Transcriptomes of Plant Gametophytes Have a Higher Proportion of Rapidly Evolving and Young Genes than Sporophytes

eproductive traits in plants tend to evolve rapidly due to various causes that include plant-pollinator coevolution and pollen competition, but the genomic basis of reproductive trait evolution is still largely unknown. To characterize evolutionary patterns of genome wide gene expression in reproductive tissues in the gametophyte and to compare them to developmental stages of the sporophyte, we analyzed evolutionary conservation and genetic diversity of protein-coding genes using microarray-based transcriptome data from three plant species, Arabidopsis thaliana, rice (Oryza sativa), and soybean (Glycine max). In all three species a significant shift in gene expression occurs during gametogenesis in which genes of younger evolutionary age and higher genetic diversity contribute significantly more to the transcriptome than in other stages. We refer to this phenomenon as “evolutionary bulge” during plant reproductive development because it differentiates the gametophyte from the sporophyte. We show that multiple, not mutually exclusive, causes may explain the bulge pattern, most prominently reduced tissue complexity of the gametophyte, a varying extent of selection on reproductive traits during gametogenesis as well as differences between male and female tissues. This highlights the importance of plant reproduction for understanding evolutionary forces determining the relationship of genomic and phenotypic variation in plants

Nature of the quantum phase transitions in the two-dimensional hardcore boson model

We use two Quantum Monte Carlo algorithms to map out the phase diagram of the two-dimensional hardcore boson Hubbard model with near ($V_1$) and next near ($V_2$) neighbor repulsion. At half filling we find three phases: Superfluid (SF), checkerboard solid and striped solid depending on the relative values of $V_1$, $V_2$ and the kinetic energy. Doping away from half filling, the checkerboard solid undergoes phase separation: The superfluid and solid phases co-exist but not as a single thermodynamic phase. As a function of doping, the transition from the checkerboard solid is therefore first order. In contrast, doping the striped solid away from half filling instead produces a striped supersolid phase: Co-existence of density order with superfluidity as a single phase. One surprising result is that the entire line of transitions between the SF and checkerboard solid phases at half filling appears to exhibit dynamical O(3) symmetry restoration. The transitions appear to be in the same universality class as the special Heisenberg point even though this symmetry is explicitly broken by the $V_2$ interaction.Comment: 10 pages, 14 eps figures, include

Quantum Monte Carlo with Directed Loops

We introduce the concept of directed loops in stochastic series expansion and path integral quantum Monte Carlo methods. Using the detailed balance rules for directed loops, we show that it is possible to smoothly connect generally applicable simulation schemes (in which it is necessary to include back-tracking processes in the loop construction) to more restricted loop algorithms that can be constructed only for a limited range of Hamiltonians (where back-tracking can be avoided). The "algorithmic discontinuities" between general and special points (or regions) in parameter space can hence be eliminated. As a specific example, we consider the anisotropic S=1/2 Heisenberg antiferromagnet in an external magnetic field. We show that directed loop simulations are very efficient for the full range of magnetic fields (zero to the saturation point) and anisotropies. In particular for weak fields and anisotropies, the autocorrelations are significantly reduced relative to those of previous approaches. The back-tracking probability vanishes continuously as the isotropic Heisenberg point is approached. For the XY-model, we show that back-tracking can be avoided for all fields extending up to the saturation field. The method is hence particularly efficient in this case. We use directed loop simulations to study the magnetization process in the 2D Heisenberg model at very low temperatures. For LxL lattices with L up to 64, we utilize the step-structure in the magnetization curve to extract gaps between different spin sectors. Finite-size scaling of the gaps gives an accurate estimate of the transverse susceptibility in the thermodynamic limit: chi_perp = 0.0659 +- 0.0002.Comment: v2: Revised and expanded discussion of detailed balance, error in algorithmic phase diagram corrected, to appear in Phys. Rev.

Development of functionally selective, small molecule agonists at kappa opioid receptors

The kappa opioid receptor (KOR) is widely expressed in the CNS and can serve as a means to modulate pain perception, stress responses, and affective reward states. Therefore, the KOR has become a prominent drug discovery target toward treating pain, depression, and drug addiction. Agonists at KOR can promote G protein coupling and βarrestin2 recruitment as well as multiple downstream signaling pathways, including ERK1/2 MAPK activation. It has been suggested that the physiological effects ofKORactivation result from different signaling cascades, with analgesia being G protein-mediated and dysphoria being mediated through βarrestin2 recruitment. Dysphoria associated with KOR activation limits the therapeutic potential in the use of KOR agonists as analgesics; therefore, it may be beneficial to develop KOR agonists that are biased toward G protein coupling and away from βarrestin2 recruitment. Here, we describe two classes of biased KOR agonists that potently activateGprotein coupling but weakly recruitβarrestin2. These potent and functionally selective small molecule compounds may prove to be useful tools for refining the therapeutic potential of KOR-directed signaling in vivo

Assessing agricultural risks of climate change in the 21st century in a global gridded crop model intercomparison

Here we present the results from an intercomparison of multiple global gridded crop models (GGCMs) within the framework of the Agricultural Model Intercomparison and Improvement Project and the Inter-Sectoral Impacts Model Intercomparison Project. Results indicate strong negative effects of climate change, especially at higher levels of warming and at low latitudes; models that include explicit nitrogen stress project more severe impacts. Across seven GGCMs, five global climate models, and four representative concentration pathways, model agreement on direction of yield changes is found in many major agricultural regions at both low and high latitudes; however, reducing uncertainty in sign of response in mid-latitude regions remains a challenge. Uncertainties related to the representation of carbon dioxide, nitrogen, and high temperature effects demonstrated here show that further research is urgently needed to better understand effects of climate change on agricultural production and to devise targeted adaptation strategies

Observation of a new chi_b state in radiative transitions to Upsilon(1S) and Upsilon(2S) at ATLAS

The chi_b(nP) quarkonium states are produced in proton-proton collisions at the Large Hadron Collider (LHC) at sqrt(s) = 7 TeV and recorded by the ATLAS detector. Using a data sample corresponding to an integrated luminosity of 4.4 fb^-1, these states are reconstructed through their radiative decays to Upsilon(1S,2S) with Upsilon->mu+mu-. In addition to the mass peaks corresponding to the decay modes chi_b(1P,2P)->Upsilon(1S)gamma, a new structure centered at a mass of 10.530+/-0.005 (stat.)+/-0.009 (syst.) GeV is also observed, in both the Upsilon(1S)gamma and Upsilon(2S)gamma decay modes. This is interpreted as the chi_b(3P) system.Comment: 5 pages plus author list (18 pages total), 2 figures, 1 table, corrected author list, matches final version in Physical Review Letter

Search for displaced vertices arising from decays of new heavy particles in 7 TeV pp collisions at ATLAS

We present the results of a search for new, heavy particles that decay at a significant distance from their production point into a final state containing charged hadrons in association with a high-momentum muon. The search is conducted in a pp-collision data sample with a center-of-mass energy of 7 TeV and an integrated luminosity of 33 pb^-1 collected in 2010 by the ATLAS detector operating at the Large Hadron Collider. Production of such particles is expected in various scenarios of physics beyond the standard model. We observe no signal and place limits on the production cross-section of supersymmetric particles in an R-parity-violating scenario as a function of the neutralino lifetime. Limits are presented for different squark and neutralino masses, enabling extension of the limits to a variety of other models.Comment: 8 pages plus author list (20 pages total), 8 figures, 1 table, final version to appear in Physics Letters

Reducing heterotic M-theory to five dimensional supergravity on a manifold with boundary

This paper constructs the reduction of heterotic $M$-theory in eleven dimensions to a supergravity model on a manifold with boundary in five dimensions using a Calabi-Yau three-fold. New results are presented for the boundary terms in the action and for the boundary conditions on the bulk fields. Some general features of dualisation on a manifold with boundary are used to explain the origin of some topological terms in the action. The effect of gaugino condensation on the fermion boundary conditions leads to a `twist' in the chirality of the gravitino which can provide an uplifting mechanism in the vacuum energy to cancel the cosmological constant after moduli stabilisation.Comment: 16 pages, RevTe

Measurement of the inclusive isolated prompt photon cross-section in pp collisions at sqrt(s)= 7 TeV using 35 pb-1 of ATLAS data

A measurement of the differential cross-section for the inclusive production of isolated prompt photons in pp collisions at a center-of-mass energy sqrt(s) = 7 TeV is presented. The measurement covers the pseudorapidity ranges |eta|<1.37 and 1.52<=|eta|<2.37 in the transverse energy range 45<=E_T<400GeV. The results are based on an integrated luminosity of 35 pb-1, collected with the ATLAS detector at the LHC. The yields of the signal photons are measured using a data-driven technique, based on the observed distribution of the hadronic energy in a narrow cone around the photon candidate and the photon selection criteria. The results are compared with next-to-leading order perturbative QCD calculations and found to be in good agreement over four orders of magnitude in cross-section.Comment: 7 pages plus author list (18 pages total), 2 figures, 4 tables, final version published in Physics Letters