Showing papers in "Lawrence Berkeley National Laboratory in 2008"

Iterative model-building, structure refinement, and density modification with the PHENIX AutoBuild Wizard

Abstract: Iterative model-building, structure refinement, and density modification with the PHENIX AutoBuild Wizard Thomas C. Terwilliger a* , Ralf W. Grosse-Kunstleve b , Pavel V. Afonine b , Nigel W. Moriarty b , Peter Zwart b , Li-Wei Hung a , Randy J. Read c , Paul D. Adams b* a b Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA Lawrence Berkeley National Laboratory, One Cyclotron Road, Bldg 64R0121, Berkeley, CA 94720, USA. c Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK. * Email: terwill@lanl.gov or PDAdams@lbl.gov Running title: The PHENIX AutoBuild Wizard Abstract The PHENIX AutoBuild Wizard is a highly automated tool for iterative model- building, structure refinement and density modification using RESOLVE or TEXTAL model- building, RESOLVE statistical density modification, and phenix.refine structure refinement. Recent advances in the AutoBuild Wizard and phenix.refine include automated detection and application of NCS from models as they are built, extensive model completion algorithms, and automated solvent molecule picking. Model completion algorithms in the AutoBuild Wizard include loop-building, crossovers between chains in different models of a structure, and side-chain optimization. The AutoBuild Wizard has been applied to a set of 48 structures at resolutions ranging from 1.1 A to 3.2 A, resulting in a mean R-factor of 0.24 and a mean free R factor of 0.29. The R-factor of the final model is dependent on the quality of the starting electron density, and relatively independent of resolution. Keywords: Model building; model completion; macromolecular models; Protein Data Bank; structure refinement; PHENIX Introduction Iterative model-building and refinement is a powerful approach to obtaining a complete and accurate macromolecular model. The approach consists of cycles of building an atomic model based on an electron density map for a macromolecular structure, refining the structure, using the refined structure as a basis for improving the map, and building a new model. This type of approach has been carried out in a semi-automated fashion for many years, with manual model-building iterating with automated refinement (Jensen, 1997). More recently, with the development first of ARP/wARP (Perrakis et al., 1999), and later other procedures including RESOLVE iterative model-building and refinement (Terwilliger,

Report to Congress on Server and Data Center Energy Efficiency: Public Law 109-431

Abstract: This report was prepared in response to the request from Congress stated in Public Law 109-431 (H.R. 5646),"An Act to Study and Promote the Use of Energy Efficient Computer Servers in the United States." This report assesses current trends in energy use and energy costs of data centers and servers in the U.S. (especially Federal government facilities) and outlines existing and emerging opportunities for improved energy efficiency. It also makes recommendations for pursuing these energy-efficiency opportunities broadly across the country through the use of information and incentive-based programs.

Data growth and its impact on the SCOP database: new developments

Abstract: The Structural Classification of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. The SCOP hierarchy comprises the following levels: Species, Protein, Family, Superfamily, Fold and Class. While keeping the original classification scheme intact, we have changed the production of SCOP in order to cope with a rapid growth of new structural data and to facilitate the discovery of new protein relationships. We describe ongoing developments and new features implemented in SCOP. A new update protocol supports batch classification of new protein structures by their detected relationships at Family and Superfamily levels in contrast to our previous sequential handling of new structural data by release date. We introduce pre-SCOP, a preview of the SCOP developmental version that enables earlier access to the information on new relationships. We also discuss the impact of worldwide Structural Genomics initiatives, which are producing new protein structures at an increasing rate, on the rates of discovery and growth of protein families and superfamilies. SCOP can be accessed at http://scop.mrc-lmb.cam.ac.uk/scop.

Seeded Growth of Highly Luminescent CdSe/CdS Nano-Heterostructures with Rod and Tetrapod Morphologies

Abstract: We have demonstrated that seeded growth of nanocrystals offers a convenient way to design nanoheterostructures with complex shapes and morphologies by changing the crystalline structure of the seed. By using Use nanocrystals with wurtzite and zinc blende structure as seeds for growth of US nanorods, we synthesized CdSe/CdS heterostructure nanorods and nanotetrapods, respectively. Both of these structures showed excellent luminescent properties, combining high photoluminescence efficiency (similar to 80 and similar to 50percent for nanorods and nanotetrapods, correspondingly), giant extinction coefficients (similar to 2 x 10(7) and similar to 1.5 x 10(8) M-1 cm (-1) at 350 nm for nanorods and nanotetrapods, correspondingly), and efficient energy transfer from the US arms into the emitting CdSe Core.

Ambient pressure photoelectron spectroscopy: a new tool for surface science and nanotechnology

Abstract: Ambient Pressure Photoelectron Spectroscopy: A new tool for surface science and nanotechnology M. Salmeron 1 and R. Schlogl 2 Lawrence Berkeley National Laboratory and Materials Science and Engineering Department, University of California, Berkeley Fritz-Haber Institute of the Max Planck Gesellshaft. Berlin. Germany

Interlayer Interaction and Electronic Screening in Multilayer Graphene

Abstract: Interlayer interaction and electronic screening in multilayer graphene Taisuke Ohta, 1, 2 Aaron Bostwick, 1 J. L. McChesney, 1, 3 Thomas Seyller, 4 Karsten Horn, 2 and Eli Rotenberg 1 Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California, USA Fritz-Haber-Institut der Max-Planck-Gesellschaft, Berlin, Germany Montana State University, Bozeman, Montana, USA Institut f¨ r Physik der Kondensierten Materie, Universit¨ t Erlangen-N¨ rnberg, Erlangen, Germany u a u (Dated: March 30, 2007) The unusual transport properties of graphene are the direct consequence of a peculiar bandstruc- ture near the Dirac point. We determine the shape of the π bands and their characteristic splitting, and find the transition from two-dimensional to bulk character for 1 to 4 layers of graphene by angle-resolved photoemission. By detailed measurements of the π bands we derive the stacking order, layer-dependent electron potential, screening length and strength of interlayer interaction by comparison with tight binding calculations, yielding a comprehensive description of multilayer graphene’s electronic structure. PACS numbers: Much recent attention has been given to the electronic structure of multilayer films of graphene, the honeycomb carbon sheet which is the building block of graphite, car- bon nanotubes, C 60 , and other mesoscopic forms of car- bon [1]. Recent progress in synthesizing or isolating mul- tilayer graphene films [2–4] has provided access to their physical properties, and revealed many interesting trans- port phenomena, including an anomalous quantum Hall effect [5, 6], ballistic electron transport at room temper- ature [7], micron-scale coherence length [7, 8] and novel many-body couplings [9]. These effects originate from the effectively massless Dirac Fermion character of the carri- ers derived from graphene’s valence bands, which exhibit a linear dispersion degenerate near the so-called Dirac point energy, E D [10]. These unconventional properties of graphene offer a new route to room temperature, molecular-scale electron- ics capable of quantum computing [6, 7]. For example, a possible switching function in bilayer graphene has been suggested by reversibly lifting the band degeneracy at the Fermi level (E F ) upon application of an electric field [11, 12]. This effect is due to a unique sensitivity of the bandstructure to the charge distribution brought about by the interplay between strong interlayer hopping and weak interlayer screening, neither of which are currently well-understood [13, 14]. In order to evaluate the interlayer screening, stack- ing order and interlayer coupling, we have systemati- cally studied the evolution of the bandstructure of one to four layers of graphene using angle-resolved photoemis- sion spectroscopy (ARPES). We demonstrate experimen- tally that the interaction between layers and the stacking sequence affect the topology of the π bands, the former inducing an electronic transition from two-dimensional (2D) to 3D (bulk) character when going from one layer to multilayer graphene. The interlayer hopping integral and screening length are determined as a function of the num- ber of graphene layers by exploiting the sensitivity of π FIG. 1: (color online) Photoemission images revealing the bandstructure of (a) single and (b) bilayer graphene along high symmetry directions, Γ-K-M-Γ. The blue dashed lines are scaled DFT bandstructure of free standing films [16]. Inset in (a) shows the 2D Brillouin zone of graphene. states to the Coulomb potential, and the layer-dependent carrier concentration is estimated. The films were synthesized on n-type (nitrogen, 1 × 10 18 cm −3 ) 6H-SiC(0001) substrates (SiCrystal AG) that were etched in hydrogen at 1550 C. Annealing in a vac- uum first removes the resulting silicate adlayer and then causes the growth of the graphene layers between 1250 to 1400 C [15]. Beyond the first layer, the samples have a ± 0.5 monolayer thickness variation; the bandstructures of different thicknesses were extracted using the method of Ref. [11]. ARPES measurements were conducted at the Electronic Structure Factory endstation at beamline 7.01 of the Advanced Light Source, equipped with a Sci- enta R4000 electron energy analyzer. The samples were cooled to ∼ 30K by liquid He. The photon energy was 94 eV with the overall energy resolution of ∼30 meV for Fig. 1 and Fig. 2(a-d). The bandstructures of a single (Fig. 1 (a)) and a bi-

Tunable plasmonic lattices of silver nanocrystals

Abstract: Silver nanocrystals are ideal building blocks for plasmonicmaterials that exhibit a wide range of unique and potentially usefuloptical phenomena. Individual nanocrystals display distinct opticalscattering spectra and can be assembled into hierarchical structures thatcouple strongly to external electromagnetic fields. This coupling, whichis mediated by surface plasmons, depends on their shape and arrangement.Here we demonstrate the bottom-up assembly of polyhedral silvernanocrystals into macroscopic two-dimensional superlattices using theLangmuir-Blodgett technique. Our ability to control interparticlespacing, density, and packing symmetry allows for tunability of theoptical response over the entire visible range. This assembly strategyoffers a new, practical approach to making novel plasmonic materials forapplication in spectroscopic sensors, sub-wavelength optics, andintegrated devices that utilize field enhancement effects.

Shotgun metaproteomics of the human distal gut microbiota

Abstract: The human gut contains a dense, complex and diverse microbial community, comprising the gut microbiome. Metagenomics has recently revealed the composition of genes in the gut microbiome, but provides no direct information about which genes are expressed or functioning. Therefore, our goal was to develop a novel approach to directly identify microbial proteins in fecal samples to gain information about the genes expressed and about key microbial functions in the human gut. We used a non-targeted, shotgun mass spectrometry-based whole community proteomics, or metaproteomics, approach for the first deep proteome measurements of thousands of proteins in human fecal samples, thus demonstrating this approach on the most complex sample type to date. The resulting metaproteomes had a skewed distribution relative to the metagenome, with more proteins for translation, energy production and carbohydrate metabolism when compared to what was earlier predicted from metagenomics. Human proteins, including antimicrobial peptides, were also identified, providing a non-targeted glimpse of the host response to the microbiota. Several unknown proteins represented previously undescribed microbial pathways or host immune responses, revealing a novel complex interplay between the human host and its associated microbes.

Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus

Abstract: Prochlorococcus is a marine cyanobacterium that numerically dominates the mid-latitude oceans and is the smallest known oxygenic phototroph. Numerous isolates from diverse areas of the world's oceans have been studied and shown to be physiologically and genetically distinct. All isolates described thus far can be assigned to either a tightly clustered high-light (HL)-adapted clade, or a more divergent low-light (LL)-adapted group. The 16S rRNA sequences of the entire Prochlorococcus group differ by at most 3percent, and the four initially published genomes revealed patterns of genetic differentiation that help explain physiological differences among the isolates. Here we describe the genomes of eight newly sequenced isolates and combine them with the first four genomes for a comprehensive analysis of the core (shared by all isolates) and flexible genes of the Prochlorococcus group, and the patterns of loss and gain of the flexible genes over the course of evolution. There are 1,273 genes that represent the core shared by all 12 genomes. They are apparently sufficient, according to metabolic reconstruction, to encode a functional cell. We describe a phylogeny for all 12 isolates by subjecting their complete proteomes to three different phylogenetic analyses. For each non-core gene, we used a maximum parsimony method to estimate which ancestor likely first acquired or lost each gene. Many of the genetic differences among isolates, especially for genes involved in outer membrane synthesis and nutrient transport, are found within the same clade. Nevertheless, we identified some genes defining HL and LL ecotypes, and clades within these broad ecotypes, helping to demonstrate the basis of HL and LL adaptations in Prochlorococcus. Furthermore, our estimates of gene gain events allow us to identify highly variable genomic islands that are not apparent through simple pairwise comparisons. These results emphasize the functional roles, especially those connected to outer membrane synthesis and transport that dominate the flexible genome and set it apart from the core. Besides identifying islands and demonstrating their role throughout the history of Prochlorococcus, reconstruction of past gene gains and losses shows that much of the variability exists at the leaves of the tree, between the most closely related strains. Finally, the identification of core and flexible genes from this 12-genome comparison is largely consistent with the relative frequency of Prochlorococcus genes found in global ocean metagenomic databases, further closing the gap between our understanding of these organisms in the lab and the wild.

Toward Production From Gas Hydrates: Current Status, Assessment of Resources, and Simulation-Based Evaluation of Technology and Potential

Abstract: Toward Production From Gas Hydrates: Current Status, Assessment of Resources, and Simulation-Based Evaluation of Technology and Potential George J. Moridis, SPE, Lawrence Berkeley National Laboratory; Timothy S. Collett, SPE, US Geological Survey; Ray Boswell, US Department of Energy; M. Kurihara, SPE, Japan Oil Engineering Company; Matthew T. Reagan, SPE, Lawrence Berkeley National Laboratory; Carolyn Koh and E. Dendy Sloan, SPE, Colorado School of Mines This paper was prepared for presentation at the 2008 SPE Unconventional Reservoirs Conference held in Keystone, Colorado, U.S.A., 10–12 February 2008. Abstract Gas hydrates are a vast energy resource with global distribution in the permafrost and in the oceans. Even if conservative estimates are considered and only a small fraction is recoverable, the sheer size of the resource is so large that it demands evaluation as a potential energy source. In this review paper, we discuss the distribution of natural gas hydrate accumulations, the status of the primary international RD Klauda and Sandler, 2005). Given the sheer magnitude of the resource, ever increasing global energy demand, and the finite volume of conventional fossil fuel reserves, gas hydrates are emerging as a potential energy source for a growing number of nations. The attractive- ness of gas hydrates is further enhanced by the environmental desirability of natural gas (as opposed to solid or liquid) fuels. Thus, the appeal of gas hydrate accumulations as future hydrocarbon gas sources is rapidly increasing and their production potential clearly demands technical and economic evaluation. The past decade has seen a marked acceleration in gas hydrate RD Paull et al., 2005), reservoir lithology, and rates and

Localized Pd Overgrowth on Cubic Pt Nanocrystals for Enhanced Electrocatalytic Oxidation of Formic Acid

Abstract: Localized Pd Overgrowth on Cubic Pt Nanocrystals for Enhanced Electrocatalytic Oxidation of Formic Acid Hyunjoo Lee †‡ , Susan E. Habas ‡ , Gabor A. Somorjai ‡ , and Peidong Yang ‡ Department of Chemical Engineering, Yonsei University, Seoul, South Korea, Department of Chemistry, University of California, Berkeley, California 94720, USA, and Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA Email: p_yang@uclink.berkeley.edu RECEIVED DATE ; Single crystalline surface such as (100), (111), (110) has been studied as an idealized platform for electrocatalytic reactions since the atomic arrangement affects a catalytic property. The secondary metal deposition on these surfaces also alters the catalytic property often showing improvement such as poisoning decrease. On the other hand, electrocatalysts used for practical purpose usually have a size on the order of nanometers. Therefore, linking the knowledge from single crystalline studies to nanoparticle catalysts is of enormous importance. Recently, the Pt nanoparticles which surface structure was preferentially oriented was synthesized and used as electrocatalysts 12 . Here, we demonstrate a rational design of a binary metallic nanocatalyst based on the single crystalline study. Clavilier et al. studied the electro-oxidation of formic acid for Pd adsorbed on Pt(100) single crystal surfaces. 5 They observed that the presence of adsorbed palladium on Pt(100) decreases self- poisoning and lowers the oxidation potential considerably. The multi-metallic nanoparticle catalysts, however, were usually prepared by co-precipitation 6 or electrodeposition 7 , and control over surface structure was not achieved. We present the synthesis and application of binary Pt/Pd nanoparticles in which Pd decorates the well-defined surface of Pt nanoparticles. Pt nanocubes fully bound by (100) surfaces acted as seeds for overgrowth of Pd. Overgrowth was observed at multiple points on each seed, predominantly at the corners. Electro-oxidation of formic acid performed on these binary Pt/Pd catalysts showed the same effects of less poisoning and lower oxidation potential expected from the single crystal study. Preparation of metal nanoparticles with shape control has often been achieved by controlling growth rates on different facets through interactions with surface-stabilizing agents. 8 However, since the catalytic activity is hindered by these surface-stabilizing agents, 9 preserving the catalytic activity of the metal surface is crucial. In this study, we used tetradecyltrimethylammonium bromide (TTAB) as a surface-stabilizing agent since it has a weak interaction with metal surfaces 9a . The cubic Pt nanoparticles used as seeds were prepared by reducing K 2 PtCl 4 dissolved in aqueous TTAB solution with NaBH 4 as previously reported. 9a A TEM image of the cubic Pt seed particles is shown in Figure S1(a). Pd was nucleated on the surface of cubic Pt seeds upon reduction of K 2 PdCl 4 by ascorbic acid in the presence of TTAB (See Supporting Information for more details). Figure 1(a) shows a low magnification TEM image of the binary Pt/Pd nanoparticles. Single, double and multiple nucleation of Pd on Pt nanoparticles was observed with nucleation occurring primarily on the corners. High resolution TEM images in Figures 1(b) show the interface of Figure 1. TEM images of (a) binary Pt/Pd nanoparticles, HR-TEM images of (b) Pt/Pd interface with an atomic resolution, (c) high Pd coverage and (d) low Pd coverage of binary Pt/Pd nanoparticles. the two metals more clearly. Pd grew on Pt surface epitaxially. Figure 1(c) and (d) show a high and low coverage of Pd on Pt surface. The formation of multiple nucleation sites of Pd on the Pt seeds rather than conformal overgrowth depends on the rate of reduction which was controlled through pH. The addition of as- made Pt seeds (pH~9) also introduces the strongly basic metaborate ion (BO 2- ) formed during the reaction of NaBH 4 with water. The higher pH increases the rate of Pd reduction, probably due to better stabilization of the oxidized form of the ascorbic acid. The increased rate of reduction may encourage the formation of multiple nucleation sites rather than the conformal overgrowth of a thin Pd shell which was observed when the Pt seeds were acidified to a neutral pH 10 . The addition of base to bring the pH of the seed solution back to ~9 once again allows for the formation of multiple nucleation sites. Fully grown cubic Pd nanoparticles with a cubic Pt seed inside, shown in Figure S1(b), were prepared by decreasing the concentration of Pt seeds along with the pH. This type of epitaxial overgrowth was demonstrated previously. 12 While both the Pt and Pd surfaces are accessible on the binary Pt/Pd nanoparticles, only the Pd surface is available on the core- shell Pt/Pd nanocubes. Pd nanoparticles without Pt seeds were also prepared as shown in Figure S1(c) for comparison.

Reversible Guest Exchange Mechanisms in Supramolecular Host-Guest Assemblies

Abstract: Reversible Guest Exchange Mechanisms in Supramolecular Host-Guest Assemblies Michael D. Pluth and Kenneth N. Raymond* Synthetic chemists have provided a wide array of supramolecular assemblies able to encapsulate guest molecules. The scope of this tutorial review focuses on supramolecular host molecules capable of reversibly encapsulating polyatomic guests. Much work has been done to determine the mechanism of guest encapsulation and guest release. This review covers common methods of monitoring and characterizing guest exchange such as NMR, UV-VIS, mass spectroscopy, electrochemistry, and calorimetry and also presents representative examples of guest exchange mechanisms. The guest exchange mechanisms of hemicarcerands, cucurbiturils, hydrogen-bonded assemblies, and metal-ligand assemblies are discussed. Special attention is given to systems which exhibit constrictive binding, a motif common in supramolecular guest exchange systems. 1. Introduction Supramolecular chemistry exemplifies the adage that the whole is often greater than the sum of the parts. By this we mean that the final structure and properties of supramolecular assemblies are often more remarkable than the simple building blocks. Most students in an introductory chemistry course have seen the dramatic difference in the properties of a supramolecular assembly and its subunits in the starch test for iodine. In the presence of iodine, the starch helical sugar polymer, composed of α-1,4-linked glucans, encapsulates a number of linear I 2 molecules (Figure 1). 1 This host-guest complex, with iodine molecules trapped inside an amylose helix, has a characteristic blue color which allows for the identification of iodine. Nature often uses simple and identical subunits as the building blocks of highly complex supramolecular assemblies, many of which have biological importance. The protein apoferritin, for example, is self-assembled from twenty-four The overall structures and properties of these assemblies are quite diverse, with internal cavities ranging from a few cubic angstroms to over a cubic nanometer. 3 Using design strategies similar to Nature, interactions such as covalent bonds, electrostatic attractions, metal-ligand bonds, and hydrogen bonding have been used to form the ‘glue’ holding subunits together. Synthetic assemblies have been used to encapsulate Fig. 2 Twenty-four identical subunits self-assemble to form the protein apoferritin. The assembled protein has octahedral symmetry and a large interior cavity. Fig. 1 In the presence of iodine, amylose, the main component of starch, forms helical polymers which encapsulate I 2 molecules. identical subunits creating an assembly with octahedral symmetry and an internal cavity of over 230 nm 3 (Figure 2). 2 This iron-transport protein can hold up to 4500 iron atoms as ferric hydrous oxides. Such assemblies often rely on a variety of weak supramolecular interactions such as hydrogen- bonding, π-π interactions, and van der Waals interactions to hold the subunits together. Following Nature’s lead, synthetic chemists have made sizable efforts in the formation of highly complex supramolecular assemblies built from simple building blocks. University of California, Department of Chemistry, Berkeley, CA 94720, USA. Fax: (+1) 510-486-5283; Tel: (+1) 510-642-7219; E-mail: raymond@socrates.berkeley.edu a variety of guest molecules, stabilize reactive intermediates, and even facilitate chemical reactions. 3, 4 Without covalent bonds to bind the guest molecules to the interior of supramolecular assemblies, guests are often free to exchange from the interior to the exterior of the host cavity. The process of reversibly exchanging one guest for another offers many questions on the mechanism of this process. Is host deformation required for guest exchange? Does the host dissociate during guest exchange? What influences do the size and chemical functionality of the guest have? These are questions relevant to guest exchange mechanisms, and often small changes in the guest or host can dramatically change the dynamics of the exchange process. Mechanistic studies of the method of guest encapsulation (ingress) and guest ejection (egress) are important for understanding how both structural and chemical features of the host are involved in guest exchange. Furthermore, as much recent focus has been placed on carrying out chemical reactions inside of synthetic supramolecular assemblies, determining the mechanism of guest exchange is imperative for understanding the often altered reactivities caused by encapsulation of reactants inside of supramolecular hosts. This review will be divided into two sections. The first part will focus on means of monitoring guest exchange and will provide references to the experimental methods outlined.

TOUGH+Hydrate v1.0 User's Manual: A Code for the Simulation of System Behavior in Hydrate-Bearing Geologic Media

Abstract: TOUGH+HYDRATE v1.0 is a new code for the simulation of the behavior of hydrate-bearing geologic systems. By solving the coupled equations of mass and heat balance, TOUGH+HYDRATE can model the non-isothermal gas release, phase behavior and flow of fluids and heat under conditions typical of common natural CH{sub 4}-hydrate deposits (i.e., in the permafrost and in deep ocean sediments) in complex geological media at any scale (from laboratory to reservoir) at which Darcy's law is valid. TOUGH+HYDRATE v1.0 includes both an equilibrium and a kinetic model of hydrate formation and dissociation. The model accounts for heat and up to four mass components, i.e., water, CH{sub 4}, hydrate, and water-soluble inhibitors such as salts or alcohols. These are partitioned among four possible phases (gas phase, liquid phase, ice phase and hydrate phase). Hydrate dissociation or formation, phase changes and the corresponding thermal effects are fully described, as are the effects of inhibitors. The model can describe all possible hydrate dissociation mechanisms, i.e., depressurization, thermal stimulation, salting-out effects and inhibitor-induced effects. TOUGH+HYDRATE is the first member of TOUGH+, the successor to the TOUGH2 [Pruess et al., 1991] family of codes for multi-component, multiphase fluid and heat flow developed at the Lawrence Berkeley National Laboratory. It is written in standard FORTRAN 95, and can be run on any computational platform (workstation, PC, Macintosh) for which such compilers are available.

Ultraconservation identifies a small subset of extremely constrained developmental enhancers

Abstract: While experimental studies have suggested that non-coding ultraconserved DNA elements are central nodes in the regulatory circuitry that specifies mammalian embryonic development, the possible functional relevance of their >200bp of perfect sequence conservation between human-mouse-rat remains obscure 1,2. Here we have compared the in vivo enhancer activity of a genome-wide set of 231 non-exonic sequences with ultraconserved cores to that of 206 sequences that are under equivalently severe human-rodent constraint (ultra-like), but lack perfect sequence conservation. In transgenic mouse assays, 50percent of the ultraconserved and 50percent of the ultra-like conserved elements reproducibly functioned as tissue-specific enhancers at embryonic day 11.5. In this in vivo assay, we observed that ultraconserved enhancers and constrained non-ultraconserved enhancers targeted expression to a similar spectrum of tissues with a particular enrichment in the developing central nervous system. A human genome-wide comparative screen uncovered ~;;2,600 non-coding elements that evolved under ultra-like human-rodent constraint and are similarly enriched near transcriptional regulators and developmental genes as the much smaller number of ultraconserved elements. These data indicate that ultraconserved elements possessing absolute human-rodent sequence conservation are not distinct from other non-coding elements that are under comparable purifying selection in mammals and suggest they are principal constituents of the cis-regulatory framework of mammalian development.

Short-lived pollutants in the Arctic: their climate impact and possible mitigation strategies

Abstract: Atmos. Chem. Phys., 8, 1723–1735, 2008 www.atmos-chem-phys.net/8/1723/2008/ © Author(s) 2008. This work is distributed under the Creative Commons Attribution 3.0 License. Atmospheric Chemistry and Physics Short-lived pollutants in the Arctic: their climate impact and possible mitigation strategies P. K. Quinn 1 , T. S. Bates 1 , E. Baum 2 , N. Doubleday 3 , A. M. Fiore 4 , M. Flanner 5 , A. Fridlind 6 , T. J. Garrett 7 , D. Koch 6 , S. Menon 8 , D. Shindell 6 , A. Stohl 9 , and S. G. Warren 10 1 NOAA 2 Clean Pacific Marine Environmental Laboratory, Seattle, WA, USA Air Task Force, Boston, MA, USA 3 Carleton University, Ottawa, ON, Canada 4 NOAA Geophysical Fluid Dynamics Laboratory, Princeton, NJ, USA 5 Advanced Study Program, NCAR, Boulder, CO, USA 6 NASA Goddard Institute for Space Sciences, New York, NY, USA 7 University of Utah, Salt Lake City, UT, USA 8 Lawrence Berkeley National Laboratory, Berkeley, CA, USA 9 Norwegian Institute for Air Research, Kjeller, Norway 10 University of Washington, Seattle, WA, USA Received: 17 October 2007 – Published in Atmos. Chem. Phys. Discuss.: 9 November 2007 Revised: 13 February 2008 – Accepted: 27 February 2008 – Published: 25 March 2008 Abstract. Several short-lived pollutants known to impact Arctic climate may be contributing to the accelerated rates of warming observed in this region relative to the global annually averaged temperature increase. Here, we present a summary of the short-lived pollutants that impact Arctic climate including methane, tropospheric ozone, and tropo- spheric aerosols. For each pollutant, we provide a descrip- tion of the major sources and the mechanism of forcing. We also provide the first seasonally averaged forcing and cor- responding temperature response estimates focused specifi- cally on the Arctic. The calculations indicate that the forc- ings due to black carbon, methane, and tropospheric ozone lead to a positive surface temperature response indicating the need to reduce emissions of these species within and outside the Arctic. Additional aerosol species may also lead to sur- face warming if the aerosol is coincident with thin, low ly- ing clouds. We suggest strategies for reducing the warming based on current knowledge and discuss directions for future research to address the large remaining uncertainties. Introduction Correspondence to: P. K. Quinn (patricia.k.quinn@noaa.gov) Arctic temperatures have increased at almost twice the global average rate over the past 100 years (IPCC, 2007). Warming in the Arctic has been accompanied by an earlier onset of spring melt, a lengthening of the melt season, and changes in the mass balance of the Greenland ice sheet (Stroeve et al., 2006; Zwally et al., 2002). In addition, Arctic sea ice extent has decreased from 1979 to 2006 in every month (Ser- reze et al., 2007). During the 2007 melt season, Arctic sea ice dropped to the lowest levels observed since satellite measure- ments began in 1979, resulting in the first recorded complete opening of the Northwest Passage (NSIDC, 2007). Impacts of ice loss include reduction of the Earth’s albedo, a positive feedback which leads to further warming. The earlier onset of spring melt is of particular concern as this is the season of maximum snow-albedo feedback (e.g., Hall and Qu, 2006). Timescales for a collapse of the Greenland ice sheet and a transition to a seasonally ice-free Arctic are highly uncer- tain, as are the regional and global impacts. However, clear ecological signals of significant and rapid response to these changes within the Arctic are already present. For example, paleolimnological data from across the Arctic have recorded striking changes in diatoms and other bioindicators corre- sponding to conditions of decreased ice cover and warming (Smol et al., 2005). Circumpolar vegetation also is showing signs of rapid change, including an expansion of shrub and tree coverage (Chapin et al., 2005). Published by Copernicus Publications on behalf of the European Geosciences Union.

The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata

Abstract: The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata Konstantinos Liolios 1 , Konstantinos Mavromatis 2 , Nektarios Tavernarakis 3 , and Nikos C. Kyrpides 2 University of Chicago, Chicago, USA, Genome Biology Program, Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, USA, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Crete, Greece. Corresponding Author: Nikos C. Kyrpides DOE Joint Genome Institute 2800 Mitchell Drive, B400 Walnut Creek, CA 94598 Phone: 925-296-5718 Fax: 925-296-5850 Email: NCKyrpides@lbl.gov

Sequence finishing and mapping of Drosophila melanogaster heterochromatin

Abstract: Genome sequences for most metazoans are incomplete due to the presence of repeated DNA in the pericentromeric heterochromatin. The heterochromatic regions of D. melanogaster contain 20 Mb of sequence amenable to mapping, sequence assembly and finishing. Here we describe the generation of 15 Mb of finished or improved heterochromatic sequence using available clone resources and assembly and mapping methods. We also constructed a BAC-based physical map that spans approximately 13 Mb of the pericentromeric heterochromatin, and a cytogenetic map that positions approximately 11 Mb of BAC contigs and sequence scaffolds in specific chromosomal locations. The integrated sequence assembly and maps greatly improve our understanding of the structure and composition of this poorly understood fraction of a metazoan genome and provide a framework for functional analyses.

Parameterized Beyond-Einstein Growth

Abstract: A single parameter, the gravitational growth index gamma, succeeds in characterizing the growth of density perturbations in the linear regime separately from the effects of the cosmic expansion. The parameter is restricted to a very narrow range for models of dark energy obeying the laws of general relativity but can take on distinctly different values in models of beyond-Einstein gravity. Motivated by the parameterized post-Newtonian (PPN) formalism for testing gravity, we analytically derive and extend the gravitational growth index, or Minimal Modified Gravity, approach to parameterizing beyond-Einstein cosmology. The analytic formalism demonstrates how to apply the growth index parameter to early dark energy, time-varying gravity, DGP braneworld gravity, and some scalar-tensor gravity.

In-situ X-ray photoelectron spectroscopy studies of water on metals and oxides at ambient conditions

Abstract: In-situ X-ray photoelectron spectroscopy studies of water metals and oxides at ambient conditions Ev Vi si ua t w tio ww n Ed .a ct itio iv n eP of DF ac .c tiv om eP DF fo rm So or ftw e d e ar ta e. ils on S Yamamoto 1 , H Bluhm 2 , K Andersson 1,3,6 , G Ketteler 4,7 , H Ogasawara 1 , M Salmeron 4,5 and A Nilsson 1,3 Stanford Synchrotron Radiation Laboratory, P.O.B. 20450, Stanford, CA 94309, USA. Lawrence Berkeley National Laboratory, Chemical Sciences Division, Berkeley, CA 94720, USA. FYSIKUM, Stockholm University, AlbaNova University Center, SE-106 91 Stockholm, Sweden. Lawrence Berkeley National Laboratory, Materials Sciences Division, Berkeley, CA 94720, USA. Department of Materials Science and Engineering, University of California, Berkeley, CA 94720, USA. E-mail: nilsson@slac.stanford.edu Running head: In-Situ XPS studies of water on metals and oxides at ambient conditions Present address: Center for Individual Nanoparticle Functionality (CINF), Department of Physics, Technical University of Denmark, Fysikvej 312, DK-2800 Kgs. Lyngby, Denmark. Present address: Department of Applied Physics, Chalmers University of Technology, SE-412 96 Goteborg, Sweden. Abstract . X-ray photoelectron spectroscopy (XPS) is a powerful tool for surface and interface analysis, providing the elemental composition of surfaces and the local chemical environment of adsorbed species. Conventional XPS experiments have been limited to ultrahigh vacuum (UHV) conditions due to a short mean free path of electrons in a gas phase. The recent advances in instrumentation coupled with third-generation synchrotron radiation sources enables in-situ XPS measurements at pressures above 5 Torr. In this review, we describe the basic design of the ambient pressure XPS setup that combines differential pumping with an electrostatic focusing. We present examples of the application of in-situ XPS to studies of water adsorption on the surface of metals and oxides including Cu(110), Cu(111), TiO 2 (110) under environmental conditions of water vapor pressure. On all these surfaces we observe a al general trend where hydroxyl groups form first, followed by molecular water adsorption. The importance of surface OH groups and their hydrogen bonding to water molecules in water adsorption on surfaces is discussed in detail.

International linear collider reference design report

Abstract: ILC-REPORT-2007-01 CHEP A07-001 (CHEP/KNU) Cockcroft-07-04 DESY 07-046 FERMILAB-TM-2382-AD-CD-DO-E-FESS-TD JAI-2007-001 JINR Dubna-E9-2007-39 JLAB-R-2007-01 KEK Report 2007-1 LNF-07/9(NT) SLAC-R-857 I NTERNATIONAL L INEAR C OLLIDER R EFERENCE D ESIGN R EPORT DR AF T A PRIL, 2007

Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks

Abstract: Bacteria of the genus Deinococcus are extremely resistant to ionizing radiation (IR), ultraviolet light (UV) and desiccation. The mesophile Deinococcus radiodurans was the first member of this group whose genome was completely sequenced. Analysis of the genome sequence of D. radiodurans, however, failed to identify unique DNA repair systems. To further delineate the genes underlying the resistance phenotypes, we report the whole-genome sequence of a second Deinococcus species, the thermophile Deinococcus geothermalis, which at its optimal growth temperature is as resistant to IR, UV and desiccation as D. radiodurans, and a comparative analysis of the two Deinococcus genomes. Many D. radiodurans genes previously implicated in resistance, but for which no sensitive phenotype was observed upon disruption, are absent in D. geothermalis. In contrast, most D. radiodurans genes whose mutants displayed a radiation-sensitive phenotype in D. radiodurans are conserved in D. geothermalis. Supporting the existence of a Deinococcus radiation response regulon, a common palindromic DNA motif was identified in a conserved set of genes associated with resistance, and a dedicated transcriptional regulator was predicted. We present the case that these two species evolved essentially the same diverse set of gene families, and that the extreme stress-resistance phenotypes of the Deinococcus lineage emerged progressively by amassing cell-cleaning systems from different sources, but not by acquisition of novel DNA repair systems. Our reconstruction of the genomic evolution of the Deinococcus-Thermus phylum indicates that the corresponding set of enzymes proliferated mainly in the common ancestor of Deinococcus. Results of the comparative analysis weaken the arguments for a role of higher-order chromosome alignment structures in resistance; more clearly define and substantially revise downward the number of uncharacterized genes that might participate in DNA repair and contribute to resistance; and strengthen the case for a role in survival of systems involved in manganese and iron homeostasis.

Weathering of Roofing Materials-An Overview

Abstract: Deliverable for CEC Task 2.6.4. Report LBNL-59724. Submitted to Construction and Building Materials, February, 2006 Weathering of Roofing Materials-An Overview Paul Berdahl, Hashem Akbari, and Ronnen Levinson Lawrence Berkeley National Laboratory Berkeley, CA 94720 and William A. Miller Oak Ridge National Laboratory Oak Ridge, TN 37831 Abstract An overview of several aspects of the weathering of roofing materials is presented. Degradation of materials initiated by ultraviolet radiation is discussed for plastics used in roofing, as well as wood and asphalt. Elevated temperatures accelerate many deleterious chemical reactions and hasten diffusion of material components. Effects of moisture include decay of wood, acceleration of corrosion of metals, staining of clay, and freeze- thaw damage. Soiling of roofing materials causes objectionable stains and reduces the solar reflectance of reflective materials. (Soiling of non-reflective materials can also increase solar reflectance.) Soiling can be attributed to biological growth (e.g., cyanobacteria, fungi, algae), deposits of organic and mineral particles, and to the accumulation of flyash, hydrocarbons and soot from combustion. 1. Introduction Roofing materials are exposed to the elements, namely wind, sunlight, rain, hail, snow, atmospheric pollution, and temperature variations and consequently degrade over time. Even the most durable materials are modified by deposition of ambient dust and debris, and may provide an opportunity for colonization by biological organisms such as cyanobacteria, fungi and algae. In this paper, we broadly review how weathering occurs and discuss several engineering strategies that are employed for improving the performance of roofing materials. We have been engaged in a multi-year project to develop and commercialize cooler, solar-reflective roofing in conjunction with a number of industrial partners. These materials can save energy used for air conditioning and improve occupant comfort. Since reflective white materials are sometimes not suitable from an architectural standpoint, the work has included materials with specified visual colors but with high near-infrared reflectance [1]. This paper is a summary of what we have learned concerning the weathering of roofing materials.

Topological Strings And (Almost) Modular Forms

Abstract: hep-th/0607100 arXiv:hep-th/0607100v2 4 May 2007 Topological Strings and (Almost) Modular Forms Mina Aganagic, 1 Vincent Bouchard, 2 Albrecht Klemm, 3 University of California, Berkeley, CA 94720, USA Mathematical Sciences Research Institute, Berkeley, CA 94720, USA University of Wisconsin, Madison, WI 53706, USA Abstract The B-model topological string theory on a Calabi-Yau threefold X has a symmetry group Γ, generated by monodromies of the periods of X. This acts on the topological string wave function in a natural way, governed by the quantum mechanics of the phase space H 3 (X). We show that, depending on the choice of polarization, the genus g topological string amplitude is either a holomorphic quasi-modular form or an almost holomorphic modular form of weight 0 under Γ. Moreover, at each genus, certain combinations of genus g amplitudes are both modular and holomorphic. We illustrate this for the local Calabi- Yau manifolds giving rise to Seiberg-Witten gauge theories in four dimensions and local IP 2 amplitudes near different points in the moduli space, which we use to give predictions for Z Gromov-Witten invariants of the orbifold C 3 /Z 3 . July 2006 and IP 1 ×IP 1 . As a byproduct, we also obtain a simple way of relating the topological string

The Genome of the Epsilonproteobacterial Chemolithoautotroph Sulfurimonas dentrificans

Abstract: Sulfur-oxidizing epsilonproteobacteria are common in a variety of sulfidogenic environments. These autotrophic and mixotrophic sulfur-oxidizing bacteria are believed to contribute substantially to the oxidative portion of the global sulfur cycle. In order to better understand the ecology and roles of sulfur-oxidizing epsilonproteobacteria, in particular those of the widespread genus Sulfurimonas, in biogeochemical cycles, the genome of Sulfurimonas denitrificans DSM1251 was sequenced. This genome has many features, including a larger size (2.2 Mbp), that suggest a greater degree of metabolic versatility or responsiveness to the environment than seen for most of the other sequenced epsilonproteobacteria. A branched electron transport chain is apparent, with genes encoding complexes for the oxidation of hydrogen, reduced sulfur compounds, and formate and the reduction of nitrate and oxygen. Genes are present for a complete, autotrophic reductive citric acid cycle. Many genes are present that could facilitate growth in the spatially and temporally heterogeneous sediment habitat from where Sulfurimonas denitrificans was originally isolated. Many resistance-nodulation-development family transporter genes (10 total) are present; of these, several are predicted to encode heavy metal efflux transporters. An elaborate arsenal of sensory and regulatory protein-encoding genes is in place, as are genes necessary to prevent and respond to oxidative stress.

Flow of mantle fluids through the ductile lower crust: Helium isotope trends

Abstract: Flow of Mantle Fluids Through the Duct,le Lower Crust: Helium Isotope Trends I B. Mack Kennedyl andlMatthijs C. van Soest ICenter for Isoto~e Geochemistry Earth Scienoes Division Lawrence Berkeley National Laboratory Berkeley, (:A 94720 2Noble Gas Geochemistry and Geochronology Laboratory School of Earth and Space Exploration Arizona State University Tempe, AZ 85287-1404 Abstract Heat and mass are injected into the shallow crust when mantle fluids are able to flow through the ductile lower crust. Minimum 3 He /4 He ratios in surface fluids from the northern Basin and Range province, western North America increase systematically from low, crustal values in the east to high, mantle values in the west, a regional trend that correlates with the rates of active crustal deformation. The highest ratios occur where the extension and shear strain rates are greatest. The correspondence of helium isotope ratios and active trans-tensional deformation indicates a deformation enhanced permeability and that mantle fluids can penetrate the ductile lithosphere in regions even where there is no significant magmatism. Superimposed on the regional trend are local, high- He/ He anomalies signifying hidden magmatic activity and/or deep fluid production with locally enhanced permeability, identifying zones with high resource potential, particularly for geothermal energy development.

TOUGHREACT User's Guide: A Simulation Program for Non-isothermal Multiphase Reactive Geochemical Transport in Variably Saturated Geologic Media, V1.2.1

Abstract: Coupled modeling of subsurface multiphase fluid and heat flow, solute transport, and chemical reactions can be applied to many geologic systems and environmental problems, including geothermal systems, diagenetic and weathering processes, subsurface waste disposal, acid mine drainage remediation, contaminant transport, and groundwater quality. TOUGHREACT has been developed as a comprehensive non-isothermal multi-component reactive fluid flow and geochemical transport simulator to investigate these and other problems. A number of subsurface thermo-physical-chemical processes are considered under various thermohydrological and geochemical conditions of pressure, temperature, water saturation, and ionic strength. TOUGHREACT can be applied to one-, two- or three-dimensional porous and fractured media with physical and chemical heterogeneity. The code can accommodate any number of chemical species present in liquid, gas and solid phases. A variety of equilibrium chemical reactions are considered, such as aqueous complexation, gas dissolution/exsolution, and cation exchange. Mineral dissolution/precipitation can take place subject to either local equilibrium or kinetic controls, with coupling to changes in porosity and permeability and capillary pressure in unsaturated systems. Chemical components can also be treated by linear adsorption and radioactive decay. The first version of the non-isothermal reactive geochemical transport code TOUGHREACT was developed (Xu and Pruess, 1998) by introducing reactive geochemistry into the more » framework of the existing multi-phase fluid and heat flow code TOUGH2 (Pruess, 1991). TOUGHREACT was further enhanced with the addition of (1) treatment of mineral-water-gas reactive-transport under boiling conditions, (2) an improved HKF activity model for aqueous species, (3) gas species diffusion coefficients calculated as a function of pressure, temperature, and molecular properties, (4) mineral reactive surface area formulations for fractured and porous media, and (5) porosity, permeability, and capillary pressure changes owing to mineral precipitation/dissolution (Sonnenthal et al., 1998, 2000, 2001; Spycher et al., 2003a). Subsequently, TOUGH2 V2 was released with additional EOS modules and features (Pruess et al., 1999). The present version of TOUGHREACT includes all of the previous extensions to the original version, along with the replacement of the original TOUGH2 (Pruess, 1991) by TOUGH2 V2 (Pruess et al., 1999). TOUGHREACT has been applied to a wide variety of problems, some of which are included as examples, such as: (1) Supergene copper enrichment (Xu et al., 2001); (2) Mineral alteration in hydrothermal systems (Xu and Pruess, 2001a; Xu et al., 2004b; Dobson et al., 2004); (3) Mineral trapping for CO{sub 2} disposal in deep saline aquifers (Xu et al., 2003b and 2004a); (4) Coupled thermal, hydrological, and chemical processes in boiling unsaturated tuff for the proposed nuclear waste emplacement site at Yucca Mountain, Nevada (Sonnenthal et al., 1998, 2001; Sonnenthal and Spycher, 2000; Spycher et al., 2003a, b; Xu et al., 2001); (5) Modeling of mineral precipitation/dissolution in plug-flow and fracture-flow experiments under boiling conditions (Dobson et al., 2003); (6) Calcite precipitation in the vadose zone as a function of net infiltration (Xu et al., 2003); and (7) Stable isotope fractionation in unsaturated zone pore water and vapor (Singleton et al., 2004). The TOUGHREACT program makes use of 'self-documenting' features. It is distributed with a number of input data files for sample problems. Besides providing benchmarks for proper code installation, these can serve as a self-teaching tutorial in the use of TOUGHREACT, and they provide templates to help jump-start new applications. The fluid and heat flow part of TOUGHREACT is derived from TOUGH2 V2, so in addition to the current manual, users must have the manual of the TOUGH2 V2 (Pruess et al., 1999). The present version of TOUGHREACT provides the following TOUGH2 fluid property or 'EOS' (equation-of-state) modules: (1) EOS1 for water, or two waters with typical applications to hydrothermal problems, (2) EOS2 for multiphase mixtures of water and CO{sub 2} also with typical applications to hydrothermal problems, (3) EOS3 for multiphase mixtures of water and air with typical applications to vadose zone and nuclear waste disposal problems, (4) EOS4 that has the same capabilities as EOS3 but with vapor pressure lowering effects due to capillary pressure, (5) EOS9 for single phase water (Richards equation) with typical applications to ambient temperature and pressure reactive geochemical transport problems, and (6) ECO2N for multiphase mixtures of water, CO{sub 2} and NaCl with typical applications to CO{sub 2} disposal in deep brine aquifers. « less

Future Air Conditioning Energy Consumption in Developing Countries and what can be done about it: The Potential of Efficiency in the Residential Sector

Abstract: The dynamics of air conditioning are of particular interest to energy analysts, both because of the high energy consumption of this product, but also its disproportionate impact on peak load. This paper addresses the special role of this end use as a driver of residential electricity consumption in rapidly developing economies. Recent history has shown that air conditioner ownership can grow grows more rapidly than economic growth in warm-climate countries. In 1990, less than a percent of urban Chinese households owned an air conditioner; by 2003 this number rose to 62 percent. The evidence suggests a similar explosion of air conditioner use in many other countries is not far behind. Room air conditioner purchases in India are currently growing at 20 percent per year, with about half of these purchases attributed to the residential sector. This paper draws on two distinct methodological elements to assess future residential air conditioner 'business as usual' electricity consumption by country/region and to consider specific alternative 'high efficiency' scenarios. The first component is an econometric ownership and use model based on household income, climate and demographic parameters. The second combines ownership forecasts and stock accounting with geographically specific efficiency scenarios within a unique analysis framework (BUENAS) developed by LBNL. The efficiency scenario module considers current efficiency baselines, available technologies, and achievable timelines for development of market transformation programs, such as minimum efficiency performance standards (MEPS) and labeling programs. The result is a detailed set of consumption and emissions scenarios for residential air conditioning.

Targeting the tumor microenvironment

Abstract: Kenny et al. Targeting the tumor microenvironment Targeting the tumor microenvironment Paraic A. Kenny, Genee Y. Lee and Mina J. Bissell Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720. For correspondence: pakenny@lbl.gov, mjbissell@lbl.gov TABLE OF CONTENTS 1. Abstract 2. Introduction 3. Heterotypic cell signaling mediators 4. Nonsteroidal anti-inflammatory drugs (NSAIDs) 5. Angiogenesis inhibitors 6. Aromatase inhibitors 7. Bisphosphonates 8. Conclusions 9. Acknowledgements 10. References

The morphologies of breast cancer cell lines in three-dimensional assays correlate with their profiles of gene expression

Abstract: * Manuscript Kenny, Lee et al. The morphologies of breast cancer cell lines in three-dimensional assays correlate with their profiles of gene expression Paraic A. Kenny* ,1 , Genee Y. Lee* ,1 , Connie A. Myers 1,3 , Richard M. Neve 1 , Jeremy R. Semeiks 1 , Paul T. Spellman 1 , Katrin Lorenz 1,4 , Eva H. Lee 1 , Mary Helen Barcellos-Hoff 1 , Ole W. Petersen 2 , Joe W. Gray 1 , Mina J. Bissell 1 *These authors contributed equally to this report. Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA. 2 Structural Cell Biology Unit , Institute of Medical Anatomy, The Panum Institute, University of Copenhagen, DK-2200 Copenhagen N, Denmark. Address for correspondence: Mina J. Bissell. Tel: +1 510 486 4365; Fax: +1 510 486 5586; Email: mjbissell@lbl.gov Running title 3D breast cancer cell transcriptomes and morphologies Current address: Division of Neuropathology, Washington University School of Medicine, St. Louis, MO 63110 Department of Molecular Medicine, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany

Where Water is Oxidized to Dioxygen: Structure of the Photosynthetic Mn4Ca Cluster from X-ray Spectroscopy

Abstract: Light-driven oxidation of water to dioxygen in plants, algae and cyanobacteria is catalyzed within photosystem II (PS II) by a Mn4Ca cluster. Although the cluster has been studied by many different methods, the structure and the mechanism have remained elusive. X-ray absorption and emission spectroscopy and EXAFS studies have been particularly useful in probing the electronic and geometric structure, and the mechanism of the water oxidation reaction. Recent progress, reviewed here, includes polarized X-ray absorption spectroscopy measurements of PS II single crystals. Analysis of those results has constrained the Mn4Ca cluster geometry to a set of three similar high-resolution structures. The structure of the cluster from the present study is unlike either the 3.0 or 3.5 Angstrom-resolution X-ray structures or other previously proposed models. The differences between the models derived from X-ray spectroscopy and crystallography are predominantly because of damage to the Mn4Ca cluster by X-rays under the conditions used for structure determination by X-ray crystallography. X-ray spectroscopy studies are also used for studying the changes in the structure of the Mn4Ca catalytic center as it cycles through the five intermediate states known as the Si-states (i=0-4). The electronic structure of the Mn4Ca cluster has been studied more recently using resonant inelastic X-ray scattering spectroscopy (RIXS), in addition to the earlier X-ray absorption and emission spectroscopy methods. These studies are revealing that the assignment of formal oxidation states is overly simplistic. A more accurate description should consider the charge density on the Mn atoms that includes the covalency of the bonds and delocalization of the charge over the cluster. The geometric and electronic structure of the Mn4Ca cluster in the S-states derived from X-ray spectroscopy are leading to a detailed understanding of the mechanism of the O-O bond formation during the photosynthetic water splitting process.