Showing papers in "Lawrence Berkeley National Laboratory in 2010"

The ground state of the electron gas by a stochastic method

Abstract: ., • ' % . ^ : K ~* B J£L~i0813_ 4JC-4 J NATIONAL RESOURCE FOR COMPUTATION IN CHEMISTRY^ '• • ' THE 81R0UND STATED 6|/THE ELECTION A - - .A r >'--H .1 ,4- v c ' M \>~ r tAWRfctftE BERKELEY LABORATORY «r National

Discovery of a Supernova Explosion at Half the Age of the Universe and its Cosmological Implications

Abstract: LBNL-41172 Discovery of a Supernova Explosion at Half the Age of the Universe and its Cosmological Implications S. Perlmutter, G. Aldering, M. Della Valle, S. Deustua, R. S. Ellis, S. Fabbro, A. Fruchter, G. Goldhaber, A. Goobar, D. E. Groom, 1. M. Hook, A. G. Kim, M. Y. Kim, R.A. Knop, C. Lidman, R. G. McMahon, P. Nugent, R. Pain, N. Panagia, C. R. Pennypacker, P. Ruiz-Lapuente, B. Schaefer & N. Walton (The Supernova Cosmology Project) This work was supported in part by the Director, Office of Science, Office of High Energy Physics, of the U.S. Department of Energy under Contract No. DE-AC03-76SF00098. DISCLAIMER This document was prepared as an account of work sponsored by the United States Government. While this document is believed to contain correct information, neither the United States Government nor any agency thereof, nor The Regents of the University of California, nor any of their employees, makes any warranty, express or implied, or assumes any legal responsibility for the accuracy, completeness, or usefulness of any infonnation, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by its trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or The Regents of the University of California. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof or The Regents of the University of California.

Observation of Single Colloidal Platinum Nanocrystal Growth Trajectories

Abstract: It is conventionally assumed that the growth of monodisperse colloidal nanocrystals requires a temporally discrete nucleation followed by monomer attachment onto the existing nuclei. However, recent studies have reported violations of this classical growth model, and have suggested that inter-particle interactions are also involved during the growth. Mechanisms of nanocrystal growth still remain controversial. Using in situ transmission electron microscopy, we show that platinum nanocrystals can grow either by monomer attachment from solution onto the existing particles or by coalescence between the particles. Surprisingly, an initially broad size distribution of the nanocrystals can spontaneously narrow. We suggest that nanocrystals take different pathways of growth based on their size- and morphology-dependent internal energies. These observations are expected to be highly relevant for other nanocrystal systems.

The NAS Parallel Benchmarks

Abstract: TITLE: The NAS Parallel Benchmarks AUTHOR: David H Bailey 1 ACRONYMS: NAS, NPB DEFINITION: The NAS Parallel Benchmarks (NPB) are a suite of parallel computer per- formance benchmarks. They were originally developed at the NASA Ames Re- search Center in 1991 to assess high-end parallel supercomputers [?]. Although they are no longer used as widely as they once were for comparing high-end sys- tem performance, they continue to be studied and analyzed a great deal in the high-performance computing community. The acronym “NAS” originally stood for the Numerical Aeronautical Simulation Program at NASA Ames. The name of this organization was subsequently changed to the Numerical Aerospace Sim- ulation Program, and more recently to the NASA Advanced Supercomputing Center, although the acronym remains “NAS.” The developers of the original NPB suite were David H. Bailey, Eric Barszcz, John Barton, David Browning, Russell Carter, LeoDagum, Rod Fatoohi, Samuel Fineberg, Paul Frederickson, Thomas Lasinski, Rob Schreiber, Horst Simon, V. Venkatakrishnan and Sisira Weeratunga. DISCUSSION: The original NAS Parallel Benchmarks consisted of eight individual bench- mark problems, each of which focused on some aspect of scientific computing. The principal focus was in computational aerophysics, although most of these benchmarks have much broader relevance, since in a much larger sense they are typical of many real-world scientific computing applications. The NPB suite grew out of the need for a more rational procedure to select new supercomputers for acquisition by NASA. The emergence of commercially available highly parallel computer systems in the late 1980s offered an attrac- tive alternative to parallel vector supercomputers that had been the mainstay of high-end scientific computing. However, the introduction of highly parallel systems was accompanied by a regrettable level of hype, not only on the part of the commercial vendors but even, in some cases, by scientists using the sys- tems. As a result, it was difficult to discern whether the new systems offered any fundamental performance advantage over vector supercomputers, and, if so, which of the parallel offerings would be most useful in real-world scientific computation. 1 Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, dhbailey@lbl.gov. Supported in part by the Director, Office of Computational and Technology Research, Division of Mathematical, Information, and Computational Sciences of the U.S. Department of Energy, under contract number DE-AC02-05CH11231.

Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels

Abstract: Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels Sung Kuk Lee, Howard Chou, Timothy S Ham, Taek Soon Lee, and Jay D Keasling ABSTRACT The ability to generate microorganisms that can produce biofuels similar to petroleum-based transportation fuels would allow the use of existing engines and infrastructure and would save an enormous amount of capital required for replacing the current infrastructure to accommodate biofuels that have properties significantly different from petroleum-based fuels. Several groups have demonstrated the feasibility of manipulating microbes to produce molecules similar to petroleum-derived products, albeit at relatively low productivity (e.g. maximum butanol production is around 20 g/L). For cost-effective production of biofuels, the fuel-producing hosts and pathways must be engineered and optimized. Advances in metabolic engineering and synthetic biology will provide new tools for metabolic engineers to better understand how to rewire the cell in order to create the desired phenotypes for the production of economically viable biofuels. INTRODUCTION Alternative transportation fuels are in high demand owing to concerns about climate change, the global petroleum supply, and energy security [ 1,2]. Currently, the most widely used biofuels are ethanol generated from starch (corn) or sugar cane and biodiesel produced from vegetable oil or animal fats [3 ]. However, ethanol is not an ideal fuel molecule in that it is not compatible with the existing fuel infrastructure for distribution and storage owing to its corrosivity and high hygroscopicity [1,4 ]. Also, it contains only about 70% of the energy content of gasoline. Biodiesel has similar problems (URL: http:// www.bdpedia.com/biodiesel/alt/alt.html): it cannot be transported in pipelines because its cloud and pour points are higher than those for petroleum diesel (petrodiesel), and its energy content is approximately 11% lower than that of petrodiesel. Furthermore, both ethanol and bio-diesel are currently produced from limited agricultural resources, even though there is a large, untapped resource of plant biomass (lignocellulose) that could be utilized as a renewable source of carbon-neutral, liquid fuels [ 5]. Microbial production of transportation fuels from renew-able lignocellulose has several advantages. First, the production is not reliant on agricultural resources commonly used for food, such as corn, sugar cane, soybean, and palm oil. Second, lignocellulose is the most abundant biopolymer on earth. Third, new biosynthetic pathways can be engineered to produce fossil-fuel replacements, including short- chain, branched-chain, and cyclic alcohols, alkanes, alkenes, esters and aromatics. The development of cost-effective and energy-efficient processes to convert lignocellulose into fuels is hampered by significant roadblocks, including the lack of genetic engineering tools for native producer organisms (non-model organ-isms), and difficulties in optimizing metabolic pathways and balancing the redox state in the engineered microbes [ 6]. Furthermore, production potentials are limited by the low activity of pathway enzymes and the inhibitory effect of fuels and byproducts from the upstream biomass processing steps on microorganisms responsible for producing fuels. Recent advances in synthetic biology and metabolic engineering will make it possible to overcome these hurdles and engineer microorganisms for the cost- effective production of biofuels from cellulosic biomass. In this review, we examine the range of choices available as potential biofuel candidates and production hosts, review the recent methods used to produce biofuels, and discuss how tools from the fields of metabolic engineering and synthetic biology can be applied to produce transportation fuels using genetically engineered micro-organisms. Liquid fuels and alternative biofuel molecules An understanding of what makes a good fuel is important in order to retool microorganisms to produce more useful alternative biofuels. The best fuel targets for the near term will be molecules that are already found in or similar to components of fossil-based fuel in order to be compatible with existing engines (spark ignition engine for gasoline, compression ignition engine for diesel fuel, and gas turbine for jet fuel). There are several relevant factors to consider when designing biofuel candidates ( Table 1). Energy contents, the combustion quality described by octane or cetane number, volatility, freezing point,

Single cell analysis: the new frontier in 'Omics'

Abstract: Single cell analysis: the new frontier in ‘Omics’ Daojing Wang 1 and Steven Bodovitz 2 1. Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 2. BioPerspectives, San Francisco, CA Corresponding author: Wang, D. (djwang@lbl.gov) Cellular heterogeneity arising from stochastic expression of genes, proteins, and metabolites is a fundamental principle of cell biology, but single cell analysis has been beyond the capabilities of ‘Omics’ technologies. This is rapidly changing with the recent examples of single cell genomics, transcriptomics, proteomics, and metabolomics. The rate of change is expected to accelerate owing to emerging technologies that range from micro/nanofluidics to microfabricated interfaces for mass spectrometry to third- and fourth-generation automated DNA sequencers. As described in this review, single cell analysis is the new frontier in Omics, and single cell Omics has the potential to transform systems biology through new discoveries derived from cellular heterogeneity. Single cell analysis: needs and applications Cellular heterogeneity Cellular heterogeneity within an isogenic cell population is a widespread event [1, 2]. Stochastic gene and protein expression at the single cell level has been clearly demonstrated in different systems using a variety of techniques [3-5]. Therefore, analyzing cell ensembles individually with high spatiotemporal resolutions will lead to a

Two distinct phases of apoptosis in mammary gland involution: proteinase-independent and -dependent pathways

Abstract: Two distinct phases of apoptosis in mammary gland involution: proteinase-independent and -dependent pathways Leif R. Lund 1,*, , John Romer 2 , Nicole Thomasset 3 , Helene Solberg 2 , Charles Pyke 2 , Mina J. Bissell 3 , Keld Dano 2 and Zena Werb 1,† Laboratory of Radiobiology and Environmental Health, University of California, San Francisco, California 94143-0750, USA Finsen Laboratory, Rigshospitalet, Strandboulevarden 49, DK-2100 Copenhagen, Denmark Life Sciences Division, Lawrence Berkeley Laboratory, Berkeley, California 94720, USA Present address 2 Author for correspondence: e-mail: zena@radlab.ucsf.edu LBNL/DOE funding & contract number: DE-AC02-05CH11231 DISCLAIMER This document was prepared as an account of work sponsored by the United States Government. While this document is believed to contain correct information, neither the United States Government nor any agency thereof, nor The Regents of the University of California, nor any of their employees, makes any warranty, express or implied, or assumes any legal responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by its trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or The Regents of the University of California. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof or The Regents of the University of California.

Normal and tumor-derived myoepithelial cells differ in their ability to interact withluminal breast epithelial cells for polarity and basement membrane deposition

Abstract: Normal and tumor-derived myoepithelial cells differ in their ability to interact with luminal breast epithelial cells for polarity and basement membrane deposition Thorarinn Gudjonsson 1 , Lone Ronnov-Jessen 2 , Rene Villadsen1, Fritz Rank 3 , Mina J. Bissell 4 and Ole William Petersen 1,* Structural Cell Biology Unit, Institute of Medical Anatomy, The Panum Institute, DK-2200 Copenhagen N, Denmark Zoophysiological Laboratory, The August Krogh Institute, DK-2100 Copenhagen O, Denmark Department of Pathology, Rigshospitalet, DK-2100 Copenhagen O, Denmark Life Sciences Division, Berkeley National Laboratory, Berkeley, CA 94720, USA Author for correspondence (e-mail: o.w.petersen@mai.ku.dk) LBNL/DOE funding & contract number: DE-AC02-05CH11231

Advancing the Frontiers in Nanocatalysis, Biointerfaces, and Renewable Energy Conversion by Innovations of Surface Techniques

Abstract: Advancing the Frontiers in Nanocatalysis, Biointerfaces, and Renewable Energy Conversion by Innovations of Surface Techniques Gabor A. Somorjai *, Heinz Frei, and Jeong Y. Park † Department of Chemistry and Lawrence Berkeley National Laboratory University of California, Berkeley Abstract The challenge of chemistry in the 21 st century is to achieve 100% selectivity of the desired product molecule in multi-path reactions (green chemistry) and develop renewable energy based processes. Surface chemistry and catalysis play key roles in this enterprise. Development of in-situ surface techniques such as high pressure scanning tunneling microscopy (STM), sum frequency generation (SFG) vibrational spectroscopy, time-resolved Fourier Transform Infrared (FT-IR) methods and ambient pressure X-ray photoelectron spectroscopy (AP-XPS) enabled the rapid advancing of three fields; nanocatalysts, biointerfaces, and renewable energy conversion chemistry. In materials nanoscience, synthetic methods have been developed to produce monodisperse metal and oxide nanoparticles (NP) in the 0.8 –10 nm range with controlled shape, oxidation states, and composition, which can be used as selective catalysts since chemical selectivity appears to be dependent on all of these experimental parameters. New spectroscopic and microscopic techniques have been developed that operate under reaction conditions and reveal the dynamic change of molecular structure of catalysts and adsorbed molecules as the reactions proceed with changes in reaction intermediates, catalyst composition, and oxidation states. SFG vibrational spectroscopy detects amino acids, peptides and proteins adsorbed at hydrophobic and hydrophilic interfaces and monitors the change of surface structure and interactions with coadsorbed water. Exothermic reactions and photons generate hot electrons in metal nanoparticles that may be utilized in chemical energy conversion. The photo-splitting of water and carbon dioxide that are important research directions in renewable energy conversion is discussed.

ChIP-seq Identification of Weakly Conserved Heart Enhancers

Abstract: Accurate control of tissue-specific gene expression plays a pivotal role in heart development, but few cardiac transcriptional enhancers have thus far been identified. Extreme non-coding sequence conservation successfully predicts enhancers active in many tissues, but fails to identify substantial numbers of heart enhancers. Here we used ChIP-seq with the enhancer-associated protein p300 from mouse embryonic day 11.5 heart tissue to identify over three thousand candidate heart enhancers genome-wide. Compared to other tissues studied at this time-point, most candidate heart enhancers are less deeply conserved in vertebrate evolution. Nevertheless, the testing of 130 candidate regions in a transgenic mouse assay revealed that most of them reproducibly function as enhancers active in the heart, irrespective of their degree of evolutionary constraint. These results provide evidence for a large population of poorly conserved heart enhancers and suggest that the evolutionary constraint of embryonic enhancers can vary depending on tissue type.

Genome Project Standards in a New Era of Sequencing

Abstract: A Joint Announcement on Genome Sequence Standards Genome project standards in a new era of sequencing P. S. G. Chain 1,2,3,4,22,* , D. V. Grafham 5,* , R. S. Fulton 6 , M. G. FitzGerald 7 , J. Hostetler 8 , D. Muzny 9 , J. C. Detter 1,10 , J. Ali 11 , B.Birren 7 , D. C. Bruce 1, 10 , C. Buhay 9 , J. R. Cole 3,4 , Y. Ding 9 , S. Dugan 9 , D. Field 12 , G. M. Garrity 3,4 , R. Gibbs 9 , T. Graves 6 , C. S. Han 1, 10 , S. H. Harrison 3 , S. Highlander 9 , P. Hugenholtz 1 , H. M. Khouri 13 , C. D. Kodira 7,23 , E. Kolker 14,15 , N. C. Kyrpides 1 , D. Lang 1,2 , A. Lapidus 1 , S. A. Malfatti 1,2 , V. Markowitz 16 , T. Metha 7 , K. E. Nelson 8 , J. Parkhill 5 , S. Pitluck 1 , X. Qin 9 , T. D. Read 17 , J. Schmutz 18 , S. Sozhamannan 19 , R. Strausberg 8 , G. Sutton 8 , N. R. Thomson 5 , J. M. Tiedje 3,4 , G. Weinstock 6 , A. Wollam 6 , and the entire GSC 20 and HMP Jumpstart 21 consortia. U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA Microbiology & Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom The Genome Center, Washington University School of Medicine, St Louis, Missouri 63108, USA The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02141, USA J. Craig Venter Institute, Rockville, Maryland 20850, USA Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada Natural Environmental Research Council Centre for Ecology and Hydrology, Oxford, Oxfordshire OX1 3SR, UK National Center for Biotechnology Information, National Library of Medicine, Rockville, Maryland 20850, USA Seattle Children’s Hospital and Research Institute, Seattle, Washington 98101, USA Biomedical & Health Informatics Division, MEBI, University of Washington School of Medicine, Seattle, Washington 98195, USA Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA Emory GRA Genomics Core, Emory University School of Medicine, Atlanta, Georgia 30322, USA HudsonAlpha Genome Sequencing Center, HudsonAlpha Institute, Huntsville, Alabama 35806, USA Biological Defense Research Directorate, Naval Medical Research Center, Silver Spring, Maryland 20910, USA Genomic Standards Consortium Human Microbiome Project Jumpstart Consortium Current address: Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA Current address: 454 Life Sciences, Branford, Connecticut 06405, USA *Address correspondence to Patrick Chain (pchain@lanl.gov) and Darren Grafham (dg1@sanger.ac.uk)

MicrobesOnline: an integrated portal for comparative and functional genomics

Abstract: Since 2003, MicrobesOnline (http://www.microbesonline.org) has been providing a community resource for comparative and functional genome analysis. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html.

The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion

Abstract: The ascomycetous fungus Nectria haematococca, (asexual name Fusarium solani), is a member of a group of .50 species known as the Fusarium solani species complex . Members of this complex have diverse biological properties including the ability to cause disease on .100 genera of plants and opportunistic infections in humans. The current research analyzed the most extensively studied member of this complex, N. haematococca mating population VI (MPVI). Several genes controlling the ability of individual isolates of this species to colonize specific habitats are located on supernumerary chromosomes. Optical mapping revealed that the sequenced isolate has 17 chromosomes ranging from 530 kb to 6.52 Mb and that the physical size of the genome, 54.43 Mb, and the number of predicted genes, 15,707, are among the largest reported for ascomycetes. Two classes of genes have contributed to gene expansion: specific genes that are not found in other fungi including its closest sequenced relative, Fusarium graminearum; and genes that commonly occur as single copies in other fungi but are present as multiple copies in N. haematococca MPVI. Some of these additional genes appear to have resulted from gene duplication events, while others may have been acquired through horizontal gene transfer. The supernumerary nature of three chromosomes, 14, 15, and 17, was confirmed by their absence in pulsed field gel electrophoresis experiments of some isolates and by demonstrating that these isolates lacked chromosome-specific sequences found on the ends of these chromosomes. These supernumerary chromosomes contain more repeat sequences, are enriched in unique and duplicated genes, and have a lower G+C content in comparison to the other chromosomes. Although the origin(s) of the extra genes and the supernumerary chromosomes is not known, the gene expansion and its large genome size are consistent with this species' diverse range of habitats. Furthermore, the presence of unique genes on supernumerary chromosomes might account for individual isolates having different environmental niches.

Aerosol indirect effects -- general circulation model intercomparison and evaluation with satellite data

Abstract: Aerosol indirect effects continue to constitute one of the most important uncertainties for anthropogenic climate perturbations. Within the international AEROCOM initiative, the representation of aerosol-cloud-radiation interactions in ten different general circulation models (GCMs) is evaluated using three satellite datasets. The focus is on stratiform liquid water clouds since most GCMs do not include ice nucleation effects, and none of the model explicitly parameterizes aerosol effects on convective clouds. We compute statistical relationships between aerosol optical depth (Ta) and various cloud and radiation quantities in a manner that is consistent between the models and the satellite data. It is found that the model-simulated influence of aerosols on cloud droplet number concentration (Nd) compares relatively well to the satellite data at least over the ocean. The relationship between Ta and liquid water path is simulated much too strongly by the models. It is shown that this is partly related to the representation of the second aerosol indirect effect in terms of autoconversion. A positive relationship between total cloud fraction (fcld) and Ta as found in the satellite data is simulated by the majority of the models, albeit less strongly than that in the satellite data in most of them. In a discussion of the hypotheses proposed in the literature to explain the satellite-derived strong fcld - Ta relationship, our results indicate that none can be identified as unique explanation. Relationships similar to the ones found in satellite data between Ta and cloud top temperature or outgoing long-wave radiation (OLR) are simulated by only a few GCMs. The GCMs that simulate a negative OLR - Ta relationship show a strong positive correlation between Ta and fcld The short-wave total aerosol radiative forcing as simulated by the GCMs is strongly influenced by the simulated anthropogenic fraction of Ta, and parameterisation assumptions such as a lower bound on Nd. Nevertheless, the strengths of the statistical relationships are good predictors for the aerosol forcings in the models. An estimate of the total short-wave aerosol forcing inferred from the combination of these predictors for the modelled forcings with the satellite-derived statistical relationships yields a global annual mean value of -1.5+-0.5 Wm-2. An alternative estimate obtained by scaling the simulated clear- and cloudy-sky forcings with estimates of anthropogenic Ta and satellite-retrieved Nd - Ta regression slopes, respectively, yields a global annual mean clear-sky (aerosol direct effect) estimate of -0.4+-0.2 Wm-2 and a cloudy-sky (aerosol indirect effect) estimate of -0.7+-0.5 Wm-2, with a total estimate of -1.2+-0.4 Wm-2.

Plant cell walls throughout evolution: towards a molecular understanding of their design principles

Abstract: Throughout their life, plants typically remain in one location utilizing sunlight for the synthesis of carbohydrates, which serve as their sole source of energy as well as building blocks of a protective extracellular matrix, called the cell wall. During the course of evolution, plants have repeatedly adapted to their respective niche,which is reflected in the changes of their body plan and the specific design of cell walls. Cell walls not only changed throughout evolution but also are constantly remodelled and reconstructed during the development of an individual plant, and in response to environmental stress or pathogen attacks. Carbohydrate-rich cell walls display complex designs, which together with the presence of phenolic polymers constitutes a barrier for microbes, fungi, and animals. Throughout evolution microbes have co-evolved strategies for efficient breakdown of cell walls. Our current understanding of cell walls and their evolutionary changes are limited as our knowledge is mainly derived from biochemical and genetic studies, complemented by a few targeted yet very informative imaging studies. Comprehensive plant cell wall models will aid in the re-design of plant cell walls for the purpose of commercially viable lignocellulosic biofuel production as well as for the timber, textile, and paper industries. Such knowledge will also be of great interest in the context of agriculture and to plant biologists in general. It is expected that detailed plant cell wall models will require integrated correlative multimodal, multiscale imaging and modelling approaches, which are currently underway.

Assembling the Marine Metagenome, One Cell at a Time

Abstract: The difficulty associated with the cultivation of most microorganisms and the complexity of natural microbial assemblages, such as marine plankton or human microbiome, hinder genome reconstruction of representative taxa using cultivation or metagenomic approaches. Here we used an alternative, single cell sequencing approach to obtain high-quality genome assemblies of two uncultured, numerically significant marine microorganisms. We employed fluorescence-activated cell sorting and multiple displacement amplification to obtain hundreds of micrograms of genomic DNA from individual, uncultured cells of two marine flavobacteria from the Gulf of Maine that were phylogenetically distant from existing cultured strains. Shotgun sequencing and genome finishing yielded 1.9 Mbp in 17 contigs and 1.5 Mbp in 21 contigs for the two flavobacteria, with estimated genome recoveries of about 91percent and 78percent, respectively. Only 0.24percent of the assembling sequences were contaminants and were removed from further analysis using rigorous quality control. In contrast to all cultured strains of marine flavobacteria, the two single cell genomes were excellent Global Ocean Sampling (GOS) metagenome fragment recruiters, demonstrating their numerical significance in the ocean. The geographic distribution of GOS recruits along the Northwest Atlantic coast coincided with ocean surface currents. Metabolic reconstruction indicated diverse potential energy sources, including biopolymer degradation, proteorhodopsin photometabolism, and hydrogen oxidation. Compared to cultured relatives, the two uncultured flavobacteria have small genome sizes, few non-coding nucleotides, and few paralogous genes, suggesting adaptations to narrow ecological niches. These features may have contributed to the abundance of the two taxa in specific regions of the ocean, and may have hindered their cultivation. We demonstrate the power of single cell DNA sequencing to generate reference genomes of uncultured taxa from a complex microbial community of marine bacterioplankton. A combination of single cell genomics and metagenomics enabled us to analyze the genome content, metabolic adaptations, and biogeography of these taxa.

Metagenome of a Versatile Chemolithoautotroph from Expanding Oceanic Dead Zones

Abstract: Oxygen minimum zones (OMZs), also known as oceanic dead zones , are widespread oceanographic features currently expanding due to global warming and coastal eutrophication. Although inhospitable to metazoan life, OMZs support a thriving but cryptic microbiota whose combined metabolic activity is intimately connected to nutrient and trace gas cycling within the global ocean. Here we report time-resolved metagenomic analyses of a ubiquitous and abundant but uncultivated OMZ microbe (SUP05) closely related to chemoautotrophic gill symbionts of deep-sea clams and mussels. The SUP05 metagenome harbors a versatile repertoire of genes mediating autotrophic carbon assimilation, sulfur-oxidation and nitrate respiration responsive to a wide range of water column redox states. Thus, SUP05 plays integral roles in shaping nutrient and energy flow within oxygen-deficient oceanic waters via carbon sequestration, sulfide detoxification and biological nitrogen loss with important implications for marine productivity and atmospheric greenhouse control.

Implications of Wide-Area Geographic Diversity for Short- Term Variability of Solar Power

Abstract: LBNL-3884E E RNEST O RLANDO L AWRENCE B ERKELEY N ATIONAL L ABORATORY Implications of Wide-Area Geographic Diversity for Short- Term Variability of Solar Power Andrew Mills and Ryan Wiser Environmental Energy Technologies Division September 2010 Download from http://eetd.lbl.gov/EA/EMP The work described in this paper was funded by the U.S. Department of Energy (Office of Energy Efficiency and Renewable Energy and Office of Electricity Delivery and Energy Reliability) under Contract No. DE-AC02-05CH11231.

Role for DNA methylation in the regulation of miR-200c and miR-141 expression in normal and cancer cells

Abstract: BACKGROUND: The microRNA-200 family participates in the maintenance of an epithelial phenotype and loss of its expression can result in epithelial to mesenchymal transition (EMT). Furthermore, the loss of expression of miR-200 family members is linked to an aggressive cancer phenotype. Regulation of the miR-200 family expression in normal and cancer cells is not fully understood. METHODOLOGY/ PRINCIPAL FINDINGS: Epigenetic mechanisms participate in the control of miR-200c and miR-141 expression in both normal and cancer cells. A CpG island near the predicted mir-200c/mir-141 transcription start site shows a striking correlation between miR-200c and miR-141 expression and DNA methylation in both normal and cancer cells, as determined by MassARRAY technology. The CpG island is unmethylated in human miR-200/miR-141 expressing epithelial cells and in miR-200c/miR-141 positive tumor cells. The CpG island is heavily methylated in human miR-200c/miR-141 negative fibroblasts and miR-200c/miR-141 negative tumor cells. Mouse cells show a similar inverse correlation between DNA methylation and miR-200c expression. Enrichment of permissive histone modifications, H3 acetylation and H3K4 trimethylation, is seen in normal miR-200c/miR-141-positive epithelial cells, as determined by chromatin immunoprecipitation coupled to real-time PCR. In contrast, repressive H3K9 dimethylation marks are present in normal miR-200c/miR-141-negative fibroblasts and miR-200c/miR-141 negative cancer cells and the permissive histone modifications are absent. The epigenetic modifier drug, 5-aza-2'-deoxycytidine, reactivates miR-200c/miR-141 expression showing that epigenetic mechanisms play a functional role in their transcriptional control. CONCLUSIONS/ SIGNIFICANCE: We report that DNA methylation plays a role in the normal cell type-specific expression of miR-200c and miR-141 and this role appears evolutionarily conserved, since similar results were obtained in mouse. Aberrant DNA methylation of the miR-200c/141 CpG island is closely linked to their inappropriate silencing in cancer cells. Since the miR-200c cluster plays a significant role in EMT, our results suggest an important role for DNA methylation in the control of phenotypic conversions in normal cells.

Metagenomic Insights into Evolution of a Heavy Metal-Contaminated Groundwater Microbial Community

Abstract: Understanding adaptation of biological communities to environmental change is a central issue in ecology and evolution. Metagenomic analysis of a stressed groundwater microbial community reveals that prolonged exposure to high concentrations of heavy metals, nitric acid and organic solvents (~;;50 years) have resulted in a massive decrease in species and allelic diversity as well as a significant loss of metabolic diversity. Although the surviving microbial community possesses all metabolic pathways necessary for survival and growth in such an extreme environment, its structure is very simple, primarily composed of clonal denitrifying ?- and ?-proteobacterial populations. The resulting community is over-abundant in key genes conferring resistance to specific stresses including nitrate, heavy metals and acetone. Evolutionary analysis indicates that lateral gene transfer could be a key mechanism in rapidly responding and adapting to environmental contamination. The results presented in this study have important implications in understanding, assessing and predicting the impacts of human-induced activities on microbial communities ranging from human health to agriculture to environmental management, and their responses to environmental changes.

The matrix metalloproteinase stromelysin-1 acts as a natural mammary tumor promoter

Abstract: The matrix metalloproteinase stromelysin-1 acts as a natural mammary tumor promoter Mark D Sternlicht *,1 , Mina J Bissell 2 and Zena Werb 1 Department of Anatomy, University of California, 513 Parnassus Avenue, HSW-1301, San Francisco, California, CA 94143-0452, USA Life Sciences Division, Lawrence Berkeley National Laboratory, California, CA 94720, USA *Corresponding Author LBNL/DOE funding & contract number: DE-AC02-05CH11231 DISCLAIMER This document was prepared as an account of work sponsored by the United States Government. While this document is believed to contain correct information, neither the United States Government nor any agency thereof, nor The Regents of the University of California, nor any of their employees, makes any warranty, express or implied, or assumes any legal responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by its trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or The Regents of the University of California. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof or The Regents of the University of California.

X-ray Absorption Spectroscopy

Abstract: This review gives a brief description of the theory and application of X-ray absorption spectroscopy, both X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS), especially, pertaining to photosynthesis. The advantages and limitations of the methods are discussed. Recent advances in extended EXAFS and polarized EXAFS using oriented membranes and single crystals are explained. Developments in theory in understanding the XANES spectra are described. The application of X-ray absorption spectroscopy to the study of the Mn4Ca cluster in Photosystem II is presented.

Cellular growth and survival are mediated by beta 1 integrins in normal human breast epithelium but not in breast carcinoma

Abstract: Cellular growth and survival are mediated by β1 integrins in normal human breast epithelium but not in breast carcinoma Anthony R. Howlett 1,4,*, Nina Bailey 1 , Caroline Damsky 2 , Ole W. Petersen 1,3 and Mina J. Bissell 1 Life Sciences Division, Lawrence Berkeley Laboratory, University of California, Berkeley, CA 94720, USA Departments of Stomatology and Anatomy, University of California, San Francisco, CA 94143, USA Structural Cell Biology Unit, Department of Medical Anatomy A, The Panum Institute, University of Copenhagen, DK-2200 Copenhagen N, Denmark Berlex BioSciences, Richmond, CA 94804, USA *Author for correspondence at address 1 LBNL/DOE funding & contract number: DE-AC02-05CH11231 DISCLAIMER This document was prepared as an account of work sponsored by the United States Government. While this document is believed to contain correct information, neither the United States Government nor any agency thereof, nor The Regents of the University of California, nor any of their employees, makes any warranty, express or implied, or assumes any legal responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by its trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or The Regents of the University of California. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof or The Regents of the University of California.

Laboratory flow experiments for visualizing carbon dioxide-induced, density-driven brine convection

Abstract: Laboratory Flow Experiments for Visualizing Carbon Dioxide-Induced, Density- Driven Brine Convection Timothy J. Kneafsey and Karsten Pruess Lawrence Berkeley National Laboratory Berkeley, California TJKneafsey@lbl.gov Abstract Injection of carbon dioxide (CO 2 ) into saline aquifers confined by low-permeability cap rock will result in a layer of CO 2 overlying the brine. Dissolution of CO 2 into the brine increases the brine density, resulting in an unstable situation in which more-dense brine overlies less-dense brine. This gravitational instability could give rise to density-driven convection of the fluid, which is a favorable process of practical interest for CO 2 storage security because it accelerates the transfer of buoyant CO 2 into the aqueous phase, where it is no longer subject to an upward buoyant drive. Laboratory flow visualization tests in transparent Hele-Shaw cells have been performed to elucidate the processes and rates of this CO2 solute-driven convection (CSC). Upon introduction of CO 2 into the system, a layer of CO 2 -laden brine forms at the CO 2 -water interface. Subsequently, small convective fingers form, which coalesce, broaden, and penetrate into the test cell. Images and time-series data of finger lengths and wavelengths are presented. Observed CO 2 uptake of the convection system indicates that the CO 2 dissolution rate is approximately constant for each test and is far greater than expected for a diffusion-only scenario. Numerical simulations of our system show good agreement with the experiments for onset time of convection and advancement of convective fingers. There are differences as well, the most prominent being the absence of cell-scale convection in the numerical simulations. This cell-scale convection observed in the experiments is probably initiated by a small temperature gradient induced by the cell illumination. Introduction Carbon dioxide (CO 2 ) injection into deep saline aquifers is a method being considered for sequestration of CO 2 . In such a scenario, the CO 2 would be injected into a permeable,

One Bacterial Cell, One Complete Genome

Abstract: While the bulk of the finished microbial genomes sequenced to date are derived from cultured bacterial and archaeal representatives, the vast majority of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes from these environmental species. Single cell genomics is a novel culture-independent approach, which enables access to the genetic material of an individual cell. No single cell genome has to our knowledge been closed and finished to date. Here we report the completed genome from an uncultured single cell of Candidatus Sulcia muelleri DMIN. Digital PCR on single symbiont cells isolated from the bacteriome of the green sharpshooter Draeculacephala minerva bacteriome allowed us to assess that this bacteria is polyploid with genome copies ranging from approximately 200-900 per cell, making it a most suitable target for single cell finishing efforts. For single cell shotgun sequencing, an individual Sulcia cell was isolated and whole genome amplified by multiple displacement amplification (MDA). Sanger-based finishing methods allowed us to close the genome. To verify the correctness of our single cell genome and exclude MDA-derived artifacts, we independently shotgun sequenced and assembled the Sulcia genome from pooled bacteriomes using a metagenomic approach, yielding a nearly identical genome. Four variations we detected appear to be genuine biological differences between the two samples. Comparison of the single cell genome with bacteriome metagenomic sequence data detected two single nucleotide polymorphisms (SNPs), indicating extremely low genetic diversity within a Sulcia population. This study demonstrates the power of single cell genomics to generate a complete, high quality, non-composite reference genome within an environmental sample, which can be used for population genetic analyzes.

Reactive transport modeling to study changes in water chemistry induced by CO2 injection at the Frio-I brine pilot

Abstract: Reactive Transport Modeling to Study Changes in Water Chemistry Induced by CO 2 Injection at the Frio-I Brine Pilot Tianfu Xu 1 , Yousif K. Kharaka 2 , Christine Doughty 1 , Barry M. Freifeld 1 , and Thomas M. Daley 1 Earth Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 U.S. Geological Survey, MS/427, 345 Middlefield Rd., Menlo Park, CA 94025 Abstract. To demonstrate the potential for geologic storage of CO 2 in saline aquifers, the Frio-I Brine Pilot was conducted, during which 1600 tons of CO 2 were injected into a high-permeability sandstone and the resulting subsurface plume of CO 2 was monitored using a variety of hydrogeological, geophysical, and geochemical techniques . Fluid samples were obtained before CO 2 injection for baseline geochemical characterization, during the CO 2 injection to track its breakthrough at a nearby observation well, and after injection to investigate changes in fluid composition and potential leakage into an overlying zone. Following CO 2 breakthrough at the observation well, brine samples showed sharp drops in pH, pronounced increases in HCO 3- and aqueous Fe, and significant shifts in the isotopic compositions of H 2 O and dissolved inorganic carbon. Based on a calibrated 1-D radial flow model, reactive transport modeling was performed for the Frio-I Brine Pilot. A simple kinetic model of Fe release from the solid to aqueous phase was developed, which can reproduce the observed increases in aqueous Fe concentration. Brine samples collected after half a year had lower Fe concentrations due to carbonate precipitation, and this trend can be also captured by our modeling. The paper provides a method for estimating potential mobile Fe inventory, and its bounding concentration in the storage formation from limited observation data. Long-term simulations show that the CO 2 plume gradually spreads outward due to capillary forces, and the gas saturation gradually decreases due to its dissolution and precipitation of carbonates. The gas phase is predicted to disappear after 500 years. Elevated aqueous CO 2 concentrations remain for a longer time, but eventually decrease due to carbonate precipitation. For the Frio-I Brine Pilot, all injected CO 2 could ultimately be sequestered as carbonate minerals. Keywords: CO 2 sequestration, Frio Formation, Water chemistry, Iron release, Reactive transport modeling

Analysis of community structure in networks of correlated data

Abstract: Analysis of community structure in networks of correlated data Sergio G´ mez, 1 Pablo Jensen, 2 and Alex Arenas 1 o Departament d’Enginyeria Inform` tica i Matem` tiques, a a Universitat Rovira i Virgili, 43007 Tarragona, Spain IXXI - Institut des Syst` mes Complexes, 5 rue du Vercors, 69007 Lyon, France e (Dated: January 16, 2009) We present a reformulation of modularity that allows the analysis of the community structure in networks of correlated data. The new modularity preserves the probabilistic semantics of the original definition even when the network is directed, weighted, signed, and has self-loops. This is the most general condition one can find in the study of any network, in particular those defined from correlated data. We apply our results to a real network of correlated data between stores in the city of Lyon (France). PACS numbers: 89.75.Hc, 02.10.Ox, 02.50.-r Complex networks are graphs representative of the in- tricate connections between elements in many natural and artificial systems [1–4], whose description in terms of statistical properties have been largely developed in the curse for a universal classification of them. However, when the networks are locally analyzed, some characteris- tics that become partially hidden in the global statistical description emerge. The most relevant perhaps is the dis- covery in many of them of community structure, meaning the existence of densely (or strongly) connected groups of nodes, with sparse (or weak) connections between these groups [5]. The study of the community structure helps to elu- cidate the organization of the networks and, eventually, could be related to the functionality of groups of nodes [6]. The most successful solutions to the community de- tection problem, in terms of accuracy and computational cost required, are those based in the optimization of a quality function called modularity proposed by Newman and Girvan [7] that allows the comparison of different partitioning of the network. The extension of modularity to weighted [8] and directed networks [9, 10] has been the first steps towards the analysis of the community struc- ture in general networks. Very often networks are defined from correlation data between elements. The common analysis of correlation matrices uses classical or advanced statistical techniques [11]. Nevertheless an alternative analysis in terms of net- works is possible. The network approach usually consist in to filter the correlation data matrix, by eliminating poorly correlated pairs according to a threshold, and by keeping unsigned the value of the correlation, produc- ing a network of positive links and no self-loops (self- correlations). Recently, some authors pointed out the possibility to analyze these networks via spectral decom- position [12, 13] . We devise also the possibility to ana- lyze them in terms of modularity to reveal the community structure (clusters) of the correlated data. However, any of these approaches can be misleading because of two facts: first, the sign of the correlation is important to avoid the mixing of correlated and anti-correlated data, and second, the existence of self-loops is critical for the determination of the community structure [9]. Here we propose a method to extract the community structure in networks of correlated data, that accounts for the exis- tence of signed correlations and self-correlations, preserv- ing the original information. To this end, we extend the modularity to the most general case of directed, weighted and signed links. We will show the performance of our method in a real network of correlations between com- mercial activities obtained from a simple physical model Given an undirected network partitioned into commu- nities, the modularity of a given partition is, up to a multiplicative constant, the probability of having edges falling within groups in the network minus the expected probability in an equivalent (null case) network with the same number of nodes, and edges placed at random pre- serving the nodes’ strength, where the strength of a node stands for the sum of the weights of its connections [15]. In mathematical form, being C i the community to which node i is assigned, modularity is expressed in terms of the weighted adjacency matrix w ij , that represents the value of the weight in the link between i and j (0 if no link exists), as [15] Q = 2w w ij − i j w i w j δ(C i , C j ) , 2w where the Kronecker delta function δ(C i , C j ) takes the values, 1 if nodes i and j are into the same community, 0 otherwise, the strengths w i = j w ij , and the total strength 2w = i w i = i j w ij . The larger the modularity the best the partitioning is, cause more deviates from the null case. Note that the optimization of the modularity cannot be performed by exhaustive search since the number of different partitions are equal to the Bell [16] or exponential numbers, which grow at least exponentially in the number of nodes N . Indeed, optimization of modularity is a NP-hard (Non- deterministic Polynomial-time hard) problem [17]. Sev-

Hetero-Epitaxial Anion Exchange Yields Single-Crystalline Hollow Nanoparticles

Abstract: Hetero-Epitaxial Anion Exchange Yields Single-Crystalline Hollow Nanoparticles Jungwon Park 1 , Haimei Zheng 1,2,3 , Young-wook Jun 1,3 , and A. Paul Alivisatos 1,3* Department of Chemistry, University of California, Berkeley, CA 94720, USA National Center for Electron Microscopy, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA

Rapid evolution of stability and productivity at the origin of a microbial mutualism

Abstract: Mutualistic interactions are taxonomically and functionally diverse Despite their ubiquity, the basic ecological and evolutionary processes underlying their origin and maintenance are poorly understood A major reason for this has been the lack of an experimentally tractable model system We examine the evolution of an experimentally imposed obligate mutualism between sulfate-reducing and methanogenic microorganisms that have no known history of prior interaction Twenty-four independent pairings (cocultures) of the bacterium Desulfovibrio vulgaris and the archaeon Methanococcus maripaludis were established and followed for 300 community doublings in two environments, one allowing for the development of a heterogeneous distribution of resources and the other not Evolved cocultures grew up to 80percent faster and were up to 30percent more productive (biomass yield per mole substrate) than the ancestors The evolutionary process was marked by periods of significant instability leading to extinction of two of the cocultures, but resulted in more stable, efficient, and productive mutualisms for most replicated pairings Comparisons of evolved cocultures with those assembled from one evolved and one ancestral mutualist showed that evolution of both species contributed to improved productivity Surprisingly, however, overall improvements in growth rate and yield were less than the sum of individual contributions, suggesting antagonistic interactions between mutations from the coevolved populations Physical constraints on the transfer of metabolites in the evolution environment affected the evolution of M maripaludis but not D vulgaris Together, these results show that challenges can imperil nascent obligate mutualisms and demonstrate the evolutionary responses that enable their persistence and future evolution