Evolution of a microbial nitrilase gene family: a comparative and environmental genomics study

BACKGROUND: Completed genomes and environmental genomic sequences are bringing a significant contribution to understanding the evolution of gene families, microbial metabolism and community eco-physiology. Here, we used comparative genomics and phylogenetic analyses in conjunction with enzymatic data to probe the evolution and functions of a microbial nitrilase gene family. Nitrilases are relatively rare in bacterial genomes, their biological function being unclear. RESULTS: We examined the genetic neighborhood of the different subfamily genes and discovered conserved gene clusters or operons associated with specific nitrilase clades. The inferred evolutionary transitions that separate nitrilases which belong to different gene clusters correlated with changes in their enzymatic properties. We present evidence that Darwinian adaptation acted during one of those transitions and identified sites in the enzyme that may have been under positive selection. CONCLUSION: Changes in the observed biochemical properties of the nitrilases associated with the different gene clusters are consistent with a hypothesis that those enzymes have been recruited to a novel metabolic pathway following gene duplication and neofunctionalization. These results demonstrate the benefits of combining environmental genomic sampling and completed genomes data with evolutionary and biochemical analyses in the study of gene families. They also open new directions for studying the functions of nitrilases and the genes they are associated with

Developing a high assurance multilevel mail server

Electronic mail (email) often contains sensitive information, which requires special handling to prevent accidental disclosure to unauthorized personnel. Using multiple systems operating at different classifications has caused a number of inefficiencies in the way email is managed and distributed. Attachments in emails have increased the likelihood that a "Trojan Horse" could be inserted in the system to obtain unauthorized access to information. To address this problem Commercial Off-The-Shelf (COTS) software for Internet Message Access Protocol (IMAP), a mail server protocol, has been adapted to a high assurance multilevel base, the Wang Federal XTS-300. The XTS-300 constrains information flow permitting information at different sensitivity levels to be stored securely. Controlled access to mail is provided to client workstations. Enhanced with a trusted computing base extension, these COTS IBM PC compatibles run a standard office productivity suite. This architecture eliminates the risk that a "Trojan horse" will pass higher sensitivity information to a lower sensitivity level.http://archive.org/details/developinghighss1094513602U.S. Marine Corps (U.S.M.C.) author.Approved for public release; distribution is unlimited

The K600 Focal Plane Polarimeter

This research was sponsored by the National Science Foundation Grant NSF PHY-931478

Benefit-Cost Analysis in Environmental, Health, and Safety Regulation: A Statement of Principles

Benefit-cost analysis can play a very important role in legislative and regulatory policy debates on improving the environment, health, and safety. It can help illustrate the tradeoffs that are inherent in public policymaking as well as make those tradeoffs more transparent. It can also help agencies set regulatory priorities. Benefit-cost analysis should be used to help decisionmakers reach a decision. Contrary to the views of some, benefit-cost analysis is neither necessary nor sufficient for designing sensible public policy. If properly done, it can be very helpful to agencies in the decisionmaking process. Decisionmakers should not be precluded from considering the economic benefits and costs of different policies in the development of regulations. Laws that prohibit costs or other factors from being considered in administrative decisionmaking are inimical to good public policy. Currently, several of the most important regulatory statutes have been interpreted to imply such prohibitions. Benefit-cost analysis should be required for all major regulatory decisions, but agency heads should not be bound by a strict benefit-cost test. Instead, they should be required to consider available benefit-cost analyses and to justify the reasons for their decision in the event that the expected costs of a regulation far exceed the expected benefits. Agencies should be encouraged to use economic analysis to help set regulatory priorities. Economic analyses prepared in support of particularly important decisions should be subjected to peer review both inside and outside government. Benefits and costs of proposed major regulations should be quantified wherever possible. Best estimates should be presented along with a description of the uncertainties. Not all benefits or costs can be easily quantified, much less translated into dollar terms. Nevertheless, even qualitative descriptions of the pros and cons associated with a contemplated action can be helpful. Care should be taken to ensure that quantitative factors do not dominate important qualitative factors in decisionmaking. The Office of Management and Budget, or some other coordinating agency, should establish guidelines that agencies should follow in conducting benefit-cost analyses. Those guidelines should specify default values for the discount rate and certain types of benefits and costs, such as the value of a small reduction in mortality risk. In addition, agencies should present their results using a standard format, which summarizes the key results and highlights major uncertainties.

Is There a Role for Benefit-Cost Analysis in Environmental, Health, and Safety Regulation?

Benefit-cost analysis has a potentially important role to play in helping inform regulatory decision-making, although it should not be the sole basis for such decision-making. This paper offers eight principles on the appropriate use of benefit-cost analysis.Environment, Health and Safety, Regulatory Reform

The K600 Focal Plane Polarimeter

This research was sponsored by the National Science Foundation Grant NSF PHY 87-1440

Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function

The first computational interaction network built from Drosophila melanogaster protein-protein and genetic interaction data allows the functional annotation of orphan genes and reveals clusters of functionally-related genes

Search for a Fourth Generation tl Quark in pp̅ Collisions at √s= 1.96 TeV

We present a search for pair production of a fourth generation tl quark and its antiparticle, followed by their decays to a W boson and a jet, based on an integrated luminosity of 5.3 fb-1 of proton-antiproton collisions at √s= 1.96 TeV collected by the D0 Collaboration at the Fermilab Tevatron Collider. We set upper limits on the tlt-l production cross section that exclude at the 95% C.L. a tl quark that decays exclusively to W + jet with a mass below 285 GeV. We observe a small excess in the µ + jets channel which reduces the mass range excluded compared to the expected limit of 320 GeV in the absence of a signal

Wy Production and Limits on Anomalous WWy Couplings in pp̅ Collisions √s = 1.96 TeV

We measure the cross section and the difference in rapidities between photons and charged leptons for inclusive W(→ lv) + y production in ey and µy final states. Using data corresponding to an integrated luminosity of 4.2 fb-1 collected with the D0 detector at the Fermilab Tevatron Collider, the measured cross section times branching fraction for the process pp̅ → Wy + X → lvy + X and the distribution of the charge-signed photon-lepton rapidity difference are found to be in agreement with the standard model. These results provide the most stringent limits on anomalous WW[1] couplings for data from hadron colliders: -0.4 \u3c ∆ky \u3c 0.4 and -0.08 \u3c λy \u3c 0.07 at the 95% C.L