bluuebunny/crossref_metadata_2025 huggingface dataset:
O atom production in water ice: Implications for O2 formation on icy satellites
Authors: Cooper Paul D. , Moore Marla H. , Hudson Reggie L.
Published: October 2010

We have found that O atoms are a primary product in the irradiation of water‐ice with 0.8 MeV protons. This observation has implications in understanding the chemical reactions that occur to produce molecular oxygen (O2) in such laboratory ices, as well as ices found on the surfaces of Ganymede and Europa, and the ice particles present in Saturn's rings. We estimate that in irradiated water‐ice, O2 can be formed at a lower limit of 0.07% by number relative to water and is in agreement with observations of the icy Jovian satellites.
Mineral quartz concentration measurements of mixed mineral dust/urban haze pollution plumes over Korea with multiwavelength aerosol Raman‐quartz lidar
Authors: Müller D. , Mattis I. , Tatarov B. , Noh Y. M. , Shin D. H. , Shin S. K. , Lee K. H. , Kim Y. J. , Sugimoto N.
Published: October 2010

We present a case study of a concentration measurement of mineral quartz immersed in East Asian urban pollution. We use a novel lidar measurement technique that uses signals from Raman scattering from quartz at ultraviolet (360 nm) wavelength. The particle‐extinction‐related Ångström exponent (wavelength pair 355/532 nm) varies around 0.7 ± 0.2 , the lidar ratio is 50–55 sr at 532 nm. The numbers indicate that the pollution plume likely consisted of a mixture of mineral dust with urban haze. Dust concentrations vary between 8–11 μg/cm3. We determined Raman quartz concentrations from measurements simultaneously carried out at 546 nm, which allows us to measure for the first time the Raman‐quartz‐related Ångström exponent of mineral dust. Values are 3–4, whereas we expect a theoretical value of 4. It is unclear if the lower values follow from retrieval uncertainties or if they are linked to the internal structure of the quartz grains.
Terrestrial gamma ray flash production by active lightning leader channels
Authors: Carlson B. E. , Lehtinen N. G. , Inan U. S.
Published: October 2010

The production of terrestrial gamma ray flashes (TGFs) requires a seed energetic electron source and a strong electric field. Lightning leaders naturally provide seed electrons by cold runaway and strong electric fields by charge accumulation on the channel. We model possible TGF production in such fields by simulating the charges and currents on the channel. The resulting electric fields then drive simulations of runaway relativistic electron avalanche and photon emission. Photon spectra and directional distributions produced by the model agree qualitatively with observations. Simulations with a variety of initial conditions indicate sufficient electric fields are produced if an unbranched channel supports a current pulse of at least 100 kA such as occurs if the channel is at least 1 km long and embedded in an ambient electric field of at least 100 kV m−1. The mechanism does not strongly depend on altitude as friction and characteristic electric field strengths scale similarly. Seed particle production is not directly simulated, but estimates of seed production rates suggest current pulse activity of ∼1 ms duration can account for TGF‐scale emission.
Occurrence and onset conditions of postsunset equatorial spread F at Jicamarca during solar minimum and maximum
Authors: Lee Chien‐Chih
Published: October 2010

The data of digisonde and the NRLMSISE‐00 model on the occurrence of postsunset equatorial spread F (ESF) at Jicamarca during solar minimum and maximum years are used in a detailed statistical analysis. The onset conditions chosen in this study are the prereversal enhancement velocity (dhF80/dt), minimum virtual height of F‐layer (h′F), gradient density scale length (L), and local linear growth rate (γ) of collisional Rayleigh‐Taylor instability. The monthly variation in ESF occurrence during solar minimum generally agrees with that during maximum. This agreement indicates that the ESF occurrence does not depend on solar activity. For the onset conditions, the differences between solar minimum and maximum exists in the monthly variations in dhF80/dt, h′F, and L, but not in γ. This consistence in monthly γ variation between two solar epochs mainly account for the solar cycle independence of ESF occurrence. Furthermore, the variations in collision frequency and recombination rate are principally responsible to the consistence in γ.
Time‐dependent volcano source monitoring using interferometric synthetic aperture radar time series: A combined genetic algorithm and Kalman filter approach
Authors: Shirzaei M. , Walter T. R.
Published: October 2010

Modern geodetic methods allow continuous monitoring of deformation fields of volcanoes. The acquired data contribute significantly to the study of the dynamics of magmatic sources prior to, during and after eruptions and intrusions. In addition to advancing the monitoring techniques, it is important to develop suitable approaches to deal with deformation time series. Here, we present, test and apply a new approach for time‐dependent, nonlinear inversion using a combination of a genetic algorithm (GA) and a Kalman filter (KF). The GA is used in the form presented by Shirzaei and Walter (2009), and the KF implementation now allows for the treatment of monitoring data as a full time series rather than as single time steps. This approach provides a flexible tool for assessing unevenly sampled and heterogeneous time series data and explains the deformation field using time‐consistent dislocation sources. Following synthetic tests, we demonstrate the merits of time‐consistent source modeling for interferometric synthetic aperture radar (InSAR) data available between 1992 and 2008 from the Campi Flegrei volcano in Italy. We obtained multiple episodes of linear velocity for the reservoir pressure change associated with a parabolic surface deformation on the volcano. These data may be interpreted via differential equations as a linear flux to the shallow reservoir that provides new insight into how both the shallow and deep reservoirs communicate beneath Campi Flegrei. The synthetic test and case study demonstrate the robustness of our approach and the ability to track and monitor the source of systems with complex dynamics. It is applicable to time‐dependent optimization problems in volcanic and tectonic environments in other tectonic environments in other areas and allows understanding of the spatiotemporal extent of a physical process in quantitative manner.
Types, models and instances: a perspective from neuroscience
Authors: Cannon Robert
Published: October 2010

In order to share neuroscience models effectively, there is a need to clearly separate out the structure, equations and parameters so that each model only specifies those bits that are unique to itself. This will enable specialized simulation tools to recognize structures they can handle without having to process the equations directly. Two projects, NeuroML2 and NineML are working in this direction. As an example, we show how the Hodgkin Huxley equations can be decomposed into separate component type definitions and parameter sets in such as way that the majority of Hodgkin-Huxley style ion channel models can be expressed in only a few lines.
MIRIAM Resources: a robust annotation and cross referencing framework
Authors: Laibe Camille , Juty Nick , Le Novère Nicolas
Published: October 2010

Background

More than ever, the era of data integration has highlighted the key requirement to reference specific data in an unambiguous and perennial way, in order to enable community-level sharing, development, exchange and reuse of information. In the field of Systems Biology, which is concerned with creating quantitative models of biological processes, these requirements have directly led to the creation of the Minimal Information Required In the Annotation of Models (MIRIAM, "http://biomodels.net/miriam/":http://biomodels.net/miriam/). MIRIAM provides a specific set of guidelines that can be implemented within any structured modelling format.

Objectives

To support the implementation of MIRIAM guidelines, we have developed MIRIAM Resources ("http://www.ebi.ac.uk/miariam/":http://www.ebi.ac.uk/miariam/). This software infrastructure facilitates the use of controlled annotations in the identification of model components. The annotation procedures described in the MIRIAM standard entail the use of a Uniform Resource Identifier (URI), thereby uniquely identifying a component without reference to its physical location.

Results

MIRIAM Resources are a set of on-line services centred around a catalogue of data types. Data types can be ontologies, such as Gene Ontology, or primary data resources available via the Web, such as UniProt and PubMed. Each of these is uniquely identified within the MIRIAM database, and information stored regarding the corresponding physical URLs (data resources) through which their associated data can be accessed. Conversion services, to generate a MIRIAM URI from a data type name and dataset identifier, and resolution services, to generate physical locations for a given MIRIAM URI, are provided through SOAP and REST Web Services. MIRIAM annotations have become widely accepted and now used and supported by various communities, such as BioModels.net, SBML, CellML and BioPAX.ConclusionThe utility of MIRIAM URIs is not restricted solely to the field of quantitative modelling; MIRIAM Resources are now used by the Proteomics Standards Initiative (PSI). MIRIAM Resources allow easy access to MIRIAM URIs, as well as associated information, and facilitate the identification, exchange, and integration of data in the Life Sciences. The source code for the entire project is available, under the GNU General Public License, at: "http://sourceforge.net/projects/miriam/":http://sourceforge.net/projects/miriam/.
Tales From the Code Front: Translating Modularity
Authors: Smith Lucian
Published: October 2010

In translating modular Antimony models to and from CellML, two differences appeared: CellML's 'black box' approach vs. Antimony's 'model composition' approach, and CellML's math-based encoding vs. Antimony's object and rule-based encoding. The latter turned out to have a much larger impact on the translation than anticipated.
SBML Level 3 Hierarchical Model Composition
Authors: Smith Lucian , Hucka Michael
Published: October 2010

A new proposal for incorporating modularity (or 'model composition') into SBML Level 3.
A community of biocurators
Authors: Gaudet Pascale
Published: October 2010

Biocuration is a difficult mission: biological data is highly heterogeneous, and there are few areas where guidelines for data preservation and exchange exist. This has hampered the speed, quantity and diversity of data possible to capture. Hence, a major challenge for the biocuration community is to explore innovative ways to capture, represent and display information. It is also essential to increase the involvement of researchers, publishers and funding agencies in this process. I will discuss the work of the International Society for Biocuration to build a community of biocurators to achieve these goals.
Melatonin as the most effective organizer of the rhythm of protein synthesis in hepatocytes in vitro and in vivo
Authors: Brodsky Vsevolod Y , Zvezdina Natalia D
Published: October 2010

Recent data has extended a large array of melatonin functions by the discovery of melatonin's involvement in the organization and regulation of the rhythm of intracellular protein synthesis. An ultradian rhythm in total protein synthesis has been detected in primary hepatocyte cultures 5 min after addition of 1–5 nM melatonin to the medium. The melatonin effect was mediated via its receptors (as shown in experiments with luzindole), leading to the cell synchronization as well as the mean rate of protein synthesis rate being increased. The chain of processes synchronizing the oscillation of the rate protein synthesis throughout the hepatocyte population includes Ca2+ fluxes {experiments with BAPTA‐AM [1,2‐bis(2‐aminophenoxy)ethane‐N,N,N′,N′‐tetraacetic acid (acetomethyl ester)]}. Inhibition of protein kinase activity (experiments with H7) inhibited the synchronizing function of melatonin. Activation of protein kinase activity results in a shift of the protein synthesis oscillation; the effect was the same as melatonin added to the culture medium. In another series of experiments, after melatonin was intraperitoneally injected to rat (0.015–0.020 μg/kg), hepatocytes were isolated and cultures established. A synchronizing effect of melatonin in vivo was detected as early as in the estimates from the direct action of melatonin on cell cultures. In the cultures obtained from old rats provided with melatonin, the amplitude of protein synthesis rhythm was enhanced, i.e. cell—cell interactions were increased, as well as rate of the protein synthesis being enhanced.
Blood and Colostrum/Milk Serum γ‐Glutamyltransferase Activity as a Predictor of Passive Transfer Status in Lambs
Authors: Maden M. , Altunok V. , Bi̇rdane F. M. , Aslan V. , Ni̇zamlioglu M.
Published: October 2010

The importance of blood and colostrum/milk serumγ‐glutamyl transferase (γ‐GT) enzyme activity was evaluated to assess passive transfer status in healthy lambs.

Thirty Akkaraman sheep (3–6 years old) were used which had normal pregnancy period and the same conditions, and the age of the lambs ranged between 0 and 15 days.

Blood and colostrum/milk samples were collected from sheep and lambs after birth, before suckling (0) and after on 1st, 3rd, 7th and 15th days. Serum immunoglobulin G (IgG) concentration was determined by the use of Single Radial Immunodiffusion method. Serumγ‐GT activity was measured, using a commercially available kit in blood and colostrum/milk samples. Correlations were carried out between immunoglobulin andγ‐GT levels. Regression models (simple and multiple) were calculated with significant data.

Linear correlation was determined between colostrum/milkγ‐GT activity and IgG concentrations and between serumγ‐GT activity and IgG concentrations in lambs on the 0 day. (r: 0.607,P: 0.001), 1st (r: 0.768,P: 0.001) and the 3rd (r: 0.603,P: 0.001) days and on the 1st (r: 0.637,P: 0.001) and 3rd (r: 0.478,P: 0.012) days in the experiment, respectively. Multivariate regression models were developed to estimate sample IgG concentration. Serum and colostrum/milk IgG concentration could be predicted using the formula: lamb serum IgG = 825 + 0.688 (lambγ‐GT) + 52 (days); colostrum/milk IgG = 832 + 0.505 (colostrum/milkγ‐GT) − 167 (days). The regression models were moderately accurate in predicting serum IgG concentration (R2 = 0.51) and colostrum/milk IgG concentration (R2 = 0.55). Test sensitivity and positive predictive values for serumγ‐GT enzyme activity were found to be 96 and 100% and for colostrum/milkγ‐GT enzyme activity were found to be 100 and 68% to prediction IgG concentration.

Serum and colostrum/milkγ‐GT activity can be used to assess passive transfer status of lambs. Along with this, regression models used to calculate serum and colostrum/milkγ‐GT activities found to be useful to estimate sample IgG concentration. The use of serum and colostrum/milkγ‐GT enzyme activity was found useful especially after birth on the 0, 1st and 3rd days.
The Distribution of Culicoides imicola in Italy: Application and Evaluation of Current Mediterranean Models Based on Climate
Authors: Calistri P. , Goffredo M. , Caporale V. , Meiswinkel R.
Published: October 2010

In August 2000 bluetongue (BT) disease appeared amongst sheep on the island of Sardinia spreading later to Sicily and to mainland Italy. The majority of areas affected by BT were surveyed for Culicoides imicola, the only proven vector of the disease known to occur in the Mediterranean region. The data from 1456 light‐trap collections, made in months with a mean temperature of 12.5°C, were used to test the accuracy of current models predicting the prevalence and abundance of C. imicola across the region. For Italy, the distribution of C. imicola was found to be very irregular and did not fit the modelled predictions. The possible reasons for this are discussed, and suggestions made as to which variables may improve this fit in the development of future risk models. In Italy, past surveys failed to reveal the presence of C. imicola, and so could be construed as evidence of its recent invasion, and thus rampant spread northwards. Although equivocal, historical records indicate that C. imicola was overlooked in the past. Six recommendations are made as to the possible future course of Culicoides research in southern Europe.
Necrotizing Stomatitis Associated with Fusobacterium necrophorum in Two Goats
Authors: Yeruham I. , Elad D.
Published: October 2010

Necrotizing stomatitis associated with Fusobacterium necrophorum in two goats is described. Arcanobacterium pyrogenes was the dominant component of the microbial flora cultured under aerobic condition. Treatment with penicillin, at a dose of 50 000 IU/kg for 6 days was used successfully in the cure of the disease.
The Use of Different Vaccination Schedules for Sows to Protect Piglets against Aujeszky's Disease
Authors: Casal J. , Planasdemunt Ll. , Varo J. A. , Martín M.
Published: October 2010

Several Aujeszky's disease virus (ADV) vaccination protocols of sows were evaluated with regard to the passive protection conferred on piglets in a recently built commercial farm. Three different groups of sows were vaccinated using a Bartha K‐61 strain. One group received an inactivated vaccine during pregnancy and the other two groups received attenuated vaccines, either during pregnancy (day 65) or on the seventh day of lactation. At farrowing, sows vaccinated during lactation had lower seroneutralization titres than those vaccinated during pregnancy either with inactivated or attenuated vaccines. Accordingly, their piglets were the ones with lower levels of maternally transferred neutralizing antibodies. At 4 weeks of age, five piglets born of each group of sows were challenged intranasally with a neurotropic strain of ADV. Piglets born of sows vaccinated during pregnancy with inactivated and attenuated vaccines gained 1.50 kg bodyweight and 2.50 kg bodyweight during 7 days, respectively, and did not show clinical signs, while piglets from sows vaccinated during the previous lactation lost 0.60 kg and presented moderate to severe clinical signs of ADV. Vaccination of sows during pregnancy provided more protection against ADV for piglets than sow vaccination before mating. Piglets born from sows vaccinated with attenuated or inactivated vaccines did not present remarkable differences on protection.
Children's perception of dinner conversation with parents in Japan
Authors: Okada Miyuki
Published: October 2010

The children's perception of dinner and dinner conversation with their parents was surveyed for sixth‐grade students of elementary school in Japan. The data were analysed from the gender of children and attending parents. The children had dinner and dinner conversation more frequently with their mother than with their father. With father attendance, girls and boys had the same frequency of dinner and dinner conversation, although, with mother attendance, girls had dinner conversation more frequently than boys. Most of the children felt happy when they had dinner with their parents. However, a lower percentage of children felt happy when having dinner conversation with their parents, thought that they were important to their parents and thought dinner conversation was useful. More children felt happy during dinner and dinner conversation with their mother than with their father. However, there was no perceived difference in the usefulness of the conversation based on the father or the mother attending. The contents of conversation were greatly affected by which parent was attending. Subjects concerning children's manners were talked about more frequently in conversation with mothers than with fathers. Children had more frequent conversations with their father about ‘social issues’ and the ‘parents’ surroundings’ than with their mother. Girls had more frequent conversations on a wider variety of subjects with their mothers than boys. Girls could more easily share in their mothers’ knowledge or sense of values through dinner conversation. Boys were, for the most part, excluded from this process in conversation with either parent.
Ab initio adiabatic and quasidiabatic potential energy surfaces of lowest four electronic states of the H++O2 system
Authors: Xavier F. George D. , Kumar Sanjay
Published: October 2010

Ab initio global adiabatic and quasidiabatic potential energy surfaces of lowest four electronic (1–4 A3″) states of the H++O2 system have been computed in the Jacobi coordinates (R,r,γ) using Dunning’s cc-pVTZ basis set at the internally contracted multireference (single and double) configuration interaction level of accuracy, which are relevant to the dynamics studies of inelastic vibrational and charge transfer processes observed in the scattering experiments. The computed equilibrium geometry parameters of the bound [HO2]+ ion in the ground electronic state and other parameters for the transition state for the isomerization process, HOO+⇌OOH+ are in good quantitative agreement with those available from the high level ab initio calculations, thus lending credence to the accuracy of the potential energy surfaces. The nonadiabatic couplings between the electronic states have been analyzed in both the adiabatic and quasidiabatic frameworks by computing the nonadiabatic coupling matrix elements and the coupling potentials, respectively. It is inferred that the dynamics of energy transfer processes in the scattering experiments carried out in the range of 9.5–23 eV would involve all the four electronic states.
Global warming induces female cuttings of Populus cathayana to allocate more biomass, C and N to aboveground organs than do male cuttings
Authors: Xu Xiao , Peng Guoquan , Wu Chengchun , Han Qingmin
Published: October 2010

We investigated differences between the sexes of a dioecious species, Populus cathayana Rehd, in biomass accumulation, biomass allocation, and carbon (C) and nitrogen (N) concentrations under elevated temperature treatments. Cuttings were subjected to three temperature regimes (control, +2°C and +4°C, respectively) in closed-top chambers. Compared with the control treatment, warming significantly increased the net photosynthesis rate, height growth, leaf dry mass, stem dry mass (SM), root dry mass (RM) and total dry mass (TM), and resulted in a higher aboveground : belowground dry mass ratio (AB) in all individuals of both sexes, except in males under the +2°C warming treatment. Furthermore, warming decreased the concentration of C in the stems in both sexes, and increased the concentration of N in the leaves of females, and consequently, resulted in a lower C : N ratio in the leaves of female cuttings than in those of male cuttings. Also, further differences between males and females were detected. In the warming treatments, females exhibited significantly higher values of SM, RM, TM and AB, and lower RM : TM and RM : foliage area ratios than did the males. However, no significant differences in these traits between the two sexes were detected under ambient temperature. Our results indicated that allocation of biomass, and the concentrations of C and N in males and females are greatly affected by an elevated temperature, and that warming benefits females, which accumulate and allocate more biomass to aboveground organs than do the males.
Development of an in vitro propagation protocol for ex situ conservation of two critically endangered species of Commersonia (Malvaceae) from Western Australia
Authors: Nikabadi Shahab , Bunn Eric , Turner Shane , Stevens Jason , Dixon Kingsley
Published: October 2010

Protocols for in vitro propagation of two critically endangered species, Commersonia adenothalia C.F.Wilkins ms and Commersonia sp. Mt Groper (R. Cranfield & D. Kabay 9157), from south-western Western Australia were established utilising both shoot and in vitro leaf explants. Regeneration from leaf explants was highest, with an average of four shoots per leaf explant per a 4-week incubation period on ½-strength Murashige and Skoog (MS) medium with 2.5 µM thidiazuron (TDZ) + 2.5 µM 3-indoleacetic acid (IAA) for C. adenothalia and 13 shoots per leaf explant on ½-strength MS medium + 4.5 µM 6-benzylaminopurine (BAP) and 2.5 µM 1-naphthaleneacetic acid (NAA) for C. sp. Mt Groper. Shoot proliferation using single shoot explants of C. adenothalia resulted in a maximum average of 3.5 shoots per shoot explant per a 5-week incubation period on ½-strength MS medium + 5 µM kinetin and 0.5 µM BAP, whereas maximum mean shoot multiplication with C. sp. Mt Groper (×30 shoots per shoot explant per a 5-week incubation period) was recorded with ½-strength MS medium + 2.5 µM kinetin and 1 µM BAP. In general, C. sp. Mt Groper was much more reactive to cytokinins than was C. adenothalia, with prolific regeneration of shoots from leaf explants or shoot explants. Both species produced roots readily on ½-strength MS medium without added hormones or with 5 µM indole-3-butyric acid (IBA) (100% rooting in 3–4 weeks) and rooted plantlets survived the transition to soil (~70% survival).
DDS, 4,4′-diaminodiphenylsulfone, extends organismic lifespan
Authors: Cho Sung Chun , Park Moon Cheol , Keam Bhumsuk , Choi Jung Min , Cho Yunje , Hyun Soonsil , Park Sang Chul , Lee Junho
Published: October 2010

DDS, 4,4′-diaminodiphenylsulfone, is the most common drug prescribed to treat Hansen disease patients. In addition to its antibacterial activity, DDS has been reported to be involved in other cellular processes that occur in eukaryotic cells. Because DDS treatment significantly enhances the antioxidant activity in humans, we examined its effect on lifespan extension. Here we show that DDS extends organismic lifespan usingCaenorhabditis elegansas a model system. DDS treatment caused a delay in aging and decreased the levels of a mitochondrial complex. The oxygen consumption rate was also significantly lowered. Consistent with these data, paraquat treatment evoked less reactive oxygen species in DDS-treated worms, and these worms were less sensitive to paraquat. Interestingly enough, all of the molecular events caused by DDS treatment were consistently reproduced in mice treated with DDS for 3 mo and in the C2C12 muscle cell line. Structural prediction identified pyruvate kinase (PK) as a protein target of DDS. Indeed, DDS bound and inhibited PK in vitro and inhibited it in vivo, and a PK mutation conferred extended lifespan ofC. elegans. Supplement of pyruvate to the media protected C2C12 cells from apoptosis caused by paraquat. Our findings establish the significance of DDS in lowering reactive oxygen species generation and extending the lifespan, which renders the rationale to examining the possible effect of DDS on human lifespan extension.
Antiretroviral therapy for tuberculosis control in nine African countries
Authors: Williams Brian G. , Granich Reuben , De Cock Kevin M. , Glaziou Philippe , Sharma Abhishek , Dye Christopher
Published: October 2010

HIV has increased the incidence of tuberculosis (TB) by up to sevenfold in African countries, but antiretroviral therapy (ART) reduces the incidence of AIDS-related TB. We use a mathematical model to investigate the short-term and long-term impacts of ART on the incidence of TB, assuming that people are tested for HIV once a year, on average, and start ART at a fixed time after HIV seroconversion or at a fixed CD4
+
cell count. We fit the model to trend data on HIV prevalence and TB incidence in nine countries in sub-Saharan Africa. If HIV-positive people start ART within 5 y of seroconversion, the incidence of AIDS-related TB in 2015 will be reduced by 48% (range: 37–55%). Long-term reductions depend sensitively on the delay to starting ART. If treatment is started 5, 2, or 1 y after HIV seroconversion, or as soon as people test positive, the incidence in 2050 will be reduced by 66% (range: 57–80%), 95% (range: 93–96%), 97.7% (range: 96.9–98.2%) and 98.4% (range: 97.8–98.9%), respectively. In the countries considered here, early ART could avert 0.71 ± 0.36 [95% confidence interval (CI)] million of 3.4 million cases of TB between 2010 and 2015 and 5.8 ± 2.9 (95% CI) million of 15 million cases between 2015 and 2050. As more countries provide ART at higher CD4
+
cell counts, the impact on TB should be investigated to test the predictions of this model.
Binding of different histone marks differentially regulates the activity and specificity of polycomb repressive complex 2 (PRC2)
Authors: Xu Chao , Bian Chuanbing , Yang Wei , Galka Marek , Ouyang Hui , Chen Chen , Qiu Wei , Liu Huadong , Jones Amanda E. , MacKenzie Farrell , Pan Patricia , Li Shawn Shun-Cheng , Wang Hengbin , Min Jinrong
Published: October 2010

The polycomb repressive complex 2 (PRC2) is the major methyltransferase for H3K27 methylation, a modification critical for maintaining repressed gene expression programs throughout development. It has been previously shown that PRC2 maintains histone methylation patterns during DNA replication in part through its ability to bind to H3K27me3. However, the mechanism by which PRC2 recognizes H3K27me3 is unclear. Here we show that the WD40 domain of EED, a PRC2 component, is a methyllysine histone-binding domain. The crystal structures of apo-EED and EED in complex respectively with five different trimethyllysine histone peptides reveal that EED binds these peptides via the top face of its β-propeller architecture. The ammonium group of the trimethyllysine is accommodated by an aromatic cage formed by three aromatic residues, while its aliphatic chain is flanked by a fourth aromatic residue. Our structural data provide an explanation for the preferential recognition of the Ala-Arg-Lys-Ser motif-containing trimethylated H3K27, H3K9, and H1K26 marks by EED over lower methylation states and other histone methyllysine marks. More importantly, we found that binding of different histone marks by EED differentially regulates the activity and specificity of PRC2. Whereas the H3K27me3 mark stimulates the histone methyltransferase activity of PRC2, the H1K26me3 mark inhibits PRC2 methyltransferase activity on the nucleosome. Moreover, H1K26me3 binding switches the specificity of PRC2 from methylating H3K27 to EED. In addition to determining the molecular basis of EED-methyllysine recognition, our work provides the biochemical characterization of how the activity of a histone methyltransferase is oppositely regulated by two histone marks.
β-Subunit myristoylation is the gatekeeper for initiating metabolic stress sensing by AMP-activated protein kinase (AMPK)
Authors: Oakhill Jonathan S. , Chen Zhi-Ping , Scott John W. , Steel Rohan , Castelli Laura A. , Ling Naomi , Macaulay S. Lance , Kemp Bruce E.
Published: October 2010

The AMP-activated protein kinase (AMPK) is an αβγ heterotrimer that acts as a master metabolic regulator to maintain cellular energy balance following increased energy demand and increases in the AMP/ATP ratio. This regulation provides dynamic control of energy metabolism, matching energy supply with demand that is essential for the function and survival of organisms. AMPK is inactive unless phosphorylated on Thr172 in the α-catalytic subunit activation loop by upstream kinases (LKB1 or calcium-calmodulin-dependent protein kinase kinase β). How a rise in AMP levels triggers AMPK α-Thr172 phosphorylation and activation is incompletely understood. Here we demonstrate unequivocally that AMP directly stimulates α-Thr172 phosphorylation provided the AMPK β-subunit is myristoylated. Loss of the myristoyl group abolishes AMP activation and reduces the extent of α-Thr172 phosphorylation. Once AMPK is phosphorylated, AMP further activates allosterically but this activation does not require β-subunit myristoylation. AMP and glucose deprivation also promote membrane association of myristoylated AMPK, indicative of a myristoyl-switch mechanism. Our results show that AMP regulates AMPK activation at the initial phosphorylation step, and that β-subunit myristoylation is important for transducing the metabolic stress signal.
Affinity purification of microRNA-133a with the cardiac transcription factor, Hand2
Authors: Vo Ngan K. , Dalton Ryan P. , Liu Ning , Olson Eric N. , Goodman Richard H.
Published: October 2010

Predictions of microRNA-mRNA interactions typically rely on bioinformatic algorithms, but these algorithms only suggest the possibility of microRNA binding and may miss important interactions as well as falsely predict others. We developed an affinity purification approach to empirically identify microRNAs associated with the 3′UTR of the mRNA encoding Hand2, a transcription factor essential for cardiac development. In addition to miR-1, a known regulator of Hand2 expression, we determined that the Hand2 3′UTR also associated with miR-133a, a microRNA cotranscribed with miR-1 in cardiac and muscle cells. Using a sequential binding assay, we showed that miR-1 and miR-133a could occupy the Hand2 3′UTR concurrently. miR-133a inhibited Hand2 expression in tissue culture models, and miR-133a double knockout mice had elevated levels of Hand2 mRNA and protein. We conclude that Hand2 is regulated by miR-133a in addition to miR-1. The affinity purification assay should be generally applicable for identifying other microRNA-mRNA interactions.
Aerobic growth at nanomolar oxygen concentrations
Authors: Stolper Daniel A. , Revsbech Niels Peter , Canfield Donald E.
Published: October 2010

Molecular oxygen (O2) is the second most abundant gas in the Earth’s atmosphere, but in many natural environments, its concentration is reduced to low or even undetectable levels. Although low-oxygen-adapted organisms define the ecology of low-oxygen environments, their capabilities are not fully known. These capabilities also provide a framework for reconstructing a critical period in the history of life, because low, but not negligible, atmospheric oxygen levels could have persisted before the “Great Oxidation” of the Earth’s surface about 2.3 to 2.4 billion years ago. Here, we show thatEscherichia coliK-12, chosen for its well-understood biochemistry, rapid growth rate, and low-oxygen-affinity terminal oxidase, grows at oxygen levels of ≤ 3 nM, two to three orders of magnitude lower than previously observed for aerobes. Our study expands both the environmental range and temporal history of aerobic organisms.
High-throughput identification of compounds targeting influenza RNA-dependent RNA polymerase activity
Authors: Su Ching-Yao , Cheng Ting-Jen R. , Lin Meng-I. , Wang Shi-Yun , Huang Wen-I. , Lin-Chu Shao-Ying , Chen Yu-Hou , Wu Chung-Yi , Lai Michael M. C. , Cheng Wei-Chieh , Wu Ying-Ta , Tsai Ming-Daw , Cheng Yih-Shyun E. , Wong Chi-Huey
Published: October 2010

As influenza viruses have developed resistance towards current drugs, new inhibitors that prevent viral replication through different inhibitory mechanisms are useful. In this study, we developed a screening procedure to search for new antiinfluenza inhibitors from 1,200,000 compounds and identified previously reported as well as new antiinfluenza compounds. Several antiinfluenza compounds were inhibitory to the influenza RNA-dependent RNA polymerase (RdRP), including nucleozin and its analogs. The most potent nucleozin analog,
3061
(FA-2), inhibited the replication of the influenza A/WSN/33 (H1N1) virus in MDCK cells at submicromolar concentrations and protected the lethal H1N1 infection of mice. Influenza variants resistant to
3061
(FA-2) were isolated and shown to have the mutation on nucleoprotein (NP) that is distinct from the recently reported resistant mutation of Y289H [Kao R, et al. (2010)
Nat Biotechnol
28:600]. Recombinant influenza carrying the Y52H NP is also resistant to
3061
(FA-2), and NP aggregation induced by
3061
(FA-2) was identified as the most likely cause for inhibition. In addition, we identified another antiinfluenza RdRP inhibitor 367 which targets PB1 protein but not NP. A mutant resistant to 367 has H456P mutation at the PB1 protein and both the recombinant influenza and the RdRP expressing the PB1 H456P mutation have elevated resistance to 367. Our high-throughput screening (HTS) campaign thus resulted in the identification of antiinfluenza compounds targeting RdRP activity.
Neutrophil elastase and myeloperoxidase regulate the formation of neutrophil extracellular traps
Authors: Papayannopoulos Venizelos , Metzler Kathleen D. , Hakkim Abdul , Zychlinsky Arturo
Published: October 2010

Neutrophils release decondensed chromatin termed neutrophil extracellular traps (NETs) to trap and kill pathogens extracellularly. Reactive oxygen species are required to initiate NET formation but the downstream molecular mechanism is unknown. We show that upon activation, neutrophil elastase (NE) escapes from azurophilic granules and translocates to the nucleus, where it partially degrades specific histones, promoting chromatin decondensation. Subsequently, myeloperoxidase synergizes with NE in driving chromatin decondensation independent of its enzymatic activity. Accordingly, NE knockout mice do not form NETs in a pulmonary model of Klebsiella pneumoniae infection, which suggests that this defect may contribute to the immune deficiency of these mice. This mechanism provides for a novel function for serine proteases and highly charged granular proteins in the regulation of chromatin density, and reveals that the oxidative burst induces a selective release of granular proteins into the cytoplasm through an unknown mechanism.
Mouse CD8α+ DCs and human BDCA3+ DCs are major producers of IFN-λ in response to poly IC
Authors: Lauterbach Henning , Bathke Barbara , Gilles Stefanie , Traidl-Hoffmann Claudia , Luber Christian A. , Fejer György , Freudenberg Marina A. , Davey Gayle M. , Vremec David , Kallies Axel , Wu Li , Shortman Ken , Chaplin Paul , Suter Mark , O’Keeffe Meredith , Hochrein Hubertus
Published: October 2010

Polyinosinic:polycytidylic acid (poly IC), a double-stranded RNA, is an effective adjuvant in vivo. IFN-λs (also termed IL-28/29) are potent immunomodulatory and antiviral cytokines. We demonstrate that poly IC injection in vivo induces large amounts of IFN-λ, which depended on hematopoietic cells and the presence of TLR3 (Toll-like receptor 3), IRF3 (IFN regulatory factor 3), IRF7, IFN-I receptor, Fms-related tyrosine kinase 3 ligand (FL), and IRF8 but not on MyD88 (myeloid differentiation factor 88), Rig-like helicases, or lymphocytes. Upon poly IC injection in vivo, the IFN-λ production by splenocytes segregated with cells phenotypically resembling CD8α+ conventional dendritic cells (DCs [cDCs]). In vitro experiments revealed that CD8α+ cDCs were the major producers of IFN-λ in response to poly IC, whereas both CD8α+ cDCs and plasmacytoid DCs produced large amounts of IFN-λ in response to HSV-1 or parapoxvirus. The nature of the stimulus and the cytokine milieu determined whether CD8α+ cDCs produced IFN-λ or IL-12p70. Human DCs expressing BDCA3 (CD141), which is considered to be the human counterpart of murine CD8α+ DCs, also produced large amounts of IFN-λ upon poly IC stimulation. Thus, IFN-λ production in response to poly IC is a novel function of mouse CD8α+ cDCs and their human equivalents.
Risk of Postdischarge Infection with Vancomycin-Resistant Enterococcus after Initial Infection or Colonization
Authors: Datta Rupak , Huang Susan S.
Published: October 2010

Postdischarge risks of vancomycin-resistant Enterococcus (VRE) infection among carriers are unknown. We conducted a retrospective cohort study of 199 patients newly detected as VRE carriers. Fifteen patients (8%) developed 27 VRE infections in the 18 months after detection. Among 10 postdischarge infections, 2 involved bacteremia and 3 resulted in readmission.
Towards suppressing H blistering by investigating the physical origin of the H–He interaction in W
Authors: Zhou Hong-Bo , Liu Yue-Lin , Jin Shuo , Zhang Ying , Luo G.-N. , Lu Guang-Hong
Published: October 2010

We investigate the physical origin of H–He interaction in W in terms of optimal charge density by calculating the energetics and diffusion properties using a first-principles method. On the one hand, we show a strong attraction between H and He in W originated from the charge density redistribution due to the presence of He, driving H segregation towards He. This can block the permeation of H into deeper bulk and thus suppress H blistering. On the other hand, we demonstrate that He, rather than H, energetically prefers to occupy the vacancy centre due to its closed-shell structure, which can block H2 formation at the vacancy centre. This is because He causes a redistribution of charge density inside the vacancy to make it ‘not optimal’ for the formation of H2 molecules, which can be treated as a preliminary nucleation of the H bubbles. We thus propose that H retention and blistering in W can be suppressed by doping the noble gas elements.
Model-based design of multi-mode feedback control in the RFX-mod experiment
Authors: Piron Lidia , Marrelli Lionello , Piovesan Paolo , Zanca Paolo
Published: October 2010

Interest in real-time control of magnetic field errors and magnetohydrodynamic (MHD) instabilities has been growing in the last decades due to the demanding stability requirements of high-performance scenarios in fusion devices. In this framework, the RFX-mod experiment (Sonato et al 2003 Fusion Eng. Des.
66 161) plays an important role. One of the main goals of RFX-mod is to explore high-plasma current regimes up to 2 MA for the first time in a reversed-field pinch. To this aim, RFX-mod is equipped with an advanced active coil system for the control of error fields and MHD modes, such as tearing and resistive-wall modes. As far as tearing modes are concerned, both controlling their edge radial magnetic field and maintaining them into slow (∼10–100 Hz) rotation are crucial to reduce both the plasma–wall interaction and the core magnetic stochasticity. In this paper, a model-based optimization of the RFX-mod feedback control is presented. The aim is to find an optimal gain set for a spectrum of multiple tearing modes, which produces the lowest possible value of the edge radial magnetic field, maintaining at the same time the modes into slow rotation and avoiding coil current saturations. These optimal gains have first been calculated offline by simulating the non-linear dynamics of a spectrum of tearing modes interacting through viscous and electromagnetic torques, using an adaptation to the RFX-mod multiple-shell layout of the model described in Zanca (2009 Plasma Phys. Control. Fusion
51 015006). This gain set has been obtained by scanning the proportional and derivative gains and has been tested in an extensive experimental campaign, showing good agreement with the model. With this approach, a reduction in the edge radial magnetic field up to 15%, with respect to discharges in which an empirical optimization was used, has been obtained. The above model proved to be a powerful tool to tune a multi-mode controller offline, which allowed us to save a large amount of experimental time.
Variation Within and AmongVitisspp. for Foliar Resistance to the Powdery Mildew PathogenErysiphe necator
Authors: Cadle-Davidson Lance , Chicoine David R. , Consolie Nancy H.
Published: October 2010

To complement existing control strategies, grape growers desire cultivars with resistance to powdery mildew caused by Erysiphe necator. Numerous disease resistance screens of diverse Vitis germplasm have been conducted previously to identify powdery mildew resistance but ratings of named cultivars were inconsistent and identities of resistant individuals in wild species were not typically provided. In the current study, controlled inoculations of a single isolate were made onto detached leaves from 1,025 Vitis accessions. The results were compared with natural epidemics in two vineyards: the cold-hardy Vitis spp. repository in Geneva, NY, in 2007–08, and a replicated vineyard of 89 Vitis accessions in Fredonia, NY in 2006–08. Of the genotypes screened using both natural infection and single-isolate inoculation, 33% were resistant to a single isolate but susceptible to diverse isolates in either or both vineyards, possibly due to race-specific resistance. This was exemplified by selection of E. necator genotypes virulent to Vitis labrusca in the Fredonia, NY vineyard, which is surrounded by production of the interspecific labrusca hybrids Concord and Niagara. Otherwise, there was good correlation of ratings between the vineyard and single-isolate ratings (r = 0.55 to 0.56) and between Geneva and Fredonia vineyard ratings (r = 0.75). No accession rated in all three screens was immune from infection. Although individual accessions of V. aestivalis, V. palmata, Vitis × doaniana, and Ampelopsis brevipedunculata were resistant in Geneva and Fredonia, each well-represented species had notable intraspecific variation in resistance. For 129 interspecific hybrids in this and previous studies, ratings infrequently corresponded among previous studies (39%) and between the current and previous studies (17 to 46%). However, three cultivars (Cayuga White, Diana, and Mars) were consistently rated as resistant across four independent studies. The results underscore the importance of uniform testing in multiple environments and the need for strategies for the development of cultivars with durable resistance.
Temporal biodiversity change in transformed landscapes: a southern African perspective
Authors: Chown Steven L.
Published: October 2010

Landscape transformation by humans is virtually ubiquitous, with several suggestions being made that the world's biomes should now be classified according to the extent and nature of this transformation. Even those areas that are thought to have a relatively limited human footprint have experienced substantial biodiversity change. This is true of both marine and terrestrial systems of southern Africa, a region of high biodiversity and including several large conservation areas. Global change drivers have had substantial effects across many levels of the biological hierarchy as is demonstrated in this review, which focuses on terrestrial systems. Interactions among drivers, such as between climate change and invasion, and between changing fire regimes and invasion, are complicating attribution of change effects and management thereof. Likewise CO
2
fertilization is having a much larger impact on terrestrial systems than perhaps commonly acknowledged. Temporal changes in biodiversity, and the seeming failure of institutional attempts to address them, underline a growing polarization of world views, which is hampering efforts to address urgent conservation needs.
Integrating spatial and temporal approaches to understanding species richness
Authors: White Ethan P. , Ernest S. K. Morgan , Adler Peter B. , Hurlbert Allen H. , Lyons S. Kathleen
Published: October 2010

Understanding species richness patterns represents one of the most fundamental problems in ecology. Most research in this area has focused on spatial gradients of species richness, with a smaller area of emphasis dedicated to understanding the temporal dynamics of richness. However, few attempts have been made to understand the linkages between the spatial and temporal patterns related to richness. Here, we argue that spatial and temporal richness patterns and the processes that drive them are inherently linked, and that our understanding of richness will be substantially improved by considering them simultaneously. The species–time–area relationship provides a case in point: successful description of the empirical spatio-temporal pattern led to a rapid development and testing of new theories. Other areas of research on species richness could also benefit from an explicitly spatio-temporal approach, and we suggest future directions for understanding the processes common to these two traditionally isolated fields of research.