Sulphate-reducing bacteria are anaerobes readily found in oxic-anoxic interfaces. Multiple defence pathways against oxidative conditions were identified in these organisms and proposed to be differentially expressed under different concentrations of oxygen, contributing to their ability to survive oxic conditions. In this study, Desulfovibrio vulgaris Hildenborough cells were exposed to the highest concentration of oxygen that sulphate-reducing bacteria are likely to encounter in natural habitats, and the global transcriptomic response was determined. 307 genes were responsive, with cellular roles in energy metabolism, protein fate, cell envelope and regulatory functions, including multiple genes encoding heat shock proteins, peptidases and proteins with heat shock promoters. Of the oxygen reducing mechanisms of D. vulgaris only the periplasmic hydrogen-dependent mechanism is up-regulated, involving the [NiFeSe]hydrogenase, formate dehydrogenase(s) and the Hmc membrane complex. The oxidative defence response concentrates on damage repair by metal-free enzymes. These data, together with the down regulation of the Fur operon, which restricts the availability of iron, and the lack of response of the PerR operon, suggest that a major effect of this oxygen stress is the inactivation and/or degradation of multiple metalloproteins present in D. vulgaris as a consequence of oxidative damage to their metal clusters.

Clouds in the tropical western Pacific are an integral part of the large scale environment. An improved understanding of the multi-scale structure of clouds and their interactions with the environment is critical to the ARM (Atmospheric Radiation Measurement) program for developing and evaluating cloud parameterizations, understanding the consequences of model biases, and providing a context for interpreting the observational data collected over the ARM Tropical Western Pacific (TWP) sites. Three-dimensional cloud resolving models (CRMs) are powerful tools for developing and evaluating cloud parameterizations. However, a significant challenge in using CRMs in the TWP is that the region lacks conventional data, so large uncertainty exists in defining the large-scale environment for clouds. This project links several aspects of the ARM program, from measurements to providing improved analyses, and from cloud-resolving modeling to climate-scale modeling and parameterization development, with the overall objective to improve the representations of clouds in climate models and to simulate and quantify resolved cloud effects on the large-scale environment. Our objectives will be achieved through a series of tasks focusing on the use of the Weather Research and Forecasting (WRF) model and ARM data. Our approach includes: -- Perform assimilation of COSMIC GPS radio occultation and other satellites …

U.S. Department of Energy (DOE) Order 450.1, Environmental Protection Program, requires each DOE site to conduct environmental monitoring. Environmental monitoring at the Waste Isolation Pilot Plant (WIPP) is conducted in order to: (a) Verify and support compliance with applicable federal, state, and local environmental laws, regulations, permits, and orders; (b) Establish baselines and characterize trends in the physical, chemical, and biological condition of effluent and environmental media; (c) Identify potential environmental problems and evaluate the need for remedial actions or measures to mitigate the problems; (d) Detect, characterize, and report unplanned releases; (e) Evaluate the effectiveness of effluent treatment and control, and pollution abatement programs; and (f) Determine compliance with commitments made in environmental impact statements, environmental assessments, safety analysis reports, or other official DOE documents. This Environmental Monitoring Plan (EMP) explains the rationale and design criteria for the environmental monitoring program, extent and frequency of monitoring and measurements, procedures for laboratory analyses, quality assurance (QA) requirements, program implementation procedures, and direction for the preparation and disposition of reports. Changes to the environmental monitoring program may be necessary to allow the use of advanced technology and new data collection techniques. This EMP will document changes in the environmental monitoring program. …

The mission of the CAVEMAN project is to provide the tools for large code systems so that those who work on them can perform source control and configuration control on UNIX-based file servers, rather than the LC Crays. An outside product called cvs has been chosen as the underlying source control system. The initials stand for {open_quotes}Concurrent Versions System{close_quotes}. It is a freeware program that runs on most UNIX stations. To quote from the cvs man page: {open_quotes}cvs is a front end to the rcs revision control system which extends the notion of revision control from a collection of files in a single directory to a hierarchical collection of directories consisting of revision controlled files. These directories and files can be combined together to form a software release. cvs provides the functions necessary to manage these software releases and to control the concurrent editing of source files among multiple software developers.{close_quotes} While cvs may be run directly, there are several tasks in the LLNL environment that it seemed either safer or easier to automate. CAVEMAN provides the needed functionality, generally in the form of wrappers to cvs.

While initially a virtual institute, the driving force behind the creation of the DOE Joint Genome Institute in Walnut Creek, California in the Fall of 1999 was the Department of Energy's commitment to sequencing the human genome. With the publication in 2004 of a trio of manuscripts describing the finished 'DOE Human Chromosomes', the Institute successfully completed its human genome mission. In the time between the creation of the Department of Energy Joint Genome Institute (DOE JGI) and completion of the Human Genome Project, sequencing and its role in biology spread to fields extending far beyond what could be imagined when the Human Genome Project first began. Accordingly, the targets of the DOE JGI's sequencing activities changed, moving from a single human genome to the genomes of large numbers of microbes, plants, and other organisms, and the community of users of DOE JGI data similarly expanded and diversified. Transitioning into operating as a user facility, the DOE JGI modeled itself after other DOE user facilities, such as synchrotron light sources and supercomputer facilities, empowering the science of large numbers of investigators working in areas of relevance to energy and the environment. The JGI's approach to being a user facility is …