Showing papers by "Lawrence Berkeley National Laboratory published in 2007"
TL;DR: A description is given of Phaser-2.1: software for phasing macromolecular crystal structures by molecular replacement and single-wavelength anomalous dispersion phasing.
Abstract: Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented in Phaser have been developed using maximum likelihood and multivariate statistics. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct solutions from noise, and for single-wavelength anomalous dispersion experimental phasing, the new algorithms, which account for correlations between F+ and F−, give better phases (lower mean phase error with respect to the phases given by the refined structure) than those that use mean F and anomalous differences ΔF. One of the design concepts of Phaser was that it be capable of a high degree of automation. To this end, Phaser (written in C++) can be called directly from Python, although it can also be called using traditional CCP4 keyword-style input. Phaser is a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community.
17,755 citations
9,432 citations
TL;DR: An anatomically comprehensive digital atlas containing the expression patterns of ∼20,000 genes in the adult mouse brain is described, providing an open, primary data resource for a wide variety of further studies concerning brain organization and function.
Abstract: Molecular approaches to understanding the functional circuitry of the nervous system promise new insights into the relationship between genes, brain and behaviour. The cellular diversity of the brain necessitates a cellular resolution approach towards understanding the functional genomics of the nervous system. We describe here an anatomically comprehensive digital atlas containing the expression patterns of approximately 20,000 genes in the adult mouse brain. Data were generated using automated high-throughput procedures for in situ hybridization and data acquisition, and are publicly accessible online. Newly developed image-based informatics tools allow global genome-scale structural analysis and cross-correlation, as well as identification of regionally enriched genes. Unbiased fine-resolution analysis has identified highly specific cellular markers as well as extensive evidence of cellular heterogeneity not evident in classical neuroanatomical atlases. This highly standardized atlas provides an open, primary data resource for a wide variety of further studies concerning brain organization and function.
4,944 citations
TL;DR: It is demonstrated that the Pt3Ni( 111) surface is 10-fold more active for the ORR than the corresponding Pt(111) surface and 90-foldMore active than the current state-of-the-art Pt/C catalysts for PEMFC.
Abstract: The slow rate of the oxygen reduction reaction (ORR) in the polymer electrolyte membrane fuel cell (PEMFC) is the main limitation for automotive applications. We demonstrated that the Pt3Ni(111) surface is 10-fold more active for the ORR than the corresponding Pt(111) surface and 90-fold more active than the current state-of-the-art Pt/C catalysts for PEMFC. The Pt3Ni(111) surface has an unusual electronic structure (d-band center position) and arrangement of surface atoms in the near-surface region. Under operating conditions relevant to fuel cells, its near-surface layer exhibits a highly structured compositional oscillation in the outermost and third layers, which are Pt-rich, and in the second atomic layer, which is Ni-rich. The weak interaction between the Pt surface atoms and nonreactive oxygenated species increases the number of active sites for O2 adsorption.
3,804 citations
TL;DR: Understanding the causes and consequences of cellular senescence has provided novel insights into how cells react to stress, especially genotoxic stress, and how this cellular response can affect complex organismal processes such as the development of cancer and ageing.
Abstract: Cells continually experience stress and damage from exogenous and endogenous sources, and their responses range from complete recovery to cell death. Proliferating cells can initiate an additional response by adopting a state of permanent cell-cycle arrest that is termed cellular senescence. Understanding the causes and consequences of cellular senescence has provided novel insights into how cells react to stress, especially genotoxic stress, and how this cellular response can affect complex organismal processes such as the development of cancer and ageing.
3,677 citations
TL;DR: Previous two-dimensional electronic spectroscopy investigations of the FMO bacteriochlorophyll complex are extended, and direct evidence is obtained for remarkably long-lived electronic quantum coherence playing an important part in energy transfer processes within this system is obtained.
Abstract: Photosynthesis provides the primary energy source for almost all life on Earth. One of its remarkable features is the efficiency with which energy is transferred within the light harvesting complexes comprising the photosynthetic apparatus. Suspicions that quantum trickery might be involved in the energy transfer processes at the core of photosynthesis are now confirmed by a new spectroscopic study. The study reveals electronic quantum beats characteristic of wavelike energy motion within the bacteriochlorophyll complex from the green sulphur bacterium Chlorobium tepidum. This wavelike characteristic of the energy transfer process can explain the extreme efficiency of photosynthesis, in that vast areas of phase space can be sampled effectively to find the most efficient path for energy transfer. A spectroscopic study has directly monitored the quantum beating arising from remarkably long-lived electronic quantum coherence in a bacteriochlorophyll complex. This wavelike characteristic of the energy transfer process can explain the extreme efficiency of photosynthesis, in that vast areas of phase space can be sampled effectively to find the most efficient path for energy transfer. Photosynthetic complexes are exquisitely tuned to capture solar light efficiently, and then transmit the excitation energy to reaction centres, where long term energy storage is initiated. The energy transfer mechanism is often described by semiclassical models that invoke ‘hopping’ of excited-state populations along discrete energy levels1,2. Two-dimensional Fourier transform electronic spectroscopy3,4,5 has mapped6 these energy levels and their coupling in the Fenna–Matthews–Olson (FMO) bacteriochlorophyll complex, which is found in green sulphur bacteria and acts as an energy ‘wire’ connecting a large peripheral light-harvesting antenna, the chlorosome, to the reaction centre7,8,9. The spectroscopic data clearly document the dependence of the dominant energy transport pathways on the spatial properties of the excited-state wavefunctions of the whole bacteriochlorophyll complex6,10. But the intricate dynamics of quantum coherence, which has no classical analogue, was largely neglected in the analyses—even though electronic energy transfer involving oscillatory populations of donors and acceptors was first discussed more than 70 years ago11, and electronic quantum beats arising from quantum coherence in photosynthetic complexes have been predicted12,13 and indirectly observed14. Here we extend previous two-dimensional electronic spectroscopy investigations of the FMO bacteriochlorophyll complex, and obtain direct evidence for remarkably long-lived electronic quantum coherence playing an important part in energy transfer processes within this system. The quantum coherence manifests itself in characteristic, directly observable quantum beating signals among the excitons within the Chlorobium tepidum FMO complex at 77 K. This wavelike characteristic of the energy transfer within the photosynthetic complex can explain its extreme efficiency, in that it allows the complexes to sample vast areas of phase space to find the most efficient path.
2,981 citations
TL;DR: The electrocatalytic trends established for extended surfaces are used to explain the activity pattern of Pt(3)M nanocatalysts as well as to provide a fundamental basis for the catalytic enhancement of cathode catalysts.
Abstract: One of the key objectives in fuel-cell technology is to improve and reduce Pt loading as the oxygen-reduction catalyst. Here, we show a fundamental relationship in electrocatalytic trends on Pt(3)M (M=Ni, Co, Fe, Ti, V) surfaces between the experimentally determined surface electronic structure (the d-band centre) and activity for the oxygen-reduction reaction. This relationship exhibits 'volcano-type' behaviour, where the maximum catalytic activity is governed by a balance between adsorption energies of reactive intermediates and surface coverage by spectator (blocking) species. The electrocatalytic trends established for extended surfaces are used to explain the activity pattern of Pt(3)M nanocatalysts as well as to provide a fundamental basis for the catalytic enhancement of cathode catalysts. By combining simulations with experiments in the quest for surfaces with desired activity, an advanced concept in nanoscale catalyst engineering has been developed.
2,774 citations
University at Buffalo1, University of Cambridge2, University of Washington3, University of Edinburgh4, Drexel University5, University of Utah6, European Bioinformatics Institute7, Lawrence Berkeley National Laboratory8, Bowling Green State University9, Massachusetts Institute of Technology10, University of Texas Southwestern Medical Center11, Stanford University12, University of Pennsylvania13
TL;DR: This work describes the OBO Foundry initiative and provides guidelines for those who might wish to become involved and describes an expanding family of ontologies designed to be interoperable and logically well formed and to incorporate accurate representations of biological reality.
Abstract: The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or 'ontologies'. Unfortunately, the very success of this approach has led to a proliferation of ontologies, which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium is pursuing a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing coordinated reform, and new ontologies are being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable and logically well formed and to incorporate accurate representations of biological reality. We describe this OBO Foundry initiative and provide guidelines for those who might wish to become involved.
2,492 citations
TL;DR: It is shown that when graphene is epitaxially grown on SiC substrate, a gap of approximately 0.26 eV is produced and it is proposed that the origin of this gap is the breaking of sublattice symmetry owing to the graphene-substrate interaction.
Abstract: Graphene has shown great application potential as the hostmaterial for next-generation electronic devices. However, despite itsintriguing properties, one of the biggest hurdles for graphene to beuseful as an electronic material is the lack of an energy gap in itselectronic spectra. This, for example, prevents the use of graphene inmaking transistors. Although several proposals have been made to open agap in graphene's electronic spectra, they all require complexengineering of the graphene layer. Here, we show that when graphene isepitaxially grown on SiC substrate, a gap of ~;0.26 eV is produced. Thisgap decreases as the sample thickness increases and eventually approacheszero when the number of layers exceeds four. We propose that the originof this gap is the breaking of sublattice symmetry owing to thegraphene-substrate interaction. We believe that our results highlight apromising direction for band gap engineering of graphene.
2,132 citations
TL;DR: These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution.
Abstract: Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
2,057 citations
University of California, Santa Cruz1, University of Arizona2, Max Planck Society3, California Institute of Technology4, University of Nottingham5, Lawrence Berkeley National Laboratory6, Columbia University7, Harvard University8, University of California, Berkeley9, University of California, Los Angeles10
TL;DR: In this paper, the authors analyzed star formation as a function of stellar mass (M☉) and redshift z in the All-Wavelength Extended Groth Strip International Survey.
Abstract: We analyze star formation (SF) as a function of stellar mass (M☉) and redshift z in the All-Wavelength Extended Groth Strip International Survey. For 2905 field galaxies, complete to 10^10(10^10.8 )M at z < 0.7(1), with Keck
spectroscopic redshifts out to z = 1.1, we compile SF rates (SFRs) from emission lines, GALEX, and Spitzer MIPS 24 µm photometry, optical-NIR M* measurements, and HST morphologies. Galaxies with reliable signs of SF form a distinct “main sequence” (MS), with a limited range of SFRs at a given M* and z (1 σ ≾ ±0.3 dex), and log (SFR) approximately proportional to log M*. The range of log (SFR) remains constant to z > 1, while the MS as a whole moves to higher SFR as z increases. The range of the SFR along the MS constrains the amplitude of episodic variations of SF and the effect of mergers on the SFR. Typical galaxies spend ∼67%(95%) of their lifetime since z = 1 within a factor of ≾2(4) of their average SFR at a given M* and z. The dominant mode of the evolution of SF since z ∼ 1 is apparently a gradual decline of the average SFR in most individual galaxies, not a decreasing frequency of starburst episodes, or a decreasing factor by which SFRs are enhanced in starbursts. LIRGs at z ∼ 1 seem to mostly reflect the high SFR typical for massive galaxies at that epoch. The smooth MS may reflect that the same set of few physical processes governs SF prior to additional quenching processes. A gradual process like gas exhaustion may play a dominant role.
TL;DR: The topological invariants of a time-reversal-invariant band structure in two dimensions are multiple copies of the ${\mathbb{Z}}_{2}$ invariant found by Kane and Mele as mentioned in this paper.
Abstract: The topological invariants of a time-reversal-invariant band structure in two dimensions are multiple copies of the ${\mathbb{Z}}_{2}$ invariant found by Kane and Mele. Such invariants protect the ``topological insulator'' phase and give rise to a spin Hall effect carried by edge states. Each pair of bands related by time reversal is described by one ${\mathbb{Z}}_{2}$ invariant, up to one less than half the dimension of the Bloch Hamiltonians. In three dimensions, there are four such invariants per band pair. The ${\mathbb{Z}}_{2}$ invariants of a crystal determine the transitions between ordinary and topological insulators as its bands are occupied by electrons. We derive these invariants using maps from the Brillouin zone to the space of Bloch Hamiltonians and clarify the connections between ${\mathbb{Z}}_{2}$ invariants, the integer invariants that underlie the integer quantum Hall effect, and previous invariants of $\mathcal{T}$-invariant Fermi systems.
TL;DR: A robust and generalized method for the culturing of various human breast cell lines in three dimensions is described and the preparation of cellular extracts from these cultures for molecular analyses are described.
Abstract: Extracellular matrix is a key regulator of normal homeostasis and tissue phenotype. Important signals are lost when cells are cultured ex vivo on two-dimensional plastic substrata. Many of these crucial microenvironmental cues may be restored using three-dimensional (3D) cultures of laminin-rich extracellular matrix (lrECM). These 3D culture assays allow phenotypic discrimination between nonmalignant and malignant mammary cells, as the former grown in a 3D context form polarized, growth-arrested acinus-like colonies whereas the latter form disorganized, proliferative and nonpolar colonies. Signaling pathways that function in parallel in cells cultured on plastic become reciprocally integrated when the cells are exposed to basement membrane-like gels. Appropriate 3D culture thus provides a more physiologically relevant approach to the analysis of gene function and cell phenotype ex vivo. We describe here a robust and generalized method for the culturing of various human breast cell lines in three dimensions and describe the preparation of cellular extracts from these cultures for molecular analyses. The procedure below describes the 3D 'embedded' assay, in which cells are cultured embedded in an lrECM gel (Fig. 1). By lrECM, we refer to the solubilized extract derived from the Engelbreth-Holm-Swarm mouse sarcoma cells. For a discussion of user options regarding 3D matrices, see Box 1. Alternatively, the 3D 'on-top' assay, in which cells are cultured on top of a thin lrECM gel overlaid with a dilute solution of lrECM, may be used as described in Box 2 (Fig. 1 and Fig. 2).
University of California, Santa Cruz1, University of Arizona2, University of Oxford3, Lawrence Berkeley National Laboratory4, Seoul National University5, University of California, Berkeley6, Princeton University7, University of Texas at Austin8, Max Planck Society9, University of Chicago10, National Taiwan University11, University of Florida12, University of Virginia13, Herzberg Institute of Astrophysics14, Johns Hopkins University15, New Mexico State University16
TL;DR: The DEEP2 and COMBO-17 surveys are compared to study luminosity functions of red and blue galaxies to z ~ 1, and the results imply that the number and total stellar mass of blue galaxies have been substantially constant since z = 1, whereas those of red galaxies (near L*) have been significantly rising as mentioned in this paper.
Abstract: The DEEP2 and COMBO-17 surveys are compared to study luminosity functions of red and blue galaxies to z ~ 1. The two surveys have different methods and sensitivities, but nevertheless results agree. After z ~ 1, M has dimmed by 1.2-1.3 mag for all colors of galaxies, * for blue galaxies has hardly changed, and * for red galaxies has at least doubled (our formal value is ~0.5 dex). Luminosity density jB has fallen by 0.6 dex for blue galaxies but has remained nearly constant for red galaxies. These results imply that the number and total stellar mass of blue galaxies have been substantially constant since z ~ 1, whereas those of red galaxies (near L*) have been significantly rising. To explain the new red galaxies, a ``mixed'' scenario is proposed in which star formation in blue cloud galaxies is quenched, causing them to migrate to the red sequence, where they merge further in a small number of stellar mergers. This mixed scenario matches the local boxy-disky transition for nearby ellipticals, as well as red sequence stellar population scaling laws such as the color-magnitude and Mg-? relations (which are explained as fossil relics from blue progenitors). Blue galaxies enter the red sequence via different quenching modes, each of which peaks at a different characteristic mass and time. The red sequence therefore likely builds up in different ways at different times and masses, and the concept of a single process that is ``downsizing'' (or upsizing) probably does not apply. Our claim in this paper of a rise in the number of red galaxies applies to galaxies near L*. Accurate counts of brighter galaxies on the steep part of the Schechter function require more accurate photometry than is currently available.
TL;DR: This work has used highly faceted cubic Pt seeds to direct the epitaxial overgrowth of a secondary metal, and demonstrates this concept with lattice-matched Pd to produce conformal shape-controlled core-shell particles, and then extends it to lattices-mismatched Au to give anisotropic growth.
Abstract: Morphological control of nanocrystals has become increasingly important, as many of their physical and chemical properties are highly shape dependent. Nanocrystal shape control for both single- and multiple-material systems, however, remains empirical and challenging. New methods need to be explored for the rational synthetic design of heterostructures with controlled morphology. Overgrowth of a different material on well-faceted seeds, for example, allows for the use of the defined seed morphology to control nucleation and growth of the secondary structure. Here, we have used highly faceted cubic Pt seeds to direct the epitaxial overgrowth of a secondary metal. We demonstrate this concept with lattice-matched Pd to produce conformal shape-controlled core-shell particles, and then extend it to lattice-mismatched Au to give anisotropic growth. Seeding with faceted nanocrystals may have significant potential towards the development of shape-controlled heterostructures with defined interfaces.
TL;DR: The results suggest that correlated protein environments preserve electronic coherence in photosynthetic complexes and allow the excitation to move coherently in space, enabling highly efficient energy harvesting and trapping in photosynthesis.
Abstract: The role of quantum coherence in promoting the efficiency of the initial stages of photosynthesis is an open and intriguing question. We performed a two-color photon echo experiment on a bacterial reaction center that enabled direct visualization of the coherence dynamics in the reaction center. The data revealed long-lasting coherence between two electronic states that are formed by mixing of the bacteriopheophytin and accessory bacteriochlorophyll excited states. This coherence can only be explained by strong correlation between the protein-induced fluctuations in the transition energy of neighboring chromophores. Our results suggest that correlated protein environments preserve electronic coherence in photosynthetic complexes and allow the excitation to move coherently in space, enabling highly efficient energy harvesting and trapping in photosynthesis.
TL;DR: In this article, the quasiparticle energies and band gaps of graphene nanoribbons were calculated using a first-principles many-electron Green's function approach within the GW approximation.
Abstract: We present calculations of the quasiparticle energies and band gaps of graphene nanoribbons (GNRs) carried out using a first-principles many-electron Green's function approach within the GW approximation. Because of the quasi-one-dimensional nature of a GNR, electron-electron interaction effects due to the enhanced screened Coulomb interaction and confinement geometry greatly influence the quasiparticle band gap. Compared with previous tight-binding and density functional theory studies, our calculated quasiparticle band gaps show significant self-energy corrections for both armchair and zigzag GNRs, in the range of 0.5-3.0 eV for ribbons of width 2.4-0.4 nm. The quasiparticle band gaps found here suggest that use of GNRs for electronic device components in ambient conditions may be viable.
TL;DR: In this article, a review of the use of small angle X-ray scattering (SAXS) for modeling macromolecular folding, unfolding, aggregation, extended conformations, flexibly linked domains, shape, conformation, and assembly state in solution, albeit at the lower resolution range of about 50 A to 10 A resolution, is presented.
Abstract: Crystallography supplies unparalleled detail on structural information critical for mechanistic analyses; however, it is restricted to describing low energy conformations of macromolecules within crystal lattices. Small angle X-ray scattering (SAXS) offers complementary information about macromolecular folding, unfolding, aggregation, extended conformations, flexibly linked domains, shape, conformation, and assembly state in solution, albeit at the lower resolution range of about 50 A to 10 A resolution, but without the size limitations inherent in NMR and electron microscopy studies. Together these techniques can allow multi-scale modeling to create complete and accurate images of macromolecules for modeling allosteric mechanisms, supramolecular complexes, and dynamic molecular machines acting in diverse processes ranging from eukaryotic DNA replication, recombination and repair to microbial membrane secretion and assembly systems. This review addresses both theoretical and practical concepts, concerns and considerations for using these techniques in conjunction with computational methods to productively combine solution scattering data with high-resolution structures. Detailed aspects of SAXS experimental results are considered with a focus on data interpretation tools suitable to model protein and nucleic acid macromolecular structures, including membrane protein, RNA, DNA, and protein-nucleic acid complexes. The methods discussed provide the basis to examine molecular interactions in solution and to study macromolecular flexibility and conformational changes that have become increasingly relevant for accurate understanding, simulation, and prediction of mechanisms in structural cell biology and nanotechnology.
TL;DR: The Genomes On Line Database (GOLD) as mentioned in this paper is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide, containing information for more than 5800 sequencing projects.
Abstract: The Genomes On Line Database (GOLD) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete and ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables and a search page. As of September 2009, GOLD contains information for more than 5800 sequencing projects, of which 1100 have been completed and their sequence data deposited in a public repository. GOLD continues to expand, moving toward the goal of providing the most comprehensive repository of metadata information related to the projects and their organisms/environments in accordance with the Minimum Information about a (Meta)Genome Sequence (MIGS/MIMS) specification. GOLD is available at: http://www.genomesonline.org and has a mirror site at the Institute of Molecular Biology and Biotechnology, Crete, Greece, at: http://gold.imbb.forth.gr/
TL;DR: In this paper, angle-resolved photoemission spectroscopy was used to show that electron-plasmon coupling plays an unusually strong role in renormalizing the bands around the Dirac crossing energy, analogous to mass renormalization by electron-boson coupling in ordinary metals.
Abstract: The effectively massless, relativistic behaviour of graphene’s charge carriers—known as Dirac fermions—is a result of its unique electronic structure, characterized by conical valence and conduction bands that meet at a single point in momentum space (at the Dirac crossing energy). The study of many-body interactions amongst the charge carriers in graphene and related systems such as carbon nanotubes, fullerenes and graphite is of interest owing to their contribution to superconductivity and other exotic ground states in these systems. Here we show, using angle-resolved photoemission spectroscopy, that electron–plasmon coupling plays an unusually strong role in renormalizing the bands around the Dirac crossing energy—analogous to mass renormalization by electron–boson coupling in ordinary metals. Our results show that electron–electron, electron–plasmon and electron–phonon coupling must be considered on an equal footing in attempts to understand the dynamics of quasiparticles in graphene and related systems.
TL;DR: In this paper, a large-scale comparison of the transcriptional profiles and 3D cell culture phenotypes of a substantial panel of human breast cancer cell lines is presented, showing that consistent differences in genes encoding signal transduction proteins emerge when even tumor cells are cultured in 3D microenvironments.
TL;DR: Phylogenetic trees from multiple methods provide strong support for the position of Amborella as the earliest diverging lineage of flowering plants, followed by Nymphaeales and Austrobaileyales, and the plastid genome trees also provide strongSupport for a sister relationship between eudicots and monocots, and this group is sister to a clade that includes Chloranthales and magnoliids.
Abstract: Angiosperms are the largest and most successful clade of land plants with >250,000 species distributed in nearly every terrestrial habitat. Many phylogenetic studies have been based on DNA sequences of one to several genes, but, despite decades of intensive efforts, relationships among early diverging lineages and several of the major clades remain either incompletely resolved or weakly supported. We performed phylogenetic analyses of 81 plastid genes in 64 sequenced genomes, including 13 new genomes, to estimate relationships among the major angiosperm clades, and the resulting trees are used to examine the evolution of gene and intron content. Phylogenetic trees from multiple methods, including model-based approaches, provide strong support for the position of Amborella as the earliest diverging lineage of flowering plants, followed by Nymphaeales and Austrobaileyales. The plastid genome trees also provide strong support for a sister relationship between eudicots and monocots, and this group is sister to a clade that includes Chloranthales and magnoliids. Resolution of relationships among the major clades of angiosperms provides the necessary framework for addressing numerous evolutionary questions regarding the rapid diversification of angiosperms. Gene and intron content are highly conserved among the early diverging angiosperms and basal eudicots, but 62 independent gene and intron losses are limited to the more derived monocot and eudicot clades. Moreover, a lineage-specific correlation was detected between rates of nucleotide substitutions, indels, and genomic rearrangements.
TL;DR: In this paper, the authors propose a structure for organo-mineral associations in soils based on recent insights concerning the molecular structure of soil organic matter (SOM), and on extensive published evidence from empirical studies of organomineral interfaces.
Abstract: In this paper, we propose a structure for organo-mineral associations in soils based on recent insights concerning the molecular structure of soil organic matter (SOM), and on extensive published evidence from empirical studies of organo-mineral interfaces. Our conceptual model assumes that SOM consists of a heterogeneous mixture of compounds that display a range of amphiphilic or surfactant-like properties, and are capable of self-organization in aqueous solution. An extension of this self-organizational behavior in solution, we suggest that SOM sorbs to mineral surfaces in a discrete zonal sequence. In the contact zone, the formation of particularly strong organo-mineral associations appears to be favored by situations where either (i) polar organic functional groups of amphiphiles interact via ligand exchange with singly coordinated mineral hydroxyls, forming stable inner-sphere complexes, or (ii) proteinaceous materials unfold upon adsorption, thus increasing adhesive strength by adding hydrophobic interactions to electrostatic binding. Entropic considerations dictate that exposed hydrophobic portions of amphiphilic molecules adsorbed directly to mineral surfaces be shielded from the polar aqueous phase through association with hydrophobic moieties of other amphiphilic molecules. This process can create a membrane-like bilayer containing a hydrophobic zone, whose components may exchange more easily with the surrounding soil solution than those in the contact zone, but which are still retained with considerable force. Sorbed to the hydrophilic exterior of hemimicellar coatings, or to adsorbed proteins, are organic molecules forming an outer region, or kinetic zone, that is loosely retained by cation bridging, hydrogen bonding, and other interactions. Organic material in the kinetic zone may experience high exchange rates with the surrounding soil solution, leading to short residence times for individual molecular fragments. The thickness of this outer region would depend more on input than on the availability of binding sites, and would largely be controlled by exchange kinetics. Movement of organics into and out of this outer region can thus be viewed as similar to a phase-partitioning process. The zonal concept of organo-mineral interactions presented here offers a new basis for understanding and predicting the retention of organic compounds, including contaminants, in soils and sediments.
TL;DR: The VISTA Enhancer Browser as discussed by the authors is a collection of more than 250 experimentally tested DNA fragments, of which more than 100 have been validated as tissue-specific enhancers, and provides digital images of whole-mount embryo staining at embryonic day 11.5 and anatomical description of the reporter gene expression pattern.
Abstract: Despite the known existence of distant-acting cis-regulatory elements in the human genome, only a small fraction of these elements has been identified and experimentally characterized in vivo. This paucity of enhancer collections with defined activities has thus hindered computational approaches for the genome-wide prediction of enhancers and their functions. To fill this void, we utilize comparative genome analysis to identify candidate enhancer elements in the human genome coupled with the experimental determination of their in vivo enhancer activity in transgenic mice [L. A. Pennacchio et al. (2006) Nature, in press]. These data are available through the VISTA Enhancer Browser (http://enhancer.lbl.gov). This growing database currently contains over 250 experimentally tested DNA fragments, of which more than 100 have been validated as tissue-specific enhancers. For each positive enhancer, we provide digital images of whole-mount embryo staining at embryonic day 11.5 and an anatomical description of the reporter gene expression pattern. Users can retrieve elements near single genes of interest, search for enhancers that target reporter gene expression to a particular tissue, or download entire collections of enhancers with a defined tissue specificity or conservation depth. These experimentally validated training sets are expected to provide a basis for a wide range of downstream computational and functional studies of enhancer function.
J. Craig Venter Institute1, University of California, Davis2, Salk Institute for Biological Studies3, Sanford-Burnham Institute for Medical Research4, University of California, Los Angeles5, University of California, Berkeley6, Lawrence Berkeley National Laboratory7, University of California, San Diego8, Brown University9
TL;DR: This work used sequence similarity clustering to explore proteins with a comprehensive dataset consisting of sequences from available databases together with 6.12 million proteins predicted from an assembly of 7.7 million Global Ocean Sampling sequences to add a great deal of diversity to known protein families and shed light on their evolution.
Abstract: Metagenomics projects based on shotgun sequencing of populations of micro-organisms yield insight into protein families. We used sequence similarity clustering to explore proteins with a comprehensive dataset consisting of sequences from available databases together with 6.12 million proteins predicted from an assembly of 7.7 million Global Ocean Sampling (GOS) sequences. The GOS dataset covers nearly all known prokaryotic protein families. A total of 3,995 medium- and large-sized clusters consisting of only GOS sequences are identified, out of which 1,700 have no detectable homology to known families. The GOS-only clusters contain a higher than expected proportion of sequences of viral origin, thus reflecting a poor sampling of viral diversity until now. Protein domain distributions in the GOS dataset and current protein databases show distinct biases. Several protein domains that were previously categorized as kingdom specific are shown to have GOS examples in other kingdoms. About 6,000 sequences (ORFans) from the literature that heretofore lacked similarity to known proteins have matches in the GOS data. The GOS dataset is also used to improve remote homology detection. Overall, besides nearly doubling the number of current proteins, the predicted GOS proteins also add a great deal of diversity to known protein families and shed light on their evolution. These observations are illustrated using several protein families, including phosphatases, proteases, ultraviolet-irradiation DNA damage repair enzymes, glutamine synthetase, and RuBisCO. The diversity added by GOS data has implications for choosing targets for experimental structure characterization as part of structural genomics efforts. Our analysis indicates that new families are being discovered at a rate that is linear or almost linear with the addition of new sequences, implying that we are still far from discovering all protein families in nature.
TL;DR: By trapping molecules between two gold electrodes with a temperature difference across them, the ability to study thermoelectricity in molecular junctions provides the opportunity to address these fundamental unanswered questions about their electronic structure and to begin exploring molecular thermoeLECTric energy conversion.
Abstract: By trapping molecules between two gold electrodes with a temperature difference across them, the junction Seebeck coefficients of 1,4-benzenedithiol (BDT), 4,4'-dibenzenedithiol, and 4,4''-tribenzenedithiol in contact with gold were measured at room temperature to be +8.7 +/- 2.1 microvolts per kelvin (muV/K), +12.9 +/- 2.2 muV/K, and +14.2 +/- 3.2 muV/K, respectively (where the error is the full width half maximum of the statistical distributions). The positive sign unambiguously indicates p-type (hole) conduction in these heterojunctions, whereas the Au Fermi level position for Au-BDT-Au junctions was identified to be 1.2 eV above the highest occupied molecular orbital level of BDT. The ability to study thermoelectricity in molecular junctions provides the opportunity to address these fundamental unanswered questions about their electronic structure and to begin exploring molecular thermoelectric energy conversion.
TL;DR: The Fifth Data Release (DR5) of the Sloan Digital Sky Survey (SDSS) was released in 2005 June and represents the completion of the SDSS-I project as mentioned in this paper, which includes five-band photometric data for 217 million objects selected over 8000 deg 2 and 1,048,960 spectra of galaxies, quasars, and stars selected from 5713 deg 2 of imaging data.
Abstract: This paper describes the Fifth Data Release (DR5) of the Sloan Digital Sky Survey (SDSS). DR5 includes all survey quality data taken through 2005 June and represents the completion of the SDSS-I project (whose successor, SDSS-II, will continue through mid-2008). It includes five-band photometric data for 217 million objects selected over 8000 deg^2 and 1,048,960 spectra of galaxies, quasars, and stars selected from 5713 deg^2 of that imaging data. These numbers represent a roughly 20% increment over those of the Fourth Data Release; all the data from previous data releases are included in the present release. In addition to "standard" SDSS observations, DR5 includes repeat scans of the southern equatorial stripe, imaging scans across M31 and the core of the Perseus Cluster of galaxies, and the first spectroscopic data from SEGUE, a survey to explore the kinematics and chemical evolution of the Galaxy. The catalog database incorporates several new features, including photometric redshifts of galaxies, tables of matched objects in overlap regions of the imaging survey, and tools that allow precise computations of survey geometry for statistical investigations.
TL;DR: Benzene hydrogenation was investigated in the presence of a surface monolayer consisting of Pt nanoparticles of different shapes (cubic and cuboctahedral) and tetradecyltrimethylammonium bromide and the catalytic selectivity was found to be strongly affected by the nanoparticle shape.
Abstract: Benzene hydrogenation was investigated in the presence of a surface monolayer consisting of Pt nanoparticles of different shapes (cubic and cuboctahedral) and tetradecyltrimethylammonium bromide (TTAB). Infrared spectroscopy indicated that TTAB binds to the Pt surface through a weak C-H...Pt bond of the alkyl chain. The catalytic selectivity was found to be strongly affected by the nanoparticle shape. Both cyclohexane and cyclohexene product molecules were formed on cuboctahedral nanoparticles, whereas only cyclohexane was produced on cubic nanoparticles. These results are the same as the product selectivities obtained on Pt(111) and Pt(100) single crystals in earlier studies. The apparent activation energy for cyclohexane production on cubic nanoparticles is 10.9 +/- 0.4 kcal/mol, while for cuboctahedral nanoparticles, the apparent activation energies for cyclohexane and cyclohexene production are 8.3 +/- 0.2 and 12.2 +/- 0.4 kcal/mol, respectively. These activation energies are lower, and corresponding turnover rates are three times higher than those obtained with single-crystal Pt surfaces.
TL;DR: In this paper, seeded growth of nanocrystals offers a convenient way to design nanoheterostructures with complex shapes and morphologies by changing the crystalline structure of the seed.
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 CdSe nanocrystals with wurtzite and zinc blende structure as seeds for growth of CdS nanorods, we synthesized CdSe/CdS heterostructure nanorods and nanotetrapods, respectively. Both of these structures showed excellent luminescent properties, combining high photoluminescence efficiency (∼80 and ∼50% for nanorods and nanotetrapods, correspondingly), giant extinction coefficients (∼2 × 107 and ∼1.5 × 108 M-1 cm-1 at 350 nm for nanorods and nanotetrapods, correspondingly), and efficient energy transfer from the CdS arms into the emitting CdSe core.