bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bursaphelenchus xylophilus: opportunities in comparative genomics and molecular host–parasite interactions
Authors: JONES JOHN T. , MOENS MAURICE , MOTA MANUEL , LI HONGMEI , KIKUCHI TAISEI 
Published: February 2008

SUMMARYMostBursaphelenchusspecies are fungal feeding nematodes that colonize dead or dying trees. However,Bursaphelenchus xylophilus, the pine wood nematode, is also a pathogen of trees and is the causal agent of pine wilt disease.B. xylophilusis native to North America and here it causes little damage to trees. Where it is introduced to new regions it causes huge damage. The most severely affected areas are found in the Far East but more recentlyB. xylophilushas been introduced into Portugal and the potential for damage here is also high. As incidence and severity of pine wilt disease are linked to temperature we suggest that climate change is likely to exacerbate the problems caused byB. xylophilusand, in addition, will extend (northwards in Europe) the range in which pine wilt disease can occur. Here we review what is currently known about the interactions ofB. xylophiluswith its hosts, including recent developments in our understanding of the molecular biology of pathogenicity in the nematode. We also examine the potential developments that could be made by more widespread use of genomics tools to understand interactions betweenB. xylophilus, bacterial pathogens that have been implicated in disease and host trees.
Vertically persistent sedimentary facies boundaries along growth anticlines and climate‐controlled sedimentation in the thrust‐sheet‐top South Pyrenean Tremp‐Graus Foreland Basin
Authors: de Boer Poppe L. , Pragt Jos S. J. , Oost Albert P. 
Published: February 2008

ABSTRACTCompression of the thrust sheet underlying the central South Pyrenean Tremp‐Graus Foreland Basin led to weak folding of the overlying basin fill during deposition of Eocene sediments. From the distribution of sedimentary facies and the presence of these folds, it is interpreted that thrusting of deep‐seated competent units was accommodated by weak synsedimentary folding with a shorter wavelength at shallower levels. This led to differential subsidence at the surface but no unconformities are observed. The slower subsidence along the active anticlines locally influenced the distribution of sedimentary facies: lateral boundaries between different sedimentary facies are found to extend (sub)vertically up to more than 60 metres within narrow zones a few 100 m to 1.5 km wide. The growth folds thus led intermittently to the fixation of the position of facies boundaries, including a fixation of the coastline, over long periods (104 to 105 years). Sediment transport paths were also influenced by the slight folding of the surface.The orientation of the weak ‘en echelon’ anticlines and of related facies boundaries agrees with the inferred compressional pattern during the Eocene.Explanations for the regular occurrence of 50–60 m thick sedimentary cycles in terms of tectonic pulses or orbitally driven climatic changes and resulting pulses in sediment yield are discussed. For cycles of shorter length (10–15 m), with durations of the order of tens of thousands of years, it is inferred that these are due to regular climatic changes, probably related to orbital forcing, and resulting cyclic alternations of arid and wet periods. Such periodic changes of climate would have caused the intermittent waxing and waning of coarse‐grained sediment
Early Tertiary palaeoenvironments and sedimentation in the NE Main Porcupine Basin (well 35/13–1), offshore western Ireland?evidence for global change in the Tertiary
Authors: Dobson M. R. , Haynes J. R. , Bannister A. D. , Levene D. G. , Petrie H. S. , Woodbridge R. A. 
Published: February 2008

ABSTRACTShell‐Agip 35/13–1 well drilled 2445 m of Tertiary sediments in the Main Porcupine Basin situated offshore west of Ireland. Early Tertiary sediments and microfossils indicate a major cycle from deep‐sea to marginal marine and terrestrial palaeoenvironments returning to deep water. By means of seismic and lithostratigraphy and petrophysical logs, three deltaic cycles can be distinguished within this major cycle. The microfaunal zonation indicates that these cycles are of late Palaeocene, early Eocene and mid/late Eocene age and, therefore, correlate broadly with the Thanet Cycle, London Clay Cycle and the Bracklesham Cycles of the Anglo‐French type sections, although they are up to an order of magnitude thicker due to rapid basin subsidence.Three major unconformities can be distinguished together with a disconformity that becomes an unconformity in the North Porcupine Basin. These surfaces are associated with both local and regional tectonic and igneous events. Detailed microfossil and lithological analyses across the major unconformities allows a reasonable matching with the global sea‐level curve and recognition of the major and medium sequence boundaries. Discrepancies during the late Eocene may relate to local faulting.The pattern of sedimentation reflects the restriction of North Atlantic circulation and the tendency to euxinic bottom conditions during the early Palaeogene. In the middle Thanetian these conditions invaded the shelf, an event recorded elsewhere in NW Europe. Discontinuous seismic reflectors indicate ‘chaotic’ sedimentation connected with more vigorous circulation and erosion in the early Oligocene. This was followed by a change to parallel bedded contourites and drifts after the cutting of the early Miocene unconformity. The study reveals the complex interplay of eustatic and oceanographic change with local and regional tectonics in the development of the basin.
Immunogenetic characteristics of immunoglobulin E in allergic disease
Authors: Davies J. M. , O'Hehir R. E. 
Published: February 2008

SummaryPatients with allergic diseases produce an excess of allergen‐specific IgE, the specific effector molecule that triggers allergic reactions. The provocation for this excess IgE production is still uncertain. Current ideas include oligoclonal expansion of allergen‐specific B cells emanating from germinal centres, activation by superantigen of a subset of B cells, or polyclonal B cells class switching to IgE due to an IL‐4 predominance. Additionally, genetic elements contribute to a propensity for increased allergen‐specific IgE production. The procedure of RT‐PCR allows for amplification of infrequent IgE mRNA transcripts from B cells of atopic individuals, and so facilitates examination of expressed Ig cDNA sequences. Better knowledge of the molecular characteristics of IgE produced by patients with allergic diseases would elucidate the immunogenetic basis for elevated allergen‐specific IgE levels. The ‘immunogenetic footprint’ of IgE transcripts may elucidate the origin and activation of IgE‐producing B cells in allergic disease. Here we review studies of the immunogenetic features of IgE in allergic diseases, highlighting the major advances and the experimental limitations.
Retinoic acid treatment of human leiomyoma cells transformed the cell phenotype to one strongly resembling myometrial cells
Authors: Malik Minnie , Webb Joy , Catherino William H. 
Published: February 2008

SummaryBackground  Uterine leiomyomas are clinically significant tumours that may develop due to an altered differentiation pathway. We have previously identified a dysregulated retinoic acid (RA) pathway that reduced retinoic exposure in human leiomyoma surgical specimens, and have shown that the leiomyoma phenotype was characterized by excessive and disorganized extracellular matrix (ECM).Objective  The goal of this study was to determine the impact of RA exposure on the disrupted ECM phenotype of leiomyomas.Design and methods  Study of immortalized and molecularly confirmed cells generated from surgical specimens of spontaneous uterine leiomyoma and matched myometrium.Results  Immortalized leiomyoma and myometrial cells retained the molecular characteristics of their progenitor tissue. Proliferation of leiomyoma cells was inhibited by all‐trans retinoic acid (ATRA). Furthermore, there was a dose‐dependent decrease in soluble extracellular collagen protein in ATRA‐treated leiomyoma cells. Exposure of leiomyoma cells to ATRA resulted in a dose‐dependent inhibition of templates for specific ECM protein production including collagen 1, collagen 4, fibronectin and versican. Notably, expression levels in treated leiomyoma cells approached those found in myometrial cells. These mRNA alterations translated into altered protein. Down‐regulation was also observed among the RA pathway genes such as CYP26A1 with exposure to ATRA. Finally, ATRA down‐regulated TGF‐β3 mRNA expression and the TGF‐β regulated genes in leiomyoma cells.Conclusion  Exposure of leiomyomas to ATRA down‐regulated cell proliferation, ECM formation, RA metabolism and TGF‐β regulation, suggesting that RA exposure can alter the leiomyoma phenotype to one that more closely approximates normal myometrium.
Left ventricular dysfunction in Klinefelter syndrome is associated to insulin resistance, abdominal adiposity and hypogonadism
Authors: Andersen N. H. , Bojesen A. , Kristensen K. , Birkebaek N. H. , Fedder J. , Bennett P. , Christiansen J. S. , Gravholt C. H. 
Published: February 2008

SummaryObjective  Epidemiological data suggest there is an increased risk of dying from heart disease among patients with Klinefelter syndrome (KS). Due to high prevalence of hypogonadism and metabolic syndrome, we speculated that patients with KS may have subclinical changes in the left ventricular function. Therefore, the aim was to assess left ventricular long axis function by tissue Doppler echocardiography in patients with KS and relate these findings to the metabolic status and testosterone levels.Design  Cross‐sectional study. Out‐patient clinic.Patients  We investigated 25 unselected patients with KS, recruited from endocrine and fertility clinics. Twenty‐five age‐matched males served as controls.Measurements  Left ventricular systolic long axis function (velocities and strain rate) assessed by tissue Doppler echocardiography related to free testosterone, fasting values of plasma glucose, insulin, homeostasis model assessment (HOMA)‐index, cholesterol and triglycerides in addition to dual energy X‐ray absorptiometry (DEXA) scan derived assessment of truncal body fat.Results  The long axis function was significantly reduced in patients with KS (peak systolic velocities 4·4 ± 1·3 vs. 5·3 ± 1·0 cm/s, P < 0·01 and strain rate –1·3 ± 0·3 vs.–1·6 ± 0·3 s−1, P < 0·01). However, the ventricular dysfunction was mainly attributed KS patients with metabolic syndrome. The peak systolic velocities were significantly correlated to truncal body fat (r = –0·72, P < 0·01) and free testosterone (r = 0·63, P < 0·01), but uncorrelated to plasma glucose, insulin and HOMA‐index.Conclusion   Systolic long axis function is decreased in patients with KS and metabolic syndrome. The decrease in myocardial systolic function was significantly related to truncal body fat and hypogonadism, but not correlated to insulin sensitivity.
Designing sampling schemes for effect monitoring of nutrient leaching from agricultural soils
Authors: Brus D. J. , Noij I. G. A. M. 
Published: February 2008

SummaryA general methodology for designing sampling schemes for monitoring is illustrated with a case study aimed at estimating the temporal change of the spatial mean P concentration in the topsoil of an agricultural field after implementation of the remediation measure. A before‐after control‐impact (BACI) sample‐pattern is proposed, with stratified random sampling as a spatial sampling design. The strata are formed as compact blocks of equal area, so that the sample locations cover the field very well. Composite sampling, where the aliquots of a composite come from different strata, is proposed in order to save laboratory costs. The numbers of composites and aliquots per composite are optimized for testing the hypothesis that the mean P concentration didn’t change or has increased. Initially, this is done for a known variogram, temporal correlation, variance of laboratory measurement error, initial mean P concentration, and time needed for fieldwork. The optimal sample size to achieve a power of 0.90 at a 10% decrease of the mean P concentration is six composites of six aliquots each. Next, the effect of uncertainty about these model parameters on the optimal sample size and on the power of the test for a fixed sample size is analyzed. This analysis showed that, to obtain a probability of 95% that the power ≥ 0.90, the sample size must be increased to 7 composites of 10 aliquots each.
Characterization of a Mediterranean litter by13C CPMAS NMR: relationships between litter depth, enzyme activities and temperature
Authors: Alarcón‐Gutiérrez E. , Floch C. , Ziarelli F. , Albrecht R. , Le Petit J. , Augur C. , Criquet S. 
Published: February 2008

SummaryOrganic matter mineralization of forest litter is catalysed by the action of different extracellular enzymes produced by microorganisms. Coupling enzyme activities with data on the general macromolecular structure of organic matter, provided by cross‐polarization magic angle spinning13C nuclear magnetic resonance (13C CPMAS NMR), allows researchers new insights into organic matter degradation processes. In this paper, the effect of the temperature of incubation on the degradation processes was evaluated in three distinct layers (OhLn, OhLv and OhLf) of an evergreen oak litter (Quercus ilexL.), located in the Mediterranean area of south‐eastern France. We studied degradation phenomena by a combination of13C CPMAS NMR and microbiological analysis. In order to determine the microbial activity of litter layers, three enzyme activities (laccase, cellulase and butyrate esterase) were measured in a 6‐month mesocosm study. Results showed an increase in the alkyl C toO‐alkyl‐C ratio and an increase of the phenolic C and carboxyl C regions, indicating a preferential degradation of polysaccharides. The aromaticity also increased with litter depth and degradation, and humification processes were more elevated at 30°C.anovashowed significant effects (P< 0.001) of increased temperature, depth and time of degradation on microbiological variables. Further information is needed about the variations in temperature and temperature‐litter response and soil functions to link fundamental understanding of carbon stabilization, climate change and global C cycling.
NMR and mass spectrometry of phosphorus in wetlands
Authors: El‐Rifai H. , Heerboth M. , Gedris T. E. , Newman S. , Orem W. , Cooper W. T. 
Published: February 2008

SummaryThere is at present little information on the long‐term stability of phosphorus sequestered in wetlands. Phosphorus sequestered during high loading periods may be relatively unstable and easily remobilized following changes in nutrient status or hydrological regime, but the chemical forms of sequestered phosphorus that do remobilize are largely unknown at this time. A lack of suitable analytical techniques has contributed to this dearth of knowledge regarding the stability of soil organic phosphorus. We analysed phosphorus in soils from the ‘head’ of Rescue Strand tree island and an adjacent marsh in the Florida Everglades by 31P nuclear magnetic resonance (NMR) spectroscopy and high‐resolution mass spectrometry. Tree islands are important areas of biodiversity within the Everglades and offer a unique opportunity to study phosphorus sequestration because they are exposed to large phosphorus loads and appear to be natural nutrient sinks. The 31P NMR profiling of extracts from surface and sediment samples in the tree island indicates that phosphorus input to Rescue Strand tree island soils is mostly in the form of inorganic ortho‐phosphate and is either refractory when deposited or rapidly recycled by the native vegetation into a stable phosphorus pool largely resistant to re‐utilization by plants or microbes. Mass spectrometry revealed the presence of inositol hexakisphosphate, a common organic monophosphate ester not previously observed in Everglades’ soils.
Spring phenology in boreal Eurasia over a nearly century time scale
Authors: DELBART NICOLAS , PICARD GHISLAIN , LE TOAN THUY , KERGOAT LAURENT , QUEGAN SHAUN , WOODWARD IAN , DYE DENNIS , FEDOTOVA VIOLETTA 
Published: February 2008

AbstractIt has been widely reported that tree leaves have tended to appear earlier in many regions of the northern hemisphere in the last few decades, reflecting climate warming. Satellite observations revealed an 8‐day advance in leaf appearance date between 1982 and 1991 in northern latitudes. In situ observations show that leaf appearance dates in Europe have advanced by an average of 6.3 days from 1959 to 1996. Modelling of leaf appearance on the basis of temperature also shows a marked advance in temperate and boreal regions from 1955 to 2002. However, before 1955, reported studies of phenological variations are restricted to local scale. Modelling, ground observations and satellite observations are here combined to analyse phenological variations in Eurasian taiga over nearly a century. The trend observed by remote sensing consists mainly in a shift at the end of the 1980s, reflecting a shift in winter and spring temperature. In western boreal Eurasia, a trend to earlier leaf appearance is evident since the mid‐1930s, although it is discontinuous. In contrast, the strong advance in leaf appearance detected over Central Siberia using satellite data in 1982–1991 is strengthened by late springs in 1983–1984; moreover, in this region the green‐up timing has displayed successive trends with opposite signs since 1920. Thus, such strong trend is not unusual if considered locally. However, the recent advance is unique in simultaneously affecting most of the Eurasian taiga, the leaf appearance dates after 1990 being the earliest in nearly a century in most of the area.
Escaping the heat: range shifts of reef coral taxa in coastal Western Australia
Authors: GREENSTEIN BENJAMIN J. , PANDOLFI JOHN M. 
Published: February 2008

AbstractOne of the most critical challenges facing ecologists today is to understand the changing geographic distribution of species in response to current and predicted global warming. Coastal Western Australia is a natural laboratory in which to assess the effect of climate change on reef coral communities over a temporal scale unavailable to studies conducted solely on modern communities. Reef corals composing Late Pleistocene reef assemblages exposed at five distinct localities along the west Australian coast were censused and the results compared with coral occurrence data published for the modern reefs offshore of each locality. The resulting comparative data set comprises modern and Late Pleistocene reef coral communities occurring over approximately 12° of latitude. For the modern reefs this gradient includes the zone of overlap between the Dampierian and Flindersian Provinces. Modern reef coral communities show a pronounced gradient in coral composition over the latitudinal range encompassed by the study, while the gradient in community composition is not as strong for Pleistocene communities. Tropical‐adapted taxa contracted their ranges north since Late Pleistocene time, emplacing two biogeographic provinces in a region in which a single province had existed previously. Beta diversity values for adjacent communities also reflect this change. Modern reefs show a distinct peak in beta diversity in the middle of the region; the peak is not matched by Pleistocene reefs. Beta diversity is correlated with distance only for comparisons between modern reefs in the north and the fossil assemblages, further supporting change in distribution of the biogeographic provinces in the study area. Coral taxa present in modern communities clearly expanded and contracted their geographic ranges in response to climate change. Those taxa that distinguish Pleistocene from modern reefs are predicted to migrate south in response to future climate change, and potentially persist in ‘temperature refugia’ as tropical reef communities farther north decline.
Summer heatwaves promote blooms of harmful cyanobacteria
Authors: JÖHNK KLAUS D. , HUISMAN JEF , SHARPLES JONATHAN , SOMMEIJER BEN , VISSER PETRA M. , STROOM JASPER M. 
Published: February 2008

AbstractDense surface blooms of toxic cyanobacteria in eutrophic lakes may lead to mass mortalities of fish and birds, and provide a serious health threat for cattle, pets, and humans. It has been argued that global warming may increase the incidence of harmful algal blooms. Here, we report on a lake experiment where intermittent artificial mixing failed to control blooms of the harmful cyanobacterium Microcystis during the summer of 2003, one of the hottest summers ever recorded in Europe. To understand this failure, we develop a coupled biological–physical model investigating how competition for light between buoyant cyanobacteria, diatoms, and green algae in eutrophic lakes is affected by the meteorological conditions of this extreme summer heatwave. The model consists of a phytoplankton competition model coupled to a one‐dimensional hydrodynamic model, driven by meteorological data. The model predicts that high temperatures favour cyanobacteria directly, through increased growth rates. Moreover, high temperatures also increase the stability of the water column, thereby reducing vertical turbulent mixing, which shifts the competitive balance in favour of buoyant cyanobacteria. Through these direct and indirect temperature effects, in combination with reduced wind speed and reduced cloudiness, summer heatwaves boost the development of harmful cyanobacterial blooms. These findings warn that climate change is likely to yield an increased threat of harmful cyanobacteria in eutrophic freshwater ecosystems.
Effects of elevated CO2 on the protein concentration of food crops: a meta‐analysis
Authors: TAUB DANIEL R. , MILLER BRIAN , ALLEN HOLLY 
Published: February 2008

AbstractMeta‐analysis techniques were used to examine the effect of elevated atmospheric carbon dioxide [CO2] on the protein concentrations of major food crops, incorporating 228 experimental observations on barley, rice, wheat, soybean and potato. Each crop had lower protein concentrations when grown at elevated (540–958  μmol mol−1) compared with ambient (315–400  μmol mol−1) CO2. For wheat, barley and rice, the reduction in grain protein concentration was ∼10–15% of the value at ambient CO2. For potato, the reduction in tuber protein concentration was 14%. For soybean, there was a much smaller, although statistically significant reduction of protein concentration of 1.4%. The magnitude of the CO2 effect on wheat grains was smaller under high soil N conditions than under low soil N. Protein concentrations in potato tubers were reduced more for plants grown at high than at low concentrations of ozone. For soybean, the ozone effect was the reverse, as elevated CO2 increased the protein concentration of soybean grown at high ozone concentrations. The magnitude of the CO2 effect also varied depending on experimental methodology. For both wheat and soybean, studies performed in open‐top chambers produced a larger CO2 effect than those performed using other types of experimental facilities. There was also indication of a possible pot artifact as, for both wheat and soybean, studies performed in open‐top chambers showed a significantly greater CO2 effect when plants were rooted in pots rather than in the ground. Studies on wheat also showed a greater CO2 effect when protein concentration was measured in whole grains rather than flour. While the magnitude of the effect of elevated CO2 varied depending on the experimental procedures, a reduction in protein concentration was consistently found for most crops. These findings suggest that the increasing CO2 concentrations of the 21st century are likely to decrease the protein concentration of many human plant foods.