bluuebunny/crossref_metadata_2025_split huggingface dataset:
Do fungal pathogens drive density-dependent mortality in established seedlings of two dominant African rain-forest trees?
Authors: Norghauer Julian M. , Newbery David M. , Tedersoo Leho , Chuyong George B. 
Published: March 2010

Abstract:Where one or a few tree species reach local high abundance, different ecological factors may variously facilitate or hinder their regeneration. Plant pathogens are thought to be one of those possible agents which drive intraspecific density-dependent mortality of tree seedlings in tropical forests. Experimental evidence for this is scarce, however. In an African rain forest at Korup, we manipulated the density of recently established seedlings (~5–8 wk old; low vs. high-density) of two dominant species of contrasting recruitment potential, and altered their exposure to pathogens using a broad-spectrum fungicide. Seedling mortality of the abundantly recruiting subcanopy tree Oubanguia alata was strongly density-dependent after 7 mo, yet fungicide-treated seedlings had slightly higher mortality than controls. By contrast, seedling mortality of the poorly recruiting large canopy-emergent tree Microberlinia bisulcata was unaffected by density or fungicide. Ectomycorrhizal colonization of M. bisulcata was not affected by density or fungicide either. For O. alata, adverse effects of fungicide on its vesicular arbuscular mycorrhizas may have offset any possible benefit of pathogen removal. We tentatively conclude that fungal pathogens are not a likely major cause of density dependence in O. alata, or of early post-establishment mortality in M. bisulcata. They do not explain the latter's currently very low recruitment rate at Korup.
Migratory connectivity and conservation of the Amur Falcon Falco amurensis: a stable isotope perspective
Authors: SYMES CRAIG T. , WOODBORNE STEPHAN 
Published: March 2010

SummaryStable isotopes (δD, δ13C, δ15N) were measured in adult and juvenile Amur Falcon Falco amurensis feathers to understand the migratory connectivity of this species. Using the OIPC (Online Isotopes in Precipitation Calculator) and a calibration curve for American Kestrels Falco sparverius we predicted the breeding range of South African Amur Falcons in the Palaearctic. δD values for juvenile feathers (mean ± SE = -58.1 ± 2.5‰, range -83.9 to -25.7‰) and predicted Palaearctic annual precipitation values indicated that juvenile Amur Falcons in South Africa originated from across their entire Palaearctic range. This rejects the leapfrog migration hypothesis and suggests the widespread movement of birds south, with a funnelling effect into the subregion where they become concentrated over a narrower distribution range. Adult δDf values were more depleted (-37.4 ± 1.8‰, range = -71.3 to -9.3‰) than predicted annual precipitation values for sites where feathers moulted in South Africa (-20.2 ± 0.9‰) but there was no correlation between δDp and δDf. This, together with significant variation of δ13C among sites and annual fluctuations in roost sizes, suggests that roost site fidelity is low in the overwintering range. Populations not confined to breeding sites in South Africa are able to move widely across the subregion, feeding on a broad range of arthropods that become seasonally abundant during the austral summer. Total population estimates for South Africa are significantly lower than global estimates so a significant proportion of the population may not overwinter in South Africa or global populations are significantly lower than estimated. In South Africa, roosts that number hundreds to thousands of individuals are often in large exotic trees, e.g. Eucalyptus sp. They are often tolerant of disturbance at roosts which may be of little concern for their conservation. Habitat changes in the overwintering range in South Africa though, particularly due to agriculture, afforestation and strip mining, may affect global population numbers. There is also concern over the persecution of birds along their migratory route.
Three-Dimensional Optical Sectioning by Scanning Confocal Electron Microscopy with a Stage-Scanning System
Authors: Hashimoto Ayako , Shimojo Masayuki , Mitsuishi Kazutaka , Takeguchi Masaki 
Published: March 2010

AbstractWe evaluated the depth resolution of annular dark-field (ADF) scanning confocal electron microscopy (SCEM) with a stage-scanning system by observation of nanoparticles. ADF-SCEM is a three-dimensional (3D) imaging technique that we recently proposed. An ADF-SCEM instrument involves a pinhole aperture before a detector for rejecting electrons from the out-of-focal plane in a specimen and an annular aperture under the specimen for collecting only scattered electrons. The stage-scanning system enables us to directly obtain optical slice images perpendicular and parallel to an optical axis at a desired position. In particular, the parallel slices visualize the elongation of nanoparticles along the optical axis, which depends on the depth resolution. ADF-SCEM effectively reduced the elongation length of the nanoparticles sufficiently to demonstrate depth sectioning, in comparison with scanning transmission electron microscopy and bright-field SCEM. The experimentally obtained length was nearly equal to the theoretically estimated one from the probe size considering the experimental conditions. Furthermore, we applied this ADF-SCEM technique to analysis of the 3D position of catalytic nanoparticles on carbon nanostructures.
Organic agriculture and climate change
Authors: Scialabba Nadia El-Hage , Müller-Lindenlauf Maria 
Published: March 2010

AbstractThis article discusses the mitigation and adaptation potential of organic agricultural systems along three main features: farming system design, cropland management and grassland and livestock management. An important potential contribution of organically managed systems to climate change mitigation is identified in the careful management of nutrients and, hence, the reduction of N2O emissions from soils. Another high mitigation potential of organic agriculture lies in carbon sequestration in soils. In a first estimate, the emission reduction potential by abstention from mineral fertilizers is calculated to be about 20% and the compensation potential by carbon sequestration to be about 40–72% of the world's current annual agricultural greenhouse gas (GHG) emissions, but further research is needed to consolidate these numbers. On the adaptation side, organic agriculture systems have a strong potential for building resilient food systems in the face of uncertainties, through farm diversification and building soil fertility with organic matter. Additionally, organic agriculture offers alternatives to energy-intensive production inputs such as synthetic fertilizers which are likely to be further limited for poor rural populations by rising energy prices. In developing countries, organic agricultural systems achieve equal or even higher yields, as compared to the current conventional practices, which translate into a potentially important option for food security and sustainable livelihoods for the rural poor in times of climate change. Certified organic products cater for higher income options for farmers and, therefore, can serve as promoters for climate-friendly farming practices worldwide.
Are biotechnology and sustainable agriculture compatible?
Authors: Ervin David E. , Glenna Leland L. , Jussaume Raymond A. 
Published: March 2010

AbstractAgricultural biotechnology has been largely opposed by advocates in the sustainable agriculture movement, despite claims by the technology's proponents that it holds the promise to deliver both production (economic) and environmental benefits, two legs of the sustainability stool. We argue in this paper that participants in this polarized debate are talking past each other because assumptions about biotechnology and sustainability remain simplistic and poorly defined. Genetically engineered (GE) herbicide-resistant and insect-resistant crop varieties are the most visible current forms of agricultural biotechnology, and thus the form of biotechnology that many in the sustainability movement react to. However, these crops represent a biotechnology option that has paid insufficient attention to the integrated and systemic requirements of sustainable agriculture. In particular, common definitions of sustainable agriculture reinforce the need to include consideration of socio-economic distributive or equity effects into any assessment of sustainability. However, the frameworks that have been proposed to assess the potential for GE crops to enhance sustainable agriculture generally neglect this essential socio-economic dimension. We present an analysis that augments the sustainability frameworks to include the full suite of environmental, economic and social impacts. A review of the latest science on each impact category reveals that crop biotechnology cannot be fully assessed with respect to fostering a more sustainable agriculture due to key gaps in evidence, especially for socio-economic distributive effects. While the first generation of GE crops generally has made progress in reducing agriculture's environmental footprint and improving adopting farmers' economic well-being, we conclude that these early products fall short of the technology's capacity to promote a more sustainable agriculture because of the failure of those developing and promoting the technology to fully engage all stakeholders and address salient equity issues. To realize the sustainability potential of biotechnology will require fundamental changes in the way public and private research and technology development and commercialization are structured and operated. We identify new approaches in these areas that could make this powerful biological science more compatible with sustainable agriculture.
MRI and MRSI Application in Neurodegeneration
Authors: Sharma Rakesh 
Published: March 2010

AbstractMRI combined with MR spectroscopy generates better information of both brain tissue composition and mesurement of metabolites or neurochemicals in multiple sclerosis(MS), Alzheimer's disease and epilepsy. New fast imaging techniques are technical advance in visualizing accurate anatomy and measurement of absolute neurochemicals in brain. Gray metter seated MS lesions is a new form of disease and lesion may appear normal on MRI but show spectroscopy peaks. High magnetic field scanners are available for fast imaging.
Structural basis for the efficient phosphorylation of AZT-MP (3′-azido-3′-deoxythymidine monophosphate) and dGMP by Plasmodium falciparum type I thymidylate kinase
Authors: Whittingham Jean L. , Carrero-Lerida Juana , Brannigan James A. , Ruiz-Perez Luis M. , Silva Ana P. G. , Fogg Mark J. , Wilkinson Anthony J. , Gilbert Ian H. , Wilson Keith S. , González-Pacanowska Dolores 
Published: March 2010

Plasmodium falciparum is the causative agent of malaria, a disease where new drug targets are required due to increasing resistance to current anti-malarials. TMPK (thymidylate kinase) is a good candidate as it is essential for the synthesis of dTTP, a critical precursor of DNA and has been much studied due to its role in prodrug activation and as a drug target. Type I TMPKs, such as the human enzyme, phosphorylate the substrate AZT (3′-azido-3′-deoxythymidine)-MP (monophosphate) inefficiently compared with type II TMPKs (e.g. Escherichia coli TMPK). In the present paper we report that eukaryotic PfTMPK (P. falciparum TMPK) presents sequence features of a type I enzyme yet the kinetic parameters for AZT-MP phosphorylation are similar to those of the highly efficient E. coli enzyme. Structural information shows that this is explained by a different juxtaposition of the P-loop and the azide of AZT-MP. Subsequent formation of the transition state requires no further movement of the PfTMPK P-loop, with no steric conflicts for the azide moiety, allowing efficient phosphate transfer. Likewise, we present results that confirm the ability of the enzyme to uniquely accept dGMP as a substrate and shed light on the basis for its wider substrate specificity. Information resulting from two ternary complexes (dTMP–ADP and AZT-MP–ADP) and a binary complex with the transition state analogue AP5dT [P1-(5′-adenosyl)-P5-(5′-thymidyl) pentaphosphate] all reveal significant differences with the human enzyme, notably in the lid region and in the P-loop which may be exploited in the rational design of Plasmodium-specific TMPK inhibitors with therapeutic potential.
A joint x-ray and neutron study on amicyanin reveals the role of protein dynamics in electron transfer
Authors: Sukumar N. , Mathews F. S. , Langan P. , Davidson V. L. 
Published: March 2010

The joint x-ray/neutron diffraction model of the Type I copper protein, amicyanin from
Paracoccus denitrificans
was determined at 1.8 Å resolution. The protein was crystallized using reagents prepared in D
2
O. About 86% of the amide hydrogen atoms are either partially or fully exchanged, which correlates well with the atomic depth of the amide nitrogen atom and the secondary structure type, but with notable exceptions. Each of the four residues that provide copper ligands is partially deuterated. The model reveals the dynamic nature of the protein, especially around the copper-binding site. A detailed analysis of the presence of deuterated water molecules near the exchange sites indicates that amide hydrogen exchange is primarily due to the flexibility of the protein. Analysis of the electron transfer path through the protein shows that residues in that region are highly dynamic, as judged by hydrogen/deuterium exchange. This could increase the rate of electron transfer by transiently shortening through-space jumps in pathways or by increasing the atomic packing density. Analysis of C-H⋯X bonding reveals previously undefined roles of these relatively weak H bonds, which, when present in sufficient number can collectively influence the structure, redox, and electron transfer properties of amicyanin.
Fast molecular tracking maps nanoscale dynamics of plasma membrane lipids
Authors: Sahl Steffen J. , Leutenegger Marcel , Hilbert Michael , Hell Stefan W. , Eggeling Christian 
Published: March 2010

We describe an optical method capable of tracking a single fluorescent molecule with a flexible choice of high spatial accuracy (∼10–20 nm standard deviation or ∼20–40 nm full-width-at-half-maximum) and temporal resolution (< 1 ms). The fluorescence signal during individual passages of fluorescent molecules through a spot of excitation light allows the sequential localization and thus spatio-temporal tracking of the molecule if its fluorescence is collected on at least three separate point detectors arranged in close proximity. We show two-dimensional trajectories of individual, small organic dye labeled lipids diffusing in the plasma membrane of living cells and directly observe transient events of trapping on < 20 nm spatial scales. The trapping is cholesterol-assisted and much more pronounced for a sphingo- than for a phosphoglycero-lipid, with average trapping times of ∼15 ms and < 4 ms, respectively. The results support previous STED nanoscopy measurements and suggest that, at least for nontreated cells, the transient interaction of a single lipid is confined to macromolecular dimensions. Our experimental approach demonstrates that fast molecular movements can be tracked with minimal invasion, which can reveal new important details of cellular nano-organization.
Structure of lactococcal phage p2 baseplate and its mechanism of activation
Authors: Sciara Giuliano , Bebeacua Cecilia , Bron Patrick , Tremblay Denise , Ortiz-Lombardia Miguel , Lichière Julie , van Heel Marin , Campanacci Valérie , Moineau Sylvain , Cambillau Christian 
Published: March 2010

Siphoviridae
is the most abundant viral family on earth which infects bacteria as well as archaea. All known siphophages infecting gram+
Lactococcus lactis
possess a baseplate at the tip of their tail involved in host recognition and attachment. Here, we report analysis of the p2 phage baseplate structure by X-ray crystallography and electron microscopy and propose a mechanism for the baseplate activation during attachment to the host cell. This ∼1 MDa,
Escherichia coli
-expressed baseplate is composed of three protein species, including six trimers of the receptor-binding protein (RBP). RBPs host-recognition domains point upwards, towards the capsid, in agreement with the electron-microscopy map of the free virion. In the presence of Ca
2+
, a cation mandatory for infection, the RBPs rotated 200° downwards, presenting their binding sites to the host, and a channel opens at the bottom of the baseplate for DNA passage. These conformational changes reveal a novel siphophage activation and host-recognition mechanism leading ultimately to DNA ejection.
ErbB3/HER3 intracellular domain is competent to bind ATP and catalyze autophosphorylation
Authors: Shi Fumin , Telesco Shannon E. , Liu Yingting , Radhakrishnan Ravi , Lemmon Mark A. 
Published: March 2010

ErbB3/HER3 is one of four members of the human epidermal growth factor receptor (EGFR/HER) or ErbB receptor tyrosine kinase family. ErbB3 binds neuregulins via its extracellular region and signals primarily by heterodimerizing with ErbB2/HER2/Neu. A recently appreciated role for ErbB3 in resistance of tumor cells to EGFR/ErbB2-targeted therapeutics has made it a focus of attention. However, efforts to inactivate ErbB3 therapeutically in parallel with other ErbB receptors are challenging because its intracellular kinase domain is thought to be an inactive pseudokinase that lacks several key conserved (and catalytically important) residues—including the catalytic base aspartate. We report here that, despite these sequence alterations, ErbB3 retains sufficient kinase activity to robustly
trans
-autophosphorylate its intracellular region—although it is substantially less active than EGFR and does not phosphorylate exogenous peptides. The ErbB3 kinase domain binds ATP with a
K
d
of approximately 1.1 μM. We describe a crystal structure of ErbB3 kinase bound to an ATP analogue, which resembles the inactive EGFR and ErbB4 kinase domains (but with a shortened αC-helix). Whereas mutations that destabilize this configuration activate EGFR and ErbB4 (and promote EGFR-dependent lung cancers), a similar mutation conversely inactivates ErbB3. Using quantum mechanics/molecular mechanics simulations, we delineate a reaction pathway for ErbB3-catalyzed phosphoryl transfer that does not require the conserved catalytic base and can be catalyzed by the “inactive-like” configuration observed crystallographically. These findings suggest that ErbB3 kinase activity within receptor dimers may be crucial for signaling and could represent an important therapeutic target.
An algorithm for interpolation in the pyramid domain‡
Authors: Guitton Antoine , Claerbout Jon 
Published: March 2010

ABSTRACTWith the pyramid transform, 2D dip spectra can be characterized by 1D prediction‐error filters (pefs) and 3D dip spectra by 2D pefs. These filters, contrary to pefs estimated in the frequency‐space domain (ω, x), are frequency independent. Therefore, one pef can be used to interpolate all frequencies. Similarly, one pef can be computed from all frequencies, thus yielding robust estimation of the filter in the presence of noise. This transform takes data from the frequency‐space domain (ω, x) to data in a frequency‐velocity domain (ω, u=ω·x) using a simple mapping procedure that leaves locations in the pyramid domain empty. Missing data in (ω, x)‐space create even more empty bins in (ω, u)‐space. We propose a multi‐stage least‐squares approach where both unknown pefs and missing data are estimated. This approach is tested on synthetic and field data examples where aliasing and irregular spacing are present.
Understanding the HER family in breast cancer: interaction with ligands, dimerization and treatments
Authors: Barros Fabrício F T , Powe Desmond G , Ellis Ian O , Green Andrew R 
Published: March 2010

Barros F F T, Powe D G, Ellis I O & Green A R (2010) Histopathology56, 560–572 Understanding the HER family in breast cancer: interaction with ligands, dimerization and treatments Breast carcinoma is the most frequent type of cancer affecting women. Among the recently described molecular and phenotypic classes of breast cancer, human epidermal growth factor receptor 2 (HER2)‐positive tumours are associated with a poor prognosis. HER2 plays an important role in cancer progression being targeted to provide predictive and prognostic information. Moreover, HER2 is related to cancer resistance against a variety of therapies; however, trastuzumab (herceptin) has proved successful in treatment of this subgroup. Nevertheless, resistance to this drug may be acquired by patients after a period of treatment, which indicates that other molecular mechanisms might influence success of this therapy. Dimerization between members of the HER family may contribute to resistance against treatments due to different combinations that trigger different downstream pathways. This is promoted by ligands, which are expressed as transmembrane precursor protein molecules and have a conserved epidermal growth factor‐like domain. Through resistance to trastuzumab, other drugs are being developed to interact in different domains of HER2 protein. It might be a good strategy to apply new drugs simultaneously to trastuzumab due to act in different domains of HER2. The study of interaction between receptors/ligands will characterize specifically their signalling pathway and understand which strategy to acquire.
High level of apoptosis and low AKT activation in mass screening as opposed to standard neuroblastoma
Authors: Sartelet Hervé , Ohta Shigeru , Barrette Stephane , Rougemont Anne‐Laure , Brevet Marie , Regairaz Marie , Harvey Isabelle , Bernard Chantal , Fabre Monique , Gaboury Louis , Oligny Luc L , Bosq Jacques , Valteau‐Couanet Dominique , Vassal Gilles 
Published: March 2010

Sartelet H, Ohta S, Barrette S, Rougemont A‐Laure, Brevet M, Regairaz M, Harvey I, Bernard C, Fabre M, Gaboury L, Oligny L L, Bosq J, Valteau‐Couanet D & Vassal G (2010) Histopathology56, 607–616 High level of apoptosis and low AKT activation in mass screening as opposed to standard neuroblastoma Aims:  Neuroblastoma is a paediatric solid tumour with a poor outcome except in children <1 year old. Based on catecholamine urinary excretion, mass screening (MS) programmes have been organized but failed to decrease the mortality of this tumour. To test the hypotheses of a spontaneous maturation/differentiation or regression, the levels of poly (ADP‐ribose) polymerase (PARP)‐1, an early apoptosis marker, of PhosphoAKT, a major apoptosis inhibitor, and of maturation/differentiation were compared in standard and in MS neuroblastomas.Methods and results:  We performed a case–control study of 55 primary tumours and 21 metastases of MS neuroblastomas. Matched controls were standard unscreened neuroblastomas and were paired according to age, stage, and MYCN amplification. The tumours were included in tissue microarrays. Immunohistochemical staining was performed using antibodies against, AKT, phosphoAKT, TRKB and PARP‐1. The expression of PARP‐1 and that of phosphoAKT were significantly higher in standard than in MS neuroblastomas independently of age and stage of the tumour. PhosphoAKT and PARP‐1 expression was significantly correlated in both tumours.Conclusions:  These data suggest that the better prognosis of patients with MS neuroblastomas compared with classical neuroblastomas was secondary to spontaneous tumour regression mediated by higher levels of apoptosis associated with low activation of AKT.