bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unusual Cu(I)/Ag(I) coordination of Escherichia coli CusF as revealed by atomic resolution crystallography and X‐ray absorption spectroscopy
Authors: Loftin Isabell R. , Franke Sylvia , Blackburn Ninian J. , McEvoy Megan M. 
Published: September 2007

AbstractElevated levels of copper or silver ions in the environment are an immediate threat to many organisms. Escherichia coli is able to resist the toxic effects of these ions through strictly limiting intracellular levels of Cu(I) and Ag(I). The CusCFBA system is one system in E. coli responsible for copper/silver tolerance. A key component of this system is the periplasmic copper/silver‐binding protein, CusF. Here the X‐ray structure and XAS data on the CusF–Ag(I) and CusF–Cu(I) complexes, respectively, are reported. In the CusF–Ag(I) structure, Ag(I) is coordinated by two methionines and a histidine, with a nearby tryptophan capping the metal site. EXAFS measurements on the CusF–Cu(I) complex show a similar environment for Cu(I). The arrangement of ligands effectively sequesters the metal from its periplasmic environment and thus may play a role in protecting the cell from the toxic ion.
Forbidden penta‐peptides
Authors: Tuller Tamir , Chor Benny , Nelson Nathan 
Published: September 2007

AbstractThere are 3,200,000 amino acid sequences of length 5 (penta‐peptides). Statistically, we expect to see a distribution of penta‐peptides that is determined by the frequency of the participating amino acids. We show, however, that not only are there thousands of such penta‐peptides that are absent from all known proteomes, but many of them are coded for multiple times in the non‐coding genomic regions. This suggests a strong selection process that prevents these peptides from being expressed. We also show that the characteristics of these forbidden penta‐peptides vary among different phylogenetic groups (e.g., eukaryotes, prokaryotes, and archaea). Our analysis provides the first steps toward understanding the “grammar” of the forbidden penta‐peptides.
Crystal structure of activin receptor type IIB kinase domain from human at 2.0 Å resolution
Authors: Han Seungil , Loulakis Pat , Griffor Matt , Xie Zhi 
Published: September 2007

AbstractActivin receptor type IIB (ActRIIB), a type II TGF‐β serine/threonine kinase receptor, is integral to the activin and myostatin signaling pathway. Ligands such as activin and myostatin bind to activin type II receptors (ActRIIA, ActRIIB), and the GS domains of type I receptors are phosphorylated by type II receptors. Myostatin, a negative regulator of skeletal muscle growth, is regarded as a potential therapeutic target and binds to ActRIIB effectively, and to a lesser extent, to ActRIIA. The high‐resolution structure of human ActRIIB kinase domain in complex with adenine establishes the conserved bilobal architecture consistent with all other catalytic kinase domains. The crystal structure reveals that the adenine has a considerably different orientation from that of the adenine moiety of ATP observed in other kinase structures due to the lack of an interaction by ribose‐phosphate moiety and the presence of tautomers with two different protonation states at the N9 nitrogen. Although the Lys217–Glu230 salt bridge is absent, the unphosphorylated activation loop of ActRIIB adopts a conformation similar to that of the fully active form. Unlike the type I TGF‐β receptor, where a partially conserved Ser280 is a gatekeeper residue, the AcRIIB structure possesses Thr265 with a back pocket supported by Phe247. Taken together, these structural features provide a molecular basis for understanding the coupled activity and recognition specificity for human ActRIIB kinase domain and for the rational design of selective inhibitors.
Regression of intestinal adenomas by vaccination with heat shock protein 105‐pulsed bone marrow‐derived dendritic cells in ApcMin/+ mice
Authors: Yokomine Kazunori , Nakatsura Tetsuya , Senju Satoru , Nakagata Naomi , Minohara Motozumi , Kira Jun–ichi , Motomura Yutaka , Kubo Tatsuko , Sasaki Yutaka , Nishimura Yasuharu 
Published: September 2007

Heat shock protein (HSP) 105 is overexpressed in various cancers, but is expressed at low levels in many normal tissues, except for the testis. A vaccination with HSP105‐pulsed bone marrow‐derived dendritic cells (BM‐DC) induced antitumor immunity without causing an autoimmune reaction in a mouse model. Because ApcMin/+ mice develop multiple adenomas throughout the intestinal tract by 4 months of age, the mice provide a clinically relevant model of human intestinal tumor. In the present study, we investigated the efficacy of the HSP105‐pulsed BM‐DC vaccine on tumor regression in the ApcMin/+ mouse. Western blot and immunohistochemical analyses revealed that the tumors of the ApcMin/+ mice endogenously overexpressed HSP105. Immunization of the ApcMin/+ mice with a HSP105‐pulsed BM‐DC vaccine at 6, 8, and 10 weeks of age significantly reduced the number of small‐intestinal polyps accompanied by infiltration of both CD4+ and CD8+ T cells in the tumors. Cell depletion experiments proved that both CD4+ and CD8+ T cells play a critical role in the activation of antitumor immunity induced by these vaccinations. These findings indicate that the HSP105‐pulsed BM‐DC vaccine can provide potent immunotherapy for tumors that appear spontaneously as a result of the inactivation of a tumor suppressor gene, such as in the ApcMin/+ mouse model. (Cancer Sci 2007; 98: 1930–1935)
Vector‐based Ape1 small interfering RNA enhances the sensitivity of human osteosarcoma cells to endostatin in vivo
Authors: Wang Dong , Zhong Zhao‐Yang , Li Meng‐Xia , Xiang De‐Bing , Li Zeng‐Peng 
Published: September 2007

Osteosarcoma is a highly vascular and extremely destructive malignancy, and the survival of patients with osteosarcoma has not improved significantly in recent years. Antiangiogenic therapy currently holds great potential in conjunction with conventional treatment modalities for osteosarcoma. However, there are examples of gradual loss of response, and perhaps acquired resistance to antiangiogenic drugs. The acquired resistance of antiangiogenesis may be associated with a lot of hypoxia‐response genes. The human apurinic/apyrimidinic endonuclease (Ape1) protein, a bifunctional redox factor and apurinic/apyrimidinic (AP) endonuclease, plays a crucial role in protecting against cell death due to hypoxia. We therefore hypothesized that Ape1 may contribute to the resistance of antiangiogenic therapy. To investigate the effect of Ape1 on the sensitivity of human osteosarcoma cells to endostatin, we constructed an Ape1 small interfering RNA expression vector, pSilenceApe1. Transfection of human osteosarcoma 9901 and HOS cells with pSilenceApe1 resulted in a dose‐dependent loss of Ape1 protein. pSilenceApe1 also significantly suppressed the expression of vascular endothelial growth factor (VEGF) protein in the 9901 cells. Combined treatment with pSilenceApe1 and recombinant human endostatin (rhES) showed potent antiangiogenic effects in the transwell chamber invasion assay. Then, 20 nude mice bearing 9901 xenografts were divided into four groups: the phosphate‐buffered saline treatment control group; the rhES treatment group (1.5 mg/kg, daily); the pSilenceApe1 treatment group (20 µg, once every 3 days); and the combination of rhES and pSilenceApe1 treatment group. pSilenceApe1 significantly suppressed the expression of Ape1 and VEGF protein in the 9901 xenografts. The tumor‐inhibition rate of the pSilenceApe1, rhES, and combination of rhES and pSilenceApe1 treatment groups was 38.23, 35.29, and 62.18%, respectively. Furthermore, a significant decrease in microvessel density with an increase in apoptosis was observed following combined treatment with pSilenceApe1 and rhES, compared with control and either agent alone in 9901 xenografts. These results indicate that Ape1 small interfering RNA could enhance the sensitivity of osteosarcoma cells to endostatin. (Cancer Sci 2007; 98: 1993–2001)
Pharmacokinetic modelling of the placental transfer of nelfinavir and its M8 metabolite: a population study using 75 maternal‐cord plasma samples
Authors: Hirt Déborah , Urien Saïk , Jullien Vincent , Firtion Ghislaine , Chappuy Hélène , Rey Elisabeth , Pons Gérard , Mandelbrot Laurent , Treluyer Jean‐Marc 
Published: September 2007

What is already known about this subject • Nelfinavir is an HIV protease inhibitor used in pregnant women, although no ex vivo and few in vivo data are available describing its transfer across the placenta. What this study adds • A population pharmacokinetic study was performed on maternal, cord plasma and amniotic fluid samples to characterize the concentration–time courses of nelfinavir and its metabolite M8 in the three compartments and to study the influence of covariates, such as weight and duration of pregnancy, on placental transfer.• The pharmacokinetics of nelfinavir and M8 were satisfactorily described by a three compartment model. The median nelfinavir fetus : maternal concentration ratio was 25% for maternal concentrations between 0.1 and 2.5 mg l−1, between the 31st and 41st week of gestation, irrespective of bodyweight. This ratio was significantly higher for M8 (a 55% increase).• To our knowledge this is the first population pharmacokinetic integrated model to describe satisfactorily the maternal‐foetal‐amniotic fluid transfer of a drug.AimsA population pharmacokinetic model was developed to characterize the transfer of nelfinavir and its active metabolite M8 from maternal to cord plasma and amniotic fluid.MethodsConcentration data were obtained from 75 women on the day of delivery and for whom maternal, umbilical plasma and amniotic fluid samples were collected. Data from 53 pregnant, 61 nonpregnant and seven consecutively pregnant and non pregnant women were then added to the database, the contents of which were analyzed using NONMEM.ResultsNelfinavir and M8 concentrations in maternal plasma, umbilical plasma and amniotic fluid were described by six connected compartments. Mean (% intersubject variability) population estimates were: absorption rate 00.67 h−1, lag time 00.87 h, oral clearance and volume of distribution: 39.5 l h−1 (53%), and 557 l for non pregnant and pregnant women, respectively, and 115 l h−1 (132%) and 1626 l, respectively, on the day of delivery, M8 formation clearance 0.77 l h−1 and M8 elimination rate constant 03.41 h−1 (74%). For nelfinavir and M8, respectively, the mother‐to‐cord parameters were 0.058 l h−1 (34%), and 00.35 h−1 (76%), the cord‐to‐amniotic fluid rate constants were 0.23 and 00.59 h−1, and the elimination rate constants from amniotic fluid were 0.36 and 00.49 h−1. The nelfinavir fetus : maternal concentration ratio was 25% for maternal concentrations between 0.1 and 2.5 mg l−1, between the 31 and 41st week of gestation.ConclusionsThe low transfer of nelfinavir from the placenta is unlikely to protect the fetus from vertical HIV‐1 transmission.
Maternal punishment practices in a rural area of Turkey
Authors: Buldukoglu Kadriye , Kukulu Kamile 
Published: September 2007

AbstractObjective  We examined a number of maternal characteristics that influence punishment practices in a rural area of Turkey.Methods  Questionnaires were filled out in face‐to‐face interviews with 539 mothers who agreed to participate in this study.Results  The majority findings of this study were as follows: all of the mothers had used various forms of punishment on their children; hitting other children was the primary reason for punishment, and hitting was the most common form of punishment used by mothers. Another interesting finding of this study was that mothers did not demonstrate the same responses to their children when they were alone as when others were present. Mothers commonly felt regret in the post‐punishment period.Conclusion  These findings can be useful in establishing parental educational programming that is directed at decreasing the rates of punishment practices.
The response of an Eastern Amazonian rain forest to drought stress: results and modelling analyses from a throughfall exclusion experiment
Authors: FISHER R. A. , WILLIAMS M. , Da COSTA A. LOLA , MALHI Y. , Da COSTA R. F. , ALMEIDA S. , MEIR P. 
Published: September 2007

AbstractWarmer and drier climates over Eastern Amazonia have been predicted as a component of climate change during the next 50–100 years. It remains unclear what effect such changes will have on forest–atmosphere exchange of carbon dioxide (CO2) and water, but the cumulative effect is anticipated to produce climatic feedback at both regional and global scales. To allow more detailed study of forest responses to soil drying, a simulated soil drought or ‘throughfall exclusion’ (TFE) experiment was established at a rain forest site in Eastern Amazonia, Brazil, for which time‐series sap flow and soil moisture data were obtained. The experiment excluded 50% of the throughfall from the soil. Sap flow data from the forest plot experiencing normal rainfall showed no limitation of transpiration throughout the two monitored dry seasons. Conversely, data from the TFE showed large dry season declines in transpiration, with tree water use restricted to 20% of that in the control plot at the peak of both dry seasons. The results were examined to evaluate the paradigm that the restriction on transpiration in the dry season was caused by limitation of soil‐to‐root water transport, driven by low soil water potential and high soil‐to‐root hydraulic resistance. This paradigm, embedded in the soil–plant–atmosphere (SPA) model and driven using on‐site measurements, provided a good explanation (R2 > 0.69) of the magnitude and timing of changes in sap flow and soil moisture. This model‐data correspondence represents a substantial improvement compared with other ecosystem models of drought stress tested in Amazonia. Inclusion of deeper rooting should lead to lower sensitivity to drought than the majority of existing models. Modelled annual GPP declined by 13–14% in response to the treatment, compared with estimated declines in transpiration of 30–40%.
Carbon mitigation by the energy crop, Miscanthus
Authors: CLIFTON‐BROWN JOHN C. , BREUER JÖERN , JONES MICHAEL B. 
Published: September 2007

AbstractBiomass crops mitigate carbon emissions by both fossil fuel substitution and sequestration of carbon in the soil. We grew Miscanthus x giganteus for 16 years at a site in southern Ireland to (i) compare methods of propagation, (ii) compare response to fertilizer application and quantify nutrient offtakes, (iii) measure long‐term annual biomass yields, (iv) estimate carbon sequestration to the soil and (v) quantify the carbon mitigation by the crop. There was no significant difference in the yield between plants established from rhizome cuttings or by micro‐propagation. Annual off‐takes of N and P were easily met by soil reserves, but soil K reserves were low in unfertilized plots. Potassium deficiency was associated with lower harvestable yield. Yields increased for 5 years following establishment but after 10 years showed some decline which could not be accounted for by the climate driven growth model MISCANMOD. Measured yields were normalized to estimate both autumn (at first frost) and spring harvests (15 March of the subsequent year). Average autumn and spring yields over the 15 harvest years were 13.4±1.1 and 9.0±0.7 t DW ha−1 yr−1 respectively. Below ground biomass in February 2002 was 20.6±4.6 t DW ha−1. Miscanthus derived soil organic carbon sequestration detected by a change in 13C signal was 8.9±2.4 t C ha−1 over 15 years. We estimate total carbon mitigation by this crop over 15 years ranged from 5.2 to 7.2 t C ha−1 yr−1 depending on the harvest time.
Monoterpene emissions from rubber trees (Hevea brasiliensis) in a changing landscape and climate: chemical speciation and environmental control
Authors: WANG YONG‐FENG , OWEN SUSAN M. , LI QING‐JUN , PEÑUELAS JOSEP 
Published: September 2007

AbstractEmissions of biogenic volatile organic compounds (VOCs) have important roles in ecophysiology and atmospheric chemistry at a wide range of spatial and temporal scales. Tropical regions are a major global source of VOC emissions and magnitude and chemical speciation of VOC emissions are highly plant‐species specific. Therefore it is important to study emissions from dominant species in tropical regions undergoing large‐scale land‐use change, for example, rubber plantations in South East Asia. Rubber trees (Hevea brasiliensis) are strong emitters of light‐dependent monoterpenes. Measurements of emissions from leaves were made in the dry season in February 2003 and at the beginning of the wet season in May 2005. Major emitted compounds were sabinene, α‐pinene and β‐pinene, but β‐ocimene and linalool also contributed significantly at low temperature and light. Cis‐ocimene was emitted with a circadian course independent of photosynthetic active radiation (PAR) and temperature changes with a maximum in the middle of the day. Total isoprenoid VOC emission potential at the beginning of the wet season (94 μg gdw−1 h−1) was almost two orders of magnitude higher than measured in the dry season (2 μg g dw−1 h−1). Composition of total emissions changed with increasing temperature or PAR ramps imposed throughout a day. As well as light and temperature, there was evidence that assimilation rate was also a factor contributing to seasonal regulating emission potential of monoterpenes from rubber trees. Results presented here contribute to a better understanding of an important source of biogenic VOC associated with land‐use change in tropical South East Asia.
Prediction of the distribution of Arctic‐nesting pink‐footed geese under a warmer climate scenario
Authors: JENSEN RIKKE A. , MADSEN JESPER , O'CONNELL MARK , WISZ MARY S. , TØMMERVIK HANS , MEHLUM FRIDTJOF 
Published: September 2007

AbstractGlobal climate change is expected to shift species ranges polewards, with a risk of range contractions and population declines of especially high‐Arctic species. We built species distribution models for Svalbard‐nesting pink‐footed geese to relate their occurrence to environmental and climatic variables, and used the models to predict their distribution under a warmer climate scenario. The most parsimonious model included mean May temperature, the number of frost‐free months and the proportion of moist and wet moss‐dominated vegetation in the area. The two climate variables are indicators for whether geese can physiologically fulfil the breeding cycle or not and the moss vegetation is an indicator of suitable feeding conditions. Projections of the distribution to warmer climate scenarios propose a large north‐ and eastward expansion of the potential breeding range on Svalbard even at modest temperature increases (1 and 2 °C increase in summer temperature, respectively). Contrary to recent suggestions regarding future distributions of Arctic wildlife, we predict that warming may lead to a further growth in population size of, at least some, Arctic breeding geese.
Developing an empirical model of stand GPP with the LUE approach: analysis of eddy covariance data at five contrasting conifer sites in Europe
Authors: MÄKELÄ ANNIKKI , PULKKINEN MINNA , KOLARI PASI , LAGERGREN FREDRIK , BERBIGIER PAUL , LINDROTH ANDERS , LOUSTAU DENIS , NIKINMAA EERO , VESALA TIMO , HARI PERTTI 
Published: September 2007

AbstractThis paper develops a statistical model for daily gross primary production (GPP) in boreal and temperate coniferous forests. The model applies the light use efficiency (LUE) approach, which estimates the conversion efficiency of daily absorbed photosynthetically active radiation (APAR) into daily GPP as a product of potential LUE and modifying factors. The latter were derived from daily total APAR and daily mean temperature, vapour pressure deficit (VPD) and soil water content (SWC). Modelling data came from five European eddy covariance measurement towers over 2–8 years. The model was tested against independent data from two AmeriFlux stations. The model with the APAR, temperature and VPD modifiers worked well in almost all the site–year combinations, but the SWC modifier only improved the fit in few cases. Geographical variation was found in the modifiers and potential LUE in site‐specific models. When a model was fitted to pooled data, differences between sites could be explained by potential LUE, leaf area and environmental conditions. The test against the AmeriFlux data corroborated this finding. The potential LUE varied from 1.9 to 3.1 g C MJ−1, and a weak correlation was found between foliar nitrogen concentration and potential LUE. Some year‐to‐year variation remained which could be captured by neither the pooled nor the site‐specific models.
Seamounts: identity crisis or split personality?
Authors: McClain Craig R. 
Published: September 2007

AbstractAt present, researchers propose that over 14,000 seamounts exist and, like their terrestrial analogues, function like islands. In addition, seamounts are described as oases, biodiversity hotspots, and lush coral/sponge gardens. Here I discuss the extent to which these tenets regarding seamounts may be inappropriate, suffer from a lack of support, and be over‐generalizations of a broad range of environmental types encountered on seamounts. Ultimately, for seamount science to progress, we need to challenge our conventional wisdom on these habitats and the extent to which all seamounts function in a similar manner.
Regional genetic diversity patterns in Antarctic hairgrass (Deschampsia antarctica Desv.)
Authors: Wouw Mark van de , Dijk Peter van , Huiskes Ad H. L. 
Published: September 2007

AbstractAim  To determine patterns in diversity of a major Antarctic plant species, including relationships of Antarctic populations with those outside the Antarctic zone.Location  Antarctic Peninsula, Maritime Antarctica, sub‐Antarctic islands, Falkland Islands and South America.Methods  Amplified fragment length polymorphisms (AFLPs) and chloroplast sequences were used to study patterns of genetic diversity in Antarctic hairgrass (Deschampsia antarctica Desv.) and the genetic relationships between populations over its distribution range. Thirty‐eight populations were sampled from a large part of the distribution of D. antarctica, and additionally, herbarium specimens were included for areas from which we could not obtain fresh samples.Results  A gradient in AFLP diversity was observed going from the Falklands southwards into the Antarctic. This gradient in diversity was also observed within the Antarctic Peninsula: diversity was lower further south. Diversity in the chloroplast genome of D. antarctica was low. Only three chloroplast haplotypes were found, each with a strong regional distribution.Main conclusions  The phylogenetic construction of AFLP marker frequencies in meta‐populations of D. antarctica supports a stepping‐stone model of colonization, whereby gene flow mainly occurs between neighbouring populations. It is concluded that long‐distance gene flow is very limited in D. antarctica. A very low diversity was found in the sub‐Antarctic islands in the Indian Ocean, indicating that these populations have experienced a recent evolutionary bottleneck.