@article{8025, abstract = {Chandelier (axoaxonic) cells (ChCs) are a distinct group of GABAergic interneurons that innervate the axon initial segments of pyramidal cells. However, their circuit role and the function of their clearly defined anatomical specificity remain unclear. Recent work has demonstrated that chandelier cells can produce depolarizing GABAergic PSPs, occasionally driving postsynaptic targets to spike. On the other hand, other work suggests that ChCs are hyperpolarizing and may have an inhibitory role. These disparate functional effects may reflect heterogeneity among ChCs. Here, using brain slices from transgenic mouse strains, we first demonstrate that, across different neocortical areas and genetic backgrounds, upper Layer 2/3 ChCs belong to a single electrophysiologically and morphologically defined population, extensively sampling Layer 1 inputs with asymmetric dendrites. Consistent with being a single cell type, we find electrical coupling between ChCs. We then investigate the effect of chandelier cell activation on pyramidal neuron spiking in several conditions, ranging from the resting membrane potential to stimuli designed to approximate in vivo membrane potential dynamics. We find that under quiescent conditions, chandelier cells are capable of both promoting and inhibiting spike generation, depending on the postsynaptic membrane potential. However, during in vivo-like membrane potential fluctuations, the dominant postsynaptic effect was a strong inhibition. Thus, neocortical chandelier cells, even from within a homogeneous population, appear to play a dual role in the circuit, helping to activate quiescent pyramidal neurons, while at the same time inhibiting active ones.}, author = {Woodruff, A. R. and McGarry, L. M. and Vogels, Tim P and Inan, M. and Anderson, S. A. and Yuste, R.}, issn = {0270-6474}, journal = {Journal of Neuroscience}, number = {49}, pages = {17872--17886}, publisher = {Society for Neuroscience}, title = {{State-dependent function of neocortical chandelier cells}}, doi = {10.1523/jneurosci.3894-11.2011}, volume = {31}, year = {2011}, } @article{8074, abstract = {Cortical neurons receive balanced excitatory and inhibitory synaptic currents. Such a balance could be established and maintained in an experience-dependent manner by synaptic plasticity at inhibitory synapses. We show that this mechanism provides an explanation for the sparse firing patterns observed in response to natural stimuli and fits well with a recently observed interaction of excitatory and inhibitory receptive field plasticity. The introduction of inhibitory plasticity in suitable recurrent networks provides a homeostatic mechanism that leads to asynchronous irregular network states. Further, it can accommodate synaptic memories with activity patterns that become indiscernible from the background state but can be reactivated by external stimuli. Our results suggest an essential role of inhibitory plasticity in the formation and maintenance of functional cortical circuitry.}, author = {Vogels, Tim P and Sprekeler, H. and Zenke, F. and Clopath, C. and Gerstner, W.}, issn = {0036-8075}, journal = {Science}, number = {6062}, pages = {1569--1573}, publisher = {American Association for the Advancement of Science}, title = {{Inhibitory plasticity balances excitation and inhibition in sensory pathways and memory networks}}, doi = {10.1126/science.1211095}, volume = {334}, year = {2011}, } @article{8464, abstract = {Nonsymmetric motion: Solid‐state NMR measurements of dipolar coupling tensors provide insight into protein dynamics. The hitherto ignored asymmetry of the dipolar coupling tensor contains valuable information about motional asymmetry, which was used in the first direct site‐resolved measurement of such tensors. Important motions such as rotamer jumps can now be directly detected in the solid state.}, author = {Schanda, Paul and Huber, Matthias and Boisbouvier, Jérôme and Meier, Beat H. and Ernst, Matthias}, issn = {1433-7851}, journal = {Angewandte Chemie International Edition}, number = {46}, pages = {11005--11009}, publisher = {Wiley}, title = {{Solid-state NMR measurements of asymmetric dipolar couplings provide insight into protein side-chain motion}}, doi = {10.1002/anie.201103944}, volume = {50}, year = {2011}, } @article{8468, author = {Lalli, Daniela and Schanda, Paul and Chowdhury, Anup and Retel, Joren and Hiller, Matthias and Higman, Victoria A. and Handel, Lieselotte and Agarwal, Vipin and Reif, Bernd and van Rossum, Barth and Akbey, Ümit and Oschkinat, Hartmut}, issn = {0925-2738}, journal = {Journal of Biomolecular NMR}, number = {4}, pages = {477--485}, publisher = {Springer Nature}, title = {{Three-dimensional deuterium-carbon correlation experiments for high-resolution solid-state MAS NMR spectroscopy of large proteins}}, doi = {10.1007/s10858-011-9578-1}, volume = {51}, year = {2011}, } @article{8469, abstract = {The accurate experimental determination of dipolar-coupling constants for one-bond heteronuclear dipolar couplings in solids is a key for the quantification of the amplitudes of motional processes. Averaging of the dipolar coupling reports on motions on time scales up to the inverse of the coupling constant, in our case tens of microseconds. Combining dipolar-coupling derived order parameters that characterize the amplitudes of the motion with relaxation data leads to a more precise characterization of the dynamical parameters and helps to disentangle the amplitudes and the time scales of the motional processes, which impact relaxation rates in a highly correlated way. Here. we describe and characterize an improved experimental protocol – based on REDOR – to measure these couplings in perdeuterated proteins with a reduced sensitivity to experimental missettings. Because such effects are presently the dominant source of systematic errors in experimental dipolar-coupling measurements, these compensated experiments should help to significantly improve the precision of such data. A detailed comparison with other commonly used pulse sequences (T-MREV, phase-inverted CP,R18 5/2, and R18 7/1) is provided.}, author = {Schanda, Paul and Meier, Beat H. and Ernst, Matthias}, issn = {1090-7807}, journal = {Journal of Magnetic Resonance}, keywords = {Nuclear and High Energy Physics, Biophysics, Biochemistry, Condensed Matter Physics}, number = {2}, pages = {246--259}, publisher = {Elsevier}, title = {{Accurate measurement of one-bond H–X heteronuclear dipolar couplings in MAS solid-state NMR}}, doi = {10.1016/j.jmr.2011.03.015}, volume = {210}, year = {2011}, } @article{8470, abstract = {Adding a new dimension: 4D or 3D proton‐detected spectra of perdeuterated protein samples with 1H labelled amides and methyl groups permit collecting unambiguous distance restraints with high sensitivity and determining protein structure by solid‐state NMR (see picture).}, author = {Huber, Matthias and Hiller, Sebastian and Schanda, Paul and Ernst, Matthias and Böckmann, Anja and Verel, René and Meier, Beat H.}, issn = {1439-4235}, journal = {ChemPhysChem}, keywords = {Physical and Theoretical Chemistry, Atomic and Molecular Physics, and Optics}, number = {5}, pages = {915--918}, publisher = {Wiley}, title = {{A proton-detected 4D solid-state NMR experiment for protein structure determination}}, doi = {10.1002/cphc.201100062}, volume = {12}, year = {2011}, } @article{8471, abstract = {Despite the importance of protein fibrils in the context of conformational diseases, information on their structure is still sparse. Hydrogen/deuterium exchange measurements of backbone amide protons allow the identification hydrogen-bonding patterns and reveal pertinent information on the amyloid β-sheet architecture. However, they provide only little information on the identity of residues exposed to solvent or buried inside the fibril core. NMR spectroscopy is a potent method for identifying solvent-accessible residues in proteins via observation of polarization transfer between chemically exchanging side-chain protons and water protons. We show here that the combined use of highly deuterated samples and fast magic-angle spinning greatly attenuates unwanted spin diffusion and allows identification of polarization exchange with the solvent in a site-specific manner. We apply this measurement protocol to HET-s(218–289) prion fibrils under different conditions (including physiological pH, where protofibrils assemble together into thicker fibrils) and demonstrate that each protofibril of HET-s(218–289), is surrounded by water, thus excluding the existence of extended dry interfibril contacts. We also show that exchangeable side-chain protons inside the hydrophobic core of HET-s(218–289) do not exchange over time intervals of weeks to months. The experiments proposed in this study can provide insight into the detailed structural features of amyloid fibrils in general.}, author = {Van Melckebeke, Hélène and Schanda, Paul and Gath, Julia and Wasmer, Christian and Verel, René and Lange, Adam and Meier, Beat H. and Böckmann, Anja}, issn = {0022-2836}, journal = {Journal of Molecular Biology}, number = {3}, pages = {765--772}, publisher = {Elsevier}, title = {{Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR}}, doi = {10.1016/j.jmb.2010.11.004}, volume = {405}, year = {2011}, } @article{8505, abstract = {The classical principle of least action says that orbits of mechanical systems extremize action; an important subclass are those orbits that minimize action. In this paper we utilize this principle along with Aubry-Mather theory to construct (Birkhoff) regions of instability for a certain three-body problem, given by a Hamiltonian system of 2 degrees of freedom. We believe that these methods can be applied to construct instability regions for a variety of Hamiltonian systems with 2 degrees of freedom. The Hamiltonian model we consider describes dynamics of a Sun-Jupiter-comet system, and under some simplifying assumptions, we show the existence of instabilities for the orbit of the comet. In particular, we show that a comet which starts close to an orbit in the shape of an ellipse of eccentricity e=0.66 can increase in eccentricity up to e=0.96. In the sequels to this paper, we extend the result to beyond e=1 and show the existence of ejection orbits. Such orbits are initially well within the range of our solar system. This might give an indication of why most objects rotating around the Sun in our solar system have relatively low eccentricity.}, author = {Galante, Joseph and Kaloshin, Vadim}, issn = {0012-7094}, journal = {Duke Mathematical Journal}, keywords = {General Mathematics}, number = {2}, pages = {275--327}, publisher = {Duke University Press}, title = {{Destruction of invariant curves in the restricted circular planar three-body problem by using comparison of action}}, doi = {10.1215/00127094-1415878}, volume = {159}, year = {2011}, } @inbook{881, author = {Fyodor Kondrashov}, booktitle = {Evolution after Gene Duplication}, pages = {57 -- 76}, publisher = {Wiley-Blackwell}, title = {{Gene Dosage and Duplication}}, doi = {10.1002/9780470619902.ch4}, year = {2011}, } @article{890, abstract = {Recent discovery of the Large-billed Reed Warbler (Acrocephalus orinus) in museums and in the wild significantly expanded our knowledge of its morphological traits and genetic variability, and revealed new data on geographical distribution of the breeding grounds, migration routes and wintering locations of this species. It is now certain that A. orinus is breeding in Central Asia; however, the precise area of distribution remains unclear. The difficulty in the further study of this species lies in the small number of known specimens, with only 13 currently available in museums, and in the relative uncertainty of the breeding area and habitat of this species. Following morphological and genetic analyses from Svensson, et al, we describe 14 new A. orinus specimens from collections of Zoological Museums of the former USSR from the territory of Central Asian states. All of these specimens were erroneously labeled as Blyth's Reed Warbler (A. dumetorum), which is thought to be a breeding species in these areas. The 14 new A. orinus specimens were collected during breeding season while most of the 85 A. dumetorum specimens from the same area were collected during the migration period. Our data indicate that the Central Asian territory previously attributed as breeding grounds of A. dumetorum is likely to constitute the breeding territory of A. orinus. This rare case of a re-description of the breeding territory of a lost species emphasizes the importance of maintenance of museum collections around the world. If the present data on the breeding grounds of A. orinus are confirmed with field observations and collections, the literature on the biology of A. dumetorum from the southern part of its range may have to be reconsidered.}, author = {Koblik, Evgeniy A and Red'Kin, Yaroslav A and Meer, Margarita S and Derelle, Romain and Golenkina, Sofia A and Fyodor Kondrashov and Arkhipov, Vladimir Y}, journal = {PLoS One}, number = {4}, publisher = {Public Library of Science}, title = {{Acrocephalus orinus: A case of Mistaken identity}}, doi = {10.1371/journal.pone.0017716}, volume = {6}, year = {2011}, } @article{90, abstract = {A popular method for generating micron-sized aerosols is to submerge ultrasonic (ω ∼ MHz) piezoelectric oscillators in a water bath. The submerged oscillator atomizes the fluid, creating droplets with radii proportional to the wavelength of the standing wave at the fluid surface. Classical theory for the Faraday instability predicts a parametric instability driving a capillary wave at the subharmonic (ω / 2) frequency. For many applications it is desirable to reduce the size of the droplets; however, using higher frequency oscillators becomes impractical beyond a few MHz. Observations are presented that demonstrate that smaller droplets may also be created by increasing the driving amplitude of the oscillator, and that this effect becomes more pronounced for large driving frequencies. It is shown that these observations are consistent with a transition from droplets associated with subharmonic (ω/2) capillary waves to harmonic (ω) capillary waves induced by larger driving frequencies and amplitudes, as predicted by a stability analysis of the capillary waves.}, author = {Higginbotham, Andrew P and Guillen, A and Jones, Nick and Donnelly, Tom and Bernoff, Andrew}, journal = {Journal of the Acoustical Society of America}, number = {5}, pages = {2694 -- 2699}, publisher = {Acoustical Society of America}, title = {{Evidence of the harmonic Faraday instability in ultrasonic atomization experiments with a deep, inviscid fluid}}, doi = {10.1121/1.3643816}, volume = {130}, year = {2011}, } @article{9143, abstract = {Understanding and predicting the response of the hydrological cycle to climate change is a major challenge with important societal implications. Much progress has been made in understanding the response of global average precipitation by considering the energy balances of the atmosphere and the surface1,2,3,4,5,6. This energetic perspective reveals that changes in temperature, greenhouse gases, aerosols, solar forcing and cloud feedbacks can all affect the global average rate of precipitation5,7,8,9,10,11. Local precipitation changes have conventionally been analysed using the water vapour budget, but here we show that the energetic approach can be extended to local changes in precipitation by including changes in horizontal energy transport. In simulations of twenty-first century climate change, this energy transport accounts for much of the spatial variability in precipitation change. We show that changes in radiative and surface sensible heat fluxes are a guide to the local precipitation response over land and at large scales, but not at small scales over the ocean, where cloud and water vapour radiative feedbacks dampen the response. The energetic approach described here helps bridge the gap between our understanding of global and regional precipitation changes. It could be applied to better understand the response of regional precipitation to different radiative forcings, including geo-engineering schemes, as well as to understand the differences between the fast and slow responses of regional precipitation to such forcings.}, author = {Muller, Caroline J and O’Gorman, P. A.}, issn = {1758-678X}, journal = {Nature Climate Change}, number = {5}, pages = {266--271}, publisher = {Springer Nature}, title = {{An energetic perspective on the regional response of precipitation to climate change}}, doi = {10.1038/nclimate1169}, volume = {1}, year = {2011}, } @article{9144, abstract = {A cloud-resolving model is used to investigate the effect of warming on high percentiles of precipitation (precipitation extremes) in the idealized setting of radiative-convective equilibrium. While this idealized setting does not allow for several factors that influence precipitation in the tropics, it does allow for an evaluation of the response of precipitation extremes to warming in simulations with resolved rather than parameterized convection. The methodology developed should also be applicable to less idealized simulations. Modeled precipitation extremes are found to increase in magnitude in response to an increase in sea surface temperature. A dry static energy budget is used to relate the changes in precipitation extremes to changes in atmospheric temperature, vertical velocity, and precipitation efficiency. To first order, the changes in precipitation extremes are captured by changes in the mean temperature structure of the atmosphere. Changes in vertical velocities play a secondary role and tend to weaken the strength of precipitation extremes, despite an intensification of updraft velocities in the upper troposphere. The influence of changes in condensate transports on precipitation extremes is quantified in terms of a precipitation efficiency; it does not change greatly with warming. Tropical precipitation extremes have previously been found to increase at a greater fractional rate than the amount of atmospheric water vapor in observations of present-day variability and in some climate model simulations with parameterized convection. But the fractional increases in precipitation extremes in the cloud-resolving simulations are comparable in magnitude to those in surface water vapor concentrations (owing to a partial cancellation between dynamical and thermodynamical changes), and are substantially less than the fractional increases in column water vapor.}, author = {Muller, Caroline J and O’Gorman, Paul A. and Back, Larissa E.}, issn = {1520-0442}, journal = {Journal of Climate}, keywords = {Atmospheric Science}, number = {11}, pages = {2784--2800}, publisher = {American Meteorological Society}, title = {{Intensification of precipitation extremes with warming in a cloud-resolving model}}, doi = {10.1175/2011jcli3876.1}, volume = {24}, year = {2011}, } @article{918, abstract = {We study theoretically the shapes of a dividing epithelial monolayer of cells lying on top of an elastic stroma. The negative tension created by cell division provokes a buckling instability at a finite wave vector leading to the formation of periodic arrays of villi and crypts. The instability is similar to the buckling of a metallic plate under compression. We use the results to rationalize the various structures of the intestinal lining observed in vivo. Taking into account the coupling between cell division and local curvature, we obtain different patterns of villi and crypts, which could explain the different morphologies of the small intestine and the colon.}, author = {Hannezo, Edouard B and Prost, Jacques and Joanny, Jean}, journal = {Physical Review Letters}, number = {7}, publisher = {American Physical Society}, title = {{Instabilities of monolayered epithelia Shape and structure of villi and crypts}}, doi = {10.1103/PhysRevLett.107.078104}, volume = {107}, year = {2011}, } @article{919, abstract = {Collective cell migration in tissues occurs throughout embryonic development, during wound healing, and in cancerous tumor invasion, yet most detailed knowledge of cell migration comes from single-cell studies. As single cells migrate, the shape of the cell body fluctuates dramatically through cyclic processes of extension, adhesion, and retraction, accompanied by erratic changes in migration direction. Within confluent cell layers, such subcellular motions must be coupled between neighbors, yet the influence of these subcellular motions on collective migration is not known. Here we study motion within a confluent epithelial cell sheet, simultaneously measuring collective migration and subcellular motions, covering a broad range of length scales, time scales, and cell densities. At large length scales and time scales collective migration slows as cell density rises, yet the fastest cells move in large, multicell groups whose scale grows with increasing cell density. This behavior has an intriguing analogy to dynamic heterogeneities found in particulate systems as they become more crowded and approach a glass transition. In addition we find a diminishing self-diffusivity of short-wavelength motions within the cell layer, and growing peaks in the vibrational density of states associated with cooperative cell-shape fluctuations. Both of these observations are also intriguingly reminiscent of a glass transition. Thus, these results provide a broad and suggestive analogy between cell motion within a confluent layer and the dynamics of supercooled colloidal and molecular fluids approaching a glass transition.}, author = {Angelini, Thomas and Hannezo, Edouard B and Trepatc, Xavier and Marquez, Manuel and Fredberg, Jeffrey and Weitz, David}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {12}, pages = {4714 -- 4719}, publisher = {PNAS}, title = {{Glass-like dynamics of collective cell migration}}, doi = {10.1073/pnas.1010059108}, volume = {108}, year = {2011}, } @article{923, abstract = {The conserved role of Notch signaling in controlling intestinal cell fate specification and homeostasis has been extensively studied. Nevertheless, the precise identity of the cells in which Notch signaling is active and the role of different Notch receptor paralogues in the intestine remain ambiguous, due to the lack of reliable tools to investigate Notch expression and function in vivo. We generated a new series of transgenic mice that allowed us, by lineage analysis, to formally prove that Notch1 and Notch2 are specifically expressed in crypt stem cells. In addition, a novel Notch reporter mouse, Hes1-EmGFP SAT, demonstrated exclusive Notch activity in crypt stem cells and absorptive progenitors. This roster of knock-in and reporter mice represents a valuable resource to functionally explore the Notch pathway in vivo in virtually all tissues.}, author = {Fré, Silvia and Hannezo, Edouard B and Šale, Sanja and Huyghe, Mathilde and Lafkas, Daniel and Kissel, Holger and Louvi, Angeliki and Greve, Jeffrey and Louvard, Daniel and Artavanis Tsakonas, Spyros}, journal = {PLoS One}, number = {10}, publisher = {Public Library of Science}, title = {{Notch lineages and activity in intestinal stem cells determined by a new set of knock in mice}}, doi = {10.1371/journal.pone.0025785}, volume = {6}, year = {2011}, } @article{9483, abstract = {Imprinted genes are expressed primarily or exclusively from either the maternal or paternal allele, a phenomenon that occurs in flowering plants and mammals. Flowering plant imprinted gene expression has been described primarily in endosperm, a terminal nutritive tissue consumed by the embryo during seed development or after germination. Imprinted expression in Arabidopsis thaliana endosperm is orchestrated by differences in cytosine DNA methylation between the paternal and maternal genomes as well as by Polycomb group proteins. Currently, only 11 imprinted A. thaliana genes are known. Here, we use extensive sequencing of cDNA libraries to identify 9 paternally expressed and 34 maternally expressed imprinted genes in A. thaliana endosperm that are regulated by the DNA-demethylating glycosylase DEMETER, the DNA methyltransferase MET1, and/or the core Polycomb group protein FIE. These genes encode transcription factors, proteins involved in hormone signaling, components of the ubiquitin protein degradation pathway, regulators of histone and DNA methylation, and small RNA pathway proteins. We also identify maternally expressed genes that may be regulated by unknown mechanisms or deposited from maternal tissues. We did not detect any imprinted genes in the embryo. Our results show that imprinted gene expression is an extensive mechanistically complex phenomenon that likely affects multiple aspects of seed development.}, author = {Hsieh, Tzung-Fu and Shin, Juhyun and Uzawa, Rie and Silva, Pedro and Cohen, Stephanie and Bauer, Matthew J. and Hashimoto, Meryl and Kirkbride, Ryan C. and Harada, John J. and Zilberman, Daniel and Fischer, Robert L.}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, number = {5}, pages = {1755--1762}, publisher = {National Academy of Sciences}, title = {{Regulation of imprinted gene expression in Arabidopsis endosperm}}, doi = {10.1073/pnas.1019273108}, volume = {108}, year = {2011}, } @misc{9522, abstract = {Little is known about chromatin remodeling events immediately after fertilization. A recent report by Autran et al. (2011) in Cell now shows that chromatin regulatory pathways that silence transposable elements are responsible for global delayed activation of gene expression in the early Arabidopsis embryo.}, author = {Zilberman, Daniel}, booktitle = {Developmental Cell}, issn = {1878-1551}, number = {6}, pages = {735--736}, publisher = {Elsevier}, title = {{Balancing parental contributions in plant embryonic gene activation}}, doi = {10.1016/j.devcel.2011.05.018}, volume = {20}, year = {2011}, } @article{967, abstract = {Motivated by recent experiments on the material Ba3NiSb 2O9, we consider a spin-one quantum antiferromagnet on a triangular lattice with the Heisenberg bilinear and biquadratic exchange interactions and a single-ion anisotropy. Using a fermionic "triplon" representation for spins, we study the phase diagram within mean-field theory. In addition to a fully gapped spin-liquid ground state, we find a state where one gapless triplon mode with a Fermi surface coexists with d+id topological pairing of the other triplons. Despite the existence of a Fermi surface, this ground state has fully gapped bulk spin excitations. Such a state has linear in-temperature specific heat and constant in-plane spin susceptibility, with an unusually high Wilson ratio.}, author = {Maksym Serbyn and Senthil, Todadri S and Lee, Patrick}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {18}, publisher = {American Physical Society}, title = {{Exotic S=1 spin-liquid state with fermionic excitations on the triangular lattice}}, doi = {10.1103/PhysRevB.84.180403}, volume = {84}, year = {2011}, } @article{968, abstract = {A Reply to the Comment by Andrei Sergeev, M. Reizer, and V. Mitin.}, author = {Maksym Serbyn and Skvortsov, Mikhail A and Varlamov, Andrei A and Galitski, Victor M}, journal = {Physical Review Letters}, number = {13}, publisher = {American Physical Society}, title = {{Serbyn et al. Reply:}}, doi = {10.1103/PhysRevLett.106.139702}, volume = {106}, year = {2011}, }