@article{17765, abstract = {Scaling relations among galaxy cluster observables, which will become available in large future samples of galaxy clusters, could be used to constrain not only cluster structure, but also cosmology. We study the utility of this approach, employing a physically motivated parametric model to describe cluster structure and applying it to the expected relation between the Sunyaev–Zel'dovich decrement (Sν) and the emission-weighted X-ray temperature (Tew). The slope and normalization of the entropy profile, the concentration of the dark matter potential, the pressure at the virial radius and the level of non-thermal pressure support as well as the mass and redshift dependence of these quantities are described by free parameters. With a suitable choice of fiducial parameter values, the cluster model satisfies several existing observational constraints. We employ a Fisher matrix approach to estimate the joint errors on cosmological and cluster structure parameters from a measurement of Sν versus Tew in a future survey. We find that different cosmological parameters affect the scaling relation differently: predominantly through the baryon fraction (Ωm and Ωb), the virial overdensity (w0 and wa for low-z clusters) and the angular diameter distance (w0 and wa for high-z clusters; ΩDE and h). We find that the cosmology constraints from the scaling relation are comparable to those expected from the number counts (dN/dz) of the same clusters. The scaling-relation approach is relatively insensitive to selection effects and it offers a valuable consistency check; combining the information from the scaling relation and dN/dz is also useful to break parameter degeneracies and help disentangle cluster physics from cosmology. Our work suggests that scaling relations should be a useful component in extracting cosmological information from large future cluster surveys.}, author = {Shang, Cien and Haiman, Zoltán and Verde, Licia}, issn = {0035-8711}, journal = {Monthly Notices of the Royal Astronomical Society}, number = {2}, pages = {1085--1104}, publisher = {Oxford University Press}, title = {{Probing cosmology and galaxy cluster structure with the Sunyaev-Zel'dovich decrement versus X-ray temperature scaling relation}}, doi = {10.1111/j.1365-2966.2009.15527.x}, volume = {400}, year = {2009}, } @article{17769, abstract = {Arguably the best hope of understanding the tail end of the re-ionization of the intergalactic medium (IGM) at redshift z > 6 is through the detection and characterization of the Gunn–Peterson damping wing absorption of the IGM in bright quasar spectra. However, the use of quasar spectra to measure the IGM damping wing requires a model of the quasar's intrinsic Lyman α emission line. Here we quantify the uncertainties in the intrinsic line shapes, and how those uncertainties affect the determination of the IGM neutral fraction. We have assembled a catalogue of high-resolution Hubble Space Telescope spectra of the emission lines of unobscured low-redshift quasars, and have characterized the variance in the shapes of their lines. We then add simulated absorption from the high-redshift IGM to these quasar spectra in order to determine the corresponding uncertainties in re-ionization constraints using current and future samples of z > 6 quasar spectra. We find that, if the redshift of the Lyman α emission line is presumed to coincide with the systemic redshift determined from metal lines, the inferred IGM neutral fraction is systematically biased to low values due to a systematic blueshift of the Lyman α line relative to the metal lines. If a similar blueshift persists in quasars at z > 6, this bias strengthens previous claims of a significant neutral hydrogen fraction at z≈ 6. The bias can be reduced by including a Lyman α blueshift in the modelling procedure, or by excising wavelengths near the Lyman α line centre from the modelling. Intrinsic Lyman α line shape variations still induce significant scatter in the inferred xIGM values. Nevertheless, this scatter still allows a robust distinction between a highly ionized (xIGM∼ 10−3) and a neutral (xIGM= 1) IGM with even a few bright quasars. We conclude that if the variations of the intrinsic Lyman α emission line shapes in high-z quasars are similar to those at low-z, this variation will not limit the usefulness of quasar spectra in probing re-ionization.}, author = {Kramer, R. H. and Haiman, Zoltán}, issn = {0035-8711}, journal = {Monthly Notices of the Royal Astronomical Society}, number = {3}, pages = {1493--1511}, publisher = {Oxford University Press}, title = {{Probing re-ionization with quasar spectra: The impact of the intrinsic Lyman α emission line shape uncertainty}}, doi = {10.1111/j.1365-2966.2009.15552.x}, volume = {400}, year = {2009}, } @article{17771, abstract = {Cold dark matter (CDM) hierarchical structure formation models predict the existence of large-scale accretion shocks between the virial and turnaround radii of clusters of galaxies. Kocsis et al. suggest that the Sunyaev–Zel'dovich signal associated with such shocks might be observable with the next generation radio interferometer, ALMA (Atacama Large Millimeter Array). We study the three-dimensional distribution of accretion shocks around individual clusters of galaxies drawn from adaptive mesh refinement (AMR) and smoothed particle hydrodynamics simulations of ΛCDM (dark energy dominated CDM) models. In relaxed clusters, we find two distinct sets of shocks. One set ("virial shocks"), with Mach numbers of 2.5–4, is located at radii 0.9–1.3 Rvir, where Rvir is the spherical infall estimate of the virial radius, covering about 40%–50% of the total surface area around clusters at these radii. Another set of stronger shocks ("external shocks") is located farther out, at about 3 Rvir, with large Mach numbers (≈100), covering about 40%–60% of the surface area. We simulate SZ surface brightness maps of relaxed massive galaxy clusters drawn from high-resolution AMR runs, and conclude that ALMA should be capable of detecting the virial shocks in massive clusters of galaxies. More simulations are needed to improve estimates of astrophysical noise and to determine optimal observational strategies.}, author = {Molnar, Sandor M. and Hearn, Nathan and Haiman, Zoltán and Bryan, Greg and Evrard, August E. and Lake, George}, issn = {0004-637X}, journal = {The Astrophysical Journal}, number = {2}, pages = {1640--1656}, publisher = {American Astronomical Society}, title = {{Accretion shocks in clusters of galaxies and their SZ signature from cosmological simulations}}, doi = {10.1088/0004-637x/696/2/1640}, volume = {696}, year = {2009}, } @article{17772, abstract = {We utilize the local velocity dispersion function (VDF) of spheroids, together with their inferred age distributions, to predict the VDF at higher redshifts (0 < z lsim 6), under the assumption that (1) most of the stars in each nearby spheroid formed in a single episode and, (2) the velocity dispersion σ remained nearly constant afterward. We assume further that a supermassive BH forms concurrently with the stars, and within ±1 Gyr of the formation of the potential well of the spheroid, and that the relation between the mass of the BH and host velocity dispersion maintains the form M BH vprop σβ with β ≈ 4, but with the normalization allowed to evolve with redshift as vprop(1 + z)α. We compute the BH mass function associated with the VDF at each redshift, and compare the accumulated total BH mass density with that inferred from the integrated quasar luminosity function (LF; the so-called Sołtan argument). This comparison is insensitive to the assumed duty cycle or Eddington ratio of quasar activity, and we find that the match between the two BH mass densities favors a relatively mild redshift evolution, with α ~ 0.33, with a positive evolution as strong as α gsim 1.3 excluded at more than 99% confidence level. A direct match between the characteristic BH mass in the VDF-based and quasar LF-based BH mass functions also yields a mean Eddington ratio of λ ~ 0.5-1 that is roughly constant within 0 lsim z lsim 3. A strong positive evolution in the M BH-σ relation is still allowed by the data if galaxies increase, on average, their velocity dispersions since the moment of formation due to dissipative processes. If we assume that the mean velocity dispersion of the host galaxies evolves as σ(z) = σ(0) × (1 + z)-γ, we find a lower limit of γ gsim 0.23 for α gsim 1.5. The latter estimate represents an interesting constraint for galaxy evolution models and can be tested through hydro simulations. This dissipative model, however, also implies a decreasing λ at higher z, at variance with several independent studies.}, author = {Shankar, Francesco and Bernardi, Mariangela and Haiman, Zoltán}, issn = {0004-637X}, journal = {The Astrophysical Journal}, number = {2}, pages = {867--878}, publisher = {American Astronomical Society}, title = {{The evolution of the mbh-σ relation inferred from the age distribution of local early-type galaxies and active galactic nuclei evolution}}, doi = {10.1088/0004-637x/694/2/867}, volume = {694}, year = {2009}, } @article{17782, abstract = {Ultraviolet (UV) radiation from early astrophysical sources could have a large impact on subsequent star formation in nearby protogalaxies, and in general on the progress of cosmological reionization. Theoretical arguments based on the absence of metals in the early Universe suggest that the first stars were likely massive, bright, yet short-lived, with lifetimes of a few million years. Here we study the radiative feedback arising from such stars using hydrodynamical simulations with transient UV backgrounds (UVBs) and persistent Lyman–Werner backgrounds (LWBs) of varying intensity. We extend our prior work in Mesinger et al., by studying a more typical region whose protogalaxies form at lower redshifts, z∼ 13–20, in the epoch likely preceding the bulk of reionization. We confirm our previous results that feedback in the relic H ii regions resulting from such transient radiation is itself transient. Feedback effects dwindle away after ∼30 per cent of the Hubble time, and the same critical specific intensity of JUV∼ 0.1 × 10^−21 erg s^−1 cm^−2 Hz^−1 sr^−1 separates positive and negative feedback regimes. This suggests that overall feedback is fairly insensitive to the large-scale environment, overdensity and redshift-dependent halo parameters, and can accurately be modelled in this regime with just the intensity of the impinging UVB. Additionally, we discover a second episode of eventual positive feedback in haloes which have not yet collapsed when their progenitor regions were exposed to the transient UVB. When exposed to the transient UVB, this gas suffers relatively little density depletion but a significant enhancement of the molecular hydrogen abundance, thus resulting in net positive feedback. This eventual positive feedback appears in all runs, regardless of the strength of the UVB. However, this feedback regime is very sensitive to the presence of Lyman–Werner radiation, and notable effects disappear under fairly modest background intensities of JLW≳ 10^−3× 10^−21 erg s^−1 cm^−2 Hz^−1 sr^−1, assuming the region is optically thin for LW photons. Nevertheless, when exposed to the same LWB, haloes inside relic H ii regions always have a higher H2 abundance and shorter cooling times than haloes outside relic H ii regions, allowing gas to cool faster once it finally begins to collapse on to the halo. We conclude that UV radiative feedback in relic H ii regions, although a complicated process, seems unlikely to have a major impact on the progress of cosmological reionization, provided that present estimates of the lifetime and luminosity of a Population III star are accurate. More likely is that the build-up of the LWB ultimately governs the feedback strength until a persistent UV background can be established.}, author = {Mesinger, Andrei and Bryan, Greg L. and Haiman, Zoltán}, issn = {0035-8711}, journal = {Monthly Notices of the Royal Astronomical Society}, number = {3}, pages = {1650--1662}, publisher = {Oxford University Press}, title = {{Relic H ii regions and radiative feedback at high redshifts}}, doi = {10.1111/j.1365-2966.2009.15404.x}, volume = {399}, year = {2009}, } @article{17797, abstract = {It is well known that an initial population of seed black holes (BHs), formed in the nuclei of low-mass galaxies at high redshift, can simultaneously explain, through their subsequent growth by mergers and accretion, both the observed evolution of the quasar luminosity function (LF) and the distribution of remnant supermassive black hole (SMBH) masses measured in local galactic nuclei. Here we consider three very different initial conditions for this scenario: models in which initial seed BHs form in either all, or only a small fraction (fbh = 0.1 or 0.01) of high-redshift dark matter halos (with Mhalo = 5 × 109 M☉ at z = 6–10). We show that with a suitable and relatively minor adjustment of two global physical parameters (the radiative efficiency and mass accretion time-scale of quasar episodes), models with fbh ≈ 0.1 and 1 can accurately reproduce the observed quasar LF at redshifts 0 < z ≲ 6, as well as the remnant SMBH mass function at z = 0. However, SMBHs remain rare, and the normalization of the high-z quasar LF and the local SMBH mass function are both significantly underpredicted, if fbh ≲ 0.01. We also show that the merger history of SMBHs, in the mass range detectable by the future Laser Interferometer Space Antenna (LISA) instrument, generically looks different as fbh is varied; this should allow LISA to deliver useful constraints on otherwise degenerate models.}, author = {Lippai, Zoltán and Frei, Zsolt and Haiman, Zoltán}, issn = {1538-4357}, journal = {The Astrophysical Journal}, number = {1}, pages = {360--368}, publisher = {American Astronomical Society}, title = {{On the occupation fraction of seed black holes in high-redshift dark matter halos}}, doi = {10.1088/0004-637x/701/1/360}, volume = {701}, year = {2009}, } @article{17805, abstract = {We report on the detection by Swift of GRB 080913, and subsequent optical/near-infrared follow-up observations by GROND, which led to the discovery of its optical/NIR afterglow and the recognition of its high-z nature via the detection of a spectral break between the i' and z' bands. Spectroscopy obtained at the ESO-VLT revealed a continuum extending down to λ = 9400 Å, and zero flux for 7500 Å<λ < 9400 Å, which we interpret as the onset of a Gunn–Peterson trough at z = 6.695± 0.025 (95.5% confidence level), making GRB 080913 the highest-redshift gamma-ray burst (GRB) to date, and more distant than the highest-redshift QSO. We note that many redshift indicators that are based on promptly available burst or afterglow properties have failed for GRB 080913. We report on our follow-up campaign and compare the properties of GRB 080913 with bursts at lower redshift. In particular, since the afterglow of this burst is fainter than typical for GRBs, we show that 2 m class telescopes can identify most high-redshift GRBs.}, author = {Greiner, J. and Krühler, T. and Fynbo, J. P. U. and Rossi, A. and Schwarz, R. and Klose, S. and Savaglio, S. and Tanvir, N. R. and McBreen, S. and Totani, T. and Zhang, B. B. and Wu, X. F. and Watson, D. and Barthelmy, S. D. and Beardmore, A. P. and Ferrero, P. and Gehrels, N. and Kann, D. A. and Kawai, N. and Yoldaş, A. Küpcü and Mészáros, P. and Milvang-Jensen, B. and Oates, S. R. and Pierini, D. and Schady, P. and Toma, K. and Vreeswijk, P. M. and Yoldaş, A. and Zhang, B. and Afonso, P. and Aoki, K. and Burrows, D. N. and Clemens, C. and Filgas, R. and Haiman, Zoltán and Hartmann, D. H. and Hasinger, G. and Hjorth, J. and Jehin, E. and Levan, A. J. and Liang, E. W. and Malesani, D. and Pyo, T.-S. and Schulze, S. and Szokoly, G. and Terada, K. and Wiersema, K.}, issn = {1538-4357}, journal = {The Astrophysical Journal}, number = {2}, pages = {1610--1620}, publisher = {American Astronomical Society}, title = {{GRB 080913 at redshift 6.7}}, doi = {10.1088/0004-637x/693/2/1610}, volume = {693}, year = {2009}, } @article{7751, abstract = {This work demonstrates that environmental conditions experienced by individuals can shape their development and affect the stability of genetic associations. The implication of this observation is that the environmental response may influence the evolution of traits in the wild. Here, we examined how the genetic architecture of a suite of sexually dimorphic traits changed as a function of environmental conditions in an unmanaged population of Soay sheep (Ovis aries) on the island of Hirta, St. Kilda, northwest Scotland. We examined the stability of phenotypic, genetic, and environmental (residual) covariance in males during the first year of life between horn length, body weight, and parasite load in environments of different quality. We then examined the same covariance structures across environments within and between the adult sexes. We found significant genotype-by-environment interactions for lamb male body weight and parasite load, leading to a change in the genetic correlation among environments. Horn length was genetically correlated with body weight in males but not females and the genetic correlation among traits within and between the sexes was dependent upon the environmental conditions experienced during adulthood. Genetic correlations were smaller in more favorable environmental conditions, suggesting that in good environments, loci are expressed that have sex-specific effects. The reduction in genetic correlation between the sexes may allow independent evolutionary trajectories for each sex. This study demonstrates that the genetic architecture of traits is not stable under temporally varying environments and highlights the fact that evolutionary processes may depend largely upon ecological conditions. ENVIRONMENTAL heterogeneity has long been recognized as an important factor influencing the evolution of fitness-related traits in the wild (Roff 2002). The evolution of a trait depends upon the selection upon it, underlying genetic variation, and to a large degree the genetic relationships with other traits (Lynch and Walsh 1998). There is evidence that selection can vary considerably from year to year (Price et al. 1984; Robinson et al. 2008) and genetic variability in quantitative traits can change in response to environmental conditions (Hoffmann and Merilä 1999; Charmantier and Garant 2005). However, we know surprisingly little about the influence of environmental conditions on genetic correlations between traits in wild populations. Laboratory evidence suggests that the environment may influence genetic relationships between traits (Sgrò and Hoffmann 2004), but estimates obtained in a controlled or in an arbitrary range of conditions show a lack of concordance with those obtained in wild habitats (Conner et al. 2003). As a result, laboratory and environment-specific estimates of genetic correlations can make predictions for a trait's evolution, but these are valid only for the environment in which they were measured. Therefore, at present, it is difficult to generalize about the evolution of a trait that is expressed in populations that experience variable environmental conditions (Steppan et al. 2002). The influence of changing environmental conditions on the G matrix (the matrix of additive genetic variance and covariances corresponding to a set of traits) has been the focus of theoretical quantitative genetic studies (e.g., Jones et al. 2003). There is evidence of genotype-by-environment interaction for many traits expressed in wild populations (Charmantier and Garant 2005) and thus we may also expect that associations between traits may depend upon the environmental conditions encountered by an individual. Genetic correlations among traits may arise from pleiotropy, where a given locus affects more than one trait (Cheverud 1988; Lynch and Walsh 1998), which may limit the potential for those traits to evolve independently. There has recently been much interest in assessing genetic correlations between the sexes (Rice and Chippindale 2001; Foerster et al. 2007; Poissant et al. 2008), but all of these predictions have also been made in average environmental conditions. For sexually dimorphic traits, expectations of between-sex genetic correlations are unclear (Lande 1980; Badyaev 2002). We might expect that the genetic determination of a trait and the patterns of genetic covariance between traits may differ both within and between the sexes, producing the differences in trait growth that are commonly observed (Lande 1980; Badyaev 2002; Roff 2002), but so far evidence suggests that genetic expression in both sexes is influenced by the same developmental pathway (Roff 2002; Jensen et al. 2003; Parker and Garant 2005). However, to our knowledge, no study has yet determined whether genetic correlations, both within and between the sexes, vary across gradients of the environmental conditions encountered by individuals in the wild (Garant et al. 2008). This study aims to assess the stability of phenotypic, genetic, and environmental (residual) associations between traits, within and between the sexes, across a range of environmental conditions experienced by a wild population. We focus on the traits of horn length, body weight, and parasite load in a feral population of Soay sheep (Ovis aries) from the island of Hirta, St. Kilda, United Kingdom. Weather conditions, population density, and consequently resource availability fluctuate from year to year, providing substantial differences between individuals in the environments they experience and thus their survival rates (Clutton-Brock and Pemberton 2004). These varying conditions, combined with a large pedigree and extensive repeated morphological measures, provide an excellent opportunity to assess the potential effects of environmental heterogeneity on genetic architecture of traits. Previous studies on this population have shown additive genetic variance for many morphological traits (Milner et al. 2000; Coltman et al. 2001; Wilson et al. 2005), genetic correlations between traits (Coltman et al. 2001), and genotype-by-environment interactions for birth weight (Wilson et al. 2006). Here we apply a random regression animal model approach to assess the extent to which quantitative genetic parameters of a range of morphological traits measured during life vary as a function of environmental conditions. We then extend this methodology to the multivariate case, testing whether the phenotypic covariance structure, and the underlying G matrix, depends on the environmental conditions experienced. Since the traits considered here are known to be sexually dimorphic and there are differences in trait growth and survival across ages, we look at sex-specific traits in lambs and then across all ages.}, author = {Robinson, Matthew Richard and Wilson, Alastair J. and Pilkington, Jill G. and Clutton-Brock, Tim H. and Pemberton, Josephine M. and Kruuk, Loeske E. B.}, issn = {0016-6731}, journal = {Genetics}, number = {4}, pages = {1639--1648}, publisher = {Genetics Society of America}, title = {{The impact of environmental heterogeneity on genetic architecture in a wild population of soay sheep}}, doi = {10.1534/genetics.108.086801}, volume = {181}, year = {2009}, } @article{8026, abstract = {Recent theoretical work has provided a basic understanding of signal propagation in networks of spiking neurons, but mechanisms for gating and controlling these signals have not been investigated previously. Here we introduce an idea for the gating of multiple signals in cortical networks that combines principles of signal propagation with aspects of balanced networks. Specifically, we studied networks in which incoming excitatory signals are normally cancelled by locally evoked inhibition, leaving the targeted layer unresponsive. Transmission can be gated 'on' by modulating excitatory and inhibitory gains to upset this detailed balance. We illustrate gating through detailed balance in large networks of integrate-and-fire neurons. We show successful gating of multiple signals and study failure modes that produce effects reminiscent of clinically observed pathologies. Provided that the individual signals are detectable, detailed balance has a large capacity for gating multiple signals.}, author = {Vogels, Tim P and Abbott, L F}, issn = {1097-6256}, journal = {Nature Neuroscience}, number = {4}, pages = {483--491}, publisher = {Springer Nature}, title = {{Gating multiple signals through detailed balance of excitation and inhibition in spiking networks}}, doi = {10.1038/nn.2276}, volume = {12}, year = {2009}, } @article{8474, abstract = {Hydrogen bonds are ubiquitous interactions in proteins, and are important for their folding and functionality. Scalar coupling constants across hydrogen bonds in the protein backbone, some as small as 0.5 Hz, can be directly measured in the solid state by NMR spectroscopy (see figure). The nuclei on both sides of the hydrogen bond can be identified and the size of the coupling constant can be measured accurately.}, author = {Schanda, Paul and Huber, Matthias and Verel, René and Ernst, Matthias and Meier, Beat H.}, issn = {1433-7851}, journal = {Angewandte Chemie International Edition}, keywords = {General Chemistry, Catalysis}, number = {49}, pages = {9322--9325}, publisher = {Wiley}, title = {{Direct detection of 3hJN' hydrogen-bond scalar couplings in proteins by solid-state NMR spectroscopy}}, doi = {10.1002/anie.200904411}, volume = {48}, year = {2009}, } @article{8475, author = {Schanda, Paul}, issn = {0079-6565}, journal = {Progress in Nuclear Magnetic Resonance Spectroscopy}, number = {3}, pages = {238--265}, publisher = {Elsevier}, title = {{Fast-pulsing longitudinal relaxation optimized techniques: Enriching the toolbox of fast biomolecular NMR spectroscopy}}, doi = {10.1016/j.pnmrs.2009.05.002}, volume = {55}, year = {2009}, } @article{8476, abstract = {Atomic-resolution information on the structure and dynamics of nucleic acids is essential for a better understanding of the mechanistic basis of many cellular processes. NMR spectroscopy is a powerful method for studying the structure and dynamics of nucleic acids; however, solution NMR studies are currently limited to relatively small nucleic acids at high concentrations. Thus, technological and methodological improvements that increase the experimental sensitivity and spectral resolution of NMR spectroscopy are required for studies of larger nucleic acids or protein−nucleic acid complexes. Here we introduce a series of imino-proton-detected NMR experiments that yield an over 2-fold increase in sensitivity compared to conventional pulse schemes. These methods can be applied to the detection of base pair interactions, RNA−ligand titration experiments, measurement of residual dipolar 15N−1H couplings, and direct measurements of conformational transitions. These NMR experiments employ longitudinal spin relaxation enhancement techniques that have proven useful in protein NMR spectroscopy. The performance of these new experiments is demonstrated for a 10 kDa TAR-TAR*GA RNA kissing complex and a 26 kDa tRNA.}, author = {Farjon, Jonathan and Boisbouvier, Jérôme and Schanda, Paul and Pardi, Arthur and Simorre, Jean-Pierre and Brutscher, Bernhard}, issn = {0002-7863}, journal = {Journal of the American Chemical Society}, number = {24}, pages = {8571--8577}, publisher = {American Chemical Society}, title = {{Longitudinal-relaxation-enhanced NMR experiments for the study of nucleic acids in solution}}, doi = {10.1021/ja901633y}, volume = {131}, year = {2009}, } @article{8477, abstract = {An optimized NMR experiment that combines the advantages of methyl-TROSY and SOFAST-HMQC has been developed. It allows the recording of high quality methyl 1H−13C correlation spectra of protein assemblies of several hundreds of kDa in a few seconds. The SOFAST-methyl-TROSY-based experiment offers completely new opportunities for the study of structural and dynamic changes occurring in molecular nanomachines while they perform their biological function in vitro.}, author = {Amero, Carlos and Schanda, Paul and Durá, M. Asunción and Ayala, Isabel and Marion, Dominique and Franzetti, Bruno and Brutscher, Bernhard and Boisbouvier, Jérôme}, issn = {0002-7863}, journal = {Journal of the American Chemical Society}, number = {10}, pages = {3448--3449}, publisher = {American Chemical Society}, title = {{Fast two-dimensional NMR spectroscopy of high molecular weight protein assemblies}}, doi = {10.1021/ja809880p}, volume = {131}, year = {2009}, } @article{8478, abstract = {Allosteric regulation is an effective mechanism of control in biological processes. In allosteric proteins a signal originating at one site in the molecule is communicated through the protein structure to trigger a specific response at a remote site. Using NMR relaxation dispersion techniques we directly observe the dynamic process through which the KIX domain of CREB binding protein communicates allosteric information between binding sites. KIX mediates cooperativity between pairs of transcription factors through binding to two distinct interaction surfaces in an allosteric manner. We show that binding the activation domain of the mixed lineage leukemia (MLL) transcription factor to KIX induces a redistribution of the relative populations of KIX conformations toward a high-energy state in which the allosterically activated second binding site is already preformed, consistent with the Monod−Wyman−Changeux (WMC) model of allostery. The structural rearrangement process that links the two conformers and by which allosteric information is communicated occurs with a time constant of 3 ms at 27 °C. Our dynamic NMR data reveal that an evolutionarily conserved network of hydrophobic amino acids constitutes the pathway through which information is transmitted.}, author = {Brüschweiler, Sven and Schanda, Paul and Kloiber, Karin and Brutscher, Bernhard and Kontaxis, Georg and Konrat, Robert and Tollinger, Martin}, issn = {0002-7863}, journal = {Journal of the American Chemical Society}, number = {8}, pages = {3063--3068}, publisher = {American Chemical Society}, title = {{Direct observation of the dynamic process underlying allosteric signal transmission}}, doi = {10.1021/ja809947w}, volume = {131}, year = {2009}, } @article{8479, abstract = {Multidimensional NMR spectroscopy is a well-established technique for the characterization of structure and fast-time-scale dynamics of highly populated ground states of biological macromolecules. The investigation of short-lived excited states that are important for molecular folding, misfolding and function, however, remains a challenge for modern biomolecular NMR techniques. Off-equilibrium real-time kinetic NMR methods allow direct observation of conformational or chemical changes by following peak positions and intensities in a series of spectra recorded during a kinetic event. Because standard multidimensional NMR methods required to yield sufficient atom-resolution are intrinsically time-consuming, many interesting phenomena are excluded from real-time NMR analysis. Recently, spatially encoded ultrafast 2D NMR techniques have been proposed that allow one to acquire a 2D NMR experiment within a single transient. In addition, when combined with the SOFAST technique, such ultrafast experiments can be repeated at high rates. One of the problems detected for such ultrafast protein NMR experiments is related to the heteronuclear decoupling during detection with interferences between the pulses and the oscillatory magnetic field gradients arising in this scheme. Here we present a method for improved ultrafast data acquisition yielding higher signal to noise and sharper lines in single-scan 2D NMR spectra. In combination with a fast-mixing device, the recording of 1H–15N correlation spectra with repetition rates of up to a few Hertz becomes feasible, enabling real-time studies of protein kinetics occurring on time scales down to a few seconds.}, author = {Gal, Maayan and Kern, Thomas and Schanda, Paul and Frydman, Lucio and Brutscher, Bernhard}, issn = {0925-2738}, journal = {Journal of Biomolecular NMR}, keywords = {Spectroscopy, Biochemistry}, pages = {1--10}, publisher = {Springer Nature}, title = {{An improved ultrafast 2D NMR experiment: Towards atom-resolved real-time studies of protein kinetics at multi-Hz rates}}, doi = {10.1007/s10858-008-9284-9}, volume = {43}, year = {2009}, } @article{8508, abstract = {We study generic unfoldings of homoclinic tangencies of two-dimensional area-preserving diffeomorphisms (conservative New house phenomena) and show that they give rise to invariant hyperbolic sets of arbitrarily large Hausdorff dimension. As applications, we discuss the size of the stochastic layer of a standard map and the Hausdorff dimension of invariant hyperbolic sets for certain restricted three-body problems. We avoid involved technical details and only concentrate on the ideas of the proof of the presented results.}, author = {Gorodetski, Anton and Kaloshin, Vadim}, issn = {0081-5438}, journal = {Proceedings of the Steklov Institute of Mathematics}, keywords = {Mathematics (miscellaneous)}, number = {1}, pages = {76--90}, publisher = {Springer Nature}, title = {{Conservative homoclinic bifurcations and some applications}}, doi = {10.1134/s0081543809040063}, volume = {267}, year = {2009}, } @article{88, abstract = {We have developed a tunable source of Mie scale microdroplet aerosols that can be used for the generation of energetic ions. To demonstrate this potential, a terawatt Ti: Al2 O3 laser focused to 2×10 19 W/cm2 was used to irradiate heavy water (D2 O) aerosols composed of micron-scale droplets. Energetic deuterium ions, which were generated in the laser-droplet interaction, produced deuterium-deuterium fusion with approximately 2×10^3 fusion neutrons measured per joule of incident laser energy. }, author = {Higginbotham, Andrew P and Semonin, Octavi and Bruce, S and Chan, C and Maindi, M and Donnelly, Tom and Maurer, M and Bang, Woosuk and Churina, I.V and Osterholz, Jens and Kim, I and Bernstein, Aaron and Ditmire, Todd}, journal = {Review of Scientific Instruments}, number = {6}, publisher = {American Institute of Physics}, title = {{Generation of Mie size microdroplet aerosols with applications in laser-driven fusion experiments}}, doi = {10.1063/1.3155302}, volume = {80}, year = {2009}, } @article{908, abstract = {Although some data link archaeal and eukaryotic translation, the overall mechanism of protein synthesis in archaea remains largely obscure. Both archaeal (aRF1) and eukaryotic (eRF1) single release factors recognize all three stop codons. The archaeal genus Methanosarcinaceae contains two aRF1 homologs, and also uses the UAG stop to encode the 22nd amino acid, pyrrolysine. Here we provide an analysis of the last stage of archaeal translation in pyrrolysine-utilizing species. We demonstrated that only one of two Methanosarcina barkeri aRF1 homologs possesses activity and recognizes all three stop codons. The second aRF1 homolog may have another unknown function. The mechanism of pyrrolysine incorporation in the Methanosarcinaceae is discussed.}, author = {Alkalaeva, Elena Z and Eliseev, Boris D and Ambrogelly, Alexandre and Vlasov, Peter K and Fyodor Kondrashov and Gundllapalli, Sarath B and Frolova, Ludmila Y and Söll, Dieter G and Kisselev, Lev L}, journal = {FEBS Letters}, number = {21}, pages = {3455 -- 3460}, publisher = {Elsevier}, title = {{Translation termination in pyrrolysine-utilizing archaea}}, doi = {10.1016/j.febslet.2009.09.044}, volume = {583}, year = {2009}, } @article{9147, abstract = {As part of an ongoing effort to develop a parameterization of wave-induced abyssal mixing, the authors derive an heuristic model for nonlinear wave breaking and energy dissipation associated with internal tides. Then the saturation and dissipation of internal tides for idealized and observed topography samples are investigated. One of the main results is that the wave-induced mixing could be more intense and more confined to the bottom than previously assumed in numerical models. Furthermore, in this model wave breaking and mixing clearly depend on the small scales of the topography below 10 km or so, which is below the current resolution of global bathymetry. This motivates the use of a statistical approach to represent the unresolved topography when addressing the role of internal tides in mixing the deep ocean.}, author = {Muller, Caroline J and Bühler, Oliver}, issn = {1520-0485}, journal = {Journal of Physical Oceanography}, keywords = {Oceanography}, number = {9}, pages = {2077--2096}, publisher = {American Meteorological Society}, title = {{Saturation of the internal tides and induced mixing in the abyssal ocean}}, doi = {10.1175/2009jpo4141.1}, volume = {39}, year = {2009}, } @article{9148, abstract = {Several observational studies have shown a tight relationship between tropical precipitation and column‐integrated water vapor. We show that the observed relationship in the tropics between column‐integrated water vapor, precipitation, and its variance can be qualitatively reproduced by a simple and physically motivated two‐layer model. It has previously been argued that features of this relationship could be explained by analogy with the theory of continuous phase transitions. Instead, our model explicitly assumes that the onset of precipitation is governed by a stability threshold involving boundary‐layer water vapor. This allows us to explain the precipitation‐humidity relationship over a broader range of water vapor values, and may explain the observed temperature dependence of the relationship.}, author = {Muller, Caroline J and Back, Larissa E. and O'Gorman, Paul A. and Emanuel, Kerry A.}, issn = {0094-8276}, journal = {Geophysical Research Letters}, keywords = {General Earth and Planetary Sciences, Geophysics}, number = {16}, publisher = {American Geophysical Union}, title = {{A model for the relationship between tropical precipitation and column water vapor}}, doi = {10.1029/2009gl039667}, volume = {36}, year = {2009}, }