bluuebunny/crossref_metadata_2025_split huggingface dataset:
The crystal structure of the C45S mutant of annelid Arenicola marina peroxiredoxin 6 supports its assignment to the mechanistically typical 2‐Cys subfamily without any formation of toroid‐shaped decamers
Authors: Smeets Aude , Loumaye Eléonore , Clippe André , Rees Jean‐François , Knoops Bernard , Declercq Jean‐Paul 
Published: March 2008

AbstractThe peroxiredoxins (PRDXs) define a superfamily of thiol‐dependent peroxidases able to reduce hydrogen peroxide, alkyl hydroperoxides, and peroxynitrite. Besides their cytoprotective antioxidant function, PRDXs have been implicated in redox signaling and chaperone activity, the latter depending on the formation of decameric high‐molecular‐weight structures. PRDXs have been mechanistically divided into three major subfamilies, namely typical 2‐Cys, atypical 2‐Cys, and 1‐Cys PRDXs, based on the number and position of cysteines involved in the catalysis. We report the structure of the C45S mutant of annelid worm Arenicola marina PRDX6 in three different crystal forms determined at 1.6, 2.0, and 2.4 Å resolution. Although A. marina PRDX6 was cloned during the search of annelid homologs of mammalian 1‐Cys PRDX6s, the crystal structures support its assignment to the mechanistically typical 2‐Cys PRDX subfamily. The protein is composed of two distinct domains: a C‐terminal domain and an N‐terminal domain exhibiting a thioredoxin fold. The subunits are associated in dimers compatible with the formation of intersubunit disulfide bonds between the peroxidatic and the resolving cysteine residues in the wild‐type enzyme. The packing of two crystal forms is very similar, with pairs of dimers associated as tetramers. The toroid‐shaped decamers formed by dimer association and observed in most typical 2‐Cys PRDXs is not present. Thus, A. marina PRDX6 presents structural features of typical 2‐Cys PRDXs without any formation of toroid‐shaped decamers, suggesting that it should function more like a cytoprotective antioxidant enzyme or a modulator of peroxide‐dependent cell signaling rather than a molecular chaperone.
Induced‐fit or preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure‐based drug design
Authors: Xu Yechun , Colletier Jacques Ph. , Jiang Hualiang , Silman Israel , Sussman Joel L. , Weik Martin 
Published: March 2008

AbstractCrystal structures of acetylcholinesterase complexed with ligands are compared with side‐chain conformations accessed by native acetylcholinesterase in molecular dynamics (MD) simulations. Several crystallographic conformations of a key residue in a specific binding site are accessed in a simulation of native acetylcholinesterase, although not seen in rotomer plots. Conformational changes upon ligand binding thus involve preexisting equilibrium dynamics. Consequently, rational drug design could benefit significantly from conformations monitored by MD simulations of native targets.
Immunohistochemical assessment of CD25 is equally sensitive and diagnostic in mastocytosis compared to flow cytometry
Authors: Baumgartner C. , Sonneck K. , Krauth M.‐T. , Kneidinger M. , Födinger M. , Hauswirth A. W. , Müllauer L. , Valent P. 
Published: March 2008

ABSTRACTBackground   Systemic mastocytosis (SM) is a clonal myeloid disorder characterized by abnormal accumulation and growth of mast cells (MC) in internal organs. In most cases, the bone marrow is involved. Expression of CD25 in bone marrow MC, with or without coexpression of CD2, is an important minor SM criterion. So far, most studies have examined CD25‐expression on MC by flow cytometry.Materials and methods   We examined the expression of CD25 in MC in patients with SM (n = 25) by immunohistochemistry (IHC) and compared these data with results obtained by flow cytometric assessment of CD25‐expression. In addition, we compared CD25‐staining results with that obtained with an antibody against CD2.Results   In a majority of all patients (> 80%), CD25 was detectable by both staining techniques. However, in one patient, CD25 was only detectable on MC by IHC, but not by flow cytometry, and in two patients in whom IHC could not be applied because of lack of compact MC infiltrates, flow cytometry revealed aberrant expression of CD25. The antibody against CD2 produced diagnostic staining results in a smaller group of patients (flow cytometry: 65%; IHC: 28% of SM cases) compared to CD25 (> 80%).Conclusions   CD25‐IHC is equally diagnostic and sensitive in SM compared to flow cytometry and thus can be recommended as a diagnostic test. Our data also suggest that the diagnostic value of CD25 exceeds that of CD2, and that optimal assessment of CD25‐expression in neoplastic MC in all patients requires the application of both techniques, flow cytometry and IHC.
C‐reactive protein and coronary composition in patients with percutaneous revascularization
Authors: Pucci A. , Brscic E. , Tessitore E. , Celeste A. , Crudelini M. , De Bernardi A. , Alberti A. , Biondi‐Zoccai G. , Sheiban I. 
Published: March 2008

ABSTRACTBackground   C‐Reactive Protein (CRP) is considered a predictive factor for cardiovascular events and its serum levels have been shown to correlate with thin cap coronary plaques in sudden coronary death. Whether serum CRP levels are associated with in vivo atherothrombotic features is unclear. We thus analysed samples from coronary atherectomy specimens obtained during percutaneous coronary intervention.Materials and methods   Patients with coronary artery disease undergoing directional atherectomy, distinguished by unstable versus stable coronary syndrome diagnosis, provided coronary specimens from culprit lesions. Assessment was conducted by means of conventional histology, morphometry and immunohistochemistry. Specific antibodies against erythrocyte‐specific protein glycophorin A, endothelial and macrophage antigens were also used.Results   There were 51 patients with unstable coronary disease and 47 patients with stable angina. Serum CRP levels ≥ 1 mg L−1 were detected in 24/98 patients, and were significantly associated with hypercellularity, macrophage infiltrates, neoangiogenesis and intraplaque haemorrhage (all P < 0·05). Furthermore, coronary plaques from patients with unstable angina contained larger atheromas, more hypercellular plaques, with abundant macrophages, neoangiogenesis and intraplaque haemorrhages and lesser fibrous tissue (all P < 0·05).Conclusions   We observed a positive correlation between increased serum CRP levels and typical pathological features of complex atherothrombotic coronary disease, confirming in vivo the mechanistic role of CRP in coronary atherothrombosis.
Sorghum ergot can develop without local Claviceps africana inoculum from nearby infected plants
Authors: Chakraborty S. , Ryley M. J. 
Published: March 2008

Batches of glasshouse‐grown flowering sorghum plants were placed in circular plots for 24 h at two field sites in southeast Queensland, Australia on 38 occasions in 2003 and 2004, to trap aerial inoculum of Claviceps africana. Plants were located 20–200 m from the centre of the plots. Batches of sorghum plants with secondary conidia of C. africana on inoculated spikelets were placed at the centre of each plot on some dates as a local point source of inoculum. Plants exposed to field inoculum were returned to a glasshouse, incubated at near‐100% relative humidity for 48 h and then at ambient relative humidity for another week before counting infected spikelets to estimate pathogen dispersal. Three times as many spikelets became infected when inoculum was present within 200 m of trap plants, but infected spikelets did not decline with increasing distance from local source within the 200 m. Spikelets also became infected on all 10 dates when plants were exposed without a local source of infected plants, indicating that infection can occur from conidia surviving in the atmosphere. In 2005, when trap plants were placed at 14 locations along a 280 km route, infected spikelets diminished with increasing distance from sorghum paddocks and infection was sporadic for distances over 1 km. Multiple regression analysis showed significant influence of moisture related weather variables on inoculum dispersal. Results suggest that sanitation measures can help reduce ergot severity at the local level, but sustainable management will require better understanding of long‐distance dispersal of C. africana inoculum.
The evolution of a thick shallow marine succession, the South Munster Basin, Ireland
Authors: QUIN JAMIE G. 
Published: March 2008

AbstractThe relatively fine‐grained Late Devonian to Early Carboniferous ‘Cork Beds’ succession of the South Munster Basin includes continuous sections of paralic facies that are over 1000 m thick and individual sandstone units over 300 m thick. However, the succession does not reflect prolonged phases when facies belts were stationary, but rather multiple stacking of small‐scale, high‐frequency sequences, each associated with pronounced migration of shorelines. What seems to have been unusual about the South Munster Basin succession was that the geographical positioning of these high‐frequency sequences was fixed. This resulted from an unusual combination of tectonics, shelf hydrodynamics, sedimentation rates and the textural maturity of the sediment within the basin. Of these, tectonics was probably most critical, particularly the juxtaposition of rapid subsidence in basinal areas and a basin margin zone (to the north) that was sufficiently up‐standing to pin the maximum extent of transgression during repeated highstands of sea‐level, yet not so upstanding as to have diverted the major regional drainage system. The embayed palaeogeography of the area may also have been influential.
Sedimentology and preservation potential of carbonate sand sheets deposited by the December 2004 Indian Ocean tsunami: South Baa Atoll, Maldives
Authors: NICHOL SCOTT L. , KENCH PAUL S. 
Published: March 2008

AbstractObservations of carbonate sand sheets deposited by the December 2004 Indian Ocean tsunami across island surfaces in the Maldives archipelago provide an opportunity to investigate tsunami flow behaviour across relatively simple coastal forms. This paper presents data on tsunami sand sheet deposits for five islands located along an east–west transect through the central atoll of South Baa. Sedimentary data include: field measurement of sand sheet planform, thickness and volume; descriptions of sedimentary structure and stratigraphic relationships with underlying surfaces; laboratory measurement of grain‐size as a proxy of settling velocity; and observations of post‐depositional changes to sand sheet characteristics two years following the Indian Ocean tsunami. Results show cross‐atoll trends in volume and form of sand sheets that are interpreted as a proxy of waning and scattering of energy, as the wave train interacted with the shallow waters and numerous islands of the atoll. On individual islands, the basin topography resulted in tsunami overwash but no return flow, so that sand sheets are the product of unidirectional flow, with evidence in grain‐size trends for minor acceleration across landward slopes. A key finding is the evidence for rapid post‐depositional changes to the form and extent of tsunami deposits. Within two years of deposition, reworking of the seaward edge of sand sheets has destroyed the thickest part of the deposit and the thinner landward part of the sand sheets has been reworked by bioturbation. This study concludes that the preservation potential of these tsunami deposits is low to moderate, with the only probable recognizable signature being local variation in the micro‐topography of island surfaces.
Palaeo‐climate controlled diagenesis of the Westphalian C & D fluvial sandstones in the Campine Basin (north‐east Belgium)
Authors: BERTIER PIETER , SWENNEN RUDY , LAGROU DAVID , LAENEN BEN , KEMPS RAYMOND 
Published: March 2008

AbstractThe Westphalian C and D fluvial sandstones in the Campine Basin (north‐east Belgium) are potential reservoirs for the sequestration of CO2 and interesting analogues of the hydrocarbon reservoirs in the Southern North Sea. Although these sandstones were deposited in a relatively short period of time, their reservoir properties and mineralogical compositions are very different. A petrographic study complemented with stable isotope analyses, fluid inclusion microthermometry and X‐ray diffraction analyses of the clay fractions of the sandstones, which were sampled from deep boreholes (>1000 m) in the Campine Basin, revealed that these differences are related mainly to the climate at the time of deposition. The most important eogenetic processes affecting the Westphalian sandstones were the generation of a pseudomatrix by physical compaction of Al‐silicates and lithic fragments that were strongly altered by extensive meteoric leaching, kaolinitization of unstable silicates and precipitation of siderite. These processes had a detrimental influence on the reservoir properties of Westphalian C sandstones, but their impact on the Westphalian D sandstones was minimal. The difference is assumed to be related to the climate at the time of deposition, which changed from tropical humid in the Westphalian C to semi‐arid/arid during the Late Westphalian D. Both the Westphalian C and D sandstones were affected by similar mesogenetic processes. Mesogenetic quartz cementation resulted from chemical compaction and illitization of kaolinite, K‐feldspar and smectitic clays. Illitization of kaolinite was controlled by the available quantities of co‐existing kaolinite and K‐feldspar and mainly affected the Westphalian D sandstones. Illitization of K‐feldspar was controlled by the K‐feldspar content. It had a much larger impact on the reservoir properties of the Westphalian D as, in these sandstones, K‐feldspar was less affected by eogenetic alteration. The illitization of smectitic clays resulted in illite, quartz and ankerite cementation in both reservoirs. This process had a more important impact on the Westphalian C reservoir, since cementation here also resulted from smectite to illite conversion in the interbedded and underlying shales. The effect of mesogenetic alterations on the reservoir properties was much less drastic than the impact of eodiagenesis. Mesogenetic alterations do exert a significant control on the properties of the Westphalian D. The vast impact of eodiagenesis on the Westphalian C sandstones made them less susceptible to mesogenetic alteration. The effect of telogenetic processes on the porosity and permeability of the Westphalian sandstones was small and restricted to the top reservoir intervals that directly underlie the Cimmerian Unconformity. No significant telogenetic alterations related to the Variscan Unconformity were observed.
The use of voltage‐sensitive dyes to monitor signal‐induced changes in membrane potential–ABA triggered membrane depolarization in guard cells†
Authors: Konrad Kai R. , Hedrich Rainer 
Published: March 2008

SummaryThe plant membrane potential reports on the activity of electrogenic plasma membrane transport processes. The membrane potential is widely used to report for early events associated with changes in light regime, hormone action or pathogen attacks. The membrane potentials of guard cells can be precisely measured with microelectrodes, but this technique is not well suited for rapid screens with large sample numbers. To provide the basis for large‐scale membrane potential recordings, we took advantage of voltage‐sensitive dyes. Using the fluorescent dyes bis‐(1,3‐dibutylbarbituric acid)‐trimethine oxonol (DiBAC4(3)) and the FLIPR Membrane Potential Assay Kit (FMP) dye we followed changes in the membrane potential in guard cells and vacuoles. Based on the fluorescence of DiBAC4(3) a method was established for quantification of the membrane potential in guard cell protoplasts which should be considered as an excellent system for high‐throughput screening of plant cells. In the absence of abscisic acid (ABA), one‐third of the guard cell protoplast population spontaneously oscillated for periods of 5‐6 min. Upon application of ABA the hyperpolarized fraction (∼50%) of the guard cell protoplast population depolarized within a few minutes. Membrane potential oscillations were terminated by ABA. Oscillations and ABA responses were found in cell populations with active anion channels. Thus time‐ and voltage‐dependent anion channels likely represent the ABA‐sensitive conductance and part of the membrane potential oscillator. The suitability of membrane potential dyes was tested on vacuoles, too. Dye‐based vacuolar membrane polarization was monitored upon ATP exposure. We conclude that voltage‐sensitive dyes provide an excellent tool for the study of changes in the membrane potential in vacuole as well as guard cell populations.
AGAMOUS‐LIKE 17, a novel flowering promoter, acts in a FT‐independent photoperiod pathway
Authors: Han Ping , García‐Ponce Berenice , Fonseca‐Salazar Gabriel , Alvarez‐Buylla Elena R. , Yu Hao 
Published: March 2008

SummaryThe photoperiod pathway is a genetically conserved pathway that affects flowering in distantly related angiosperms. Here we report a novel flowering promoter AGAMOUS‐LIKE 17 (AGL17) acting in the photoperiod pathway of Arabidopsis. AGL17 transcripts were detectable in various plant organs with the highest expression in the root. Under long‐day conditions, expression of AGL17 gradually increased in the aerial part of seedlings during the floral transition. Overexpression of AGL17 caused early flowering, while loss of function of AGL17 exhibited late flowering, particularly under long days. Analysis of AGL17 expression in various flowering‐time mutants showed that its transcripts were significantly reduced in the photoperiod pathway mutant co‐1. Correspondingly, AGL17 expression was upregulated in transgenic plants overexpressing CONSTANS (CO) and also when CO activity was induced by light. Genetic analysis further showed that overexpression of AGL17 could partially suppress the late flowering of co‐1. These results suggest that AGL17 acts to promote flowering and is positively controlled by the photoperiod pathway regulator CO. In contrast, another target of CO, FLOWERING LOCUS T (FT), did not affect AGL17 expression, and vice versa. The expression of two floral meristem identity genes LEAFY (LFY) and APETALA1 (AP1) decreased in agl17‐1, while LFY and AP1 could be rapidly induced by AGL17 using a functional estradiol‐inducible system. These findings indicate that AGL17 ultimately promotes flowering via regulation of LFY and AP1.
Productivism, Post‐Productivism and European Agricultural Reform: The Case of Sugar
Authors: Ward Neil , Jackson Peter , Russell Polly , Wilkinson Katy 
Published: March 2008

AbstractChanges in European agricultural policy and institutions over the past two decades have been characterised as a transition from a productivist to a post‐productivist framework. This account of policy change has been accused of being overly structuralist and deterministic. This article makes the case for taking a commodity‐specific approach to analysing European agricultural policy reform to contribute to understanding the specificities and contingencies of agricultural productivism, the interplay between external and internal pressures which help drive the reform process and the implications of the material properties of foods in understanding regulatory change. Drawing on original interview material and other secondary sources, the article examines the recent reform of the European Union sugar regime – widely regarded as the last bastion of the highly regulated and protectionist Common Agricultural Policy. It argues that the case of sugar sheds new light on the processes through which the productivist order is being dismantled, highlighting the importance of world trade and international development concerns in shaping agricultural policy change in the EU.
Gender and Work in Norwegian Family Farm Businesses
Authors: Bjørkhaug Hilde , Blekesaune Arild 
Published: March 2008

AbstractThe traditional way of organising agricultural production in Norway has been through family farming. A family farm is defined by the ownership of the farm through kinship over a number of generations. This article examines structural changes on Norwegian family farms based on the impact of increased competition and falling prices and subsidies. The strategy traditionally employed has been to increase total household income on the farm through working off‐farm. We map changes in income allocation and work strategies on Norwegian family farms over time, changes in income allocation and work strategies among men and women on family farms over time and we show income allocation and work strategies among men and women as farmers and as farmers’ spouses. Through a quantitative analysis of data on Norwegian farmers from 1987 until 2004, we show that there are continuing changes in work and income allocation on Norwegian farms. The trend is a higher dependence on off‐farm income. However, this development is not only explained by more off‐farm work by farmers – which is an indication of lower value of farm work itself – but to a large degree this is a result of the increasing off‐farm work of farm women. While at the same time more women are entering agriculture as farmers, we find clear evidence of differences in the organisation of farms operated by men and women. While male farmers are professionalising as ‘one‐man farmers,’ female farmers to a larger degree depend (voluntarily or not) on their partner's assistance in the farm work.
Re‐thinking the Transformation of Organics: The Role of the UK Government in Shaping British Organic Food and Farming
Authors: Tomlinson Isobel 
Published: March 2008

AbstractThe focus of international scholarship on the contemporary transformation of organic food and farming has been a rather narrow preoccupation with the ‘conventionalisation thesis’ that describes a process whereby the structure and ideology of the expanding organic sector is seen increasingly to resemble that of the conventional food and farming sector that it has traditionally opposed. This study seeks to contribute to this literature by examining the role of the UK government in shaping the British organic sector since 1980, when it first began to engage seriously with organic farming. It draws on the analysis of a wide range of government and organic movement publications for the period 1980–2006, as well as a programme of semi‐structured interviews with key organic policy actors during this time frame. By analysing the way in which the UK government has discursively constructed three separate story‐lines about organics, this study argues that the effects of government action on British organic food and farming are best described as a process of containment. Further, it posits the need to move on from the rather reductionist focus offered by the conventionalisation thesis to more nuanced approaches to the transformation of contemporary food and farming that account for different geographical contexts, and the particular roles of different actors actively constructing what ‘organics’ is.