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  • Blackwell Publishing Ltd  (30,697)
  • Nature Publishing Group (NPG)
  • 2020-2024  (14)
  • 2005-2009  (6,665)
  • 1985-1989  (28,447)
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  • 1
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    Toward an adequate level of detail in flood risk assessments (2023)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2024-01-24
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Flood risk assessments require different disciplines to understand and model the underlying components hazard, exposure, and vulnerability. Many methods and data sets have been refined considerably to cover more details of spatial, temporal, or process information. We compile case studies indicating that refined methods and data have a considerable effect on the overall assessment of flood risk. But are these improvements worth the effort? The adequate level of detail is typically unknown and prioritization of improvements in a specific component is hampered by the lack of an overarching view on flood risk. Consequently, creating the dilemma of potentially being too greedy or too wasteful with the resources available for a risk assessment. A “sweet spot” between those two would use methods and data sets that cover all relevant known processes without using resources inefficiently. We provide three key questions as a qualitative guidance toward this “sweet spot.” For quantitative decision support, more overarching case studies in various contexts are needed to reveal the sensitivity of the overall flood risk to individual components. This could also support the anticipation of unforeseen events like the flood event in Germany and Belgium in 2021 and increase the reliability of flood risk assessments.〈/p〉
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Description: BMBF http://dx.doi.org/10.13039/501100002347
    Description: Federal Environment Agency http://dx.doi.org/10.13039/501100010809
    Description: http://howas21.gfz-potsdam.de/howas21/
    Description: https://www.umwelt.niedersachsen.de/startseite/themen/wasser/hochwasser_amp_kustenschutz/hochwasserrisikomanagement_richtlinie/hochwassergefahren_und_hochwasserrisikokarten/hochwasserkarten-121920.html
    Description: https://download.geofabrik.de/europe/germany.html
    Description: https://emergency.copernicus.eu/mapping/list-of-components/EMSN024
    Description: https://data.jrc.ec.europa.eu/collection/id-0054
    Description: https://oasishub.co/dataset/surface-water-flooding-footprinthurricane-harvey-august-2017-jba
    Description: https://www.wasser.sachsen.de/hochwassergefahrenkarte-11915.html
    Keywords: ddc:551.48 ; decision support ; extreme events ; integrated flood risk management ; risk assessment
    Language: English
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  • 2
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    Small lateral air pressure gradients generated by a large chamber system have a strong effect on CO2 transport in soil (2023)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2024-02-09
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Gas transport in soils is usually assumed to be purely diffusive, although several studies have shown that non‐diffusive processes can significantly enhance soil gas transport. These processes include barometric air pressure changes, wind‐induced pressure pumping and static air pressure fields generated by wind interacting with obstacles. The associated pressure gradients in the soil can cause advective gas fluxes that are much larger than diffusive fluxes. However, the contributions of the respective transport processes are difficult to separate. We developed a large chamber system to simulate pressure fields and investigate their influence on soil gas transport. The chamber consists of four subspaces in which pressure is regulated by fans that blow air in or out of the chamber. With this setup, we conducted experiments with oscillating and static pressure fields. CO〈sub〉2〈/sub〉 concentrations were measured along two soil profiles beneath the chamber. We found a significant relationship between static lateral pressure gradients and the change in the CO〈sub〉2〈/sub〉 profiles (R〈sup〉2〈/sup〉 = 0.53; 〈italic toggle="no"〉p〈/italic〉‐value 〈2e‐16). Even small pressure gradients between −1 and 1 Pa relative to ambient pressure resulted in an increase or decrease in CO〈sub〉2〈/sub〉 concentrations of 8% on average in the upper soil, indicating advective flow of air in the pore space. Positive pressure gradients resulted in decreasing, negative pressure gradients in increasing CO〈sub〉2〈/sub〉 concentrations. The concentration changes were probably caused by an advective flow field in the soil beneath the chamber generated by the pressure gradients. No effect of oscillating pressure fields was observed in this study. The results indicate that static lateral pressure gradients have a substantial impact on soil gas transport and therefore are an important driver of gas exchange between soil and atmosphere. Lateral pressure gradients in a comparable range can be induced under windy conditions when wind interacts with terrain features. They can also be caused by chambers used for flux measurements at high wind speed or by fans used for head‐space mixing within the chambers, which yields biased flux estimates.〈/p〉
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Keywords: ddc:631.4 ; advective flux ; chamber flux measurements ; static air pressure fields ; wind‐induced pressure pumping
    Language: English
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  • 3
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    Redoxtrons – An experimental system to study redox processes within the capillary fringe (2023)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2023-11-18
    Description: Spatiotemporal characterisation of the soil redox status within the capillary fringe (CF) is a challenging task. Air‐filled porosities (ε), oxygen concentration (O〈sub〉2〈/sub〉) and soil redox potential (EH) are interrelated soil variables within active biogeochemical domains such as the CF. We investigated the impact of water table (WT) rise and drainage in an undisturbed topsoil and subsoil sample taken from a Calcaric Gleysol for a period of 46 days. We merged 1D (EH and matric potential) and 2D (O〈sub〉2〈/sub〉) systems to monitor at high spatiotemporal resolution redox dynamics within self‐constructed redoxtron housings and complemented the data set by a 3D pore network characterization using X‐ray microtomography (X‐ray μCT). Depletion of O〈sub〉2〈/sub〉 was faster in the organic matter‐ and clay‐rich aggregated topsoil and the CF extended 〉10 cm above the artificial WT. The homogeneous and less‐aggregated subsoil extended only 4 cm above the WT as indicated by ε–O〈sub〉2〈/sub〉–EH data during saturation. After drainage, 2D O〈sub〉2〈/sub〉 imaging revealed a fast aeration towards the lower depths of the topsoil, which agrees with the connected ε derived by X‐ray μCT (ε〈sub〉CT_conn〈/sub〉) of 14.9% of the total porosity. However, small‐scaled anoxic domains with O〈sub〉2〈/sub〉 saturation 〈5% were apparent even after lowering the WT (down to 0.25 cm〈sup〉2〈/sup〉 in size) for 23 days. These domains remained a nucleus for reducing soil conditions (E〈sub〉H〈/sub〉 〈 −100 mV), which made it challenging to characterise the soil redox status in the CF. In contrast, the subsoil aeration reached O〈sub〉2〈/sub〉 saturation after 8 days for the complete soil volume. Values of ε〈sub〉CT_conn〈/sub〉 around zero in the subsoil highlighted that soil aeration was independent of this parameter suggesting that other variables such as microbial activity must be considered when predicting the soil redox status from ε alone. The use of redoxtrons in combination with localised redox‐measurements and image based pore space analysis resulted in a better 2D/3D characterisation of the pore system and related O〈sub〉2〈/sub〉 transport properties. This allowed us to analyse the distribution and activity of microbiological niches highly associated with the spatiotemporal variable redox dynamics in soil environments. Highlights: The time needed to turn from reducing to oxidising (period where all platinum electrodes feature E〈sub〉H〈/sub〉 〉 300 mV) condition differ for two samples with contrasting soil structure. The subsoil with presumably low O〈sub〉2〈/sub〉 consumption rates aerated considerably faster than the topsoil and exclusively by O〈sub〉2〈/sub〉 diffusion through medium‐ and fine‐sized pores. To derive the soil redox status based upon the triplet ε–O〈sub〉2〈/sub〉–E〈sub〉H〈/sub〉 is challenging at present in heterogeneous soil domains and larger soil volumes than 250 cm〈sup〉3〈/sup〉. Undisturbed soil sampling along with 2D/3D redox measurement systems (e.g., redoxtrons) improve our understanding of redox dynamics within the capillary fringe.
    Keywords: ddc:631.4 ; environmental monitoring ; incubation experiments ; redox processes ; soil reducing conditions ; undisturbed soil ; X‐ray microtomography
    Language: English
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  • 4
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    The dilemma of analytical method changes for soil organic carbon in long‐term experiments (2023)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2023-11-17
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈sec xmlns:mml="http://www.w3.org/1998/Math/MathML" id="ejss13362-sec-1003" xml:lang="en"〉 〈p xml:lang="en"〉Long‐term experiments (LTEs) have provided data to modellers and agronomists to investigate changes and dynamics of soil organic carbon (SOC) under different cropping systems. As treatment changes have occurred due to agricultural advancements, so too have analytical soil methods. This may lead to method bias over time, which could affect the robust interpretation of data and conclusions drawn. This study aims to quantify differences in SOC due to changes in dry combustion methods over time, using soil samples of a LTE established in 1963 that focuses on mineral and organic fertilizer management in the temperate zone of Northeast Germany. For this purpose, 1059 soil samples, collected between 1976 and 2008, have been analysed twice, once with their historical laboratory method right after sampling, and a second time in 2016 when all samples were analysed using the same elementary analyser. In 9 of 11 soil sampling campaigns, a paired 〈italic toggle="no"〉t〈/italic〉‐test provided evidence for significant differences in the historical SOC values when compared with the re‐analysed concentrations of the same LTE sample. In the sampling years 1988 and 2004, the historical analysis obtained about 0.9 g kg〈sup〉−1〈/sup〉 lower SOC compared with the re‐analysed one. For 1990 and 1998, this difference was about 0.4 g kg〈sup〉−1〈/sup〉. Correction factors, an approach often used to correct for different analytical techniques, could only be applied for 5 of 11 sampling campaigns to account for constant and proportional systematic method error. For this particular LTE, the interpretation of SOC changes due to agronomic management (here fertilization) deviates depending on the analytical method used, which may weaken the explanatory power of the historical data. We demonstrate that analytical method changes over time present one of many challenges in the interpretation of time series data of SOC dynamics. Therefore, LTE site managers need to ensure providing all necessary protocols and data in order to retrace method changes and if necessary recalculate SOC.〈/p〉 〈/sec〉〈sec xmlns:mml="http://www.w3.org/1998/Math/MathML" id="ejss13362-sec-0003" xml:lang="en"〉 〈title〉Highlights〈/title〉 〈p xml:lang="en"〉〈list list-type="bullet" id="ejss13362-list-0001"〉 〈list-item id="ejss13362-li-0001"〉〈p〉A total of 1059 LTE soil samples taken between 1976 and 2008 were re‐analysed for SOC in 2016〈/p〉〈/list-item〉 〈list-item id="ejss13362-li-0002"〉〈p〉Several methodological changes for SOC determination led to significant different SOC concentration in the same sample〈/p〉〈/list-item〉 〈list-item id="ejss13362-li-0003"〉〈p〉Interpretation and time series of LTE soil data suffer from consideration of analytical method changes and poor documentation of the same〈/p〉〈/list-item〉 〈list-item id="ejss13362-li-0004"〉〈p〉Soil archive establishment, thorough method protocols and diligent proficiency testing after soil method changes ameliorate the dilemma〈/p〉〈/list-item〉 〈/list〉〈/p〉 〈/sec〉
    Description: Brandenburger Staatsministerium für Wissenschaft, Forschung und Kultur http://dx.doi.org/10.13039/501100004581
    Description: Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100004937
    Description: https://doi.org/10.4228/zalf-acge-b683
    Keywords: ddc:631.4 ; Bland–Altman ; carbon stocks ; data trueness ; Deming regression ; method bias ; soil archive ; soil survey
    Language: English
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  • 5
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    Optimised use of data fusion and memory‐based learning with an Austrian soil library for predictions with infrared data (2023)
    Blackwell Publishing Ltd | Oxford, UK
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    Publication Date: 2023-12-12
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Infrared spectroscopy in the visible to near‐infrared (vis–NIR) and mid‐infrared (MIR) regions is a well‐established approach for the prediction of soil properties. Different data fusion and training approaches exist, and the optimal procedures are yet undefined and may depend on the heterogeneity present in the set and on the considered scale. The objectives were to test the usefulness of partial least squares regressions (PLSRs) for soil organic carbon (SOC), total carbon (C〈sub〉t〈/sub〉), total nitrogen (N〈sub〉t〈/sub〉) and pH using vis–NIR and MIR spectroscopy for an independent validation after standard calibration (use of a general PLSR model) or using memory‐based learning (MBL) with and without spiking for a national spectral database. Data fusion approaches were simple concatenation of spectra, outer product analysis (OPA) and model averaging. In total, 481 soils from an Austrian forest soil archive were measured in the vis–NIR and MIR regions, and regressions were calculated. Fivefold calibration‐validation approaches were carried out with a region‐related split of spectra to implement independent validations with n ranging from 47 to 99 soils in different folds. MIR predictions were generally superior over vis–NIR predictions. For all properties, optimal predictions were obtained with data fusion, with OPA and spectra concatenation outperforming model averaging. The greatest robustness of performance was found for OPA and MBL with spiking with 〈italic toggle="no"〉R〈/italic〉〈sup〉2〈/sup〉 ≥ 0.77 (N), 0.85 (SOC), 0.86 (pH) and 0.88 (C〈sub〉t〈/sub〉) in the validations of all folds. Overall, the results indicate that the combination of OPA for vis–NIR and MIR spectra with MBL and spiking has a high potential to accurately estimate properties when using large‐scale soil spectral libraries as reference data. However, the reduction of cost‐effectiveness using two spectrometers needs to be weighed against the potential increase in accuracy compared to a single MIR spectroscopy approach.〈/p〉
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Keywords: ddc:631.4 ; data fusion ; independent validation ; infrared spectroscopy ; MBL ; nitrogen ; outer product analysis ; pH ; soil organic carbon ; spiking ; total carbon
    Language: English
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  • 6
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    Importance of catchment hydrological processes and calibration of hydrological‐hydrodynamic rainfall‐runoff models in small rural catchments (2023)
    Blackwell Publishing Ltd | Oxford, UK
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    Publication Date: 2024-01-19
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉In recent years, many two‐dimensional (2D) hydrodynamic models have been extended to include the direct rainfall method (DRM). This allows their application as a hydrological‐hydrodynamic model for the determination of floodplains in one model system. In previous studies on DRM, the role of catchment hydrological processes (CaHyPro) and its interaction with the calibration process was not investigated in detail. In the present, case‐oriented study, the influence of the spatiotemporal distribution of the processes precipitation and runoff formation in combination with the 2D model HEC‐RAS is investigated. In a further step, a conceptual approach for event‐based interflow is integrated. The study is performed on the basis of a single storm event in a small rural catchment (low mountain range, 38 km〈sup〉2〈/sup〉) in Hesse (Germany). The model results are evaluated against six quality criteria and compared to a simplified baseline model. Finally, the calibrated improved model is contrasted with a calibrated baseline model. The results show the enhancement of the model results due to the integration of the CaHyPro and highlight its interplay with the calibrated model parameters.〈/p〉
    Keywords: ddc:551.48 ; 2D hydrodynamic modeling ; calibration ; direct rainfall modeling ; hydrological processes ; radar data ; runoff formation
    Language: English
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  • 7
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    BODIUM—A systemic approach to model the dynamics of soil functions (2023)
    Blackwell Publishing Ltd | Oxford, UK
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    Publication Date: 2024-01-26
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉The increasing demand for biomass for food, animal feed, fibre and bioenergy requires optimization of soil productivity, while at the same time, protecting other soil functions such as nutrient cycling and buffering, carbon storage, habitat for biological activity and water filter and storage. Therefore, one of the main challenges for sustainable agriculture is to produce high yields while maintaining all the other soil functions. Mechanistic simulation models are an essential tool to fully understand and predict the complex interactions between physical, biological and chemical processes of soils that generate those functions. We developed a soil model to simulate the impact of various agricultural management options and climate change on soil functions by integrating the relevant processes mechanistically and in a systemic way. As a special feature, we include the dynamics of soil structure induced by tillage and biological activity, which is especially relevant in arable soils. The model operates on a 1D soil profile consisting of a number of discrete layers with dynamic thickness. We demonstrate the model performance by simulating crop growth, root growth, nutrient and water uptake, nitrogen cycling, soil organic matter turnover, microbial activity, water distribution and soil structure dynamics in a long‐term field experiment including different crops and different types and levels of fertilization. The model is able to capture essential features that are measured regularly including crop yield, soil organic carbon, and soil nitrogen. In this way, the plausibility of the implemented processes and their interactions is confirmed. Furthermore, we present the results of explorative simulations comparing scenarios with and without tillage events to analyse the effect of soil structure on soil functions. Since the model is process‐based, we are confident that the model can also be used to predict quantities that have not been measured or to estimate the effect of management measures and climate states not yet been observed. The model thus has the potential to predict the site‐specific impact of management decisions on soil functions, which is of great importance for the development of a sustainable agriculture that is currently also on the agenda of the ‘Green Deal’ at the European level.〈/p〉
    Description: Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100002347
    Description: https://git.ufz.de/bodium/bodium_v1.0
    Keywords: ddc:631.4 ; agriculture ; computational model ; simulation ; soil microbiology ; soil structure ; sustainable soil
    Language: English
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  • 8
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    Temperature and soil moisture change microbial allocation of pesticide‐derived carbon (2023)
    Blackwell Publishing Ltd | Oxford, UK
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    Publication Date: 2024-03-18
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Temperature and soil moisture are known to control pesticide mineralization. Half‐life times (DT〈sub〉50〈/sub〉) derived from pesticide mineralization curves generally indicate longer residence times at low soil temperature and moisture but do not consider potential changes in the microbial allocation of pesticide‐derived carbon (C). We aimed to determine carbon use efficiency (CUE, formation of new biomass relative to total C uptake) to better understand microbial utilization of pesticide‐derived C under different environmental conditions and to support the conventional description of degradation dynamics based on mineralization. We performed a microcosm experiment at two MCPA (2‐methyl‐4‐chlorophenoxyacetic acid) concentrations (1 and 20 mg kg〈sup〉−1〈/sup〉) and defined 20°C/pF 1.8 as optimal and 10°C/pF 3.5 as limiting environmental conditions. After 4 weeks, 70% of the initially applied MCPA was mineralized under optimal conditions but MCPA mineralization reached less than 25% under limiting conditions. However, under limiting conditions, an increase in CUE was observed, indicating a shift towards anabolic utilization of MCPA‐derived C. In this case, increased C assimilation implied C storage or the formation of precursor compounds to support resistance mechanisms, rather than actual growth since we did not find an increase in the 〈italic toggle="no"〉tfdA〈/italic〉 gene relevant to MCPA degradation. We were able to confirm the assumption that under limiting conditions, C assimilation increases relative to mineralization and that C redistribution, may serve as an explanation for the difference between mineralization and MCPA dissipation‐derived degradation dynamics. In addition, by introducing CUE to the temperature‐ and moisture‐dependent degradation of pesticides, we can capture the underlying microbial constraints and adaptive mechanisms to changing environmental conditions.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Changing environmental conditions alter the MCPA degradation dynamics and the allocation of pesticide‐derived carbon to anabolic or catabolic metabolism.〈boxed-text position="anchor" content-type="graphic" id="ejss13417-blkfxd-0001" xml:lang="en"〉 〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:13510754:media:ejss13417:ejss13417-toc-0001"〉 〈/graphic〉 〈/boxed-text〉〈/p〉
    Description: Collaborative Research Center 1253 CAMPOS (DFG)
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Description: DFG Priority Program 2322 “Soil System”
    Description: Ellrichshausen Foundation
    Description: Research Training Group “Integrated Hydrosystem modeling”
    Description: https://doi.org/10.5281/zenodo.5081655
    Keywords: ddc:631.4 ; anabolism ; carbon use efficiency ; catabolism ; effect of soil moisture and temperature ; gene‐centric process model ; MCPA biodegradation
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  • 9
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    Fifty years after deep‐ploughing: Effects on yield, roots, nutrient stocks and soil structure (2023)
    Blackwell Publishing Ltd | Oxford, UK
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    Publication Date: 2024-05-30
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Deep‐ploughing far beyond the common depth of 30 cm was used more than 50 years ago in Northern Germany with the aim to break root‐restricting layers and thereby improve access to subsoil water and nutrient resources. We hypothesized that effects of this earlier intervention on soil properties and yields prevailed after 50 years. Hence, we sampled two sandy soils and one silty soil (Cambisols and a Luvisol) of which half of the field had been deep‐ploughed 50 years ago (soils then re‐classified as Treposols). The adjacent other half was not deep‐ploughed and thus served as the control. At all the three sites, both deep‐ploughed and control parts were then conventionally managed over the last 50 years. We assessed yields during the dry year 2019 and additionally in 2020, and rooting intensity at the year of sampling (2019), as well as changes in soil structure, carbon and nutrient stocks in that year. We found that deep‐ploughing improved yields in the dry spell of 2019 at the sandy sites, which was supported by a more general pattern of higher NDVI indices in deep‐ploughed parts for the period from 2016 to 2021 across varying weather conditions. Subsoil stocks of soil organic carbon and total plant‐available phosphorus were enhanced by 21%–199% in the different sites. Root biomass in the subsoil was reduced due to deep‐ploughing at the silty site and was increased or unaffected at the sandy sites. Overall, the effects of deep‐ploughing were site‐specific, with reduced bulk density in the buried topsoil stripes in the subsoil of the sandy sites, but with elevated subsoil density in the silty site. Hence, even 50 years after deep‐ploughing, changes in soil properties are still detectable, although effect size differed among sites.〈/p〉
    Description: BonaRes http://dx.doi.org/10.13039/501100022576
    Keywords: ddc:631.4 ; aggregates ; carbon sequestration ; deep‐ploughing ; macronutrients ; subsoil ; Treposol
    Language: English
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  • 10
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    Non‐exchangeable stable hydrogen isotope ratios in clay minerals and soil clay fractions: A method test (2022)
    Blackwell Publishing Ltd | Oxford, UK
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    Publication Date: 2023-01-20
    Description: Stable hydrogen isotope ratios (δ2H values) in structural hydroxyl groups of pedogenic clay minerals are inherited from the surrounding water at the time of their formation. Only non‐exchangeable H preserves the environmental forensic and paleoclimate information (δ2Hn value). To measure δ2Hn values in structural H of clay minerals and soil clay fractions, we adapted a steam equilibration method by accounting for high hygroscopicity. Our δ2Hn values for USGS57 biotite (−95.3 ± SD 0.9‰) and USGS58 muscovite (30.7 ± 1.4‰) differed slightly but significantly from the reported δ2H values (−91.5 ± 2.4‰ and −28.4 ± 1.6‰), because the minerals contained 1.1%–4.4% of exchangeable H. The low SD of replicate measurements (n = 3) confirmed a high precision. The clay separation method including destruction of Fe oxides, carbonates and soil organic matter, and dispersion did not significantly change the δ2Hn values of five different clay minerals. However, we were unable to remove all organic matter from the soil clay fractions resulting in an estimated bias of 1‰ in two samples and 15‰ in the carbon‐richest sample. Our results demonstrate that δ2Hn values of structural H of clay minerals and soil clay fractions can be reliably measured without interference from atmospheric water and the method used to separate the soil clay fraction. Highlights We tested steam equilibration to determine stable isotope ratios of structural H in clay. Gas‐tight capsule sealing in Ar atmosphere was necessary to avoid remoistening. Our steam equilibration method showed a high accuracy and precision. The clay separation method did not change stable isotope ratios of structural H in clay.
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Keywords: ddc:549 ; controlled isotope exchange technique ; deuterium ; montmorillonite ; soil clay separation ; soil organic matter removal ; steam equilibration ; structural H ; USGS57 biotite ; vermiculite ; δ2H
    Language: English
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  • 11
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    Potential erodibility of semi‐arid steppe soils derived from aggregate stability tests (2022)
    Koza, Moritz ; Pöhlitz, Julia ; Prays, Aleksey ; [et al.]
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2023-01-26
    Description: Erosion is a severe threat to the sustainable use of agricultural soils. However, the structural resistance of soil against the disruptive forces steppe soils experience under field conditions has not been investigated. Therefore, 132 topsoils under grass‐ and cropland covering a large range of physico‐chemical soil properties (sand: 2–76%, silt: 18–80%, clay: 6–30%, organic carbon: 7.3–64.2 g kg−1, inorganic carbon: 0.0–8.5 g kg−1, pH: 4.8–9.5, electrical conductivity: 32–946 μS cm−1) from northern Kazakhstan were assessed for their potential erodibility using several tests. An adjusted drop‐shatter method (low energy input of 60 Joule on a 250‐cm3 soil block) was used to estimate the stability of dry soil against weak mechanical forces, such as saltating particles striking the surface causing wind erosion. Three wetting treatments with various conditions and energies (fast wetting, slow wetting, and wet shaking) were applied to simulate different disruptive effects of water. Results indicate that aggregate stability was higher for grassland than cropland soils and declined with decreasing soil organic carbon content. The results of the drop‐shatter test suggested that 29% of the soils under cropland were at risk of wind erosion, but only 6% were at high risk (i.e. erodible fraction 〉60%). In contrast, the fast wetting treatment revealed that 54% of the samples were prone to become “very unstable” and 44% “unstable” during heavy rain or snowmelt events. Even under conditions comparable to light rain events or raindrop impact, 53–59% of the samples were “unstable.” Overall, cropland soils under semi‐arid conditions seem much more susceptible to water than wind erosion. Considering future projections of increasing precipitation in Kazakhstan, we conclude that the risk of water erosion is potentially underestimated and needs to be taken into account when developing sustainable land use strategies. Highlights Organic matter is the important binding agent enhancing aggregation in steppe topsoils. Tillage always declines aggregate stability even without soil organic carbon changes. All croplands soil are prone to wind or water erosion independent of their soil properties. Despite the semi‐arid conditions, erosion risk by water seems higher than by wind.
    Description: Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100002347
    Keywords: ddc:631.4 ; climate change ; land use ; soil organic carbon ; soil texture ; water erosion ; wind erosion
    Language: English
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  • 12
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    Vertical SOC distribution and aromatic carbon in centuries old charcoal‐rich Technosols (2022)
    Bonhage, Alexander ; Raab, Thomas ; Schneider, Anna ; [et al.]
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2023-01-21
    Description: Charcoal‐rich Technosols on century‐old relict charcoal hearths (RCHs) are the subject of ongoing research regarding potential legacy effects that result from historic charcoal production and subsequent charcoal amendments on forest soil properties and forest ecosystems today. RCHs consist mostly of Auh horizons that are substantially enriched in soil organic carbon (SOC), of which the largest part seems to be of pyrogenic origin (PyC). However, the reported range of SOC and PyC contents in RCH soil also suggests that they are enriched in nonpyrogenic SOC. RCH soils are discussed as potential benchmarks for the long‐term influence of biochar amendment and the post‐wildfire influences on soil properties. In this study, we utilised a large soil sample dataset (n = 1245) from 52 RCH sites in north‐western Connecticut, USA, to quantify SOC contents by total element analysis. The contents of condensed highly aromatic carbon as a proxy for black carbon (BC) were predicted by using a modified benzene polycarboxylated acid (BPCA) marker method in combination with diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy‐based partial least square regression (r2 = 0.89). A high vertical spatial sampling resolution allowed the identification of soil organic matter (SOM) enrichment and translocation processes. The results show an average 75% and 1862% increase in TOC and BPCA‐derived carbon, respectively, for technogenic Auh horizons compared to reference soils. In addition to an increase in aromatic properties, increased carboxylic properties of the RCH SOC suggest self‐humification effects of degrading charcoal and thereby the continuing formation of leachable aromatic carbon compounds, which could have effects on pedogenic processes in buried soils. Indeed, we show BPCA‐derived carbon concentrations in intermediate technogenic Cu horizons and buried top/subsoils that suggest vertical translocation of highly aromatic carbon originating in RCH Auh horizons. Topmost Auh horizons showed a gradual decrease in total organic carbon (TOC) contents with increasing depth, suggesting accumulation of recent, non‐pyrogenic SOM. Lower aliphatic absorptions in RCH soil spectra suggest different SOM turnover dynamics compared to reference soils. Furthermore, studied RCH soils featured additional TOC enrichment, which cannot be fully explained now. Highlights BC to TOC ratio and high resolution vertical SOC distribution in 52 RCH sites were studied. RCH soils non‐BC pool was potentially different to reference soils. RCH soils feature TOC accumulation in the topmost horizon. There is BC translocation into buried soils on RCH sites.
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Keywords: ddc:631.4 ; benzene polycarboxylated acid marker (BPCA) ; black carbon ; charcoal degradation ; charcoal kiln ; pyrogenic carbon ; relict charcoal hearth ; biochar
    Language: English
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  • 13
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    Defining Hydrogeological Site Similarity with Hierarchical Agglomerative Clustering (2022)
    Blackwell Publishing Ltd | Malden, US
    Details
    Publication Date: 2024-02-28
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Hydrogeological information about an aquifer is difficult and costly to obtain, yet essential for the efficient management of groundwater resources. Transferring information from sampled sites to a specific site of interest can provide information when site‐specific data is lacking. Central to this approach is the notion of site similarity, which is necessary for determining relevant sites to include in the data transfer process. In this paper, we present a data‐driven method for defining site similarity. We apply this method to selecting groups of similar sites from which to derive prior distributions for the Bayesian estimation of hydraulic conductivity measurements at sites of interest. We conclude that there is now a unique opportunity to combine hydrogeological expertise with data‐driven methods to improve the predictive ability of stochastic hydrogeological models.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉〈italic〉Article impact statement〈/italic〉: This article introduces hierarchical clustering as a method for defining a notion of site similarity; the aim of this method is to improve the derivation of prior distributions in Bayesian methods in hydrogeology.〈/p〉
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Description: https://github.com/GeoStat-Bayesian/geostatDB
    Description: https://github.com/GeoStat-Bayesian/exPrior
    Description: https://github.com/GeoStat-Bayesian/siteSimilarity
    Keywords: ddc:551.49 ; hydrogeological sites ; hydrogeological modeling
    Language: English
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  • 14
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    Reducing tillage intensity benefits the soil micro‐ and mesofauna in a global meta‐analysis (2022)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2024-03-22
    Description: Soil fauna drives crucial processes of energy and nutrient cycling in agricultural systems, and influences the quality of crops and pest incidence. Soil tillage is the most influential agricultural manipulation of soil structure, and has a profound influence on soil biology and its provision of ecosystem services. The objective of this study was to quantify through meta‐analyses the effects of reducing tillage intensity on density and diversity of soil micro‐ and mesofaunal communities, and how these effects vary among different pedoclimatic conditions and interact with concurrent management practices. We present the results of a global meta‐analysis of available literature data on the effects of different tillage intensities on taxonomic and functional groups of soil micro‐ and mesofauna. We collected paired observations (conventional vs. reduced forms of tillage/no‐tillage) from 133 studies across 33 countries. Our results show that reduced tillage intensity or no‐tillage increases the total density of springtails (+35%), mites (+23%), and enchytraeids (+37%) compared to more intense tillage methods. The meta‐analyses for different nematode feeding groups, life‐forms of springtails, and taxonomic mite groups showed higher densities under reduced forms of tillage compared to conventional tillage on omnivorous nematodes (+53%), epedaphic (+81%) and hemiedaphic (+84%) springtails, oribatid (+43%) and mesostigmatid (+57%) mites. Furthermore, the effects of reduced forms of tillage on soil micro‐ and mesofauna varied with depth, climate and soil texture, as well as with tillage method, tillage frequency, concurrent fertilisation, and herbicide application. Our findings suggest that reducing tillage intensity can have positive effects on the density of micro‐ and mesofaunal communities in areas subjected to long‐term intensive cultivation practices. Our results will be useful to support decision making on the management of soil faunal communities and will facilitate modelling efforts of soil biology in global agroecosystems. HIGHLIGHTS Global meta‐analysis to estimate the effect of reducing tillage intensity on micro‐ and mesofauna Reduced tillage or no‐tillage has positive effects on springtail, mite and enchytraeid density Effects vary among nematode feeding groups, springtail life forms and mite suborders Effects vary with texture, climate and depth and depend on the tillage method and frequency
    Description: Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100002347
    Description: https://doi.org/10.20387/bonares-eh0f-hj28
    Keywords: ddc:631.4 ; agricultural land use ; conservation agriculture ; conventional agriculture ; soil biodiversity ; soil cultivation
    Language: English
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  • 15
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    Coots use hatch order to learn to recognize and reject conspecific brood parasitic chicks (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-12-18
    Description: Avian brood parasites and their hosts provide model systems for investigating links between recognition, learning, and their fitness consequences. One major evolutionary puzzle has continued to capture the attention of naturalists for centuries: why do hosts of brood parasites generally fail to recognize parasitic offspring after they have hatched from the egg, even when the host and parasitic chicks differ to almost comic degrees? One prominent theory to explain this pattern proposes that the costs of mistakenly learning to recognize the wrong offspring make recognition maladaptive. Here we show that American coots, Fulica americana, can recognize and reject parasitic chicks in their brood by using learned cues, despite the fact that the hosts and the brood parasites are of the same species. A series of chick cross-fostering experiments confirm that coots use first-hatched chicks in a brood as referents to learn to recognize their own chicks and then discriminate against later-hatched parasitic chicks in the same brood. When experimentally provided with the wrong reference chicks, coots can be induced to discriminate against their own offspring, confirming that the learning errors proposed by theory can exist. However, learning based on hatching order is reliable in naturally parasitized coot nests because host eggs hatch predictably ahead of parasite eggs. Conversely, a lack of reliable information may help to explain why the evolution of chick recognition is not more common in hosts of most interspecific brood parasites.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shizuka, Daizaburo -- Lyon, Bruce E -- England -- Nature. 2010 Jan 14;463(7278):223-6. doi: 10.1038/nature08655. Epub 2009 Dec 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California 95064, USA. shizuka@biology.ucsc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20016486" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Birds/*parasitology/*physiology ; British Columbia ; Cues ; Discrimination Learning/*physiology ; Feeding Behavior/physiology ; Genetic Fitness ; Nesting Behavior/*physiology ; Ovum/growth & development ; Pattern Recognition, Visual/physiology ; Survival Rate ; Time Factors ; Wetlands
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 16
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    Origins and functional impact of copy number variation in the human genome (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-10-09
    Description: Structural variations of DNA greater than 1 kilobase in size account for most bases that vary among human genomes, but are still relatively under-ascertained. Here we use tiling oligonucleotide microarrays, comprising 42 million probes, to generate a comprehensive map of 11,700 copy number variations (CNVs) greater than 443 base pairs, of which most (8,599) have been validated independently. For 4,978 of these CNVs, we generated reference genotypes from 450 individuals of European, African or East Asian ancestry. The predominant mutational mechanisms differ among CNV size classes. Retrotransposition has duplicated and inserted some coding and non-coding DNA segments randomly around the genome. Furthermore, by correlation with known trait-associated single nucleotide polymorphisms (SNPs), we identified 30 loci with CNVs that are candidates for influencing disease susceptibility. Despite this, having assessed the completeness of our map and the patterns of linkage disequilibrium between CNVs and SNPs, we conclude that, for complex traits, the heritability void left by genome-wide association studies will not be accounted for by common CNVs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3330748/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3330748/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Conrad, Donald F -- Pinto, Dalila -- Redon, Richard -- Feuk, Lars -- Gokcumen, Omer -- Zhang, Yujun -- Aerts, Jan -- Andrews, T Daniel -- Barnes, Chris -- Campbell, Peter -- Fitzgerald, Tomas -- Hu, Min -- Ihm, Chun Hwa -- Kristiansson, Kati -- Macarthur, Daniel G -- Macdonald, Jeffrey R -- Onyiah, Ifejinelo -- Pang, Andy Wing Chun -- Robson, Sam -- Stirrups, Kathy -- Valsesia, Armand -- Walter, Klaudia -- Wei, John -- Wellcome Trust Case Control Consortium -- Tyler-Smith, Chris -- Carter, Nigel P -- Lee, Charles -- Scherer, Stephen W -- Hurles, Matthew E -- 077006/Z/05/Z/Wellcome Trust/United Kingdom -- 077008/Wellcome Trust/United Kingdom -- 077009/Wellcome Trust/United Kingdom -- 077014/Wellcome Trust/United Kingdom -- 088340/Wellcome Trust/United Kingdom -- GM081533/GM/NIGMS NIH HHS/ -- HG004221/HG/NHGRI NIH HHS/ -- Canadian Institutes of Health Research/Canada -- England -- Nature. 2010 Apr 1;464(7289):704-12. doi: 10.1038/nature08516. Epub 2009 Oct 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19812545" target="_blank"〉PubMed〈/a〉
    Keywords: Continental Population Groups/genetics ; DNA Copy Number Variations/*genetics ; Gene Duplication ; Genetic Predisposition to Disease/*genetics ; Genome, Human/*genetics ; Genome-Wide Association Study ; Genotype ; Haplotypes/genetics ; Humans ; Mutagenesis/*genetics ; Oligonucleotide Array Sequence Analysis ; Polymorphism, Single Nucleotide/genetics ; Reproducibility of Results
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 17
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    Reprogramming towards pluripotency requires AID-dependent DNA demethylation (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-12-23
    Description: Reprogramming of somatic cell nuclei to yield induced pluripotent stem (iPS) cells makes possible derivation of patient-specific stem cells for regenerative medicine. However, iPS cell generation is asynchronous and slow (2-3 weeks), the frequency is low (〈0.1%), and DNA demethylation constitutes a bottleneck. To determine regulatory mechanisms involved in reprogramming, we generated interspecies heterokaryons (fused mouse embryonic stem (ES) cells and human fibroblasts) that induce reprogramming synchronously, frequently and fast. Here we show that reprogramming towards pluripotency in single heterokaryons is initiated without cell division or DNA replication, rapidly (1 day) and efficiently (70%). Short interfering RNA (siRNA)-mediated knockdown showed that activation-induced cytidine deaminase (AID, also known as AICDA) is required for promoter demethylation and induction of OCT4 (also known as POU5F1) and NANOG gene expression. AID protein bound silent methylated OCT4 and NANOG promoters in fibroblasts, but not active demethylated promoters in ES cells. These data provide new evidence that mammalian AID is required for active DNA demethylation and initiation of nuclear reprogramming towards pluripotency in human somatic cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2906123/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2906123/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bhutani, Nidhi -- Brady, Jennifer J -- Damian, Mara -- Sacco, Alessandra -- Corbel, Stephane Y -- Blau, Helen M -- AG009521/AG/NIA NIH HHS/ -- AG024987/AG/NIA NIH HHS/ -- AI007328/AI/NIAID NIH HHS/ -- R01 AG009521/AG/NIA NIH HHS/ -- R01 AG009521-25/AG/NIA NIH HHS/ -- R01 AG024987/AG/NIA NIH HHS/ -- R01 AG024987-05/AG/NIA NIH HHS/ -- T32 AI007328/AI/NIAID NIH HHS/ -- U01 HL100397/HL/NHLBI NIH HHS/ -- England -- Nature. 2010 Feb 25;463(7284):1042-7. doi: 10.1038/nature08752.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Baxter Laboratory for Stem Cell Biology, Institute for Stem Cell Biology and Regenerative Medicine, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305-5175, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20027182" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Division ; Cell Fusion ; Cell Line ; Cells, Cultured ; Cellular Reprogramming/genetics/*physiology ; Chromatin Immunoprecipitation ; Cytidine Deaminase/deficiency/genetics/*metabolism ; DNA/chemistry/genetics/metabolism ; *DNA Methylation ; DNA Replication ; Embryonic Stem Cells/cytology/metabolism ; Fibroblasts/cytology/metabolism ; Gene Expression Regulation ; Gene Knockdown Techniques ; Homeodomain Proteins/genetics ; Humans ; Induced Pluripotent Stem Cells/*cytology/enzymology/*metabolism ; Lung/cytology/embryology ; Mice ; Models, Biological ; Octamer Transcription Factor-3/genetics ; Promoter Regions, Genetic/genetics ; Time Factors
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 18
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    The sequence and de novo assembly of the giant panda genome (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-12-17
    Description: Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3951497/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3951497/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Ruiqiang -- Fan, Wei -- Tian, Geng -- Zhu, Hongmei -- He, Lin -- Cai, Jing -- Huang, Quanfei -- Cai, Qingle -- Li, Bo -- Bai, Yinqi -- Zhang, Zhihe -- Zhang, Yaping -- Wang, Wen -- Li, Jun -- Wei, Fuwen -- Li, Heng -- Jian, Min -- Li, Jianwen -- Zhang, Zhaolei -- Nielsen, Rasmus -- Li, Dawei -- Gu, Wanjun -- Yang, Zhentao -- Xuan, Zhaoling -- Ryder, Oliver A -- Leung, Frederick Chi-Ching -- Zhou, Yan -- Cao, Jianjun -- Sun, Xiao -- Fu, Yonggui -- Fang, Xiaodong -- Guo, Xiaosen -- Wang, Bo -- Hou, Rong -- Shen, Fujun -- Mu, Bo -- Ni, Peixiang -- Lin, Runmao -- Qian, Wubin -- Wang, Guodong -- Yu, Chang -- Nie, Wenhui -- Wang, Jinhuan -- Wu, Zhigang -- Liang, Huiqing -- Min, Jiumeng -- Wu, Qi -- Cheng, Shifeng -- Ruan, Jue -- Wang, Mingwei -- Shi, Zhongbin -- Wen, Ming -- Liu, Binghang -- Ren, Xiaoli -- Zheng, Huisong -- Dong, Dong -- Cook, Kathleen -- Shan, Gao -- Zhang, Hao -- Kosiol, Carolin -- Xie, Xueying -- Lu, Zuhong -- Zheng, Hancheng -- Li, Yingrui -- Steiner, Cynthia C -- Lam, Tommy Tsan-Yuk -- Lin, Siyuan -- Zhang, Qinghui -- Li, Guoqing -- Tian, Jing -- Gong, Timing -- Liu, Hongde -- Zhang, Dejin -- Fang, Lin -- Ye, Chen -- Zhang, Juanbin -- Hu, Wenbo -- Xu, Anlong -- Ren, Yuanyuan -- Zhang, Guojie -- Bruford, Michael W -- Li, Qibin -- Ma, Lijia -- Guo, Yiran -- An, Na -- Hu, Yujie -- Zheng, Yang -- Shi, Yongyong -- Li, Zhiqiang -- Liu, Qing -- Chen, Yanling -- Zhao, Jing -- Qu, Ning -- Zhao, Shancen -- Tian, Feng -- Wang, Xiaoling -- Wang, Haiyin -- Xu, Lizhi -- Liu, Xiao -- Vinar, Tomas -- Wang, Yajun -- Lam, Tak-Wah -- Yiu, Siu-Ming -- Liu, Shiping -- Zhang, Hemin -- Li, Desheng -- Huang, Yan -- Wang, Xia -- Yang, Guohua -- Jiang, Zhi -- Wang, Junyi -- Qin, Nan -- Li, Li -- Li, Jingxiang -- Bolund, Lars -- Kristiansen, Karsten -- Wong, Gane Ka-Shu -- Olson, Maynard -- Zhang, Xiuqing -- Li, Songgang -- Yang, Huanming -- Wang, Jian -- Wang, Jun -- R01 HG003229/HG/NHGRI NIH HHS/ -- R01 HG003229-05/HG/NHGRI NIH HHS/ -- England -- Nature. 2010 Jan 21;463(7279):311-7. doi: 10.1038/nature08696. Epub 2009 Dec 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉BGI-Shenzhen, Shenzhen 518083, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20010809" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Animals ; China ; Conserved Sequence/genetics ; Contig Mapping ; Diet/veterinary ; Dogs ; Evolution, Molecular ; Female ; Fertility/genetics/physiology ; Genome/*genetics ; *Genomics ; Heterozygote ; Humans ; Multigene Family/genetics ; Polymorphism, Single Nucleotide/genetics ; Receptors, G-Protein-Coupled/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Synteny/genetics ; Ursidae/classification/*genetics/physiology
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 19
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    A comprehensive catalogue of somatic mutations from a human cancer genome (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-12-18
    Description: All cancers carry somatic mutations. A subset of these somatic alterations, termed driver mutations, confer selective growth advantage and are implicated in cancer development, whereas the remainder are passengers. Here we have sequenced the genomes of a malignant melanoma and a lymphoblastoid cell line from the same person, providing the first comprehensive catalogue of somatic mutations from an individual cancer. The catalogue provides remarkable insights into the forces that have shaped this cancer genome. The dominant mutational signature reflects DNA damage due to ultraviolet light exposure, a known risk factor for malignant melanoma, whereas the uneven distribution of mutations across the genome, with a lower prevalence in gene footprints, indicates that DNA repair has been preferentially deployed towards transcribed regions. The results illustrate the power of a cancer genome sequence to reveal traces of the DNA damage, repair, mutation and selection processes that were operative years before the cancer became symptomatic.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3145108/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3145108/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pleasance, Erin D -- Cheetham, R Keira -- Stephens, Philip J -- McBride, David J -- Humphray, Sean J -- Greenman, Chris D -- Varela, Ignacio -- Lin, Meng-Lay -- Ordonez, Gonzalo R -- Bignell, Graham R -- Ye, Kai -- Alipaz, Julie -- Bauer, Markus J -- Beare, David -- Butler, Adam -- Carter, Richard J -- Chen, Lina -- Cox, Anthony J -- Edkins, Sarah -- Kokko-Gonzales, Paula I -- Gormley, Niall A -- Grocock, Russell J -- Haudenschild, Christian D -- Hims, Matthew M -- James, Terena -- Jia, Mingming -- Kingsbury, Zoya -- Leroy, Catherine -- Marshall, John -- Menzies, Andrew -- Mudie, Laura J -- Ning, Zemin -- Royce, Tom -- Schulz-Trieglaff, Ole B -- Spiridou, Anastassia -- Stebbings, Lucy A -- Szajkowski, Lukasz -- Teague, Jon -- Williamson, David -- Chin, Lynda -- Ross, Mark T -- Campbell, Peter J -- Bentley, David R -- Futreal, P Andrew -- Stratton, Michael R -- 077012/Z/05/Z/Wellcome Trust/United Kingdom -- 088340/Wellcome Trust/United Kingdom -- 093867/Wellcome Trust/United Kingdom -- England -- Nature. 2010 Jan 14;463(7278):191-6. doi: 10.1038/nature08658. Epub 2009 Dec 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20016485" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Cell Line, Tumor ; DNA Damage/genetics ; DNA Mutational Analysis ; DNA Repair/genetics ; Gene Dosage/genetics ; Genes, Neoplasm/*genetics ; Genome, Human/*genetics ; Humans ; Loss of Heterozygosity/genetics ; Male ; Melanoma/etiology/genetics ; MicroRNAs/genetics ; Mutagenesis, Insertional/genetics ; Mutation/*genetics ; Neoplasms/etiology/*genetics ; Polymorphism, Single Nucleotide/genetics ; Precision Medicine ; Sequence Deletion/genetics ; Ultraviolet Rays
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Phylogenies reveal new interpretation of speciation and the Red Queen (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-12-17
    Description: The Red Queen describes a view of nature in which species continually evolve but do not become better adapted. It is one of the more distinctive metaphors of evolutionary biology, but no test of its claim that speciation occurs at a constant rate has ever been made against competing models that can predict virtually identical outcomes, nor has any mechanism been proposed that could cause the constant-rate phenomenon. Here we use 101 phylogenies of animal, plant and fungal taxa to test the constant-rate claim against four competing models. Phylogenetic branch lengths record the amount of time or evolutionary change between successive events of speciation. The models predict the distribution of these lengths by specifying how factors combine to bring about speciation, or by describing how rates of speciation vary throughout a tree. We find that the hypotheses that speciation follows the accumulation of many small events that act either multiplicatively or additively found support in 8% and none of the trees, respectively. A further 8% of trees hinted that the probability of speciation changes according to the amount of divergence from the ancestral species, and 6% suggested speciation rates vary among taxa. By comparison, 78% of the trees fit the simplest model in which new species emerge from single events, each rare but individually sufficient to cause speciation. This model predicts a constant rate of speciation, and provides a new interpretation of the Red Queen: the metaphor of species losing a race against a deteriorating environment is replaced by a view linking speciation to rare stochastic events that cause reproductive isolation. Attempts to understand species-radiations or why some groups have more or fewer species should look to the size of the catalogue of potential causes of speciation shared by a group of closely related organisms rather than to how those causes combine.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Venditti, Chris -- Meade, Andrew -- Pagel, Mark -- England -- Nature. 2010 Jan 21;463(7279):349-52. doi: 10.1038/nature08630. Epub 2009 Dec 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biological Sciences, University of Reading, Reading, Berkshire, RG6 6BX, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20010607" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Animals ; *Genetic Speciation ; *Models, Biological ; *Phylogeny ; Selection, Genetic ; Stochastic Processes
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    Time-reversal symmetry breaking and spontaneous Hall effect without magnetic dipole order (2009)
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    Publication Date: 2009-12-17
    Description: Spin liquids are magnetically frustrated systems, in which spins are prevented from ordering or freezing, owing to quantum or thermal fluctuations among degenerate states induced by the frustration. Chiral spin liquids are a hypothetical class of spin liquids in which the time-reversal symmetry is macroscopically broken in the absence of an applied magnetic field or any magnetic dipole long-range order. Even though such chiral spin-liquid states were proposed more than two decades ago, an experimental realization and observation of such states has remained a challenge. One of the characteristic order parameters in such systems is a macroscopic average of the scalar spin chirality, a solid angle subtended by three nearby spins. In previous experimental reports, however, the spin chirality was only parasitic to the non-coplanar spin structure associated with a magnetic dipole long-range order or induced by the applied magnetic field, and thus the chiral spin-liquid state has never been found. Here, we report empirical evidence that the time-reversal symmetry can be broken spontaneously on a macroscopic scale in the absence of magnetic dipole long-range order. In particular, we employ the anomalous Hall effect to directly probe the broken time-reversal symmetry for the metallic frustrated magnet Pr(2)Ir(2)O(7). An onset of the Hall effect is observed at zero field in the absence of uniform magnetization, within the experimental accuracy, suggesting an emergence of a chiral spin liquid. The origin of this spontaneous Hall effect is ascribed to chiral spin textures, which are inferred from the magnetic measurements indicating the spin ice-rule formation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Machida, Yo -- Nakatsuji, Satoru -- Onoda, Shigeki -- Tayama, Takashi -- Sakakibara, Toshiro -- England -- Nature. 2010 Jan 14;463(7278):210-3. doi: 10.1038/nature08680. Epub 2009 Dec 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉[1] Institute for Solid State Physics, University of Tokyo, Kashiwa 277-8581, Japan [2] Present addresses: Department of Physics, Tokyo Institute of Technology, Meguro 152-8551, Japan (Y.M.); Department of Physics, University of Toyama, Toyama 930-8555, Japan (T.T.).〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20010605" target="_blank"〉PubMed〈/a〉
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    Three-dimensional structure determination from a single view (2009)
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    Publication Date: 2009-12-18
    Description: The ability to determine the structure of matter in three dimensions has profoundly advanced our understanding of nature. Traditionally, the most widely used schemes for three-dimensional (3D) structure determination of an object are implemented by acquiring multiple measurements over various sample orientations, as in the case of crystallography and tomography, or by scanning a series of thin sections through the sample, as in confocal microscopy. Here we present a 3D imaging modality, termed ankylography (derived from the Greek words ankylos meaning 'curved' and graphein meaning 'writing'), which under certain circumstances enables complete 3D structure determination from a single exposure using a monochromatic incident beam. We demonstrate that when the diffraction pattern of a finite object is sampled at a sufficiently fine scale on the Ewald sphere, the 3D structure of the object is in principle determined by the 2D spherical pattern. We confirm the theoretical analysis by performing 3D numerical reconstructions of a sodium silicate glass structure at 2 A resolution, and a single poliovirus at 2-3 nm resolution, from 2D spherical diffraction patterns alone. Using diffraction data from a soft X-ray laser, we also provide a preliminary demonstration that ankylography is experimentally feasible by obtaining a 3D image of a test object from a single 2D diffraction pattern. With further development, this approach of obtaining complete 3D structure information from a single view could find broad applications in the physical and life sciences.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Raines, Kevin S -- Salha, Sara -- Sandberg, Richard L -- Jiang, Huaidong -- Rodriguez, Jose A -- Fahimian, Benjamin P -- Kapteyn, Henry C -- Du, Jincheng -- Miao, Jianwei -- England -- Nature. 2010 Jan 14;463(7278):214-7. doi: 10.1038/nature08705. Epub 2009 Dec 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉[1] Department of Physics and Astronomy, [2] California NanoSystems Institute.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20016484" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Cryoelectron Microscopy ; Glass/*chemistry ; Imaging, Three-Dimensional/*methods ; Lasers ; Molecular Conformation ; Molecular Dynamics Simulation ; Molecular Imaging/*methods ; Poliovirus/*chemistry/ultrastructure ; *Scattering, Radiation ; Silicates/*chemistry ; X-Rays
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    Crystal structure of DNA-PKcs reveals a large open-ring cradle comprised of HEAT repeats (2009)
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    Publication Date: 2009-12-22
    Description: Broken chromosomes arising from DNA double-strand breaks result from endogenous events such as the production of reactive oxygen species during cellular metabolism, as well as from exogenous sources such as ionizing radiation. Left unrepaired or incorrectly repaired they can lead to genomic changes that may result in cell death or cancer. DNA-dependent protein kinase (DNA-PK), a holoenzyme that comprises the DNA-PK catalytic subunit (DNA-PKcs) and the heterodimer Ku70/Ku80, has a major role in non-homologous end joining-the main pathway in mammals used to repair double-strand breaks. DNA-PKcs is a serine/threonine protein kinase comprising a single polypeptide chain of 4,128 amino acids and belonging to the phosphatidylinositol-3-OH kinase (PI(3)K)-related protein family. DNA-PKcs is involved in the sensing and transmission of DNA damage signals to proteins such as p53, setting off events that lead to cell cycle arrest. It phosphorylates a wide range of substrates in vitro, including Ku70/Ku80, which is translocated along DNA. Here we present the crystal structure of human DNA-PKcs at 6.6 A resolution, in which the overall fold is clearly visible, to our knowledge, for the first time. The many alpha-helical HEAT repeats (helix-turn-helix motifs) facilitate bending and allow the polypeptide chain to fold into a hollow circular structure. The carboxy-terminal kinase domain is located on top of this structure, and a small HEAT repeat domain that probably binds DNA is inside. The structure provides a flexible cradle to promote DNA double-strand-break repair.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2811870/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2811870/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sibanda, Bancinyane L -- Chirgadze, Dimitri Y -- Blundell, Tom L -- 079281/Wellcome Trust/United Kingdom -- A3846/Cancer Research UK/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2010 Jan 7;463(7277):118-21. doi: 10.1038/nature08648. Epub 2009 Dec 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Cambridge, Old Addenbrooke's site, 80 Tennis Court Road, Cambridge CB2 1GA, UK. lynn@cryst.bioc.cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20023628" target="_blank"〉PubMed〈/a〉
    Keywords: Antigens, Nuclear/chemistry ; Catalytic Domain ; Crystallography, X-Ray ; DNA/metabolism ; DNA Breaks, Double-Stranded ; DNA-Activated Protein Kinase/*chemistry/metabolism ; DNA-Binding Proteins/chemistry ; HeLa Cells ; *Helix-Turn-Helix Motifs ; Humans ; Models, Molecular ; Nuclear Proteins/*chemistry/metabolism ; Protein Folding ; Protein Structure, Secondary
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    Preventing the return of fear in humans using reconsolidation update mechanisms (2009)
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    Publication Date: 2009-12-17
    Description: Recent research on changing fears has examined targeting reconsolidation. During reconsolidation, stored information is rendered labile after being retrieved. Pharmacological manipulations at this stage result in an inability to retrieve the memories at later times, suggesting that they are erased or persistently inhibited. Unfortunately, the use of these pharmacological manipulations in humans can be problematic. Here we introduce a non-invasive technique to target the reconsolidation of fear memories in humans. We provide evidence that old fear memories can be updated with non-fearful information provided during the reconsolidation window. As a consequence, fear responses are no longer expressed, an effect that lasted at least a year and was selective only to reactivated memories without affecting others. These findings demonstrate the adaptive role of reconsolidation as a window of opportunity to rewrite emotional memories, and suggest a non-invasive technique that can be used safely in humans to prevent the return of fear.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3640262/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3640262/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schiller, Daniela -- Monfils, Marie-H -- Raio, Candace M -- Johnson, David C -- Ledoux, Joseph E -- Phelps, Elizabeth A -- K05 MH067048/MH/NIMH NIH HHS/ -- P50 MH058911/MH/NIMH NIH HHS/ -- R01 MH038774/MH/NIMH NIH HHS/ -- R01 MH046516/MH/NIMH NIH HHS/ -- R21 MH072279/MH/NIMH NIH HHS/ -- R37 MH038774/MH/NIMH NIH HHS/ -- Canadian Institutes of Health Research/Canada -- England -- Nature. 2010 Jan 7;463(7277):49-53. doi: 10.1038/nature08637. Epub 2009 Dec 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Neural Science, New York University, New York, New York 10003, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20010606" target="_blank"〉PubMed〈/a〉
    Keywords: Conditioning, Classical/*physiology ; Cues ; Electrodes ; Electroshock ; Extinction, Psychological/*physiology ; Fear/*physiology/*psychology ; Humans ; Memory/*physiology ; Models, Neurological ; Models, Psychological ; Neuronal Plasticity/*physiology ; Photic Stimulation ; Time Factors
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    A structural explanation for the binding of endocytic dileucine motifs by the AP2 complex (2009)
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    Publication Date: 2009-01-14
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4340503/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4340503/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kelly, Bernard T -- McCoy, Airlie J -- Spate, Kira -- Miller, Sharon E -- Evans, Philip R -- Honing, Stefan -- Owen, David J -- 090909/Wellcome Trust/United Kingdom -- MC_U105178845/Medical Research Council/United Kingdom -- England -- Nature. 2008 Dec 18;456(7224):976-79. doi: 10.1038/nature07422.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19140243" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Protein Complex 2/*chemistry/genetics/*metabolism ; Amino Acid Motifs ; Animals ; Antigens, CD4/*chemistry/*metabolism ; Binding Sites ; Conserved Sequence ; *Endocytosis ; Humans ; Leucine/*metabolism ; Mice ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Subunits/chemistry/genetics/metabolism ; Rats
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    Wanted: cyber-czars (2009)
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    Publication Date: 2009-04-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2009 Apr 23;458(7241):945. doi: 10.1038/458945a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19396091" target="_blank"〉PubMed〈/a〉
    Keywords: Computer Security/standards/statistics & numerical data/*trends ; European Union ; Federal Government ; Internet/*standards ; *Leadership ; Research/*trends ; United States
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    No bull: genes for better milk (2009)
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    Publication Date: 2009-01-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dalton, Rex -- England -- Nature. 2009 Jan 22;457(7228):369. doi: 10.1038/457369a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19158758" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Breeding/economics/*methods ; Cattle/*genetics ; Dairying/economics/*methods ; Female ; Internationality ; Male ; Milk/*secretion/*standards ; Oligonucleotide Array Sequence Analysis ; Polymorphism, Single Nucleotide/genetics ; United States ; United States Department of Agriculture
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    Two types of dopamine neuron distinctly convey positive and negative motivational signals (2009)
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    Publication Date: 2009-05-19
    Description: Midbrain dopamine neurons are activated by reward or sensory stimuli predicting reward. These excitatory responses increase as the reward value increases. This response property has led to a hypothesis that dopamine neurons encode value-related signals and are inhibited by aversive events. Here we show that this is true only for a subset of dopamine neurons. We recorded the activity of dopamine neurons in monkeys (Macaca mulatta) during a Pavlovian procedure with appetitive and aversive outcomes (liquid rewards and airpuffs directed at the face, respectively). We found that some dopamine neurons were excited by reward-predicting stimuli and inhibited by airpuff-predicting stimuli, as the value hypothesis predicts. However, a greater number of dopamine neurons were excited by both of these stimuli, inconsistent with the hypothesis. Some dopamine neurons were also excited by both rewards and airpuffs themselves, especially when they were unpredictable. Neurons excited by the airpuff-predicting stimuli were located more dorsolaterally in the substantia nigra pars compacta, whereas neurons inhibited by the stimuli were located more ventromedially, some in the ventral tegmental area. A similar anatomical difference was observed for their responses to actual airpuffs. These findings suggest that different groups of dopamine neurons convey motivational signals in distinct manners.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2739096/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2739096/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Matsumoto, Masayuki -- Hikosaka, Okihide -- Z01 EY000415-05/Intramural NIH HHS/ -- England -- Nature. 2009 Jun 11;459(7248):837-41. doi: 10.1038/nature08028. Epub 2009 May 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Sensorimotor Research, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892-4435, USA. matsumotom@nei.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19448610" target="_blank"〉PubMed〈/a〉
    Keywords: Air ; Animals ; Appetitive Behavior/physiology ; Conditioning, Classical/physiology ; Dopamine/*metabolism ; Macaca mulatta/*physiology ; Models, Neurological ; *Motivation ; Neurons/*physiology ; Reward
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    Costing the earth (2009)
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    Publication Date: 2009-11-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sukhdev, Pavan -- England -- Nature. 2009 Nov 19;462(7271):277. doi: 10.1038/462277a. Epub 2009 Nov 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Economics of Ecosystems and Biodiversity (TEEB) project, United Nations Campus, Hermann-Ehlers-Strasse 10, 53113 Bonn, Germany. teeb@unep-teeb.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19915547" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biodiversity ; *Conservation of Natural Resources ; Fresh Water ; Government ; Humans ; Poverty
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    More than hot air (2009)
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    Publication Date: 2009-04-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2009 Apr 23;458(7241):945-6. doi: 10.1038/458945b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19396090" target="_blank"〉PubMed〈/a〉
    Keywords: Air Pollution/prevention & control ; Environmental Monitoring/*legislation & jurisprudence ; *Federal Government ; *Greenhouse Effect ; Humans ; Public Health/*legislation & jurisprudence ; United States ; United States Environmental Protection Agency/*legislation & jurisprudence
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    Optically controlled locking of the nuclear field via coherent dark-state spectroscopy (2009)
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    Publication Date: 2009-06-26
    Description: A single electron or hole spin trapped inside a semiconductor quantum dot forms the foundation for many proposed quantum logic devices. In group III-V materials, the resonance and coherence between two ground states of the single spin are inevitably affected by the lattice nuclear spins through the hyperfine interaction, while the dynamics of the single spin also influence the nuclear environment. Recent efforts have been made to protect the coherence of spins in quantum dots by suppressing the nuclear spin fluctuations. However, coherent control of a single spin in a single dot with simultaneous suppression of the nuclear fluctuations has yet to be achieved. Here we report the suppression of nuclear field fluctuations in a singly charged quantum dot to well below the thermal value, as shown by an enhancement of the single electron spin dephasing time T(2)*, which we measure using coherent dark-state spectroscopy. The suppression of nuclear fluctuations is found to result from a hole-spin assisted dynamic nuclear spin polarization feedback process, where the stable value of the nuclear field is determined only by the laser frequencies at fixed laser powers. This nuclear field locking is further demonstrated in a three-laser measurement, indicating a possible enhancement of the electron spin T(2)* by a factor of several hundred. This is a simple and powerful method of enhancing the electron spin coherence time without use of 'spin echo'-type techniques. We expect that our results will enable the reproducible preparation of the nuclear spin environment for repetitive control and measurement of a single spin with minimal statistical broadening.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, Xiaodong -- Yao, Wang -- Sun, Bo -- Steel, Duncan G -- Bracker, Allan S -- Gammon, Daniel -- Sham, L J -- England -- Nature. 2009 Jun 25;459(7250):1105-9. doi: 10.1038/nature08120.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The H. M. Randall Laboratory of Physics, The University of Michigan, Ann Arbor, Michigan 48109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19553994" target="_blank"〉PubMed〈/a〉
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    Science journalism: Breaking the convention? (2009)
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    Publication Date: 2009-06-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brumfiel, Geoff -- England -- Nature. 2009 Jun 25;459(7250):1050-1. doi: 10.1038/4591050a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19553969" target="_blank"〉PubMed〈/a〉
    Keywords: Computer Communication Networks/*trends ; Congresses as Topic/ethics/*trends ; Journalism/ethics/*trends ; Research
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    Climate-control plans scrutinized (2009)
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    Publication Date: 2009-09-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brumfiel, Geoff -- England -- Nature. 2009 Sep 3;461(7260):19. doi: 10.1038/461019a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19727173" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/chemistry ; Carbon Dioxide/analysis/*isolation & purification ; Conservation of Energy Resources/trends ; Ecosystem ; Fossil Fuels ; Great Britain ; *Greenhouse Effect ; Hydrogen-Ion Concentration ; Research/economics/standards ; *Research Design ; Societies, Scientific
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    Battlefield: hitting the supporters of biotechnology (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-10-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Katzek, Jens A -- England -- Nature. 2009 Oct 15;461(7266):875. doi: 10.1038/461875a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19829352" target="_blank"〉PubMed〈/a〉
    Keywords: *Biotechnology/manpower/standards ; *Communication ; *Food, Genetically Modified/adverse effects/standards ; Humans ; Lobbying ; Oryza/metabolism ; Plants, Genetically Modified/adverse effects ; *Public Opinion ; *Research Personnel ; beta Carotene/administration & dosage/metabolism
    Print ISSN: 0028-0836
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    Disease-corrected haematopoietic progenitors from Fanconi anaemia induced pluripotent stem cells (2009)
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    Publication Date: 2009-06-02
    Description: The generation of induced pluripotent stem (iPS) cells has enabled the derivation of patient-specific pluripotent cells and provided valuable experimental platforms to model human disease. Patient-specific iPS cells are also thought to hold great therapeutic potential, although direct evidence for this is still lacking. Here we show that, on correction of the genetic defect, somatic cells from Fanconi anaemia patients can be reprogrammed to pluripotency to generate patient-specific iPS cells. These cell lines appear indistinguishable from human embryonic stem cells and iPS cells from healthy individuals. Most importantly, we show that corrected Fanconi-anaemia-specific iPS cells can give rise to haematopoietic progenitors of the myeloid and erythroid lineages that are phenotypically normal, that is, disease-free. These data offer proof-of-concept that iPS cell technology can be used for the generation of disease-corrected, patient-specific cells with potential value for cell therapy applications.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2720823/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2720823/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Raya, Angel -- Rodriguez-Piza, Ignasi -- Guenechea, Guillermo -- Vassena, Rita -- Navarro, Susana -- Barrero, Maria Jose -- Consiglio, Antonella -- Castella, Maria -- Rio, Paula -- Sleep, Eduard -- Gonzalez, Federico -- Tiscornia, Gustavo -- Garreta, Elena -- Aasen, Trond -- Veiga, Anna -- Verma, Inder M -- Surralles, Jordi -- Bueren, Juan -- Izpisua Belmonte, Juan Carlos -- R01 HL053670/HL/NHLBI NIH HHS/ -- R01 HL053670-14/HL/NHLBI NIH HHS/ -- England -- Nature. 2009 Jul 2;460(7251):53-9. doi: 10.1038/nature08129. Epub 2009 May 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Regenerative Medicine in Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19483674" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line ; Cellular Reprogramming ; Fanconi Anemia/*pathology/*therapy ; Health ; Hematopoietic Stem Cells/*cytology/metabolism ; Humans ; Pluripotent Stem Cells/*cytology/metabolism
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    Frequent inactivation of A20 in B-cell lymphomas (2009)
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    Publication Date: 2009-05-05
    Description: A20 is a negative regulator of the NF-kappaB pathway and was initially identified as being rapidly induced after tumour-necrosis factor-alpha stimulation. It has a pivotal role in regulation of the immune response and prevents excessive activation of NF-kappaB in response to a variety of external stimuli; recent genetic studies have disclosed putative associations of polymorphic A20 (also called TNFAIP3) alleles with autoimmune disease risk. However, the involvement of A20 in the development of human cancers is unknown. Here we show, using a genome-wide analysis of genetic lesions in 238 B-cell lymphomas, that A20 is a common genetic target in B-lineage lymphomas. A20 is frequently inactivated by somatic mutations and/or deletions in mucosa-associated tissue lymphoma (18 out of 87; 21.8%) and Hodgkin's lymphoma of nodular sclerosis histology (5 out of 15; 33.3%), and, to a lesser extent, in other B-lineage lymphomas. When re-expressed in a lymphoma-derived cell line with no functional A20 alleles, wild-type A20, but not mutant A20, resulted in suppression of cell growth and induction of apoptosis, accompanied by downregulation of NF-kappaB activation. The A20-deficient cells stably generated tumours in immunodeficient mice, whereas the tumorigenicity was effectively suppressed by re-expression of A20. In A20-deficient cells, suppression of both cell growth and NF-kappaB activity due to re-expression of A20 depended, at least partly, on cell-surface-receptor signalling, including the tumour-necrosis factor receptor. Considering the physiological function of A20 in the negative modulation of NF-kappaB activation induced by multiple upstream stimuli, our findings indicate that uncontrolled signalling of NF-kappaB caused by loss of A20 function is involved in the pathogenesis of subsets of B-lineage lymphomas.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kato, Motohiro -- Sanada, Masashi -- Kato, Itaru -- Sato, Yasuharu -- Takita, Junko -- Takeuchi, Kengo -- Niwa, Akira -- Chen, Yuyan -- Nakazaki, Kumi -- Nomoto, Junko -- Asakura, Yoshitaka -- Muto, Satsuki -- Tamura, Azusa -- Iio, Mitsuru -- Akatsuka, Yoshiki -- Hayashi, Yasuhide -- Mori, Hiraku -- Igarashi, Takashi -- Kurokawa, Mineo -- Chiba, Shigeru -- Mori, Shigeo -- Ishikawa, Yuichi -- Okamoto, Koji -- Tobinai, Kensei -- Nakagama, Hitoshi -- Nakahata, Tatsutoshi -- Yoshino, Tadashi -- Kobayashi, Yukio -- Ogawa, Seishi -- England -- Nature. 2009 Jun 4;459(7247):712-6. doi: 10.1038/nature07969. Epub 2009 May 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Genomics Project, Department of Pediatrics, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19412163" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Apoptosis/physiology ; Cell Line ; Cysteine Endopeptidases/*genetics/*metabolism ; DNA-Binding Proteins ; Gene Expression ; *Gene Silencing ; Genome/genetics ; Humans ; Intracellular Signaling Peptides and Proteins/*genetics/*metabolism ; Lymphoma, B-Cell/*genetics/*physiopathology ; Mice ; NF-kappa B/genetics/metabolism ; Nuclear Proteins/*genetics/*metabolism
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    Bidirectional promoters generate pervasive transcription in yeast (2009)
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    Publication Date: 2009-01-27
    Description: Genome-wide pervasive transcription has been reported in many eukaryotic organisms, revealing a highly interleaved transcriptome organization that involves hundreds of previously unknown non-coding RNAs. These recently identified transcripts either exist stably in cells (stable unannotated transcripts, SUTs) or are rapidly degraded by the RNA surveillance pathway (cryptic unstable transcripts, CUTs). One characteristic of pervasive transcription is the extensive overlap of SUTs and CUTs with previously annotated features, which prompts questions regarding how these transcripts are generated, and whether they exert function. Single-gene studies have shown that transcription of SUTs and CUTs can be functional, through mechanisms involving the generated RNAs or their generation itself. So far, a complete transcriptome architecture including SUTs and CUTs has not been described in any organism. Knowledge about the position and genome-wide arrangement of these transcripts will be instrumental in understanding their function. Here we provide a comprehensive analysis of these transcripts in the context of multiple conditions, a mutant of the exosome machinery and different strain backgrounds of Saccharomyces cerevisiae. We show that both SUTs and CUTs display distinct patterns of distribution at specific locations. Most of the newly identified transcripts initiate from nucleosome-free regions (NFRs) associated with the promoters of other transcripts (mostly protein-coding genes), or from NFRs at the 3' ends of protein-coding genes. Likewise, about half of all coding transcripts initiate from NFRs associated with promoters of other transcripts. These data change our view of how a genome is transcribed, indicating that bidirectionality is an inherent feature of promoters. Such an arrangement of divergent and overlapping transcripts may provide a mechanism for local spreading of regulatory signals-that is, coupling the transcriptional regulation of neighbouring genes by means of transcriptional interference or histone modification.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2766638/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2766638/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, Zhenyu -- Wei, Wu -- Gagneur, Julien -- Perocchi, Fabiana -- Clauder-Munster, Sandra -- Camblong, Jurgi -- Guffanti, Elisa -- Stutz, Francoise -- Huber, Wolfgang -- Steinmetz, Lars M -- P01 HG000205/HG/NHGRI NIH HHS/ -- P01 HG000205-19/HG/NHGRI NIH HHS/ -- R01 GM068717/GM/NIGMS NIH HHS/ -- R01 GM068717-06/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Feb 19;457(7232):1033-7. doi: 10.1038/nature07728. Epub 2009 Jan 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19169243" target="_blank"〉PubMed〈/a〉
    Keywords: Gene Expression Profiling ; Gene Expression Regulation, Fungal/*genetics ; Genes, Fungal/genetics ; Genes, Overlapping/genetics ; Genome, Fungal/genetics ; Models, Genetic ; Nucleosomes ; Promoter Regions, Genetic/*genetics ; RNA Stability/genetics ; RNA, Fungal/*genetics ; RNA, Untranslated/genetics ; Saccharomyces cerevisiae/classification/*genetics ; Saccharomyces cerevisiae Proteins/genetics ; Transcription, Genetic/*genetics
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    A magnificence to share (2009)
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    Publication Date: 2009-04-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2009 Apr 16;458(7240):808. doi: 10.1038/458808a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19369979" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antarctic Regions ; *Ecosystem ; International Cooperation/*legislation & jurisprudence ; Travel/*legislation & jurisprudence
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    Astronomers lose access to military data (2009)
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    Publication Date: 2009-06-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brumfiel, Geoff -- England -- Nature. 2009 Jun 18;459(7249):896-7. doi: 10.1038/459897a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19536225" target="_blank"〉PubMed〈/a〉
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    Steven Chu prepares for power (2009)
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    Publication Date: 2009-01-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dalton, Rex -- England -- Nature. 2009 Jan 15;457(7227):241. doi: 10.1038/457241a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19148062" target="_blank"〉PubMed〈/a〉
    Keywords: Conservation of Energy Resources/*trends ; History, 20th Century ; History, 21st Century ; United States ; United States Government Agencies/*organization & administration
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    Interrogation: has abuse been reduced by psychologists? (2009)
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    Publication Date: 2009-07-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Summers, Frank -- England -- Nature. 2009 Jul 9;460(7252):173. doi: 10.1038/460173a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19587745" target="_blank"〉PubMed〈/a〉
    Keywords: Prisoners/*psychology ; Psychology/*statistics & numerical data ; Societies, Scientific ; Torture/*statistics & numerical data ; United States
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    Pore architecture and ion sites in acid-sensing ion channels and P2X receptors (2009)
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    Publication Date: 2009-07-31
    Description: Acid-sensing ion channels are proton-activated, sodium-selective channels composed of three subunits, and are members of the superfamily of epithelial sodium channels, mechanosensitive and FMRF-amide peptide-gated ion channels. These ubiquitous eukaryotic ion channels have essential roles in biological activities as diverse as sodium homeostasis, taste and pain. Despite their crucial roles in biology and their unusual trimeric subunit stoichiometry, there is little knowledge of the structural and chemical principles underlying their ion channel architecture and ion-binding sites. Here we present the structure of a functional acid-sensing ion channel in a desensitized state at 3 A resolution, the location and composition of the approximately 8 A 'thick' desensitization gate, and the trigonal antiprism coordination of caesium ions bound in the extracellular vestibule. Comparison of the acid-sensing ion channel structure with the ATP-gated P2X(4) receptor reveals similarity in pore architecture and aqueous vestibules, suggesting that there are unanticipated yet common structural and mechanistic principles.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2845979/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2845979/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gonzales, Eric B -- Kawate, Toshimitsu -- Gouaux, Eric -- F32 GM083615/GM/NIGMS NIH HHS/ -- F32 GM083615-01/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Jul 30;460(7255):599-604. doi: 10.1038/nature08218.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vollum Institute, Oregon Health and Science University, 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19641589" target="_blank"〉PubMed〈/a〉
    Keywords: Acid Sensing Ion Channels ; Animals ; Binding Sites ; CHO Cells ; Cell Line ; Cesium/metabolism ; Chickens/*physiology ; Cricetinae ; Cricetulus ; Crystallization ; Humans ; Ions/metabolism ; *Models, Molecular ; Nerve Tissue Proteins/*chemistry ; Protein Structure, Tertiary ; Receptors, Purinergic P2/*chemistry ; Receptors, Purinergic P2X ; Sodium Channels/*chemistry ; Zebrafish/*physiology
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    X-ray observation of a transient hemiaminal trapped in a porous network (2009)
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    Publication Date: 2009-10-02
    Description: X-ray crystallography is the method of choice for the direct structural analysis of crystalline compounds. Extending its use to the in situ mapping of chemical transformations could provide valuable insights, as illustrated by time-resolved X-ray crystallography studies; however, the transient nature of unstable reaction intermediates often poses a significant challenge. It has recently been demonstrated that standard chemical reactions can occur within the pores of porous coordination networks and that the robust crystallinity of these networks facilitates in situ X-ray analysis of the adducts and products. Here we show that such systems even enable X-ray observations of reaction intermediates that are usually transient and non-isolable. Our proof-of-concept demonstration examines the simple and ubiquitous reaction between an amine and an aldehyde, which normally form a very short-lived hemiaminal that then yields the Schiff-base product. The mechanism of this reaction has been exhaustively examined, but the hemiaminal intermediate has only rarely been observed. We first determine the structure of a porous network with an aromatic amine embedded in it, then diffuse an aldehyde substrate into the material to transform the amine into a hemiaminal intermediate that is kinetically trapped and thus amenable to X-ray analysis, and finally raise the temperature of the system to obtain the imine product and determine its structure. These results establish that porous network materials provide a means of obtaining sequential X-ray-based snapshots of the structural transformations that occur during chemical reactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kawamichi, Takehide -- Haneda, Tsuyoshi -- Kawano, Masaki -- Fujita, Makoto -- England -- Nature. 2009 Oct 1;461(7264):633-5. doi: 10.1038/nature08326.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Applied Chemistry, School of Engineering, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19794489" target="_blank"〉PubMed〈/a〉
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    Religious belief and the history of science (2009)
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    Publication Date: 2009-09-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goode, Scott -- England -- Nature. 2009 Sep 10;461(7261):167. doi: 10.1038/461167d.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19741681" target="_blank"〉PubMed〈/a〉
    Keywords: History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; *Religion and Science ; Research Personnel/*history/psychology/standards
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    Fluid dynamics: Rotating convection on the edge (2009)
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    Publication Date: 2009-01-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Read, Peter L -- England -- Nature. 2009 Jan 15;457(7227):270-1. doi: 10.1038/457270a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19148088" target="_blank"〉PubMed〈/a〉
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    A fly by any other name (2009)
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    Publication Date: 2009-01-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dalton, Rex -- England -- Nature. 2009 Jan 22;457(7228):368. doi: 10.1038/457368a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19158757" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Drosophila/*classification ; Drosophila melanogaster/classification ; Species Specificity ; *Terminology as Topic
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    The ITQ-37 mesoporous chiral zeolite (2009)
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    Publication Date: 2009-05-02
    Description: The synthesis of crystalline molecular sieves with pore dimensions that fill the gap between microporous and mesoporous materials is a matter of fundamental and industrial interest. The preparation of zeolitic materials with extralarge pores and chiral frameworks would permit many new applications. Two important steps in this direction include the synthesis of ITQ-33, a stable zeolite with 18 x 10 x 10 ring windows, and the synthesis of SU-32, which has an intrinsically chiral zeolite structure and where each crystal exhibits only one handedness. Here we present a germanosilicate zeolite (ITQ-37) with extralarge 30-ring windows. Its structure was determined by combining selected area electron diffraction (SAED) and powder X-ray diffraction (PXRD) in a charge-flipping algorithm. The framework follows the SrSi(2) (srs) minimal net and forms two unique cavities, each of which is connected to three other cavities to form a gyroidal channel system. These cavities comprise the enantiomorphous srs net of the framework. ITQ-37 is the first chiral zeolite with one single gyroidal channel. It has the lowest framework density (10.3 T atoms per 1,000 A(3)) of all existing 4-coordinated crystalline oxide frameworks, and the pore volume of the corresponding silica polymorph would be 0.38 cm(3) g(-1).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sun, Junliang -- Bonneau, Charlotte -- Cantin, Angel -- Corma, Avelino -- Diaz-Cabanas, Maria J -- Moliner, Manuel -- Zhang, Daliang -- Li, Mingrun -- Zou, Xiaodong -- England -- Nature. 2009 Apr 30;458(7242):1154-7. doi: 10.1038/nature07957.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Chemistry and Berzelii Centre, EXSELENT on Porous Materials, Stockholm University, SE-106 91, Stockholm, Sweden.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19407798" target="_blank"〉PubMed〈/a〉
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    Direct observation of a pressure-induced metal-to-semiconductor transition in lithium (2009)
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    Publication Date: 2009-03-13
    Description: Lithium, the lightest metal, has long been considered to have a 'simple' electronic structure that can be well explained within the nearly-free-electron model. But lithium does not stay 'simple' under compression: rather than becoming more free-electron-like as pressure is increased, first-principles calculations suggest that it transforms into a semi-metal or semiconductor. Experimentally, it has been shown that dense lithium adopts low-symmetry structures; there is also evidence that its resistivity increases with pressure. However, the electronic transport properties of lithium have so far not been directly monitored as a function of increasing static pressure. Here we report electrical resistance measurements on lithium in a diamond anvil cell up to pressures of 105 GPa, which reveal a significant increase in electrical resistivity and a change in its temperature dependence near 80 GPa. Our data thus provide unambiguous experimental evidence for a pressure-induced metal-to-semiconductor transition in a 'simple' metallic element.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Matsuoka, Takahiro -- Shimizu, Katsuya -- England -- Nature. 2009 Mar 12;458(7235):186-9. doi: 10.1038/nature07827.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉KYOKUGEN, Center for Quantum Science and Technology under Extreme Conditions, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan. matsuoka@djebel.mp.es.osaka-u.ac.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19279633" target="_blank"〉PubMed〈/a〉
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    A role for self-gravity at multiple length scales in the process of star formation (2009)
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    Publication Date: 2009-01-06
    Description: Self-gravity plays a decisive role in the final stages of star formation, where dense cores (size approximately 0.1 parsecs) inside molecular clouds collapse to form star-plus-disk systems. But self-gravity's role at earlier times (and on larger length scales, such as approximately 1 parsec) is unclear; some molecular cloud simulations that do not include self-gravity suggest that 'turbulent fragmentation' alone is sufficient to create a mass distribution of dense cores that resembles, and sets, the stellar initial mass function. Here we report a 'dendrogram' (hierarchical tree-diagram) analysis that reveals that self-gravity plays a significant role over the full range of possible scales traced by (13)CO observations in the L1448 molecular cloud, but not everywhere in the observed region. In particular, more than 90 per cent of the compact 'pre-stellar cores' traced by peaks of dust emission are projected on the sky within one of the dendrogram's self-gravitating 'leaves'. As these peaks mark the locations of already-forming stars, or of those probably about to form, a self-gravitating cocoon seems a critical condition for their existence. Turbulent fragmentation simulations without self-gravity-even of unmagnetized isothermal material-can yield mass and velocity power spectra very similar to what is observed in clouds like L1448. But a dendrogram of such a simulation shows that nearly all the gas in it (much more than in the observations) appears to be self-gravitating. A potentially significant role for gravity in 'non-self-gravitating' simulations suggests inconsistency in simulation assumptions and output, and that it is necessary to include self-gravity in any realistic simulation of the star-formation process on subparsec scales.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3817203/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3817203/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goodman, Alyssa A -- Rosolowsky, Erik W -- Borkin, Michelle A -- Foster, Jonathan B -- Halle, Michael -- Kauffmann, Jens -- Pineda, Jaime E -- P41 RR013218/RR/NCRR NIH HHS/ -- P41 RR013218-12/RR/NCRR NIH HHS/ -- U54 EB005149/EB/NIBIB NIH HHS/ -- U54 EB005149-05/EB/NIBIB NIH HHS/ -- U54-EB005149/EB/NIBIB NIH HHS/ -- England -- Nature. 2009 Jan 1;457(7225):63-6. doi: 10.1038/nature07609.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Initiative in Innovative Computing at Harvard, Cambridge, Massachusetts 02138, USA. agoodman@cfa.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19122636" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Astronomy ; Carbon Monoxide/analysis ; Computer Simulation ; *Gravitation ; Stars, Celestial/*chemistry
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    Healthy outlook (2009)
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    Publication Date: 2009-04-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2009 Apr 16;458(7240):807-8. doi: 10.1038/458807b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19369978" target="_blank"〉PubMed〈/a〉
    Keywords: China ; Communicable Diseases, Emerging/epidemiology ; Community Health Services/*trends ; Delivery of Health Care/*trends ; Drug Prescriptions/economics/statistics & numerical data ; Hospitals, County/trends ; Humans ; Medical Informatics/trends ; Medical Records
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    Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay (2009)
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    Publication Date: 2009-03-27
    Description: Toll-like receptors (TLRs) recognize microbial components, and evoke inflammation and immune responses. TLR stimulation activates complex gene expression networks that regulate the magnitude and duration of the immune reaction. Here we identify the TLR-inducible gene Zc3h12a as an immune response modifier that has an essential role in preventing immune disorders. Zc3h12a-deficient mice suffered from severe anaemia, and most died within 12 weeks. Zc3h12a(-/-) mice also showed augmented serum immunoglobulin levels and autoantibody production, together with a greatly increased number of plasma cells, as well as infiltration of plasma cells to the lung. Most Zc3h12a(-/-) splenic T cells showed effector/memory characteristics and produced interferon-gamma in response to T-cell receptor stimulation. Macrophages from Zc3h12a(-/-) mice showed highly increased production of interleukin (IL)-6 and IL-12p40 (also known as IL12b), but not TNF, in response to TLR ligands. Although the activation of TLR signalling pathways was normal, Il6 messenger RNA decay was severely impaired in Zc3h12a(-/-) macrophages. Overexpression of Zc3h12a accelerated Il6 mRNA degradation via its 3'-untranslated region (UTR), and destabilized RNAs with 3'-UTRs for genes including Il6, Il12p40 and the calcitonin receptor gene Calcr. Zc3h12a contains a putative amino-terminal nuclease domain, and the expressed protein had RNase activity, consistent with a role in the decay of Il6 mRNA. Together, these results indicate that Zc3h12a is an essential RNase that prevents immune disorders by directly controlling the stability of a set of inflammatory genes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Matsushita, Kazufumi -- Takeuchi, Osamu -- Standley, Daron M -- Kumagai, Yutaro -- Kawagoe, Tatsukata -- Miyake, Tohru -- Satoh, Takashi -- Kato, Hiroki -- Tsujimura, Tohru -- Nakamura, Haruki -- Akira, Shizuo -- P01 AI070167/AI/NIAID NIH HHS/ -- England -- Nature. 2009 Apr 30;458(7242):1185-90. doi: 10.1038/nature07924. Epub 2009 Mar 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Host Defense, WPI Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19322177" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions/genetics/metabolism ; Anemia/complications/genetics ; Animals ; Autoantibodies/blood/immunology ; Autoimmune Diseases/complications/immunology ; Cell Line ; Cytokines/biosynthesis/genetics ; Fetal Diseases/immunology ; Humans ; Immunity/*genetics/*immunology ; Inflammation Mediators/metabolism ; Interleukin-6/genetics ; Macrophages, Peritoneal/immunology/metabolism ; Mice ; Plasma Cells/cytology ; *RNA Stability ; Ribonucleases/deficiency/genetics/*metabolism ; T-Lymphocytes/immunology
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    NOAA chief ready to tackle climate (2009)
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    Publication Date: 2009-04-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dalton, Rex -- Witze, Alexandra -- England -- Nature. 2009 Mar 26;458(7237):396. doi: 10.1038/458396a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19334300" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Ecosystem ; *Greenhouse Effect ; History, 20th Century ; History, 21st Century ; Leadership ; Marine Biology ; United States ; United States Government Agencies/*organization & administration
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    Canadian government reaffirms support for science and discovery (2009)
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    Publication Date: 2009-04-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Goodyear, Gary -- England -- Nature. 2009 Apr 16;458(7240):830. doi: 10.1038/458830c.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19370007" target="_blank"〉PubMed〈/a〉
    Keywords: Canada ; *Federal Government ; Fellowships and Scholarships/economics ; Research Personnel/*economics ; Science/*economics
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    Linking the p53 tumour suppressor pathway to somatic cell reprogramming (2009)
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    Publication Date: 2009-08-12
    Description: Reprogramming somatic cells to induced pluripotent stem (iPS) cells has been accomplished by expressing pluripotency factors and oncogenes, but the low frequency and tendency to induce malignant transformation compromise the clinical utility of this powerful approach. We address both issues by investigating the mechanisms limiting reprogramming efficiency in somatic cells. Here we show that reprogramming factors can activate the p53 (also known as Trp53 in mice, TP53 in humans) pathway. Reducing signalling to p53 by expressing a mutated version of one of its negative regulators, by deleting or knocking down p53 or its target gene, p21 (also known as Cdkn1a), or by antagonizing reprogramming-induced apoptosis in mouse fibroblasts increases reprogramming efficiency. Notably, decreasing p53 protein levels enabled fibroblasts to give rise to iPS cells capable of generating germline-transmitting chimaeric mice using only Oct4 (also known as Pou5f1) and Sox2. Furthermore, silencing of p53 significantly increased the reprogramming efficiency of human somatic cells. These results provide insights into reprogramming mechanisms and suggest new routes to more efficient reprogramming while minimizing the use of oncogenes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735889/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735889/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kawamura, Teruhisa -- Suzuki, Jotaro -- Wang, Yunyuan V -- Menendez, Sergio -- Morera, Laura Batlle -- Raya, Angel -- Wahl, Geoffrey M -- Izpisua Belmonte, Juan Carlos -- 5 R01 CA061449/CA/NCI NIH HHS/ -- 5 R01 CA100845/CA/NCI NIH HHS/ -- R01 CA061449/CA/NCI NIH HHS/ -- R01 CA061449-30/CA/NCI NIH HHS/ -- R01 CA100845/CA/NCI NIH HHS/ -- R01 CA100845-05/CA/NCI NIH HHS/ -- R33 HL088293/HL/NHLBI NIH HHS/ -- R33 HL088293-03/HL/NHLBI NIH HHS/ -- England -- Nature. 2009 Aug 27;460(7259):1140-4. doi: 10.1038/nature08311. Epub 2009 Aug 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19668186" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cells, Cultured ; Cellular Reprogramming/*physiology ; Cyclin-Dependent Kinase Inhibitor p21/deficiency/genetics/metabolism ; Down-Regulation ; Embryo, Mammalian/cytology ; Female ; Fibroblasts/cytology/metabolism ; Humans ; Keratinocytes ; Male ; Mice ; Mice, Inbred C57BL ; Pluripotent Stem Cells/*cytology/*metabolism ; Tumor Suppressor Protein p53/deficiency/genetics/*metabolism
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    The proportionality of global warming to cumulative carbon emissions (2009)
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    Publication Date: 2009-06-12
    Description: The global temperature response to increasing atmospheric CO(2) is often quantified by metrics such as equilibrium climate sensitivity and transient climate response. These approaches, however, do not account for carbon cycle feedbacks and therefore do not fully represent the net response of the Earth system to anthropogenic CO(2) emissions. Climate-carbon modelling experiments have shown that: (1) the warming per unit CO(2) emitted does not depend on the background CO(2) concentration; (2) the total allowable emissions for climate stabilization do not depend on the timing of those emissions; and (3) the temperature response to a pulse of CO(2) is approximately constant on timescales of decades to centuries. Here we generalize these results and show that the carbon-climate response (CCR), defined as the ratio of temperature change to cumulative carbon emissions, is approximately independent of both the atmospheric CO(2) concentration and its rate of change on these timescales. From observational constraints, we estimate CCR to be in the range 1.0-2.1 degrees C per trillion tonnes of carbon (Tt C) emitted (5th to 95th percentiles), consistent with twenty-first-century CCR values simulated by climate-carbon models. Uncertainty in land-use CO(2) emissions and aerosol forcing, however, means that higher observationally constrained values cannot be excluded. The CCR, when evaluated from climate-carbon models under idealized conditions, represents a simple yet robust metric for comparing models, which aggregates both climate feedbacks and carbon cycle feedbacks. CCR is also likely to be a useful concept for climate change mitigation and policy; by combining the uncertainties associated with climate sensitivity, carbon sinks and climate-carbon feedbacks into a single quantity, the CCR allows CO(2)-induced global mean temperature change to be inferred directly from cumulative carbon emissions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Matthews, H Damon -- Gillett, Nathan P -- Stott, Peter A -- Zickfeld, Kirsten -- England -- Nature. 2009 Jun 11;459(7248):829-32. doi: 10.1038/nature08047.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Geography, Planning and Environment, Concordia University, 1455 de Maisonneuve Blvd W., Montreal, Quebec, H3G 1M8, Canada. dmatthew@alcor.concordia.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19516338" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/chemistry ; Carbon Dioxide/*analysis ; Feedback ; *Greenhouse Effect ; Models, Theoretical ; *Temperature ; Uncertainty
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    Photonics: One-way road for light (2009)
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    Publication Date: 2009-10-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yablonovitch, Eli -- England -- Nature. 2009 Oct 8;461(7265):744-5. doi: 10.1038/461744a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19812665" target="_blank"〉PubMed〈/a〉
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    Adaptive immune features of natural killer cells (2009)
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    Publication Date: 2009-01-13
    Description: In an adaptive immune response, naive T cells proliferate during infection and generate long-lived memory cells that undergo secondary expansion after a repeat encounter with the same pathogen. Although natural killer (NK) cells have traditionally been classified as cells of the innate immune system, they share many similarities with cytotoxic T lymphocytes. We use a mouse model of cytomegalovirus infection to show that, like T cells, NK cells bearing the virus-specific Ly49H receptor proliferate 100-fold in the spleen and 1,000-fold in the liver after infection. After a contraction phase, Ly49H-positive NK cells reside in lymphoid and non-lymphoid organs for several months. These self-renewing 'memory' NK cells rapidly degranulate and produce cytokines on reactivation. Adoptive transfer of these NK cells into naive animals followed by viral challenge results in a robust secondary expansion and protective immunity. These findings reveal properties of NK cells that were previously attributed only to cells of the adaptive immune system.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674434/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674434/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sun, Joseph C -- Beilke, Joshua N -- Lanier, Lewis L -- AI068129/AI/NIAID NIH HHS/ -- R01 AI068129/AI/NIAID NIH HHS/ -- R01 AI068129-09/AI/NIAID NIH HHS/ -- England -- Nature. 2009 Jan 29;457(7229):557-61. doi: 10.1038/nature07665. Epub 2009 Jan 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology and the Cancer Research Institute, University of California, San Francisco, California 94143, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19136945" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/deficiency/genetics ; Adoptive Transfer ; Animals ; Cell Proliferation ; Immunologic Memory/*immunology ; Killer Cells, Natural/*cytology/*immunology ; Lymphoid Tissue/immunology ; Mice ; Mice, Congenic ; Mice, Inbred C57BL ; *Models, Immunological ; Muromegalovirus/immunology/physiology ; Phenotype ; T-Lymphocytes, Cytotoxic/immunology
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    Metamaterials: Ideal focus (2009)
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    Publication Date: 2009-05-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brumfiel, Geoff -- England -- Nature. 2009 May 28;459(7246):504-5. doi: 10.1038/459504a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19478762" target="_blank"〉PubMed〈/a〉
    Keywords: Humans ; *Lenses ; Optical Processes ; Technology/*instrumentation
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    Lab hazard (2009)
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    Publication Date: 2009-05-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dance, Amber -- England -- Nature. 2009 Apr 2;458(7238):664-5. doi: 10.1038/nj7238-664a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19444985" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Laboratory/immunology ; Asthma/immunology ; Hypersensitivity/epidemiology/*immunology ; Occupational Diseases/epidemiology/*etiology/mortality ; *Occupational Exposure/statistics & numerical data ; *Research Personnel
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    Synthetic biology: The yin and yang of nature (2009)
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    Publication Date: 2009-01-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gore, Jeff -- van Oudenaarden, Alexander -- K99 GM085279/GM/NIGMS NIH HHS/ -- R00 GM085279/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Jan 15;457(7227):271-2. doi: 10.1038/457271a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19148089" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Clocks/*physiology ; Circadian Rhythm/*physiology ; Escherichia coli ; *Feedback, Physiological ; Gene Expression Regulation/*genetics ; Genes, Synthetic/*genetics ; Genetic Engineering ; *Models, Biological
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    Soft colloids make strong glasses (2009)
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    Publication Date: 2009-11-06
    Description: Glass formation in colloidal suspensions has many of the hallmarks of glass formation in molecular materials. For hard-sphere colloids, which interact only as a result of excluded volume, phase behaviour is controlled by volume fraction, phi; an increase in phi drives the system towards its glassy state, analogously to a decrease in temperature, T, in molecular systems. When phi increases above phi* approximately 0.53, the viscosity starts to increase significantly, and the system eventually moves out of equilibrium at the glass transition, phi(g) approximately 0.58, where particle crowding greatly restricts structural relaxation. The large particle size makes it possible to study both structure and dynamics with light scattering and imaging; colloidal suspensions have therefore provided considerable insight into the glass transition. However, hard-sphere colloidal suspensions do not exhibit the same diversity of behaviour as molecular glasses. This is highlighted by the wide variation in behaviour observed for the viscosity or structural relaxation time, tau(alpha), when the glassy state is approached in supercooled molecular liquids. This variation is characterized by the unifying concept of fragility, which has spurred the search for a 'universal' description of dynamic arrest in glass-forming liquids. For 'fragile' liquids, tau(alpha) is highly sensitive to changes in T, whereas non-fragile, or 'strong', liquids show a much lower T sensitivity. In contrast, hard-sphere colloidal suspensions are restricted to fragile behaviour, as determined by their phi dependence, ultimately limiting their utility in the study of the glass transition. Here we show that deformable colloidal particles, when studied through their concentration dependence at fixed temperature, do exhibit the same variation in fragility as that observed in the T dependence of molecular liquids at fixed volume. Their fragility is dictated by elastic properties on the scale of individual colloidal particles. Furthermore, we find an equivalent effect in molecular systems, where elasticity directly reflects fragility. Colloidal suspensions may thus provide new insight into glass formation in molecular systems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mattsson, Johan -- Wyss, Hans M -- Fernandez-Nieves, Alberto -- Miyazaki, Kunimasa -- Hu, Zhibing -- Reichman, David R -- Weitz, David A -- England -- Nature. 2009 Nov 5;462(7269):83-6. doi: 10.1038/nature08457.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics and Harvard School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA. johanm@chalmers.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19890327" target="_blank"〉PubMed〈/a〉
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    Adaptation of HIV-1 to human leukocyte antigen class I (2009)
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    Publication Date: 2009-02-27
    Description: The rapid and extensive spread of the human immunodeficiency virus (HIV) epidemic provides a rare opportunity to witness host-pathogen co-evolution involving humans. A focal point is the interaction between genes encoding human leukocyte antigen (HLA) and those encoding HIV proteins. HLA molecules present fragments (epitopes) of HIV proteins on the surface of infected cells to enable immune recognition and killing by CD8(+) T cells; particular HLA molecules, such as HLA-B*57, HLA-B*27 and HLA-B*51, are more likely to mediate successful control of HIV infection. Mutation within these epitopes can allow viral escape from CD8(+) T-cell recognition. Here we analysed viral sequences and HLA alleles from 〉2,800 subjects, drawn from 9 distinct study cohorts spanning 5 continents. Initial analysis of the HLA-B*51-restricted epitope, TAFTIPSI (reverse transcriptase residues 128-135), showed a strong correlation between the frequency of the escape mutation I135X and HLA-B*51 prevalence in the 9 study cohorts (P = 0.0001). Extending these analyses to incorporate other well-defined CD8(+) T-cell epitopes, including those restricted by HLA-B*57 and HLA-B*27, showed that the frequency of these epitope variants (n = 14) was consistently correlated with the prevalence of the restricting HLA allele in the different cohorts (together, P 〈 0.0001), demonstrating strong evidence of HIV adaptation to HLA at a population level. This process of viral adaptation may dismantle the well-established HLA associations with control of HIV infection that are linked to the availability of key epitopes, and highlights the challenge for a vaccine to keep pace with the changing immunological landscape presented by HIV.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3148020/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3148020/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kawashima, Yuka -- Pfafferott, Katja -- Frater, John -- Matthews, Philippa -- Payne, Rebecca -- Addo, Marylyn -- Gatanaga, Hiroyuki -- Fujiwara, Mamoru -- Hachiya, Atsuko -- Koizumi, Hirokazu -- Kuse, Nozomi -- Oka, Shinichi -- Duda, Anna -- Prendergast, Andrew -- Crawford, Hayley -- Leslie, Alasdair -- Brumme, Zabrina -- Brumme, Chanson -- Allen, Todd -- Brander, Christian -- Kaslow, Richard -- Tang, James -- Hunter, Eric -- Allen, Susan -- Mulenga, Joseph -- Branch, Songee -- Roach, Tim -- John, Mina -- Mallal, Simon -- Ogwu, Anthony -- Shapiro, Roger -- Prado, Julia G -- Fidler, Sarah -- Weber, Jonathan -- Pybus, Oliver G -- Klenerman, Paul -- Ndung'u, Thumbi -- Phillips, Rodney -- Heckerman, David -- Harrigan, P Richard -- Walker, Bruce D -- Takiguchi, Masafumi -- Goulder, Philip -- 1 R01 AI067073/AI/NIAID NIH HHS/ -- G0500384/Medical Research Council/United Kingdom -- G0501777/Medical Research Council/United Kingdom -- G108/626/Medical Research Council/United Kingdom -- R01 AI046995/AI/NIAID NIH HHS/ -- R01 AI046995-10/AI/NIAID NIH HHS/ -- R01 AI060460/AI/NIAID NIH HHS/ -- R01 AI064060/AI/NIAID NIH HHS/ -- R01 AI064060-06A1/AI/NIAID NIH HHS/ -- R01AI46995/AI/NIAID NIH HHS/ -- R01AI64060/AI/NIAID NIH HHS/ -- Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2009 Apr 2;458(7238):641-5. doi: 10.1038/nature07746. Epub 2009 Feb 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Viral Immunology, Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Kumamoto 860-0811, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19242411" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; CD8-Positive T-Lymphocytes/immunology ; Cohort Studies ; Epitopes, T-Lymphocyte/chemistry/genetics/immunology ; HIV Antigens/chemistry/genetics/immunology ; HIV-1/genetics/*immunology/physiology ; HLA-B Antigens/genetics/*immunology ; Humans ; Internationality ; Leukocytes/*immunology ; Polymorphism, Genetic ; gag Gene Products, Human Immunodeficiency Virus/chemistry/genetics/immunology
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    Sweden likely winner for neutron source (2009)
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    Publication Date: 2009-06-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brumfiel, Geoff -- England -- Nature. 2009 Jun 4;459(7247):626. doi: 10.1038/459626a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19494879" target="_blank"〉PubMed〈/a〉
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    US AIDS programme 'essential and expensive' (2009)
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    Publication Date: 2009-04-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2009 Apr 9;458(7239):693. doi: 10.1038/458693b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19360057" target="_blank"〉PubMed〈/a〉
    Keywords: Acquired Immunodeficiency Syndrome/*economics/mortality/*therapy ; Africa ; Costs and Cost Analysis ; Government Programs/*economics ; United States
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    Elite and stochastic models for induced pluripotent stem cell generation (2009)
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    Publication Date: 2009-07-03
    Description: Induced pluripotent stem cells offer unprecedented potential for disease research, drug screening, toxicology and regenerative medicine. However, the process of reprogramming is inefficient and often incomplete. Here I consider reasons for bottlenecks in induced pluripotent stem cell generation, and propose a model in which most or all cells have the potential to become pluripotent.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yamanaka, Shinya -- England -- Nature. 2009 Jul 2;460(7251):49-52. doi: 10.1038/nature08180.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan. yamanaka@cira.kyoto-u.ac.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19571877" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Differentiation ; Cell Lineage ; *Cellular Reprogramming/genetics ; Epigenesis, Genetic ; Humans ; Mice ; *Models, Biological ; Pluripotent Stem Cells/*cytology/metabolism ; Stochastic Processes ; Transduction, Genetic
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    Recession Watch: No time for nationalism (2009)
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    Publication Date: 2009-02-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sunami, Atsushi -- Kurokawa, Kiyoshi -- England -- Nature. 2009 Feb 19;457(7232):960-1. doi: 10.1038/457960a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Graduate Institute for Policy Studies in Tokyo. sunami-atsushi@grips.ac.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19225502" target="_blank"〉PubMed〈/a〉
    Keywords: Emigrants and Immigrants ; Financing, Government/history ; Foreign Professional Personnel ; History, 20th Century ; History, 21st Century ; International Cooperation ; Japan ; *Public Policy ; Research/economics/*history/manpower/*trends
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    Fusion dreams delayed (2009)
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    Publication Date: 2009-05-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brumfiel, Geoff -- England -- Nature. 2009 May 28;459(7246):488-9. doi: 10.1038/459488a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19478747" target="_blank"〉PubMed〈/a〉
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    A high-mobility electron-transporting polymer for printed transistors (2009)
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    Publication Date: 2009-01-23
    Description: Printed electronics is a revolutionary technology aimed at unconventional electronic device manufacture on plastic foils, and will probably rely on polymeric semiconductors for organic thin-film transistor (OTFT) fabrication. In addition to having excellent charge-transport characteristics in ambient conditions, such materials must meet other key requirements, such as chemical stability, large solubility in common solvents, and inexpensive solution and/or low-temperature processing. Furthermore, compatibility of both p-channel (hole-transporting) and n-channel (electron-transporting) semiconductors with a single combination of gate dielectric and contact materials is highly desirable to enable powerful complementary circuit technologies, where p- and n-channel OTFTs operate in concert. Polymeric complementary circuits operating in ambient conditions are currently difficult to realize: although excellent p-channel polymers are widely available, the achievement of high-performance n-channel polymers is more challenging. Here we report a highly soluble ( approximately 60 g l(-1)) and printable n-channel polymer exhibiting unprecedented OTFT characteristics (electron mobilities up to approximately 0.45-0.85 cm(2) V(-1) s(-1)) under ambient conditions in combination with Au contacts and various polymeric dielectrics. Several top-gate OTFTs on plastic substrates were fabricated with the semiconductor-dielectric layers deposited by spin-coating as well as by gravure, flexographic and inkjet printing, demonstrating great processing versatility. Finally, all-printed polymeric complementary inverters (with gain 25-65) have been demonstrated.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yan, He -- Chen, Zhihua -- Zheng, Yan -- Newman, Christopher -- Quinn, Jordan R -- Dotz, Florian -- Kastler, Marcel -- Facchetti, Antonio -- England -- Nature. 2009 Feb 5;457(7230):679-86. doi: 10.1038/nature07727. Epub 2009 Jan 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Polyera Corporation, 8045 Lamon Avenue, Skokie, Illinois 60077, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19158674" target="_blank"〉PubMed〈/a〉
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    Whistleblowers at risk as science fails to correct itself (2009)
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    Publication Date: 2009-08-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reich, Eugenie Samuel -- England -- Nature. 2009 Aug 20;460(7258):949. doi: 10.1038/460949c.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cambridge, Massachusetts 02139, USA eugenie.reich@gmail.com.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19693062" target="_blank"〉PubMed〈/a〉
    Keywords: Physics ; Risk ; Science/*standards ; *Scientific Misconduct ; *Whistleblowing
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    Reconstructing Indian population history (2009)
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    Publication Date: 2009-09-26
    Description: India has been underrepresented in genome-wide surveys of human variation. We analyse 25 diverse groups in India to provide strong evidence for two ancient populations, genetically divergent, that are ancestral to most Indians today. One, the 'Ancestral North Indians' (ANI), is genetically close to Middle Easterners, Central Asians, and Europeans, whereas the other, the 'Ancestral South Indians' (ASI), is as distinct from ANI and East Asians as they are from each other. By introducing methods that can estimate ancestry without accurate ancestral populations, we show that ANI ancestry ranges from 39-71% in most Indian groups, and is higher in traditionally upper caste and Indo-European speakers. Groups with only ASI ancestry may no longer exist in mainland India. However, the indigenous Andaman Islanders are unique in being ASI-related groups without ANI ancestry. Allele frequency differences between groups in India are larger than in Europe, reflecting strong founder effects whose signatures have been maintained for thousands of years owing to endogamy. We therefore predict that there will be an excess of recessive diseases in India, which should be possible to screen and map genetically.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842210/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842210/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reich, David -- Thangaraj, Kumarasamy -- Patterson, Nick -- Price, Alkes L -- Singh, Lalji -- HG004168/HG/NHGRI NIH HHS/ -- R01 HG006399/HG/NHGRI NIH HHS/ -- U01 HG004168/HG/NHGRI NIH HHS/ -- U01 HG004168-03/HG/NHGRI NIH HHS/ -- England -- Nature. 2009 Sep 24;461(7263):489-94. doi: 10.1038/nature08365.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. reich@genetics.med.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19779445" target="_blank"〉PubMed〈/a〉
    Keywords: Asia/ethnology ; Chromosomes, Human, Y/genetics ; Continental Population Groups/genetics ; DNA, Mitochondrial/genetics ; Ethnic Groups/*genetics ; Europe/ethnology ; Female ; Founder Effect ; Gene Frequency ; Genes, Recessive/genetics ; Genetic Variation/*genetics ; Genetics, Medical ; Genetics, Population ; Genome, Human/genetics ; Genomics ; Genotype ; Geography ; Humans ; India ; Language ; Linkage Disequilibrium/genetics ; Male ; Middle East/ethnology ; *Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Principal Component Analysis
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    Emissions: Canada should not be isolating itself (2009)
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    Publication Date: 2009-12-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Suzuki, David -- England -- Nature. 2009 Dec 10;462(7274):720. doi: 10.1038/462720a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20010664" target="_blank"〉PubMed〈/a〉
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    Early warnings (2009)
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    Publication Date: 2009-04-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2009 Apr 9;458(7239):679. doi: 10.1038/458679a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19360033" target="_blank"〉PubMed〈/a〉
    Keywords: Biomarkers/analysis ; *Early Detection of Cancer ; Humans ; Mass Screening/*standards ; Neoplasms/*diagnosis/mortality
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    HMGB proteins function as universal sentinels for nucleic-acid-mediated innate immune responses (2009)
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    Publication Date: 2009-11-06
    Description: The activation of innate immune responses by nucleic acids is crucial to protective and pathological immunities and is mediated by the transmembrane Toll-like receptors (TLRs) and cytosolic receptors. However, it remains unknown whether a mechanism exists that integrates these nucleic-acid-sensing systems. Here we show that high-mobility group box (HMGB) proteins 1, 2 and 3 function as universal sentinels for nucleic acids. HMGBs bind to all immunogenic nucleic acids examined with a correlation between affinity and immunogenic potential. Hmgb1(-/-) and Hmgb2(-/-) mouse cells are defective in type-I interferon and inflammatory cytokine induction by DNA or RNA targeted to activate the cytosolic nucleic-acid-sensing receptors; cells in which the expression of all three HMGBs is suppressed show a more profound defect, accompanied by impaired activation of the transcription factors interferon regulatory factor 3 (IRF3) and nuclear factor (NF)-kappaB. The absence of HMGBs also severely impairs the activation of TLR3, TLR7 and TLR9 by their cognate nucleic acids. Our results therefore indicate a hierarchy in the nucleic-acid-mediated activation of immune responses, wherein the selective activation of nucleic-acid-sensing receptors is contingent on the more promiscuous sensing of nucleic acids by HMGBs. These findings may have implications for understanding the evolution of the innate immune system and for the treatment of immunological disorders.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yanai, Hideyuki -- Ban, Tatsuma -- Wang, ZhiChao -- Choi, Myoung Kwon -- Kawamura, Takeshi -- Negishi, Hideo -- Nakasato, Makoto -- Lu, Yan -- Hangai, Sho -- Koshiba, Ryuji -- Savitsky, David -- Ronfani, Lorenza -- Akira, Shizuo -- Bianchi, Marco E -- Honda, Kenya -- Tamura, Tomohiko -- Kodama, Tatsuhiko -- Taniguchi, Tadatsugu -- England -- Nature. 2009 Nov 5;462(7269):99-103. doi: 10.1038/nature08512.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology, Graduate School of Medicine and Faculty of Medicine, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19890330" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Cytosol/immunology ; DNA/immunology ; HMGB Proteins/deficiency/genetics/*immunology/*metabolism ; HMGB1 Protein/deficiency/genetics/immunology/metabolism ; HMGB2 Protein/deficiency/genetics/immunology/metabolism ; Immunity, Innate/*immunology ; Interferon Regulatory Factor-3/metabolism ; Mice ; Mice, Inbred C57BL ; Models, Immunological ; NF-kappa B/metabolism ; Nucleic Acids/*immunology ; Nucleotides/chemistry/immunology/metabolism ; RNA/immunology ; Signal Transduction ; Toll-Like Receptors/immunology ; Virus Diseases/immunology/virology
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    Austria quits CERN after 50 years (2009)
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    Publication Date: 2009-05-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brumfiel, Geoff -- England -- Nature. 2009 May 14;459(7244):151. doi: 10.1038/459151a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19444178" target="_blank"〉PubMed〈/a〉
    Keywords: Austria ; Biotechnology/economics/organization & administration/trends ; Laboratories/*organization & administration ; *Physics/economics/trends ; Switzerland
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    Cancer-associated IDH1 mutations produce 2-hydroxyglutarate (2009)
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    Publication Date: 2009-11-26
    Description: Mutations in the enzyme cytosolic isocitrate dehydrogenase 1 (IDH1) are a common feature of a major subset of primary human brain cancers. These mutations occur at a single amino acid residue of the IDH1 active site, resulting in loss of the enzyme's ability to catalyse conversion of isocitrate to alpha-ketoglutarate. However, only a single copy of the gene is mutated in tumours, raising the possibility that the mutations do not result in a simple loss of function. Here we show that cancer-associated IDH1 mutations result in a new ability of the enzyme to catalyse the NADPH-dependent reduction of alpha-ketoglutarate to R(-)-2-hydroxyglutarate (2HG). Structural studies demonstrate that when arginine 132 is mutated to histidine, residues in the active site are shifted to produce structural changes consistent with reduced oxidative decarboxylation of isocitrate and acquisition of the ability to convert alpha-ketoglutarate to 2HG. Excess accumulation of 2HG has been shown to lead to an elevated risk of malignant brain tumours in patients with inborn errors of 2HG metabolism. Similarly, in human malignant gliomas harbouring IDH1 mutations, we find markedly elevated levels of 2HG. These data demonstrate that the IDH1 mutations result in production of the onco-metabolite 2HG, and indicate that the excess 2HG which accumulates in vivo contributes to the formation and malignant progression of gliomas.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2818760/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2818760/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dang, Lenny -- White, David W -- Gross, Stefan -- Bennett, Bryson D -- Bittinger, Mark A -- Driggers, Edward M -- Fantin, Valeria R -- Jang, Hyun Gyung -- Jin, Shengfang -- Keenan, Marie C -- Marks, Kevin M -- Prins, Robert M -- Ward, Patrick S -- Yen, Katharine E -- Liau, Linda M -- Rabinowitz, Joshua D -- Cantley, Lewis C -- Thompson, Craig B -- Vander Heiden, Matthew G -- Su, Shinsan M -- P01 CA104838/CA/NCI NIH HHS/ -- P01 CA104838-05/CA/NCI NIH HHS/ -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 CA105463/CA/NCI NIH HHS/ -- R01 CA105463-06/CA/NCI NIH HHS/ -- R21 CA128620/CA/NCI NIH HHS/ -- England -- Nature. 2009 Dec 10;462(7274):739-44. doi: 10.1038/nature08617. Epub .〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Agios Pharmaceuticals, Cambridge, Massachusetts 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19935646" target="_blank"〉PubMed〈/a〉
    Keywords: Arginine/genetics ; Brain Neoplasms/*genetics/*metabolism/pathology ; Catalytic Domain ; Cell Line ; Crystallography, X-Ray ; Disease Progression ; Enzyme Assays ; Glioma/genetics/metabolism/pathology ; Glutarates/*metabolism ; Histidine/genetics/metabolism ; Humans ; Isocitrate Dehydrogenase/*genetics/*metabolism ; Ketoglutaric Acids/metabolism ; Models, Molecular ; Mutant Proteins/*genetics/*metabolism ; Mutation/genetics ; Protein Conformation
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    Long-range oncogenic activation of Igh-c-myc translocations by the Igh 3' regulatory region (2009)
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    Publication Date: 2009-12-17
    Description: B-cell malignancies, such as human Burkitt's lymphoma, often contain translocations that link c-myc or other proto-oncogenes to the immunoglobulin heavy chain locus (IgH, encoded by Igh). The nature of elements that activate oncogenes within such translocations has been a long-standing question. Translocations within Igh involve DNA double-strand breaks initiated either by the RAG1/2 endonuclease during variable, diversity and joining gene segment (V(D)J) recombination, or by activation-induced cytidine deaminase (AID, also known as AICDA) during class switch recombination (CSR). V(D)J recombination in progenitor B (pro-B) cells assembles Igh variable region exons upstream of mu constant region (Cmu) exons, which are the first of several sets of C(H) exons ('C(H) genes') within a C(H) locus that span several hundred kilobases (kb). In mature B cells, CSR deletes Cmu and replaces it with a downstream C(H) gene. An intronic enhancer (iEmu) between the variable region exons and Cmu promotes V(D)J recombination in developing B cells. Furthermore, the Igh 3' regulatory region (Igh3'RR) lies downstream of the C(H) locus and modulates CSR by long-range transcriptional enhancement of C(H) genes. Transgenic mice bearing iEmu or Igh3'RR sequences fused to c-myc are predisposed to B lymphomas, demonstrating that such elements can confer oncogenic c-myc expression. However, in many B-cell lymphomas, Igh-c-myc translocations delete iEmu and place c-myc up to 200 kb upstream of the Igh3'RR. Here we address the oncogenic role of the Igh3'RR by inactivating it in two distinct mouse models for B-cell lymphoma with Igh-c-myc translocations. We show that the Igh3'RR is dispensable for pro-B-cell lymphomas with V(D)J recombination-initiated translocations, but is required for peripheral B-cell lymphomas with CSR-associated translocations. As the Igh3'RR is not required for CSR-associated Igh breaks or Igh-c-myc translocations in peripheral B-cell lymphoma progenitors, we conclude that this regulatory region confers oncogenic activity by long-range and developmental stage-specific activation of translocated c-myc genes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2802177/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2802177/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gostissa, Monica -- Yan, Catherine T -- Bianco, Julia M -- Cogne, Michel -- Pinaud, Eric -- Alt, Frederick W -- CA92625/CA/NCI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Dec 10;462(7274):803-7. doi: 10.1038/nature08633.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20010689" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions/*genetics ; Alleles ; Animals ; Cells, Cultured ; Chromosome Breakpoints ; Gene Rearrangement, B-Lymphocyte/*genetics ; Genes, Immunoglobulin Heavy Chain/*genetics ; Genes, myc/*genetics ; Immunoglobulin Class Switching/genetics ; Lymphoma, B-Cell/*genetics/pathology ; Mice ; Mice, Transgenic ; Regulatory Sequences, Nucleic Acid/*genetics ; Translocation, Genetic/*genetics
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    Global Darwin: long kept under wraps in Pakistan (2009)
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    Publication Date: 2009-12-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kayani, Saheeb Ahmed -- England -- Nature. 2009 Dec 24;462(7276):984. doi: 10.1038/462984b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20033020" target="_blank"〉PubMed〈/a〉
    Keywords: *Biological Evolution ; History, 20th Century ; History, 21st Century ; Humans ; Pakistan ; *Religion and Science ; Science/history
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    Too small to overlook (2009)
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    Publication Date: 2009-07-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Maynard, Andrew -- Rejeski, David -- England -- Nature. 2009 Jul 9;460(7252):174. doi: 10.1038/460174a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Project on Emerging Nanotechnologies at the Woodrow Wilson International Center for Scholars, 1300 Pennsylvania Avenue, Washington DC 20004-3027, USA. andrew.maynard@wilsoncenter.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19587746" target="_blank"〉PubMed〈/a〉
    Keywords: *Government Regulation ; Guidelines as Topic ; Humans ; Internationality ; Nanostructures/standards ; Nanotechnology/economics/*legislation & jurisprudence/*standards/statistics & ; numerical data ; *Risk Management/legislation & jurisprudence/standards ; Safety/legislation & jurisprudence/standards
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    Malaria: The gatekeeper revealed (2009)
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    Publication Date: 2009-06-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reiff, Sarah B -- Striepen, Boris -- England -- Nature. 2009 Jun 18;459(7249):918-9. doi: 10.1038/459918a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19536248" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Humans ; Malaria, Falciparum/drug therapy/*parasitology ; Models, Biological ; Plasmodium falciparum/*metabolism ; Protein Binding ; Protein Transport ; Protozoan Proteins/antagonists & inhibitors/*metabolism ; Vacuoles/metabolism/parasitology
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    Modulation of microRNA processing by p53 (2009)
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    Publication Date: 2009-07-25
    Description: MicroRNAs (miRNAs) have emerged as key post-transcriptional regulators of gene expression, involved in diverse physiological and pathological processes. Although miRNAs can function as both tumour suppressors and oncogenes in tumour development, a widespread downregulation of miRNAs is commonly observed in human cancers and promotes cellular transformation and tumorigenesis. This indicates an inherent significance of small RNAs in tumour suppression. However, the connection between tumour suppressor networks and miRNA biogenesis machineries has not been investigated in depth. Here we show that a central tumour suppressor, p53, enhances the post-transcriptional maturation of several miRNAs with growth-suppressive function, including miR-16-1, miR-143 and miR-145, in response to DNA damage. In HCT116 cells and human diploid fibroblasts, p53 interacts with the Drosha processing complex through the association with DEAD-box RNA helicase p68 (also known as DDX5) and facilitates the processing of primary miRNAs to precursor miRNAs. We also found that transcriptionally inactive p53 mutants interfere with a functional assembly between Drosha complex and p68, leading to attenuation of miRNA processing activity. These findings suggest that transcription-independent modulation of miRNA biogenesis is intrinsically embedded in a tumour suppressive program governed by p53. Our study reveals a previously unrecognized function of p53 in miRNA processing, which may underlie key aspects of cancer biology.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Suzuki, Hiroshi I -- Yamagata, Kaoru -- Sugimoto, Koichi -- Iwamoto, Takashi -- Kato, Shigeaki -- Miyazono, Kohei -- England -- Nature. 2009 Jul 23;460(7254):529-33. doi: 10.1038/nature08199.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Pathology, Graduate School of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19626115" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line ; DNA Damage/physiology ; Gene Expression Regulation ; HCT116 Cells ; Humans ; MicroRNAs/*metabolism ; Mutation ; *RNA Processing, Post-Transcriptional ; Ribonuclease III/metabolism ; Tumor Suppressor Protein p53/genetics/*metabolism
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    Optical manipulation of nanoparticles and biomolecules in sub-wavelength slot waveguides (2009)
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    Publication Date: 2009-01-06
    Description: The ability to manipulate nanoscopic matter precisely is critical for the development of active nanosystems. Optical tweezers are excellent tools for transporting particles ranging in size from several micrometres to a few hundred nanometres. Manipulation of dielectric objects with much smaller diameters, however, requires stronger optical confinement and higher intensities than can be provided by these diffraction-limited systems. Here we present an approach to optofluidic transport that overcomes these limitations, using sub-wavelength liquid-core slot waveguides. The technique simultaneously makes use of near-field optical forces to confine matter inside the waveguide and scattering/adsorption forces to transport it. The ability of the slot waveguide to condense the accessible electromagnetic energy to scales as small as 60 nm allows us also to overcome the fundamental diffraction problem. We apply the approach here to the trapping and transport of 75-nm dielectric nanoparticles and lambda-DNA molecules. Because trapping occurs along a line, rather than at a point as with traditional point traps, the method provides the ability to handle extended biomolecules directly. We also carry out a detailed numerical analysis that relates the near-field optical forces to release kinetics. We believe that the architecture demonstrated here will help to bridge the gap between optical manipulation and nanofluidics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Allen H J -- Moore, Sean D -- Schmidt, Bradley S -- Klug, Matthew -- Lipson, Michal -- Erickson, David -- England -- Nature. 2009 Jan 1;457(7225):71-5. doi: 10.1038/nature07593.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19122638" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophage lambda/genetics ; DNA, Viral/*analysis ; Electrons ; Kinetics ; Micromanipulation/instrumentation/*methods ; Nanoparticles/*analysis ; *Optical Tweezers ; Optics and Photonics/*instrumentation/*methods
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    Tough climate (2009)
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    Publication Date: 2009-04-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2009 Apr 9;458(7239):679-80. doi: 10.1038/458679b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19360032" target="_blank"〉PubMed〈/a〉
    Keywords: *Greenhouse Effect ; National Academy of Sciences (U.S.) ; *Policy Making ; United States
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    Collision debris increases risk to Earth-observing satellites (2009)
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    Publication Date: 2009-04-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brumfiel, Geoff -- England -- Nature. 2009 Apr 16;458(7240):814. doi: 10.1038/458814b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19369993" target="_blank"〉PubMed〈/a〉
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    Biologists napping while work militarized (2009)
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    Publication Date: 2009-08-21
    Description: As researchers discover more agents that alter mental states, the Chemical Weapons Convention needs modification to help ensure that the life sciences are not used for hostile purposes, says Malcolm Dando.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dando, Malcolm -- England -- Nature. 2009 Aug 20;460(7258):950-1. doi: 10.1038/460950a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Peace Studies, University of Bradford, Richmond Road, Bradford, BD7 IDP, UK. mrdando@bradford.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19693065" target="_blank"〉PubMed〈/a〉
    Keywords: Biological Warfare Agents/ethics/legislation & jurisprudence ; Central Nervous System/drug effects ; *Chemical Warfare Agents/adverse effects/standards ; Fentanyl/adverse effects ; Humans ; International Cooperation ; Military Science/*ethics/legislation & jurisprudence ; Riot Control Agents, Chemical/adverse effects
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    Cancer: The fat and the furious (2009)
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    Publication Date: 2009-09-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gottlieb, Eyal -- England -- Nature. 2009 Sep 3;461(7260):44-5. doi: 10.1038/461044a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19727186" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Anoikis/physiology ; Autophagy ; Breast Neoplasms/*metabolism/*pathology ; Cell Adhesion ; Cell Survival ; Epithelial Cells/cytology/*metabolism/pathology ; Extracellular Matrix/*metabolism ; Glucose/metabolism ; Humans ; Receptor, ErbB-2/genetics/*metabolism
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    Obituary: Herbert Frank York (1921-2009) (2009)
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    Publication Date: 2009-07-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉May, Michael M -- England -- Nature. 2009 Jul 9;460(7252):189. doi: 10.1038/460189a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19587758" target="_blank"〉PubMed〈/a〉
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    Welcome, nature chemistry (2009)
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    Publication Date: 2009-04-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2009 Apr 9;458(7239):680. doi: 10.1038/458680a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19360034" target="_blank"〉PubMed〈/a〉
    Keywords: *Chemistry ; *Periodicals as Topic
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    The remnants of galaxy formation from a panoramic survey of the region around M31 (2009)
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    Publication Date: 2009-09-04
    Description: In hierarchical cosmological models, galaxies grow in mass through the continual accretion of smaller ones. The tidal disruption of these systems is expected to result in loosely bound stars surrounding the galaxy, at distances that reach 10-100 times the radius of the central disk. The number, luminosity and morphology of the relics of this process provide significant clues to galaxy formation history, but obtaining a comprehensive survey of these components is difficult because of their intrinsic faintness and vast extent. Here we report a panoramic survey of the Andromeda galaxy (M31). We detect stars and coherent structures that are almost certainly remnants of dwarf galaxies destroyed by the tidal field of M31. An improved census of their surviving counterparts implies that three-quarters of M31's satellites brighter than M(v) = -6 await discovery. The brightest companion, Triangulum (M33), is surrounded by a stellar structure that provides persuasive evidence for a recent encounter with M31. This panorama of galaxy structure directly confirms the basic tenets of the hierarchical galaxy formation model and reveals the shared history of M31 and M33 in the unceasing build-up of galaxies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McConnachie, Alan W -- Irwin, Michael J -- Ibata, Rodrigo A -- Dubinski, John -- Widrow, Lawrence M -- Martin, Nicolas F -- Cote, Patrick -- Dotter, Aaron L -- Navarro, Julio F -- Ferguson, Annette M N -- Puzia, Thomas H -- Lewis, Geraint F -- Babul, Arif -- Barmby, Pauline -- Bienayme, Olivier -- Chapman, Scott C -- Cockcroft, Robert -- Collins, Michelle L M -- Fardal, Mark A -- Harris, William E -- Huxor, Avon -- Mackey, A Dougal -- Penarrubia, Jorge -- Rich, R Michael -- Richer, Harvey B -- Siebert, Arnaud -- Tanvir, Nial -- Valls-Gabaud, David -- Venn, Kimberly A -- England -- Nature. 2009 Sep 3;461(7260):66-9. doi: 10.1038/nature08327.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉NRC Herzberg Institute of Astrophysics, 5071 West Saanich Road, Victoria, British Columbia, Canada V9E 2E7. alan.mcconnachie@nrc-cnrc.gc.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19727194" target="_blank"〉PubMed〈/a〉
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    Obituary: Norman E. Borlaug (1914-2009) (2009)
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    Publication Date: 2009-10-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Swaminathan, M S -- England -- Nature. 2009 Oct 15;461(7266):894. doi: 10.1038/461894a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉M. S. Swaminathan Research Foundation, Third Cross Street, Taramani Institutional Area, Chennai 600 113, India. chairman@mssrf.res.in〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19829366" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/*history ; Breeding/history ; Food Supply/history ; History, 20th Century ; History, 21st Century ; Humans ; Plant Diseases/genetics/microbiology ; Triticum/genetics/physiology
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    A bill against rights (2009)
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    Publication Date: 2009-04-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2009 Apr 2;458(7238):550. doi: 10.1038/458550a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19340028" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Enteral Nutrition/ethics/utilization ; Female ; Humans ; Italy ; Living Wills/ethics/*legislation & jurisprudence ; *Patients ; *Physicians ; Right to Die/ethics/*legislation & jurisprudence ; Young Adult
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    Stably maintained dendritic spines are associated with lifelong memories (2009)
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    Publication Date: 2009-12-01
    Description: Changes in synaptic connections are considered essential for learning and memory formation. However, it is unknown how neural circuits undergo continuous synaptic changes during learning while maintaining lifelong memories. Here we show, by following postsynaptic dendritic spines over time in the mouse cortex, that learning and novel sensory experience lead to spine formation and elimination by a protracted process. The extent of spine remodelling correlates with behavioural improvement after learning, suggesting a crucial role of synaptic structural plasticity in memory formation. Importantly, a small fraction of new spines induced by novel experience, together with most spines formed early during development and surviving experience-dependent elimination, are preserved and provide a structural basis for memory retention throughout the entire life of an animal. These studies indicate that learning and daily sensory experience leave minute but permanent marks on cortical connections and suggest that lifelong memories are stored in largely stably connected synaptic networks.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4724802/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4724802/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Guang -- Pan, Feng -- Gan, Wen-Biao -- R01 NS047325/NS/NINDS NIH HHS/ -- England -- Nature. 2009 Dec 17;462(7275):920-4. doi: 10.1038/nature08577. Epub 2009 Nov 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Neurobiology Program, The Helen and Martin Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, Department of Physiology and Neuroscience, New York University School of Medicine, New York, New York 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19946265" target="_blank"〉PubMed〈/a〉
    Keywords: Aging/physiology ; Animals ; Dendritic Spines/metabolism/*physiology ; Forelimb/physiology ; Memory/*physiology ; Mice ; Motor Cortex/cytology/physiology ; Motor Skills/physiology ; Neuronal Plasticity/physiology ; Pyramidal Cells/metabolism ; Synapses/*metabolism ; Time Factors
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    Korean satellite misses orbit (2009)
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    Publication Date: 2009-04-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brumfiel, Geoff -- England -- Nature. 2009 Apr 9;458(7239):685. doi: 10.1038/458685a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19360047" target="_blank"〉PubMed〈/a〉
    Keywords: Korea ; Pacific Ocean ; *Spacecraft
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    Histone H4 lysine 16 acetylation regulates cellular lifespan (2009)
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    Publication Date: 2009-06-12
    Description: Cells undergoing developmental processes are characterized by persistent non-genetic alterations in chromatin, termed epigenetic changes, represented by distinct patterns of DNA methylation and histone post-translational modifications. Sirtuins, a group of conserved NAD(+)-dependent deacetylases or ADP-ribosyltransferases, promote longevity in diverse organisms; however, their molecular mechanisms in ageing regulation remain poorly understood. Yeast Sir2, the first member of the family to be found, establishes and maintains chromatin silencing by removing histone H4 lysine 16 acetylation and bringing in other silencing proteins. Here we report an age-associated decrease in Sir2 protein abundance accompanied by an increase in H4 lysine 16 acetylation and loss of histones at specific subtelomeric regions in replicatively old yeast cells, which results in compromised transcriptional silencing at these loci. Antagonizing activities of Sir2 and Sas2, a histone acetyltransferase, regulate the replicative lifespan through histone H4 lysine 16 at subtelomeric regions. This pathway, distinct from existing ageing models for yeast, may represent an evolutionarily conserved function of sirtuins in regulation of replicative ageing by maintenance of intact telomeric chromatin.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2702157/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2702157/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dang, Weiwei -- Steffen, Kristan K -- Perry, Rocco -- Dorsey, Jean A -- Johnson, F Brad -- Shilatifard, Ali -- Kaeberlein, Matt -- Kennedy, Brian K -- Berger, Shelley L -- R01 AG025549/AG/NIA NIH HHS/ -- R01 AG025549-01A2/AG/NIA NIH HHS/ -- R01 AG025549-03/AG/NIA NIH HHS/ -- R01 CA089455/CA/NCI NIH HHS/ -- England -- Nature. 2009 Jun 11;459(7248):802-7. doi: 10.1038/nature08085.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Gene Expression and Regulation Program, The Wistar Institute Philadelphia, Pennsylvania 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19516333" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Acetyltransferases/metabolism ; Cell Division ; Chromatin/genetics/metabolism ; Epistasis, Genetic ; Gene Expression Regulation, Fungal ; Gene Silencing ; Histone Acetyltransferases ; Histone Deacetylase Inhibitors ; Histone Deacetylases/deficiency/metabolism ; Histones/*chemistry/genetics/*metabolism ; Lysine/*metabolism ; Mutant Proteins/genetics/metabolism ; Mutation ; Saccharomyces cerevisiae/*cytology/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Silent Information Regulator Proteins, Saccharomyces cerevisiae/antagonists & ; inhibitors/deficiency/metabolism ; Sirtuin 2 ; Sirtuins/antagonists & inhibitors/deficiency/metabolism ; Telomere/genetics/metabolism ; Transcription, Genetic
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    Human DAZL, DAZ and BOULE genes modulate primordial germ-cell and haploid gamete formation (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-10-30
    Description: The leading cause of infertility in men and women is quantitative and qualitative defects in human germ-cell (oocyte and sperm) development. Yet, it has not been possible to examine the unique developmental genetics of human germ-cell formation and differentiation owing to inaccessibility of germ cells during fetal development. Although several studies have shown that germ cells can be differentiated from mouse and human embryonic stem cells, human germ cells differentiated in these studies generally did not develop beyond the earliest stages. Here we used a germ-cell reporter to quantify and isolate primordial germ cells derived from both male and female human embryonic stem cells. By silencing and overexpressing genes that encode germ-cell-specific cytoplasmic RNA-binding proteins (not transcription factors), we modulated human germ-cell formation and developmental progression. We observed that human DAZL (deleted in azoospermia-like) functions in primordial germ-cell formation, whereas closely related genes DAZ and BOULE (also called BOLL) promote later stages of meiosis and development of haploid gametes. These results are significant to the generation of gametes for future basic science and potential clinical applications.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3133736/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3133736/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kee, Kehkooi -- Angeles, Vanessa T -- Flores, Martha -- Nguyen, Ha Nam -- Reijo Pera, Renee A -- R01 HD047721/HD/NICHD NIH HHS/ -- R01 HD047721-06/HD/NICHD NIH HHS/ -- R01HD047721/HD/NICHD NIH HHS/ -- U54 HD055764/HD/NICHD NIH HHS/ -- U54 HD055764-015755/HD/NICHD NIH HHS/ -- U54HD055764/HD/NICHD NIH HHS/ -- England -- Nature. 2009 Nov 12;462(7270):222-5. doi: 10.1038/nature08562. Epub 2009 Oct 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Human Embryonic Stem Cell Research and Education, Institute for Stem Cell Biology & Regenerative Medicine, Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford University, Palo Alto, California 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19865085" target="_blank"〉PubMed〈/a〉
    Keywords: Bone Morphogenetic Proteins/metabolism ; Cell Count ; *Cell Differentiation ; Cell Line ; Cellular Reprogramming ; Embryonic Stem Cells/cytology/metabolism ; Female ; Gene Expression ; Gene Silencing ; Genes, Reporter ; Germ Cells/*cytology/*metabolism ; *Haploidy ; Humans ; Male ; Meiosis ; Organ Specificity ; RNA-Binding Proteins/genetics/*metabolism
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Snowdrift game dynamics and facultative cheating in yeast (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-04-08
    Description: The origin of cooperation is a central challenge to our understanding of evolution. The fact that microbial interactions can be manipulated in ways that animal interactions cannot has led to a growing interest in microbial models of cooperation and competition. For the budding yeast Saccharomyces cerevisiae to grow on sucrose, the disaccharide must first be hydrolysed by the enzyme invertase. This hydrolysis reaction is performed outside the cytoplasm in the periplasmic space between the plasma membrane and the cell wall. Here we demonstrate that the vast majority ( approximately 99 per cent) of the monosaccharides created by sucrose hydrolysis diffuse away before they can be imported into the cell, serving to make invertase production and secretion a cooperative behaviour. A mutant cheater strain that does not produce invertase is able to take advantage of and invade a population of wild-type cooperator cells. However, over a wide range of conditions, the wild-type cooperator can also invade a population of cheater cells. Therefore, we observe steady-state coexistence between the two strains in well-mixed culture resulting from the fact that rare strategies outperform common strategies-the defining features of what game theorists call the snowdrift game. A model of the cooperative interaction incorporating nonlinear benefits explains the origin of this coexistence. We are able to alter the outcome of the competition by varying either the cost of cooperation or the glucose concentration in the media. Finally, we note that glucose repression of invertase expression in wild-type cells produces a strategy that is optimal for the snowdrift game-wild-type cells cooperate only when competing against cheater cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2888597/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2888597/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gore, Jeff -- Youk, Hyun -- van Oudenaarden, Alexander -- K99 GM085279/GM/NIGMS NIH HHS/ -- K99 GM085279-01/GM/NIGMS NIH HHS/ -- R01 GM068957/GM/NIGMS NIH HHS/ -- R01 GM068957-04/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 May 14;459(7244):253-6. doi: 10.1038/nature07921. Epub 2009 Apr 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19349960" target="_blank"〉PubMed〈/a〉
    Keywords: Coculture Techniques ; Competitive Behavior/drug effects ; Cooperative Behavior ; Diffusion ; *Game Theory ; Glucose/*metabolism ; *Models, Biological ; Saccharomyces cerevisiae/*cytology/enzymology/genetics/*metabolism ; beta-Fructofuranosidase/genetics/metabolism
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    Ancient ivory figurine deserves a more thoughtful label (2009)
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    Publication Date: 2009-06-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McDonnell, Anna -- England -- Nature. 2009 Jun 18;459(7249):909. doi: 10.1038/459909b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19536241" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Female ; Fertility ; History, Ancient ; Humans ; Pregnancy ; Sculpture/*history
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    Crystal structure of the ATP-gated P2X(4) ion channel in the closed state (2009)
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    Publication Date: 2009-07-31
    Description: P2X receptors are cation-selective ion channels gated by extracellular ATP, and are implicated in diverse physiological processes, from synaptic transmission to inflammation to the sensing of taste and pain. Because P2X receptors are not related to other ion channel proteins of known structure, there is at present no molecular foundation for mechanisms of ligand-gating, allosteric modulation and ion permeation. Here we present crystal structures of the zebrafish P2X(4) receptor in its closed, resting state. The chalice-shaped, trimeric receptor is knit together by subunit-subunit contacts implicated in ion channel gating and receptor assembly. Extracellular domains, rich in beta-strands, have large acidic patches that may attract cations, through fenestrations, to vestibules near the ion channel. In the transmembrane pore, the 'gate' is defined by an approximately 8 A slab of protein. We define the location of three non-canonical, intersubunit ATP-binding sites, and suggest that ATP binding promotes subunit rearrangement and ion channel opening.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2720809/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2720809/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kawate, Toshimitsu -- Michel, Jennifer Carlisle -- Birdsong, William T -- Gouaux, Eric -- U54 GM075026/GM/NIGMS NIH HHS/ -- U54 GM075026-04/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Jul 30;460(7255):592-8. doi: 10.1038/nature08198.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vollum Institute, Oregon Health and Science University, 3181 Southwest Sam Jackson Park Road, Oregon 97239, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19641588" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Animals ; Binding Sites ; Cell Line ; Crystallography, X-Ray ; Gadolinium/metabolism ; Humans ; Ion Channels/antagonists & inhibitors/*chemistry ; Membrane Proteins/chemistry ; *Models, Molecular ; Protein Binding ; Protein Folding ; Protein Structure, Tertiary ; Purinergic P2 Receptor Antagonists ; Receptors, Purinergic P2/*chemistry ; Receptors, Purinergic P2X4 ; Zebrafish/*physiology ; Zebrafish Proteins/antagonists & inhibitors/*chemistry
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    Increased mortality and AIDS-like immunopathology in wild chimpanzees infected with SIVcpz (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-07-25
    Description: African primates are naturally infected with over 40 different simian immunodeficiency viruses (SIVs), two of which have crossed the species barrier and generated human immunodeficiency virus types 1 and 2 (HIV-1 and HIV-2). Unlike the human viruses, however, SIVs do not generally cause acquired immunodeficiency syndrome (AIDS) in their natural hosts. Here we show that SIVcpz, the immediate precursor of HIV-1, is pathogenic in free-ranging chimpanzees. By following 94 members of two habituated chimpanzee communities in Gombe National Park, Tanzania, for over 9 years, we found a 10- to 16-fold higher age-corrected death hazard for SIVcpz-infected (n = 17) compared to uninfected (n = 77) chimpanzees. We also found that SIVcpz-infected females were less likely to give birth and had a higher infant mortality rate than uninfected females. Immunohistochemistry and in situ hybridization of post-mortem spleen and lymph node samples from three infected and two uninfected chimpanzees revealed significant CD4(+) T-cell depletion in all infected individuals, with evidence of high viral replication and extensive follicular dendritic cell virus trapping in one of them. One female, who died within 3 years of acquiring SIVcpz, had histopathological findings consistent with end-stage AIDS. These results indicate that SIVcpz, like HIV-1, is associated with progressive CD4(+) T-cell loss, lymphatic tissue destruction and premature death. These findings challenge the prevailing view that all natural SIV infections are non-pathogenic and suggest that SIVcpz has a substantial negative impact on the health, reproduction and lifespan of chimpanzees in the wild.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872475/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872475/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Keele, Brandon F -- Jones, James Holland -- Terio, Karen A -- Estes, Jacob D -- Rudicell, Rebecca S -- Wilson, Michael L -- Li, Yingying -- Learn, Gerald H -- Beasley, T Mark -- Schumacher-Stankey, Joann -- Wroblewski, Emily -- Mosser, Anna -- Raphael, Jane -- Kamenya, Shadrack -- Lonsdorf, Elizabeth V -- Travis, Dominic A -- Mlengeya, Titus -- Kinsel, Michael J -- Else, James G -- Silvestri, Guido -- Goodall, Jane -- Sharp, Paul M -- Shaw, George M -- Pusey, Anne E -- Hahn, Beatrice H -- HHSN266200400088C/PHS HHS/ -- P30 AI 27767/AI/NIAID NIH HHS/ -- P30 AI027767/AI/NIAID NIH HHS/ -- P30 AI027767-21A17134/AI/NIAID NIH HHS/ -- R01 AI058715/AI/NIAID NIH HHS/ -- R01 AI058715-06A1/AI/NIAID NIH HHS/ -- R01 AI50529/AI/NIAID NIH HHS/ -- R01 AI58715/AI/NIAID NIH HHS/ -- R37 AI050529/AI/NIAID NIH HHS/ -- R37 AI050529-06A1/AI/NIAID NIH HHS/ -- RR-00165/RR/NCRR NIH HHS/ -- T32 GM008111/GM/NIGMS NIH HHS/ -- U19 AI067854/AI/NIAID NIH HHS/ -- U19 AI067854-059010/AI/NIAID NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Jul 23;460(7254):515-9. doi: 10.1038/nature08200.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19626114" target="_blank"〉PubMed〈/a〉
    Keywords: Acquired Immunodeficiency Syndrome/pathology ; Africa ; Animals ; Animals, Wild ; CD4-Positive T-Lymphocytes/immunology ; Female ; Humans ; Male ; Molecular Sequence Data ; Pan troglodytes/*virology ; Prevalence ; Simian Acquired Immunodeficiency ; Syndrome/epidemiology/immunology/*mortality/*pathology ; Simian Immunodeficiency Virus/*physiology
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    Graphene gets ready for the big time (2009)
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    Publication Date: 2009-03-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brumfiel, Geoff -- England -- Nature. 2009 Mar 26;458(7237):390-1. doi: 10.1038/458390a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19325592" target="_blank"〉PubMed〈/a〉
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    White organic light-emitting diodes with fluorescent tube efficiency (2009)
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    Publication Date: 2009-05-16
    Description: The development of white organic light-emitting diodes (OLEDs) holds great promise for the production of highly efficient large-area light sources. High internal quantum efficiencies for the conversion of electrical energy to light have been realized. Nevertheless, the overall device power efficiencies are still considerably below the 60-70 lumens per watt of fluorescent tubes, which is the current benchmark for novel light sources. Although some reports about highly power-efficient white OLEDs exist, details about structure and the measurement conditions of these structures have not been fully disclosed: the highest power efficiency reported in the scientific literature is 44 lm W(-1) (ref. 7). Here we report an improved OLED structure which reaches fluorescent tube efficiency. By combining a carefully chosen emitter layer with high-refractive-index substrates, and using a periodic outcoupling structure, we achieve a device power efficiency of 90 lm W(-1) at 1,000 candelas per square metre. This efficiency has the potential to be raised to 124 lm W(-1) if the light outcoupling can be further improved. Besides approaching internal quantum efficiency values of one, we have also focused on reducing energetic and ohmic losses that occur during electron-photon conversion. We anticipate that our results will be a starting point for further research, leading to white OLEDs having efficiencies beyond 100 lm W(-1). This could make white-light OLEDs, with their soft area light and high colour-rendering qualities, the light sources of choice for the future.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reineke, Sebastian -- Lindner, Frank -- Schwartz, Gregor -- Seidler, Nico -- Walzer, Karsten -- Lussem, Bjorn -- Leo, Karl -- England -- Nature. 2009 May 14;459(7244):234-8. doi: 10.1038/nature08003.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Angewandte Photophysik, George-Bahr-Strasse 1, D-01062 Dresden, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19444212" target="_blank"〉PubMed〈/a〉
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