bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-resolution NMR studies of structure and dynamics of human ERp27 indicate extensive interdomain flexibility
Authors: Amin Nader T. , Wallis A. Katrine , Wells Stephen A. , Rowe Michelle L. , Williamson Richard A. , Howard Mark J. , Freedman Robert B. 
Published: December 2012

ERp27 (endoplasmic reticulum protein 27.7 kDa) is a homologue of PDI (protein disulfide-isomerase) localized to the endoplasmic reticulum. ERp27 is predicted to consist of two thioredoxin-fold domains homologous with the non-catalytic b and b′ domains of PDI. The structure in solution of the N-terminal b-like domain of ERp27 was solved using high-resolution NMR data. The structure confirms that it has the thioredoxin fold and that ERp27 is a member of the PDI family. 15N-NMR relaxation data were obtained and ModelFree analysis highlighted limited exchange contributions and slow internal motions, and indicated that the domain has an average order parameter S2 of 0.79. Comparison of the single-domain structure determined in the present study with the equivalent domain within full-length ERp27, determined independently by X-ray diffraction, indicated very close agreement. The domain interface inferred from NMR data in solution was much more extensive than that observed in the X-ray structure, suggesting that the domains flex independently and that crystallization selects one specific interdomain orientation. This led us to apply a new rapid method to simulate the flexibility of the full-length protein, establishing that the domains show considerable freedom to flex (tilt and twist) about the interdomain linker, consistent with the NMR data.
The timing of abscission affects dispersal distance in a wind‐dispersed tropical tree
Authors: Maurer Kyle D. , Bohrer Gil , Medvigy David , Wright S. Joseph 
Published: December 2012

Summary

Seed dispersal is a short‐term phenomenon with long‐term consequences for population survival and spread. Physiological mechanisms that target the release of seeds to particular sets of environmental conditions that maximize the probability of long‐distance dispersal should evolve if long dispersal distance enhances fitness.

In this study, we use high‐frequency censuses of seeds actually dispersed, high‐frequency within‐canopy meteorological observations and long‐term measurements of above‐canopy wind to investigate the environmental conditions that control the timing of seed abscission at different time‐scales for a wind‐dispersed tropical tree, Luehea seemannii.

We show that seed abscission follows a typical seasonal pattern, is rare at night and is most prevalent during periods of prolonged updrafts, higher temperature, with negative feedback when the heat canopy flux is relatively high.

We use phenomenological (super‐WALD) and mechanistic (coupled Eulerian–Lagrangian closure) models to estimate the relative effects of the timing of seed release at different subannual temporal scales (seconds–hours) on the resulting long‐term (season–decade) dispersal kernels. We find that periods of high wind speed increase the probability of long‐distance dispersal between 100–1000 m, but decrease the probability at distances further than 1000 m relative to unbiased environmental conditions. We also find abscission during updrafts to increase the probability of long‐distance dispersal at distances greater than 100 m.

Synthesis: We observe preferential abscission during updrafts in a tropical wind‐dispersed tree. We use mechanistic models and long‐term wind statistics to estimate the dispersal consequences of preferential seed release in specific environmental conditions. We find that the timing of the dispersal season may be influenced by wind conditions that maximize long‐distance dispersal; however, there are likely other environmental factors essential for their determination. Our approach provides a method to bridge between small turbulence scales and large ecosystem scales to predict dispersal kernels. These findings shed light on the evolutionary processes that drive optimization of the timing of seed abscission and may be incorporated into plant population movement models to increase their accuracy and predictive power.
Functional diversity among seed dispersal kernels generated by carnivorous mammals
Authors: González‐Varo Juan P. , López‐Bao José V. , Guitián José 
Published: December 2012

Summary

Knowledge of the spatial scale of the dispersal service provided by important seed dispersers (i.e. common and/or keystone species) is essential to our understanding of their role on plant ecology, ecosystem functioning and, ultimately, biodiversity conservation.

Carnivores are the main mammalian frugivores and seed dispersers in temperate climate regions. However, information on the seed dispersal distances they generate is still very limited. We focused on two common temperate carnivores differing in body size and spatial ecology – red fox (Vulpes vulpes) and European pine marten (Martes martes) – for evaluating possible functional diversity in their seed dispersal kernels.

We measured dispersal distances using colour‐coded seed mimics embedded in experimental fruits that were offered to the carnivores in feeding stations (simulating source trees). The exclusive colour code of each simulated tree allowed us to assign the exact origin of seed mimics found later in carnivore faeces. We further designed an explicit sampling strategy aiming to detect the longest dispersal events; as far we know, the most robust sampling scheme followed for tracking carnivore‐dispersed seeds.

We found a marked functional heterogeneity among both species in their seed dispersal kernels according to their home range size: multimodality and long‐distance dispersal in the case of the fox and unimodality and short‐distance dispersal in the case of the marten (maximum distances = 2846 and 1233 m, respectively). As a consequence, emergent kernels at the guild level (overall and in two different years) were highly dependent on the relative contribution of each carnivore species.

Our results provide the first empirical evidence of functional diversity among seed dispersal kernels generated by carnivorous mammals. Moreover, they illustrate for the first time how seed dispersal kernels strongly depend on the relative contribution of different disperser species, thus on the composition of local disperser assemblages. These findings provide a key starting point for understanding and modelling plant population processes that include mammal‐mediated seed dispersal, such as connectivity, range expansion and colonization.
Urease gene‐containing Archaea dominate autotrophic ammonia oxidation in two acid soils
Authors: Lu Lu , Jia Zhongjun 
Published: December 2012

SummaryThe metabolic traits of ammonia‐oxidizing archaea (AOA) and bacteria (AOB) interacting with their environment determine the nitrogen cycle at the global scale. Ureolytic metabolism has long been proposed as a mechanism for AOB to cope with substrate paucity in acid soil, but it remains unclear whether urea hydrolysis could afford AOA greater ecological advantages. By combining DNA‐based stable isotope probing (SIP) and high‐throughput pyrosequencing, here we show that autotrophic ammonia oxidation in two acid soils was predominately driven by AOA that contain ureC genes encoding the alpha subunit of a putative archaeal urease. In urea‐amended SIP microcosms of forest soil (pH 5.40) and tea orchard soil (pH 3.75), nitrification activity was stimulated significantly by urea fertilization when compared with water‐amended soils in which nitrification resulted solely from the oxidation of ammonia generated through mineralization of soil organic nitrogen. The stimulated activity was paralleled by changes in abundance and composition of archaeal amoA genes. Time‐course incubations indicated that archaeal amoA genes were increasingly labelled by 13CO2 in both microcosms amended with water and urea. Pyrosequencing revealed that archaeal populations were labelled to a much greater extent in soils amended with urea than water. Furthermore, archaeal ureC genes were successfully amplified in the 13C‐DNA, and acetylene inhibition suggests that autotrophic growth of urease‐containing AOA depended on energy generation through ammonia oxidation. The sequences of AOB were not detected, and active AOA were affiliated with the marine Group 1.1a‐associated lineage. The results suggest that ureolytic N metabolism could afford AOA greater advantages for autotrophic ammonia oxidation in acid soil, but the mechanism of how urea activates AOA cells remains unclear.
Capping Direct Payments in the CAP: Another Paper Tiger?  Plafonnement des aides directes: simple tigre de papier?  Kappung der Direktzahlungen: Noch ein Papiertiger?
Authors: Sahrbacher Christoph , Sahrbacher Amanda , Balmann Alfons , Ostermeyer Arlette , Schoenau Franziska 
Published: December 2012

summaryCapping Direct Payments in the CAP: Another Paper Tiger?One of the goals set by the European Commission while preparing the upcoming reform of the CAP is to reach a more equitable distribution of direct payments between Member States. Direct payments should also be more justifiable in the eyes of taxpayers. In its proposal published in October 2011, the EC suggests dividing direct payments into a basic and a greening component. The basic component should be subject to so‐called capping, a mechanism that applies progressive cuts in the basic payment and introduces a ceiling at €300,000. However, salaries could be subtracted before capping. It is expected that regions will suffer most where large field crop farms are predominant. Therefore, simulation experiments are implemented to assess farms’ reactions to capping in an East German large‐scale farming region. Results show that only a few farms are affected by capping and even fewer farms undergo substantial losses in both profit and size. Farms potentially affected by capping rather adapt by investing in labour‐intensive production. However, farm growth is hindered in farms affected by capping, whereas at the same time small farms do not benefit either. In the long‐term, capping potentially leads to structural inefficiencies and competitive distortions that may cause higher welfare losses than those gained with the reduction of direct payments.
How Do Incomes in Agriculture Compare with Those in the Rest of the Economy?  Comment les revenus en agriculture se situent‐ils par rapport à ceux du reste de l’économie ?  Wie schneiden Einkommen in der Landwirtschaft im Vergleich zu anderen Einkommen ab?
Authors: Hill Berkeley 
Published: December 2012

summaryHow Do Incomes in Agriculture Compare with Those in the Rest of the Economy?In the period in which changes to the post‐2013 CAP are being considered, the European Commission has asserted that incomes in agriculture compare unfavourably with those in the rest of the economy, at a level typically of about 50 per cent or less. This assessment, made on the basis of average returns to the factor labour, should not be interpreted as indicating the relative incomes of farmers and their families. Though no EU‐wide working system for generating household‐level income data exists, evidence from seven Member States points to situations of approximate parity and, at worst, differences that are far smaller than the Commission’s observation implies, other than perhaps in Poland. Also it is clear that, because of short‐term movements in the earnings from farming, it is not advisable to rely too heavily on figures for single years. If the CAP is to take the core legal objective of ensuring a ‘fair standard of living of the agricultural community’ seriously, and to improve its efficiency in doing so, reliable household level income data need to be provided.
From Economic Research to Policy in 32 Years  De la recherche en économie à la politique : 32 ans d’expérience  In 32 Jahren aus der Wirtschaftsforschung in die Politik
Authors: Bowbrick Peter 
Published: December 2012

summaryFrom Economic Research to Policy in 32 YearsThe European Commission has recently reformed its system of horticultural standards, acting on economic research which was published 32 years ago and accepted immediately by academic economists. The delay may have cost €10 to €15 billion a year in higher costs and prices, reduced health and environmental damage. One reason for the delay may be that top government economists based their decisions on the economics that was orthodox when they were undergraduates. Action was taken by researchers and civil servants to suppress unwelcome research results. Key economic decisions were made not by economists, but by civil service horticulturists and grading inspectors who blocked reform, possibly because they felt their expertise was not valued or their jobs were threatened. Action was taken to prevent a knowledgeable outsider from carrying out a review because civil servants did not like a book he published 20 years earlier. Such actions have a chilling effect: consultants or academics who say what they think can have their careers destroyed. Systems used outside the EU could have speeded change: for example, regular policy reviews using independent reviewers – academics, consultants or international organisations. Strict selection procedures for consultants, strictly enforced, are essential. Publication of reviews is important.
Climate warming increases biodiversity of small rodents by favoring rare or less abundant species in a grassland ecosystem
Authors: JIANG Guangshun , LIU Jun , XU Lei , YU Guirui , HE Honglin , ZHANG Zhibin 
Published: December 2012

AbstractOur Earth is facing the challenge of accelerating climate change, which imposes a great threat to biodiversity. Many published studies suggest that climate warming may cause a dramatic decline in biodiversity, especially in colder and drier regions. In this study, we investigated the effects of temperature, precipitation and a normalized difference vegetation index on biodiversity indices of rodent communities in the current or previous year for both detrended and nondetrended data in semi‐arid grassland of Inner Mongolia during 1982–2006. Our results demonstrate that temperature showed predominantly positive effects on the biodiversity of small rodents; precipitation showed both positive and negative effects; a normalized difference vegetation index showed positive effects; and cross‐correlation function values between rodent abundance and temperature were negatively correlated with rodent abundance. Our results suggest that recent climate warming increased the biodiversity of small rodents by providing more benefits to population growth of rare or less abundant species than that of more abundant species in Inner Mongolia grassland, which does not support the popular view that global warming would decrease biodiversity in colder and drier regions. We hypothesized that higher temperatures might benefit rare or less abundant species (with smaller populations and more folivorous diets) by reducing the probability of local extinction and/or by increasing herbaceous food resources.
Phenotypic plasticity is maintained despite geographical isolation in an African cichlid fish, Pseudocrenilabrus multicolor
Authors: WIENS Kirsten E. , CRISPO Erika , CHAPMAN Lauren J. 
Published: December 2012

AbstractGene flow among populations in different selective environments should favor the evolution of phenotypic plasticity over local adaptation. Plasticity in development is a common response to long‐term hypoxia in some widespread African fishes, including Pseudocrenilabrus multicolor, a cichlid that exploits both normoxic (high oxygen) rivers/lakes and hypoxic (low oxygen) swamps. Previous studies have shown that fish from normoxic and hypoxic sites differ in many traits, including gill size, brain size and body shape, and that much of this variation reflects developmental plasticity. However, these earlier studies focused on areas in Uganda where gene flow between swamp and river or lake populations is high. In this study we tested the hypothesis that P. multicolor from a relatively isolated lake population (Lake Saka, Uganda) exhibit low levels of plasticity in traits related to oxygen uptake. Multiple broods of P. multicolor from Lake Saka were reared under low and high dissolved oxygen, and traits related to gill size, brain mass and body shape were quantified. Surprisingly, both gill size and brain mass showed high levels of developmental plasticity. We suggest that high levels of plasticity, particularly in the gill size of P. multicolor, reflects low costs of maintaining the plastic response, even in relatively isolated populations.
Ecological scale and seasonal heterogeneity in the spatial behaviors of giant pandas
Authors: ZHANG Zejun , SHEPPARD James K. , SWAISGOOD Ronald R. , WANG Guan , NIE Yonggang , WEI Wei , ZHAO Naxun , WEI Fuwen 
Published: December 2012

AbstractWe report on the first study to track the spatial behaviors of wild giant pandas (Ailuropoda melanoleuca) using high‐resolution global positioning system (GPS) telemetry. Between 2008 and 2009, 4 pandas (2 male and 2 female) were tracked in Foping Reserve, China for an average of 305 days (± 54.8 SE). Panda home ranges were larger than those of previous very high frequency tracking studies, with a bimodal distribution of space‐use and distinct winter and summer centers of activity. Home range sizes were larger in winter than in summer, although there was considerable individual variability. All tracked pandas exhibited individualistic, unoriented and multiphasic movement paths, with a high level of tortuosity within seasonal core habitats and directed, linear, large‐scale movements between habitats. Pandas moved from low elevation winter habitats to high elevation (>2000 m) summer habitats in May, when temperatures averaged 17.5 °C (± 0.3 SE), and these large‐scale movements took <1 month to complete. The peak in panda mean elevation occurred in Jul, after which they began slow, large‐scale movements back to winter habitats that were completed in Nov. An adult female panda made 2 longdistance movements during the mating season. Pandas remain close to rivers and streams during winter, possibly reflecting the elevated water requirements to digest their high‐fiber food. Panda movement path tortuosity and first‐passage‐time as a function of spatial scale indicated a mean peak in habitat search effort and patch use of approximately 700 m. Despite a high degree of spatial overlap between panda home ranges, particularly in winter, we detected neither avoidance nor attraction behavior between conspecifics.
Annual survival and site fidelity of free‐ranging white‐tailed deer (Odocoileus virginianus): comparative demography before (1983–1992) and after (1993–2005) spatial confinement
Authors: WEBB Stephen L. , GEE Kenneth L. 
Published: December 2012

AbstractSurvival and movement are important demographic variables influencing the dynamics of large herbivores with implications for management and evolution of life‐history strategies. Management practices such as spatial confinement and harvest regulation attempt to control survival and movement for the sustainability of harvested deer populations, but a paucity of long‐term data exists on these management practices. We examined annual survival and site fidelity of free‐ranging white‐tailed deer (Odocoileus virginianus) over 10 years (1983–1992) to compare demographic parameters after spatial confinement (1993–2005). We used capture records (n = 174; 104 females, 70 males), marked deer recaptures (n = 42), and dead recoveries (n = 68) to estimate sex‐specific, age‐specific and time‐specific parameters. We found that annual female survival was 50% from 1983–1987 during a period of intense harvest, but increased to 93.7% after intense harvesting was eliminated. Prior to spatial confinement, annual survival of marked male deer averaged 36.7%–42.5%. After spatial confinement, annual survival increased on average for males (58%–99%) and females (77%–98%). Females showed high levels of site fidelity (>99%) prior to spatial confinement, whereas males showed much less site fidelity (≤4.5% for the 2 top‐ranking models). During spatial confinement, the semi‐impermeable fence effectively increased site fidelity of males (≥56%). These results stem from long‐term study (23 years) of a large herbivore experiencing changes to life‐history, resulting from changes in management that were applied to the population and aimed at altering population demographics, for sustainability of a harvestable population of deer.
Towards understanding the low prevalence of Helicobacter pylori in Malays: Genetic variants among Helicobacter pylori‐negative ethnic Malays in the north‐eastern region of Peninsular Malaysia and Han Chinese and South Indians
Authors: Maran Sathiya , Lee Yeong Yeh , Xu Shu Hua , Raj Mahendra Sundramoorthy , Abdul Majid Noorizan , Choo Keng Ee , Zilfalil Bin Alwi , Graham David Y. 
Published: December 2012

ObjectivesTo identify gene polymorphisms that differ between Malays, Han Chinese and South Indians, and to identify candidate genes for the investigation of their role in protecting Malays from Helicobacter pylori (H. pylori) infection.MethodsMalay participants born and residing in Kelantan with a documented absence of H. pylori infection were studied. Venous blood was used for genotyping using the Affymetrix 50K Xba I kit. CEL files from 141 Han Chinese and 76 South Indians were analyzed to compare their allele frequency with that of the Malays using fixation index (FST) calculation. The single nucleotide polymorphisms (SNPs) with the highest allele frequency (outliers) were then examined for their functional characteristics using F‐SNP software and the Entrez Gene database.Results:In all, 37 Malays were enrolled in the study; of whom 7 were excluded for low genotyping call rates. The average FST estimated from the genome‐wide data were 0.038 (Malays in Kelantan vs the South Indians), 0.015 (Malays in Kelantan vs Han Chinese) and 0.066 (Han Chinese vs South Indians), respectively. The outlier gene variants present in Malays with functional characteristics were C7orf10 (FST 0.29988), TSTD2 (FST 0.43278), SMG7 (FST 0.29877) and XPA (FST 0.43393 and 0.43644).ConclusionGenetic variants possibly related to protection against H. pylori infection in ethnic Malays from the north‐eastern region of Peninsular Malaysia were identified for testing in subsequent trials among infected and uninfected Malays.