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Bacteria from phyla lacking cultivated representatives are widespread in natural systems and some have very small genomes. Here we test the hypothesis that these cells are small and thus might be enriched by filtration for coupled genomic and ultrastructural characterization. Metagenomic analysis of groundwater that passed through a ~0.2-μm filter reveals a(More)
Reproducible images of uncoated DNA in the atomic force microscope (AFM) have been obtained by imaging plasmid DNA on mica in n-propanol. Specially sharpened AFM tips give images with reproducible features several nanometers in size along the DNA. Plasmids can be dissected in propanol by increasing the force applied by the AFM tip at selected locations.
Fully understanding the biology of acid mine drainage (AMD) is central to our ability to control and manipulate its environmental impact. Although genomics and biogeochemical methods are relatively well established in the field, their combination with high-resolution imaging of intact members of microbial biofilm communities has not yet reached its full(More)
The goal of the work reported here is to understand the precise molecular mechanism of the process of DNA packaging in dsDNA bacteriophages. Cryo-EM was used to directly visualize the architecture of the DNA inside the capsid and thus to measure fundamental physical parameters such as inter-strand distances, local curvatures, and the degree of order. We(More)
The LBNL/NERSC Visportal effort explores ways to deliver advanced Remote/Distributed Visualization (RDV) capabilities through a Grid-enabled web-portal interface. The effort focuses on latency tolerant distributed visualization algorithms, GUI designs that are more appropriate for the capabilities of web interfaces , and refactoring parallel-distributed(More)
Significant problems facing all experimental and computational sciences arise from growing data size and complexity. Common to all these problems is the need to perform efficient data I/O on diverse computer architectures. In our scientific application, the largest parallel particle simulations generate vast quantities of six-dimensional data. Such a(More)
Protein-based assemblies with ordered nanometer-scale features in three dimensions are of interest as functional nanomaterials but are difficult to generate. Here we report that a truncated S-layer protein assembles into stable bilayers, which we characterized using cryogenic-electron microscopy, tomography, and X-ray spectroscopy. We find that emergence of(More)
SciDAC has had a major impact on computational beam dynamics and the design of particle accelerators. Particle accelerators-which account for half of the facilities in the DOE Office of Science Facilities for the Future of Science 20 Year Outlook-are crucial for US scientific, industrial, and economic competitiveness. Thanks to SciDAC, accelerator design(More)
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