Earth Life Science Institute
Earth Life Science Institute
Mookherjee M.,Florida State University |
Tsuchiya J.,Ehime University |
Tsuchiya J.,Earth Life Science Institute |
Hariharan A.,Cornell University
Physics of the Earth and Planetary Interiors | Year: 2016
We examined the equation of state and high-pressure elasticity of the hydrous aluminosilicate mineral topaz-OH (Al2SiO4(OH)2) using first principles simulation. Topaz-OH is a hydrous phase in the Al2O3-SiO2-H2O (ASH) ternary system, which is relevant for the mineral phase relations in the hydrated sedimentary layer of subducting slabs. Based on recent neutron diffraction experiments, it is known that the protons in the topaz-OH exhibit positional disorder with half occupancy over two distinct crystallographic sites. In order to adequately depict the proton environment in the topaz-OH, we examined five crystal structure models with distinct configuration for the protons in topaz-OH. Upon full geometry optimization we find two distinct space group, an orthorhombic Pbnm and a monoclinic P21/c for topaz-OH. The topaz-OH with the monoclinic P21/c space group has a lower energy compared to the orthorhombic Pbmn space group symmetry. The pressure-volume results for the monoclinic topaz-OH is well represented by a third order Birch-Murnaghan formulation, with V0mon=348.63 (±0.04)Å3, K0mon=164.7 (±0.04)GPa, and K0mon=4.24 (±0.05). The pressure-volume results for the orthorhombic topaz-OH is well represented by a third order Birch-Murnaghan formulation, with V0orth=352.47 (±0.04)Å3, K0orth=166.4 (±0.06)GPa, and K0orth=4.03 (±0.04). While the bulk moduli are very similar for both the monoclinic and orthorhombic topaz-OH, the shear elastic constants and the shear moduli are very sensitive to the position of the proton, orientation of the O-H dipole, and the space group symmetry. The S-wave anisotropy for the orthorhombic and monoclinic topaz-OH are also quite distinct.In the hydrated sedimentary layer of subducting slabs, transformation of a mineral assemblage consisting of coesite (SiO2) and diaspore (AlOOH) to topaz-OH (Al2SiO4(OH)2) is likely to be accompanied by an increase in density, compressional velocity, and shear wave velocity. However, further studies of physical properties and lattice preferred orientation of several key hydrous aluminosilicates needs to be prioritized for gaining better insight into the transport of water via subduction of sediments. © 2015 Elsevier B.V.
Rainey E.S.G.,University of California at Los Angeles |
Hernlund J.W.,University of California at Berkeley |
Hernlund J.W.,Earth Life Science Institute |
Kavner A.,University of California at Los Angeles
Journal of Applied Physics | Year: 2013
We present TempDAC, a 3-D numerical model for calculating the steady-state temperature distribution for continuous wave laser-heated experiments in the diamond anvil cell. TempDAC solves the steady heat conduction equation in three dimensions over the sample chamber, gasket, and diamond anvils and includes material-, temperature-, and direction-dependent thermal conductivity, while allowing for flexible sample geometries, laser beam intensity profile, and laser absorption properties. The model has been validated against an axisymmetric analytic solution for the temperature distribution within a laser-heated sample. Example calculations illustrate the importance of considering heat flow in three dimensions for the laser-heated diamond anvil cell. In particular, we show that a "flat top" input laser beam profile does not lead to a more uniform temperature distribution or flatter temperature gradients than a wide Gaussian laser beam. © 2013 AIP Publishing LLC.
Taylor T.,University of York |
Bedau M.,Reed College |
Channon A.,Keele University |
Ackley D.,University of New Mexico |
And 21 more authors.
Artificial Life | Year: 2016
We describe the content and outcomes of the First Workshop on Open-Ended Evolution: Recent Progress and Future Milestones (OEE1), held during the ECAL 2015 conference at the University of York, UK, in July 2015. We briefly summarize the content of the workshop's talks, and identify the main themes that emerged from the open discussions. Two important conclusions from the discussions are: (1) the idea of pluralism about OEE - it seems clear that there is more than one interesting and important kind of OEE; and (2) the importance of distinguishing observable behavioral hallmarks of systems undergoing OEE from hypothesized underlying mechanisms that explain why a system exhibits those hallmarks. We summarize the different hallmarks and mechanisms discussed during the workshop, and list the specific systems that were highlighted with respect to particular hallmarks and mechanisms. We conclude by identifying some of the most important open research questions about OEE that are apparent in light of the discussions. The York workshop provides a foundation for a follow-up OEE2 workshop taking place at the ALIFE XV conference in Cancún, Mexico, in July 2016. Additional materials from the York workshop, including talk abstracts, presentation slides, and videos of each talk, are available at http://alife.org/ws/oee1. © 2016 Massachusetts Institute of Technology. Published under a Creative Commons Attribution 3.0 Unported (CC BY) license.
Taki-Nakano N.,Tokyo Institute of Technology |
Taki-Nakano N.,Mitsubishi Group |
Ohzeki H.,Mitsubishi Group |
Kotera J.,Mitsubishi Group |
And 2 more authors.
Biochimica et Biophysica Acta - General Subjects | Year: 2014
Background Jasmonates are plant lipid-derived oxylipins that act as key signaling compounds when plants are under oxidative stress, but little is known about their functions in mammalian cells. Here we investigated whether jasmonates could protect human neuroblastoma SH-SY5Y cells against oxidative stress-induced toxicity. Methods The cells were pretreated with individual jasmonates for 24 h and exposed to hydrogen peroxide (H2O2) for 24 h. Before the resulting cytotoxicity, intracellular reactive oxygen species (ROS) levels, and mitochondrial membrane potential were measured. We also measured intracellular glutathione (GSH) levels and investigated changes in the signaling cascade mediated by nuclear factor erythroid 2-related factor 2 (Nrf2) in cells treated with 12-oxo phytodienoic acid (OPDA). Results Among the jasmonates, only OPDA suppressed H2O2-induced cytotoxicity. OPDA pretreatment also inhibited the H2O2-induced ROS increase and mitochondrial membrane potential decrease. In addition, OPDA induced the nuclear translocation of Nrf2 and increased intracellular GSH level and the expression of the Nrf2-regulated phase II antioxidant enzymes heme oxygenase-1, NADPH quinone oxidoreductase 1, and glutathione reductase. Finally, the cytoprotective effects of OPDA were reduced by siRNA-induced knockdown of Nrf2. Conclusions These results demonstrated that among jasmonates, only OPDA suppressed oxidative stress-induced death of human neuroblastoma cells, which occurred via activation of the Nrf2 pathway. General significance Plant-derived oxylipin OPDA may have the potential to provide protection against oxidative stress-related diseases. © 2014 The Authors.
Mitchell R.N.,California Institute of Technology |
Mitchell R.N.,Yale University |
Raub T.D.,University of St. Andrews |
Silva S.C.,University of Connecticut |
Kirschvink J.L.,Earth Life Science Institute
American Journal of Science | Year: 2015
Charles Darwin suspected that the Cambrian "explosion" might be an artifact of fossil preservation. A more recent, initially controversial hypothesis that repeated true polar wander (TPW) triggered the Ediacaran-Cambrian explosion of animal life has been supported by numerous paleomagnetic and geochronologic refinements. These data imply 75° of TPW between 535 and 515 million years ago, coinciding with the paleontologically observed rise in metazoan diversity and disparity. We show here that this evolutionary trend is explained simply by the well known ecology-driven increase of diversity in low latitudes, coupled by other ecological effects as well as the enhanced deposition of sedimentary rocks during TPW-driven sea-level transgressions. During the Cambrian TPW event, Laurentia and parts of Gondwanaland moved into the equatorial zone while experiencing local TPW-induced transgressions; these areas dominate the paleontological record of the time. Although diversity might thus be considered partly artifactual, TPW acted on Cambrian biogeography to increase net diversity; and enhanced rates of origination and extinction also could increase disparity, especially if Early Cambrian TPW occurred at a time when genetic regulatory networks were critically poised for expansion and exaptation.
Yuzawa Y.,Tokyo Institute of Technology |
Shimojima M.,Tokyo Institute of Technology |
Sato R.,Tokyo Institute of Technology |
Mizusawa N.,Hosei University |
And 9 more authors.
Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids | Year: 2014
We characterized certain physiological functions of cyanobacterial monoglucosyldiacylglycerol using a Synechocystis sp. PCC 6803 mutant in which the gene for monoglucosyldiacylglycerol synthase had been disrupted and its function complemented by inclusion of an Arabidopsis monogalactosyldiacylglycerol synthase gene. By using this method, we prepared the first viable monoglucosyldiacylglycerol-deficient mutant of cyanobacterium and found that monoglucosyldiacylglycerol is not essential for its growth and photosynthesis under a set of "normal growth conditions" when monogalactosyldiacylglycerol is adequately supplied by the Arabidopsis monogalactosyldiacylglycerol synthase. The mutant had healthy thylakoid membranes and normal pigment content. The membrane lipid composition of the mutant was similar with that of WT except lack of monoglucosyldiacylglycerol and a slight increase in the level of phosphatidylglycerol at both normal and low temperatures. However, the ratio of unsaturated fatty acids in monogalactosyldiacylglycerol and digalactosyldiacylglycerol was reduced in the mutant compared with WT. Although the growth of the mutant was indistinguishable with that of WT at normal growth temperature, it was markedly retarded at low temperature compared with that of WT. Our data indicated the possibility that cyanobacterial monogalactosyldiacylglycerol-synthesis pathway might be required for the adequate unsaturation level of fatty acids in galactolipids and affect the low-temperature sensitivity. © 2013 The Author.
Mookherjee M.,Cornell University |
Tsuchiya J.,Ehime University |
Tsuchiya J.,Earth Life Science Institute
Physics of the Earth and Planetary Interiors | Year: 2015
We have used first principles simulation based on density functional theory to calculate the equation of state and elasticity of superhydrous phase B, Mg10Si3O14(OH)4. The pressure-volume results for superhydrous phase B is well represented by a third order Birch-Murnaghan formulation, with K0=161.8 (±0.2)GPa and K0'=4.4 (±0.01). The calculated full elastic tensor at 0GPa is in good agreement with Brillouin scattering results, with the compressional elastic constants: c11=329.5GPa, c22=294.9GPa, c33=306.8GPa, the shear elastic constants - c44=99.8GPa, c55=98GPa, and c66=99GPa; the off-diagonal elastic constants c12=82.5GPa, c13=84.6GPa, and c23=98.7GPa. At the depths corresponding to the mantle transition zone, the aggregate sound wave velocities for superhydrous phase B is slower compared to dry ringwoodite which is the dominant mineral phase. However, hydrous ringwoodite bulk sound velocities are comparable to that of superhydrous phase B. Majoritic garnet, the second most abundant mineral in the transition zone, has bulk sound wave velocities slower than superhydrous phase B. An assemblage consisting of hydrous ringwoodite, superhydrous phase B, and majorite garnet could account for the low velocities observed in certain subduction zone settings at depths corresponding to the base of the transition zone and upper mantle. Superhydrous phase B exhibits moderate single-crystal elastic anisotropy with AVP~3% and AVS~5% at the base of the transition zone. Single-crystal elastic anisotropy of other dense hydrous magnesium silicate phases phase such as hydrous phase D is significantly larger at these conditions and might play a major role in explaining the observed mid mantle seismic anisotropy. © 2014 Elsevier B.V.