Type III restriction-modification enzymes: a historical perspective

Restriction endonucleases interact with DNA at specific sites leading to cleavage of DNA. Bacterial DNA is protected from restriction endonuclease cleavage by modifying the DNA using a DNA methyltransferase. Based on their molecular structure, sequence recognition, cleavage position and cofactor requirements, restriction-modification (R-M) systems are classified into four groups. Type III R-M enzymes need to interact with two separate unmethylated DNA sequences in inversely repeated head-to-head orientations for efficient cleavage to occur at a defined location (25-27 bp downstream of one of the recognition sites). Like the Type I R-M enzymes, Type III R-M enzymes possess a sequence-specific ATPase activity for DNA cleavage. ATP hydrolysis is required for the long-distance communication between the sites before cleavage. Different models, based on 1D diffusion and/or 3D-DNA looping, exist to explain how the long-distance interaction between the two recognition sites takes place. Type III R-M systems are found in most sequenced bacteria. Genome sequencing of many pathogenic bacteria also shows the presence of a number of phase-variable Type III R-M systems, which play a role in virulence. A growing number of these enzymes are being subjected to biochemical and genetic studies, which, when combined with ongoing structural analyses, promise to provide details for mechanisms of DNA recognition and catalysis.

DEEP WASHINGTON PHOTOMETRY OF INCONSPICUOUS STAR CLUSTER CANDIDATES IN THE LARGE MAGELLANIC CLOUD

We present deep Washington photometry of 45 poorly populated star cluster candidates in the Large Magellanic Cloud (LMC). We have performed a systematic study to estimate the parameters of the cluster candidates by matching theoretical isochrones to the cleaned and dereddened cluster color-magnitude diagrams. We were able to estimate the basic parameters for 33 clusters, out of which 23 are identified as single clusters and 10 are found to be members of double clusters. The other 12 cluster candidates have been classified as possible clusters/asterisms. About 50% of the true clusters are in the 100-300 Myr age range, whereas some are older or younger. We have discussed the distribution of age, location, and reddening with respect to field, as well as the size of true clusters. The sizes and masses of the studied sample are found to be similar to that of open clusters in the Milky Way. Our study adds to the lower end of cluster mass distribution in the LMC, suggesting that the LMC, apart from hosting rich clusters, also has formed small, less massive open clusters in the 100-300 Myr age range.

A theoretical perspective of the Telepinu Myth : archetypes and initiation rites in historical contexts

Abstract: Research on the Telepinu Myth (CTH 324) has shown that it is an inexhaustibly rich document and that therefore the different, and sometimes conflicting, lines of analysis need to be pursued further. In the light of the symbolic evidence presented by this mythological tradition, we propose to focus on the privileged position granted to spatial symbols and to hypothesize the function this Myth served in specific contexts of the Hittite history, characterized by the increase and reduction of lands under Hittite jurisdiction. In this regard, we propose to evaluate the symbolic function that the Telepinu Myth displayed in order to rebuild the sacred space of the territories governed by the Hittites, when they were undergoing changes brought about by increased political and military contact with neighboring societies.

The degree of predictability of earthquakes in several regions of China: statistical analysis of historical data

The stress release model, a stochastic version of the elastic-rebound theory, is applied to the historical earthquake data from three strong earthquake-prone regions of China, including North China, Southwest China, and the Taiwan seismic regions. The results show that the seismicity along a plate boundary (Taiwan) is more active than in intraplate regions (North and Southwest China). The degree of predictability or regularity of seismic events in these seismic regions, based on both the Akaike information criterion (AIC) and fitted sensitivity parameters, follows the order Taiwan, Southwest China, and North China, which is further identified by numerical simulations. (c) 2004 Elsevier Ltd. All rights reserved.

Model of sources: a proposal for the hierarchy, merging strategy and representation of the information sources in virtual models of historical buildings

Contributed to: Fusion of Cultures: XXXVIII Annual Conference on Computer Applications and Quantitative Methods in Archaeology – CAA2010 (Granada, Spain, Apr 6-9, 2010)

Imminent Geologic and Hydrologic Hazards on Fort Ord BLM Land

The Bureau of Land Management acquired 7,500 acres of land as part of the re-use of the decommissioned Fort Ord Army base. A variety of geologic hazards exist on the landscape including gully erosion, mass wasting, and decaying earthen dams. This short report highlights a few critical areas that deserve closer evaluation and remediation. Of particular concern are decaying earthen dams and mass wasting of tall stream banks that may impact BLM infrastructure or adjacent urban development. (Document contains 13 paGES)

Summary report on water quantity and quality studies of Vancouver Lake, Washington

Vancouver Lake, located adjacent to the Columbia River and just north of the Vancouver-Portland metropolitan area, is a "dying" lake. Although all lakes die naturally in geologic time through the process of eutrophication,* Vancouver Lake is dying more rapidly due to man's activities and due to the resultant increased accumulation of sediment, chemicals, and wastes. Natural eutrophication takes thousands of years, whereas man-made modifications can cause the death of a lake in decades. Vancouver Lake does, however, have the potential of becoming a valuable water resource asset for the area, due particularly to its location near the Columbia River which can be used as a source of "flushing" water to improve the quality of Vancouver Lake. (Document pdf contains 59 pages) Community interest in Vancouver Lake has waxed and waned. Prior to World War II, there were relatively few plans for discussions about the Lake and its surrounding land area. A plan to drain the Lake for farming was prohibited by the city council and county commissioners. Interest increased in 1945 when the federal government considered developing the Lake as a berthing harbor for deactivated ships at which time a preliminary proposal was prepared by the City. The only surface water connection between Vancouver Lake and the Columbia River, except during floods, is Lake River. The Lake now serves as a receiving body of water for Lake River tidal flow and surface flow from creeks and nearby land areas. Seasonally, these flows are heavily laden with sediment, septic tank drainage, fertilizers and drainage from cattle yards. Construction and gravel pit operations increase the sediment loads entering the Lake from Burnt Bridge Creek and Salmon Creek (via Lake River by tidal action). The tidal flats at the north end of Vancouver Lake are evidence of this accumulation. Since 1945, the buildup of sediment and nutrients created by man's activities has accelerated the growth of the large water plants and algae which contribute to the degeneration of the Lake. Flooding from the Columbia River, as in 1968, has added to the deposition in Vancouver Lake. The combined effect of these human and natural activities has changed Vancouver Lake into a relatively useless body of shallow water supporting some wildlife, rough fish, and shallow draft boats. It is still pleasant to view from the hills to the east. Because precipitation and streamflow are the lowest during the summer and early fall, water quantity and quality conditions are at their worst when the potential of the Lake for water-based recreation is the highest. Increased pollution of the Lake has caused a larger segment of the community to become concerned. Land use and planning studies were undertaken on the Columbia River lowlands and a wide variety of ideas were proposed for improving the quality of the water-land environment in order to enhance the usefulness of the area. In 1966, the College of Engineering Research Division at Washington State University (WSU0 in Pullman, Washington, was contacted by the Port of Vancouver to determine possible alternatives for restoring Vancouver Lake. Various proposals were prepared between 1966 and 1969. During the summer and fall of 1967, a study was made by WSU on the existing water quality in the Lake. In 1969, the current studies were funded to establish a data base for considering a broad range of alternative solutions for improving the quantity and quality of Vancouver Lake. Until these studies were undertaken, practically no data on a continuous nature were available on Vancouver Lake, Lake River, or their tributaries. (Document pdf contains 59 pages)

Mechanical and Chemical Control of Smooth Cordgrass in Waillapa Bay, Washington

We evaluated four methods to control smooth cordgrass (Spartina alterniflora Loisel), hereafter spartina, in Willapa Bay, Washington: mowing, mowing plus herbicide combination, herbicide only for clones, and aerial application of herbicide for meadows. (PDF has 7 pages.)

Non-target Impacts to Eelgrass from Treatments to Control Spartina in Willapa Bay, Washington

Four methods to control the smooth cordgrass Spartina (Spartina alterniflora) and the footwear worn by treatment personnelat several sites in Willapa Bay, Washington were evaluatedto determine the non-target impacts to eelgrass (Zostera japonica). Clone-sized infestations of Spartina were treated bymowing or a single hand-spray application of Rodeo® formulatedat 480 g L-1acid equivalence (ae) of the isopropylaminesalt of glyphosate (Monsanto Agricultural Co., St. Louis, MO;currently Dow AgroSciences, Indianapolis, IN) with the nonionic surfactant LI 700® (2% v/v) or a combination of mowing and hand spraying. An aerial application of Rodeo® with X-77 Spreader® (0.13% v/v) to a 2-ha meadow was also investigated. Monitoring consisted of measuring eelgrass shoot densities and percent cover pre-treatment and 1-yr post-treatment. Impacts to eelgrass adjacent to treated clones were determined 1 m from the clones and compared to a control 5-m away. Impacts from footwear were assessed at 5 equidistant intervals along a 10-m transect on mudflat and an untreated control transect at each of the three clone treatment sites. Impacts from the aerial application were determined by comparing shoot densities and percent cover 1, 3 and 10 m from the edge of the treated Spartina meadow to that at comparable distances from an untreated meadow. Methods utilized to control Spartina clones did not impact surrounding eelgrass at two of three sites. Decreases in shoot densities observed at the third site were consistent across treatments. Most impacts to eelgrass from the footwear worn by treatment personnel were negligible and those that were significant were limited to soft mud substrate. The aerial application of the herbicide was associated with reductions in eelgrass (shoot density and percent cover) at two of the three sampling distances, but reductions on the control plot were greater. We conclude that the unchecked spread of Spartina is a far greater threat to the survival and health of eelgrass than that from any of the control measures we studied. The basis for evaluating control measures for Spartina should be efficacy and logistical constraints and not impacts to eelgrass. PDF is 7 pages.

The Impact of Endothall on the Aquatic Plant Community of Kress Lake, Washington

CA dense mat-forming population of Eurasian watermilfoil ( Myriophyllum spicatum L . ) was interfering with fishing and recreation in a small western Washington lake. A low concentration (1.5 mg/L active ingredient) of the herbicide endothall formulated as Aquathol® K was used in 2000 to attempt to selectively control the Eurasian watermilfoil. Aquatic plant biomass and frequency data were collected before treatment, ten weeks after treatment and during the growing season for 3 additional years. Macrophyte data were analyzed to assess the herbicide’s impacts on Eurasian watermilfoil as well as the rest of the aquatic plant community. Results showed a significant decrease in Eurasian watermilfoil biomass and frequency 10 weeks after treatment. The Eurasian watermilfoil continued to be present, but at a significantly reduced level through the remainder of the study (3 years after treatment). Of the native plant species, large-leaf pondweed ( Potamogeton amplifolius Tucker . ) frequency and biomass was significantly reduced after treatment. Common elodea ( Elodea canadensis Rich.), muskgrass ( Chara sp. Vallaint.) and bladderwort ( Utricularia sp. L.) all increased significantly after treatment. (PDF has 6 pages.)

Limnology in Argentina: an historical account.

This short review includes major books, articles and episodes concerned with studies on inland waters that have affected the development of limnology in Argentina.

Relationship between water quality, watermilfoil frequency, and weevil distribution in the State of Washington

During the summer of 1997, we surveyed 50 waterbodies in Washington State to determine the distribution of the aquatic weevil Euhrychiopsis lecontei Dietz. We collected data on water quality and the frequency of occurrence of watermilfoil species within selected watermilfoil beds to compare the waterbodies and determine if they were related to the distribution E. lecontei . We found E. lecontei in 14 waterbodies, most of which were in eastern Washington. Only one lake with weevils was located in western Washington. Weevils were associated with both Eurasian ( Myriophyllum spicatum L.) and northern watermilfoil ( M. sibiricum K.). Waterbodies with E. lecontei had significantly higher ( P < 0.05) pH (8.7 ± 0.2) (mean ± 2SE), specific conductance (0.3 ± 0.08 mS cm -1 ) and total alkalinity (132.4 ± 30.8 mg CaCO 3 L -1 ). We also found that weevil presence was related to surface water temperature and waterbody location ( = 24.3, P ≤ 0.001) and of all the models tested, this model provided the best fit (Hosmer- Lemeshow goodness-of-fit = 4.0, P = 0.9). Our results suggest that in Washington State E. lecontei occurs primarily in eastern Washington in waterbodies with pH ≥ 8.2 and specific conductance ≥ 0.2 mS cm -1 . Furthermore, weevil distribution appears to be correlated with waterbody location (eastern versus western Washington) and surface water temperature.