bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of monomer sequences on conformations of copolymers grafted on spherical nanoparticles: A Monte Carlo simulation study
Authors: Seifpour Arezou , Spicer Philip , Nair Nitish , Jayaraman Arthi
Published: April 2010

Functionalizing nanoparticles with organic ligands, such as oligomers, polymers, DNA, and proteins, is an attractive way to manipulate the interfacial interactions between the nanoparticles and the medium the particles are placed in, and thus control the nanoparticle assembly. In this paper we have conducted a Monte Carlo simulation study on copolymer grafted spherical nanoparticles to show the tremendous potential of using monomer sequence on the copolymers to tune the grafted chain conformation, and thus the effective interactions between copolymer grafted nanoparticles. We have studied AB copolymers with alternating, multiblock, or diblock sequences, where either A monomers or B monomers have monomer-monomer attractive interactions. Our focus has been to show the nontrivial effect of monomer sequence on the conformations of the grafted copolymers at various particle diameters, grafting densities, copolymer chain lengths, and monomer-monomer interactions in an implicit small molecule solvent. We observe that the monomer sequence, particle diameter, and grafting density dictate whether (a) the grafted chains aggregate to bring attractive monomers from multiple grafted chains together (interchain and intrachain monomer aggregation) if the enthalpy gained by doing so offsets the entropic loss caused by stretching of chains, or (b) each grafted chain folds onto itself to bring its attractive monomers together (only intrachain monomer aggregation) if the entropic loss from interchain aggregation cannot be overcome by the enthalpic gain. For six copolymers of chain length N=24 grafted on a spherical particle of diameter D=4, interchain and intrachain monomer aggregation occurs, and the radius of gyration varies nonmonotonically with increasing blockiness of the monomer sequence. At larger particle diameters the grafted chains transition to purely intrachain monomer aggregation. The radius of gyration varies monotonically with monomer sequence for intrachain monomer aggregation because as the sequence becomes blockier (like monomers are grouped together), the copolymer chain has to fold less compactly to maximize the enthalpically favorable contacts while maintaining high conformational entropy. The radius of gyration of alternating and diblock copolymers scales with chain length N through a power law ⟨Rg2⟩1/2=αNν with the prefactor α and scaling exponent ν, varying with monomer sequence and monomer-monomer attraction strength.
Improving the density functional theory description of water with self-consistent polarization
Authors: Murdachaew Garold , Mundy Christopher J. , Schenter Gregory K.
Published: April 2010

We applied the self-consistent polarization density functional theory (SCP-DFT) to water. SCP-DFT requires only minimal parametrization, self-consistently includes the dispersion interaction neglected by standard DFT functionals, and has a cost similar to standard DFT despite its improved performance. Compared to the DFT functionals BLYP and BLYP-D (where the latter contains a simple dispersion correction), SCP-DFT yields interaction energies per molecule and harmonic frequencies of clusters in better agreement with experiment, with errors in the former of only a few tenths of a kcal/mol. BLYP and BLYP-D underbind and overbind the clusters, respectively, by up to about 1 kcal/mol. For liquid water, both BLYP and SCP-DFT predict radial distribution functions that are similar and overstructured compared to experiment. However, SCP-DFT improves over BLYP in predicting the experimental enthalpy of vaporization. A decomposition of the dimer interaction energy attempts to rationalize the performance of SCP-DFT. The SCP-DFT approach holds promise as an efficient and accurate method for describing large hydrogen-bonded systems, and has the potential to model complex systems with minimal parametrization.
Time dependent measurements of nitrous oxide and carbon dioxide collisional relaxation processes by a frequency down-chirped quantum cascade laser: Rapid passage signals and the time dependence of collisional processes
Authors: Tasinato Nicola , Hay Kenneth G. , Langford Nigel , Duxbury Geoffrey , Wilson David
Published: April 2010

Intrapulse quantum cascade laser spectrometers are able to produce both saturation and molecular alignment of the gas sample. This is due to the rapid sweep of the radiation through the absorption features. The intrapulse time domain spectra closely resemble those recorded in coherent optical nutation experiments. In the present paper, the frequency down-chirped technique is employed to investigate the nitrous oxide–foreign gas collisions. We have demonstrated that the measurements may be characterized by the induced polarization dominated and collision dominated measurement limits. The first of these is directly related to the time dependence of the long range collision cross sections. Among the collisional partners considered, carbon dioxide shows a very unusual behavior of rapid polarization damping, resulting in the production of symmetrical line shapes at very low gas buffer pressures. In the collision dominated regime, the pressure broadening parameters, which we have derived, are comparable at slow chirp rates, with those derived from other experimental methods. By comparing the pressure broadening coefficients of Ar, N2, and CO2 with those of He, making use of the chirp rate independence of the pressure broadening by helium, we have shown that at higher chirp rates there is clear evidence of the chirp-rate dependence of the pressure broadening parameters of N2 and CO2.
Communications: When diffraction rules the stereodynamics of rotationally inelastic collisions
Authors: Lemeshko Mikhail , Jambrina Pablo G. , de Miranda Marcelo P. , Friedrich Bretislav
Published: April 2010

Following upon our recent work on vector correlations in the Ar–NO collisions [Lemeshko and Friedrich, Phys. Chem. Chem. Phys. 12, 1038 (2010)], we compare model results with close-coupling calculations for a range of channels and collision energies for the He–NO system. The striking agreement between the model and exact polarization moments indicates that the stereodynamics of rotationally inelastic atom-molecule collisions at thermal energies is governed by diffraction of matter waves from a two-dimensional repulsive core of the atom-molecule potential. Furthermore, the model polarization moments characterizing the He–NO, He–O2, He–OH, and He–CaH stereodynamics are found to coalesce into a single, distinctive pattern, which can serve as a “fingerprint” to identify diffraction-driven stereodynamics in future work.
Phase behavior of a two-dimensional and confined in slitlike pores square-shoulder, square-well fluid
Authors: Rżysko W. , Patrykiejew A. , Sokołowski S. , Pizio O.
Published: April 2010

We report the phase diagrams for a square-shoulder, square-well fluids in two dimensions (2D), as well as confined in slitlike pores. The diagrams are obtained by histogram reweighting Monte Carlo simulations. The critical points are located by using finite size scaling analysis. Our calculations indicate that the phase behavior of the systems investigated is distinct from that observed in three dimensions. In particular, we have not found the liquid-liquid transition that occurs in the bulk.
Dewetting-induced globule-coil transitions of model polymers and possible implications high-temperature and low-pressure unfolding of proteins
Authors: Sumi Tomonari , Imazaki Nobuyuki , Sekino Hideo
Published: April 2010

A thermodynamic analysis of high-temperature and low-pressure unfolding of proteins using a coarse-grained multiscale simulation combined with a liquid-state density-functional theory is presented. In this study, a hydrophobic polymer chain is employed as a probe molecule for investigating qualitative changes in a hydration free energy surface acting on proteins with changes in temperature and pressure. When water is heated so that its vapor pressure is equal to the atmospheric pressure, it boils. Long-ranged dewetting or drying caused by a hydrophobic planar wall and a large hydrophobic solute surface is significantly enhanced as it approaches the liquid-vapor coexistence curve of water. In this study, we demonstrate that high-temperature and low-pressure unfolding of the polymer chain is interpreted as dewetting-induced unfolding that occurs as it approaches the liquid-vapor coexistence. The unfolding of proteins due to high-temperature and low-pressure denaturation enhances the long-ranged dewetting or drying around them. The long-ranged dewetting phenomenon is considered to be originating from positive changes in both volume and entropy due to the high-temperature and low-pressure denaturation of the proteins.
Pulsed current wave shaping with a transmission line by utilizing superposition of a forward and a backward voltage wave for fast capillary Z-pinch discharge
Authors: Sakai Y. , Takahashi S. , Watanabe M. , Kim G.-H. , Hotta E.
Published: April 2010

By using a water transmission line, current wave shaping was demonstrated for a fast capillary Z-pinch discharge recombination soft x-ray laser study. The pulsed power system consists of a water capacitor, a gap switch, a transmission line, and a capillary plasma load. A voltage wave initiated at the water capacitor propagates toward the capillary load through the transmission line. Control of the pulse delay that occurred in the transmission line provides the superposition of the forward and the backward voltage waves effectively in order to perform current wave shaping with higher current amplitude and rapid current decay.
A practical method to avoid zero-point leak in molecular dynamics calculations: Application to the water dimer
Authors: Czakó Gábor , Kaledin Alexey L. , Bowman Joel M.
Published: April 2010

We report the implementation of a previously suggested method to constrain a molecular system to have mode-specific vibrational energy greater than or equal to the zero-point energy in quasiclassical trajectory calculations [J. M. Bowman et al., J. Chem. Phys. 91, 2859 (1989); W. H. Miller et al., J. Chem. Phys. 91, 2863 (1989)]. The implementation is made practical by using a technique described recently [G. Czakó and J. M. Bowman, J. Chem. Phys. 131, 244302 (2009)], where a normal-mode analysis is performed during the course of a trajectory and which gives only real-valued frequencies. The method is applied to the water dimer, where its effectiveness is shown by computing mode energies as a function of integration time. Radial distribution functions are also calculated using constrained quasiclassical and standard classical molecular dynamics at low temperature and at 300 K and compared to rigorous quantum path integral calculations.
Delineation of sediment sources to a coastal wetland in the Great Barrier Reef catchment: influence of climate variability and land clearing since European arrival
Authors: Douglas Grant B. , Kuhnen Mio , Radke Lynda C. , Hancock Gary , Brooke Brendan , Palmer Mark J. , Pietsch Tim , Ford Phillip W. , Trefry Michael G. , Packett R. (Bob)
Published: April 2010

Environmental context. Undisturbed sediments provide a record to past events in a catchment. In this study we examine changes in sources of sediment and their variation over the past century due to changes in climate and extensive modification of the catchment after European settlement. We also highlight how multiple lines of forensic evidence acquired from the sediments can be used to reconstruct catchment history over a range of timescales.
Abstract. Enhanced delivery of sediment and nutrients to the Great Barrier Reef has the potential to profoundly influence ecological processes in this natural icon. Within the Fitzroy River Basin (FRB) of north-eastern Australia, natural impoundments such as Crescent Lagoon provide an invaluable archive of accumulated sediment that can be dated using multiple techniques to reconstruct the history of sediment export. During the last century, net rates of accumulation of sediment remain similar; however, large variations in sediment sources are apparent. A major sedimentary and geochemical discontinuity is present between ~45 to 29 years before present. Within this time interval a redox front is preserved corresponding to a change in organic matter influx; C3 plant detritus derived from the onset of broadscale agriculture within the FRB provided an assimilable carbon source resulting in more reducing conditions within the sediments. Statistical correlations demonstrate a notable correspondence between some sediment fractions supporting the notion of a short-lived disturbance to the sedimentation regime in the 1960–70s.
Anisole nitration during gamma-irradiation of aqueous nitrite and nitrate solutions: free radical versus ionic mechanisms
Authors: Elias Gracy , Mincher Bruce J. , Mezyk Stephen P. , Cullen Thomas D. , Martin Leigh R.
Published: April 2010

Environmental context. The nitration of aromatic compounds is an important source of toxic, carcinogenic, and mutagenic species in the atmosphere. Gas phase nitration typically occurs by free radical reactions. Condensed-phase free radical reactions may also be relevant in fog and cloud water in polluted areas, in urban aerosols with low pH, in water treatment using advanced oxidation processes such as e-beam irradiation, and in nuclear waste treatment applications. This paper discusses research towards an improved understanding of nitration of aromatic compounds in the condensed phase under conditions conducive to free radical formation. Abstract. In the irradiated, acidic condensed phase, radiation-enhanced nitrous acid-catalysed, nitrosonium ion, electrophilic aromatic substitution followed by oxidation reactions dominated over radical addition reactions for anisole. This ionic mechanism would predominate in urban atmospheric aerosols and nuclear fuel dissolutions. Irradiated neutral nitrate anisole solutions were dominated by mixed nitrosonium/nitronium ion electrophilic aromatic substitution reactions, but with lower product yields. Solutions such as these might be encountered in water treatment by e-beam irradiation. Irradiation of neutral nitrite anisole solutions resulted in a statistical substitution pattern for nitroanisole products, suggesting non-electrophilic free radical reactions involving the •NO2 radical. Although often proposed as an atmospheric nitrating agent, NO2 radical is unlikely to have an important effect in the acidic condensed phase in the presence of more reactive, competing species such as nitrous acid.
Aeolian iron mobilisation by dust - acid interactions and their implications for soluble iron deposition to the ocean: a test involving potential anthropogenic organic acidic species
Authors: Luo Chao , Gao Yuan
Published: April 2010

Environmental context. Studying the input of atmospheric soluble iron to the ocean is important as the soluble form of iron is bioavailable for phytoplankton uptake in the surface ocean to support photosynthesis. In this paper, the effect of organic acidic species on atmospheric iron dissolution is addressed through a global model for the first time. The new results contribute to a better understanding of iron dissolution processes in the atmosphere and the role of atmospheric iron in ocean biogeochemical cycles.
Abstract. Dust deposition is a major source of iron in certain oceanic regions. Many atmospheric processes, such as heterogeneous reactions with acidic species, may convert insoluble iron in dust to soluble forms that become bioavailable for phytoplankton uptake in the surface ocean. Here we report for the first time the effects of organic acidic species on iron dissolution using laboratory-measured conversion rates by oxalate, simulated in a global model to estimate soluble iron fluxes to the ocean. With the complexity and limited data from measurements relating to different sources for oxalate, we focus on the effect of oxalate of anthropogenic origin in this work as a first-step testing, and we apply a scaling factor for oxalate based on its relationship with aerosol sulfate observed by in situ measurements in the continental sites. The results show better correlation with the observations than the work including inorganic acids alone, suggesting the contribution of organic acids to Fe dissolution. However, the simulated iron solubility is lower than that derived from measurements, suggesting additional processes may contribute to Fe dissolution that should be included in the model. Total deposition of soluble iron to the global ocean including the effect by anthropogenic oxalate is ~0.34 Tg year–1.
Are Arctic Ocean ecosystems exceptionally vulnerable to global emissions of mercury? A call for emphasised research on methylation and the consequences of climate change
Authors: Macdonald R. W. , Loseto L. L.
Published: April 2010

Environmental context. Mercury is a global contaminant that has entered Arctic food webs in sufficient quantity to put at risk the health of top predators and humans that consume them. Recent research has discovered a photochemical process unique to the Arctic that leads to mercury deposition on frozen surfaces after polar sunrise, but the connection between mercury deposition and entry into food webs remains tenuous and poorly understood. We propose here that the Arctic Ocean’s sensitivity to the global mercury cycle depends far more on neglected post-deposition processes that lead to methylation within the ice–ocean system, and the vulnerability of these processes to changes occurring in the cryosphere.
Abstract. Emissions, atmospheric transport and deposition have formed the emphasis of recent research to understand Hg trends in Arctic marine biota, with the expressed objective of predicting how biotic trends might respond to emission controls. To answer the question of whether the Arctic Ocean might be especially vulnerable to global mercury (Hg) contamination and how biota might respond to emission controls requires a distinction between the supply of Hg from source regions and the processes within the Arctic Ocean that sequester and convert mercury to monomethyl Hg (MeHg). Atmospheric Mercury Depletion Events (AMDEs) provide a unique Hg deposition process in the Arctic; however, AMDEs have yet to be linked quantitatively with Hg uptake in marine food webs. The difficulty in implicating AMDEs or emissions to biotic trends lie in the ocean where several poorly understood processes lead to MeHg production and biomagnification. We propose that sensitivity of the Arctic Ocean’s ecosystem to Hg lies not so much in the deposition process as in methylation processes within the ocean, Hg inputs from large drainage basins, and the vulnerability these to climate change. Future research needs to be better balanced across the entire Hg cycle.
Assessment of metal - extracellular polymeric substances interactions by asymmetrical flow field-flow fractionation coupled to inductively coupled plasma mass spectrometry
Authors: Alasonati Enrica , Dubascoux Stephane , Lespes Gaetane , Slaveykova Vera I.
Published: April 2010

Environmental context. Extracellular polymeric substances (EPS) are soluble polymers that are liberated from microorganisms and represent an important component of the natural organic matter in the aquatic and terrestrial environment. These substances affect nutrient and toxic metal cycling, both owing to their metal binding properties and their effect on aggregation and sedimentation. In order to obtain more information on their role in metal transport, EPS size (molar mass) distributions and the associated Ca, Cd and Pb were measured by using asymmetrical flow field-flow fractionation coupled to inductively coupled plasma mass spectrometry. Abstract. Extracellular polymeric substances (EPSs) excreted by the bacterium Sinorhizobium meliloti and associated Ca, Cd and Pb were characterised by asymmetrical flow field-flow fractionation coupled with UV spectrophotometry and inductively coupled plasma mass spectrometry in terms of molar-mass distributions, number- and weight-average molar masses and polydispersity index. Two major populations with weight-average molar masses of 74 × 103 and 1.35 × 106 g mol–1 were obtained for the EPS. Characterisation of the whole EPS–metal interactions evidenced the preferential binding of Ca and Cd to the low molar mass fraction, whereas Pb associated mainly with the high molar mass (HMM) fraction. Comparison with the EPS produced by exoY-mutant, deficient in HMM-EPS excretion, confirmed the preferential binding of Pb to the high molar mass fraction. Enrichment of the EPS with increasing metal concentrations induced the formation of aggregates, which was most pronounced in the presence of 10–4 mol L–1 Pb.
Design and analysis of synthetic carbon fixation pathways
Authors: Bar-Even Arren , Noor Elad , Lewis Nathan E. , Milo Ron
Published: April 2010

Carbon fixation is the process by which CO
2
is incorporated into organic compounds. In modern agriculture in which water, light, and nutrients can be abundant, carbon fixation could become a significant growth-limiting factor. Hence, increasing the fixation rate is of major importance in the road toward sustainability in food and energy production. There have been recent attempts to improve the rate and specificity of Rubisco, the carboxylating enzyme operating in the Calvin–Benson cycle; however, they have achieved only limited success. Nature employs several alternative carbon fixation pathways, which prompted us to ask whether more efficient novel synthetic cycles could be devised. Using the entire repertoire of approximately 5,000 metabolic enzymes known to occur in nature, we computationally identified alternative carbon fixation pathways that combine existing metabolic building blocks from various organisms. We compared the natural and synthetic pathways based on physicochemical criteria that include kinetics, energetics, and topology. Our study suggests that some of the proposed synthetic pathways could have significant quantitative advantages over their natural counterparts, such as the overall kinetic rate. One such cycle, which is predicted to be two to three times faster than the Calvin–Benson cycle, employs the most effective carboxylating enzyme, phosphoenolpyruvate carboxylase, using the core of the naturally evolved C4 cycle. Although implementing such alternative cycles presents daunting challenges related to expression levels, activity, stability, localization, and regulation, we believe our findings suggest exciting avenues of exploration in the grand challenge of enhancing food and renewable fuel production via metabolic engineering and synthetic biology.
Large scale dynamics in flux driven gyrokinetic turbulence
Authors: Sarazin Y. , Grandgirard V. , Abiteboul J. , Allfrey S. , Garbet X. , Ghendrih Ph. , Latu G. , Strugarek A. , Dif-Pradalier G.
Published: April 2010

The turbulent transport governed by the toroidal ion temperature gradient driven instability is analysed with the full-f global gyrokinetic code GYSELA (Grandgirard et al
2007 Plasma Phys. Control. Fusion
49 B173) when the system is driven by a prescribed heat source. Weak, yet finite, collisionality governs a neoclassical ion heat flux that can compete with the turbulent driven transport. In turn, the ratio of turbulent to neoclassical transport increases with the source magnitude, resulting in the degradation of confinement with additional power. The turbulent flux exhibits avalanche-like events, characterized by intermittent outbursts which propagate ballistically roughly at the diamagnetic velocity. Locally, the temperature gradient can drop well below the linear stability threshold. Large outbursts are found to correlate with streamer-like structures of the convection cells albeit their Fourier spectrum departs significantly from that of the most unstable linear modes. Last, the poloidal rotation of turbulent eddies is essentially governed by the radial electric field at moderate density gradient.
Influences of ballooning modes with moderate wave number on MHD equilibrium in LHD
Authors: Miura H. , Nakajima N.
Published: April 2010

In order to investigate the influences of ballooning modes with moderate wave numbers on MHD equilibrium, fully three-dimensional nonlinear MHD simulations with or without a large parallel thermal conductivity κ∥ are carried out for a fairly Mercier-unstable low-β MHD equilibrium in the inward-shifted Large Helical Device (LHD) configuration, which is considered to be avoided by pressure profile control in experiments. In the case without a κ∥ corresponding to a nearly non-dissipative plasma, such ballooning modes are so dangerous that a pressure collapse occurs in the core region and the plasma expands beyond the outermost flux surface. On the other hand, pressure deformation is limited in the core region for the case with a large κ∥, because ballooning modes with moderate wave numbers are significantly suppressed by κ∥. Since the core pressure collapse in a low-β plasma will become an obstacle on the way to attaining a high-β plasma in experiments, the operation regime or pressure profile in the inward-shifted LHD configuration might be restricted, at the least low-β regime, which is consistent with the experimental observation.
Effects of resonant magnetic perturbations on the dynamics of transport barrier relaxations in fusion plasmas
Authors: Leconte M. , Beyer P. , Garbet X. , Benkadda S.
Published: April 2010

The dynamics of transport barrier relaxation oscillations in the presence of resonant magnetic perturbations (RMPs) is investigated with a 3D global fluid code which simulates resistive ballooning turbulence in tokamak edge plasmas. The results reproduce qualitatively the stabilizing effect of RMPs and share common characteristics with ELM control experiments. It is found that this stabilization is due to a modification of the geometrical properties of the barrier.
Altered Lipid Droplet Dynamics in Hepatocytes Lacking Triacylglycerol Hydrolase Expression
Authors: Wang Huajin , Wei Enhui , Quiroga Ariel D. , Sun Xuejin , Touret Nicolas , Lehner Richard
Published: April 2010

Lipid droplets (LDs) form from the endoplasmic reticulum (ER) and grow in size by obtaining triacylglycerols (TG). Triacylglycerol hydrolase (TGH), a lipase residing in the ER, is involved in the mobilization of TG stored in LDs for the secretion of very-low-density lipoproteins. In this study, we investigated TGH-mediated changes in cytosolic LD dynamics. We have found that TGH deficiency resulted in decreased size and increased number of LDs in hepatocytes. Using fluorescent fatty acid analogues to trace LD formation, we observed that TGH deficiency did not affect the formation of nascent LDs on the ER. However, the rate of lipid transfer into preformed LDs was significantly slower in the absence of TGH. Absence of TGH expression resulted in increased levels of membrane diacylglycerol and augmented phospholipid synthesis, which may be responsible for the delayed lipid transfer. Therefore, altered maturation (growth) rather than nascent formation (de novo synthesis) may be responsible for the observed morphological changes of LDs in TGH-deficient hepatocytes.
Mug28, a Meiosis-specific Protein ofSchizosaccharomyces pombe, Regulates Spore Wall Formation
Authors: Shigehisa Akira , Okuzaki Daisuke , Kasama Takashi , Tohda Hideki , Hirata Aiko , Nojima Hiroshi
Published: April 2010

The meiosis-specific mug28+gene of Schizosaccharomyces pombe encodes a putative RNA-binding protein with three RNA recognition motifs (RRMs). Live observations of meiotic cells that express Mug28 tagged with green fluorescent protein (GFP) revealed that Mug28 is localized in the cytoplasm, and accumulates around the nucleus from metaphase I to anaphase II. Disruption of mug28+generated spores with low viability, due to the aberrant formation of the forespore membrane (FSM). Visualization of the FSM in living cells expressing GFP-tagged Psy1, an FSM protein, indicated that mug28Δ cells harbored abnormal FSMs that contained buds, and had a delayed disappearance of Meu14, a leading edge protein. Electron microscopic observation revealed that FSM formation was abnormal in mug28Δ cells, showing bifurcated spore walls that were thicker than the nonbifurcated spore walls of the wild type. Analysis of Mug28 mutants revealed that RRM3, in particular phenylalanin-466, is of primary importance for the proper localization of Mug28, spore viability, and FSM formation. Together, we conclude that Mug28 is essential for the proper maturation of the FSM and the spore wall.
Promoter DNA Methylation Patterns of Differentiated Cells Are Largely Programmed at the Progenitor Stage
Authors: Sørensen Anita L. , Jacobsen Bente Marie , Reiner Andrew H. , Andersen Ingrid S. , Collas Philippe
Published: April 2010

Mesenchymal stem cells (MSCs) isolated from various tissues share common phenotypic and functional properties. However, intrinsic molecular evidence supporting these observations has been lacking. Here, we unravel overlapping genome-wide promoter DNA methylation patterns between MSCs from adipose tissue, bone marrow, and skeletal muscle, whereas hematopoietic progenitors are more epigenetically distant from MSCs as a whole. Commonly hypermethylated genes are enriched in signaling, metabolic, and developmental functions, whereas genes hypermethylated only in MSCs are associated with early development functions. We find that most lineage-specification promoters are DNA hypomethylated and harbor a combination of trimethylated H3K4 and H3K27, whereas early developmental genes are DNA hypermethylated with or without H3K27 methylation. Promoter DNA methylation patterns of differentiated cells are largely established at the progenitor stage; yet, differentiation segregates a minor fraction of the commonly hypermethylated promoters, generating greater epigenetic divergence between differentiated cell types than between their undifferentiated counterparts. We also show an effect of promoter CpG content on methylation dynamics upon differentiation and distinct methylation profiles on transcriptionally active and inactive promoters. We infer that methylation state of lineage-specific promoters in MSCs is not a primary determinant of differentiation capacity. Our results support the view of a common origin of mesenchymal progenitors.
Insulin-regulated Aminopeptidase Is a Key Regulator of GLUT4 Trafficking by Controlling the Sorting of GLUT4 from Endosomes to Specialized Insulin-regulated Vesicles
Authors: Jordens Ingrid , Molle Dorothee , Xiong Wenyong , Keller Susanna R. , McGraw Timothy E.
Published: April 2010

Insulin stimulates glucose uptake by regulating translocation of the GLUT4 glucose transporter from intracellular compartments to the plasma membrane. In the absence of insulin GLUT4 is actively sequestered away from the general endosomes into GLUT4-specialized compartments, thereby controlling the amount of GLUT4 at the plasma membrane. Here, we investigated the role of the aminopeptidase IRAP in GLUT4 trafficking. In unstimulated IRAP knockdown adipocytes, plasma membrane GLUT4 levels are elevated because of increased exocytosis, demonstrating an essential role of IRAP in GLUT4 retention. Current evidence supports the model that AS160 RabGAP, which is required for basal GLUT4 retention, is recruited to GLUT4 compartments via an interaction with IRAP. However, here we show that AS160 recruitment to GLUT4 compartments and AS160 regulation of GLUT4 trafficking were unaffected by IRAP knockdown. These results demonstrate that AS160 is recruited to membranes by an IRAP-independent mechanism. Consistent with a role independent of AS160, we showed that IRAP functions in GLUT4 sorting from endosomes to GLUT4-specialized compartments. This is revealed by the relocalization of GLUT4 to endosomes in IRAP knockdown cells. Although IRAP knockdown has profound effects on GLUT4 traffic, GLUT4 knockdown does not affect IRAP trafficking, demonstrating that IRAP traffics independent of GLUT4. In sum, we show that IRAP is both cargo and a key regulator of the insulin-regulated pathway.
Risk factors for the evolutionary emergence of pathogens
Authors: Alexander H. K. , Day T.
Published: April 2010

Recent outbreaks of novel infectious diseases (e.g. SARS, influenza H1N1) have highlighted the threat of cross-species pathogen transmission. When first introduced to a population, a pathogen is often poorly adapted to its new host and must evolve in order to escape extinction. Theoretical arguments and empirical studies have suggested various factors to explain why some pathogens emerge and others do not, including host contact structure, pathogen adaptive pathways and mutation rates. Using a multi-type branching process, we model the spread of an introduced pathogen evolving through several strains. Extending previous models, we use a network-based approach to separate host contact patterns from pathogen transmissibility. We also allow for arbitrary adaptive pathways. These generalizations lead to novel predictions regarding the impact of hypothesized risk factors. Pathogen fitness depends on the host population in which it circulates, and the ‘riskiest’ contact distribution and adaptive pathway depend on initial transmissibility. Emergence probability is sensitive to mutation probabilities and number of adaptive steps required, with the possibility of large adaptive steps (e.g. simultaneous point mutations or recombination) having a dramatic effect. In most situations, increasing overall mutation probability increases the risk of emergence; however, notable exceptions arise when deleterious mutations are available.
The formation of subglacial streams and mega-scale glacial lineations
Authors: Fowler A. C.
Published: April 2010

The instability theory of drumlin formation has been very successful in predicting the existence of ribbed moraine, as well as its amplitude and wavelength. However, the theory as it stands has not yet been shown to have the capability of predicting the existence of three-dimensional bedforms—drumlins—or their more extreme cousins, mega-scale glacial lineations. We extend the instability theory to include a dynamic description of the local subglacial drainage system, and in particular, we show that a uniform water-film flow between ice and deformable subglacial till is unstable, and that as a consequence, lineations will form. Predictions of the transverse wavelengths are consistent with observations.
Fronts, jumps and secondary introductions suggested as different invasion patterns in marine species, with an increase in spread rates over time
Authors: Mineur Frédéric , Davies Andrew J. , Maggs Christine A. , Verlaque Marc , Johnson Mark P.
Published: April 2010

Not all introduced (invasive) species in a region will spread from a single point of introduction. Long-distance dispersal or further introductions can obscure the pattern of spread, but the regional importance of such processes is difficult to gauge. These difficulties are further compounded when information on the multiple scale process of invasive species range expansion is reduced to one-dimensional estimates of spread (e.g. km yr
−1
). We therefore compared the results of two different metrics of range expansion: maximum linear rate of spread and accumulation of occupied grid squares (50 × 50 km) over time. An analysis of records for 54 species of introduced marine macrophytes in the Mediterranean and northeast Atlantic revealed cases where the invasion process was probably missed (e.g. Atlantic
Bonnemaisonia hamifera
) and suggested cases of secondary introductions or erratic jump dispersal (
Dasysiphonia
sp. and
Womersleyella setacea
). A majority of species analysed showed evidence for an accumulation of invaded sites without a clear invasion front. Estimates of spread rate are increasing for more recent introductions. The increase is greater than can be accounted for by temporally varying search effort and implies a historical increase in vector efficiency and/or a decreased resistance of native communities to invasion.
The evolution of migration in a seasonal environment
Authors: Griswold Cortland K. , Taylor Caz M. , Norris D. Ryan
Published: April 2010

Despite the fact that migration occurs in a wide variety of taxa worldwide, little is known about the conditions under which migration is expected to evolve from an ancestral resident population. We develop a model that focuses on ecological factors affecting the evolution of migration in a seasonal environment within a genetically explicit framework. We model the evolution of migration for two common types of migration: ‘shared breeding
’
where migrants share a breeding ground with residents and migrate to a separate non-breeding area, versus ‘shared non-breeding’, where migrants share a non-breeding ground with residents and migrate to a separate breeding area. Ecologically, migration is more easily established in the shared-breeding case versus the shared-non-breeding case. Genetically, the additive effect of a migratory allele affects its establishment more in the shared-non-breeding case versus the shared-breeding case, whereas the dominance effect of the allele affects its establishment more in the shared-breeding case versus the shared-non-breeding case. Generally, migratory alleles can invade even when residents are competitively superior to migrants during the shared season. Partial migration occurs when the population is polymorphic for migratory and non-migratory alleles, and is dependent upon which season is shared and the additive and dominance behaviour of the migratory allele.
Human cytomegalovirus UL141 promotes efficient downregulation of the natural killer cell activating ligand CD112
Authors: Prod'homme Virginie , Sugrue Daniel M. , Stanton Richard J. , Nomoto Akio , Davies James , Rickards Carole R. , Cochrane Daniel , Moore Melanie , Wilkinson Gavin W. G. , Tomasec Peter
Published: April 2010

Human cytomegalovirus (HCMV) UL141 induces protection against natural killer cell-mediated cytolysis by downregulating cell surface expression of CD155 (nectin-like molecule 5; poliovirus receptor), a ligand for the activating receptor DNAM-1 (CD226). However, DNAM-1 is also recognized to bind a second ligand, CD112 (nectin-2). We now show that HCMV targets CD112 for proteasome-mediated degradation by 48 h post-infection, thus removing both activating ligands for DNAM-1 from the cell surface during productive infection. Significantly, cell surface expression of both CD112 and CD155 was restored when UL141 was deleted from the HCMV genome. While gpUL141 alone is sufficient to mediate retention of CD155 in the endoplasmic reticulum, UL141 requires assistance from additional HCMV-encoded functions to suppress expression of CD112.
Resistance pathways of human immunodeficiency virus type 1 against the combination of zidovudine and lamivudine
Authors: Theys K. , Deforche K. , Libin P. , Camacho R. J. , Van Laethem K. , Vandamme A.-M.
Published: April 2010

A better understanding of human immunodeficiency virus type 1 drug-resistance evolution under the selective pressure of combination treatment is important for the design of long-term effective treatment strategies. We applied Bayesian network learning to sequences from patients treated with the reverse transcriptase inhibitor combination of zidovudine (AZT) and lamivudine (3TC) to identify the role of many treatment-selected mutations in the development of resistance. Based on the Bayesian network structure, anin vivofitness landscape was built, reflecting the necessary selective pressure under treatment, to evolve naive sequences to sequences obtained from patients treated with the combination. This landscape, combined with an evolutionary model, was used to predict resistance evolution in longitudinal sequence pairs. In our analysis, mutations 41L, 70R, 184V and 215F/Y were identified as major resistance mutations to the combination of AZT and 3TC, as they were associated directly with treatment experience. The network also suggested a possible role in resistance development for a number of novel mutations. Estimated fitness, using the landscape, correlated significantly within vitroresistance phenotype in genotype–phenotype pairs (R2=0.70). Variation in predicted evolution under selective pressure correlated significantly with observedin vivoevolution during AZT plus 3CT treatment. In conclusion, we confirmed current knowledge on resistance development to the combination of AZT and 3CT, but additional novel mutations were identified. Moreover, a model to predict resistance evolution during AZT and 3CT treatment has been built and validated.
A novel seven‐helix transmembrane protein BTP1 of Botrytis cinerea controls the expression of GST‐encoding genes, but is not essential for pathogenicity
Authors: GRONOVER CHRISTIAN SCHULZE , SCHUMACHER JULIA , HANTSCH PHILLIP , TUDZYNSKI BETTINA
Published: April 2010

To gain new insights into the signalling mechanisms of the grey mould Botrytis cinerea, which causes several pre‐ and post‐harvest diseases on a variety of host plants, we cloned, sequenced and functionally characterized a gene, btp1, encoding a novel 391‐amino acid transmembrane protein. The protein BTP1 shows similarity to the transmembrane protein pth11, which is essential for appressorium formation and successful colonization of plant tissue in the rice blast fungus Magnaporthe grisea. Analyses of the deduced amino acid sequence of btp1 predicted a seven α‐helical transmembrane topology, which is known to be typical for G protein‐coupled receptors (GPCRs) and therefore the protein is thought to play a role in mediation of extracellular signals to intracellular effectors. The gene is located next to the gene bcgstII encoding a new putative glutathione S‐transferase, and both genes are transcribed in opposite directions from the same promoter. BcGSTII shows similarity to the glutathione S‐transferase GSTII of Schizosaccharomyces pombe, a protein thought to be involved in detoxification of several antifungal drugs. From the sequence similarity of BTP1 to GPCRs, and its expression in planta, we suggested that it might play a role in mediation of plant signals and therefore in pathogenicity. However, targeted gene replacement of btp1 did not result in a phenotype markedly affecting either pathogenicity or sensitivity to chemical stress when compared with the wild‐type strain; however, the ten‐fold dilution of conidial suspension used for the pathogenicity assay resulted in slight reduction of virulence. Visible symptom development of the mutants on bean plants was also different from the wild‐type. The brownish ring, which appears at the margin of secondary lesions in wild‐type infections, was brighter and almost absent in Δbtp1 mutants. Interestingly, deletion of btp1 not only affected the expression of the physically linked bcgstII gene, but in addition the expression of the other two GST‐encoding genes in B. cinerea for bcgstI was down‐regulated, bcgstII was slightly up‐regulated and bcgstIII was strongly up‐regulated in the mutant.
Chlorovirus: a genus of Phycodnaviridae that infects certain chlorella‐like green algae
Authors: KANG MING , DUNIGAN DAVID D. , VAN ETTEN JAMES L.
Published: April 2010

Taxonomy: Chlorella viruses are assigned to the family Phycodnaviridae, genusChlorovirus, and are divided into three species:ChlorellaNC64A viruses,ChlorellaPbi viruses andHydra viridis Chlorellaviruses. Chlorella viruses are large, icosahedral, plaque‐forming, dsDNA viruses that infect certain unicellular, chlorella‐like green algae. The type member isParamecium bursariachlorella virus 1 (PBCV‐1).

Physical properties: Chlorella virus particles are large (molecular weight ∼1 × 109 Da) and complex. The virion of PBCV‐1 contains more than 100 different proteins; the major capsid protein, Vp54, comprises ∼40% of the virus protein. Cryoelectron microscopy and three‐dimensional image reconstruction of PBCV‐1 virions indicate that the outer glycoprotein‐containing capsid shell is icosahedral and surrounds a lipid bilayered membrane. The diameter of the viral capsid ranges from 1650 Å along the two‐ and three‐fold axes to 1900 Å along the five‐fold axis. The virus contains 5040 copies of Vp54, and the triangulation number is 169. The PBCV‐1 genome is a linear, 330 744‐bp, non‐permuted dsDNA with covalently closed hairpin ends. The PBCV‐1 genome contains ∼375 protein‐encoding genes and 11 tRNA genes. About 50% of the protein‐encoding genes match proteins in the databases.

Hosts: ChlorellaNC64A andChlorellaPbi, the hosts for NC64A viruses and Pbi viruses, respectively, are endosymbionts of the protozoanParamecium bursaria. However, they can be grown in the laboratory free of both the paramecium and the virus. These two chlorella species are hosts to viruses that have been isolated from fresh water collected around the world. The host for hydra chlorella virus, a symbiotic chlorella fromHydra viridis, has not been grown independently of its host; thus the virus can only be obtained from chlorella cells freshly released from hydra.
Seasonal diet preferences of black rhinoceros in three arid South African National Parks
Authors: Buk Kenneth Gregers , Knight Mike H.
Published: April 2010

Black rhinoceros diet and browse availability was investigated in Augrabies Falls (AFNP), Karoo (KRNP) and Vaalbos National Parks (VNP) in South Africa. Rhino tracks were followed and 18,804 standard bite volumes recorded. Browse availability of each plant species was recorded by measuring 14,800 plants and calculating reachable browse volume. The diet comprised 51, 53 and 41 plant species in AFNP, KRNP and VNP, respectively, but three species accounted for more than 65% of the diet in each park, making diet less diverse than available browse in AFNP and KRNP. Browse availability explained 14%, 15% and 52% of diet selection in AFNP, KRNP and VNP, with consumption of most plant species significantly different from availability. A few plant species were so highly preferred that browsing intensities were unsustainable, while some common species were totally rejected. Pressure on the eaten browse averaged 4.4%, 14.5% and 1.3% annually of the volume in AFNP, KRNP and VNP. In the dry season, there was a two to sevenfold increase in browsing pressure on species with actively photosynthesizing tissues. A few key species, includingMonechmaandZygophyllumspecies, were identified as potential early warning indicators of black rhino browsing impact.
Survey of childhood cancer survivors who stopped follow‐up physician visits
Authors: Maeda Naoko , Horibe Keizo , Kato Koji , Kojima Seiji , Tsurusawa Masahito
Published: April 2010

Background:  Childhood cancer cure rates have increased remarkably; however, survivors face an increased risk of morbidity and mortality. Survivors may benefit from anticipatory guidance and periodic surveillance to minimize morbidity and mortality.

Methods:  Subjects included 114 5‐year survivors of childhood cancer who were diagnosed and treated in three hospitals in Nagoya between 1975 and 2001 and who stopped follow‐up physician visits during the preceding 2 years. We conducted a survey of their socioeconomic status, knowledge about their diagnosis and late effects of treatment received, and current hospital attendance patterns.

Results:  Eighty‐eight of 114 subjects replied. Sixty‐six survivors knew about their disease, but only 26 knew about possible late effects of cancer treatment. Although 78 respondents indicated they were healthy and had no trouble in their daily lives, 46 had at least one chronic condition. In response to the question regarding why they did not visit the hospital regularly, many subjects responded that the physician‐in‐charge told them they did not need to visit the hospital anymore; others thought it was unnecessary to consult a physician because they were in good health.

Conclusions:  Some cancer survivors who stop follow‐up physician visits may still be suffering from cancer‐related illnesses. Both survivor‐related and physician‐related barriers contribute to cancer survivors stopping follow‐up physician visits. To ensure that survivors undergo appropriate follow‐up visits, it is necessary to educate survivors, their families, and medical staff about the late effects of cancer and its treatment and the importance of long‐term follow up.