@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}, } @article{9453, abstract = {Parent-of-origin-specific (imprinted) gene expression is regulated in Arabidopsis thaliana endosperm by cytosine demethylation of the maternal genome mediated by the DNA glycosylase DEMETER, but the extent of the methylation changes is not known. Here, we show that virtually the entire endosperm genome is demethylated, coupled with extensive local non-CG hypermethylation of small interfering RNA–targeted sequences. Mutation of DEMETER partially restores endosperm CG methylation to levels found in other tissues, indicating that CG demethylation is specific to maternal sequences. Endosperm demethylation is accompanied by CHH hypermethylation of embryo transposable elements. Our findings demonstrate extensive reconfiguration of the endosperm methylation landscape that likely reinforces transposon silencing in the embryo.}, author = {Hsieh, Tzung-Fu and Ibarra, Christian A. and Silva, Pedro and Zemach, Assaf and Eshed-Williams, Leor and Fischer, Robert L. and Zilberman, Daniel}, issn = {1095-9203}, journal = {Science}, keywords = {Multidisciplinary}, number = {5933}, pages = {1451--1454}, publisher = {American Association for the Advancement of Science}, title = {{Genome-wide demethylation of Arabidopsis endosperm}}, doi = {10.1126/science.1172417}, volume = {324}, year = {2009}, } @inproceedings{964, abstract = {A theory of the fluctuation-induced Nernst efl'ect is developed for a two-dimensional superconductor in a perpendicular magnetic field. First, we derive a simple phenomenological formula for the Nernst coefficient, which naturally explains the giant Nernst signal due to fluctuating Cooper pairs. The latter signal is shown to be large even far from the transition and may exceed by orders of magnitude the Fermi liquid terms. We also present a complete microscopic calculation of the Nernst coefficient for arbitrary magnetic fields and temperatures, which is based on the standard definition of heat current vertices. It is shown that the magnitude and the behavior of the Nernst signal observed experimentally in disordered superconducting films can be well understood on the basis of superconducting fluctuation theory.}, author = {Maksym Serbyn and Skvortsov, Mikhail A and Varlamov, Andrei A and Galitski, Victor M}, pages = {140 -- 145}, publisher = {American Institute of Physics}, title = {{Giant nernst effect due to fluctuating cooper Pairs in superconductors}}, doi = {10.1063/1.3149485}, volume = {1134}, year = {2009}, } @misc{5392, abstract = {We consider probabilistic automata on infinite words with acceptance defined by safety, reachability, Büchi, coBüchi and limit-average conditions. We consider quantitative and qualitative decision problems. We present extensions and adaptations of proofs of [GO09] and present a precise characterization of the decidability and undecidability frontier of the quantitative and qualitative decision problems.}, author = {Chatterjee, Krishnendu}, issn = {2664-1690}, pages = {17}, publisher = {IST Austria}, title = {{Probabilistic automata on infinite words: Decidability and undecidability results}}, doi = {10.15479/AT:IST-2009-0004}, year = {2009}, } @misc{5393, abstract = {Gist is a tool that (a) solves the qualitative analysis problem of turn-based probabilistic games with ω-regular objectives; and (b) synthesizes reasonable environment assumptions for synthesis of unrealizable specifications. Our tool provides efficient implementations of several reduction based techniques to solve turn-based probabilistic games, and uses the analysis of turn-based probabilistic games for synthesizing environment assumptions for unrealizable specifications.}, author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Jobstmann, Barbara and Radhakrishna, Arjun}, issn = {2664-1690}, pages = {12}, publisher = {IST Austria}, title = {{Gist: A solver for probabilistic games}}, doi = {10.15479/AT:IST-2009-0003}, year = {2009}, } @misc{5394, abstract = {We consider two-player games played on graphs with request-response and finitary Streett objectives. We show these games are PSPACE-hard, improving the previous known NP-hardness. We also improve the lower bounds on memory required by the winning strategies for the players.}, author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Horn, Florian}, issn = {2664-1690}, pages = {11}, publisher = {IST Austria}, title = {{Improved lower bounds for request-response and finitary Streett games}}, doi = {10.15479/AT:IST-2009-0002}, year = {2009}, } @misc{5395, abstract = {We study observation-based strategies for partially-observable Markov decision processes (POMDPs) with omega-regular objectives. An observation-based strategy relies on partial information about the history of a play, namely, on the past sequence of observa- tions. We consider the qualitative analysis problem: given a POMDP with an omega-regular objective, whether there is an observation-based strategy to achieve the objective with probability 1 (almost-sure winning), or with positive probability (positive winning). Our main results are twofold. First, we present a complete picture of the computational complexity of the qualitative analysis of POMDPs with parity objectives (a canonical form to express omega-regular objectives) and its subclasses. Our contribution consists in establishing several upper and lower bounds that were not known in literature. Second, we present optimal bounds (matching upper and lower bounds) on the memory required by pure and randomized observation-based strategies for the qualitative analysis of POMDPs with parity objectives and its subclasses.}, author = {Chatterjee, Krishnendu and Doyen, Laurent and Henzinger, Thomas A}, issn = {2664-1690}, pages = {20}, publisher = {IST Austria}, title = {{Qualitative analysis of partially-observable Markov decision processes}}, doi = {10.15479/AT:IST-2009-0001}, year = {2009}, } @article{599, abstract = {The human CDK8 subcomplex (CDK8, cyclin C, Med12, and Med13) negatively regulates transcription in ways not completely defined; past studies suggested CDK8 kinase activity was required for its repressive function. Using a reconstituted transcription system together with recombinant or endogenous CDK8 subcomplexes, we demonstrate that, in fact, Med12 and Med13 are critical for subcomplex-dependent repression, whereas CDK8 kinase activity is not. A hallmark of activated transcription is efficient reinitiation from promoter-bound scaffold complexes that recruit a series of pol II enzymes to the gene. Notably, the CDK8 submodule strongly represses even reinitiation events, suggesting a means to fine tune transcript levels. Structural and biochemical studies confirm the CDK8 submodule binds the Mediator leg/tail domain via the Med13 subunit, and this submodule-Mediator association precludes pol II recruitment. Collectively, these results reveal the CDK8 subcomplex functions as a simple switch that controls the Mediator-pol II interaction to help regulate transcription initiation and reinitiation events. As Mediator is generally required for expression of protein-coding genes, this may reflect a common mechanism by which activated transcription is shut down in human cells.}, author = {Knuesel, Matthew and Meyer, Krista and Bernecky, Carrie A and Taatjes, Dylan}, journal = {Genes and Development}, number = {4}, pages = {439 -- 451}, publisher = {Cold Spring Harbor Laboratory Press}, title = {{The human CDK8 subcomplex is a molecular switch that controls Mediator coactivator function}}, doi = {10.1101/gad.1767009}, volume = {23}, year = {2009}, } @article{6144, abstract = {Behaviours evolve by iterations of natural selection, but we have few insights into the molecular and neural mechanisms involved. Here we show that some Caenorhabditis elegans wild strains switch between two foraging behaviours in response to subtle changes in ambient oxygen. This finely tuned switch is conferred by a naturally variable hexacoordinated globin, GLB-5. GLB-5 acts with the atypical soluble guanylate cyclases1,2,3, which are a different type of oxygen binding protein, to tune the dynamic range of oxygen-sensing neurons close to atmospheric (21%) concentrations. Calcium imaging indicates that one group of these neurons is activated when oxygen rises towards 21%, and is inhibited as oxygen drops below 21%. The soluble guanylate cyclase GCY-35 is required for high oxygen to activate the neurons; GLB-5 provides inhibitory input when oxygen decreases below 21%. Together, these oxygen binding proteins tune neuronal and behavioural responses to a narrow oxygen concentration range close to atmospheric levels. The effect of the glb-5 gene on oxygen sensing and foraging is modified by the naturally variable neuropeptide receptor npr-1 (refs 4, 5), providing insights into how polygenic variation reshapes neural circuit function.}, author = {Persson, Annelie and Gross, Einav and Laurent, Patrick and Busch, Karl Emanuel and Bretes, Hugo and de Bono, Mario}, issn = {0028-0836}, journal = {Nature}, number = {7241}, pages = {1030--1033}, publisher = {Springer Nature}, title = {{Natural variation in a neural globin tunes oxygen sensing in wild Caenorhabditis elegans}}, doi = {10.1038/nature07820}, volume = {458}, year = {2009}, } @article{6145, author = {Cohen, Merav and Reale, Vincenzina and Olofsson, Birgitta and Knights, Andrew and Evans, Peter and de Bono, Mario}, issn = {1550-4131}, journal = {Cell Metabolism}, number = {4}, pages = {375--385}, publisher = {Elsevier}, title = {{Coordinated regulation of foraging and metabolism in C. elegans by RFamide neuropeptide signaling}}, doi = {10.1016/j.cmet.2009.02.003}, volume = {9}, year = {2009}, } @article{7080, abstract = {We show evidence that a structural martensitic transition is related to significant changes in the electronic structure, as revealed in thermodynamic measurements made in high magnetic fields. The effect of the magnetic field is considered unusual as many influential investigations of martensitic transitions have emphasized that the structural transitions are primarily lattice dynamical and are driven by the entropy due to the phonons. We provide a theoretical framework, which can be used to describe the effect of the magnetic field on the lattice dynamics in which the field dependence originates from the dielectric constant.}, author = {Yang, X.-D. and Riseborough, P.S. and Modic, Kimberly A and Fisher, R.A. and Opeil, C.P. and Finlayson, T.R. and Cooley, J.C. and Smith, J.L. and Goddard, P.A. and Silhanek, A.V. and Lashley, J.C.}, issn = {1478-6443}, journal = {Philosophical Magazine}, number = {22-24}, pages = {2083--2091}, publisher = {Taylor & Francis}, title = {{Influence of magnetic fields on structural martensitic transitions}}, doi = {10.1080/14786430902865518}, volume = {89}, year = {2009}, } @article{7319, abstract = {In the first paper of this series, an experimental technique for measuring the current-density distribution with a resolution better than the sub-millimeter scale of the channel and rib structures in the flow-field plates of polymer electrolyte fuel cells (PEFCs) was introduced. This method is extended to the determination of local membrane resistance with the same spatial resolution in the present paper. The combined measurement of current and resistance allows for investigating the interaction of mass- and charge-transport processes, which determine the local rate distribution across the domain of channels and ribs. Therewith, the influence of relevant operating parameters such as reactant composition, dew points, and cell compression on local current generation is investigated. The results show that the distribution of water and oxidant across the channel and rib are the main reasons for significant current gradients on a scale smaller than a millimeter. Humidity variation mainly affects the membrane resistance under the channel, while reactant concentration predominantly influences current generation under the rib-covered cell area.}, author = {Reum, Mathias and Freunberger, Stefan Alexander and Wokaun, Alexander and Büchi, Felix N.}, issn = {0013-4651}, journal = {Journal of The Electrochemical Society}, number = {3}, publisher = {The Electrochemical Society}, title = {{Measuring the current distribution with sub-millimeter resolution in PEFCs: II. Impact of operating parameters}}, doi = {10.1149/1.3043422}, volume = {156}, year = {2009}, } @inproceedings{752, abstract = {Set agreement is a fundamental problem in distributed computing in which processes collectively choose a small subset of values from a larger set of proposals. The impossibility of fault-tolerant set agreement in asynchronous networks is one of the seminal results in distributed computing. The complexity of set agreement in synchronous networks has also been a significant research challenge. Real systems, however, are neither purely synchronous nor purely asynchronous. Rather, they tend to alternate between periods of synchrony and periods of asynchrony. In this paper, we analyze the complexity of set agreement in a "partially synchronous" setting, presenting the first (asymptotically) tight bound on the complexity of set agreement in such systems. We introduce a novel technique for simulating, in fault-prone asynchronous shared memory, executions of an asynchronous and failure-prone messagepassing system in which some fragments appear synchronous to some processes. We use this technique to derive a lower bound on the round complexity of set agreement in a partially synchronous system by a reduction from asynchronous wait-free set agreement. We also present an asymptotically matching algorithm that relies on a distributed asynchrony detection mechanism to decide as soon as possible during periods of synchrony. By relating environments with differing degrees of synchrony, our simulation technique is of independent interest. In particular, it allows us to obtain a new lower bound on the complexity of early deciding k-set agreement complementary to that of [12], and to re-derive the combinatorial topology lower bound of [13] in an algorithmic way.}, author = {Alistarh, Dan-Adrian and Gilbert, Seth and Guerraoui, Rachid and Travers, Corentin}, pages = {943 -- 953}, publisher = {Springer}, title = {{Of choices, failures and asynchrony: the many faces of set agreement}}, doi = {10.1007/978-3-642-10631-6_95}, volume = {5878 LNCS}, year = {2009}, } @article{3428, abstract = {In this issue of Molecular Cell, Davies et al. (2009) work out a sequence of active cellular events that lead to the death of Escherichia coli in the presence of the drug hydroxyurea.}, author = {Bollenbach, Mark Tobias and Kishony, Roy}, journal = {Molecular Cell}, number = {5}, pages = {728 -- 729}, publisher = {Cell Press}, title = {{Hydroxyurea triggers cellular responses that actively cause bacterial cell death}}, doi = {10.1016/j.molcel.2009.11.027}, volume = {36}, year = {2009}, }