bluuebunny/crossref_metadata_2025 huggingface dataset:
Forest cover change patterns in Myanmar (Burma) 1990–2000
Authors: LEIMGRUBER PETER , KELLY DANIEL S. , STEININGER MARC K. , BRUNNER JAKE , MÜLLER THOMAS , SONGER MELISSA
Published: December 2005

Myanmar is one of the most forested countries in mainland South-east Asia. These forests support a large number of important species and endemics and have great value for global efforts in biodiversity conservation. Landsat satellite imagery from the 1990s and 2000s was used to develop a countrywide forest map and estimate deforestation. The country has retained much of its forest cover, but forests have declined by 0.3% annually. Deforestation varied considerably among administrative units, with central and more populated states and divisions showing the highest losses. Ten deforestation hotspots had annual deforestation rates well above the countrywide average. Major reasons for forest losses in these hotspots stemmed from increased agricultural conversion, fuelwood consumption, charcoal production, commercial logging and plantation development. While Myanmar continues to be a stronghold for closed canopy forests, several areas have been experiencing serious deforestation. Most notable are the mangrove forests in the Ayeyarwady delta region and the remaining dry forests at the northern edge of the central dry zone.
The importance of the lexicon in tagging biological text
Authors: SMITH LAWRENCE H. , RINDFLESCH THOMAS C. , WILBUR W. JOHN
Published: December 2005

A part-of-speech tagger is a fundamental and indispensable tool in computational linguistics, typically employed at the critical early stages of processing. Although taggers are widely available that achieve high accuracy in very general domains, these do not perform nearly as well when applied to novel specialized domains, and this is especially true with biological text. We present a stochastic tagger that achieves over 97.44% accuracy on MEDLINE abstracts. A primary component of the tagger is its lexicon which enumerates the permitted parts-of-speech for the 10000 words most frequently occurring in MEDLINE. We present evidence for the conclusion that the lexicon is as vital to tagger accuracy as a training corpus, and more important than previously thought.
Lake surface water temperature retrieval using advanced very high resolution radiometer and Moderate Resolution Imaging Spectroradiometer data: Validation and feasibility study
Authors: Oesch D. C. , Jaquet J.‐M. , Hauser A. , Wunderle S.
Published: December 2005

In this study we prove the feasibility of the advanced very high resolution radiometer (AVHRR) and Moderate Resolution Imaging Spectroradiometer sea surface temperature algorithms to derive operational lake surface water temperature (LSWT). A validation study covering 2 years was done using data from the AVHRR on NOAA 12, 15, 16, and 17, the MODIS on TERRA, and AQUA and with different method‐ingested in situ data from different sized lakes. Best results were found for NOAA 16 nighttime data at Lake Geneva (bias of 0.18 K and standard deviation of 0.73 K) and TERRA nighttime data at Lake Constance (satellite‐buoy bias of −0.08 K and standard deviation of 0.92 K). For all sensor families an overall scatter ranging from 0.9 to 1.6 K was found. Bias of MODIS is larger, −1.73 to 1.9 K, than the one of the AVHRR (−0.28 to 1.5 K). The current orbital configuration of the platforms used revealed the diurnal evolution of the lake surface temperature amplitude from space. The damped mixing found for a typical calm and clear‐sky regime is different from open ocean conditions. As the main error source, we found undetected cloudy pixel. Furthermore, the physical difference between skin and bulk temperature, especially its relation to the diurnal thermocline, solar insolation, and wind stress contributes to the bias and scatter within the match‐up data set. The data sets have been validated to allow further application for LSWT climatology and assimilation into numerical weather prediction models.
Accurate consideration of metal losses at waveguide junctions using admittance and impedance integral equation formulations
Authors: Taroncher M. , Hueso J. , Cogollos S. , Gimeno B. , Boria V. E. , Vidal A. , Esteban H. , Guglielmi M.
Published: December 2005

At higher frequencies, metal loss effects in passive waveguide components become more pronounced and hazardous. In this paper, we propose two integral equation techniques, based on the generalized admittance and impedance matrices, for the accurate consideration of losses in the metal walls of waveguide junctions. Both techniques have been evaluated in terms of accuracy and numerical efficiency, and conclusions are drawn regarding the best properties of the admittance parameter formulation. Finally, combining such technique with a classical perturbative method for considering propagation losses, we have successfully predicted all loss effects in two real waveguide filters used for commercial applications.
Structural and petrological constraints on the tectonic evolution of the garnet‐lherzolite facies Higashi‐akaishi peridotite body, Sanbagawa belt, SW Japan
Authors: Mizukami Tomoyuki , Wallis Simon R.
Published: December 2005

The Higashi‐akaishi peridotite body in the Sanbagawa metamorphic belt is a unique example of a kilometer‐scale body including garnet‐lherzolite facies rocks from an oceanic subduction‐type orogen. In this body, four distinct deformational phases D1, D2, D3, and D4 can be defined. The tectonic significance of D1 is unclear. Microstructural observations and application of garnet‐orthopyroxene geothermobarometry suggest that D2 took place during high‐temperature subduction up to depths of ∼100 km (from 2.3 GPa to above 2.8 GPa at temperature of 700–800°C) or more. D3 represents a major phase of exhumation. After exhumation the Higashi‐akaishi body became juxtaposed with the adjacent Besshi and Eclogite units at a depth of around 35 km (1 GPa). The common history of the two units after D3 is shown by the intertectonic growth of tremolite between D3 and D4 that corresponds to a stage of intertectonic growth of plagioclase in the Besshi and Eclogite units. Both the spatial distribution and the estimated pressure‐temperature (P‐T) conditions of this intertectonic phase of mineral growth in the different units are in excellent agreement. The development of an antigorite schistosity during the late stage of D2 indicates an anticlockwise P‐T path with cooling at depths of around 100 km. The association of the antigorite‐bearing fabric and the onset of exhumation after the D2 stage suggest that the density decrease due to antigorite formation may have been sufficient to trigger the exhumation of dense ultramafic body from UHP conditions in subduction zones. Syn‐D2 water introduction and the anticlockwise P‐T path are expected when convection in the mantle wedge brings peridotite toward a subduction boundary through mantle wedge or when peridotite is dragged down along a subduction boundary that is progressively cooling immediately after initiation of subduction.
Constraints on climate change from a multi‐thousand member ensemble of simulations
Authors: Piani C. , Frame D. J. , Stainforth D. A. , Allen M. R.
Published: December 2005

The first multi thousand member “perturbed physics” ensemble simulation of present and future climate, completed by the distributed computing project climateprediction.net, is used to search for constraints on the response to increasing greenhouse gas levels among present day observable climate variables. The search is conducted with a systematic statistical methodology to identify correlations between observables and the quantities we wish to predict, namely the climate sensitivity and the climate feedback parameter. A sensitivity analysis is conducted to ensure that results are minimally dependent on the parameters of the methodology. Our best estimate of climate sensitivity is 3.3 K. When an internally consistent representation of the origins of model‐data discrepancy is used to calculate the probability density function of climate sensitivity, the 5th and 95th percentiles are 2.2 K and 6.8 K respectively. These results are sensitive, particularly the upper bound, to the representation of the origins of model‐data discrepancy.
On RCM‐based projections of change in southern African summer climate
Authors: Tadross Mark , Jack Chris , Hewitson Bruce
Published: December 2005

Two regional climate models (RCMs) are used to downscale 10 years of control and 10 years of future (2070–2079) southern African climate, as simulated by the HadAM3 general circulation model forced with the A2 SRES emissions scenario. Changes in early and late summer season total rainfall, rain days and average surface temperature are presented for the projected future climate. The two RCMs indicate broadly consistent changes over the region as a whole. However, time‐ and location‐dependent differences are apparent, especially in the simulated magnitude of change, due to different representations of each model's internal physics and local hydrological cycle.
Relative importance of fluvial input and wave energy in controlling the timescale for distributary‐channel avulsion
Authors: Swenson John B.
Published: December 2005

Existing avulsion models are decoupled from nearshore processes. Here, I explore quantitatively how the interplay of wave energy with fluvial input of sediment and water controls the aggradation rate and avulsion timescale of a single distributary channel. My approach rigorously couples a diffusive, moving‐boundary theory of fluvial morphodynamics with a diffusive treatment of shoreface morphodynamics. I use this deterministic model to quantify the time required for channel‐belt superelevation, normalized with channel depth, to attain a threshold value for nodal avulsion at a specified channel location. Increasing the long‐term wave energy relative to fluvial input by an order of magnitude increases longshore sediment dispersal, thereby reducing the rate of channel‐belt aggradation and associated seaward extension and increasing the avulsion timescale by a factor of approximately 50. Far‐field processes eventually limit the ability of wave energy to suppress avulsion.
Estuaries are not so unique
Authors: Prandle David , Lane Andrew , Manning Andrew J.
Published: December 2005

The applicability of recent theories relating tides and river flow to estuarine bathymetry has been assessed against observations from UK estuaries. These theories, combined with observations, show that variations between estuaries are limited by how tides and river flow control sediments and bathymetry. Typical ages were determined from differences between theoretical and observed depths for Rias (11000 years), Coastal Plain (15000 years) and Bar‐Built (100 years) estuaries. The theories can explain the estuarine bathymetry without needing to account for the sediments, suggesting that it is the bathymetry which determines the sediment regime within the estuary.
Evolution and characteristics of global Pc5 ULF waves during a high solar wind speed interval
Authors: Rae I. J. , Donovan E. F. , Mann I. R. , Fenrich F. R. , Watt C. E. J. , Milling D. K. , Lester M. , Lavraud B. , Wild J. A. , Singer H. J. , Rème H. , Balogh A.
Published: December 2005

We present an interval of extremely long‐lasting narrow‐band Pc5 pulsations during the recovery phase of a large geomagnetic storm. These pulsations occurred continuously for many hours and were observed throughout the magnetosphere and in the dusk‐sector ionosphere. The subject of this paper is the favorable radial alignment of the Cluster, Polar, and geosynchronous satellites in the dusk sector during a 3‐hour subset of this interval that allows extensive analysis of the global nature of the pulsations and the tracing of their energy transfer from the solar wind to the ground. Virtually monochromatic large‐amplitude pulsations were observed by the CANOPUS magnetometer chain at dusk for several hours, during which the Cluster spacecraft constellation traversed the dusk magnetopause. The solar wind conditions were very steady, the solar wind speed was fast, and time series analysis of the solar wind dynamic pressure shows no significant power concentrated in the Pc5 band. The pulsations are observed in both geosynchronous electron and magnetic field data over a wide range of local times while Cluster is in the vicinity of the magnetopause providing clear evidence of boundary oscillations with the same periodicity as the ground and geosynchronous pulsations. Furthermore, the Polar spacecraft crossed the equatorial dusk magnetosphere outside of geosynchronous orbit (L ∼ 6–9) and observed significant electric and magnetic perturbations around the same quasi‐stable central frequency (1.4–1.6 mHz). The Poynting vector observed by the Polar spacecraft associated with these pulsations has strong field‐aligned oscillations, as expected for standing Alfvén waves, as well as a nonzero azimuthal component, indicating a downtail component to the energy propagation. In the ionosphere, ground‐based magnetometers observed signatures characteristic of a field‐line resonance, and HF radars observed flows as a direct consequence of the energy input. We conclude that the most likely explanations is that magnetopause oscillations couple energy to field lines close to the location of Polar, setting up standing Alfvén waves along the resonant field lines which are then also observed in the ionosphere. In the absence of monochromatic dynamic pressure variations in the solar wind, this event is a potential example where discrete frequency pulsations in the magnetosphere result from the excitation of a magnetospheric waveguide mode, perhaps excited via the Kelvin‐Helmoltz instability or via overreflection at the duskside magnetopause.
Electron density images of the middle‐ and high‐latitude magnetosphere in response to the solar wind
Authors: Tu Jiannan , Song Paul , Reinisch Bodo W. , Huang Xueqin , Green James L. , Frey Harald U. , Reiff Patricia H.
Published: December 2005

Electron density distributions and plasma dynamics in the middle‐ and high‐latitude dayside magnetosphere are studied with observations from the IMAGE radio plasma imager. Remote measurements of the electron densities along magnetic field lines were made before and during a magnetic storm when the solar wind and interplanetary magnetic field (IMF) impinging on the magnetopause varied considerably. Several regions of different density distribution characteristics, including plasmasphere, plasma trough, subauroral/auroral density depletion, density enhancements in the aurora/cusp, and polar cap, are identified in “two‐dimensional images,” i.e., along the satellite orbit and field lines. The plasma dynamics, such as the plasma refilling in the outer plasmasphere and the plasma acceleration in the aurora/cusp region, are inferred from density gradients along the field lines. It is shown that the densities and locations of the plasma regions vary in accordance with the solar wind, particularly with the IMF variations for the case examined. In the partial recovery phase of the magnetic storm when the IMF was northward, the density depletion region expanded to wider latitude range and extended to lower altitudes, with much lower densities than those in the density depletion regions of the other RPI measurement periods. The density enhancements associated with the aurora/cusp region were not visible, possibly because of the diffusive nature of the dayside aurora and higher‐latitude location of the cusp during this period. At the peak of the storm, characterized by a persistent southward IMF Bz, all plasma regions moved to lower L shells. The results imply that the solar wind/IMF effects should be included in any statistical study of the electron density distributions in these regions.
Geophysical constraints on the composition and structure of the Martian interior
Authors: Sohl Frank , Schubert Gerald , Spohn Tilman
Published: December 2005

Most recent Martian interior structure models are based on the planet's polar moment of inertia C, although the mean moment of inertia I is required for constructing spherically symmetric models of planetary interiors. Using the improved value of C/MpRp2 recently obtained from a combined reanalysis of the entire set of radio science data collected during the last three decades and accounting for the rotationally and topographically induced shape of the planet's gravitational field, we find a mean moment‐of‐inertia factor of I/MpRp2 = 0.3635 ± 0.0012. The new lower value suggests a core radius several tens of kilometers larger if other parameters like core density, crust density, and crust thickness are fixed. It further implies that the Martian crust is several tens of kilometers thicker than previously thought if crust and mantle densities and core size are given. Moreover, the Martian mantle may be less dense, about several tens of kg m−3, with a smaller iron content than previously thought if crust thickness and core size are specified. The mantle density of Mars is relatively well determined by the planet's moment of inertia factor if crust thickness and density are specified.
Electromagnetic diffraction at skew incidence by a wedge with anisotropic impedance faces
Authors: Yuan Fei , Zhu Guo Qiang
Published: December 2005

The asymptotic expressions for the total field excited by a plane wave obliquely incident on a wedge with anisotropic impedance faces are represented in the framework of the uniform geometrical theory of diffraction. The problem of decoupling the functional difference equations is solved by applying the perturbation technique on the basis of two analytical solutions: normal incidence and grazing to the edge incidence. The numerical results agree well with those presented in published papers and provide a uniform and continuous behavior of the field dependent upon the skewness of the incident wave outside the wedge region.
CD16b associates with high-density, detergent-resistant membranes in human neutrophils
Authors: Fernandes Maria J. G. , Rollet-Labelle Emmanuelle , Paré Guillaume , Marois Sébastien , Tremblay Marie-Lisane , Teillaud Jean-Luc , Naccache Paul H.
Published: December 2005

CD16b is unique in that it is the only Fc receptor linked to the plasma membrane by a GPI (glycosylphosphatidylinositol) anchor. GPI-anchored proteins often preferentially localize to DRMs (detergent-resistant membranes) that are rich in sphingolipids and cholesterol and play an important role in signal transduction. Even though the responses to CD16b engagement have been intensively investigated, the importance of DRM integrity for CD16b signalling has not been characterized in human neutrophils. We provide direct evidence that CD16b constitutively partitions with both low- and high-density DRMs. Moreover, upon CD16b engagement, a significant increase in the amount of the receptor is observed in high-density DRMs. Similarly to CD16b, CD11b also resides in low- and high-density DRMs. In contrast with CD16b, the partitioning of CD11b in DRMs does not change in response to CD16b engagement. We also provide evidence for the implication of Syk in CD16b signalling and its partitioning to DRMs in resting and activated PMNs (polymorphonuclear neutrophils). Additionally, DRM-disrupting agents, such as nystatin and methyl-β-cyclodextrin, alter cellular responses to CD16b receptor ligation. Notably, a significant increase in the mobilization of intracellular Ca2+ and in tyrosine phosphorylation of intracellular substrates after CD16b engagement is observed. Altogether, the results of this study provide evidence that high-density DRMs play a role in CD16b signalling in human neutrophils.
SMAD 8 binding to mice Msx1 basal promoter is required for transcriptional activation
Authors: Binato Renata , Alvarez Martinez Cristina E. , Pizzatti Luciana , Robert Benoit , Abdelhay Eliana
Published: December 2005

The Msx1 gene in mice has been proven to be induced by BMP (bone morphogenetic protein) proteins, and three binding sites for SMAD, an intracellular BMP signalling transducer, have already been identified in its promoter. Gel shift analyses were performed and they demonstrated that the consensus found very near the transcription start site, a region designed BP (basal promoter), is functional for binding nuclear proteins from 10.5, 11.5 and 13.5 dpc (days post-coitum) embryos. Notably, this binding occurs only when the SMAD-binding consensus sequence is maintained, suggesting that it is required for the formation of a protein complex over BP. Binding of purified SMAD 1 and SMAD 4 as well as supershift assay with SMAD 1/SMAD 5/SMAD 8 antibody proved that a SMAD protein is present in this complex. Transfection assays in cell cultures with fragments from BP driving the expression of luciferase confirmed that only in the presence of the SMAD consensus site is Msx1 expression activated. A proteomic analysis of the complex components after immunoprecipitation identified several proteins necessary to activate transcription including SMAD 8. Our results suggest that BMP2/BMP4 signalling through SMAD 8 is required for transcriptional activation of the mouse Msx1 gene.
Expression of UCP3 in CHO cells does not cause uncoupling, but controls mitochondrial activity in the presence of glucose
Authors: Mozo Julien , Ferry Gilles , Studeny Aurélie , Pecqueur Claire , Rodriguez Marianne , Boutin Jean A. , Bouillaud Frédéric
Published: December 2005

The proton-transport activity of UCP1 (uncoupling protein 1) triggers mitochondrial uncoupling and thermogenesis. The exact role of its close homologues, UCP2 and UCP3, is unclear. Mounting evidence associates them with the control of mitochondrial superoxide production. Using CHO (Chinese-hamster ovary) cells stably expressing UCP3 or UCP1, we found no evidence for respiration uncoupling. The explanation lies in the absence of an appropriate activator of UCP protonophoric function. Accordingly, the addition of retinoic acid uncouples the respiration of the UCP1-expressing clone, but not that of the UCP3-expressing ones. In a glucose-containing medium, the extent of the hyperpolarization of mitochondria by oligomycin was close to 22 mV in the five UCP3-expressing clones, contrasting with the variable values observed with the 15 controls. Our observations suggest that, when glycolysis and mitochondria generate ATP, and in the absence of appropriate activators of proton transport, UCPs do not transport protons (uncoupling), but rather other ions of physiological relevance that control mitochondrial activity. A model is proposed using the known passive transport of pyruvate by UCP1.
The hnRNPs F and H2 bind to similar sequences to influence gene expression
Authors: Alkan Serkan A. , Martincic Kathleen , Milcarek Christine
Published: December 2005

The hnRNPs (heterogeneous nuclear ribonucleoproteins) F and H2 share a similar protein structure. Both have been implicated as regulating polyadenylation, but hnRNP H2 had a positive effect, whereas hnRNP F acted negatively. We therefore carried out side-by-side comparisons of their RNA-binding and in vivo actions. The binding of the CstF2 (64 kDa cleavage stimulatory factor) to SV40 (simian virus 40) late pre-mRNA substrates containing a downstream GRS (guanine-rich sequence) was reduced by hnRNP F, but not by hnRNP H2, in a UV-cross-linking assay. Point mutations of the 14-nt GRS influenced the binding of purified hnRNP F or H2 in parallel. Co-operative binding of the individual proteins to RNA was lost with mutations of the GRS in the G1−5 or G12−14 regions; both regions seem to be necessary for optimal interactions. Using a reporter green fluorescent protein assay with the GRS inserted downstream of the poly(A) (polyadenine) signal, expression in vivo was diminished by a mutant G1−5 sequence which decreased binding of both hnRNPs (SAA20) and was enhanced by a 12–14-nt mutant that showed enhanced hnRNP F or H2 binding (SAA10). Using small interfering RNA, down-regulation of hnRNP H2 levels diminished reporter expression, confirming that hnRNP H2 confers a positive influence; in contrast, decreasing hnRNP F levels had a negligible influence on reporter expression with the intact GRS. A pronounced diminution in reporter expression was seen with the SAA20 mutant for both. Thus the relative levels of hnRNP F and H2 in cells, as well as the target sequences in the downstream GRS on pre-mRNA, influence gene expression.
Archaeal Pyrococcus furiosus thymidylate synthase 1 is an RNA-binding protein
Authors: Kanai Akio , Sato Asako , Imoto Jun , Tomita Masaru
Published: December 2005

Using a stem–loop RNA oligonucleotide (19-mer) containing an AUG sequence in the loop region as a probe, we screened the protein library from a hyperthermophilic archaeon, Pyrococcus furiosus, and found that a flavin-dependent thymidylate synthase, Pf-Thy1 (Pyrococcus furiosus thymidylate synthase 1), possessed RNA-binding activity. Recombinant Pf-Thy1 was able to bind to the stem–loop structure at a high temperature (75 °C) with an apparent dissociation constant of 0.6 μM. A similar stem–loop RNA structure was located around the translation start AUG codon of Pf-Thy1 RNA, and gel-shift analysis revealed that Pf-Thy1 could also bind to this stem–loop structure. In vitro translation analysis using chimaeric constructs containing the stem–loop sequence in their Pf-Thy1 RNA and a luciferase reporter gene indicated that the stem–loop structure acted as an inhibitory regulator of translation by preventing the binding of its Shine–Dalgarno-like sequence by positioning it in the stem region. Addition of Pf-Thy1 into the in vitro translation system also inhibited translation. These results suggested that this class of thymidylate synthases may autoregulate their own translation in a manner analogous to that of the well characterized thymidylate synthase A proteins, although there is no significant amino acid sequence similarity between them.
Tid1 is a Smad-binding protein that can modulate Smad7 activity in developing embryos
Authors: Torregroza Ingrid , Evans Todd
Published: December 2005

In a search for binding partners to Smad8, we identified the chicken homologue of the mammalian Tid1 protein (cTid1), which is a regulator of apoptosis related to the Drosophila tumour suppressor Tid56. The cTid1 coding sequence is highly conserved with mammalian Tid1, including the DnaJ domain that interacts with Hsp70 (heat-shock protein 70). The cTid1 gene is widely expressed with transcripts enriched in the developing blood islands of the embryonic-yolk sac. We show that cTid1 can bind to other members of the Smad family and that highest binding activity occurs with the negative regulatory Smad7, through the conserved MH2 domain. This interaction can have functional relevance in vivo, since co-expression of Tid1 blocks the dorsalizing and BMP (bone morphogenetic protein)-dependent regulatory activity of Smad7 in developing Xenopus embryos. The finding that these proteins can interact suggests the potential for linking two important cell survival/apoptosis pathways.
Role of MKK3 and p38 MAPK in cytokine-induced death of insulin-producing cells
Authors: Makeeva Natalia , Myers Jason W. , Welsh Nils
Published: December 2005

The aim of the present investigation was to elucidate further the importance of p38 MAPK (mitogen-activated protein kinase) in nitric oxide- and cytokine-induced β-cell death. For this purpose, isolated human islets were treated with d-siRNA (diced small interfering RNA) and then exposed to the nitric oxide donor DETA/NONOate [2,2′-(hydroxynitrosohydrazono)bis-ethanamine]. We observed that cells treated with p38α-specific d-siRNA, but not with d-siRNA targeting GL3 (a firefly luciferase siRNA plasmid) or PKCδ (protein kinase Cδ), were protected against nitric oxide-induced death. This was paralleled by an increased level of Bcl-XL (B-cell leukaemia/lymphoma-X long). For an in-depth study of the mechanisms of p38 activation, MKK3 (MAPK kinase 3), MKK6 and their dominant-negative mutants were overexpressed in insulin-producing RIN-5AH cells. In transient transfections, MKK3 overexpression resulted in increased p38 phosphorylation, whereas in stable MKK3-overexpressing RIN-5AH clones, the protein levels of p38 and JNK (c-Jun N-terminal kinase) were decreased, resulting in unaffected phospho-p38 levels. In addition, a long-term MKK3 overexpression did not affect cell death rates in response to the cytokines interleukin-1β and interferon-γ, whereas a short-term MKK3 expression resulted in increased cytokine-induced RIN-5AH cell death. The MKK3-potentiating effect on cytokine-induced cell death was abolished by a nitric oxide synthase inhibitor, and MKK3-stimulated p38 phosphorylation was enhanced by inhibitors of phosphatases. Finally, as the dominant-negative mutant of MKK3 did not affect cytokine-induced p38 phosphorylation, and as wild-type MKK3 did not influence p38 autophosphorylation, it may be that p38 is activated by MKK3/6-independent pathways in response to cytokines and nitric oxide. In addition, it is likely that a long-term increase in p38 activity is counteracted by both a decreased expression of the p38, JNK and p42 genes as well as an increased dephosphorylation of p38.
Probing the substrate binding site of Candida tenuis xylose reductase (AKR2B5) with site-directed mutagenesis
Authors: Kratzer Regina , Leitgeb Stefan , Wilson David K. , Nidetzky Bernd
Published: December 2005

Little is known about how substrates bind to CtXR (Candida tenuis xylose reductase; AKR2B5) and other members of the AKR (aldo–keto reductase) protein superfamily. Modelling of xylose into the active site of CtXR suggested that Trp23, Asp50 and Asn309 are the main components of pentose-specific substrate-binding recognition. Kinetic consequences of site-directed substitutions of these residues are reported. The mutants W23F and W23Y catalysed NADH-dependent reduction of xylose with only 4 and 1% of the wild-type efficiency (kcat/Km) respectively, but improved the wild-type selectivity for utilization of ketones, relative to xylose, by factors of 156 and 471 respectively. Comparison of multiple sequence alignment with reported specificities of AKR members emphasizes a conserved role of Trp23 in determining aldehyde-versus-ketone substrate selectivity. D50A showed 31 and 18% of the wild-type catalytic-centre activities for xylose reduction and xylitol oxidation respectively, consistent with a decrease in the rates of the chemical steps caused by the mutation, but no change in the apparent substrate binding constants and the pattern of substrate specificities. The 30-fold preference of the wild-type for D-galactose compared with 2-deoxy-D-galactose was lost completely in N309A and N309D mutants. Comparison of the 2.4 Å (1 Å=0.1 nm) X-ray crystal structure of mutant N309D bound to NAD+ with the previous structure of the wild-type holoenzyme reveals no major structural perturbations. The results suggest that replacement of Asn309 with alanine or aspartic acid disrupts the function of the original side chain in donating a hydrogen atom for bonding with the substrate C-2(R) hydroxy group, thus causing a loss of transition-state stabilization energy of 8–9 kJ/mol.
Biotinylation of glycan chains in β2 glycoprotein I induces dimerization of the molecule and its detection by the human autoimmune anti-cardiolipin antibody EY2C9
Authors: Dupuy d'Angeac Arnaud , Stefas Ilias , Graafland Hubert , de Lamotte Frédéric , Rucheton Marcel , Palais Caroline , Eriksson Anna-Karin , Bosc Priscille , Rosé Caroline , Chicheportiche Robert
Published: December 2005

Binding of β2GPI (β2 glycoprotein I), a human plasma protein, to AnPLs (anionic phospholipids) plays a key role in the formation of antiphospholipid antibodies involved in autoimmune diseases like antiphospholipid syndrome or systemic lupus erythematosus. We recently showed that binding of β2GPI to AnPLs was enhanced by biotinylation of its glycan chains with biotin-hydrazide. In the present study, we investigated why this chemical modification of β2GPI increased both its affinity for AnPLs and its recognition by anti-cardiolipin antibodies. Electrophoretic analysis showed that: (i) high molecular mass β2GPI (dimers and other oligomers) covalently coupled by imine bonds, were present in variable amounts in oxidized β2GPI and in β2GPI-bh (β2GPI-biotin-hydrazide), but were absent in native β2GPI; (ii) binding of β2GPI-bh to phosphatidylserine-coated microtitre plates generated high molecular mass polymers in a time-dependent manner. Native β2GPI did not polymerize in these conditions. These polymers did not bind more strongly to AnPLs than the monomer β2GPI. However, in solution at 1 μM β2GPI-bh essentially appeared as a dimer as revealed by light-scattering analysis. SPR (surface plasmon resonance) analysis showed that the increased affinity of β2GPI-bh for AnPL monolayers was due to a lower dissociation rate constant compared with native β2GPI. Finally, the monoclonal human aCL (auto-immune anti-cardiolipin antibody) EY2C9 bound to β2GPI-bh but did not bind to monomeric native and oxidized β2GPI. It is likely that the dimeric quaternary structure of β2GPI-bh is in fact responsible for the appearance of the epitopes targeted by the EY2C9 antibody.
MAPK interacts with occludin and mediates EGF-induced prevention of tight junction disruption by hydrogen peroxide
Authors: Basuroy Shyamali , Seth Ankur , Elias Bertha , Naren Anjaparavanda P. , Rao Radhakrishna
Published: December 2005

The MAPK (mitogen-activated protein kinase) pathway is a major intracellular signalling pathway involved in EGF (epithelial growth factor) receptor-mediated cell growth and differentiation. A novel function of MAPK activity in the mechanism of EGF-mediated protection of TJs (tight junctions) from H2O2 was examined in Caco-2 cell monolayers. EGF-mediated prevention of H2O2-induced increase in paracellular permeability was associated with the prevention of H2O2-induced Tyr-phosphorylation, Thr-dephosphorylation and cellular redistribution of occludin and ZO-1 (zonula occludin-1). EGF also prevented H2O2-induced disruption of the actin cytoskeleton and the dissociation of occludin and ZO-1 from the actin-rich detergent-insoluble fractions. MEK (MAPK/ERK kinase, where ERK stands for extracellular signal related kinase) inhibitors, PD98059 and U0126, completely blocked these protective effects of EGF on TJs. EGF rapidly increased the levels of phosphorylated MEK (p-MEK) in detergent-soluble fractions and phosphorylated ERK (p-ERK) in detergent-insoluble fractions. p-ERK was colocalized and co-immunoprecipitated with occludin. GST (glutathione S-transferase) pull-down assay showed that the C-terminal tail of occludin binds to p-ERK in Caco-2 cell extracts. Pair-wise binding studies using recombinant proteins demonstrated that ERK1 directly interacts with the C-terminal tail of occludin. Therefore the present study shows that ERK interacts with the C-terminal region of occludin and mediates the prevention of H2O2-induced disruption of TJs by EGF.
Nkx3.1 binds and negatively regulates the transcriptional activity of Sp-family members in prostate-derived cells
Authors: Simmons Steven O. , Horowitz Jonathan M.
Published: December 2005

Nkx3.1 is a homeodomain-containing transcription factor that is expressed early in the development of the prostate gland and is believed to play an important role in the differentiation of prostatic epithelia. Loss of Nkx3.1 protein expression is often an early event in prostate tumorigenesis, and the abundance of Nkx3.1-negative epithelial cells increases with disease progression. In a number of systems, homeodomain proteins collaborate with zinc-finger-containing transcription factors to bind and regulate target genes. In the present paper, we report that Nkx3.1 collaborates with Sp-family members in the regulation of PSA (prostate-specific antigen) in prostate-derived cells. Nkx3.1 forms protein complexes with Sp proteins that are dependent on their respective DNA-binding domains and an N-terminal segment of Nkx3.1, and Nkx3.1 negatively regulates Sp-mediated transcription via Trichostatin A-sensitive and -insensitive mechanisms. A distal 1000 bp portion of the PSA promoter is required for transrepression by Nkx3.1, although Nkx3.1 DNA-binding activity is itself not required. We conclude that Nkx3.1 negatively regulates Sp-mediated transcription via the tethering of histone deacetylases and/or by inhibiting the association of Sp proteins with co-activators.
The shed ectodomain of type XIII collagen associates with the fibrillar fibronectin matrix and may interfere with its assembly in vitro
Authors: Väisänen Marja-Riitta , Väisänen Timo , Tu Hongmin , Pirilä Päivi , Sormunen Raija , Pihlajaniemi Taina
Published: December 2005

Type XIII collagen is a transmembrane collagen, which is known to exist also as a soluble variant due to ectodomain shedding. Earlier studies with the recombinant ectodomain have shown it to interact in vitro with a number of extracellular matrix proteins, e.g. Fn (fibronectin). In view of its strong binding to Fn, we examined in the present study whether the released soluble ectodomain can bind to the fibrillar Fn matrix under cell-culture conditions and, if so, influence its assembly. In this study, we demonstrate that the type XIII collagen ectodomain of mammalian cells can associate with Fn fibres and may eventually hamper incorporation of the fibrillar Fn meshwork. The association between type XIII collagen and Fn was implicated to be mediated by the C-terminal end of type XIII collagen and the N-terminal end of Fn. The results presented here imply that the shedding of the type XIII collagen ectodomain results in a biologically active molecule capable of remodelling the structure of the pericellular matrix.
Differential regulation of glutamate–cysteine ligase subunit expression and increased holoenzyme formation in response to cysteine deprivation
Authors: Lee Jeong-In , Kang Joann , Stipanuk Martha H.
Published: December 2005

GCL (glutamate–cysteine ligase) is a heterodimer of a GCLC (GCL catalytic subunit) that possesses all of the enzymatic activity and a GCLM (GCL modifier subunit) that alters the Ki of GCLC for GSH. We hypothesized that the expression of GCLM and the association of GCLM with GCLC were responsible for the apparent increase in GCL activity state observed in the liver of rats fed low-protein diets or in hepatocytes cultured in low-sulphur amino acid-containing medium. Therefore we conducted a series of studies using rats and a human hepatoma (HepG2/C3A) cell line to assess the role of GCLM and holoenzyme formation in the regulation of GCL activity in response to sulphur amino acid intake or availability. Increases in GCL activity in rat liver, as well as in HepG2 cells, were due to the additive effects of changes in the amount of GCLC and the kcat for GCLC. The increase in the kcat for GCLC was associated with increased holoenzyme formation, which was associated with an increase in the molar ratio of GCLM to GCLC. Furthermore, our results indicate that the GCLM level in rat liver is always limiting and that up-regulation of the GCLM level results in increased holoenzyme formation and an increase in the kcat. This is the first report demonstrating that the catalytic efficiency of rat GCL is increased by holoenzyme formation and the first demonstration of differential up-regulation of the GCL subunits in response to cysteine deprivation.
Physical and functional interactions between Escherichia coli MutY and endonuclease VIII
Authors: Lu A-Lien , Lee Chih-Yung , Li Lina , Li Xianghong
Published: December 2005

Both GO (7,8-dihydro-8-oxoguanine) and hoU (5-hydroxyuracil) are highly mutagenic because DNA polymerase frequently misincorporates adenine opposite these damaged bases. In Escherichia coli, MutY DNA glycosylase can remove misincorporated adenine opposite G or GO on the template strand during DNA replication. MutY remains bound to the product that contains an AP (apurinic/apyrimidinic) site. Endo VIII (endonuclease VIII) can remove oxidized pyrimidine and weakly remove GO by its DNA glycosylase and β/δ-elimination activities. In the present paper, we demonstrate that Endo VIII can promote MutY dissociation from AP/G, but not from AP/GO, and can promote β/δ-elimination on the products of MutY. MutY interacts physically with Endo VIII through its C-terminal domain. MutY has a moderate affinity for DNA containing a hoU/A mismatch, which is a substrate of Endo VIII. MutY competes with Endo VIII and inhibits Endo VIII activity on DNA that contains a hoU/A mismatch. Moreover, MutY has a weak adenine glycosylase activity on hoU/A mismatches. These results suggest that MutY may have some role in reducing the mutagenic effects of hoU.
Stronger control of ATP/ADP by proton leak in pancreatic β-cells than skeletal muscle mitochondria
Authors: Affourtit Charles , Brand Martin D.
Published: December 2005

Pancreatic beta cells respond to rising blood glucose concentrations by increasing their oxidative metabolism, which leads to an increased ATP/ADP ratio, closure of KATP channels, depolarization of the plasma membrane potential, influx of calcium and the eventual secretion of insulin. Such a signalling mechanism implies that the ATP/ADP ratio is flexible in beta cells (β-cells), which is in contrast with other cell types (e.g. muscle and liver) that maintain a stable ATP/ADP poise while respiring at widely varying rates. To determine whether this difference in flexibility is accounted for by mitochondrial peculiarities, we performed a top-down metabolic control analysis to quantitatively assess how ATP/ADP is controlled in mitochondria isolated from rat skeletal muscle and cultured beta cells. We show that the ATP/ADP ratio is more strongly controlled (approx. 7.5-fold) by proton leak in beta cells than in muscle. The comparatively high importance of proton leak in beta cell mitochondria (relative to phosphorylation) is evidenced furthermore by its relatively high level of control over membrane potential and overall respiratory activity. Modular-kinetic analysis of oxidative phosphorylation reveals that these control differences can be fully explained by a higher relative leak activity in beta cell mitochondria, which results in a comparatively high contribution of proton leak to the overall respiratory activity in this system.
Cyclic nucleotide phosphodiesterases as targets for treatment of haematological malignancies
Authors: Lerner Adam , Epstein Paul M.
Published: December 2005

The cAMP signalling pathway has emerged as a key regulator of haematopoietic cell proliferation, differentiation and apoptosis. In parallel, general understanding of the biology of cyclic nucleotide PDEs (phosphodiesterases) has advanced considerably, revealing the remarkable complexity of this enzyme system that regulates the amplitude, kinetics and location of intracellular cAMP-mediated signalling. The development of therapeutic inhibitors of specific PDE gene families has resulted in a growing appreciation of the potential therapeutic application of PDE inhibitors to the treatment of immune-mediated illnesses and haematopoietic malignancies. This review summarizes the expression and function of PDEs in normal haematopoietic cells and the evidence that family-specific inhibitors will be therapeutically useful in myeloid and lymphoid malignancies.
The adipocyte life cycle hypothesis
Authors: Smith Jessica , Al-Amri Maha , Dorairaj Prabhakaran , Sniderman Allan
Published: December 2005

The adipocyte life cycle hypothesis states that the metabolic properties of an adipocyte vary predictably during its life cycle: that as an adipocyte matures, it accumulates triacylglycerol (triglyceride) and becomes larger; that the rates of triacylglycerol synthesis and lipolysis are matched within adipocytes and that larger adipocytes, in general, have greater rates of triacylglycerol synthesis and, concurrently, greater rates of lipolysis and, therefore, larger adipocytes have greater rates of transmembrane fatty acid flux; and that the secretion of cytokines can also be related to adipocyte size with larger adipocytes having a more unfavourable profile of cytokine secretion than smaller adipocytes. Adipocyte location is an important modifier of this relationship and the favoured sites of adipocyte proliferation are a function of gender and the position within the life cycle of the organism at which proliferation occurs. The adipocyte life cycle hypothesis posits that the metabolic consequences of obesity depend on whether expansion of adipose tissue is achieved primarily by an increase in adipocyte number or adipocyte size. This hypothesis may explain a variety of previously unanswered clinical puzzles such as the vulnerability of many peoples from South East Asia to the adverse metabolic consequences of obesity.
Manipulation of systemic oxygen flux by acute exercise and normobaric hypoxia: implications for reactive oxygen species generation
Authors: Davison Gareth W. , Morgan Rhian M. , Hiscock Natalie , Garcia Juan M. , Grace Fergal , Boisseau Natalie , Davies Bruce , Castell Linda , McEneny Jane , Young Ian S. , Hullin David , Ashton Tony , Bailey Damian M.
Published: December 2005

Maximal exercise in normoxia results in oxidative stress due to an increase in free radical production. However, the effect of a single bout of moderate aerobic exercise performed in either relative or absolute normobaric hypoxia on free radical production and lipid peroxidation remains unknown. To examine this, we randomly matched {according to their normobaric normoxic V̇O2peak [peak V̇O2 (oxygen uptake)]} and assigned 30 male subjects to a normoxia (n=10), a hypoxia relative (n=10) or a hypoxia absolute (n=10) group. Each group was required to exercise on a cycle ergometer at 55% of V̇O2peak for 2 h double-blinded to either a normoxic or hypoxic condition [FiO2 (inspired fraction of O2)=0.21 and 0.16 respectively]. ESR (electron spin resonance) spectroscopy in conjunction with ex vivo spin trapping was utilized for the direct detection of free radical species. The main findings show that moderate intensity exercise increased plasma-volume-corrected free radical and lipid hydroperoxide concentration (pooled rest compared with exercise data, P<0.05); however, there were no selective differences between groups (state×group interaction, P>0.05). The delta change in free radical concentration was moderately correlated with systemic V̇O2 (r2=0.48, P<0.05). The hyperfine coupling constants recorded from the ESR spectra [aN=13.8 Gauss, and aHβ=1.9 Gauss; where 1 Gauss=10−4 T (telsa)] are suggestive of oxygen-centred free radical species formed via the decomposition of lipid hydroperoxides. Peripheral leucocyte and neutrophil cells and total CK (creatine kinase) activity all increased following sustained exercise (pooled rest compared with exercise data, P<0.05), but no selective differences were observed between groups (state×group interaction, P>0.05). We conclude that a single bout of moderate aerobic exercise increases secondary free radical species. There is also evidence of exercise-induced muscle damage, possibly caused by the increase in free radical generation.
Antibody- and Fc-receptor-based therapeutics for malaria
Authors: Shi Jianguo , Mcintosh Richard S. , Pleass Richard J.
Published: December 2005

Abs (antibodies) are complex glycoproteins that play a crucial role in protective immunity to malaria, but their effectiveness in mediating resistance can be enhanced by genetically engineered modifications that improve on nature. These Abs also aid investigation of immune mechanisms operating to control the disease and are valuable tools in developing neutralization assays for vaccine design. This review explores how this might be achieved.