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Sample records for fork leonaradian age

  1. Integrated Outcrop and Subsurface Studies of the Interwell Environment of Carbonate Reservoirs: Clear Fork (Leonaradian Age) Reservoirs, West Texas and New Mexico, Semi-Annual

    SciTech Connect

    Ruppel, Stephen C.; Jennings, James W.; Laubach, Stephen E.

    2001-11-29

    Outcrop studies include stratigraphic and petrophysical analysis. Analysis of the detailed sequence- and cycle-scale architecture of the Clear Fork reservoir-equivalent outcrops in Apache Canyon is nearly complete. This work reveals two high-frequency transgressive-regressive sequences (HFS) in the lower Clear Fork composite depositional sequence and three HFS in the basal middle Clear Fork composite depositional sequence. A 1,800-ft transect of 1-inch-diameter samples was collected from one cycle at the Apache Canyon outcrop. The transect was sampled with 5-ft spacing, but there were some gaps due to cover and cliff, resulting in 181 samples. Permeability, porosity, and grain density were measured, and the spatial statistics are being analyzed geostatistically.

  2. Integrated Outcrop and Subsurface Studies of the Interwell Environment of Carbonate Reservoirs: Clear Fork (Leonaradian Age) Reservoirs, West Texas and New Mexico

    SciTech Connect

    Lucia, F.J.; Ruppel, S.C.

    2001-02-01

    Characterization of cycle and facies architecture on lower Clear Fork and lowermost upper Clear Fork equivalent outcrops in Apache Canyon of Sierra Diablo was complete. The focus of detailed study in Apache Canyon has been the upper Clear Fork section because this interval contains the productive interval in South Wasson field, the preliminary subsurface study area. Parts of three high-frequency sequences (HFS), each 60 to 100 ft thick, are present on the south wall of Apache Canyon. HFS's display an upper-deepening or backstepping pattern associated with longer-term sea level rise. Each HFS is composed of upward-shallowing cycles whose thickness, facies composition, and continuity vary within and between HFS's.

  3. Integrated Outcrop and Subsurface Studies of the Interwell Environment of Carbonate Reservoirs: Clear Fork (Leonaradian Age) Reservoirs, West Texas and New Mexico

    SciTech Connect

    Lucia, F. Jerry; Jennings, Jr., James W.

    2001-05-08

    A preliminary reservoir model was constructed for the Lower Clear Fork of the South Wasson Clear Fork reservoir. The model was constructed by calibrating high-frequency cycles observed in cores to the porosity log. The rock fabrics mostly fall in petrophysical class 1, and cross plots of porosity and water saturation could not be used to identify rock fabrics. Data from two limestone fields and one dolostone field were presented to support the contention that grain-dominated fabrics have higher porosity than mud-dominated fabrics do and that this difference is retained when the limestone is dolomitized.

  4. INTEGRATED OUTCROP AND SUBSURFACE STUDIES OF THE INTERWELL ENVIRONMENT OF CARBONATE RESERVOIRS: CLEAR FORK (LEONARADIAN AGE) RESERVOIRS, WEST TEXAS AND NEW MEXICO

    SciTech Connect

    James W. Jennings, Jr.; F. Jerry Lucia

    2001-10-01

    Petrophysical heterogeneity in the South Wasson Clear Fork (SWCF) reservoir and other shallow-water platform carbonates in the Permian Basin and elsewhere is composed of a large-scale stratigraphically controlled component and a small-scale poorly correlated component. The large-scale variability exists as a flow-unit scale petrophysical layering that is laterally persistent at interwell scales and produces highly stratified reservoir behavior. Capturing the rate-enhancing effect of the small-scale variability requires carefully controlled averaging procedures at four levels of scaleup. Porosity can be easily scaled using arithmetic averaging procedures. Permeability, however, requires carefully controlled power-averaging procedures. Effective permeability is increased at every scaleup level.

  5. Along Middle Fork Road toward North Fork of the Crazy ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Along Middle Fork Road toward North Fork of the Crazy Woman Creek Bridge, view to west - North Fork of Crazy Woman Creek Bridge, Spanning North Fork of Crazy Woman Creek at Middle Fork Road, Buffalo, Johnson County, WY

  6. INTEGRATED OUTCROP AND SUBSURFACE STUDIES OF THE INTERWELL ENVIRONMENT OF CARBONATE RESERVOIRS: CLEAR FORK (LEONARDIAN-AGE) RESERVOIRS, WEST TEXAS AND NEW MEXICO

    SciTech Connect

    F. Jerry Lucia

    2002-01-31

    This is the final report of the project ''Integrated Outcrop and Subsurface Studies of the Interwell Environment of Carbonate Reservoirs: Clear Fork (Leonardian-Age) Reservoirs, West Texas and New Mexico'', Department of Energy contract no. DE-AC26-98BC15105 and is the third in a series of similar projects funded jointly by the U.S. Department of Energy and The University of Texas at Austin, Bureau of Economic Geology, Reservoir Characterization Research Laboratory for Carbonates. All three projects focus on the integration of outcrop and subsurface data for the purpose of developing improved methods for modeling petrophysical properties in the interwell environment. The first project, funded by contract no. DE-AC22-89BC14470, was a study of San Andres outcrops in the Algerita Escarpment, Guadalupe Mountains, Texas and New Mexico, and the Seminole San Andres reservoir, Permian Basin. This study established the basic concepts for constructing a reservoir model using sequence-stratigraphic principles and rock-fabric, petrophysical relationships. The second project, funded by contract no. DE-AC22-93BC14895, was a study of Grayburg outcrops in the Brokeoff Mountains, New Mexico, and the South Cowden Grayburg reservoir, Permian Basin. This study developed a sequence-stratigraphic succession for the Grayburg and improved methods for locating remaining hydrocarbons in carbonate ramp reservoirs. The current study is of the Clear Fork Group in Apache Canyon, Sierra Diablo Mountains, West Texas, and the South Wasson Clear Fork reservoir, Permian Basin. The focus was on scales of heterogeneity, imaging high- and low-permeability layers, and the impact of fractures on reservoir performance. In this study (1) the Clear Fork cycle stratigraphy is defined, (2) important scales of petrophysical variability are confirmed, (3) a unique rock-fabric, petrophysical relationship is defined, (4) a porosity method for correlating high-frequency cycles and defining rock-fabric flow layers

  7. Metals-contaminated benthic invertebrates in the Clark Fork River, Montana: Effects on age-0 brown trout and rainbow trout

    USGS Publications Warehouse

    Woodward, Daniel F.; Farag, Aïda M.; Bergman, Harold L.; Delonay, Aaron J.; Little, Edward E.; Smiths, Charlie E.; Barrows, Frederic T.

    1995-01-01

    Benthic organisms in the upper Clark Fork River have recently been implicated as a dietary source of metals that may be a chronic problem for young-of-the-year rainbow trout (Oncorhynchus mykiss). In this present study, early life stage brown trout (Salmo trutta) and rainbow trout were exposed for 88 d to simulated Clark Fork River water and a diet of benthic invertebrates collected from the river. These exposures resulted in reduced growth and elevated levels of metals in the whole body of both species. Concentrations of As, Cd, Cu, and Pb increased in whole brown trout; in rainbow trout, As and Cd increased in whole fish, and As also increased in liver. Brown trout on the metals-contaminated diets exhibited constipation, gut impaction, increased cell membrane damage (lipid peroxidation), decreased digestive enzyme production (zymogen), and a sloughing of intestinal mucosal epithelial cells. Rainbow trout fed the contaminated diets exhibited constipation and reduced feeding activity. We believe that the reduced standing crop of trout in the Clark Fork River results partly from chronic effects of metals contamination in benthic invertebrates that are important as food for young-of-the-year fish.

  8. Regulation of Replication Fork Advance and Stability by Nucleosome Assembly

    PubMed Central

    Prado, Felix; Maya, Douglas

    2017-01-01

    The advance of replication forks to duplicate chromosomes in dividing cells requires the disassembly of nucleosomes ahead of the fork and the rapid assembly of parental and de novo histones at the newly synthesized strands behind the fork. Replication-coupled chromatin assembly provides a unique opportunity to regulate fork advance and stability. Through post-translational histone modifications and tightly regulated physical and genetic interactions between chromatin assembly factors and replisome components, chromatin assembly: (1) controls the rate of DNA synthesis and adjusts it to histone availability; (2) provides a mechanism to protect the integrity of the advancing fork; and (3) regulates the mechanisms of DNA damage tolerance in response to replication-blocking lesions. Uncoupling DNA synthesis from nucleosome assembly has deleterious effects on genome integrity and cell cycle progression and is linked to genetic diseases, cancer, and aging. PMID:28125036

  9. Regulation of Replication Fork Advance and Stability by Nucleosome Assembly.

    PubMed

    Prado, Felix; Maya, Douglas

    2017-01-24

    The advance of replication forks to duplicate chromosomes in dividing cells requires the disassembly of nucleosomes ahead of the fork and the rapid assembly of parental and de novo histones at the newly synthesized strands behind the fork. Replication-coupled chromatin assembly provides a unique opportunity to regulate fork advance and stability. Through post-translational histone modifications and tightly regulated physical and genetic interactions between chromatin assembly factors and replisome components, chromatin assembly: (1) controls the rate of DNA synthesis and adjusts it to histone availability; (2) provides a mechanism to protect the integrity of the advancing fork; and (3) regulates the mechanisms of DNA damage tolerance in response to replication-blocking lesions. Uncoupling DNA synthesis from nucleosome assembly has deleterious effects on genome integrity and cell cycle progression and is linked to genetic diseases, cancer, and aging.

  10. 1. View of Clark Fork Vehicle Bridge facing west. Panorama ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. View of Clark Fork Vehicle Bridge facing west. Panorama showing the entire span of bridge from north shore of the Clark Fork River. - Clark Fork Vehicle Bridge, Spanning Clark Fork River, serves Highway 200, Clark Fork, Bonner County, ID

  11. 3. View of Clark Fork Vehicle Bridge facing southwest. Bridge ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    3. View of Clark Fork Vehicle Bridge facing southwest. Bridge from north shore of Clark Fork River. - Clark Fork Vehicle Bridge, Spanning Clark Fork River, serves Highway 200, Clark Fork, Bonner County, ID

  12. 7. View of Clark Fork Vehicle Bridge facing northwest. Bridge ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    7. View of Clark Fork Vehicle Bridge facing northwest. Bridge from south shore of Clark Fork River showing 4 1/2 spans. - Clark Fork Vehicle Bridge, Spanning Clark Fork River, serves Highway 200, Clark Fork, Bonner County, ID

  13. 4. View of Clark Fork Vehicle Bridge facing northeast. Bridge ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    4. View of Clark Fork Vehicle Bridge facing northeast. Bridge from south shoreof Clark Fork River showing 4 spans. - Clark Fork Vehicle Bridge, Spanning Clark Fork River, serves Highway 200, Clark Fork, Bonner County, ID

  14. 2. View of Clark Fork Vehicle Bridge facing northeast. Bridge ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    2. View of Clark Fork Vehicle Bridge facing northeast. Bridge from south shore of Clark Fork River showing 4 1/2 spans. - Clark Fork Vehicle Bridge, Spanning Clark Fork River, serves Highway 200, Clark Fork, Bonner County, ID

  15. Tuning Forks and Monitor Screens.

    ERIC Educational Resources Information Center

    Harrison, M. A. T.

    2000-01-01

    Defines the vibrations of a tuning fork against a computer monitor screen as a pattern that can illustrate or explain physical concepts like wave vibrations, wave forms, and phase differences. Presents background information and demonstrates the experiment. (Author/YDS)

  16. 22. View of Clark Fork Vehicle Bridge facing downwest side. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    22. View of Clark Fork Vehicle Bridge facing down-west side. Looking at road deck and vertical laced channel. - Clark Fork Vehicle Bridge, Spanning Clark Fork River, serves Highway 200, Clark Fork, Bonner County, ID

  17. 8. View of Clark Fork Vehicle Bridge facing southwest. Looking ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    8. View of Clark Fork Vehicle Bridge facing southwest. Looking at understructure of northernmost span. - Clark Fork Vehicle Bridge, Spanning Clark Fork River, serves Highway 200, Clark Fork, Bonner County, ID

  18. 11. View of Clark Fork Vehicle Bridge facing northwest. Southernmost ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    11. View of Clark Fork Vehicle Bridge facing northwest. Southernmost span. Plaque was originally located where striped traffic sign is posted. - Clark Fork Vehicle Bridge, Spanning Clark Fork River, serves Highway 200, Clark Fork, Bonner County, ID

  19. 21. View of Clark Fork Vehicle Bridge facing west. Looking ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    21. View of Clark Fork Vehicle Bridge facing west. Looking at bridge deck, guard rail, juncture of two bridge spans. - Clark Fork Vehicle Bridge, Spanning Clark Fork River, serves Highway 200, Clark Fork, Bonner County, ID

  20. 12. View of Clark Fork Vehicle Bridge facing south. Approach ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    12. View of Clark Fork Vehicle Bridge facing south. Approach from the north road. Plaque was originally located where striped traffic sign is posted. - Clark Fork Vehicle Bridge, Spanning Clark Fork River, serves Highway 200, Clark Fork, Bonner County, ID

  1. 18. View of Clark Fork Vehicle Bridge facing north. Looking ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    18. View of Clark Fork Vehicle Bridge facing north. Looking at north concrete abutment and timber stringers. - Clark Fork Vehicle Bridge, Spanning Clark Fork River, serves Highway 200, Clark Fork, Bonner County, ID

  2. 20. View of Clark Fork Vehicle Bridge facing up. Looking ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    20. View of Clark Fork Vehicle Bridge facing up. Looking at understructure of northernmost span. - Clark Fork Vehicle Bridge, Spanning Clark Fork River, serves Highway 200, Clark Fork, Bonner County, ID

  3. 19. View of Clark Fork Vehicle Bridge facing north. Looking ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    19. View of Clark Fork Vehicle Bridge facing north. Looking at north abutment and underside of northernmost span. - Clark Fork Vehicle Bridge, Spanning Clark Fork River, serves Highway 200, Clark Fork, Bonner County, ID

  4. Multiple pathways process stalled replication forks.

    PubMed

    Michel, Bénédicte; Grompone, Gianfranco; Florès, Maria-Jose; Bidnenko, Vladimir

    2004-08-31

    Impairment of replication fork progression is a serious threat to living organisms and a potential source of genome instability. Studies in prokaryotes have provided evidence that inactivated replication forks can restart by the reassembly of the replication machinery. Several strategies for the processing of inactivated replication forks before replisome reassembly have been described. Most of these require the action of recombination proteins, with different proteins being implicated, depending on the cause of fork arrest. The action of recombination proteins at blocked forks is not necessarily accompanied by a strand-exchange reaction and may prevent rather than repair fork breakage. These various restart pathways may reflect different structures at stalled forks. We review here the different strategies of fork processing elicited by different kinds of replication impairments in prokaryotes and the variety of roles played by recombination proteins in these processes.

  5. Replication fork instability and the consequences of fork collisions from rereplication

    PubMed Central

    Alexander, Jessica L.; Orr-Weaver, Terry L.

    2016-01-01

    Replication forks encounter obstacles that must be repaired or bypassed to complete chromosome duplication before cell division. Proteomic analysis of replication forks suggests that the checkpoint and repair machinery travels with unperturbed forks, implying that they are poised to respond to stalling and collapse. However, impaired fork progression still generates aberrations, including repeat copy number instability and chromosome rearrangements. Deregulated origin firing also causes fork instability if a newer fork collides with an older one, generating double-strand breaks (DSBs) and partially rereplicated DNA. Current evidence suggests that multiple mechanisms are used to repair rereplication damage, yet these can have deleterious consequences for genome integrity. PMID:27898391

  6. 5. View of Clark Fork Vehicle Bridge facing east. Bridge ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. View of Clark Fork Vehicle Bridge facing east. Bridge from south shore of Clark Fork River-southernmost span. 1900-era Northern Pacific Railway Bridge in background. - Clark Fork Vehicle Bridge, Spanning Clark Fork River, serves Highway 200, Clark Fork, Bonner County, ID

  7. Pathways of mammalian replication fork restart.

    PubMed

    Petermann, Eva; Helleday, Thomas

    2010-10-01

    Single-molecule analyses of DNA replication have greatly advanced our understanding of mammalian replication restart. Several proteins that are not part of the core replication machinery promote the efficient restart of replication forks that have been stalled by replication inhibitors, suggesting that bona fide fork restart pathways exist in mammalian cells. Different models of replication fork restart can be envisaged, based on the involvement of DNA helicases, nucleases, homologous recombination factors and the importance of DNA double-strand break formation.

  8. 2. PLANK COVERED BRANCH FLUME ON THE SOUTH FORK OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    2. PLANK COVERED BRANCH FLUME ON THE SOUTH FORK OF THE TULE RIVER MIDDLE FORK AND CONCRETE DIVERSION DAM SPILLING WATER. VIEW TO SOUTHEAST. - Tule River Hydroelectric Project, Water Conveyance System, Middle Fork Tule River, Springville, Tulare County, CA

  9. 16 CFR 1512.13 - Requirements for front fork.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... REGULATIONS REQUIREMENTS FOR BICYCLES Regulations § 1512.13 Requirements for front fork. The front fork shall... fork test, § 1512.18(k)(1), without visible evidence of fracture. Sidewalk bicycles need not meet...

  10. Research reactor fork users manual

    SciTech Connect

    Hsue, S.T.; Menlove, H.O.; Bosler, G.E.; Dye, H.R.; Walton, G.; Halbig, J.K.; Siebelist, R.

    1993-11-01

    This manual describes the design features and operating characteristics of the research reactor fork. The system includes an ion chamber for gross gamma-ray counting, fission chambers for neutron counting, and a collimated high-resolution spectroscopy system for gamma-ray measurements. The neutron and ion chamber measurements are designed to be made underwater in spent-fuel cooling ponds. The neutron and gamma-ray detectors have been designed with high efficiencies to accommodate the relatively low emission rates of neutrons and gamma rays from low-burnup, research-type reactor fuel. This manual presents the design, performance, and test results for the system.

  11. Fifth-wheel fork truck adapter

    NASA Technical Reports Server (NTRS)

    Smith, P. L.

    1969-01-01

    Standard fifth wheel mounted on a rectangular steel structure adapted for use with a fork lift truck provides a fast, safe, and economical way of maneuvering semitrailers in close quarters at plants and warehouses. One operator can move and locate a semitrailer without dismounting from a fork lift truck.

  12. Training Guidelines: Fork Lift Truck Driving.

    ERIC Educational Resources Information Center

    Ceramics, Glass, and Mineral Products Industry Training Board, Harrow (England).

    This manual of operative training guidelines for fork lift truck driving has been developed by the Ceramics, Glass and Mineral Products Industry Training Board (Great Britain) in consultation with a number of firms which manufacture fork lift trucks or which already have training--programs for their use. The purpose of the guidelines is to assist…

  13. 21 CFR 882.1525 - Tuning fork.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Tuning fork. 882.1525 Section 882.1525 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES NEUROLOGICAL DEVICES Neurological Diagnostic Devices § 882.1525 Tuning fork. (a) Identification. A tuning...

  14. 21 CFR 882.1525 - Tuning fork.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Tuning fork. 882.1525 Section 882.1525 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES NEUROLOGICAL DEVICES Neurological Diagnostic Devices § 882.1525 Tuning fork. (a) Identification. A tuning...

  15. 21 CFR 882.1525 - Tuning fork.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Tuning fork. 882.1525 Section 882.1525 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES NEUROLOGICAL DEVICES Neurological Diagnostic Devices § 882.1525 Tuning fork. (a) Identification. A tuning...

  16. 21 CFR 882.1525 - Tuning fork.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Tuning fork. 882.1525 Section 882.1525 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES NEUROLOGICAL DEVICES Neurological Diagnostic Devices § 882.1525 Tuning fork. (a) Identification. A tuning...

  17. 21 CFR 882.1525 - Tuning fork.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Tuning fork. 882.1525 Section 882.1525 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES NEUROLOGICAL DEVICES Neurological Diagnostic Devices § 882.1525 Tuning fork. (a) Identification. A tuning...

  18. 23. View of Clark Fork Vehicle Bridge facing upwest side. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    23. View of Clark Fork Vehicle Bridge facing up-west side. Looking at structural connection of top chord, vertical laced channel and diagonal bars. - Clark Fork Vehicle Bridge, Spanning Clark Fork River, serves Highway 200, Clark Fork, Bonner County, ID

  19. 13. View of Clark Fork Vehicle Bridge facing south. Concrete ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    13. View of Clark Fork Vehicle Bridge facing south. Concrete barrier blocks access. Plaque was originally located where strioed traffic sign is posted at right. - Clark Fork Vehicle Bridge, Spanning Clark Fork River, serves Highway 200, Clark Fork, Bonner County, ID

  20. 14. View of Clark Fork Vehicle Bridge facing north. Approach ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    14. View of Clark Fork Vehicle Bridge facing north. Approach from the south. Concrete barrier blocks access. Plaque was originally located where striped traffic sign is posted at right. - Clark Fork Vehicle Bridge, Spanning Clark Fork River, serves Highway 200, Clark Fork, Bonner County, ID

  1. 24. View of one of the plaques from Clark Fork ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    24. View of one of the plaques from Clark Fork Vehicle Bridge. Presently located at the Bonner County Historical Museum in Sandpoint, Idaho. A plaque was attached at each end of the bridge. Only one remains. - Clark Fork Vehicle Bridge, Spanning Clark Fork River, serves Highway 200, Clark Fork, Bonner County, ID

  2. South Fork Holston River basin 1988 biomonitoring

    SciTech Connect

    Saylor, C.F.; Ahlstedt, S.A.

    1990-06-01

    There is concern over the effects of shifts in land use use practices on the aquatic fauna of streams in the South Fork Holston River basin in northwestern North Carolina and southwestern Virginia. Trout reproduction has noticeably declined in the Watauga River subbasin. The Watauga River and Elk River subbasins have been subjected to commercial and resort development. The Middle fork Holston River and the upper South Fork Holston River subbasins have been affected by agricultural and mining activities, respectively (Cox, 1986). To aid reclamation and management of the South Fork Holston basin, Tennessee Valley Authority (TVA) biologists conducted biomonitoring--including index of biotic integrity and macroinvertebrate sampling--on the Middle Fork Holston, South Fork Holston, Watauga, and Elk Rivers to assess cumulative impairment related to changes in habitat and pollutant loading in these subbasins. Biomonitoring can detect environmental degradation, help document problem areas, and assist in development of strategies for managing water quality. This report discusses the methods and materials and results of the biomonitoring of South Fork Holston River Basin. 13 refs., 5 figs., 12 tabs.

  3. DNA REPAIR. Mus81 and converging forks limit the mutagenicity of replication fork breakage.

    PubMed

    Mayle, Ryan; Campbell, Ian M; Beck, Christine R; Yu, Yang; Wilson, Marenda; Shaw, Chad A; Bjergbaek, Lotte; Lupski, James R; Ira, Grzegorz

    2015-08-14

    Most spontaneous DNA double-strand breaks (DSBs) result from replication-fork breakage. Break-induced replication (BIR), a genome rearrangement-prone repair mechanism that requires the Pol32/POLD3 subunit of eukaryotic DNA Polδ, was proposed to repair broken forks, but how genome destabilization is avoided was unknown. We show that broken fork repair initially uses error-prone Pol32-dependent synthesis, but that mutagenic synthesis is limited to within a few kilobases from the break by Mus81 endonuclease and a converging fork. Mus81 suppresses template switches between both homologous sequences and diverged human Alu repetitive elements, highlighting its importance for stability of highly repetitive genomes. We propose that lack of a timely converging fork or Mus81 may propel genome instability observed in cancer.

  4. Mus81 and converging forks limit the mutagenicity of replication fork breakage

    PubMed Central

    Mayle, Ryan; Campbell, Ian M.; Beck, Christine R.; Yu, Yang; Wilson, Marenda; Shaw, Chad A.; Bjergbaek, Lotte; Lupski, James R.; Ira, Grzegorz

    2016-01-01

    Most spontaneous DNA double-strand breaks (DSBs) result from replication-fork breakage. Break-induced replication (BIR), a genome rearrangement-prone repair mechanism that requires the Pol32/POLD3 subunit of eukaryotic DNA Polδ, was proposed to repair broken forks, but how genome destabilization is avoided was unknown. We show that broken fork repair initially uses error-prone Pol32-dependent synthesis, but that mutagenic synthesis is limited to within a few kilobases from the break by Mus81 endonuclease and a converging fork. Mus81 suppresses template switches between both homologous sequences and diverged human Alu repetitive elements, highlighting its importance for stability of highly repetitive genomes. We propose that lack of a timely converging fork or Mus81 may propel genome instability observed in cancer. PMID:26273056

  5. 5. Roaring Fork Motor Nature Trail, vista at stop three. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. Roaring Fork Motor Nature Trail, vista at stop three. - Great Smoky Mountains National Park Roads & Bridges, Roaring Fork Motor Nature Trail, Between Cherokee Orchard Road & U.S. Route 321, Gatlinburg, Sevier County, TN

  6. 2. Roaring Fork Motor Nature Trail, road view before first ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    2. Roaring Fork Motor Nature Trail, road view before first stop. - Great Smoky Mountains National Park Roads & Bridges, Roaring Fork Motor Nature Trail, Between Cherokee Orchard Road & U.S. Route 321, Gatlinburg, Sevier County, TN

  7. 1. Roaring Fork Motor Nature Trail, entrance sign. Great ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. Roaring Fork Motor Nature Trail, entrance sign. - Great Smoky Mountains National Park Roads & Bridges, Roaring Fork Motor Nature Trail, Between Cherokee Orchard Road & U.S. Route 321, Gatlinburg, Sevier County, TN

  8. 7. Roaring Fork Motor Nature Trail, rocks along edge of ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    7. Roaring Fork Motor Nature Trail, rocks along edge of road. - Great Smoky Mountains National Park Roads & Bridges, Roaring Fork Motor Nature Trail, Between Cherokee Orchard Road & U.S. Route 321, Gatlinburg, Sevier County, TN

  9. 3. Roaring Fork Motor Nature Trail, view between second and ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    3. Roaring Fork Motor Nature Trail, view between second and third stops - Great Smoky Mountains National Park Roads & Bridges, Roaring Fork Motor Nature Trail, Between Cherokee Orchard Road & U.S. Route 321, Gatlinburg, Sevier County, TN

  10. 11. Roaring Fork Motor Nature Trail, boulders along road after ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    11. Roaring Fork Motor Nature Trail, boulders along road after stop 13. - Great Smoky Mountains National Park Roads & Bridges, Roaring Fork Motor Nature Trail, Between Cherokee Orchard Road & U.S. Route 321, Gatlinburg, Sevier County, TN

  11. Roaring Fork Motor Nature Trail, Title Sheet Great Smoky ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Roaring Fork Motor Nature Trail, Title Sheet - Great Smoky Mountains National Park Roads & Bridges, Roaring Fork Motor Nature Trail, Between Cherokee Orchard Road & U.S. Route 321, Gatlinburg, Sevier County, TN

  12. 9. Roaring Fork Motor Nature Trail, Reagan House. Great ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    9. Roaring Fork Motor Nature Trail, Reagan House. - Great Smoky Mountains National Park Roads & Bridges, Roaring Fork Motor Nature Trail, Between Cherokee Orchard Road & U.S. Route 321, Gatlinburg, Sevier County, TN

  13. 6. Roaring Fork Motor Nature Trail, road view after stop ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    6. Roaring Fork Motor Nature Trail, road view after stop four. - Great Smoky Mountains National Park Roads & Bridges, Roaring Fork Motor Nature Trail, Between Cherokee Orchard Road & U.S. Route 321, Gatlinburg, Sevier County, TN

  14. 12. Roaring Fork Motor Nature Trail, place of a thousand ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    12. Roaring Fork Motor Nature Trail, place of a thousand drips, view from road. - Great Smoky Mountains National Park Roads & Bridges, Roaring Fork Motor Nature Trail, Between Cherokee Orchard Road & U.S. Route 321, Gatlinburg, Sevier County, TN

  15. 12. PLANK BRIDGE ON OLD ROAD NEAR NORTH FORK VIRGIN ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    12. PLANK BRIDGE ON OLD ROAD NEAR NORTH FORK VIRGIN RIVER BRIDGE, FACING EAST - Zion-Mount Carmel Highway, Virgin River Bridge, Spanning North Fork of Virgin River on Zion-Mount Carmel Highway, Springdale, Washington County, UT

  16. South Fork Latrine showing north and west sides, general view ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    South Fork Latrine showing north and west sides, general view to southeast - Fort McKinley, South Fork Latrine, West side of East Side Drive, approximately 225 feet south of Weymouth Way, Great Diamond Island, Portland, Cumberland County, ME

  17. South Fork Latrine, east elevation showing structure in context, view ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    South Fork Latrine, east elevation showing structure in context, view west - Fort McKinley, South Fork Latrine, West side of East Side Drive, approximately 225 feet south of Weymouth Way, Great Diamond Island, Portland, Cumberland County, ME

  18. South Fork Latrine, oblique view showing south and east sides; ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    South Fork Latrine, oblique view showing south and east sides; view northwest - Fort McKinley, South Fork Latrine, West side of East Side Drive, approximately 225 feet south of Weymouth Way, Great Diamond Island, Portland, Cumberland County, ME

  19. 15. INSIDE VIEW OF FLUME, LOOKING DOWNSTREAM, LEFT FORK TO ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    15. INSIDE VIEW OF FLUME, LOOKING DOWNSTREAM, LEFT FORK TO SETTLING BASIN, SHOWING RIGHT FORK WITH GATE IN PLACE AND A FEW NEEDLES IN PLACE - Electron Hydroelectric Project, Along Puyallup River, Electron, Pierce County, WA

  20. 8. Roaring Fork Motor Nature Trail, handbuilt rock pile. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    8. Roaring Fork Motor Nature Trail, hand-built rock pile. - Great Smoky Mountains National Park Roads & Bridges, Roaring Fork Motor Nature Trail, Between Cherokee Orchard Road & U.S. Route 321, Gatlinburg, Sevier County, TN

  1. Pathological Changes of von Economo Neuron and Fork Neuron in Neuropsychiatric Diseases.

    PubMed

    Liu, Jia; Wang, Lu-ning; Arzberger, Thomas; Zhu, Ming-wei

    2016-02-01

    von Economo neuron (VEN) is a bipolar neuron characterized by a large spindle-shaped soma. VEN is generally distributed in the layer V of anterior insular lobe and anterior cingulate cortex. Fork neuron is another featured bipolar neuron. In recent years,many studies have illustrated that VEN and fork neurons are correlated with complicated cognition such as self-consciousness and social emotion. Studies in the development and morpholigies of these two neurons as well as their pathological changes in various neurological and psychiatric disorders have found that the abnormal number and functions of VEN can cause corresponding dysfunctions in social recognition and emotions both during the neuro-developmental stages of childhood and during the nerve degeneration in old age stage. Therefore, more attentions should be paid on the research of VEN and fork neurons in neuropsychiatric diseases.

  2. Resonant tuning fork detector for electromagnetic radiation.

    PubMed

    Pohlkötter, Andreas; Willer, Ulrike; Bauer, Christoph; Schade, Wolfgang

    2009-02-01

    A mechanical quartz microresonator (tuning fork) is used to detect electromagnetic radiation. The detection scheme is based on forces created due to the incident electromagnetic radiation on the piezoelectric tuning fork. A force can be created due to the transfer of the photon momentum of the incident electromagnetic radiation. If the surfaces of the tuning fork are nonuniformly heated, a second force acts on it, the so-called photophoretic force. These processes occur for all wavelengths of the incident radiation, making the detector suitable for sensing of ultraviolet, visible, and mid-infrared light, even THz-radiation. Here the detector is characterized in the visible range; noise analysis is performed for 650 nm and 5.26 microm. A linear power characteristic and the dependence on pulse lengths of the incoming light are shown. Examples for applications for the visible and mid-infrared spectral region are given by 2f and absorption spectroscopy of oxygen and nitric oxide, respectively.

  3. 27 CFR 9.113 - North Fork of Long Island.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2011-04-01 2011-04-01 false North Fork of Long Island... North Fork of Long Island. (a) Name. The name of the viticultural area described in this section is “North Fork of Long Island.” (b) Approved maps. The appropriate maps for determining the boundaries...

  4. 27 CFR 9.113 - North Fork of Long Island.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false North Fork of Long Island... North Fork of Long Island. (a) Name. The name of the viticultural area described in this section is “North Fork of Long Island.” (b) Approved maps. The appropriate maps for determining the boundaries...

  5. 27 CFR 9.113 - North Fork of Long Island.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2013-04-01 2013-04-01 false North Fork of Long Island... North Fork of Long Island. (a) Name. The name of the viticultural area described in this section is “North Fork of Long Island.” (b) Approved maps. The appropriate maps for determining the boundaries...

  6. 27 CFR 9.113 - North Fork of Long Island.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2014-04-01 2014-04-01 false North Fork of Long Island... North Fork of Long Island. (a) Name. The name of the viticultural area described in this section is “North Fork of Long Island.” (b) Approved maps. The appropriate maps for determining the boundaries...

  7. 27 CFR 9.113 - North Fork of Long Island.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2012-04-01 2012-04-01 false North Fork of Long Island... North Fork of Long Island. (a) Name. The name of the viticultural area described in this section is “North Fork of Long Island.” (b) Approved maps. The appropriate maps for determining the boundaries...

  8. Environment of deposition of Clear Fork Formation: Yoakum County, Texas

    SciTech Connect

    Moore, B.K.

    1987-05-01

    The Clear Fork Formation is Permian (Leonardian) in age and constitutes a major oil-bearing unit in the Permian basin of west Texas. In Yoakum County, west Texas, the upper Clear Fork carbonates record a subtidal upward-shoaling sequence of deposition. A small bryozoan-algal patch reef is situated within these carbonates near the southern edge of the North Basin platform. The reef is completely dolomitized, but paramorphic replacement has facilitated a study of the paleoecology, lateral variations, and community succession within this buildup. Build-ups of this type are scarcely known in strata of Permian age. The reef was apparently founded on a coquina horizon at the base of the buildup. The reef apparently had a low-relief, dome-shaped morphology. The trapping and binding of sediment by bryozoa appear to have been the main constructional process. A significant role was also played by encrusting forams and the early precipitation of submarine cements, both of which added rigidity to the structure. The reef also contains a low-diversity community of other invertebrates. Algal constituents predominate at the basinward edge of the buildup. The reef was formed entirely subaqueously on a broad, relatively shallow tropical marine carbonate shelf environment. An understanding of the lithofacies distribution and paragenesis within this sequence will provide information on porosity variations and the nature and distribution of permeability barriers. Such information is useful in reservoir modeling studies and for secondary recovery techniques in shelf-edge carbonate reservoirs of this type.

  9. Grand Forks - East Grand Forks Urban Water Resources Study. Social and Environmental Inventory.

    DTIC Science & Technology

    1979-01-01

    Utilities 107-108 FIGUR~ES Figure Number Title Pag 14 Projected Population - Region 67 1 5 Projected Population - Grand Forks County 68 Study Area 16...Projected Population - Polk County Study Area 68 17 Planning Regions 105 TABLES Tale Number Title Pg 21 Historic Sites in the Grand Forks Area 61I 22...of Indians, traders and settlers; and those related to the populations which currently reside in the area. The information on archeology and history

  10. Homologous recombination as a replication fork escort: fork-protection and recovery.

    PubMed

    Costes, Audrey; Lambert, Sarah A E

    2012-12-27

    Homologous recombination is a universal mechanism that allows DNA repair and ensures the efficiency of DNA replication. The substrate initiating the process of homologous recombination is a single-stranded DNA that promotes a strand exchange reaction resulting in a genetic exchange that promotes genetic diversity and DNA repair. The molecular mechanisms by which homologous recombination repairs a double-strand break have been extensively studied and are now well characterized. However, the mechanisms by which homologous recombination contribute to DNA replication in eukaryotes remains poorly understood. Studies in bacteria have identified multiple roles for the machinery of homologous recombination at replication forks. Here, we review our understanding of the molecular pathways involving the homologous recombination machinery to support the robustness of DNA replication. In addition to its role in fork-recovery and in rebuilding a functional replication fork apparatus, homologous recombination may also act as a fork-protection mechanism. We discuss that some of the fork-escort functions of homologous recombination might be achieved by loading of the recombination machinery at inactivated forks without a need for a strand exchange step; as well as the consequence of such a model for the stability of eukaryotic genomes.

  11. Geohydrologic appraisal of water resources of the South Fork, Long Island, New York

    USGS Publications Warehouse

    Nemickas, Bronius; Koszalka, Edward J.

    1982-01-01

    The ground-water resources of the South Fork of Long Island, N.Y., were investigated from April 1974 to September 1977. The study area encompasses 137 square miles and includes the eastern part of the Town of Southampton and the entire Town of East Hampton. The South Fork consists of a Paleozoic basement complex that is overlain by Cretaceous and Pleistocene sediments. The surficial material is composed of Late Wisconsinan glacial and glaciofluvial deposits in association with beach and marsh deposits of Recent age. Till underlies most of the eastern part of the South Fork. Precipitation is the sole source of fresh ground water on the South Fork. Average annual precipitation recorded at Bridgehampton from 1931-76 is 45 inches; about half this amount reaches the ground-water reservoir. It is estimated that overland runoff amounts to 0.5 inches per year, and evapotranspiration is 23 inches per year. Thus, recharge equals approximately 22 inches per year. Hydraulic conductivity and transmissivity of the Magothy (Cretaceous) and upper glacial (Pleistocene) aquifers on the South Fork were estimated from aquifer tests and specific-capacity data. The average horizontal hydraulic conductivity of the Magothy aquifer is 70 feet per day, and of the upper glacial aquifer 350 feet per day. Transmissivity of the Magothy aquifer on the South Fork ranges from 600 to 24,100 feet squared per day; transmissivity of the upper glacial aquifer ranges from 5,400 feet to 22,700 feet squared per day. No potable water is available from the underlying Lloyd aquifer. The position of the freshwater to saline-water interface is depicted in maps. In the southern part of the area, the freshwater reservoir follows the Ghyben-Herzberg principle, but in the northern part, the depth to interface is less than expected owing to a greater degree of anisotropy of the geologic units. Total public-supply pumpage on the South Fork is estimated to be about 3 Mgal/day, (million gallons per day). Public

  12. Bedload measurements, East Fork River, Wyoming.

    PubMed

    Leopold, L B; Emmett, W W

    1976-04-01

    A bedload trap in the riverbed provided direct quantitative measurement of debris-transport rate in the East Fork River, Wyoming, a basin of 466 km(2) drainage area. Traction load moves only during the spring snow melt season. Data collected in three spring runoff seasons during which a peak flow of 45 m(3)/s occurred showed that transport rate is correlated with power expenditure of the flowing water and at high flows becomes directly proportional to power as suggested by Bagnold.

  13. Environmental Inventory: Little South Fork Cumberland River.

    DTIC Science & Technology

    1981-11-01

    28 2.2.4.1 Paleo-Indian Tradition ---------- 28 2.2.4.2 Archaic Tradition --------------- 29 2.2.4.3 Woodland Tradition...Soils as Woodland ----------- 128 3.7.4.1 Woodland Suitability Grouping of Soils ------------- 129 3.7.5 Use of the Soils for Wildlife ---------- 133...Stations on the Little South Fork Cumberland River in June and September 1978 and July 1979 - 94 12. Woodland Management Interpretations by Woodland

  14. North Fork Snoqualmie River Basin Wildlife Study.

    DTIC Science & Technology

    1981-03-01

    more recent origin, never having been a natural lake. 118 Shoreline materials arv still in the process of washing into the depths of the South Fork...10-12 Twin Peaks - Philippa Lake 9 12-24 Bessemer Mountain 13 Total 52-55 44-64 , Estimates provided by John Cook (Olympic Taxidermy, Renton, Wash...organisms which use resources efficient- ly. This process results in wildlife populations which are balanced with their environments. When resources

  15. Needs assessment for the Greenway Grand Forks-East Grand Forks development and public education

    NASA Astrophysics Data System (ADS)

    Munski, Laura

    Following the flood of 1997, the U.S. Army Corps of Engineers included the Greenway Grand Forks---East Grand Forks (the Greenway) as a flood control measure for Grand Forks, North Dakota and East Grand Forks, Minnesota. It extends along both the Red River of the North and the Red Lake River, encompassing 2200 acres of land. The cities of Grand Forks and East Grand Forks hired consultants to assist with the postflood planning process. The planning process culminated with the Red River of the North Greenway Final Report (Flink, 1998). The purpose of this study was to determine if the development of the Greenway addressed the objectives of the planning report. The history of the land adjacent to the rivers was reviewed to document the progression of riverfront development. Anecdotal evidence was collected, field observations were made, city council minutes were reviewed, Greenway Technical Committee members were interviewed, Greenway Technical Committee minutes were reviewed, and the Greenway Grand Forks---East Grand Forks survey results were reviewed to determine if the objectives of the Red River of the North Greenway Final Report were addressed. A cross section survey was designed by Laura Munski for this dissertation research. The survey was approved by the Greenway Technical Committee. The survey collected both quantitative and qualitative data from the community. The purpose of the survey portion of the research project was to ascertain how residents were kept informed of activities on the Greenway and what amenities residents were using on the Greenway and to solicit their comments regarding the Greenway. The results of the survey research were used in both marketing and event planning for the Greenway. The singular qualitative survey question gave respondents an opportunity to share their comments regarding the Greenway. The qualitative data analysis provided insight to the amenities and educational programs desired by respondents, their concerns regarding the

  16. Bedload measurements, East Fork River, Wyoming

    PubMed Central

    Leopold, Luna B.; Emmett, William W.

    1976-01-01

    A bedload trap in the riverbed provided direct quantitative measurement of debris-transport rate in the East Fork River, Wyoming, a basin of 466 km2 drainage area. Traction load moves only during the spring snow melt season. Data collected in three spring runoff seasons during which a peak flow of 45 m3/s occurred showed that transport rate is correlated with power expenditure of the flowing water and at high flows becomes directly proportional to power as suggested by Bagnold. PMID:16592302

  17. 14. Roaring Fork Motor Nature Trail, Place of a thousand ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    14. Roaring Fork Motor Nature Trail, Place of a thousand drips, view with three culvert pipes. - Great Smoky Mountains National Park Roads & Bridges, Roaring Fork Motor Nature Trail, Between Cherokee Orchard Road & U.S. Route 321, Gatlinburg, Sevier County, TN

  18. 33 CFR 117.315 - New River, South Fork.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false New River, South Fork. 117.315 Section 117.315 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements Florida § 117.315 New River, South Fork. (a) The...

  19. South Fork Telephone Switchboard Building, oblique view of (W) and ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    South Fork Telephone Switchboard Building, oblique view of (W) and (S) sides, view to northeast - Fort McKinley, South Fork Telephone Switchboard Building, South side of Weymouth Way, approximately 100 feet west of East Side Drive, Great Diamond Island, Portland, Cumberland County, ME

  20. South Fork Telephone Switchboard Building, interior west room showing hardwood ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    South Fork Telephone Switchboard Building, interior west room showing hardwood floor; view south - Fort McKinley, South Fork Telephone Switchboard Building, South side of Weymouth Way, approximately 100 feet west of East Side Drive, Great Diamond Island, Portland, Cumberland County, ME

  1. South Fork Telephone Switchboard Building, oblique view of east side; ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    South Fork Telephone Switchboard Building, oblique view of east side; view northwest - Fort McKinley, South Fork Telephone Switchboard Building, South side of Weymouth Way, approximately 100 feet west of East Side Drive, Great Diamond Island, Portland, Cumberland County, ME

  2. South Fork Latrine, interior showing head with steel tank mounted ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    South Fork Latrine, interior showing head with steel tank mounted to wall; view south - Fort McKinley, South Fork Latrine, West side of East Side Drive, approximately 225 feet south of Weymouth Way, Great Diamond Island, Portland, Cumberland County, ME

  3. South Fork Telephone Switchboard Building, general view in setting showing ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    South Fork Telephone Switchboard Building, general view in setting showing (N) side; view (S) - Fort McKinley, South Fork Telephone Switchboard Building, South side of Weymouth Way, approximately 100 feet west of East Side Drive, Great Diamond Island, Portland, Cumberland County, ME

  4. DNA Copy Number Control Through Inhibition of Replication Fork Progression

    PubMed Central

    Nordman, Jared T.; Kozhevnikova, Elena N.; Verrijzer, C. Peter; Pindyurin, Alexey V.; Andreyeva, Evgeniya N.; Shloma, Victor V.; Zhimulev, Igor F.; Orr-Weaver, Terry L.

    2014-01-01

    Summary Proper control of DNA replication is essential to ensure faithful transmission of genetic material and to prevent chromosomal aberrations that can drive cancer progression and developmental disorders. DNA replication is regulated primarily at the level of initiation and is under strict cell cycle regulation. Importantly, DNA replication is highly influenced by developmental cues. In Drosophila, specific regions of the genome are repressed for DNA replication during differentiation by the SNF2 domain-containing protein SUUR through an unknown mechanism. We demonstrate that SUUR is recruited to active replication forks and mediates repression of DNA replication by directly inhibiting replication fork progression instead of functioning as a replication fork barrier. Mass-spec identification of SUUR associated proteins identified the replicative helicase member CDC45 as a SUUR-associated protein, supporting a role for SUUR directly at replication forks. Our results reveal that control of eukaryotic DNA copy number can occur through inhibition of replication fork progression. PMID:25437540

  5. The Fork+ burnup measurement system: Design and first measurement campaign

    SciTech Connect

    Olson, C.E.; Bronowski, D.R.; McMurtry, W.; Ewing, R.; Jordan, R.; Rivard, D.

    1998-12-31

    Previous work with the original Fork detector showed that burnup as determined by reactor records could be accurately allocated to spent nuclear fuel assemblies. The original Fork detector, designed by Los Alamos National Laboratory, used an ion chamber to measure gross gamma count and a fission chamber to measure neutrons from an activation source, {sup 244}Cm. In its review of the draft Topical Report on Burnup Credit, the US Nuclear Regulatory Commission indicated it felt uncomfortable with a measurement system that depended on reactor records for calibration. The Fork+ system was developed at Sandia National Laboratories under the sponsorship of the Electric Power Research Institute with the aim of providing this independent measurement capability. The initial Fork+ prototype was used in a measurement campaign at the Maine Yankee reactor. The campaign confirmed the applicability of the sensor approach in the Fork+ system and the efficiency of the hand-portable Fork+ prototype in making fuel assembly measurements. It also indicated potential design modifications that will be necessary before the Fork+ can be used effectively on high-burnup spent fuel.

  6. New interpretation of Clarks Fork field, northern Bighorn basin, Montana

    SciTech Connect

    Johnson, J.S.; Lindsley-Griffin, N.

    1986-08-01

    Clarks Fork field is located at the northern edge of the Bighorn basin (T9S, R22E) in Carbon County, Montana. Production was first established in 1944 by General Petroleum Corporation in the Cretaceous Peay Sandstone (basal Frontier) and was later extended to the Cretaceous Greybull (1949) and Lakota (1956) sandstones by British American. Total cumulative hydrocarbons from this field are 1,1789,193 bbl of oil and 3,061,522 mcf of gas, with Lakota sandstones being most productive. Lakota production occurs from a structural-stratigraphic trap in an east-west-trending channel on the axis of Clarks Fork anticline, geographically near the center of the township. Our structural reinterpretation of Clarks Fork field suggests that Elk Basin anticline is a northwest extension of the Elk Basin field anticline. The Elk Basin thrust truncates the north limb of the fold and does not strike to the northwest, as shown by earlier interpretations. They interpret a northwest-striking thrust in the center of the township as a splay off the Elk Basin thrust, and have named it the Clarks Fork thrust. The Clarks Fork anticline is located on the hanging wall of Clarks Fork thrust. Subsurface maps indicate the Clarks Fork area has not been fully developed. Stratigraphic traps in the Lakota and Greybull sandstones are present in several areas of the township. Structural traps in the center and northwest portions of the township may also exist.

  7. Fork gratings based on ferroelectric liquid crystals.

    PubMed

    Ma, Y; Wei, B Y; Shi, L Y; Srivastava, A K; Chigrinov, V G; Kwok, H-S; Hu, W; Lu, Y Q

    2016-03-21

    In this article, we disclose a fork grating (FG) based on the photo-aligned ferroelectric liquid crystal (FLC). The Digital Micro-mirror Device based system is used as a dynamic photomask to generated different holograms. Because of controlled anchoring energy, the photo alignment process offers optimal conditions for the multi-domain FLC alignment. Two different electro-optical modes namely DIFF/TRANS and DIFF/OFF switchable modes have been proposed where the diffraction can be switched either to no diffraction or to a completely black state, respectively. The FLC FG shows high diffraction efficiency and fast response time of 50µs that is relatively faster than existing technologies. Thus, the FLC FG may pave a good foundation toward optical vertices generation and manipulation that could find applications in a variety of devices.

  8. Chemical and biological sensing using tuning forks

    DOEpatents

    Tao, Nongjian; Boussaad, Salah

    2012-07-10

    A device for sensing a chemical analyte is disclosed. The device is comprised of a vibrating structure having first and second surfaces and having an associated resonant frequency and a wire coupled between the first and second surfaces of the vibrating structure, wherein the analyte interacts with the wire and causes a change in the resonant frequency of the vibrating structure. The vibrating structure can include a tuning fork. The vibrating structure can be comprised of quartz. The wire can be comprised of polymer. A plurality of vibrating structures are arranged in an array to increase confidence by promoting a redundancy of measurement or to detect a plurality of chemical analytes. A method of making a device for sensing a chemical analyte is also disclosed.

  9. Determining Absolute Zero Using a Tuning Fork

    NASA Astrophysics Data System (ADS)

    Goldader, Jeffrey D.

    2008-04-01

    The Celsius and Kelvin temperature scales, we tell our students, are related. We explain that a change in temperature of 1°C corresponds to a change of 1 Kelvin and that atoms and molecules have zero kinetic energy at zero Kelvin, -273°C. In this paper, we will show how students can derive the relationship between the Celsius and Kelvin temperature scales using a simple, well-known physics experiment. By making multiple measurements of the speed of sound at different temperatures, using the classic physics experiment of determining the speed of sound with a tuning fork and variable-length tube, they can determine the temperature at which the speed of sound is zero—absolute zero.

  10. Wireless tuning fork gyroscope for biomedical applications

    NASA Astrophysics Data System (ADS)

    Abraham, Jose K.; Varadan, Vijay K.; Whitchurch, Ashwin K.; Sarukesi, K.

    2003-07-01

    This paper presents the development of a Bluetooth enabled wireless tuning fork gyroscope for the biomedical applications, including gait phase detection system, human motion analysis and physical therapy. This gyroscope is capable of measuring rotation rates between -90 and 90 and it can read the rotation information using a computer. Currently, the information from a gyroscope can trigger automobile airbag deployment during rollover, improve the accuracy and reliability of GPS navigation systems and stabilize moving platforms such as automobiles, airplanes, robots, antennas, and industrial equipment. Adding wireless capability to the existing gyroscope could help to expand its applications in many areas particularly in biomedical applications, where a continuous patient monitoring is quite difficult. This wireless system provides information on several aspects of activities of patients for real-time monitoring in hospitals.

  11. Little Known Facts about the Common Tuning Fork.

    ERIC Educational Resources Information Center

    Ong, P. P.

    2002-01-01

    Explains the physical principles of the tuning fork which has a common use in teaching laboratories. Includes information on its vibration, frequency of vibration, elasticity, and reasons for having two prongs. (YDS)

  12. 17. DETAIL VIEW OF WHAT APPEARS TO BE STIRRING FORK ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    17. DETAIL VIEW OF WHAT APPEARS TO BE STIRRING FORK THAT MIXED COFFEE BEANS AS THEY WERE HUSKED - Hacienda Cafetalera Santa Clara, Coffee Mill, KM 19, PR Route 372, Hacienda La Juanita, Yauco Municipio, PR

  13. 9. VIEW OF WHEEL RACK FOR BORING MILL. Fork loading ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    9. VIEW OF WHEEL RACK FOR BORING MILL. Fork loading crane, manufactured by Cleveland Tramrail, 2-1/2 ton capacity. - Juniata Shops, Erecting Shop & Machine Shop, East of Fourth Avenue, between Fourth & Fifth Streets, Altoona, Blair County, PA

  14. 8. VIEW OF WHEEL RACK FOR BORING MILL. Fork loading ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    8. VIEW OF WHEEL RACK FOR BORING MILL. Fork loading crane, manufactured by Cleveland Tramrail, 2-1/2 ton capacity. - Juniata Shops, Erecting Shop & Machine Shop, East of Fourth Avenue, between Fourth & Fifth Streets, Altoona, Blair County, PA

  15. TRAIP regulates replication fork recovery and progression via PCNA

    PubMed Central

    Feng, Wanjuan; Guo, Yingying; Huang, Jun; Deng, Yiqun; Zang, Jianye; Huen, Michael Shing-Yan

    2016-01-01

    PCNA is a central scaffold that coordinately assembles replication and repair machineries at DNA replication forks for faithful genome duplication. Here, we describe TRAIP (RNF206) as a novel PCNA-interacting factor that has important roles during mammalian replicative stress responses. We show that TRAIP encodes a nucleolar protein that migrates to stalled replication forks, and that this is accomplished by its targeting of PCNA via an evolutionarily conserved PIP box on its C terminus. Accordingly, inactivation of TRAIP or its interaction with the PCNA clamp compromised replication fork recovery and progression, and leads to chromosome instability. Together, our findings establish TRAIP as a component of the mammalian replicative stress response network, and implicate the TRAIP-PCNA axis in recovery of stalled replication forks. PMID:27462463

  16. 9. EEL RIVER SOUTH FORK BRIDGE, OLD HIGHWAY 101. NORTH ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    9. EEL RIVER SOUTH FORK BRIDGE, OLD HIGHWAY 101. NORTH OF LEGGETT, HUMBOLDT COUNTY, CALIFORNIA. LOOKING W. - Redwood National & State Parks Roads, California coast from Crescent City to Trinidad, Crescent City, Del Norte County, CA

  17. 8. EEL RIVER SOUTH FORK BRIDGE, OLD HIGHWAY 101. NORTH ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    8. EEL RIVER SOUTH FORK BRIDGE, OLD HIGHWAY 101. NORTH OF LEGGETT, HUMBOLDT COUNTY, CALIFORNIA. LOOKING N. - Redwood National & State Parks Roads, California coast from Crescent City to Trinidad, Crescent City, Del Norte County, CA

  18. 117. Laurel Fork Viaduct. Elevation view of this 545 1939 ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    117. Laurel Fork Viaduct. Elevation view of this 545 1939 steel girder viaduct. Example of structure with plain reinforced concrete arches. Looking northwest. - Blue Ridge Parkway, Between Shenandoah National Park & Great Smoky Mountains, Asheville, Buncombe County, NC

  19. Assembly of Slx4 signaling complexes behind DNA replication forks.

    PubMed

    Balint, Attila; Kim, TaeHyung; Gallo, David; Cussiol, Jose Renato; Bastos de Oliveira, Francisco M; Yimit, Askar; Ou, Jiongwen; Nakato, Ryuichiro; Gurevich, Alexey; Shirahige, Katsuhiko; Smolka, Marcus B; Zhang, Zhaolei; Brown, Grant W

    2015-08-13

    Obstructions to replication fork progression, referred to collectively as DNA replication stress, challenge genome stability. In Saccharomyces cerevisiae, cells lacking RTT107 or SLX4 show genome instability and sensitivity to DNA replication stress and are defective in the completion of DNA replication during recovery from replication stress. We demonstrate that Slx4 is recruited to chromatin behind stressed replication forks, in a region that is spatially distinct from that occupied by the replication machinery. Slx4 complex formation is nucleated by Mec1 phosphorylation of histone H2A, which is recognized by the constitutive Slx4 binding partner Rtt107. Slx4 is essential for recruiting the Mec1 activator Dpb11 behind stressed replication forks, and Slx4 complexes are important for full activity of Mec1. We propose that Slx4 complexes promote robust checkpoint signaling by Mec1 by stably recruiting Dpb11 within a discrete domain behind the replication fork, during DNA replication stress.

  20. Environmental Assessment Deicer Recovery at Grand Forks AFB, North Dakota

    DTIC Science & Technology

    2004-12-15

    completed application to this office for further review. We also request the opportunity for complete review of applications for renewal or...NO 58205~6434 September 30, 2004 ND SHPO Ref.: 97 .. Q527av, Draft FONSI, Deicer Recovery Operation, Grand Forks AFB, NO. Dear Ms. Strom: We have...reviewed the Finding ofNo Significant Impact for a deicer recovery operation (draft version) at the Grand Forks Air Force Base, NO. We have no

  1. Environmental Assessment Tent City at Grand Forks AFB, North Dakota

    DTIC Science & Technology

    2004-11-15

    thunderstorms. Winters are long and severe with almost continuous snow cover. The spring and fall seasons are generally short transition periods. The...from the northwest during the late fall, winter, and spring , and from the southeast during the summer. Grand Forks County is included in the ND Air...drainage system. At Manvel, ND, approximately 10 miles northeast of Grand Forks AFB, the mean discharge of the Turtle River is 50.3 feet cubed per

  2. Force regulated dynamics of RPA on a DNA fork

    PubMed Central

    Kemmerich, Felix E.; Daldrop, Peter; Pinto, Cosimo; Levikova, Maryna; Cejka, Petr; Seidel, Ralf

    2016-01-01

    Replication protein A (RPA) is a single-stranded DNA binding protein, involved in most aspects of eukaryotic DNA metabolism. Here, we study the behavior of RPA on a DNA substrate that mimics a replication fork. Using magnetic tweezers we show that both yeast and human RPA can open forked DNA when sufficient external tension is applied. In contrast, at low force, RPA becomes rapidly displaced by the rehybridization of the DNA fork. This process appears to be governed by the binding or the release of an RPA microdomain (toehold) of only few base-pairs length. This gives rise to an extremely rapid exchange dynamics of RPA at the fork. Fork rezipping rates reach up to hundreds of base-pairs per second, being orders of magnitude faster than RPA dissociation from ssDNA alone. Additionally, we show that RPA undergoes diffusive motion on ssDNA, such that it can be pushed over long distances by a rezipping fork. Generally the behavior of both human and yeast RPA homologs is very similar. However, in contrast to yeast RPA, the dissociation of human RPA from ssDNA is greatly reduced at low Mg2+ concentrations, such that human RPA can melt DNA in absence of force. PMID:27016742

  3. Single strand transposition at the host replication fork

    PubMed Central

    Lavatine, Laure; He, Susu; Caumont-Sarcos, Anne; Guynet, Catherine; Marty, Brigitte; Chandler, Mick; Ton-Hoang, Bao

    2016-01-01

    Members of the IS200/IS605 insertion sequence family differ fundamentally from classical IS essentially by their specific single-strand (ss) transposition mechanism, orchestrated by the Y1 transposase, TnpA, a small HuH enzyme which recognizes and processes ss DNA substrates. Transposition occurs by the ‘peel and paste’ pathway composed of two steps: precise excision of the top strand as a circular ss DNA intermediate; and subsequent integration into a specific ssDNA target. Transposition of family members was experimentally shown or suggested by in silico high-throughput analysis to be intimately coupled to the lagging strand template of the replication fork. In this study, we investigated factors involved in replication fork targeting and analysed DNA-binding properties of the transposase which can assist localization of ss DNA substrates on the replication fork. We showed that TnpA interacts with the β sliding clamp, DnaN and recognizes DNA which mimics replication fork structures. We also showed that dsDNA can facilitate TnpA targeting ssDNA substrates. We analysed the effect of Ssb and RecA proteins on TnpA activity in vitro and showed that while RecA does not show a notable effect, Ssb inhibits integration. Finally we discuss the way(s) in which integration may be directed into ssDNA at the replication fork. PMID:27466393

  4. Chk1 promotes replication fork progression by controlling replication initiation.

    PubMed

    Petermann, Eva; Woodcock, Mick; Helleday, Thomas

    2010-09-14

    DNA replication starts at initiation sites termed replication origins. Metazoan cells contain many more potential origins than are activated (fired) during each S phase. Origin activation is controlled by the ATR checkpoint kinase and its downstream effector kinase Chk1, which suppresses origin firing in response to replication blocks and during normal S phase by inhibiting the cyclin-dependent kinase Cdk2. In addition to increased origin activation, cells deficient in Chk1 activity display reduced rates of replication fork progression. Here we investigate the causal relationship between increased origin firing and reduced replication fork progression. We use the Cdk inhibitor roscovitine or RNAi depletion of Cdc7 to inhibit origin firing in Chk1-inhibited or RNAi-depleted cells. We report that Cdk inhibition and depletion of Cdc7 can alleviate the slow replication fork speeds in Chk1-deficient cells. Our data suggest that increased replication initiation leads to slow replication fork progression and that Chk1 promotes replication fork progression during normal S phase by controlling replication origin activity.

  5. Replication fork dynamics and the DNA damage response.

    PubMed

    Jones, Rebecca M; Petermann, Eva

    2012-04-01

    Prevention and repair of DNA damage is essential for maintenance of genomic stability and cell survival. DNA replication during S-phase can be a source of DNA damage if endogenous or exogenous stresses impair the progression of replication forks. It has become increasingly clear that DNA-damage-response pathways do not only respond to the presence of damaged DNA, but also modulate DNA replication dynamics to prevent DNA damage formation during S-phase. Such observations may help explain the developmental defects or cancer predisposition caused by mutations in DNA-damage-response genes. The present review focuses on molecular mechanisms by which DNA-damage-response pathways control and promote replication dynamics in vertebrate cells. In particular, DNA damage pathways contribute to proper replication by regulating replication initiation, stabilizing transiently stalled forks, promoting replication restart and facilitating fork movement on difficult-to-replicate templates. If replication fork progression fails to be rescued, this may lead to DNA damage and genomic instability via nuclease processing of aberrant fork structures or incomplete sister chromatid separation during mitosis.

  6. 77 FR 47058 - Middle Fork American River Hydroelectric Project Placer County Water Agency; Notice of Draft...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-07

    ... Energy Regulatory Commission Middle Fork American River Hydroelectric Project Placer County Water Agency... comments on the draft environmental impact statement for the Middle Fork American River Project No. 2079... project. This meeting is posted on the Commission's calendar located at...

  7. Geology and ground water resources of Grand Forks County

    USGS Publications Warehouse

    Hansen, Dan E.; Kume, Jack; Kelly, T.E.; Paulson, Q.F.

    1970-01-01

    Grand Forks County in northeastern North Dakota is underlain by glacial drift, westward-dipping Paleozoic and Mesozoic sedimentary rocks and Precambrian igneous and metamorphic rocks. Glacial drift that covers the bedrock reaches a maximum thickness of 455 feet. It can be differentiated into 5 drift sheets, each of which in turn can be separated into till units, lake clay and silt units, and sand and gravel units. Relief on the bedrock surface is much greater than that on the present glacial topography. In western Grand Forks County, the bedrock rises 600 feet from east to west at the Pembina escarpment, whereas the surface elevations rise only 300 feet.

  8. Bank stability and channel width adjustment, East Fork River, Wyoming.

    USGS Publications Warehouse

    Andrews, E.D.

    1982-01-01

    Frequent surveys of eight cross sections located in self-formed reaches of the East Fork River, Wyoming, during the 1974 snowmelt flood showed a close relation between channel morphology and scour and fill. Those cross sections narrower than the mean reach width filled at discharges less than bankfull and scoured at discharges greater than bankfull. Those cross sections wider than the mean reach width scoured at discharges less than bankfull and filled at discharges greater than bankfull. Bank stability, and to some extent the adjustment of stream channel width, in the East Fork River study reach appears to be controlled by the processes of scour and fill. -from Author

  9. Replication Termination: Containing Fork Fusion-Mediated Pathologies in Escherichia coli

    PubMed Central

    Dimude, Juachi U.; Midgley-Smith, Sarah L.; Stein, Monja; Rudolph, Christian J.

    2016-01-01

    Duplication of bacterial chromosomes is initiated via the assembly of two replication forks at a single defined origin. Forks proceed bi-directionally until they fuse in a specialised termination area opposite the origin. This area is flanked by polar replication fork pause sites that allow forks to enter but not to leave. The precise function of this replication fork trap has remained enigmatic, as no obvious phenotypes have been associated with its inactivation. However, the fork trap becomes a serious problem to cells if the second fork is stalled at an impediment, as replication cannot be completed, suggesting that a significant evolutionary advantage for maintaining this chromosomal arrangement must exist. Recently, we demonstrated that head-on fusion of replication forks can trigger over-replication of the chromosome. This over-replication is normally prevented by a number of proteins including RecG helicase and 3’ exonucleases. However, even in the absence of these proteins it can be safely contained within the replication fork trap, highlighting that multiple systems might be involved in coordinating replication fork fusions. Here, we discuss whether considering the problems associated with head-on replication fork fusion events helps us to better understand the important role of the replication fork trap in cellular metabolism. PMID:27463728

  10. 16 CFR 1512.14 - Requirements for fork and frame assembly.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 16 Commercial Practices 2 2010-01-01 2010-01-01 false Requirements for fork and frame assembly... SUBSTANCES ACT REGULATIONS REQUIREMENTS FOR BICYCLES Regulations § 1512.14 Requirements for fork and frame assembly. The fork and frame assembly shall be tested for strength by application of a load of 890 N...

  11. 16 CFR 1512.14 - Requirements for fork and frame assembly.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 16 Commercial Practices 2 2011-01-01 2011-01-01 false Requirements for fork and frame assembly... SUBSTANCES ACT REGULATIONS REQUIREMENTS FOR BICYCLES Regulations § 1512.14 Requirements for fork and frame assembly. The fork and frame assembly shall be tested for strength by application of a load of 890 N...

  12. 77 FR 39675 - Wallowa-Whitman National Forest, Baker County, OR; North Fork Burnt River Mining

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-05

    ...-Whitman National Forest, Baker County, OR; North Fork Burnt River Mining AGENCY: Forest Service, USDA... North Fork Burnt River Mining Record of Decision will replace and supercede the 2004 North Fork Burnt River Mining Record of Decision only where necessary to address the inadequacies identified by the...

  13. Hydraulic geometry and sediment data for the South Fork Salmon River, Idaho, 1985-86

    USGS Publications Warehouse

    Williams, Rhea P.; O'Dell, Ivalou; Megahan, Walter F.

    1989-01-01

    Hydraulic geometry, suspended-sediment, and bedload samples were collected at three sites in the upper reach of the South Fork Salmon River drainage basin from April 1985 to June 1986. Sites selected were South Fork Salmon River near Krassel Ranger Station, Buckhorn Creek, and North Fork Lick Creek. Results of the data collection are presented in this report.

  14. Reconnaissance of ground-water resources in the North Fork Gunnison River basin, southwestern Colorado

    USGS Publications Warehouse

    Ackerman, D.J.; Brooks, Tom

    1986-01-01

    Aquifers of large areal extent in the North Fork Gunnison River basin are found in the alluvium and bedrock. Alluvial aquifers yielded water with dissolved solids concentrations ranging from 43 to 2,300 mg/L. Dissolved solids concentrations of water samples from the Mesaverde Formation of Late Cretaceous age and the Dakota Sandstone and Burro Canyon Formations of Late and Early Cretaceous age ranged from 56 to 3,200 mg/L. Dissolved solids concentrations of water samples from Mancos Shale ranged from 1,800 to 8,200 mg/L. Most wells in the North Fork Gunnison River basin are at altitudes below 7,500 ft, yield from 2 to 40 gal/min and are completed in alluvial sand and gravel, sandstone , or fractured bedrock. Springs generally are at altitudes above 7,000 ft, discharge from perched water tables at geologic contacts, have calcium magnesium bicarbonate water types, and are much less saline than water from wells. (Author 's abstract)

  15. Mechanism of DNA Replication in Drosophila Chromosomes: Structure of Replication Forks and Evidence for Bidirectionality

    PubMed Central

    Kriegstein, Henry J.; Hogness, David S.

    1974-01-01

    The replicating chromosomal DNA in Drosophila melanogaster cleavage nuclei has been visualized in the electron microscope as a serial array of closely spaced replicated regions created by pairs of diverging replication forks. The fine structure of the forks is very similar to that observed for the replication forks of bidirectionally replicating bacteriophage DNAs. However, the mean length of the single-stranded gaps in Drosophila forks is less than 200 nucleotide residues, much shorter than the gaps in phage forks. This difference in gap length corresponds to the observed difference in the size of Okazaki fragments from Drosophila and phage. Images PMID:4204203

  16. 80. Laurel Fork Creek Bridge #2. Example of a concrete ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    80. Laurel Fork Creek Bridge #2. Example of a concrete slab bridge with T beams. It was built in 1937 and the wing walls were faced with stone to blend with its surroundings. Looking northeast. - Blue Ridge Parkway, Between Shenandoah National Park & Great Smoky Mountains, Asheville, Buncombe County, NC

  17. Forks and combs and DNA: the synthesis of branched oligodeoxyribonucleotides.

    PubMed Central

    Horn, T; Urdea, M S

    1989-01-01

    Nucleoside phosphoramidite derivatives containing two protected primary hydroxyl functions have been incorporated into synthetic oligonucleotides as 'branching monomers'. With selective deprotection, multiple identical copies of an additional oligonucleotide can be incorporated to form fork- or comb-like structures for use as signal amplification materials in nucleic acid hybridization assays. Images PMID:2780317

  18. New histone supply regulates replication fork speed and PCNA unloading

    PubMed Central

    Mejlvang, Jakob; Feng, Yunpeng; Alabert, Constance; Neelsen, Kai J.; Jasencakova, Zuzana; Zhao, Xiaobei; Lees, Michael; Sandelin, Albin; Pasero, Philippe; Lopes, Massimo

    2014-01-01

    Correct duplication of DNA sequence and its organization into chromatin is central to genome function and stability. However, it remains unclear how cells coordinate DNA synthesis with provision of new histones for chromatin assembly to ensure chromosomal stability. In this paper, we show that replication fork speed is dependent on new histone supply and efficient nucleosome assembly. Inhibition of canonical histone biosynthesis impaired replication fork progression and reduced nucleosome occupancy on newly synthesized DNA. Replication forks initially remained stable without activation of conventional checkpoints, although prolonged histone deficiency generated DNA damage. PCNA accumulated on newly synthesized DNA in cells lacking new histones, possibly to maintain opportunity for CAF-1 recruitment and nucleosome assembly. Consistent with this, in vitro and in vivo analysis showed that PCNA unloading is delayed in the absence of nucleosome assembly. We propose that coupling of fork speed and PCNA unloading to nucleosome assembly provides a simple mechanism to adjust DNA replication and maintain chromatin integrity during transient histone shortage. PMID:24379417

  19. NEW APPROACHES: Speed of sound in tuning fork metal

    NASA Astrophysics Data System (ADS)

    Narayanan, V. Anantha; Narayanan, Radha

    1996-11-01

    A procedure to find the speed of sound in tuning fork metal is described. The formula needed is extracted from the literature and explained. Since the equipment needed for this project is readily available in most high school and introductory level college science laboratories, this exercise can be done without any additional cost.

  20. 27 CFR 9.65 - North Fork of Roanoke.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2014-04-01 2014-04-01 false North Fork of Roanoke. 9.65 Section 9.65 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY ALCOHOL AMERICAN VITICULTURAL AREAS Approved American Viticultural Areas §...

  1. 27 CFR 9.65 - North Fork of Roanoke.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2012-04-01 2012-04-01 false North Fork of Roanoke. 9.65 Section 9.65 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS AMERICAN VITICULTURAL AREAS Approved American Viticultural Areas §...

  2. 134. FORKS DIVERSION, HIGH LINE AND LOW LINE CANALS, TWIN ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    134. FORKS DIVERSION, HIGH LINE AND LOW LINE CANALS, TWIN FALLS COUNTY, SOUTH OF HANSEN, IDAHO; VIEW OF LOW LINE AND POWER GATES, WEST VIEW. - Milner Dam & Main Canal: Twin Falls Canal Company, On Snake River, 11 miles West of city of Burley, Idaho, Twin Falls, Twin Falls County, ID

  3. 132. FORKS DIVERSION, HIGH LINE AND LOW LINE CANALS, TWIN ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    132. FORKS DIVERSION, HIGH LINE AND LOW LINE CANALS, TWIN FALLS COUNTY, SOUTH OF HANSEN, IDAHO; POWER GATES FOR HYDRO-ELECTRIC. - Milner Dam & Main Canal: Twin Falls Canal Company, On Snake River, 11 miles West of city of Burley, Idaho, Twin Falls, Twin Falls County, ID

  4. Endonuclease EEPD1 Is a Gatekeeper for Repair of Stressed Replication Forks*

    PubMed Central

    Kim, Hyun-Suk; Nickoloff, Jac A.; Wu, Yuehan; Williamson, Elizabeth A.; Sidhu, Gurjit Singh; Reinert, Brian L.; Jaiswal, Aruna S.; Srinivasan, Gayathri; Patel, Bhavita; Kong, Kimi; Burma, Sandeep; Lee, Suk-Hee; Hromas, Robert A.

    2017-01-01

    Replication is not as continuous as once thought, with DNA damage frequently stalling replication forks. Aberrant repair of stressed replication forks can result in cell death or genome instability and resulting transformation to malignancy. Stressed replication forks are most commonly repaired via homologous recombination (HR), which begins with 5′ end resection, mediated by exonuclease complexes, one of which contains Exo1. However, Exo1 requires free 5′-DNA ends upon which to act, and these are not commonly present in non-reversed stalled replication forks. To generate a free 5′ end, stalled replication forks must therefore be cleaved. Although several candidate endonucleases have been implicated in cleavage of stalled replication forks to permit end resection, the identity of such an endonuclease remains elusive. Here we show that the 5′-endonuclease EEPD1 cleaves replication forks at the junction between the lagging parental strand and the unreplicated DNA parental double strands. This cleavage creates the structure that Exo1 requires for 5′ end resection and HR initiation. We observed that EEPD1 and Exo1 interact constitutively, and Exo1 repairs stalled replication forks poorly without EEPD1. Thus, EEPD1 performs a gatekeeper function for replication fork repair by mediating the fork cleavage that permits initiation of HR-mediated repair and restart of stressed forks. PMID:28049724

  5. Fork rotation and DNA precatenation are restricted during DNA replication to prevent chromosomal instability.

    PubMed

    Schalbetter, Stephanie A; Mansoubi, Sahar; Chambers, Anna L; Downs, Jessica A; Baxter, Jonathan

    2015-08-18

    Faithful genome duplication and inheritance require the complete resolution of all intertwines within the parental DNA duplex. This is achieved by topoisomerase action ahead of the replication fork or by fork rotation and subsequent resolution of the DNA precatenation formed. Although fork rotation predominates at replication termination, in vitro studies have suggested that it also occurs frequently during elongation. However, the factors that influence fork rotation and how rotation and precatenation may influence other replication-associated processes are unknown. Here we analyze the causes and consequences of fork rotation in budding yeast. We find that fork rotation and precatenation preferentially occur in contexts that inhibit topoisomerase action ahead of the fork, including stable protein-DNA fragile sites and termination. However, generally, fork rotation and precatenation are actively inhibited by Timeless/Tof1 and Tipin/Csm3. In the absence of Tof1/Timeless, excessive fork rotation and precatenation cause extensive DNA damage following DNA replication. With Tof1, damage related to precatenation is focused on the fragile protein-DNA sites where fork rotation is induced. We conclude that although fork rotation and precatenation facilitate unwinding in hard-to-replicate contexts, they intrinsically disrupt normal chromosome duplication and are therefore restricted by Timeless/Tipin.

  6. Homologous recombination restarts blocked replication forks at the expense of genome rearrangements by template exchange.

    PubMed

    Lambert, Sarah; Mizuno, Ken'ichi; Blaisonneau, Joël; Martineau, Sylvain; Chanet, Roland; Fréon, Karine; Murray, Johanne M; Carr, Antony M; Baldacci, Giuseppe

    2010-08-13

    Template switching induced by stalled replication forks has recently been proposed to underlie complex genomic rearrangements. However, the resulting models are not supported by robust physical evidence. Here, we analyzed replication and recombination intermediates in a well-defined fission yeast system that blocks replication forks. We show that, in response to fork arrest, chromosomal rearrangements result from Rad52-dependent nascent strand template exchange occurring during fork restart. This template exchange occurs by both Rad51-dependent and -independent mechanisms. We demonstrate that Rqh1, the BLM homolog, limits Rad51-dependent template exchange without affecting fork restart. In contrast, we report that the Srs2 helicase promotes both fork restart and template exchange. Our data demonstrate that template exchange occurs during recombination-dependent fork restart at the expense of genome rearrangements.

  7. Termination of DNA replication forks: "Breaking up is hard to do".

    PubMed

    Bailey, Rachael; Priego Moreno, Sara; Gambus, Agnieszka

    2015-01-01

    To ensure duplication of the entire genome, eukaryotic DNA replication initiates from thousands of replication origins. The replication forks move through the chromatin until they encounter forks from neighboring origins. During replication fork termination forks converge, the replisomes disassemble and topoisomerase II resolves the daughter DNA molecules. If not resolved efficiently, terminating forks result in genomic instability through the formation of pathogenic structures. Our recent findings shed light onto the mechanism of replisome disassembly upon replication fork termination. We have shown that termination-specific polyubiquitylation of the replicative helicase component - Mcm7, leads to dissolution of the active helicase in a process dependent on the p97/VCP/Cdc48 segregase. The inhibition of terminating helicase disassembly resulted in a replication termination defect. In this extended view we present hypothetical models of replication fork termination and discuss remaining and emerging questions in the DNA replication termination field.

  8. Oak Grove Fork Habitat Improvement Project, 1988 Annual Report.

    SciTech Connect

    Bettin, Scott

    1989-04-01

    The Lower Oak Grove Fork of the Clackamas River is a fifth-order tributary of the Clackamas River drainage supporting depressed runs of coho and chinook salmon, and summer and winter steelhead. Habitat condition rating for the Lower Oak Grove is good, but smelt production estimates are below the average for Clackamas River tributaries. Limiting factors in the 3.8 miles of the Lower Oak Grove supporting anadromous fish include an overall lack of quality spawning and rearing habitat. Beginning in 1986. measures to improve fish habitat in the Lower Oak Grove were developed in coordination with the Oregon Department of Fish and Wildlife (ODF&W) and Portland General Electric (PGE) fisheries biologists. Prior to 1986, no measures had been applied to the stream to mitigate for PGE's storage and regulation of flows in the Oak Grove Fork (Timothy Lake, Harriet Lake). Catchable rainbow trout are stocked by ODF&W two or three times a year during the trout fishing season in the lowermost portion of the Oak Grove Fork near two Forest Service campgrounds (Ripplebrook and Rainbow). The 1987 field season marked the third year of efforts to improve fish habitat of the Lower Oak Grove Fork and restore anadromous fish production. The efforts included the development of an implementation plan for habitat improvement activities in the Lower Oak Grove Fork. post-project monitoring. and maintenance of the 1986 improvement structures. No new structures were constructed or placed in 1987. Fiscal year 1988 brought a multitude of changes which delayed implementation of plans developed in 1987. The most prominent change was the withdrawal of the proposed Spotted Owl Habitat Area (SOHA) which overlapped the Oak Grove project implementation area. Another was the change in the Forest Service biologist responsible for implementation and design of this project.

  9. South Fork John Day River Habitat Enhancement Project : Annual Reports 1986, 1987 and Final Report.

    SciTech Connect

    Wiley, Ron

    1993-05-01

    The South Fork John Day River (SFJDR) contains important wild summer steelhead habitat. Adult fish annually return to the drainage to spawn. All tributaries accessible to steelhead are used for spawning. Additionally, juvenile steelhead rear in the SFJDR and its tributaries from two to three years before migrating to the ocean. The role of the SFJDR in rearing juvenile steelhead, particularly from age 1+ to smolt, is vital to the system as a whole. Many, if not all, of the tributaries produce juveniles in numbers exceeding the stream's capacity to rear to smolt. These fish migrate to the SFJDR and are reared to smolt there. Factors limiting steelhead production in the SFJDR are: Poor quantity and quality of pool habitat; low summer flows; high water temperatures; and excessive sediment load. During September 1986, 1,500 boulders were placed in 14 reaches of the South Fork John Day River approximately between RM 14 and RM 25. A number of smaller boulders were also placed by the contract or rather than return them to the rock pit. The boulders were placed in a variety of configurations, each determined as best fitted to specific site features (such as, depth, flow, velocity, bank condition, existing or potential riparian cover). It is estimated this project will provide rearing area for an additional 7,500 summer steelhead smolts.

  10. Aging

    PubMed Central

    Park, Dong Choon

    2013-01-01

    Aging is initiated based on genetic and environmental factors that operate from the time of birth of organisms. Aging induces physiological phenomena such as reduction of cell counts, deterioration of tissue proteins, tissue atrophy, a decrease of the metabolic rate, reduction of body fluids, and calcium metabolism abnormalities, with final progression onto pathological aging. Despite the efforts from many researchers, the progression and the mechanisms of aging are not clearly understood yet. Therefore, the authors would like to introduce several theories which have gained attentions among the published theories up to date; genetic program theory, wear-and-tear theory, telomere theory, endocrine theory, DNA damage hypothesis, error catastrophe theory, the rate of living theory, mitochondrial theory, and free radical theory. Although there have been many studies that have tried to prevent aging and prolong life, here we introduce a couple of theories which have been proven more or less; food, exercise, and diet restriction. PMID:24653904

  11. Top1- and Top2-mediated topological transitions at replication forks ensure fork progression and stability and prevent DNA damage checkpoint activation.

    PubMed

    Bermejo, Rodrigo; Doksani, Ylli; Capra, Thelma; Katou, Yuki-Mori; Tanaka, Hirokazu; Shirahige, Katsuhiko; Foiani, Marco

    2007-08-01

    DNA topoisomerases solve topological problems during chromosome metabolism. We investigated where and when Top1 and Top2 are recruited on replicating chromosomes and how their inactivation affects fork integrity and DNA damage checkpoint activation. We show that, in the context of replicating chromatin, Top1 and Top2 act within a 600-base-pair (bp) region spanning the moving forks. Top2 exhibits additional S-phase clusters at specific intergenic loci, mostly containing promoters. TOP1 ablation does not affect fork progression and stability and does not cause activation of the Rad53 checkpoint kinase. top2 mutants accumulate sister chromatid junctions in S phase without affecting fork progression and activate Rad53 at the M-G1 transition. top1 top2 double mutants exhibit fork block and processing and phosphorylation of Rad53 and gamma H2A in S phase. The exonuclease Exo1 influences fork processing and DNA damage checkpoint activation in top1 top2 mutants. Our data are consistent with a coordinated action of Top1 and Top2 in counteracting the accumulation of torsional stress and sister chromatid entanglement at replication forks, thus preventing the diffusion of topological changes along large chromosomal regions. A failure in resolving fork-related topological constrains during S phase may therefore result in abnormal chromosome transitions, DNA damage checkpoint activation, and chromosome breakage during segregation.

  12. Scanning Probe Microscopy of DNA with a Quartz Tuning Fork

    NASA Astrophysics Data System (ADS)

    King, G. M.; Nunes, G., Jr.

    2001-03-01

    Quartz tuning-forks have recently been put to use as highly sensitive force detectors in atomic force microscopy (AFM).(F.J.Giessibl et al.), Science 289, 422 (2000). In this study we have applied a home-built, tuning-fork based AFM to the investigation of single and double stranded DNA (ssDNA and dsDNA). We operate the microscope in the non-contact mode (typical tip amplitude ~1 nm) with a variety of tips (e.g. Si, Si_3N_4, W). Here we report on recent results showing that the apparent height of plasmid dsDNA on mica substrates depends on both the tip material and imaging frequency shift. This talk will also review our efforts to probe ssDNA with a chemically functionalized tip. Current and future prospects for this dynamic-mode, chemically-sensitive force microscopy technique will be discussed.

  13. A single-element tuning fork piezoelectric linear actuator.

    PubMed

    Friend, James R; Satonobu, Jun; Nakamura, Kentaro; Ueha, Sadayuki; Stutts, Daniel S

    2003-02-01

    This paper describes the design of a piezoelectric tuning-fork, dual-mode motor. The motor uses a single multilayer piezoelectric element in combination with tuning fork and shearing motion to form an actuator using a single drive signal. Finite-element analysis was used in the design of the motor, and the process is described along with the selection of the device's materials and its performance. Swaging was used to mount the multilayer piezoelectric element within the stator. Prototypes of the 25-mm long bidirectional actuator achieved a maximum linear no-load speed of 16.5 cm/s, a maximum linear force of 1.86 N, and maximum efficiency of 18.9%.

  14. Optimal information provision for maximizing flow in a forked lattice.

    PubMed

    Imai, Takeaki; Nishinari, Katsuhiro

    2015-06-01

    In a forked road, the provision of inappropriate information to car drivers sometimes leads to undesirable situations such as one-sided congestion, which is called the hunting phenomenon in real traffic. To address such problems, we propose a forked exclusion model and investigate the behavior of traffic flow in two routes, providing various types of information to a limited number of traveling particles according to the share rate of information. To analytically understand the phenomena, we develop a coarse-grained representation of the model. By analyzing the model, we find the most effective types of information to minimize particles' travel time and the existence of an optimal share rate according to route conditions.

  15. Optimal information provision for maximizing flow in a forked lattice

    NASA Astrophysics Data System (ADS)

    Imai, Takeaki; Nishinari, Katsuhiro

    2015-06-01

    In a forked road, the provision of inappropriate information to car drivers sometimes leads to undesirable situations such as one-sided congestion, which is called the hunting phenomenon in real traffic. To address such problems, we propose a forked exclusion model and investigate the behavior of traffic flow in two routes, providing various types of information to a limited number of traveling particles according to the share rate of information. To analytically understand the phenomena, we develop a coarse-grained representation of the model. By analyzing the model, we find the most effective types of information to minimize particles' travel time and the existence of an optimal share rate according to route conditions.

  16. South Fork Clearwater River Habitat Enhancement, Nez Perce National Forest.

    SciTech Connect

    Siddall, Phoebe

    1992-04-01

    In 1984, the Nez Perce National forest and the Bonneville Power Administration entered into a contractual agreement which provided for improvement of spring chinook salmon and summer steelhead trout habitat in south Fork Clearwater River tributaries. Project work was completed in seven main locations: Crooked River, Red River, Meadow Creek Haysfork Gloryhole, Cal-Idaho Gloryhole, Fisher Placer and Leggett Placer. This report describes restoration activities at each of these sites.

  17. Environmental Assessment: Demolish 452 at Grand Forks Air Force Base

    DTIC Science & Technology

    2005-12-01

    humid with frequent thunderstorms. Winters are long and severe with almost continuous snow cover. The spring and fall seasons are generally short...direction is generally from the northwest during the late fall, winter, and spring , and from the southeast during the summer. Grand Forks County is...to Lake Winnipeg, Canada. The Red River drainage basin is part of the Hudson Bay drainage system. At Manvel, ND, approximately 10 miles northeast

  18. Geomorphological Analysis of North Fork, Toutle River, Washington: 1980- 1984

    DTIC Science & Technology

    1994-03-01

    north flank of Mount St. Helens and included glacial ice, modern dacite dome, and a mixture of andesite and minor amounts of basalt lava flows...and basalt form the former domes. During emplacement this deposit also consisted of snow and large blocks of ice from the glaciers on the north flank of...north side of Mount St. Helens. Consequently,the North Fork Unit features as its dominant 23 materials the dark colored mixed basalt deposits and the

  19. Environmental Assessment Housing Transfer at Grand Forks AFB, North Dakota

    DTIC Science & Technology

    2005-01-27

    tallgrass prairie that once was dominant in this region. Plants thriving in this preserve include western wheatgrass, slender wheatgrass, big bluestem...Palustrine Forested type wetlands. Vegetation is robust at GFAFB wetlands, and they are characterized as typical prairie potholes found within the...grassland and wetland habitats for wildlife in Grand Forks County. Pastures, meadows, and other non-cultivated areas create a prairie -land mosaic

  20. East Fork Watershed Cooperative: Toward better system-scale ...

    EPA Pesticide Factsheets

    The East Fork Watershed Cooperative is a group intent on understanding how to best manage water quality in a large mixed-use Midwestern watershed system. The system contains a reservoir that serves as a source of drinking water and is popular for water recreation. The reservoir is experience harmful algal blooms. The system including the reservoir has become a significant case study for EPA ORD research and development. The Cooperative includes affiliates from the USACE, the OHIO EPA, the USGS, the USDA, and local Soil and Water Conservation districts as well as utility operators and water quality protection offices. The presentation includes a description of the water quality monitoring and modeling program in the watershed, followed by the results of using the watershed model to estimate the costs associated with nutrient reduction to Harsha Lake, and then ends with an explanation of temporal changes observed for important factors controlling harmful algae in Harsha Lake and how this lake relates to other reservoirs in the Ohio River Basin. This presentation is an invited contribution to the Ohio River Basin Water Quality Workshop sponsored by the US ACE and the US EPA. The presentation describes the activities of the East Fork Watershed Cooperative and the knowledge it has gained to help better manage a case study watershed system over the last few years. The East Fork of the Little Miami River is the focal watershed. It is a significant tributary to the Lit

  1. Replication patterns and organization of replication forks in Vibrio cholerae.

    PubMed

    Stokke, Caroline; Waldminghaus, Torsten; Skarstad, Kirsten

    2011-03-01

    We have investigated the replication patterns of the two chromosomes of the bacterium Vibrio cholerae grown in four different media. By combining flow cytometry and quantitative real-time PCR with computer simulations, we show that in rich media, V. cholerae cells grow with overlapping replication cycles of both the large chromosome (ChrI) and the small chromosome (ChrII). In Luria-Bertani (LB) medium, initiation occurs at four copies of the ChrI origin and two copies of the ChrII origin. Replication of ChrII was found to occur at the end of the ChrI replication period in all four growth conditions. Novel cell-sorting experiments with marker frequency analysis support these conclusions. Incubation with protein synthesis inhibitors indicated that the potential for initiation of replication of ChrII was present at the same time as that of ChrI, but was actively delayed until much of ChrI was replicated. Investigations of the localization of SeqA bound to new DNA at replication forks indicated that the forks were co-localized in pairs when cells grew without overlapping replication cycles and in higher-order structures during more rapid growth. The increased degree of fork organization during rapid growth may be a means by which correct segregation of daughter molecules is facilitated.

  2. The Yampa Bed - A Regionally Extensive Tonstein in the Williams Fork Formation, Northwestern Piceance Creek and Southern Sand Wash Basins, Colorado

    USGS Publications Warehouse

    Brownfield, Michael E.; Johnson, Edward A.

    2008-01-01

    A regionally persistent and distinctive unit of Upper Cretaceous age is here formally named the Yampa Bed of the Williams Fork Formation for exposures in the Yampa, Danforth Hills, and Grand Hogback coal fields, Moffat and Routt Counties, northwest Colorado; the name is derived from the Yampa River valley. The type section was measured in the NE? SW? sec. 6, T. 5 N., R. 91 W., about 8 miles south of Craig, Colo., where the bed is 38 inches thick and lies within the C-D coal bed in the lower part of the Williams Fork Formation, about 165 feet above the Trout Creek Sandstone Member of the Iles Formation. The Yampa Bed is dated at 72.2 ? .1 mega-annum using the K-Ar method. Regionally, the Yampa Bed is a 0.5- to 5-ft-thick, regionally persistent tonstein that can be readily identified in several different lithofacies in the lower part of the Williams Fork Formation. The unit is useful as a regional datum in the correlation of facies within the Williams Fork, and it is easily recognized on geophysical logs by its low resistivity response. Evidence suggests that it is a diagenetically altered airfall ash.

  3. Human RECQ1 promotes restart of replication forks reversed by DNA topoisomerase I inhibition.

    PubMed

    Berti, Matteo; Ray Chaudhuri, Arnab; Thangavel, Saravanabhavan; Gomathinayagam, Shivasankari; Kenig, Sasa; Vujanovic, Marko; Odreman, Federico; Glatter, Timo; Graziano, Simona; Mendoza-Maldonado, Ramiro; Marino, Francesca; Lucic, Bojana; Biasin, Valentina; Gstaiger, Matthias; Aebersold, Ruedi; Sidorova, Julia M; Monnat, Raymond J; Lopes, Massimo; Vindigni, Alessandro

    2013-03-01

    Topoisomerase I (TOP1) inhibitors are an important class of anticancer drugs. The cytotoxicity of TOP1 inhibitors can be modulated by replication fork reversal through a process that requires poly(ADP-ribose) polymerase (PARP) activity. Whether regressed forks can efficiently restart and what factors are required to restart fork progression after fork reversal are still unknown. We have combined biochemical and EM approaches with single-molecule DNA fiber analysis to identify a key role for human RECQ1 helicase in replication fork restart after TOP1 inhibition that is not shared by other human RecQ proteins. We show that the poly(ADP-ribosyl)ation activity of PARP1 stabilizes forks in the regressed state by limiting their restart by RECQ1. These studies provide new mechanistic insights into the roles of RECQ1 and PARP in DNA replication and offer molecular perspectives to potentiate chemotherapeutic regimens based on TOP1 inhibition.

  4. Human RECQ1 promotes restart of replication forks reversed by DNA topoisomerase I inhibition

    PubMed Central

    Berti, Matteo; Chaudhuri, Arnab Ray; Thangavel, Saravanabhavan; Gomathinayagam, Shivasankari; Kenig, Sasa; Vujanovic, Marko; Odreman, Federico; Glatter, Timo; Graziano, Simona; Mendoza-Maldonado, Ramiro; Marino, Francesca; Lucic, Bojana; Biasin, Valentina; Gstaiger, Matthias; Aebersold, Ruedi; Sidorova, Julia M.; Monnat, Raymond J.; Lopes, Massimo; Vindigni, Alessandro

    2014-01-01

    SUMMARY Topoisomerase I (TOP1) inhibitors are an important class of anticancer drugs. The cytotoxicity of TOP1 inhibitors can be modulated by replication fork reversal, in a process that requires PARP activity. Whether regressed forks can efficiently restart and the factors required to restart fork progression after fork reversal are still unknown. Here we combined biochemical and electron microscopy approaches with single-molecule DNA fiber analysis, to identify a key role for human RECQ1 helicase in replication fork restart after TOP1 inhibition, not shared by other human RecQ proteins. We show that the poly(ADPribosyl)ation activity of PARP1 stabilizes forks in their regressed state by limiting their restart by RECQ1. These studies provide new mechanistic insights into the roles of RECQ1 and PARP in DNA replication and offer molecular perspectives to potentiate chemotherapeutic regimens based on TOP1 inhibition. PMID:23396353

  5. Rad51-mediated replication fork reversal is a global response to genotoxic treatments in human cells

    PubMed Central

    Zellweger, Ralph; Dalcher, Damian; Mutreja, Karun; Berti, Matteo; Schmid, Jonas A.; Herrador, Raquel; Vindigni, Alessandro

    2015-01-01

    Replication fork reversal protects forks from breakage after poisoning of Topoisomerase 1. We here investigated fork progression and chromosomal breakage in human cells in response to a panel of sublethal genotoxic treatments, using other topoisomerase poisons, DNA synthesis inhibitors, interstrand cross-linking inducers, and base-damaging agents. We used electron microscopy to visualize fork architecture under these conditions and analyzed the association of specific molecular features with checkpoint activation. Our data identify replication fork uncoupling and reversal as global responses to genotoxic treatments. Both events are frequent even after mild treatments that do not affect fork integrity, nor activate checkpoints. Fork reversal was found to be dependent on the central homologous recombination factor RAD51, which is consistently present at replication forks independently of their breakage, and to be antagonized by poly (ADP-ribose) polymerase/RECQ1-regulated restart. Our work establishes remodeling of uncoupled forks as a pivotal RAD51-regulated response to genotoxic stress in human cells and as a promising target to potentiate cancer chemotherapy. PMID:25733714

  6. The fork and the kinase: a DNA replication tale from a CHK1 perspective.

    PubMed

    González Besteiro, Marina A; Gottifredi, Vanesa

    2015-01-01

    Replication fork progression is being continuously hampered by exogenously introduced and naturally occurring DNA lesions and other physical obstacles. Checkpoint kinase 1 (Chk1) is activated at replication forks that encounter damaged DNA. Subsequently, Chk1 inhibits the initiation of new replication factories and stimulates the firing of dormant origins (those in the vicinity of stalled forks). Chk1 also avoids fork collapse into DSBs (double strand breaks) and promotes fork elongation. At the molecular level, the current model considers stalled forks as the site of Chk1 activation and the nucleoplasm as the location where Chk1 phosphorylates target proteins. This model certainly serves to explain how Chk1 modulates origin firing, but how Chk1 controls the fate of stalled forks is less clear. Interestingly, recent reports demonstrating that Chk1 phosphorylates chromatin-bound proteins and even holds kinase-independent functions might shed light on how Chk1 contributes to the elongation of damaged DNA. Indeed, such findings have unveiled a puzzling connection between Chk1 and DNA lesion bypass, which might be central to promoting fork elongation and checkpoint attenuation. In summary, Chk1 is a multifaceted and versatile signaling factor that acts at ongoing forks and replication origins to determine the extent and quality of the cellular response to replication stress.

  7. The carpenter fork bed, a new - and older - Black-shale unit at the base of the New Albany shale in central Kentucky: Characterization and significance

    USGS Publications Warehouse

    Barnett, S.F.; Ettensohn, F.R.; Norby, R.D.

    1996-01-01

    Black shales previously interpreted to be Late Devonian cave-fill or slide deposits are shown to be much older Middle Devonian black shales only preserved locally in Middle Devonian grabens and structural lows in central Kentucky. This newly recognized - and older -black-shale unit occurs at the base of the New Albany Shale and is named the Carpenter Fork Bed of the Portwood Member of the New Albany Shale after its only known exposure on Carpenter Fork in Boyle County, central Kentucky; two other occurrences are known from core holes in east-central Kentucky. Based on stratigraphic position and conodont biostratigraphy, the unit is Middle Devonian (Givetian: probably Middle to Upper P. varcus Zone) in age and occurs at a position represented by an unconformity atop the Middle Devonian Boyle Dolostone and its equivalents elsewhere on the outcrop belt. Based on its presence as isolated clasts in the overlying Duffin Bed of the Portwood Member, the former distribution of the unit was probably much more widespread - perhaps occurring throughout western parts of the Rome trough. Carpenter Fork black shales apparently represent an episode of subsidence or sea-level rise coincident with inception of the third tectophase of the Acadian orogeny. Deposition, however, was soon interrupted by reactivation of several fault zones in central Kentucky, perhaps in response to bulge migration accompanying start of the tectophase. As a result, much of central Kentucky was uplifted and tilted, and the Carpenter Fork Bed was largely eroded from the top of the Boyle, except in a few structural lows like the Carpenter Fork graben where a nearly complete record of Middle to early Late Devonian deposition is preserved.

  8. MIDDLE FORK OF THE JUDITH RIVER WILDERNESS STUDY AREA, MONTANA.

    USGS Publications Warehouse

    Reynolds, Mitchell W.; Hamilton, Michael

    1984-01-01

    The Middle Fork of the Judith River Wilderness Study Area in Montana has several prospects containing local small inferred resources and several exposed mineral occurrences bearing silver, lead, copper, and gold along its north and west edges with no identified resource potential. Geologic, geophysical, and geochemical studies, conducted to appraise the mineral resources of the study area, identified no other anomalous concentrations of metallic elements. A gem-quality sapphire resource, present near the east boundary, cannot be identified within the study area. The area holds little promise for the occurrence of other mineral or energy resources.

  9. 78 FR 48292 - Amendment of Class D Airspace; Grand Forks AFB, ND

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-08

    ... Federal Aviation Administration 14 CFR Part 71 Amendment of Class D Airspace; Grand Forks AFB, ND AGENCY: Federal Aviation Administration (FAA), DOT. ACTION: Final rule. SUMMARY: This action amends Class D... Federal Register a notice of proposed rulemaking (NPRM) to amend Class D airspace for Grand Forks AFB,...

  10. HLTF's Ancient HIRAN Domain Binds 3' DNA Ends to Drive Replication Fork Reversal.

    PubMed

    Kile, Andrew C; Chavez, Diana A; Bacal, Julien; Eldirany, Sherif; Korzhnev, Dmitry M; Bezsonova, Irina; Eichman, Brandt F; Cimprich, Karlene A

    2015-06-18

    Stalled replication forks are a critical problem for the cell because they can lead to complex genome rearrangements that underlie cell death and disease. Processes such as DNA damage tolerance and replication fork reversal protect stalled forks from these events. A central mediator of these DNA damage responses in humans is the Rad5-related DNA translocase, HLTF. Here, we present biochemical and structural evidence that the HIRAN domain, an ancient and conserved domain found in HLTF and other DNA processing proteins, is a modified oligonucleotide/oligosaccharide (OB) fold that binds to 3' ssDNA ends. We demonstrate that the HIRAN domain promotes HLTF-dependent fork reversal in vitro through its interaction with 3' ssDNA ends found at forks. Finally, we show that HLTF restrains replication fork progression in cells in a HIRAN-dependent manner. These findings establish a mechanism of HLTF-mediated fork reversal and provide insight into the requirement for distinct fork remodeling activities in the cell.

  11. 76 FR 35909 - Temporary Concession Contract for Big South Fork National Recreation Area, TN/KY

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-20

    ... National Recreation Area, TN/KY. SUMMARY: Pursuant to 36 CFR 51.24, public notice is hereby given that the...] Temporary Concession Contract for Big South Fork National Recreation Area, TN/KY AGENCY: National Park... visitor services within Big South Fork National Recreation Area, Tennessee and Kentucky, for a term not...

  12. 33 CFR 208.26 - Altus Dam and Reservoir, North Fork Red River, Okla.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Fork Red River, Okla. 208.26 Section 208.26 Navigation and Navigable Waters CORPS OF ENGINEERS..., North Fork Red River, Okla. The Bureau of Reclamation, or its designated agent, shall operate the Altus... of runoff from the area above the dam exceeds the volume of water necessary to raise the...

  13. 33 CFR 208.26 - Altus Dam and Reservoir, North Fork Red River, Okla.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... Fork Red River, Okla. 208.26 Section 208.26 Navigation and Navigable Waters CORPS OF ENGINEERS..., North Fork Red River, Okla. The Bureau of Reclamation, or its designated agent, shall operate the Altus... of runoff from the area above the dam exceeds the volume of water necessary to raise the...

  14. First report of anther smut caused by Microbotryum violaceum on forked catchfly in Turkey

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Forked catchfly (Silene dichotoma Ehrh.), family Caryophyllaceae, is a common and native plant in rangelands and pastures in Turkey. It is also an introduced plant that is widely distributed in North America. In May, 2007 about 20 forked catchfly plants on the campus of Ondokuz Mayis University, i...

  15. Origin & Evolution of the Grand Forks Human Nutrition Research Center, 1970-90

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the early 1960s William E Cornatzer, MD, PhD, suggested the need for increased USDA research concerning human nutrition, and creation of the Grand Forks Human Nutrition Laboratory (Grand Forks Human Nutrition Research Center). He shared ideas with Senator Milton R. Young of North Dakota, who requ...

  16. Active Control of Repetitive Structural Transitions between Replication Forks and Holliday Junctions by Werner Syndrome Helicase

    PubMed Central

    Shin, Soochul; Lee, Jinwoo; Yoo, Sangwoon; Kulikowicz, Tomasz; Bohr, Vilhelm A.; Ahn, Byungchan; Hohng, Sungchul

    2016-01-01

    SUMMARY The reactivation of stalled DNA replication via fork regression invokes Holliday junction formation, branch migration, and the recovery of the replication fork after DNA repair or error-free DNA synthesis. The coordination mechanism for these DNA structural transitions by molecular motors, however, remains unclear. Here we perform single-molecule fluorescence experiments with Werner syndrome protein (WRN) and model replication forks. The Holliday junction is readily formed once the lagging arm is unwound, and migrated unidirectionally with 3.2 ± 0.03 bases/s velocity. The recovery of the replication fork was controlled by branch migration reversal of WRN, resulting in repetitive fork regression. The Holliday junction formation, branch migration, and migration direction reversal are all ATP dependent, revealing that WRN uses the energy of ATP hydrolysis to actively coordinate the structural transitions of DNA. PMID:27427477

  17. 77 FR 64125 - Notice of Proposed Withdrawal Extension and Notification of a Public Meeting for the East Fork...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-18

    ... for the East Fork Elk Winter Range; WY AGENCY: Bureau of Land Management, Interior. ACTION: Notice... States mining laws, to protect the East Fork Elk Winter Range and elk natural feeding grounds in Fremont... mineral estate from location or entry under the United States mining laws, to protect the East Fork...

  18. 59 FR- Prohibited Acts in West Little and North Fork Owyhee National Wild and Scenic River Area

    Federal Register 2010, 2011, 2012, 2013, 2014

    1994-12-15

    ... INTERIOR [OR-030-03-1220-04: GS-043] Prohibited Acts in West Little and North Fork Owyhee National Wild and... and restrictions within the boundaries of the West Little and North Fork Owyhee Rivers as established in the Main, West Little and North Fork Owyhee National Wild and Scenic Rivers Management...

  19. Depositional environments, reservoir trends, and diagenesis of Red Fork sandstones in parts of Blaine, Caddo, and Custer counties, Oklahoma

    SciTech Connect

    Johnson, C.L.

    1984-04-01

    The Red Fork sandstone was divided into the upper and lower Red Fork which are separated by a consistent marker bed. The Red Fork interval thickens markedly across the study area from 250 ft (75 m) in the northeast to over 1300 ft (400 m) in the southwest. Most of the thickening is within the lower Red Fork. The lower Red Fork is believed to have been deposited in shelf-to-basin transitional terrain. Sands were located in delta-front, submarine-channel-fill, and possible submarine-fan terrain. The upper Red Fork is believed to represent the maximum progradation of a deltaic complex. Sandstones of the lower Red Fork are sublithic to lithic arenites; the upper Red Fork is sublithic arenite. The dominant lithic fraction is mudstone fragments. The main diagenetic alterations of both the upper and lower Red Fork sandstones were destruction of primary porosity by compaction and cementation. Dissolution chiefly of mud fragments has produced well-developed secondary porosity. Clays of the lower Red Fork mainly are authigenic chlorite; clays of the upper Red Fork primarily are authigenic kaolinite. Present oil and gas production from Red Fork sandstones is most abundant from localities on the paleoshelf.

  20. CtIP mediates replication fork recovery in a FANCD2-regulated manner.

    PubMed

    Yeo, Jung Eun; Lee, Eu Han; Hendrickson, Eric A; Sobeck, Alexandra

    2014-07-15

    Fanconi anemia (FA) is a chromosome instability syndrome characterized by increased cancer predisposition. Within the FA pathway, an upstream FA core complex mediates monoubiquitination and recruitment of the central FANCD2 protein to sites of stalled replication forks. Once recruited, FANCD2 fulfills a dual role towards replication fork recovery: (i) it cooperates with BRCA2 and RAD51 to protect forks from nucleolytic degradation and (ii) it recruits the BLM helicase to promote replication fork restart while suppressing new origin firing. Intriguingly, FANCD2 and its interaction partners are also involved in homologous recombination (HR) repair of DNA double-strand breaks, hinting that FANCD2 utilizes HR proteins to mediate replication fork recovery. One such candidate is CtIP (CtBP-interacting protein), a key HR repair factor that functions in complex with BRCA1 and MRE11, but has not been investigated as putative player in the replication stress response. Here, we identify CtIP as a novel interaction partner of FANCD2. CtIP binds and stabilizes FANCD2 in a DNA damage- and FA core complex-independent manner, suggesting that FANCD2 monoubiquitination is dispensable for its interaction with CtIP. Following cellular treatment with a replication inhibitor, aphidicolin, FANCD2 recruits CtIP to transiently stalled, as well as collapsed, replication forks on chromatin. At stalled forks, CtIP cooperates with FANCD2 to promote fork restart and the suppression of new origin firing. Both functions are dependent on BRCA1 that controls the step-wise recruitment of MRE11, FANCD2 and finally CtIP to stalled replication forks, followed by their concerted actions to promote fork recovery.

  1. Quartz tuning fork as a probe of surface oscillations

    NASA Astrophysics Data System (ADS)

    Todoshchenko, I.; Savin, A.; Haataja, M.; Kaikkonen, J.-P.; Hakonen, P. J.

    2017-02-01

    Quartz tuning forks are high-quality mechanical oscillators widely used in low temperature physics as viscometers, thermometers, and pressure sensors. We demonstrate that a fork placed in liquid helium near the surface of solid helium is very sensitive to the oscillations of the solid-liquid interface. We developed a double-resonance read-out technique, which allowed us to detect oscillations of the surface with an accuracy of 1 Å in 10 s. Using this technique, we have investigated crystallization waves in 4He down to 10 mK. In contrast to previous studies of crystallization waves, our measurement scheme has very low dissipation, on the order of 20 pW, which allows us to carry out experiments even at sub-mK temperatures. We propose to use this scheme in the search for crystallization waves in 3He, which exist only at temperatures well below 0.5 mK. The suggested technique can also be used for accurate displacement detection in a large variety of systems.

  2. Forked grating coupler optical vortex beam interface for silicon photonics

    NASA Astrophysics Data System (ADS)

    Nadovich, Christopher T.; Kosciolek, Derek J.; Jemison, William D.; Crouse, David T.

    2016-09-01

    The forked grating coupler (FGC) is a novel low-profile device compatible with silicon photonics that is capable of sensitive detection or efficient radiation of Optical Vortex (OV) light beams conveying orbital optical angular momentum (OAM). The FGC device combines the idea of a Bragg coupler with the forked hologram to create an integrated optics device that can selectively and efficiently couple selected optical vortex modes at near-normal incidence into planar confined dielectric waveguide modes of a photonic IC. FGCs retain many of the advantages of Bragg couplers, including convenience of placement and fabrication, reasonable bandwidth, small size, and CMOS process compatibility. In this work, prototype designs of FGC structures for 1550 nm wavelength have been developed for implementation on silicon on insulator (SOI) substrate. Fully vectorial three-dimensional (3D) electromagnetic simulation has allowed performance to be optimized over a range of structural parameters. Results have been evaluated against optical performance metrics including overall efficiency, mode match efficiency, and crosstalk between OV modes. Candidate FGC devices have been fabricated on SOI with e-beam lithography and tested optically. Tolerance to etch depth error has been evaluated.

  3. Replication Fork Stability Confers Chemoresistance in BRCA-deficient Cells

    PubMed Central

    Chaudhuri, Arnab Ray; Callen, Elsa; Ding, Xia; Gogola, Ewa; Duarte, Alexandra A.; Lee, Ji-Eun; Wong, Nancy; Lafarga, Vanessa; Calvo, Jennifer A.; Panzarino, Nicholas J.; John, Sam; Day, Amanda; Crespo, Anna Vidal; Shen, Binghui; Starnes, Linda M.; de Ruiter, Julian R.; Daniel, Jeremy A.; Konstantinopoulos, Panagiotis A.; Cortez, David; Cantor, Sharon B.; Fernandez-Capetillo, Oscar; Ge, Kai; Jonkers, Jos; Rottenberg, Sven; Sharan, Shyam K.; Nussenzweig, André

    2016-01-01

    Brca1- and Brca2-deficient cells have reduced capacity to repair DNA double-strand breaks (DSBs) by homologous recombination (HR) and consequently are hypersensitive to DNA damaging agents, including cisplatin and poly(ADP-ribose) polymerase (PARP) inhibitors. Here we show that loss of the MLL3/4 complex protein, PTIP, protects Brca1/2-deficient cells from DNA damage and rescues the lethality of Brca2-deficient embryonic stem cells. However, PTIP deficiency does not restore HR activity at DSBs. Instead, its absence inhibits the recruitment of the MRE11 nuclease to stalled replication forks, which in turn protects nascent DNA strands from extensive degradation. More generally, acquisition of PARPi and cisplatin resistance is associated with replication fork (RF) protection in Brca2-deficient tumor cells that do not develop Brca2 reversion mutations. Disruption of multiple proteins, including PARP1 and CHD4, leads to the same end point of RF protection, highlighting the complexities by which tumor cells evade chemotherapeutic interventions and acquire drug resistance. PMID:27443740

  4. Depositional environments of the Red Fork Sandstone in Custer and Roger Mills Counties, southwestern Oklahoma

    SciTech Connect

    Tolson, P.M. )

    1993-09-01

    The Desmoinesian Red Fork formation is a prolific, overpressured gas-producing sequence of interbedded sandstones and shales. Total thickness ranges from less than 100 ft (northeast) to more than 1100 ft (south). Isopach maps suggest that syndepositional faulting controlled major depositional trends. The lower Red Fork, whose base is defined by a persistent, hot, black shale (sequence boundary ), is mainly deep-marine shale and siltstone. Two major shallowing-upward deltaic sequences separated by a marine transgression are evident in the middle (50-400-ft thick) and upper (30-250-ft thick) Red Fork. The middle Red Fork is marine dominated and was deposited into a relatively deep basin on a steep, unstable delta-front slope. In contrast, the upper Red Fork deltaic sequence is more fluvial dominated and was deposited in shallower water. The upper Red Fork is overlain by the Pink lime interval which appears to be shallow-marine/lagoonal black shale. The Pink lime contains fish scales, coffee-ground to branch-size lignitic plant debris, and brackish to shallow-marine ostracodes, linguloid brachiopods, Tasmanites algae, and gastropods. Most of the Red Fork has an easterly, possibly Ouachita Mountain area source. The prolific Southwest Leedey field has a different mineral assemblage and diagenetic sequence and may have a northern source.

  5. Geomorphic Characterization of the Middle Fork Saline River: Garland, Perry, and Saline Counties, Arkansas

    USGS Publications Warehouse

    Pugh, Aaron L.; Garday, Thomas J.; Redman, Ronald

    2008-01-01

    This report was prepared to help address concerns raised by local residents, State, and Federal agencies about the current geomorphic conditions of the Middle Fork Saline River. Over the past 30 years the Middle Fork Saline River Basin has experienced a marked increase in urbanization. The report summarizes the Middle Fork?s current (2003) channel characteristics at nine stream reaches in the upper 91 square miles of the basin. Assessments at each study reach included comparing measured stream geometry dimensions (cross-sectional area, top width, and mean depth) at bankfull stage to regional hydraulic geometry curves for the Ouachita Mountains Physiographic Province of Arkansas and Oklahoma, evaluations of streambed materials and sinuosity, and classification of individual stream reach types. When compared to the Ouachita Mountains? regional hydraulic geometry curves for natural, stable, stream reaches, five of the nine study reaches had slightly smaller crosssectional areas, longer top widths, and shallower depths. Streambed material analysis indicates that the Middle Fork is a bedrock influenced, gravel dominated stream with lesser amounts of sand and cobbles. Slight increases in sinuosity from 1992 to 2002 at seven of the nine study reaches indicate a slight decrease in stream channel slope. Analyses of the Middle Fork?s hydraulic geometry and sinuosity indicate that the Middle Fork is currently overly wide and shallow, but is slowly adjusting towards a deeper, narrower hydraulic geometry. Using the Rosgen system of channel classification, the two upstream study reaches classified as B4c/1 stream types; which were moderately entrenched, riffle dominated channels, with infrequently spaced pools. The downstream seven study reaches classified as C4/1 stream types; which were slightly entrenched, meandering, gravel-dominated, riffle/ pool channels with well developed flood plains. Analyses of stream reach types suggest that the downstream reaches of the Middle Fork

  6. Effects of Transposable Elements on the Expression of the Forked Gene of Drosophila Melanogaster

    PubMed Central

    Hoover, K. K.; Chien, A. J.; Corces, V. G.

    1993-01-01

    The products of the forked gene are involved in the formation and/or maintenance of a temporary fibrillar structure within the developing bristle rudiment of Drosophila melanogaster. Mutations in the forked locus alter this structure and result in aberrant development of macrochaetae, microchaetae and trichomes. The locus has been characterized at the molecular level by walking, mutant characterization and transcript analysis. Expression of the six forked transcripts is temporally restricted to midlate pupal development. At this time, RNAs of 6.4, 5.6, 5.4, 2.5, 1.9 and 1.1 kilobases (kb) are detected by Northern analysis. The coding region of these RNAs has been found to be within a 21-kb stretch of genomic DNA. The amino terminus of the proteins encoded by the 5.4- and 5.6-kb forked transcripts contain tandem copies of ankyrin-like repeats that may play an important role in the function of forked-encoded products. The profile of forked RNA expression is altered in seven spontaneous mutations characterized during this study. Three forked mutations induced by the insertion of the gypsy retrotransposon contain a copy of this element inserted into an intron of the gene. In these mutants, the 5.6-, 5.4- and 2.5-kb forked mRNAs are truncated via recognition of the polyadenylation site in the 5' long terminal repeat of the gypsy retrotransposon. These results help explain the role of the forked gene in fly development and further our understanding of the role of transposable elements in mutagenesis. PMID:8244011

  7. Finite Element Analysis of Electrically Excited Quartz Tuning Fork Devices

    PubMed Central

    Oria, Roger; Otero, Jorge; González, Laura; Botaya, Luis; Carmona, Manuel; Puig-Vidal, Manel

    2013-01-01

    Quartz Tuning Fork (QTF)-based Scanning Probe Microscopy (SPM) is an important field of research. A suitable model for the QTF is important to obtain quantitative measurements with these devices. Analytical models have the limitation of being based on the double cantilever configuration. In this paper, we present an electromechanical finite element model of the QTF electrically excited with two free prongs. The model goes beyond the state-of-the-art of numerical simulations currently found in the literature for this QTF configuration. We present the first numerical analysis of both the electrical and mechanical behavior of QTF devices. Experimental measurements obtained with 10 units of the same model of QTF validate the finite element model with a good agreement. PMID:23722828

  8. Quartz-enhanced photoacoustic spectroscopy exploiting tuning fork overtone modes

    NASA Astrophysics Data System (ADS)

    Sampaolo, A.; Patimisco, P.; Dong, L.; Geras, A.; Scamarcio, G.; Starecki, T.; Tittel, F. K.; Spagnolo, V.

    2015-12-01

    We report on a quartz-enhanced photoacoustic sensor (QEPAS) based on a custom-made quartz tuning fork (QTF) to operate in both the fundamental and the first overtone vibrational mode resonances. The QTF fundamental mode resonance falls at ˜3 kHz and the first overtone at ˜18 kHz. Electrical tests showed that the first overtone provides a higher quality factor and increased piezoelectric current peak values, with respect to the fundamental flexural mode. To evaluate the QTF acousto-electric energy conversion efficiency, we operated the QEPAS in the near-IR and selected water vapor as the target gas. The first overtone resonance provides a QEPAS signal-to-noise ratio ˜5 times greater with respect to that measured for the fundamental mode. These results open the way to employing QTF overtone vibrational modes for QEPAS based trace gas sensing.

  9. Geochemical map of the North Fork John Day River Roadless Area, Grant County, Oregon

    USGS Publications Warehouse

    Evans, James G.

    1986-01-01

    The North Fork John Day River Roadless Area comprised 21,210 acres in the Umatilla and Wallowa-Whitman National Forests, Grant County, Oregon, about 30 miles northwest of Baker, Oregon. The irregularly shaped area extends for about 1 mile on both sides of a 25-mile segment of the North Fork John Day River from Big Creek on the west to North Fork John Day Campground on the east. Most of the roadless area is in the northern half of the Desolation Butte 15-minute quadrangle. The eastern end of the area is in parts of the Granite and Trout Meadows 7½-minute quadrangles.

  10. Chromatin-associated degradation is defined by UBXN-3/FAF1 to safeguard DNA replication fork progression

    PubMed Central

    Franz, André; Pirson, Paul A.; Pilger, Domenic; Halder, Swagata; Achuthankutty, Divya; Kashkar, Hamid; Ramadan, Kristijan; Hoppe, Thorsten

    2016-01-01

    The coordinated activity of DNA replication factors is a highly dynamic process that involves ubiquitin-dependent regulation. In this context, the ubiquitin-directed ATPase CDC-48/p97 recently emerged as a key regulator of chromatin-associated degradation in several of the DNA metabolic pathways that assure genome integrity. However, the spatiotemporal control of distinct CDC-48/p97 substrates in the chromatin environment remained unclear. Here, we report that progression of the DNA replication fork is coordinated by UBXN-3/FAF1. UBXN-3/FAF1 binds to the licensing factor CDT-1 and additional ubiquitylated proteins, thus promoting CDC-48/p97-dependent turnover and disassembly of DNA replication factor complexes. Consequently, inactivation of UBXN-3/FAF1 stabilizes CDT-1 and CDC-45/GINS on chromatin, causing severe defects in replication fork dynamics accompanied by pronounced replication stress and eventually resulting in genome instability. Our work identifies a critical substrate selection module of CDC-48/p97 required for chromatin-associated protein degradation in both Caenorhabditis elegans and humans, which is relevant to oncogenesis and aging. PMID:26842564

  11. Cancer therapy and replication stress: forks on the road to perdition.

    PubMed

    Kotsantis, Panagiotis; Jones, Rebecca M; Higgs, Martin R; Petermann, Eva

    2015-01-01

    Deregulated DNA replication occurs in cancer where it contributes to genomic instability. This process is a target of cytotoxic therapies. Chemotherapies exploit high DNA replication in cancer cells by modifying the DNA template or by inhibiting vital enzymatic activities that lead to slowing or stalling replication fork progression. Stalled replication forks can be converted into toxic DNA double-strand breaks resulting in cell death, i.e., replication stress. While likely crucial for many cancer treatments, replication stress is poorly understood due to its complexity. While we still know relatively little about the role of replication stress in cancer therapy, technical advances in recent years have shed new light on the effect that cancer therapeutics have on replication forks and the molecular mechanisms that lead from obstructed fork progression to cell death. This chapter will give an overview of our current understanding of replication stress in the context of cancer therapy.

  12. The DNA helicase Pfh1 promotes fork merging at replication termination sites to ensure genome stability

    PubMed Central

    Steinacher, Roland; Osman, Fekret; Dalgaard, Jacob Z.; Lorenz, Alexander; Whitby, Matthew C.

    2012-01-01

    Bidirectionally moving DNA replication forks merge at termination sites composed of accidental or programmed DNA–protein barriers. If merging fails, then regions of unreplicated DNA can result in the breakage of DNA during mitosis, which in turn can give rise to genome instability. Despite its importance, little is known about the mechanisms that promote the final stages of fork merging in eukaryotes. Here we show that the Pif1 family DNA helicase Pfh1 plays a dual role in promoting replication fork termination. First, it facilitates replication past DNA–protein barriers, and second, it promotes the merging of replication forks. A failure of these processes in Pfh1-deficient cells results in aberrant chromosome segregation and heightened genome instability. PMID:22426535

  13. Probing Liquid ^4He with Quartz Tuning Forks Using a Novel Multifrequency Lock-in Technique

    NASA Astrophysics Data System (ADS)

    Bradley, D. I.; Haley, R. P.; Kafanov, S.; Noble, M. T.; Pickett, G. R.; Tsepelin, V.; Vonka, J.; Wilcox, T.

    2016-09-01

    We report on a novel technique to measure quartz tuning forks, and possibly other vibrating objects, in a quantum fluid using a multifrequency lock-in amplifier. The multifrequency technique allows to measure the resonance curve of a vibrating object much faster than a conventional single frequency lock-in amplifier technique. Forks with resonance frequencies of 12 kHz and 16 kHz were excited and measured electro-mechanically either at a single frequency or at up to 40 different frequencies simultaneously around the same mechanical mode. The response of each fork was identical for both methods and validates the use of the multifrequency lock-in technique to probe properties of liquid helium at low fork velocities. Using both methods we measured the resonance frequency and drag of two 25-μ m-wide quartz tuning forks immersed in liquid ^4He in the temperature range from 4.2 K to 1.5 K at saturated vapour pressure. The damping and shift of resonance frequency experienced by both tuning forks at low velocities are well described by hydrodynamic contributions in the framework of the two-fluid model. The sensitivity of the 25-μ m-wide tuning forks is larger compared to similar 75-μ m-wide forks and in combination with the faster multifrequency lock-in technique could be used to improve thermometry in liquid ^4He. The multifrequency technique could also be used for studies of the onset of non-linear phenomena such as quantum turbulence and cavitation in superfluids.

  14. Environmental Assessment: Demolish CASS Switch Stations Buildings 644, 645, 646 at Grand Forks Air Force Base

    DTIC Science & Technology

    2006-06-01

    Winters are long and severe with almost continuous snow cover. The spring and fall seasons are generally short transition periods. The average...during the late fall, winter, and spring , and from the southeast during the summer. Grand Forks County is included in the ND Air Quality Control...approximately 10 miles northeast of Grand Forks AFB, the mean discharge of the Turtle River is 50.3 feet cubed per second (ft3/s). Peak flows result from

  15. Environmental Assessment: Construct Airfield Lighting Vault and Demolish Building 531 at Grand Forks Air Force Base

    DTIC Science & Technology

    2007-08-01

    frequent thunderstorms. Winters are long and severe with almost continuous snow cover. The spring and fall seasons are generally short transition periods...from the northwest during the late fall, winter, and spring , and from the southeast during the summer. Grand Forks County is included in the ND Air...Manvel, ND, approximately 10 miles northeast of Grand Forks AFB, the mean discharge of the Turtle River is 50.3 feet cubed per second (ft3/s). Peak

  16. Environmental Assessment: Demolish Buildings 212, 218, 819, 820 at Grand Forks Air Force Base

    DTIC Science & Technology

    2007-01-31

    Winters are long and severe with almost continuous snow cover. The spring and fall seasons are generally short transition periods. The average annual...during the late fall, winter, and spring , and from the southeast during the summer. Grand Forks County is included in the ND Air Quality Control...approximately 10 miles northeast of Grand Forks AFB, the mean discharge of the Turtle River is 50.3 feet cubed per second (ft3/s). Peak flows result from

  17. The Sound Field around a Tuning Fork and the Role of a Resonance Box

    ERIC Educational Resources Information Center

    Bogacz, Bogdan F.; Pedziwiatr, Antoni T.

    2015-01-01

    Atypical two-tine tuning fork is barely audible when held vibrating at an arm's length. It is enough, however, to touch its base to a table or, better, to a resonance box and the emitted sound becomes much louder. An inquiring student may pose questions: (1) Why is a bare tuning fork such a weak emitter of sound? (2) What is the role of the…

  18. Linking habitat quality with trophic performance of steelhead along forest gradients in the South Fork Trinity River Watershed, California

    USGS Publications Warehouse

    McCarthy, Sarah G.; Duda, Jeffrey J.; Emlen, John M.; Hodgson, Garth R.; Beauchamp, David A.

    2009-01-01

    We examined invertebrate prey, fish diet, and energy assimilation in relation to habitat variation for steelhead Oncorhynchus mykiss (anadromous rainbow trout) and rainbow trout in nine low-order tributaries of the South Fork Trinity River, northern California. These streams spanned a range of environmental conditions, which allowed us to use bioenergetics modeling to determine the relative effects of forest cover, stream temperature, season, and fish age on food consumption and growth efficiency. Evidence of seasonal shifts in reliance on aquatic versus terrestrial food sources was detected among forest cover categories and fish ages, although these categories were not robust indicators of O. mykiss condition and growth efficiency. Consumption estimates were generally less than 20% of maximum consumption, and fish lost weight in some streams during summer low-flow conditions when stream temperatures exceeded 15°C. Current 100-year climate change projections for California threaten to exacerbate negative growth patterns and may undermine the productivity of this steelhead population, which is currently not listed as endangered or threatened. To demonstrate the potential effect of global warming on fish growth, we ran three climate change scenarios in two representative streams. Simulated temperature increases ranging from 1.4°C to 5.5°C during the summer and from 1.5°C to 2.9C during the winter amplified the weight loss; estimated average growth for age-1 fish was 0.4–4.5 times lower than normal (low to high estimated temperature increase) in the warm stream and 0.05–0.8 times lower in the cool stream. We conclude that feeding rate and temperature during the summer currently limit the growth and productivity of steelhead and rainbow trout in low-order streams in the South Fork Trinity River basin and predict that climate change will have detrimental effects on steelhead growth as well as on macroinvertebrate communities and stream ecosystems in general.

  19. DNA2 drives processing and restart of reversed replication forks in human cells

    PubMed Central

    Thangavel, Saravanabhavan; Berti, Matteo; Levikova, Maryna; Pinto, Cosimo; Gomathinayagam, Shivasankari; Vujanovic, Marko; Zellweger, Ralph; Moore, Hayley; Lee, Eu Han; Hendrickson, Eric A.; Cejka, Petr; Stewart, Sheila; Lopes, Massimo

    2015-01-01

    Accurate processing of stalled or damaged DNA replication forks is paramount to genomic integrity and recent work points to replication fork reversal and restart as a central mechanism to ensuring high-fidelity DNA replication. Here, we identify a novel DNA2- and WRN-dependent mechanism of reversed replication fork processing and restart after prolonged genotoxic stress. The human DNA2 nuclease and WRN ATPase activities functionally interact to degrade reversed replication forks with a 5′-to-3′ polarity and promote replication restart, thus preventing aberrant processing of unresolved replication intermediates. Unexpectedly, EXO1, MRE11, and CtIP are not involved in the same mechanism of reversed fork processing, whereas human RECQ1 limits DNA2 activity by preventing extensive nascent strand degradation. RAD51 depletion antagonizes this mechanism, presumably by preventing reversed fork formation. These studies define a new mechanism for maintaining genome integrity tightly controlled by specific nucleolytic activities and central homologous recombination factors. PMID:25733713

  20. Multiple mechanisms contribute to double-strand break repair at rereplication forks in Drosophila follicle cells

    PubMed Central

    Alexander, Jessica L.; Beagan, Kelly; Orr-Weaver, Terry L.; McVey, Mitch

    2016-01-01

    Rereplication generates double-strand breaks (DSBs) at sites of fork collisions and causes genomic damage, including repeat instability and chromosomal aberrations. However, the primary mechanism used to repair rereplication DSBs varies across different experimental systems. In Drosophila follicle cells, developmentally regulated rereplication is used to amplify six genomic regions, two of which contain genes encoding eggshell proteins. We have exploited this system to test the roles of several DSB repair pathways during rereplication, using fork progression as a readout for DSB repair efficiency. Here we show that a null mutation in the microhomology-mediated end-joining (MMEJ) component, polymerase θ/mutagen-sensitive 308 (mus308), exhibits a sporadic thin eggshell phenotype and reduced chorion gene expression. Unlike other thin eggshell mutants, mus308 displays normal origin firing but reduced fork progression at two regions of rereplication. We also find that MMEJ compensates for loss of nonhomologous end joining to repair rereplication DSBs in a site-specific manner. Conversely, we show that fork progression is enhanced in the absence of both Drosophila Rad51 homologs, spindle-A and spindle-B, revealing homologous recombination is active and actually impairs fork movement during follicle cell rereplication. These results demonstrate that several DSB repair pathways are used during rereplication in the follicle cells and their contribution to productive fork progression is influenced by genomic position and repair pathway competition. Furthermore, our findings illustrate that specific rereplication DSB repair pathways can have major effects on cellular physiology, dependent upon genomic context. PMID:27849606

  1. Note: Enhanced energy harvesting from low-frequency magnetic fields utilizing magneto-mechano-electric composite tuning-fork.

    PubMed

    Yang, Aichao; Li, Ping; Wen, Yumei; Yang, Chao; Wang, Decai; Zhang, Feng; Zhang, Jiajia

    2015-06-01

    A magnetic-field energy harvester using a low-frequency magneto-mechano-electric (MME) composite tuning-fork is proposed. This MME composite tuning-fork consists of a copper tuning fork with piezoelectric Pb(Zr(1-x)Ti(x))O3 (PZT) plates bonded near its fixed end and with NdFeB magnets attached at its free ends. Due to the resonance coupling between fork prongs, the MME composite tuning-fork owns strong vibration and high Q value. Experimental results show that the proposed magnetic-field energy harvester using the MME composite tuning-fork exhibits approximately 4 times larger maximum output voltage and 7.2 times higher maximum power than the conventional magnetic-field energy harvester using the MME composite cantilever.

  2. Mcm10: A Dynamic Scaffold at Eukaryotic Replication Forks

    PubMed Central

    Baxley, Ryan M.; Bielinsky, Anja-Katrin

    2017-01-01

    To complete the duplication of large genomes efficiently, mechanisms have evolved that coordinate DNA unwinding with DNA synthesis and provide quality control measures prior to cell division. Minichromosome maintenance protein 10 (Mcm10) is a conserved component of the eukaryotic replisome that contributes to this process in multiple ways. Mcm10 promotes the initiation of DNA replication through direct interactions with the cell division cycle 45 (Cdc45)-minichromosome maintenance complex proteins 2-7 (Mcm2-7)-go-ichi-ni-san GINS complex proteins, as well as single- and double-stranded DNA. After origin firing, Mcm10 controls replication fork stability to support elongation, primarily facilitating Okazaki fragment synthesis through recruitment of DNA polymerase-α and proliferating cell nuclear antigen. Based on its multivalent properties, Mcm10 serves as an essential scaffold to promote DNA replication and guard against replication stress. Under pathological conditions, Mcm10 is often dysregulated. Genetic amplification and/or overexpression of MCM10 are common in cancer, and can serve as a strong prognostic marker of poor survival. These findings are compatible with a heightened requirement for Mcm10 in transformed cells to overcome limitations for DNA replication dictated by altered cell cycle control. In this review, we highlight advances in our understanding of when, where and how Mcm10 functions within the replisome to protect against barriers that cause incomplete replication. PMID:28218679

  3. Bioavailability of mercury in East Fork Poplar Creek soils

    SciTech Connect

    Barnett, M.O.; Turner, R.R.

    1995-05-01

    The initial risk assessment for the East Fork Poplar Creek (EFPC) floodplain in Oak Ridge, Tennessee, a superfund site heavily contaminated with mercury, was based upon a reference dose for mercuric chloride, a soluble mercury compound not expected to be present in the floodplain, which is frequently saturated with water. Previous investigations had suggested mercury in the EFPC floodplain was less soluble and therefore less bioavailable than mercuric chloride, possibly making the results of the risk assessment unduly conservative. A bioavailability study, designed to measure the amount of mercury available for absorption in a child`s digestive tract, the most critical risk endpoint and pathway, was performed on twenty soils from the EFPC floodplain. The average percentage of mercury released during the study for the twenty soils was 5.3%, compared to 100% of the compound mercuric chloride subjected to the same conditions. Alteration of the procedure to test additional conditions possible during soil digestion did not appreciably alter the results. Therefore, use of a reference dose for mercuric chloride in the EFPC risk assessment without inclusion of a corresponding bioavailability factor may be unduly conservative.

  4. BIOLOGICAL MONITORING PROGRAM FOR EAST FORK POPLAR CREEK

    SciTech Connect

    ADAMS, S.M.; ASHWOOD, T.L.; BEATY, T.W.; BRANDT, C.C.

    1997-10-24

    In May 1985, a National Pollutant Discharge Elimination System (NPDES) permit was issued for the Oak Ridge Y-12 Plant. As a condition of the permit a Biological Monitoring and Abatement Program (BMAP) was developed to demonstrate that the effluent limitations established for the Y- 12 Plant protect the classified uses of the receiving stream (East Fork Poplar Creek; EFPC), in particular, the growth and propagation of aquatic life (Lear et al. 1989). A second objective of the BMAP is to document the ecological effects resulting from the implementation of a water pollution control program designed to eliminate direct discharges of wastewaters to EFPC and to minimize the inadvertent release of pollutants to the environment. Because of the complex nature of the discharges to EFPC and the temporal and spatial variability in the composition of the discharges, a comprehensive, integrated approach to biological monitoring was developed. A new permit was issued to the Y-12 Plant on April 28, 1995 and became effective on July 1, 1995. Biological monitoring continues to be required under the new permit. The BMAP consists of four major tasks that reflect different but complementary approaches to evaluating the effects of the Y-12 Plant discharges on the aquatic integrity of EFPC. These tasks are (1) toxicity monitoring, (2) biological indicator studies, (3) bioaccumulation studies, and (4) ecological surveys of the periphyton, benthic macroinvertebrate, and fish communities.

  5. Biological monitoring program for East Fork Poplar Creek

    SciTech Connect

    Adams, S.M.; Ashwood, T.L.; Beaty, T.W.; Brandt, C.C.; Christensen, S.W.; Cicerone, D.S.; Greeley, M.S. Jr.; Hill, W.R.; Kszos, L.S.

    1997-04-18

    In May 1985, a National Pollutant Discharge Elimination System (NPDES) permit was issued for the Oak Ridge Y-12 Plant. As a condition of the permit, a Biological Monitoring and Abatement Program (BMAP) was developed to demonstrate that the effluent limitations established for the Y-12 Plant protect the classified uses of the receiving stream (East Fork Poplar Creek; EFPC), in particular, the growth and propagation of aquatic life (Lear et al. 1989). A second objective of the BMAP is to document the ecological effects resulting from the implementation of a water pollution control program designed to eliminate direct discharges of wastewaters to EFPC and to minimize the inadvertent release of pollutants to the environment. Because of the complex nature of the discharges to EFPC and the temporal and spatial variability in the composition of the discharges, a comprehensive, integrated approach to biological monitoring was developed. A new permit was issued to the Y-12 Plant on April 28, 1995 and became effective on July 1, 1995. Biological monitoring continues to be required under the new permit. The BMAP consists of four major tasks that reflect different but complementary approaches to evaluating the effects of the Y-12 Plant discharges on the aquatic integrity of EFPC. These tasks are (1) toxicity monitoring, (2) biological indicator studies, (3) bioaccumulation studies, and (4) ecological surveys of the periphyton, benthic macroinvertebrate, and fish communities.

  6. BIOLOGICAL MONITORING PROGRAM FOR EAST FORK POPLAR CREEK

    SciTech Connect

    ADAMS, S.M.; BEATY, T.W.; BRANDT, C.C.; CHRISTENSEN, S.W.; CICERONE, D.S.

    1998-09-09

    In May 1985, a National Pollutant Discharge Elimination System (NPDES) permit was issued for the Oak Ridge Y-12 Plant. As a condition of the permit, a Biological Monitoring and Abatement Program (BMAP) was developed to demonstrate that the effluent limitations established for the Y-12 Plant protect the classified uses of the receiving stream (East Fork Poplar Creek; EFPC), in particular, the growth and propagation of aquatic life (Lear et al. 1989). A second objective of the BMAP is to document the ecological effects resulting from the implementation of a water pollution control program designed to eliminate direct discharges of wastewaters to EFPC and to minimize the inadvertent release of pollutants to the environment. Because of the complex nature of the discharges to EFPC and the temporal and spatial variability in the composition of the discharges, a comprehensive, integrated approach to biological monitoring was developed. A new permit was issued to the Y-12 Plant on April 28, 1995 and became effective on July 1, 1995. Biological monitoring continues to be required under the new permit. The BMAP consists of four major tasks that reflect different but complementary approaches to evaluating the effects of the Y-12 Plant discharges on the aquatic integrity of EFPC. These tasks are (1) toxicity monitoring, (2) biological indicator studies, (3) bioaccumulation studies, and (4) ecological surveys of the periphyton, benthic macroinvertebrate, and fish communities.

  7. CDK1 phosphorylates WRN at collapsed replication forks

    PubMed Central

    Palermo, Valentina; Rinalducci, Sara; Sanchez, Massimo; Grillini, Francesca; Sommers, Joshua A.; Brosh, Robert M.; Zolla, Lello; Franchitto, Annapaola; Pichierri, Pietro

    2016-01-01

    Regulation of end-processing is critical for accurate repair and to switch between homologous recombination (HR) and non-homologous end joining (NHEJ). End resection is a two-stage process but very little is known about regulation of the long-range resection, especially in humans. WRN participates in one of the two alternative long-range resection pathways mediated by DNA2 or EXO1. Here we demonstrate that phosphorylation of WRN by CDK1 is essential to perform DNA2-dependent end resection at replication-related DSBs, promoting HR, replication recovery and chromosome stability. Mechanistically, S1133 phosphorylation of WRN is dispensable for relocalization in foci but is involved in the interaction with the MRE11 complex. Loss of WRN phosphorylation negatively affects MRE11 foci formation and acts in a dominant negative manner to prevent long-range resection altogether, thereby licensing NHEJ at collapsed forks. Collectively, we unveil a CDK1-dependent regulation of the WRN-DNA2-mediated resection and identify an undescribed function of WRN as a DSB repair pathway switch. PMID:27634057

  8. Quartz tuning-fork oscillations in He II and drag coefficient

    NASA Astrophysics Data System (ADS)

    Gritsenko, I. A.; Zadorozhko, A. A.; Neoneta, A. S.; Chagovets, V. K.; Sheshin, G. A.

    2011-07-01

    The temperature dependencies of drag coefficient for quartz tuning forks of various geometric dimensions, immersed in the He II, were determined experimentally in the temperature range 0.1-3 K. It is identified, that these dependencies are similar, but the values of drag coefficient are different for tuning forks with different geometric dimensions. It is shown, that the obtained specific drag coefficient depends only on the temperature and frequency of vibrations, when the value of drag coefficient is normalized to the surface area of moving tuning-fork prong. The temperature dependencies of normalized drag coefficient for the tuning forks of various dimensions, wire, and microsphere, oscillating in the Не II, are compared. It is shown, that in the ballistic regime of scattering of quasiparticles, these dependencies are identical and have a slope proportional to T4, which is determined by the density of thermal excitations. In the hydrodynamic regime at T > 0.5 K, the behavior of the temperature dependence of specific drag coefficient is affected by the size and frequency of vibrating body. The empirical relation, which allows to describe the behavior of specific drag coefficient for vibrating tuning forks, microsphere, and wire everywhere over the temperature region and at various frequencies, is proposed.

  9. Triplex structures induce DNA double strand breaks via replication fork collapse in NER deficient cells

    PubMed Central

    Kaushik Tiwari, Meetu; Adaku, Nneoma; Peart, Natoya; Rogers, Faye A.

    2016-01-01

    Structural alterations in DNA can serve as natural impediments to replication fork stability and progression, resulting in DNA damage and genomic instability. Naturally occurring polypurine mirror repeat sequences in the human genome can create endogenous triplex structures evoking a robust DNA damage response. Failures to recognize or adequately process these genomic lesions can result in loss of genomic integrity. Nucleotide excision repair (NER) proteins have been found to play a prominent role in the recognition and repair of triplex structures. We demonstrate using triplex-forming oligonucleotides that chromosomal triplexes perturb DNA replication fork progression, eventually resulting in fork collapse and the induction of double strand breaks (DSBs). We find that cells deficient in the NER damage recognition proteins, XPA and XPC, accumulate more DSBs in response to chromosomal triplex formation than NER-proficient cells. Furthermore, we demonstrate that XPC-deficient cells are particularly prone to replication-associated DSBs in the presence of triplexes. In the absence of XPA or XPC, deleterious consequences of triplex-induced genomic instability may be averted by activating apoptosis via dual phosphorylation of the H2AX protein. Our results reveal that damage recognition by XPC and XPA is critical to maintaining replication fork integrity and preventing replication fork collapse in the presence of triplex structures. PMID:27298253

  10. NEK8 regulates DNA damage-induced RAD51 foci formation and replication fork protection

    PubMed Central

    Abeyta, Antonio; Castella, Maria; Jacquemont, Celine; Taniguchi, Toshiyasu

    2017-01-01

    ABSTRACT Proteins essential for homologous recombination play a pivotal role in the repair of DNA double strand breaks, DNA inter-strand crosslinks and replication fork stability. Defects in homologous recombination also play a critical role in the development of cancer and the sensitivity of these cancers to chemotherapy. RAD51, an essential factor for homologous recombination and replication fork protection, accumulates and forms immunocytochemically detectable nuclear foci at sites of DNA damage. To identify kinases that may regulate RAD51 localization to sites of DNA damage, we performed a human kinome siRNA library screen, using DNA damage-induced RAD51 foci formation as readout. We found that NEK8, a NIMA family kinase member, is required for efficient DNA damage-induced RAD51 foci formation. Interestingly, knockout of Nek8 in murine embryonic fibroblasts led to cellular sensitivity to the replication inhibitor, hydroxyurea, and inhibition of the ATR kinase. Furthermore, NEK8 was required for proper replication fork protection following replication stall with hydroxyurea. Loading of RAD51 to chromatin was decreased in NEK8-depleted cells and Nek8-knockout cells. Single-molecule DNA fiber analyses revealed that nascent DNA tracts were degraded in the absence of NEK8 following treatment with hydroxyurea. Consistent with this, Nek8-knockout cells showed increased chromosome breaks following treatment with hydroxyurea. Thus, NEK8 plays a critical role in replication fork stability through its regulation of the DNA repair and replication fork protection protein RAD51. PMID:27892797

  11. South Fork Snake River/Palisades Wildlife Mitigation Project: Environmental assessment

    SciTech Connect

    1995-09-01

    BPA proposes to fund the implementation of the South Fork Snake River Programmatic Management Plan to compensate for losses of wildlife and wildlife habitat due to hydroelectric development at Palisades Dam. The Idaho Department of Fish and Game drafted the plan, which was completed in May 1993. This plan recommends land and conservation easement acquisition and wildlife habitat enhancement measures. These measures would be implemented on selected lands along the South Fork of the Snake River between Palisades Dam and the confluence with the Henry`s Fork, and on portions of the Henry`s Fork located in Bonneville, Madison, and Jefferson Counties, Idaho. BPA has prepared an Environmental Assessment evaluating the proposed project. The EA also incorporates by reference the analyses in the South Fork Snake River Activity/Operations Plan and EA prepared jointly in 1991 by the Bureau of Land Management and the Forest Service. Based on the analysis in the EA, BPA has determined that the proposed action is not a major Federal action significantly affecting the quality of the human environment within the meaning of the National Environmental Policy Act (NEPA) of 1969. Therefore, the preparation of an Environmental Impact Statement (EIS) is not required and BPA is issuing this FONSI.

  12. Biological Monitoring Program for East Fork Poplar Creek

    SciTech Connect

    Adams, S.M.; Christensen, S.W.; Greeley, M.S.jr; Hill, W.R.; Kszos, L.A.; McCarthy, J.F.; Peterson, M.J.; Ryon, M.G.; Smith, J.G.; Southworth, G.R.; Stewart, A.J.

    1998-10-15

    In May 1985, a National Pollutant Discharge Elimination System (NPDES) permit was issued for the Oak Ridge Y-12 Plant. As a condition of the permit, a Biologicai Monitoring and Abatement Program (BMAP) was developed to demonstrate that the effluent limitations established for the Y-12 Plant protect the classified uses of the receiving stream (East Fork Poplar Creek; EFPC), in particular, the growth and propagation of aquatic life (Lear et al. 1989). A second objective of the BMAP is to document the ecological effects resulting from the implementation of a water pollution control program designed to eliminate direct discharges of wastewaters to EFPC and to minimize the inadvertent release of pollutants to the environment. Because of the compiex nature of the discharges to EFPC and the temporal and spatial variability in the composition of the discharges, a comprehensive, integrated approach to biological monitoring was developed. A new permit was issued to the Y-12 Plant on April 28, 1995 and became effective on July 1, 1995. Biological monitoring continues to be required under the new permit. The BMAP consists of four major tasks that reflect different but complementary approaches to evaluating the effects of the Y-12 Plant discharges on the aquatic integrity of EFPC, These tasks are (1) toxicity monitoring, (2) biological indicator studies, (3) bioaccumuiation studies, and (4) ecological surveys of the periphyton, benthic macro invertebrate, and fish communities. Monitoring is currently being conducted at five sites, although sites maybe excluded and/or others added depending upon the specific objectives of the various tasks. Criteria used in selecting the sites include: (1) location of sampling sites used in other studies, (2) known or suspected sources of downstream impacts, (3) proximity to U.S. Department of Energy (DOE) Oak Ridge Reservation (ORR) boundaries, (4) concentration of mercury in the adjacent floodplain, (5) appropriate habitat distribution, and (6

  13. Regional Ecorisk Field investigation, upper Clark Fork River Basin

    SciTech Connect

    Pastorok, R.; LaTier, A.; Ginn, T.

    1995-12-31

    The Regional Ecorisk Field Investigation was conducted at the Clark Fork River Superfund Site (Montana) to evaluate the relationships between plant communities and tailings deposits in riparian habitats and to evaluate food-chain transfer of trace elements to selected wildlife species. Stations were selected to represent a range of vegetation biomass (or cover) values and apparent impact of trace elements, with some areas of lush vegetation, some areas of mostly unvegetated soil (e.g., < 30 percent plant cover), and a gradient in between. For the evaluation of risk to wildlife, bioaccumulation of metals was evaluated in native or naturalized plants, terrestrial invertebrates, and the deer mouse (Peromyscus maniculatus). Potential reproductive effects in the deer mouse were evaluated by direct measurements. For other wildlife species, bioaccumulation data were interpreted in the context of food web exposure models. Total biomass and species richness of riparian plant communities are related to tailings content of soil as indicated by pH and metals concentrations. Risk to populations of omnivorous small mammals such as the deer mouse was not significant. Relative abundance and reproductive condition of the deer mouse were normal, even in areas of high metals enrichment. Based on exposure models and site-specific tissue residue data for dietary species, risk to local populations of predators such as red fox and American kestrel that feed on deer mice and terrestrial invertebrates is not significant. Risk to herbivores related to metals bioaccumulation in plant tissues is not significant. Population level effects in deer and other large wildlife are not expected because of the large home ranges of such species and compensatory demographic factors.

  14. Multiple critical velocities in oscillatory flow of superfluid 4He due to quartz tuning forks

    NASA Astrophysics Data System (ADS)

    Schmoranzer, D.; Jackson, M. J.; Tsepelin, V.; Poole, M.; Woods, A. J.; Človečko, M.; Skrbek, L.

    2016-12-01

    We report recent investigations into the transition to turbulence in superfluid 4He, realized experimentally by measuring the drag forces acting on two custom-made quartz tuning forks with fundamental resonances at 6.5 kHz and 55.5 kHz, in the temperature range 10 mK to 2.17 K. In pure superfluid in the zero temperature limit, three distinct critical velocities were observed with both tuning forks. We discuss the significance of all critical velocities and associate the third critical velocity reported here with the development of large vortical structures in the flow, which thus starts to mimic turbulence in classical fluids. The interpretation of our results is directly linked to previous experimental work with oscillators such as tuning forks, grids, and vibrating wires, focusing on the behavior of purely superfluid 4He at very low temperatures.

  15. Replication Fork Protection Factors Controlling R-Loop Bypass and Suppression

    PubMed Central

    Chang, Emily Yun-Chia; Stirling, Peter C.

    2017-01-01

    Replication–transcription conflicts have been a well-studied source of genome instability for many years and have frequently been linked to defects in RNA processing. However, recent characterization of replication fork-associated proteins has revealed that defects in fork protection can directly or indirectly stabilize R-loop structures in the genome and promote transcription–replication conflicts that lead to genome instability. Defects in essential DNA replication-associated activities like topoisomerase, or the minichromosome maintenance (MCM) helicase complex, as well as fork-associated protection factors like the Fanconi anemia pathway, both appear to mitigate transcription–replication conflicts. Here, we will highlight recent advances that support the concept that normal and robust replisome function itself is a key component of mitigating R-loop coupled genome instability. PMID:28098815

  16. FANCD2 regulates BLM complex functions independently of FANCI to promote replication fork recovery.

    PubMed

    Chaudhury, Indrajit; Sareen, Archana; Raghunandan, Maya; Sobeck, Alexandra

    2013-07-01

    Fanconi Anemia (FA) and Bloom Syndrome share overlapping phenotypes including spontaneous chromosomal abnormalities and increased cancer predisposition. The FA protein pathway comprises an upstream core complex that mediates recruitment of two central players, FANCD2 and FANCI, to sites of stalled replication forks. Successful fork recovery depends on the Bloom's helicase BLM that participates in a larger protein complex ('BLMcx') containing topoisomerase III alpha, RMI1, RMI2 and replication protein A. We show that FANCD2 is an essential regulator of BLMcx functions: it maintains BLM protein stability and is crucial for complete BLMcx assembly; moreover, it recruits BLMcx to replicating chromatin during normal S-phase and mediates phosphorylation of BLMcx members in response to DNA damage. During replication stress, FANCD2 and BLM cooperate to promote restart of stalled replication forks while suppressing firing of new replication origins. In contrast, FANCI is dispensable for FANCD2-dependent BLMcx regulation, demonstrating functional separation of FANCD2 from FANCI.

  17. Maps showing mines, quarries, prospects, and exposures in the Devils Fork Roadless Area, Scott County, Virginia

    USGS Publications Warehouse

    Behum, Paul T.

    1984-01-01

    The Devils Fork Roadless Area is located at the eastern edge of the Appalachian coal region and is within the Cumberland Mountain section of the Appalachian Plateau physiographic province. Most of the area is drained by Devil Fork and its tributaries. Clinch Rock Branch of Straight Creek, Roddy Branch of Valley Creek, and Stinking Creek, all tributary to the Clinch River, drain small fringe tracts. Altitudes range from about 1,550 ft on the lower part of Straight Fork to about 3,490 ft at Cox Place on Little Mountain. Vegetation varies from mixed hardwoods in the uplands to thickets of conifer, rhododendron, and laurel in moist protected areas, as in coves along drainage courses.

  18. Replication Fork Protection Factors Controlling R-Loop Bypass and Suppression.

    PubMed

    Chang, Emily Yun-Chia; Stirling, Peter C

    2017-01-14

    Replication-transcription conflicts have been a well-studied source of genome instability for many years and have frequently been linked to defects in RNA processing. However, recent characterization of replication fork-associated proteins has revealed that defects in fork protection can directly or indirectly stabilize R-loop structures in the genome and promote transcription-replication conflicts that lead to genome instability. Defects in essential DNA replication-associated activities like topoisomerase, or the minichromosome maintenance (MCM) helicase complex, as well as fork-associated protection factors like the Fanconi anemia pathway, both appear to mitigate transcription-replication conflicts. Here, we will highlight recent advances that support the concept that normal and robust replisome function itself is a key component of mitigating R-loop coupled genome instability.

  19. South Fork Clearwater River Habitat Enhancement, Crooked and Red Rivers : Annual Report, 1989.

    SciTech Connect

    Baer, William H.

    1990-01-01

    In 1983, the Nez Perce National Forest and the Bonneville Power Administration entered into an interagency agreement to enhance and improve habitat for two anadromous fish species, spring chinook salmon (Oncorhynchus tshawyscha) and summer steelhead trout (Onchorhyncus mykiss), in the South Fork Clearwater River tributaries. The South Fork Clearwater River was dammed in 1927 for hydroelectric development. Anadromous fish runs were virtually eliminated until the dam was removed in 1962. To complicate the problem, upstream spawning and rearing habitats were severely impacted by dredge and hydraulic mining, road building, timber harvest, and over-grazing. Fish habitat improvement projects under the above contract are being carried out in two major tributaries to the South Fork Clearwater River. Both the Red River and the Crooked River projects began in 1983 and will be completed in 1990. 12 figures., 1 tab.

  20. 76 FR 50171 - Notice of Intent To Prepare an Environmental Impact Statement for the Henrys Fork Salinity...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-12

    ... the Henrys Fork Salinity Control Project Plan, Sweetwater and Uinta Counties, WY; Daggett and Summit... Statement (EIS) for the Henrys Fork Salinity Control Project Plan (SCPP). The NRCS will be the lead agency... Improvements'' alternative assumes a salinity control project will be implemented. Existing financial...

  1. 77 FR 66865 - Record of Decision for the Oil and Gas Management Plan, Big South Fork National River and...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-07

    ... National Park Service Record of Decision for the Oil and Gas Management Plan, Big South Fork National River... (ROD) for the Oil and Gas Management Plan (Plan) for Big South Fork National River and Recreation Area and Obed Wild and Scenic River. On September 5, 2012, the Southeast Regional Director, approved...

  2. 33 CFR 165.552 - Security Zone; Oyster Creek Generation Station, Forked River, Ocean County, New Jersey.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 2 2013-07-01 2013-07-01 false Security Zone; Oyster Creek Generation Station, Forked River, Ocean County, New Jersey. 165.552 Section 165.552 Navigation and Navigable... Coast Guard District § 165.552 Security Zone; Oyster Creek Generation Station, Forked River,...

  3. 33 CFR 165.552 - Security Zone; Oyster Creek Generation Station, Forked River, Ocean County, New Jersey.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 2 2014-07-01 2014-07-01 false Security Zone; Oyster Creek Generation Station, Forked River, Ocean County, New Jersey. 165.552 Section 165.552 Navigation and Navigable... Coast Guard District § 165.552 Security Zone; Oyster Creek Generation Station, Forked River,...

  4. 33 CFR 165.552 - Security Zone; Oyster Creek Generation Station, Forked River, Ocean County, New Jersey.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 2 2012-07-01 2012-07-01 false Security Zone; Oyster Creek Generation Station, Forked River, Ocean County, New Jersey. 165.552 Section 165.552 Navigation and Navigable... Coast Guard District § 165.552 Security Zone; Oyster Creek Generation Station, Forked River,...

  5. HLTF’s Ancient HIRAN Domain Binds 3′-DNA Ends to Drive Replication Fork Reversal

    PubMed Central

    Kile, Andrew C.; Chavez, Diana A.; Bacal, Julien; Eldirany, Sherif; Korzhnev, Dmitry M.; Bezsonova, Irina; Eichman, Brandt F.; Cimprich, Karlene A.

    2015-01-01

    Summary Stalled replication forks are a critical problem for the cell because they can lead to complex genome rearrangements that underlie cell death and disease. Processes such as DNA damage tolerance and replication fork reversal protect stalled forks from these events. A central mediator of these DNA damage responses in humans is the Rad5-related DNA translocase, HLTF. Here, we present biochemical and structural evidence that the HIRAN domain, an ancient and conserved domain found in HLTF and other DNA processing proteins, is a modified oligonucleotide/oligosaccharide (OB) fold that binds to 3′-ssDNA ends. We demonstrate that the HIRAN domain promotes HLTF-dependent fork reversal in vitro, through its interaction with 3′-ssDNA ends found at forks. Finally, we show that HLTF restrains replication fork progression in cells in a HIRAN-dependent manner. These findings establish a mechanism of HLTF-mediated fork reversal and provide insight into the requirement for distinct fork remodeling activities in the cell. PMID:26051180

  6. Integrating Salmon Recovery, Clean Water Act Compliance, Restoration, and Climate Change Impacts in the South Fork Nooksack River

    EPA Science Inventory

    "The South Fork Nooksack River (SFNR) is an important tributary to the Nooksack River, Bellingham Bay, and the Salish Sea. The South Fork Nooksack River comprises one of the 22 independent populations of spring Chinook in the Puget Sound Chinook Evolutionarily Significant Un...

  7. 33 CFR 165.552 - Security Zone; Oyster Creek Generation Station, Forked River, Ocean County, New Jersey.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Security Zone; Oyster Creek Generation Station, Forked River, Ocean County, New Jersey. 165.552 Section 165.552 Navigation and Navigable... Coast Guard District § 165.552 Security Zone; Oyster Creek Generation Station, Forked River,...

  8. 33 CFR 165.552 - Security Zone; Oyster Creek Generation Station, Forked River, Ocean County, New Jersey.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 2 2011-07-01 2011-07-01 false Security Zone; Oyster Creek Generation Station, Forked River, Ocean County, New Jersey. 165.552 Section 165.552 Navigation and Navigable... Coast Guard District § 165.552 Security Zone; Oyster Creek Generation Station, Forked River,...

  9. Recombination occurs within minutes of replication blockage by RTS1 producing restarted forks that are prone to collapse

    PubMed Central

    Nguyen, Michael O; Jalan, Manisha; Morrow, Carl A; Osman, Fekret; Whitby, Matthew C

    2015-01-01

    The completion of genome duplication during the cell cycle is threatened by the presence of replication fork barriers (RFBs). Following collision with a RFB, replication proteins can dissociate from the stalled fork (fork collapse) rendering it incapable of further DNA synthesis unless recombination intervenes to restart replication. We use time-lapse microscopy and genetic assays to show that recombination is initiated within ∼10 min of replication fork blockage at a site-specific barrier in fission yeast, leading to a restarted fork within ∼60 min, which is only prevented/curtailed by the arrival of the opposing replication fork. The restarted fork is susceptible to further collapse causing hyper-recombination downstream of the barrier. Surprisingly, in our system fork restart is unnecessary for maintaining cell viability. Seemingly, the risk of failing to complete replication prior to mitosis is sufficient to warrant the induction of recombination even though it can cause deleterious genetic change. DOI: http://dx.doi.org/10.7554/eLife.04539.001 PMID:25806683

  10. Metamorphism and plutonism around the middle and south forks of the Feather River, California

    USGS Publications Warehouse

    Hietanen, Anna Martta

    1976-01-01

    The area around the Middle and South Forks of the Feather River provides information on metamorphic and igneous processes that bear on the origin of andesitic and granitic magmas in general and on the variation of their potassium content in particular. In the north, the area joins the Pulga and Bucks Lake quadrangles studied previously. Tectonically, this area is situated in the southern part of an arcuate segment of the Nevadan orogenic belt in the northwestern Sierra Nevada. The oldest rocks are metamorphosed calcalkaline island-arc-type andesite, dacite, and sodarhyolite with interbedded tuff layers (the Franklin Canyon Formation), all probably correlative with Devonian rocks in the Klamath Mountains. Younger rocks form a sequence of volcanic, volcaniclastic, and sedimentary rocks including some limestone (The Horseshoe Bend Formation), probably Permian in age. All the volcanic and sedimentary rocks were folded and recrystallized to the greenschist facies during the Nevadan (Jurassic) orogeny and were invaded by monzotonalitic magmas shortly thereafter. A second lineation and metamorphism to the epidote-amphibolite facies developed in a narrow zone around the plutons. In light of the concept of plate tectonics, it is suggested that the early (Devonian?) island-arc-type andesite, dacite, and sodarhyolite (the Franklin Canyon Formation) were derived from the mantle above a Benioff zone by partial melting of peridotite in hydrous conditions. The water was probably derived from an oceanic plate descending to the mantle. Later (Permian?) magmas were mainly basaltic; some discontinuous layers of potassium-rich rhyolite indicate a change into anhydrous conditions and a deeper level of magma generation. The plutonic magmas that invaded the metamorphic rocks at the end of the Jurassic may contain material from the mantle, the subducted oceanic lithosphere, and the downfolded metamorphic rocks. The ratio of partial melts from these three sources may have changed with time

  11. Regulating telomere length from the inside out: the replication fork model

    PubMed Central

    2016-01-01

    Telomere length is regulated around an equilibrium set point. Telomeres shorten during replication and are lengthened by telomerase. Disruption of the length equilibrium leads to disease; thus, it is important to understand the mechanisms that regulate length at the molecular level. The prevailing protein-counting model for regulating telomerase access to elongate the telomere does not explain accumulating evidence of a role of DNA replication in telomere length regulation. Here I present an alternative model: the replication fork model that can explain how passage of a replication fork and regulation of origin firing affect telomere length. PMID:27401551

  12. The Sound Field Around a Tuning Fork and the Role of a Resonance Box

    NASA Astrophysics Data System (ADS)

    Bogacz, Bogdan F.; Pedziwiatr, Antoni T.

    2015-02-01

    Atypical two-tine tuning fork is barely audible when held vibrating at an arm's length. It is enough, however, to touch its base to a table or, better, to a resonance box and the emitted sound becomes much louder. An inquiring student may pose questions: Why is a bare tuning fork such a weak emitter of sound?What is the role of the resonance box?Where does energy connected with larger intensity of emitted acoustic waves come from?

  13. Endonuclease cleavage of blocked replication forks: An indirect pathway of DNA damage from antitumor drug-topoisomerase complexes

    NASA Astrophysics Data System (ADS)

    Hong, George; Kreuzer, Kenneth N.

    2003-04-01

    The cytotoxicity of several important antitumor drugs depends on formation of the covalent topoisomerase-DNA cleavage complex. However, cellular processes such as DNA replication are necessary to convert the cleavage complex into a cytotoxic lesion, but the molecular mechanism of this conversion and the precise nature of the cytotoxic lesion are unknown. Using a bacteriophage T4 model system, we have previously shown that antitumor drug-induced cleavage complexes block replication forks in vivo. In this report, we show that these blocked forks can be cleaved by T4 endonuclease VII to create overt DNA breaks. The accumulation of blocked forks increased in endonuclease VII-deficient infections, suggesting that endonuclease cleavage contributes to fork processing in vivo. Furthermore, purified endonuclease VII cleaved the blocked forks in vitro close to the branch points. These results suggest that an indirect pathway of branched-DNA cleavage contributes to the cytotoxicity of antitumor drugs that target DNA topoisomerases.

  14. Fluvial sediment in Salem Fork watershed, West Virginia

    USGS Publications Warehouse

    Flint, R.F.

    1972-01-01

    Suspended sediment discharged from the 8.32-square-mile Salem Fork study area in Harrison County, W. Va., averaged 3,500 tons per year during the first 4-year period of investigation and 1,770 tons per year during the second 4-year period. The difference as attributed to increased flow control, effected by the completion of detention structures and other conservation measures, the absence of appreciable sediment-producing construction activities, and a reduction of the amounts of rainfall and runoff during the second 4-year period. Particle-size distribution of the suspended sediment discharged from the watershed remained unchanged during the two 4-year periods. Although sand and some silt were deposited in upstream reservoirs, sands and other sediments were evidently entrained in the flow below the reservoirs. During the 7.75-year period, reservoir 11A had a trap efficiency of 88 percent. The average annual sediment yield of subwatershed 11A was 1.31 tons per acre, or 837 tons per square mile. Outflow from reservoir 11A occurred during 81 percent of the investigation 'period, October 1954 to June 1962, and 78 percent of the sediment discharge from the reservoir occurred during less than 6 percent of the investigation period. A comparison of particle-size distribution of inflow sediment with that of outflow sediment revealed that practically all sands and some silts entering reservoir 11A were deposited in the reservoir. Chemical analyses of inflow water and the particle-size analyses suggested that flocculation of fine sediments occurred in the reservoir. Analysis of the sediment data collected at the outflow of reservoir 9 during 1956-62 revealed that the average annual sediment discharge was 128,000 pounds per year. Limited particle-size data suggested that practically no sand was discharged from reservoir 9, even though the inflow contained sand. Average annual inflow to reservoirs 11A and 9 compared favorably with average annual runoff for the entire watershed

  15. EEPD1 Rescues Stressed Replication Forks and Maintains Genome Stability by Promoting End Resection and Homologous Recombination Repair

    PubMed Central

    Wu, Yuehan; Lee, Suk-Hee; Williamson, Elizabeth A.; Reinert, Brian L.; Cho, Ju Hwan; Xia, Fen; Jaiswal, Aruna Shanker; Srinivasan, Gayathri; Patel, Bhavita; Brantley, Alexis; Zhou, Daohong; Shao, Lijian; Pathak, Rupak; Hauer-Jensen, Martin; Singh, Sudha; Kong, Kimi; Wu, Xaiohua; Kim, Hyun-Suk; Beissbarth, Timothy; Gaedcke, Jochen; Burma, Sandeep; Nickoloff, Jac A.; Hromas, Robert A.

    2015-01-01

    Replication fork stalling and collapse is a major source of genome instability leading to neoplastic transformation or cell death. Such stressed replication forks can be conservatively repaired and restarted using homologous recombination (HR) or non-conservatively repaired using micro-homology mediated end joining (MMEJ). HR repair of stressed forks is initiated by 5’ end resection near the fork junction, which permits 3’ single strand invasion of a homologous template for fork restart. This 5’ end resection also prevents classical non-homologous end-joining (cNHEJ), a competing pathway for DNA double-strand break (DSB) repair. Unopposed NHEJ can cause genome instability during replication stress by abnormally fusing free double strand ends that occur as unstable replication fork repair intermediates. We show here that the previously uncharacterized Exonuclease/Endonuclease/Phosphatase Domain-1 (EEPD1) protein is required for initiating repair and restart of stalled forks. EEPD1 is recruited to stalled forks, enhances 5’ DNA end resection, and promotes restart of stalled forks. Interestingly, EEPD1 directs DSB repair away from cNHEJ, and also away from MMEJ, which requires limited end resection for initiation. EEPD1 is also required for proper ATR and CHK1 phosphorylation, and formation of gamma-H2AX, RAD51 and phospho-RPA32 foci. Consistent with a direct role in stalled replication fork cleavage, EEPD1 is a 5’ overhang nuclease in an obligate complex with the end resection nuclease Exo1 and BLM. EEPD1 depletion causes nuclear and cytogenetic defects, which are made worse by replication stress. Depleting 53BP1, which slows cNHEJ, fully rescues the nuclear and cytogenetic abnormalities seen with EEPD1 depletion. These data demonstrate that genome stability during replication stress is maintained by EEPD1, which initiates HR and inhibits cNHEJ and MMEJ. PMID:26684013

  16. Recent sedimentation and surface-water flow patterns on the flood plain of the North Fork Forked Deer River, Dyer County, Tennessee

    USGS Publications Warehouse

    Wolfe, W.J.; Diehl, T.H.

    1993-01-01

    Sedimentation in the 19th and 20th centuries has had a major effect on surface-water drainage conditions along a 7-mile section of the North, Fork Forked Deer River flood plain, Dyer County, Tenn. During the century prior to 1930, 5 to 12 feet of sediment were deposited over much of the flood plain, resulting in channel obstruction and widespread flooding. The estimated bankfull capacity of the natural channel before it was channelized in 19 16 was comparable to the base flow of the river during the 1980's. Ditching of the river between 191i6 and 1;9,21 was followed by reductions in sedimentation rates over parts of the flood plain. However, the effects of sedimentation have persisted. Occlusions along the natural channel of the river have divided this stream reach into a series of sloughs. These sloughs continue to fill with sediment and are surrounded by ponds that have expanded since 1941. Degradation of the North Fork Forked Deer ditch may eventually reduce ponding over much of the flood plain. Active incision of headcuts in both banks of the ditch is enhancing the drainage of widespread ponded areas. These headcuts likely will have limited effect on drainage of most tributaries. The highest recent sedimentation rates, in places more than 0.2 foot per year, are concentrated near the flood-plain margin along tributary streams. In conjunction with beaver dams and debris, ongoing sedimentation has blocked flow in several tributaries, posing a flood hazard to agricultural land near the flood-plain margin. The occluded tributaries likely will continue to overflow unless they are periodically dredged or their sediment loads are reduced.

  17. Channelization and floodplain forests: Impacts of accelerated sedimentation and valley plug formation on floodplain forests of the Middle Fork Forked Deer River, Tennessee, USA

    USGS Publications Warehouse

    Oswalt, S.N.; King, S.L.

    2005-01-01

    We evaluated the severe degradation of floodplain habitats resulting from channelization and concomitant excessive coarse sedimentation on the Middle Fork Forked Deer River in west Tennessee from 2000 to 2003. Land use practices have resulted in excessive sediment in the tributaries and river system eventually resulting in sand deposition on the floodplain, increased overbank flooding, a rise in the groundwater table, and ponding of upstream timber. Our objectives were to: (1) determine the composition of floodplain vegetation communities along the degraded river reach, (2) to isolate relationships among these communities, geomorphic features, and environmental variables and (3) evaluate successional changes based on current stand conditions. Vegetation communities were not specifically associated with predefined geomorphic features; nevertheless, hydrologic and geomorphic processes as a result of channelization have clearly affected vegetation communities. The presence of valley plugs and continued degradation of upstream reaches and tributaries on the impacted study reach has arrested recovery of floodplain plant communities. Historically common species like Liquidambar styraciflua L. and Quercus spp. L. were not important, with importance values (IV) less than 1, and occurred in less than 20% of forested plots, while Acer rubrum L., a disturbance-tolerant species, was the most important species on the site (IV = 78.1) and occurred in 87% of forested plots. The results of this study also indicate that channelization impacts on the Middle Fork Forked Deer River are more temporally and spatially complex than previously described for other river systems. Rehabilitation of this system necessitates a long-term, landscape-scale solution that addresses watershed rehabilitation in a spatially and temporally hierarchical manner. ?? 2005 Elsevier B.V. All rights reserved.

  18. Storm water control plan for the Lower East Fork Poplar Creek Operable Unit, Oak Ridge, Tennessee

    SciTech Connect

    1996-04-01

    This document provides the Environmental Restoration Program with information about the erosion and sediment control, storm water management, maintenance, and reporting and record keeping practices to be employed during Phase II of the remediation project for the Lower East Fork Poplar Creek (LEFPC) Operable Unit.

  19. 75 FR 25197 - Shasta Trinity National Forest, South Fork Management Unit, California Salt Timber Harvest and...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-07

    ... Forest Service Shasta Trinity National Forest, South Fork Management Unit, California Salt Timber Harvest... statement for the Salt Timber Harvest and Fuels Reduction Project (Salt Project). A supplemental environmental impact statement will be prepared for the Salt Project to supplement wildlife management...

  20. Numerical performance analysis of quartz tuning fork-based force sensors

    NASA Astrophysics Data System (ADS)

    Dagdeviren, Omur E.; Schwarz, Udo D.

    2017-01-01

    Quartz tuning fork-based force sensors where one prong is immobilized onto a holder while the other one is allowed to oscillate freely (‘qPlus’ configuration) are in widespread use for high-resolution scanning probe microscopy applications. Due to the small size of the tuning forks (≈3 mm) and the complexity of the sensor assemblies, the reliable and repeatable manufacturing of the sensors has been challenging. In this paper, we investigate the contribution of the amount and location of the epoxy glue used to attach the tuning fork to its holder on the sensor’s performance. Towards this end, we use finite element analysis to model the entire sensor assembly and to perform static and dynamic numerical simulations. Our analysis reveals that increasing the thickness of the epoxy layer between prong and holder results in a decrease of the sensor’s spring constant, eigenfrequency, and quality factor while showing an increasing deviation from oscillation in its primary modal shape. Adding epoxy at the sides of the tuning fork also leads to a degradation of the quality factor even though in this case, spring constant and eigenfrequency rise in tandem with a lessening of the deviation from its ideal modal shape.

  1. NUTRIENT CONCENTRATIONS IN FLOWING WATERS OF THE SOUTH FORK BROAD RIVER, GEORGIA WATERSHED

    EPA Science Inventory

    The South Fork Broad River (SFBR) drains about 635 km2 of the Georgia Piedmont. The SFBR watershed is primarily rural and undeveloped although the human population increased by about 25% between 1990 and 2000. Forestry and agriculture are the main land uses. Agriculture consis...

  2. Human HLTF mediates postreplication repair by its HIRAN domain-dependent replication fork remodelling

    PubMed Central

    Achar, Yathish Jagadheesh; Balogh, David; Neculai, Dante; Juhasz, Szilvia; Morocz, Monika; Gali, Himabindu; Dhe-Paganon, Sirano; Venclovas, Česlovas; Haracska, Lajos

    2015-01-01

    Defects in the ability to respond properly to an unrepaired DNA lesion blocking replication promote genomic instability and cancer. Human HLTF, implicated in error-free replication of damaged DNA and tumour suppression, exhibits a HIRAN domain, a RING domain, and a SWI/SNF domain facilitating DNA-binding, PCNA-polyubiquitin-ligase, and dsDNA-translocase activities, respectively. Here, we investigate the mechanism of HLTF action with emphasis on its HIRAN domain. We found that in cells HLTF promotes the filling-in of gaps left opposite damaged DNA during replication, and this postreplication repair function depends on its HIRAN domain. Our biochemical assays show that HIRAN domain mutant HLTF proteins retain their ubiquitin ligase, ATPase and dsDNA translocase activities but are impaired in binding to a model replication fork. These data and our structural study indicate that the HIRAN domain recruits HLTF to a stalled replication fork, and it also provides the direction for the movement of the dsDNA translocase motor domain for fork reversal. In more general terms, we suggest functional similarities between the HIRAN, the OB, the HARP2, and other domains found in certain motor proteins, which may explain why only a subset of DNA translocases can carry out fork reversal. PMID:26350214

  3. NUTRIENT CONCENTRATIONS IN FLOWING WATERS OF THE SOUTH FORK BROAD RIVER, GEORGIA WATERSHED

    EPA Science Inventory

    We monitored concentrations of nutrients, dissolved organic matter (DOM) and other parameters in 17 headwater streams, at three sites on the main stem, and in three major tributaries near their confluence with the South Fork Broad River on a monthly basis for over a year. Concent...

  4. East Fork Watershed Cooperative: Toward better system-scale watershed management

    EPA Science Inventory

    The East Fork Watershed Cooperative is a group intent on understanding how to best manage water quality in a large mixed-use Midwestern watershed system. The system contains a reservoir that serves as a source of drinking water and is popular for water recreation. The reservoir i...

  5. Mammalian RAD52 Functions in Break-Induced Replication Repair of Collapsed DNA Replication Forks.

    PubMed

    Sotiriou, Sotirios K; Kamileri, Irene; Lugli, Natalia; Evangelou, Konstantinos; Da-Ré, Caterina; Huber, Florian; Padayachy, Laura; Tardy, Sebastien; Nicati, Noemie L; Barriot, Samia; Ochs, Fena; Lukas, Claudia; Lukas, Jiri; Gorgoulis, Vassilis G; Scapozza, Leonardo; Halazonetis, Thanos D

    2016-12-15

    Human cancers are characterized by the presence of oncogene-induced DNA replication stress (DRS), making them dependent on repair pathways such as break-induced replication (BIR) for damaged DNA replication forks. To better understand BIR, we performed a targeted siRNA screen for genes whose depletion inhibited G1 to S phase progression when oncogenic cyclin E was overexpressed. RAD52, a gene dispensable for normal development in mice, was among the top hits. In cells in which fork collapse was induced by oncogenes or chemicals, the Rad52 protein localized to DRS foci. Depletion of Rad52 by siRNA or knockout of the gene by CRISPR/Cas9 compromised restart of collapsed forks and led to DNA damage in cells experiencing DRS. Furthermore, in cancer-prone, heterozygous APC mutant mice, homozygous deletion of the Rad52 gene suppressed tumor growth and prolonged lifespan. We therefore propose that mammalian RAD52 facilitates repair of collapsed DNA replication forks in cancer cells.

  6. 76 FR 46721 - Salmon-Challis National Forest, ID; Upper North Fork HFRA Ecosystem Restoration Project...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-03

    ... County and the State of Idaho. Lemhi County's Wildfire Prevention Plan has designated the North Fork... the potential for large-scale, high-intensity wildfires that threaten human life, property, and... uncharacteristic high-intensity wildfires and landscape restoration needs in the project. It is important...

  7. Inferring Causes of Biological Impairment in the Clear Fork Watershed, West Virginia (Final)

    EPA Science Inventory

    The Clear Fork, WV case study illustrates a causal assessment in a watershed using the USEPA stressor identification process described on www.epa.gov/caddis. This case study demonstrates that a watershed-wide causal assessment has several advantages for making analysis practical,...

  8. 78 FR 74005 - Amendment of Class D and Class E Airspace; Grand Forks, ND

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-10

    ... MSL within a 4.2-mile radius of Grand Forks International Airport. This Class D airspace area is... airspace extending upward from the surface to and including 3,400 feet MSL within a 4.9-mile radius of....9-mile radius to 5.6 miles south of the airport, excluding that airspace within the Grand...

  9. A chloroplast DNA helicase II from pea that prefers fork-like replication structures

    PubMed

    Tuteja; Phan

    1998-11-01

    A DNA helicase, called chloroplast DNA (ctDNA) helicase II, was purified to apparent homogeneity from pea (Pisum sativum). The enzyme contained intrinsic, single-stranded, DNA-dependent ATPase activity and an apparent molecular mass of 78 kD on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The DNA helicase was markedly stimulated by DNA substrates with fork-like replication structures. A 5'-tailed fork was more active than the 3'-tailed fork, which itself was more active than substrates without a fork. The direction of unwinding was 3' to 5' along the bound strand, and it failed to unwind blunt-ended duplex DNA. DNA helicase activity required only ATP or dATP hydrolysis. The enzyme also required a divalent cation (Mg2+>Mn2+>Ca2+) for its unwinding activity and was inhibited at 200 mM KCl or NaCl. This enzyme could be involved in the replication of ctDNA. The DNA major groove-intercalating ligands nogalamycin and daunorubicin were inhibitory to unwinding (Ki approximately 0.85 &mgr;M and 2.2 &mgr;M, respectively) and ATPase (Ki approximately 1.3 &mgr;M and 3.0 &mgr;M, respectively) activities of pea ctDNA helicase II, whereas ellipticine, etoposide (VP-16), and camptothecin had no effect on the enzyme activity. These ligands may be useful in further studies of the mechanisms of chloroplast helicase activities.

  10. Inferring Causes of Biological Impairment in the Clear Fork Watershed, West Virginia (Final)

    EPA Science Inventory

    EPA announced the availability of the final report, Inferring Causes of Biological Impairment in the Clear Fork Watershed, West Virginia. This study illustrates a causal assessment in a watershed using the US EPA stressor identification process described on the www.epa....

  11. Double Moutain Fork Brazos River between Lubbock and Buffalo Lakes, Texas

    USGS Publications Warehouse

    Joerns, J.O.

    1955-01-01

    The purpose of this investigation was to study quantity, quality, and possible sources of the low flow and spring inflow of the Double Mountain Fork of the Brazos River between the Lubbock sewage disposal plant, 3 miles southeast of Lubbock, and a County Road crossing about 15 miles downstream and 4.2 miles northeast of Slaton, Lubbock County (fig. 1).

  12. Human HLTF mediates postreplication repair by its HIRAN domain-dependent replication fork remodelling

    DOE PAGES

    Achar, Yathish Jagadheesh; Balogh, David; Neculai, Dante; ...

    2015-09-08

    Defects in the ability to respond properly to an unrepaired DNA lesion blocking replication promote genomic instability and cancer. Human HLTF, implicated in error-free replication of damaged DNA and tumour suppression, exhibits a HIRAN domain, a RING domain, and a SWI/SNF domain facilitating DNA-binding, PCNA-polyubiquitin-ligase, and dsDNA-translocase activities, respectively. Here, we investigate the mechanism of HLTF action with emphasis on its HIRAN domain. We found that in cells HLTF promotes the filling-in of gaps left opposite damaged DNA during replication, and this postreplication repair function depends on its HIRAN domain. Our biochemical assays show that HIRAN domain mutant HLTF proteinsmore » retain their ubiquitin ligase, ATPase and dsDNA translocase activities but are impaired in binding to a model replication fork. These data and our structural study indicate that the HIRAN domain recruits HLTF to a stalled replication fork, and it also provides the direction for the movement of the dsDNA translocase motor domain for fork reversal. We suggest functional similarities between the HIRAN, the OB, the HARP2, and other domains found in certain motor proteins, which may explain why only a subset of DNA translocases can carry out fork reversal.« less

  13. EFFECTS OF HABITAT DEGRADATION ON BIOLOGICAL ENDPOINTS IN THE SOUTH FORK BROAD RIVER BASIN, GEORGIA

    EPA Science Inventory

    Many of the streams of the lower Piedmont ecoregion in Georgia have been negatively impacted to some degree by habitat degradation due primarily to sedimentation. The South Fork of the Broad River watershed has been designated as sediment impacted under Section 303(d) of the Clea...

  14. LIFE HISTORY MONITORING OF SALMONIDS IN THE WEST FORK SMITH RIVER, UMPQUA BASIN, OREGON

    EPA Science Inventory

    As a life-cycle monitoring basin for the Oregon Salmon Plan, the Oregon Department of Fish and Wildlife has estimated adult returns, distribution and smolt outmigration of coho, chinook and winter steelhead in the West Fork Smith River since 1998. In 2001/2002, the Environmenta...

  15. 16 CFR Figure 1 to Part 1512 - Bicycle Front Fork Cantilever Bending Test Rig

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 16 Commercial Practices 2 2014-01-01 2014-01-01 false Bicycle Front Fork Cantilever Bending Test Rig 1 Figure 1 to Part 1512 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION FEDERAL HAZARDOUS SUBSTANCES ACT REGULATIONS REQUIREMENTS FOR BICYCLES Pt. 1512, Fig. 1 Figure 1 to Part 1512—Bicycle...

  16. 16 CFR Figure 1 to Part 1512 - Bicycle Front Fork Cantilever Bending Test Rig

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 16 Commercial Practices 2 2011-01-01 2011-01-01 false Bicycle Front Fork Cantilever Bending Test Rig 1 Figure 1 to Part 1512 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION FEDERAL HAZARDOUS SUBSTANCES ACT REGULATIONS REQUIREMENTS FOR BICYCLES Pt. 1512, Fig. 1 Figure 1 to Part 1512—Bicycle...

  17. 16 CFR Figure 1 to Part 1512 - Bicycle Front Fork Cantilever Bending Test Rig

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 16 Commercial Practices 2 2012-01-01 2012-01-01 false Bicycle Front Fork Cantilever Bending Test Rig 1 Figure 1 to Part 1512 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION FEDERAL HAZARDOUS SUBSTANCES ACT REGULATIONS REQUIREMENTS FOR BICYCLES Pt. 1512, Fig. 1 Figure 1 to Part 1512—Bicycle...

  18. 16 CFR Figure 1 to Part 1512 - Bicycle Front Fork Cantilever Bending Test Rig

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 16 Commercial Practices 2 2013-01-01 2013-01-01 false Bicycle Front Fork Cantilever Bending Test Rig 1 Figure 1 to Part 1512 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION FEDERAL HAZARDOUS SUBSTANCES ACT REGULATIONS REQUIREMENTS FOR BICYCLES Pt. 1512, Fig. 1 Figure 1 to Part 1512—Bicycle...

  19. 16 CFR Figure 1 to Part 1512 - Bicycle Front Fork Cantilever Bending Test Rig

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 16 Commercial Practices 2 2010-01-01 2010-01-01 false Bicycle Front Fork Cantilever Bending Test Rig 1 Figure 1 to Part 1512 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION FEDERAL HAZARDOUS SUBSTANCES ACT REGULATIONS REQUIREMENTS FOR BICYCLES Pt. 1512, Fig. 1 Figure 1 to Part 1512—Bicycle...

  20. Archaeal Hel308 helicase targets replication forks in vivo and in vitro and unwinds lagging strands.

    PubMed

    Guy, Colin P; Bolt, Edward L

    2005-01-01

    Mutations in mammalian and Drosophila Hel308 and PolQ paralogues cause genome instability but their helicase functions are mysterious. By in vivo and in vitro analysis, we show that Hel308 from archaea (Hel308a) may act at stalled replication forks. Introducing hel308a into Escherichia coli dnaE strains that conditionally accumulate stalled forks caused synthetic lethality, an effect indistinguishable from E.coli RecQ. Further analysis in vivo indicated that the effect of hel308a is exerted independently of homologous recombination. The minimal biochemical properties of Hel308a protein were the same as human Hel308. We describe how helicase actions of Hel308a at fork structures lead specifically to displacement of lagging strands. The invading strand of D-loops is also targeted. Using archaeal Hel308, we propose models of action for the helicase domain of PolQ, promoting loading of the translesion polymerase domain. We speculate that removal of lagging strands at stalled forks by Hel308 promotes the formation of initiation zones, priming restart of lagging strand synthesis.

  1. Risks at the DNA Replication Fork: Effects upon Carcinogenesis and Tumor Heterogeneity

    PubMed Central

    Mertz, Tony M.; Harcy, Victoria; Roberts, Steven A.

    2017-01-01

    The ability of all organisms to copy their genetic information via DNA replication is a prerequisite for cell division and a biological imperative of life. In multicellular organisms, however, mutations arising from DNA replication errors in the germline and somatic cells are the basis of genetic diseases and cancer, respectively. Within human tumors, replication errors additionally contribute to mutator phenotypes and tumor heterogeneity, which are major confounding factors for cancer therapeutics. Successful DNA replication involves the coordination of many large-scale, complex cellular processes. In this review, we focus on the roles that defects in enzymes that normally act at the replication fork and dysregulation of enzymes that inappropriately damage single-stranded DNA at the fork play in causing mutations that contribute to carcinogenesis. We focus on tumor data and experimental evidence that error-prone variants of replicative polymerases promote carcinogenesis and on research indicating that the primary target mutated by APOBEC (apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like) cytidine deaminases is ssDNA present at the replication fork. Furthermore, we discuss evidence from model systems that indicate replication stress and other cancer-associated metabolic changes may modulate mutagenic enzymatic activities at the replication fork. PMID:28117753

  2. Human HLTF mediates postreplication repair by its HIRAN domain-dependent replication fork remodelling

    SciTech Connect

    Achar, Yathish Jagadheesh; Balogh, David; Neculai, Dante; Juhasz, Szilvia; Morocz, Monika; Gali, Himabindu; Dhe-Paganon, Sirano; Venclovas, Česlovas; Haracska, Lajos

    2015-09-08

    Defects in the ability to respond properly to an unrepaired DNA lesion blocking replication promote genomic instability and cancer. Human HLTF, implicated in error-free replication of damaged DNA and tumour suppression, exhibits a HIRAN domain, a RING domain, and a SWI/SNF domain facilitating DNA-binding, PCNA-polyubiquitin-ligase, and dsDNA-translocase activities, respectively. Here, we investigate the mechanism of HLTF action with emphasis on its HIRAN domain. We found that in cells HLTF promotes the filling-in of gaps left opposite damaged DNA during replication, and this postreplication repair function depends on its HIRAN domain. Our biochemical assays show that HIRAN domain mutant HLTF proteins retain their ubiquitin ligase, ATPase and dsDNA translocase activities but are impaired in binding to a model replication fork. These data and our structural study indicate that the HIRAN domain recruits HLTF to a stalled replication fork, and it also provides the direction for the movement of the dsDNA translocase motor domain for fork reversal. We suggest functional similarities between the HIRAN, the OB, the HARP2, and other domains found in certain motor proteins, which may explain why only a subset of DNA translocases can carry out fork reversal.

  3. Structure of the replication fork in ultraviolet light-irradiated human cells.

    PubMed Central

    Cordeiro-Stone, M; Schumacher, R I; Meneghini, R

    1979-01-01

    The DNA extracted from xeroderma pigmentosum human fibroblasts previously irradiated with 12.5 J/m2 of UV light and pulse-labeled for 45 min with radioactive and (or) heavy precursors, was used to determine the structural characteristics of the replication fork. Density equilibrium centrifugation experiments showed that a fork moved 6 micrometer in 45 min and bypassed 3 pyrimidine dimers in both strands. The same length was covered in 15-20 min in control cells. The delay in irradiated cells was apparently due to pyrimidine dimers acting as temporary blocks to the fork movement. Evidence for this interpretation comes from kinetics of incorporation of [3H]thymidine into DNA, which show that the time necessary to attain a new stable level of DNA synthesis in irradiated cells is equivalent to that required for the replication fork to cover the interdimer distance in one strand. On the other hand, the action of S1 nuclease on DNA synthesized soon after irradiation gives rise to a bimodal distribution in neutral sucrose gradients, one peak corresponding to 43 X 10(6) daltons and the other to 3 X 10(6) daltons. These two DNA species are generated by the attack of the S1 nuclease on single-stranded regions associated with the replication fork. A possible explanation for these results is given by a model according to which there is a delayed bypass of the dimer in the leading strand and the appearance of gaps opposite pyrimidine dimers in the lagging strand, as a direct consequence of the discontinuous mode of DNA replication. In terms of the model, the DNA of 43 X 10(6) daltons corresponds to the leading strand, linked to the unreplicated branch of the forks, whereas the piece of 3 X 10(6) daltons is the intergap DNA coming from the lagging strand. Pulse and chase experiments reveal that the low molecular weight DNA grows in a pattern that suggests that more than one gap may be formed per replication fork. PMID:233582

  4. Dissolved-Solids Load in Henrys Fork Upstream from the Confluence with Antelope Wash, Wyoming, Water Years 1970-2009

    USGS Publications Warehouse

    Foster, Katharine; Kenney, Terry A.

    2010-01-01

    Annual dissolved-solids load at the mouth of Henrys Fork was estimated by using data from U.S. Geological Survey streamflow-gaging station 09229500, Henrys Fork near Manila, Utah. The annual dissolved-solids load for water years 1970-2009 ranged from 18,300 tons in 1977 to 123,300 tons in 1983. Annual streamflows for this period ranged from 14,100 acre-feet in 1977 to 197,500 acre-feet in 1983. The 25-percent trimmed mean dissolved-solids load for water years 1970-2009 was 44,300 tons per year at Henrys Fork near Manila, Utah. Previous simulations using a SPAtially Referenced Regression On Watershed attributes (SPARROW) model for dissolved solids specific to water year 1991 conditions in the Upper Colorado River Basin predicted an annual dissolved-solids load of 25,000 tons for the Henrys Fork Basin upstream from Antelope Wash. On the basis of computed dissolved-solids load data from Henrys Fork near Manila, Utah, together with estimated annual dissolved-solids load from Antelope Wash and Peoples Canal, this prediction was adjusted to 37,200 tons. As determined by simulations with the Upper Colorado River Basin SPARROW model, approximately 56 percent (14,000 tons per year) of the dissolved-solids load at Henrys Fork upstream from Antelope Wash is associated with the 21,500 acres of irrigated agricultural lands in the upper Henrys Fork Basin.

  5. Mechanism of chromosomal DNA replication initiation and replication fork stabilization in eukaryotes.

    PubMed

    Wu, LiHong; Liu, Yang; Kong, DaoChun

    2014-05-01

    Chromosomal DNA replication is one of the central biological events occurring inside cells. Due to its large size, the replication of genomic DNA in eukaryotes initiates at hundreds to tens of thousands of sites called DNA origins so that the replication could be completed in a limited time. Further, eukaryotic DNA replication is sophisticatedly regulated, and this regulation guarantees that each origin fires once per S phase and each segment of DNA gets duplication also once per cell cycle. The first step of replication initiation is the assembly of pre-replication complex (pre-RC). Since 1973, four proteins, Cdc6/Cdc18, MCM, ORC and Cdt1, have been extensively studied and proved to be pre-RC components. Recently, a novel pre-RC component called Sap1/Girdin was identified. Sap1/Girdin is required for loading Cdc18/Cdc6 to origins for pre-RC assembly in the fission yeast and human cells, respectively. At the transition of G1 to S phase, pre-RC is activated by the two kinases, cyclindependent kinase (CDK) and Dbf4-dependent kinase (DDK), and subsequently, RPA, primase-polα, PCNA, topoisomerase, Cdc45, polδ, and polɛ are recruited to DNA origins for creating two bi-directional replication forks and initiating DNA replication. As replication forks move along chromatin DNA, they frequently stall due to the presence of a great number of replication barriers on chromatin DNA, such as secondary DNA structures, protein/DNA complexes, DNA lesions, gene transcription. Stalled forks must require checkpoint regulation for their stabilization. Otherwise, stalled forks will collapse, which results in incomplete DNA replication and genomic instability. This short review gives a concise introduction regarding the current understanding of replication initiation and replication fork stabilization.

  6. Life-history notes on Cambarus hubbsi creaser (Hubbs crayfish) from the South Fork Spring River, Arkansas

    USGS Publications Warehouse

    Larson, E.R.; Magoulick, Daniel D.

    2011-01-01

    Many crayfish species native to the southeastern United States are imperiled due to small range sizes and anthropogenic impacts such as habitat loss and introduction of non-native species. Furthermore, effective management of crayfish is limited by the scarcity of life-history and ecological data for many of these species. We report results of the first life-history study of the crayfish Cambarus hubbsi (Hubbs Crayfish). We collected 466 Hubbs Crayfish from the South Fork Spring River, AR throughout 2006 and recorded carapace lengths, wet weights, indicators of reproductive activity, and number of eggs on ovigerous females. Using length-frequency distributions, we identified four Hubbs Crayfish age classes and evaluated growth rates by plotting size by season (winter, spring, summer, autumn). Male Hubbs Crayfish were more common than females in all seasons except autumn, and males weighed more at equivalent lengths than females. Reproductive activity in Hubbs Crayfish peaked in late winter and spring, and ovigerous females were collected in March, April, and June. Ovigerous females were age II or III and carried few eggs relative to co-occurring crayfish of the genus Orconectes. Compared to these Orconectes species, Hubbs Crayfish is comparatively slow growing, long lived, with low reproductive potential, and as a result may be categorized as a K life-history strategist. Based on this species' life-history strategy and previously documented habitat specificity and taxonomic distinctiveness, Hubbs Crayfish may require monitoring and management attention normally reserved for species with smaller ranges.

  7. Seasonal Alterations in Park Visitation, Amenity Use, and Physical Activity — Grand Forks, North Dakota, 2012–2013

    PubMed Central

    Johnson, LuAnn

    2014-01-01

    Introduction Park amenities promote visitation and physical activity during summer. Physical activity declines during winter. Identifying park amenities that promote visitation during winter would increase year-round activity. The purpose of this study was to determine how park visitation, amenity choice, and physical activity intensity change across seasons. Methods Physical activity intensity of children and adults was assessed at 16 parks in Grand Forks, North Dakota, during summer and fall of 2012, and winter and spring of 2013. Results Park visitation was highest in spring and lowest in winter. Amenity use varied by season. Parks with water splash pads were visited more during summer, and playgrounds and open spaces were visited more during spring. Ice rinks were visited most in winter. Physical activity intensity was lowest in summer and highest in winter for each age group. The activity intensity observed for all young age groups ranged from 2.7 to 2.9 metabolic equivalents in summer and greater than 3 metabolic equivalents in all other seasons. Adults’ mean activity intensity was greater than 3 metabolic equivalents in winter. Conclusion Information on park visitation, amenity use, and activity intensity across seasons is valuable; it can be used when designing or redesigning parks in order to promote year-round physical activity. Redesigning parks in cold climates to include ice rinks, sledding hills, cross-country skiing, and indoor areas for physical activity would increase winter visitation and allow the park to serve as a year-round resource for physical activity. PMID:25211503

  8. Directionality of replication fork movement determined by two-dimensional native-native DNA agarose gel electrophoresis.

    PubMed

    Ivessa, Andreas S

    2013-01-01

    The analysis of replication intermediates by the neutral-neutral two-dimensional agarose gel technique allows determining the chromosomal positions where DNA replication initiates, whether replication forks pause or stall at specific sites, or whether two DNA molecules undergo DNA recombination events. This technique does not, however, immediately tell in which direction replication forks migrate through the DNA region under investigation. Here, we describe the procedure to determine the direction of replication fork progression by carrying out a restriction enzyme digest of DNA imbedded in agarose after the completion of the first dimension of a 2D gel.

  9. Evaluation of Lower East Fork Poplar Creek Mercury Sources

    SciTech Connect

    Watson, David B.; Brooks, Scott C.; Mathews, Teresa J.; Bevelhimer, Mark S.; DeRolph, Chris; Brandt, Craig C.; Peterson, Mark J.; Ketelle, Richard

    2016-06-01

    This report summarizes a 3-year research project undertaken to better understand the nature and magnitude of mercury (Hg) fluxes in East Fork Poplar Creek (EFPC). This project addresses the requirements of Action Plan 1 in the 2011 Oak Ridge Reservation-wide Comprehensive Environmental Response, Compensation, and Liability Act Five Year Review (FYR). The Action Plan is designed to address a twofold 2011 FYR issue: (1) new information suggests mobilization of mercury from the upper and lower EFPC streambeds and stream banks is the primary source of mercury export during high-flow conditions, and (2) the current Record of Decision did not address the entire hydrologic system and creek bank or creek bed sediments. To obtain a more robust watershed-scale understanding of mercury sources and processes in lower EFPC (LEFPC), new field and laboratory studies were coupled with existing data from multiple US Department of Energy programs to develop a dynamic watershed and bioaccumulation model. LEFPC field studies for the project focused primarily on quantification of streambank erosion and an evaluation of mercury dynamics in shallow groundwater adjacent to LEFPC and potential connection to the surface water. The approach to the stream bank study was innovative in using imagery from kayak floats’ surveys from the headwaters to the mouth of EFPC to estimate erosion, coupled with detailed bank soil mercury analyses. The goal of new field assessments and modeling was to generate a more holistic and quantitative understanding of the watershed and the sources, flux, concentration, transformation, and bioaccumulation of inorganic mercury (IHg) and methylmercury (MeHg). Model development used a hybrid approach that dynamically linked a spreadsheet-based physical and chemical watershed model to a systems dynamics, mercury bioaccumulation model for key fish species. The watershed model tracks total Hg and MeHg fluxes and concentrations by examining upstream inputs, floodplain

  10. Flood-inundation maps for the East Fork White River at Columbus, Indiana

    USGS Publications Warehouse

    Lombard, Pamela J.

    2013-01-01

    Digital flood-inundation maps for a 5.4-mile reach of the East Fork White River at Columbus, Indiana, from where the Flatrock and Driftwood Rivers combine to make up East Fork White River to just upstream of the confluence of Clifty Creek with the East Fork White River, were created by the U.S. Geological Survey (USGS) in cooperation with the Indiana Department of Transportation. The inundation maps, which can be accessed through the USGS Flood Inundation Mapping Science Web site at http://water.usgs.gov/osw/flood_inundation, depict estimates of the areal extent of flooding corresponding to selected water levels (stages) at USGS streamgage 03364000, East Fork White River at Columbus, Indiana. Current conditions at the USGS streamgage may be obtained on the Internet from the USGS National Water Information System (http://waterdata.usgs.gov/in/nwis/uv/?site_no=03364000&agency_cd=USGS&). The National Weather Service (NWS) forecasts flood hydrographs for the East Fork White River at Columbus, Indiana at their Advanced Hydrologic Prediction Service (AHPS) flood warning system Website (http://water.weather.gov/ahps/), that may be used in conjunction with the maps developed in this study to show predicted areas of flood inundation. In this study, flood profiles were computed for the stream reach by means of a one-dimensional step-backwater model. The hydraulic model was calibrated by using the most current stage-discharge relation at USGS streamgage 03364000, East Fork White River at Columbus, Indiana. The calibrated hydraulic model was then used to determine 15 water-surface profiles for flood stages at 1-foot (ft) intervals referenced to the streamgage datum and ranging from bankfull to approximately the highest recorded water level at the streamgage. The simulated water-surface profiles were then combined with a geographic information system digital elevation model (derived from Light Detection and Ranging (LiDAR) data), having a 0.37-ft vertical accuracy and a 1.02 ft

  11. A distinct replication fork protection pathway connects Fanconi anemia tumor suppressors to RAD51-BRCA1/2.

    PubMed

    Schlacher, Katharina; Wu, Hong; Jasin, Maria

    2012-07-10

    Genes mutated in patients with Fanconi anemia (FA) interact with the DNA repair genes BRCA1 and BRCA2/FANCD1 to suppress tumorigenesis, but the molecular functions ascribed to them cannot fully explain all of their cellular roles. Here, we show a repair-independent requirement for FA genes, including FANCD2, and BRCA1 in protecting stalled replication forks from degradation. Fork protection is surprisingly rescued in FANCD2-deficient cells by elevated RAD51 levels or stabilized RAD51 filaments. Moreover, FANCD2-mediated fork protection is epistatic with RAD51 functions, revealing an unanticipated fork protection pathway that connects FA genes to RAD51 and the BRCA1/2 breast cancer suppressors. Collective results imply a unified molecular mechanism for repair-independent functions of FA, RAD51, and BRCA1/2 proteins in preventing genomic instability and suppressing tumorigenesis.

  12. Moonlighting at replication forks - a new life for homologous recombination proteins BRCA1, BRCA2 and RAD51.

    PubMed

    Kolinjivadi, Arun Mouli; Sannino, Vincenzo; de Antoni, Anna; Técher, Hervé; Baldi, Giorgio; Costanzo, Vincenzo

    2017-01-12

    Coordination between DNA replication and DNA repair ensures maintenance of genome integrity, which is lost in cancer cells. Emerging evidence has linked homologous recombination (HR) proteins RAD51, BRCA1 and BRCA2 to the stability of nascent DNA. This function appears to be distinct from double-strand break (DSB) repair and is in part due to the prevention of MRE11-mediated degradation of nascent DNA at stalled forks. The role of RAD51 in fork protection resembles the activity described for its prokaryotic orthologue RecA, which prevents nuclease-mediated degradation of DNA and promotes replication fork restart in cells challenged by DNA-damaging agents. Here, we examine the mechanistic aspects of HR-mediated fork protection, addressing the crosstalk between HR and replication proteins.

  13. Using Caffeine as a Water Quality Indicator in the Ambient Monitoring Program for Third Fork Creek Watershed, Durham, North Carolina

    PubMed Central

    Spence, Porché L

    2015-01-01

    Caffeine has been suggested as a chemical indicator for domestic wastewater in freshwater systems, although it is not included in water quality monitoring programs. The Third Fork Creek watershed in Durham, NC, is highly urbanized, with a history of receiving untreated wastewater from leaking and overflowing sanitary sewers. The poor water quality originating in the Third Fork Creek watershed threatens its intended uses and jeopardizes drinking water, aquatic life, and recreational activities provided by Jordan Lake. Organic waste contaminants have been detected in both Third Fork Creek watershed and Jordan Lake; however, the sampling periods were temporary, resulting in a few samples collected during nonstorm periods. It is recommended that (1) the concentration of caffeine and other organic waste contaminants are determined during storm and nonstorm periods and (2) caffeine is monitored regularly with traditional water quality indicators to evaluate the health of Third Fork Creek watershed. PMID:26157335

  14. FANCD2-controlled chromatin access of the Fanconi-associated nuclease FAN1 is crucial for the recovery of stalled replication forks.

    PubMed

    Chaudhury, Indrajit; Stroik, Daniel R; Sobeck, Alexandra

    2014-11-01

    Fanconi anemia (FA) is a cancer predisposition syndrome characterized by cellular hypersensitivity to DNA interstrand cross-links (ICLs). Within the FA pathway, an upstream core complex monoubiquitinates and recruits the FANCD2 protein to ICLs on chromatin. Ensuing DNA repair involves the Fanconi-associated nuclease 1 (FAN1), which interacts selectively with monoubiquitinated FANCD2 (FANCD2(Ub)) at ICLs. Importantly, FANCD2 has additional independent functions: it binds chromatin and coordinates the restart of aphidicolin (APH)-stalled replication forks in concert with the BLM helicase, while protecting forks from nucleolytic degradation by MRE11. We identified FAN1 as a new crucial replication fork recovery factor. FAN1 joins the BLM-FANCD2 complex following APH-mediated fork stalling in a manner dependent on MRE11 and FANCD2, followed by FAN1 nuclease-mediated fork restart. Surprisingly, APH-induced activation and chromatin recruitment of FAN1 occur independently of the FA core complex or the FAN1 UBZ domain, indicating that the FANCD2(Ub) isoform is dispensable for functional FANCD2-FAN1 cross talk during stalled fork recovery. In the absence of FANCD2, MRE11 exonuclease-promoted access of FAN1 to stalled forks results in severe FAN1-mediated nucleolytic degradation of nascent DNA strands. Thus, FAN1 nuclease activity at stalled replication forks requires tight regulation: too little inhibits fork restart, whereas too much causes fork degradation.

  15. Environmental Assessment - Construct a Ground-to-Air Transmitter and Receiver (GATR) Facility at Grand Forks Air Force Base

    DTIC Science & Technology

    2006-06-06

    are long and severe with almost continuous snow cover. The spring and fall seasons are generally short transition periods. The average annual...the late fall, winter, and spring , and from the southeast during the summer. Grand Forks County is included in the ND Air Quality Control Region...approximately 10 miles northeast of Grand Forks AFB, the mean discharge of the Turtle River is 50.3 feet cubed per second (ft3/s). Peak flows

  16. Hydrologic, water-quality, and biological characteristics of the North Fork Flathead River, Montana, water years 2007-2008

    USGS Publications Warehouse

    Mills, Taylor J.; Schweiger, E. William; Mast, M. Alisa; Clow, David W.

    2012-01-01

    In water year 2007, the U.S. Geological Survey, in cooperation with the National Park Service, began a 2-year study to collect hydrologic, water-quality, and biological data to provide a baseline characterization of the North Fork Flathead River from the United States-Canada border to its confluence with the Middle Fork of the Flathead River near Columbia Falls, Montana. Although mining in the Canadian portion of the North Fork Basin was banned in 2010 by a Memorandum of Understanding issued by the Province of British Columbia, baseline characterization was deemed important for the evaluation of any potential future changes in hydrology, water quality, or aquatic biology in the basin. The North Fork Basin above Columbia Falls (including Canada) drains an area of 1,564 square miles, and the study area encompasses the portion of the basin in Montana, which is 1,126 square miles. Seasonal patterns in the hydrology of the North Fork are dominated by the accumulation and melting of seasonal snowpack in the basin. Low-flow conditions occurred during the late-summer, fall, and winter months, and high-flow conditions coincided with the spring snowmelt. Substantial gains in streamflow occurred along the study reach of the North Fork, 85 percent of which were accounted for by tributary inflows during low-flow conditions, indicating unmeasured streamflow inputs along the main stem were 15 percent or less.

  17. The RecQ DNA helicase Rqh1 constrains Exonuclease 1-dependent recombination at stalled replication forks

    PubMed Central

    Osman, Fekret; Ahn, Jong Sook; Lorenz, Alexander; Whitby, Matthew C.

    2016-01-01

    DNA double-strand break (DSB) repair by homologous recombination (HR) involves resection of the break to expose a 3′ single-stranded DNA tail. In budding yeast, resection occurs in two steps: initial short-range resection, performed by Mre11-Rad50-Xrs2 and Sae2; and long-range resection catalysed by either Exo1 or Sgs1-Dna2. Here we use genetic assays to investigate the importance of Exo1 and the Sgs1 homologue Rqh1 for DNA repair and promotion of direct repeat recombination in the fission yeast Schizosaccharomyces pombe. We find that Exo1 and Rqh1 function in alternative redundant pathways for promoting survival following replication fork breakage. Exo1 promotes replication fork barrier-induced direct repeat recombination but intriguingly limits recombination induced by fork breakage. Direct repeat recombination induced by ultraviolet light depends on either Exo1 or Rqh1. Finally, we show that Rqh1 plays a major role in limiting Exo1-dependent direct repeat recombination induced by replication fork stalling but only a minor role in constraining recombination induced by fork breakage. The implications of our findings are discussed in the context of the benefits that long-range resection may bring to processing perturbed replication forks. PMID:26957021

  18. The RecQ DNA helicase Rqh1 constrains Exonuclease 1-dependent recombination at stalled replication forks.

    PubMed

    Osman, Fekret; Ahn, Jong Sook; Lorenz, Alexander; Whitby, Matthew C

    2016-03-09

    DNA double-strand break (DSB) repair by homologous recombination (HR) involves resection of the break to expose a 3' single-stranded DNA tail. In budding yeast, resection occurs in two steps: initial short-range resection, performed by Mre11-Rad50-Xrs2 and Sae2; and long-range resection catalysed by either Exo1 or Sgs1-Dna2. Here we use genetic assays to investigate the importance of Exo1 and the Sgs1 homologue Rqh1 for DNA repair and promotion of direct repeat recombination in the fission yeast Schizosaccharomyces pombe. We find that Exo1 and Rqh1 function in alternative redundant pathways for promoting survival following replication fork breakage. Exo1 promotes replication fork barrier-induced direct repeat recombination but intriguingly limits recombination induced by fork breakage. Direct repeat recombination induced by ultraviolet light depends on either Exo1 or Rqh1. Finally, we show that Rqh1 plays a major role in limiting Exo1-dependent direct repeat recombination induced by replication fork stalling but only a minor role in constraining recombination induced by fork breakage. The implications of our findings are discussed in the context of the benefits that long-range resection may bring to processing perturbed replication forks.

  19. A rotary pumping model for helicase function of MCM proteins at a distance from replication forks.

    PubMed

    Laskey, Ronald A; Madine, Mark A

    2003-01-01

    We propose an integrated model for eukaryotic DNA replication to explain the following problems: (1) How is DNA spooled through fixed sites of replication? (2) What and where are the helicases that unwind replicating DNA? (3) Why are the best candidates for replicative helicases, namely mini-chromosome maintenance (MCM) proteins, not concentrated at the replication fork? (4) How do MCM proteins spread away from loading sites at origins of replication? We draw on recent discoveries to argue that the MCM hexameric ring is a rotary motor that pumps DNA along its helical axis by simple rotation, such that the movement resembles that of a threaded bolt through a nut, and we propose that MCM proteins act at a distance from the replication fork to unwind DNA. This model would place DNA replication in a growing list of processes, such as recombination and virus packaging, that are mediated by ring-shaped ATPases pumping DNA by helical rotation.

  20. Bend and refractive index sensing based on the tuning fork fiber

    NASA Astrophysics Data System (ADS)

    Sun, Bo; Li, Xuyou; Yu, Yingying; He, Kunpeng

    2015-08-01

    A fiber-optic based on the tuning fork structure is investigated for bend and refractive index (RI). The new bend/RI sensor based on the tuning fork structure is ease of fabrication, low cost, and simple signal acquisition. The operation principle relies on the power coupling of two cores inputted into light simultaneously. The beam-propagation method (BPM) is employed for modeling the propagation of light along the optical fiber sensing device proposed. The simulation results show that it exhibits very high sensitivity, accuracy and wide dynamic range in making curvature and RI measurements. The bending sensitivity is about 0.01184 W/m-1 at curvatures ranging from 0 to 50 m-1, the RI sensitivity is about -1.5557, -22.3031 and -102.44878 W/RIU at refractive indexes ranging from 1.33-1.418, 1.418-1.45 and 1.45-1.456, respectively.

  1. Acute MUS81 depletion leads to replication fork slowing and a constitutive DNA damage response

    PubMed Central

    Xing, Meichun; Wang, Xiaohui; Palmai-Pallag, Timea; Shen, Huahao; Helleday, Thomas; Hickson, Ian D.; Ying, Songmin

    2015-01-01

    The MUS81 protein belongs to a conserved family of DNA structure-specific nucleases that play important roles in DNA replication and repair. Inactivation of the Mus81 gene in mice has no major deleterious consequences for embryonic development, although cancer susceptibility has been reported. We have investigated the role of MUS81 in human cells by acutely depleting the protein using shRNAs. We found that MUS81 depletion from human fibroblasts leads to accumulation of ssDNA and a constitutive DNA damage response that ultimately activates cellular senescence. Moreover, we show that MUS81 is required for efficient replication fork progression during an unperturbed S-phase, and for recovery of productive replication following replication stalling. These results demonstrate essential roles for the MUS81 nuclease in maintenance of replication fork integrity. PMID:26415217

  2. Highly transcribed RNA polymerase II genes are impediments to replication fork progression in Saccharomyces cerevisiae

    PubMed Central

    Azvolinsky, Anna; Giresi, Paul G.; Lieb, Jason D.; Zakian, Virginia A.

    2009-01-01

    SUMMARY Replication forks face multiple obstacles that slow their progression. By two-dimensional gel analysis, yeast forks pause at stable DNA protein complexes, and this pausing is greatly increased in the absence of the Rrm3 helicase. We used a genome wide approach to identify 96 sites of very high DNA polymerase binding in wild type cells. Most of these binding sites were not previously identified pause sites. Rather, the most highly represented genomic category among high DNA polymerase binding sites was the open reading frames (ORFs) of highly transcribed RNA polymerase II genes. Twice as many pause sites were identified in rrm3 compared to wild type cells as pausing in this strain occurred at both highly transcribed RNA polymerase II genes and the previously identified protein DNA complexes. ORFs of highly transcribed RNA polymerase II genes are the first class of natural pause sites that are not exacerbated in rrm3 cells. PMID:19560424

  3. Impacts of hikers on aquatic invertebrates in the North Fork of the Virgin River, Utah

    USGS Publications Warehouse

    Caires, A.M.; Vinson, M.R.; Brasher, A.M.D.

    2010-01-01

    Effects of in-stream hiking on benthic standing stocks and drifting aquatic invertebrates and on organic matter were examined in the North Fork of the Virgin River, Zion National Park, Washington County, Utah. Densities of drifting aquatic invertebrates and organic matter increased with increasing numbers of hikers and reached a threshold level at high numbers of hikers. However, there was no apparent longer-term effect on standing stocks of benthic invertebrates or on organic matter. Densities of benthic invertebrates and organic matter did not differ among sites. Results suggest that in-stream hiking in the North Fork of the Virgin River increases drifting by invertebrates, but invertebrates from nearby undisturbed patches readily colonize impacted reaches.

  4. Initial Geomorphic Responses to Removal of Milltown Dam, Clark Fork River, Montana, USA

    NASA Astrophysics Data System (ADS)

    Wilcox, A. C.; Brinkerhoff, D.; Woelfle-Erskine, C.

    2008-12-01

    The removal of Milltown Dam on the Clark Fork River, Montana, USA, is creating a field-scale experiment on upstream and downstream responses to dam removal and on how gravel-bed rivers respond to sediment pulses. Milltown Dam was removed in 2008, reconnecting the Clark Fork River to its upstream basin in terms of sediment transport and fish passage. This dam removal is especially notable because (1) it is the largest dam removal to date in the United States in terms of the volume of reservoir sediment potentially available for downstream transport (over 3 million m3; 1.7 million m3 are being mechanically removed); and (2) the dam is the downstream end of the largest Superfund site in the United States, the Clark Fork Complex, and reservoir sediments are composed largely of contaminated mine tailings. Data collection on pre- and post-dam removal channel morphology, bed sediment characteristics, and sediment loads are being used to investigate spatial and temporal patterns of sediment transport and deposition associated with this dam removal. In the first several months following breaching of the dam, snowmelt runoff with a 3-year recurrence interval peak caused substantial erosion and downstream transport of metals-laden sediments from Milltown reservoir. Reservoir sediments in the Clark Fork arm of Milltown reservoir eroded at levels far exceeding modeling predictions as a result of both incision to the new base level created by dam removal and bank retreat of over 200 m in reaches upstream of a constructed bypass reach and remediation area. Copper and other metals in these eroded reservoir sediments provide a tracer for identifying whether sediment deposits observed downstream of the dam originated from Milltown reservoir or uncontaminated tributaries and indicate that Milltown sediments have reached over 200 km downstream. Downstream deposition has been greatest along channel margins and in side-channel areas, whereas the transport capacity of the active channel

  5. New species of Triplocania Roesler with forewing M3 forked (Psocodea: 'Psocoptera': Ptiloneuridae), from Brazil.

    PubMed

    Da Silva Neto, Alberto Moreira; Rafael, José Albertino; Aldrete, Alfonso N García

    2014-07-16

    Four new Brazilian species of Triplocania with forewing M3 forked are described and illustrated based on male specimens, namely: Triplocania lamasi n.sp. (Mato Grosso: Brazil), Triplocania mariateresae n.sp. (Rio de Janeiro: Brazil), Triplocania newi n.sp. (Tocantins: Brazil) and Triplocania plaumanni n.sp. (Santa Catarina: Brasil). They differ from all the other species in the genus, in which the males are known, by the hypandrium and phallosome structures.

  6. Slow Replication Fork Velocity of Homologous Recombination-Defective Cells Results from Endogenous Oxidative Stress

    PubMed Central

    Magdalou, Indiana; Machon, Christelle; Dardillac, Elodie; Técher, Hervé; Guitton, Jérôme; Debatisse, Michelle; Lopez, Bernard S.

    2016-01-01

    Replications forks are routinely hindered by different endogenous stresses. Because homologous recombination plays a pivotal role in the reactivation of arrested replication forks, defects in homologous recombination reveal the initial endogenous stress(es). Homologous recombination-defective cells consistently exhibit a spontaneously reduced replication speed, leading to mitotic extra centrosomes. Here, we identify oxidative stress as a major endogenous source of replication speed deceleration in homologous recombination-defective cells. The treatment of homologous recombination-defective cells with the antioxidant N-acetyl-cysteine or the maintenance of the cells at low O2 levels (3%) rescues both the replication fork speed, as monitored by single-molecule analysis (molecular combing), and the associated mitotic extra centrosome frequency. Reciprocally, the exposure of wild-type cells to H2O2 reduces the replication fork speed and generates mitotic extra centrosomes. Supplying deoxynucleotide precursors to H2O2-exposed cells rescued the replication speed. Remarkably, treatment with N-acetyl-cysteine strongly expanded the nucleotide pool, accounting for the replication speed rescue. Remarkably, homologous recombination-defective cells exhibit a high level of endogenous reactive oxygen species. Consistently, homologous recombination-defective cells accumulate spontaneous γH2AX or XRCC1 foci that are abolished by treatment with N-acetyl-cysteine or maintenance at 3% O2. Finally, oxidative stress stimulated homologous recombination, which is suppressed by supplying deoxynucleotide precursors. Therefore, the cellular redox status strongly impacts genome duplication and transmission. Oxidative stress should generate replication stress through different mechanisms, including DNA damage and nucleotide pool imbalance. These data highlight the intricacy of endogenous replication and oxidative stresses, which are both evoked during tumorigenesis and senescence initiation

  7. Brief reconnaissance study for the addition of hydropower for Carr Fork Dam, Sassafras, Kentucky

    SciTech Connect

    Gebhard, T.G. Jr.

    1982-05-24

    The feasibility of retrofitting the Carr Fork Dam near Hazard, KY for power generation was examined. This dam has a developable head of 80 ft and was built in 1975 to provide flood protection. The study of environmental, institutional, safety, and economic factors showed that the total investment cost would be $909,600 and that hydroelectric power development at this site is not feasible unless a higher price could be obtained for the power sold. (LCL)

  8. Tumor Suppression by BRCA-1: A Critical Role at DNA Replication Forks

    DTIC Science & Technology

    2006-10-01

    free extracts derived from Xenopus laevis eggs that support: 1. Semi-conservative, cell-cycle regulated DNA replication; 2. Many facets of the DNA...extracts derived from Xenopus laevis eggs that support: 1. Semi-conservative, cell-cycle regulated DNA replication; 2. Many facets of the DNA damage...assess the consequences of complete loss of BRCA1/BARD1 on fork progression and stalling. BODY Cell-free systems derived from Xenopus eggs can

  9. Slow Replication Fork Velocity of Homologous Recombination-Defective Cells Results from Endogenous Oxidative Stress.

    PubMed

    Wilhelm, Therese; Ragu, Sandrine; Magdalou, Indiana; Machon, Christelle; Dardillac, Elodie; Técher, Hervé; Guitton, Jérôme; Debatisse, Michelle; Lopez, Bernard S

    2016-05-01

    Replications forks are routinely hindered by different endogenous stresses. Because homologous recombination plays a pivotal role in the reactivation of arrested replication forks, defects in homologous recombination reveal the initial endogenous stress(es). Homologous recombination-defective cells consistently exhibit a spontaneously reduced replication speed, leading to mitotic extra centrosomes. Here, we identify oxidative stress as a major endogenous source of replication speed deceleration in homologous recombination-defective cells. The treatment of homologous recombination-defective cells with the antioxidant N-acetyl-cysteine or the maintenance of the cells at low O2 levels (3%) rescues both the replication fork speed, as monitored by single-molecule analysis (molecular combing), and the associated mitotic extra centrosome frequency. Reciprocally, the exposure of wild-type cells to H2O2 reduces the replication fork speed and generates mitotic extra centrosomes. Supplying deoxynucleotide precursors to H2O2-exposed cells rescued the replication speed. Remarkably, treatment with N-acetyl-cysteine strongly expanded the nucleotide pool, accounting for the replication speed rescue. Remarkably, homologous recombination-defective cells exhibit a high level of endogenous reactive oxygen species. Consistently, homologous recombination-defective cells accumulate spontaneous γH2AX or XRCC1 foci that are abolished by treatment with N-acetyl-cysteine or maintenance at 3% O2. Finally, oxidative stress stimulated homologous recombination, which is suppressed by supplying deoxynucleotide precursors. Therefore, the cellular redox status strongly impacts genome duplication and transmission. Oxidative stress should generate replication stress through different mechanisms, including DNA damage and nucleotide pool imbalance. These data highlight the intricacy of endogenous replication and oxidative stresses, which are both evoked during tumorigenesis and senescence initiation

  10. Hydrology and water chemistry of shallow aquifers along the upper Clark Fork, western Montana

    USGS Publications Warehouse

    Nimick, D.A.

    1993-01-01

    Shallow ground-water resources in western Montana have been developed primarily in Quaternary alluvium and Tertiary deposits, although bedrock supplies water to wells locally. Well-yield and trans- missivity values were largest (medians of 40 gallons per minute and 970 feet squared per day, respec- tively) in alluvium and smallest (medians of 15 gallons per minute and 130 feet squared per day, respectively) in bedrock. Chemical composition of ground water was dominated by calcium, magnesium, and bicarbonate derived from dissolution of carbonate minerals. Other water types may be the result of ion exchange (increased sodium) and mixing of geothermal water or leachate from mine wastes (increased sulfate). Although concen- trations of arsenic were relatively small (maximum of 20 micrograms per liter), they were somewhat larger in alluvium within 300 feet of the Clark Fork. Elevated concentrations of cadmium (maximum of 6 micrograms per liter) were measured in water from one well downgradient from tailings ponds. Although mining and smelting activities have resulted in widespread distribution of contami- nants in the Clark Fork valley, this study indicates that ground water contains elevated concentrations of trace elements only locally. Streamflow data indicate significant ground-water inflow to the Clark Fork in two reaches. Between Racetrack and Garrison, irrigation-return flow probably augments naturally occurring ground-water discharge. Between Jens and Cramer Creek, geo- thermal water from bedrock flows through alluvium to the river. In the Clark Fork, the maximum arsenic concentration was 8.1 micrograms per liter; copper and manganese concentrations were largest at Warm Springs (maximums of 14 and 350 micrograms per liter, respectively) and decreased downstream.

  11. Environmental Assessment: Building Addition Building 233 at Grand Forks AFB, North Dakota

    DTIC Science & Technology

    2004-03-22

    construction methods. With respect to construction, we have the following comments: 1. All necessary measures must be taken to minimize fugitive dust...scheduled in the area. In addition, we believe the proposed activities are consistent with the State Implementation Plan for the Control of Air...0527, Draft EA, Addition to Building 233, Grand Forks AFB, ND. Dear Ms. Durako: We have reviewed: Environmental Assessment: Building Addition

  12. Environmental Assessment: Construct Mass/Mobility Parking Lot at Grand Forks AFB, North Dakota

    DTIC Science & Technology

    2004-02-13

    2003 ND SHPO Ref.: 97 .. 0527, Draft EA, Mass/Mobility Parking Lot, Grand Forks AFB, ND. Dear Ms. Durako: We have reviewed: Environmental Assessment...specific project. If you have any questions please contact Duane Klinner at (701) 328-3576. Sincerely, cZ:~ Merlan E. Paaverud, Jr. State Historic... we have reviewed the projeet and foresee no identiftable conflict with wildlife or wildlife habitat based on 1M information provided. D .. Q

  13. Environmental Assessment: Construct Fire Station at Grand Forks Air Force Base

    DTIC Science & Technology

    2006-03-01

    Base Development CEQ Council on Environmental Quality CES Civil Engineer Squadron CEV Environmental Management Flight CFR Code of Federal...Act RAPCON Radar Approach Control USACE U.S. Army Corps of Engineers USAF U.S. Air Force VII SECTION 1 Purpose of and Need for Action 1.1...SPONSORING/MONITORING AGENCY NAME(S) AND ADDRESS(ES) 319 Civil Engineer Squadron, 525 Tuskegee Airmen Blvd, Grand Forks AFB, ND, 58205-6434 10

  14. Gaussian Random Fields Methods for Fork-Join Network with Synchronization Constraints

    DTIC Science & Technology

    2014-12-22

    research papers, under review in Mathematics of Operations Research (minor revision) and Annals of Applied Probability. One paper was on the finalist...2.00 1.00 Hongyuan Lu, Guodong Pang. Heavy Traffic Limits for A Fork-Join Network In the Halfin-Whitt Regime, Annals of Applied Probability (11 2014...fellowships for further studies in science , mathematics, engineering or technology fields: Student Metrics This section only applies to graduating

  15. On bandwidth characteristics of tuning fork micro-gyroscope with mechanically coupled sense mode.

    PubMed

    Ni, Yunfang; Li, Hongsheng; Huang, Libin; Ding, Xukai; Wang, Haipeng

    2014-07-21

    The bandwidth characteristics of a tuning fork micro-gyroscope with mechanically coupled sense mode were investigated in this paper to provide some references for mechanical bandwidth design. The concept of sense mode mechanical coupling is introduced first. Theoretical frequency response analyses were then carried out on the mechanical part of the gyroscope. Equations representing the relationships between the differential output signal and the frequency of the input angular rate were deduced in full frequency range and further simplified in low frequency range. Based on these equations, bandwidth characteristics under ideal and non-ideal conditions are discussed. Analytical results show that under ideal conditions, the bandwidth characteristics of a tuning fork micro-gyroscope are similar to those of a single mass micro-gyroscope, but under non-ideal conditions, especially when sense mass and/or stiffness are asymmetric, the bandwidth characteristics would be quite different because the in-phase mode would participate in the anti-phase vibration response. Experimental verifications were carried out on two micro-gyroscope prototypes designed in our laboratory. The deduced equations and analytical results can be used in guiding the mechanical bandwidth design of tuning fork micro-gyroscopes with mechanically coupled sense mode.

  16. Nucleoid occlusion prevents cell division during replication fork arrest in Bacillus subtilis

    PubMed Central

    Bernard, Remi; Marquis, Kathleen A.; Rudner, David Z.

    2010-01-01

    Summary How bacteria respond to chromosome replication stress has been traditionally studied using temperature-sensitive mutants and chemical inhibitors. These methods inevitably arrest all replication and lead to induction of transcriptional responses and inhibition of cell division. Here, we used repressor proteins bound to operator arrays to generate a single stalled replication fork. These replication roadblocks impeded replisome progression on one arm, leaving replication of the other arm and re-initiation unaffected. Remarkably, despite robust generation of RecA-GFP filaments and a strong block to cell division during the roadblock, patterns of gene expression were not significantly altered. Consistent with these findings, division inhibition was not mediated by the SOS-induced regulator YneA nor by RecA-independent repression of ftsL. In support of the idea that nucleoid occlusion prevents inappropriate cell division during fork arrest, immature FtsZ-rings formed adjacent to the DNA mass but rarely on top of it. Furthermore, mild alterations in chromosome compaction resulted in cell division that guillotined the DNA. Strikingly, the nucleoid occlusion protein Noc had no discernable role in division inhibition. Our data indicate that Noc-independent nucleoid occlusion prevents inappropriate cell division during replication fork arrest. They further suggest that Bacillus subtilis normally manages replication stress rather than inducing a stress-response. PMID:20807205

  17. Replication-fork stalling and processing at a single psoralen interstrand crosslink in Xenopus egg extracts.

    PubMed

    Le Breton, Cyrille; Hennion, Magali; Arimondo, Paola B; Hyrien, Olivier

    2011-04-15

    Interstrand crosslink (ICL)-inducing agents block the separation of the two DNA strands. They prevent transcription and replication and are used in clinics for the treatment of cancer and skin diseases. Here, we have introduced a single psoralen ICL at a specific site in plasmid DNA using a triplex-forming-oligonucleotide (TFO)-psoralen conjugate and studied its repair in Xenopus egg extracts that support nuclear assembly and replication of plasmid DNA. Replication forks arriving from either side stalled at the psoralen ICL. In contrast to previous observations with other ICL-inducing agents, the leading strands advanced up to the lesion without any prior pausing. Subsequently, incisions were introduced on one parental strand on both sides of the ICL. These incisions could be detected whether one or both forks reached the ICL. Using small molecule inhibitors, we found that the ATR-Chk1 pathway, but not the ATM-Chk2 pathway, stimulated both the incision step and the subsequent processing of the broken replication intermediates. Our results highlight both similarities and differences in fork stalling and repair induced by psoralen and by other ICL-forming agents.

  18. On Bandwidth Characteristics of Tuning Fork Micro-Gyroscope with Mechanically Coupled Sense Mode

    PubMed Central

    Ni, Yunfang; Li, Hongsheng; Huang, Libin; Ding, Xukai; Wang, Haipeng

    2014-01-01

    The bandwidth characteristics of a tuning fork micro-gyroscope with mechanically coupled sense mode were investigated in this paper to provide some references for mechanical bandwidth design. The concept of sense mode mechanical coupling is introduced first. Theoretical frequency response analyses were then carried out on the mechanical part of the gyroscope. Equations representing the relationships between the differential output signal and the frequency of the input angular rate were deduced in full frequency range and further simplified in low frequency range. Based on these equations, bandwidth characteristics under ideal and non-ideal conditions are discussed. Analytical results show that under ideal conditions, the bandwidth characteristics of a tuning fork micro-gyroscope are similar to those of a single mass micro-gyroscope, but under non-ideal conditions, especially when sense mass and/or stiffness are asymmetric, the bandwidth characteristics would be quite different because the in-phase mode would participate in the anti-phase vibration response. Experimental verifications were carried out on two micro-gyroscope prototypes designed in our laboratory. The deduced equations and analytical results can be used in guiding the mechanical bandwidth design of tuning fork micro-gyroscopes with mechanically coupled sense mode. PMID:25051030

  19. The progression of replication forks at natural replication barriers in live bacteria

    PubMed Central

    Moolman, M. Charl; Tiruvadi Krishnan, Sriram; Kerssemakers, Jacob W.J.; de Leeuw, Roy; Lorent, Vincent; Sherratt, David J.; Dekker, Nynke H.

    2016-01-01

    Protein–DNA complexes are one of the principal barriers the replisome encounters during replication. One such barrier is the Tus–ter complex, which is a direction dependent barrier for replication fork progression. The details concerning the dynamics of the replisome when encountering these Tus–ter barriers in the cell are poorly understood. By performing quantitative fluorescence microscopy with microfuidics, we investigate the effect on the replisome when encountering these barriers in live Escherichia coli cells. We make use of an E. coli variant that includes only an ectopic origin of replication that is positioned such that one of the two replisomes encounters a Tus–ter barrier before the other replisome. This enables us to single out the effect of encountering a Tus–ter roadblock on an individual replisome. We demonstrate that the replisome remains stably bound after encountering a Tus–ter complex from the non-permissive direction. Furthermore, the replisome is only transiently blocked, and continues replication beyond the barrier. Additionally, we demonstrate that these barriers affect sister chromosome segregation by visualizing specific chromosomal loci in the presence and absence of the Tus protein. These observations demonstrate the resilience of the replication fork to natural barriers and the sensitivity of chromosome alignment to fork progression. PMID:27166373

  20. Brown trout avoidance of metals in water characteristic of the Clark Fork River, Montana

    USGS Publications Warehouse

    Woodward, Daniel F.; Hansen, James A.; Bergman, Harold L.; Delonay, Aaron J.; Little, Edward E.

    1995-01-01

    The avoidance response of brown trout (Salmo trutta) to mixtures of cadmium, copper, lead, and zinc was determined in water simulating the Clark Fork River, Montana. Effects of acidification on the avoidance response were also evaluated. Tests were conducted in a cylindrical chamber that received reference water at one end and metal-contaminated water at the other; a distinct boundary formed at the center where the chamber drained. A 1 × mixture of the four metals (Cd, 1.1 μg/L; Cu, 12 μg/L; Pb, 3.2 μg/L; and Zn, 55 μg/L) that was representative of the ambient metals concentrations of the Clark Fork River resulted in avoidance by brown trout. Brown trout also avoided 0.5×, 2×, 4×, and 10× mixtures but not a 0.1 × mixture. A reduction in pH from 8.0 to either 7.0, 6.0, or 5.0 resulted in significant avoidance. Avoidance reactions to metals, similar to those observed in our laboratory experiments, may contribute to the depression of brown trout populations in the Clark Fork River.

  1. A tip-attached tuning fork sensor for the control of DNA translocation through a nanopore

    NASA Astrophysics Data System (ADS)

    Hyun, Changbae; Kaur, Harpreet; Huang, Tao; Li, Jiali

    2017-02-01

    In this work, we demonstrate that a tuning fork can be used as a force detecting sensor for manipulating DNA molecules and for controlling the DNA translocation rate through a nanopore. One prong of a tuning fork is glued with a probe tip which DNA molecules can be attached to. To control the motion and position of the tip, the tuning fork is fixed to a nanopositioning system which has sub-nanometer position control. A fluidic chamber is designed to fulfill many requirements for the experiment: for the access of a DNA-attached tip approaching to a nanopore, for housing a nanopore chip, and for measuring ionic current through a solid-state nanopore with a pair of electrodes. The location of a nanopore is first observed by transmission electron microscopy, and then is determined inside the liquid chambers with an optical microscope combined with local scanning the probe tip on the nanopore surface. When a DNA-immobilized tip approaches a membrane surface near a nanopore, free ends of the immobilized DNA strings can be pulled and trapped into the pore by an applied voltage across the nanopore chip, resulting in an ionic current reduction through the nanopore. The trapped DNA molecules can be lifted up from the nanopore at a user controlled speed. This integrated apparatus allows manipulation of biomolecules (DNA, RNA, and proteins) attached to a probe tip with sub-nanometer precision, and simultaneously allows measurement of the biomolecules by a nanopore device.

  2. Stream Habitat Modeling to Support Water Management Decisions for the North Fork Shenandoah River, Virginia

    NASA Astrophysics Data System (ADS)

    Averett, A.; Persinger, J. W.; Orth, D. J.

    2005-05-01

    The Shenandoah River and its tributaries, the North Fork and South Fork, represent an excellent model of a multiple use river. Due to documented fish kills, frequent low flow events, and proximity to the Washington D.C. metropolitan area, there is growing concern regarding the sustainability of this natural resource. In 1999, a four-year IFIM (Instream Flow Incremental Methodology) study was initiated to evaluate the response of hydraulics and fish habitat to low flow conditions in the North Fork Shenandoah River (NFSR) basin. Habitat suitability criteria were developed onsite for guilds of riffle, fast generalist, pool-run, and pool-cover fishes. Habitat responses to stream flows were quantified for these habitat guilds and habitat conditions conducive to nuisance algal blooms. In addition, we compared usable habitat conditions under baseline and alternative hydrologic time series corresponding to water use restrictions. Model results were used to identify aquatic conservation flows and establish a stepwise process for implementing aquatic conservation flow management in the NFSR basin. This process will facilitate the adoption of water use conservation measures at appropriate times during future extreme droughts.

  3. Establishing a context for river rehabilitation, North Fork Gunnison River, Colorado.

    PubMed

    Jaquette, Christopher; Wohl, Ellen; Cooper, David

    2005-05-01

    Initial river rehabilitation efforts along the North Fork Gunnison River in Colorado focused on the use of in-stream structures and channel stabilization to create a single-thread channel with pools along a braided river. These efforts were based on the assumption that the river's braided planform results primarily from land use during the past century. In order to establish a context for further rehabilitation, we evaluated the possibility that the river might be braided as a result of processes independent of land use. We estimated volume, grain-size distribution, and lithology of sediment sources along the river corridor and evaluated the planform stability of the river during the past century using historical sources, aerial photographs covering 1939-1997, and comparison of bankfull discharge and gradient in the study area to values published for braided and meandering rivers. Our results indicate that the North Fork Gunnison River has been primarily braided in its lower reaches during the past few hundred years, although the channel planform tends toward a single-thread channel during decades of lower precipitation and discharge. Although land use is not the primary cause of braiding along the North Fork Gunnison River, it has decreased channel stability, and rehabilitation efforts should be designed to reduce these effects. Our results illustrate the importance of planning river rehabilitation measures within a historical context that accounts for both catchment-scale and reach-scale controls on channel processes and planform.

  4. Vibration amplitude of a tip-loaded quartz tuning fork during shear force microscopy scanning.

    PubMed

    Sandoz, P; Friedt, J-M; Carry, E

    2008-08-01

    This Note reports on experimental results obtained with a recently published vision method for in-plane vibration measurement [Sandoz et al., Rev. Sci. Instrum. 78, 023706 (2007)]. The latter is applied to a tip-loaded quartz tuning fork frequently used in scanning probe microscopy for shear-force monitoring of the tip-sample distance. The vibration amplitude of the tip-loaded prong is compared to that of the free one and the damping induced by tip-surface interactions is measured. The tuning-fork behavior is characterized during approaches from free space to surface contact. Tip-surface contact is clearly identified by a drastic reduction in the prong vibration amplitude. However, no differences were observed between hydrophilic and hydrophobic surfaces. Experiments reported here show that the vibration amplitude of the quartz tuning fork in free space is a good estimate of the vibration amplitude of the tip interacting with the sample surface during shear force sample-tip feedback. The experimental setup for measuring the amplitude is easily integrated in an inverted microscope setup on which the shear force microscope is installed for simultaneous scanning probe and optical microscopy analysis of the sample.

  5. Vibration amplitude of a tip-loaded quartz tuning fork during shear force microscopy scanning

    NASA Astrophysics Data System (ADS)

    Sandoz, P.; Friedt, J.-M.; Carry, É.

    2008-08-01

    This Note reports on experimental results obtained with a recently published vision method for in-plane vibration measurement [Sandoz et al., Rev. Sci. Instrum. 78, 023706 (2007)]. The latter is applied to a tip-loaded quartz tuning fork frequently used in scanning probe microscopy for shear-force monitoring of the tip-sample distance. The vibration amplitude of the tip-loaded prong is compared to that of the free one and the damping induced by tip-surface interactions is measured. The tuning-fork behavior is characterized during approaches from free space to surface contact. Tip-surface contact is clearly identified by a drastic reduction in the prong vibration amplitude. However, no differences were observed between hydrophilic and hydrophobic surfaces. Experiments reported here show that the vibration amplitude of the quartz tuning fork in free space is a good estimate of the vibration amplitude of the tip interacting with the sample surface during shear force sample-tip feedback. The experimental setup for measuring the amplitude is easily integrated in an inverted microscope setup on which the shear force microscope is installed for simultaneous scanning probe and optical microscopy analysis of the sample.

  6. Flood-inundation maps for the East Fork White River near Bedford, Indiana

    USGS Publications Warehouse

    Fowler, Kathleen K.

    2014-01-01

    Digital flood-inundation maps for an 1.8-mile reach of the East Fork White River near Bedford, Indiana (Ind.) were created by the U.S. Geological Survey (USGS) in cooperation with the Indiana Department of Transportation. The inundation maps, which can be accessed through the USGS Flood Inundation Mapping Science Web site at http://water.usgs.gov/osw/flood_inundation/ depict estimates of the areal extent and depth of flooding corresponding to selectedwater levels (stages) at USGS streamgage 03371500, East Fork White River near Bedford, Ind. Current conditions for estimating near-real-time areas of inundation using USGS streamgage information may be obtained on the Internet at http://waterdata.usgs.gov/in/nwis/uv?site_no=03371500. In addition, information has been provided to the National Weather Service (NWS) for incorporation into their Advanced Hydrologic Prediction Service (AHPS) flood warning system (http://water.weather.gov/ahps/). The NWS forecasts flood hydrographs at many places that are often colocated with USGS streamgages, including the East Fork White River near Bedford, Ind. NWS-forecasted peak-stage information may be used in conjunction with the maps developed in this study to show predicted areas of flood inundation. For this study, flood profiles were computed for the East Fork White River reach by means of a one-dimensional step-backwater model. The hydraulic model was calibrated by using the most current stage-discharge relations at USGS streamgage 03371500, East Fork White River near Bedford, Ind., and documented high-water marks from the flood of June 2008. The calibrated hydraulic model was then used to determine 20 water-surface profiles for flood stages at 1-foot intervals referenced to the streamgage datum and ranging from bankfull to the highest stage of the current stage-discharge rating curve. The simulated water-surface profiles were then combined with a geographic information system (GIS) digital elevation model (DEM, derived from

  7. Flood-inundation maps for the East Fork White River at Shoals, Indiana

    USGS Publications Warehouse

    Boldt, Justin A.

    2016-05-06

    Digital flood-inundation maps for a 5.9-mile reach of the East Fork White River at Shoals, Indiana (Ind.), were created by the U.S. Geological Survey (USGS) in cooperation with the Indiana Office of Community and Rural Affairs. The flood-inundation maps, which can be accessed through the USGS Flood Inundation Mapping Science Web site at http://water.usgs.gov/osw/flood_inundation/ depict estimates of the areal extent and depth of flooding corresponding to selected water levels (stages) at the USGS streamgage on the East Fork White River at Shoals, Ind. (USGS station number 03373500). Near-real-time stages at this streamgage may be obtained on the Internet from the USGS National Water Information System at http://waterdata.usgs.gov/ or the National Weather Service (NWS) Advanced Hydrologic Prediction Service (AHPS) at http://water.weather.gov/ahps/, which also forecasts flood hydrographs at this site (NWS AHPS site SHLI3). NWS AHPS forecast peak stage information may be used in conjunction with the maps developed in this study to show predicted areas of flood inundation.Flood profiles were computed for the East Fork White River reach by means of a one-dimensional, step-backwater model developed by the U.S. Army Corps of Engineers. The hydraulic model was calibrated by using the current stage-discharge relation (USGS rating no. 43.0) at USGS streamgage 03373500, East Fork White River at Shoals, Ind. The calibrated hydraulic model was then used to compute 26 water-surface profiles for flood stages at 1-foot (ft) intervals referenced to the streamgage datum and ranging from approximately bankfull (10 ft) to the highest stage of the current stage-discharge rating curve (35 ft). The simulated water-surface profiles were then combined with a geographic information system (GIS) digital elevation model (DEM), derived from light detection and ranging (lidar) data, to delineate the area flooded at each water level. The areal extent of the 24-ft flood-inundation map was

  8. Replication Terminator Protein-Based Replication Fork-Arrest Systems in Various Bacillus Species

    PubMed Central

    Griffiths, A. A.; Andersen, P. A.; Wake, R. G.

    1998-01-01

    The replication terminator protein (RTP) of Bacillus subtilis interacts with its cognate DNA terminators to cause replication fork arrest, thereby ensuring that the forks approaching one another at the conclusion of a round of replication meet within a restricted terminus region. A similar situation exists in Escherichia coli, but it appears that the fork-arrest systems in these two organisms have evolved independently of one another. In the present work, RTP homologs in four species closely related to B. subtilis (B. atrophaeus, B. amyloliquefaciens, B. mojavensis, and B. vallismortis) have been identified and characterized. An RTP homolog could not be identified in another closely related species, B. licheniformis. The nucleotide and amino acid changes from B. subtilis among the four homologs are consistent with the recently established phylogenetic tree for these species. The GC contents of the rtp genes raise the possibility that these organisms arose within this branch of the tree by horizontal transfer into a common ancestor after their divergence from B. licheniformis. Only 5 amino acid residue positions were changed among the four homologs, despite an up to 17.2% change in the nucleotide sequence, a finding that highlights the importance of the precise folded structure to the functioning of RTP. The absence of any significant change in the proposed DNA-binding region of RTP emphasizes the importance of its high affinity for the DNA terminator in its functioning. By coincidence, the single change (E30K) found in the B. mojavensis RTP corresponds exactly to that purposefully introduced by others into B. subtilis RTP to implicate a crucial role for E30 in the fork-arrest mechanism. The natural occurrence of this variant is difficult to reconcile with such an implication, and it was shown directly that RTP.E30K functions normally in fork arrest in B. subtilis in vivo. Additional DNA terminators were identified in the new RTP homolog-containing strains, allowing

  9. Nucleolytic processing of aberrant replication intermediates by an Exo1-Dna2-Sae2 axis counteracts fork collapse-driven chromosome instability

    PubMed Central

    Colosio, Arianna; Frattini, Camilla; Pellicanò, Grazia; Villa-Hernández, Sara; Bermejo, Rodrigo

    2016-01-01

    Problems during DNA replication underlie genomic instability and drive malignant transformation. The DNA damage checkpoint stabilizes stalled replication forks thus counteracting aberrant fork transitions, DNA breaks and chromosomal rearrangements. We analyzed fork processing in checkpoint deficient cells by coupling psoralen crosslinking with replication intermediate two-dimensional gel analysis. This revealed a novel role for Exo1 nuclease in resecting reversed replication fork structures and counteracting the accumulation of aberrant intermediates resembling fork cleavage products. Genetic analyses demonstrated a functional interplay of Exo1 with Mus81, Dna2 and Sae2 nucleases in promoting cell survival following replication stress, suggestive of concerted nucleolytic processing of stalled forks. While Mus81 and other Structure Specific Endonucleases do not contribute to obvious collapsed fork transitions, Dna2 promotes reversed fork resection likely by facilitating Exo1 access to nascent strands. Instead, Sae2 cooperates with Exo1 in counteracting putative fork cleavage events linked to double strand breaks formation and increased gross chromosomal rearrangement rates. Our data indicate that in checkpoint deficient cells diverse nuclease activities interface to eliminate aberrant replication intermediates and prevent chromosome instability. PMID:27672038

  10. Nucleolytic processing of aberrant replication intermediates by an Exo1-Dna2-Sae2 axis counteracts fork collapse-driven chromosome instability.

    PubMed

    Colosio, Arianna; Frattini, Camilla; Pellicanò, Grazia; Villa-Hernández, Sara; Bermejo, Rodrigo

    2016-12-15

    Problems during DNA replication underlie genomic instability and drive malignant transformation. The DNA damage checkpoint stabilizes stalled replication forks thus counteracting aberrant fork transitions, DNA breaks and chromosomal rearrangements. We analyzed fork processing in checkpoint deficient cells by coupling psoralen crosslinking with replication intermediate two-dimensional gel analysis. This revealed a novel role for Exo1 nuclease in resecting reversed replication fork structures and counteracting the accumulation of aberrant intermediates resembling fork cleavage products. Genetic analyses demonstrated a functional interplay of Exo1 with Mus81, Dna2 and Sae2 nucleases in promoting cell survival following replication stress, suggestive of concerted nucleolytic processing of stalled forks. While Mus81 and other Structure Specific Endonucleases do not contribute to obvious collapsed fork transitions, Dna2 promotes reversed fork resection likely by facilitating Exo1 access to nascent strands. Instead, Sae2 cooperates with Exo1 in counteracting putative fork cleavage events linked to double strand breaks formation and increased gross chromosomal rearrangement rates. Our data indicate that in checkpoint deficient cells diverse nuclease activities interface to eliminate aberrant replication intermediates and prevent chromosome instability.

  11. Effects of controlled burning of chaparral on streamflow and sediment characteristics, East Fork Sycamore Creek, central Arizona

    USGS Publications Warehouse

    Baldys, Stanley; Hjalmarson, H.W.

    1994-01-01

    The effects of controlled burning of part of a chaparral-covered drainage basin on streamflow and sediment characteristics were studied in the upper reaches of the Sycamore Creek basin in central Arizona. A paired-watershed method was used to analyze data collected in two phases separated by the controlled burning of 45 percent of the East Fork Sycamore Creek drainage basin by the U.S. Forest Service on October 31, 1981. Statistically significant increases in streamflow in East Fork occurred from October 26, 1982, through August 25, 1984. Streamflow for August 26, 1984, through the end of data collection for the study on May 31, 1986, was generally at or less than preburn levels. An increase in the percentage of time that flow occurred in East Fork was noted for water years 1983 and 1984. No increase in the magnitude of instantaneous peak flows as a result of the burn was discernable at statistically significant levels. Suspended-sediment yields computed for data collected during water year 1983 were significantly greater in the East Fork drainage basin, 546 tons per square mile, than in the West Fork drainage basin, 22.6 tons per square mile. Suspended-sediment yields computed for East Fork and West Fork for water year 1985, 38.3 and 13.3 tons per square mile, respectively, were much closer in yield. These more uniform yields indicate a possible return to preburn conditions. Data collection did not begin until 11 months after the burn; therefore, the largest increases in streamflow and sediment yields, which commonly occur during the year after a burn, may not have been measured. During the second through fourth years after the burn, smaller increases in stream- flow and sediment yields were found in this study than were found in similar studies in this region.

  12. THE WERNER AND BLOOM SYNDROME PROTEINS HELP RESOLVE REPLICATION BLOCKAGE BY CONVERTING (REGRESSED) HOLLIDAY JUNCTIONS TO FUNCTIONAL REPLICATION FORKS

    PubMed Central

    Machwe, Amrita; Karale, Rajashree; Xu, Xioahua; Liu, Yilun; Orren, David K.

    2011-01-01

    Cells cope with blockage of replication fork progression in a manner so that DNA synthesis can be completed and genomic instability minimized. Models for resolution of blocked replication involve fork regression to form Holliday junction structures. The human RecQ helicases WRN and BLM (deficient in Werner and Bloom syndromes, respectively) are critical for maintaining genomic stability and postulated to function in accurate resolution of replication blockage. Consistent with this notion, WRN and BLM localize to sites of blocked replication after certain DNA damaging treatments and exhibit enhanced activity on replication and recombination intermediates. Here we examined the actions of WRN and BLM on a special Holliday junction substrate reflective of a regressed replication fork. Our results demonstrate that, in reactions requiring ATP hydrolysis, both WRN and BLM convert this Holliday junction substrate primarily to a four-stranded replication fork structure, suggesting they target the Holliday junction to initiate branch migration. In agreement, the Holliday junction binding protein RuvA inhibits the WRN- and BLM-mediated conversion reactions. Importantly, this conversion product is suitable for replication with its leading daughter strand readily extended by DNA polymerases. Furthermore, binding to and conversion of this Holliday junction is optimal in low MgCl2, suggesting that WRN and BLM preferentially act on the square planar (open) conformation of Holliday junctions. Our findings suggest that, subsequent to fork regression events, WRN and/or BLM could re-establish functional replication forks to help overcome fork blockage. Such a function is highly consistent with phenotypes associated with WRN- and BLM-deficient cells. PMID:21736299

  13. Environmental Statement for Lavon Dam and Reservoir Modification and East Fork Channel Improvement - Pertaining to East Fork Channel and Levee Improvement Increment I. Supplement.

    DTIC Science & Technology

    1977-01-01

    Fork Channel and Levee Improvement Increment .p I ON0TRACT OR GRANT NUMBER.) US Army Corps of Engineers u l F t W o r t h , T X .... .- - -- 9...the abaract ontered in Blook 20 I dlfforent be- r Report) IS. SUPPLEMENTARY NOTES IS. KEY WORDS (Continue on reovere side It necosary and Idontdir by...0 ’ ’ % I N" ’S S S S S I S I S S S I S I S / S - S S I 5 I S IIN I S / S aeAf"- d"b* mm AR r -kp ’ r do~ -dC -4W% P* ~ qbb IELEVATION IN 360 I (1 It

  14. The Late Cretaceous Middle Fork caldera, its resurgent intrusion, and enduring landscape stability in east-central Alaska

    USGS Publications Warehouse

    Bacon, Charles R.; Dusel-Bacon, Cynthia; Aleinikoff, John N.; Slack, John F.

    2014-01-01

    The Middle Fork is a relatively well preserved caldera within a broad region of Paleozoic metamorphic rocks and Mesozoic plutons bounded by northeast-trending faults. In the relatively downdropped and less deeply exhumed crustal blocks, Cretaceous–Early Tertiary silicic volcanic rocks attest to long-term stability of the landscape. Within the Middle Fork caldera, the granite porphyry is interpreted to have been exposed by erosion of thick intracaldera tuff from an asymmetric resurgent dome. The Middle Fork of the North Fork of the Fortymile River incised an arcuate valley into and around the caldera fill on the west and north and may have cut down from within an original caldera moat. The 70 Ma land surface is preserved beneath proximal outflow tuff at the west margin of the caldera structure and beneath welded outflow tuff 16–23 km east-southeast of the caldera in a paleovalley. Within ∼50 km of the Middle Fork caldera are 14 examples of Late Cretaceous (?)–Tertiary felsic volcanic and hypabyssal intrusive rocks that range in area from <1 km2 to ∼100 km2. Rhyolite dome clusters north and northwest of the caldera occupy tectonic basins associated with northeast-trending faults and are relatively little eroded. Lava of a latite complex, 12–19 km northeast of the caldera, apparently flowed into the paleovalley of the Middle Fork of the North Fork of the Fortymile River. To the northwest of the Middle Fork caldera, in the Mount Harper crustal block, mid-Cretaceous plutonic rocks are widely exposed, indicating greater total exhumation. To the southeast of the Middle Fork block, the Mount Veta block has been uplifted sufficiently to expose a ca. 68–66 Ma equigranular granitic pluton. Farther to the southeast, in the Kechumstuk block, the flat-lying outflow tuff remnant in Gold Creek and a regionally extensive high terrace indicate that the landscape there has been little modified since 70 Ma other than entrenchment of tributaries in response to post–2

  15. Oxidative damage to poultry: from farm to fork.

    PubMed

    Estévez, M

    2015-06-01

    Poultry and poultry meat are particularly susceptible to oxidative reactions. Oxidation processes have been for decades the focus of animal and meat scientists owing to the negative impact of these reactions on animal growth, performance, and food quality. Lipid oxidation has been recognized a major threat to the quality of processed poultry products. The recent discoveries on the occurrence of protein oxidation in muscle foods have increased the scientific and technological interest in a topic that broadens the horizons of food biochemistry into innovative fields. Furthermore, in recent years we have witnessed a growing interest in consumers on the impact of diet and oxidation on health and aging. Hence, the general description of oxidative reactions as harmful phenomena goes beyond the actual impact on animal production and food quality and reaches the potential influence of oxidized foods on consumer health. Likewise, the current antioxidant strategies aim for the protection of the living tissues, the food systems, and a potential health benefit in the consumer upon ingestion. Along these lines, the application of phytochemicals and other microelements (Se, Cu) with antioxidant potential in the feeds or directly in the meat product are strategies of substantial significance. The present paper reviews in a concise manner the most relevant and novel aspects of the mechanisms and consequences of oxidative reactions in poultry and poultry meat, and describes current antioxidant strategies against these undesirable reactions.

  16. Hydrology of the North Fork of the Right Fork of Miller Creek, Carbon County, Utah, before, during, and after underground coal mining

    USGS Publications Warehouse

    Slaughter, C.B.; Freethey, G.W.; Spangler, L.E.

    1995-01-01

    From 1988-92 the U.S. Geological Survey, in cooperation with the Utah Division of Oil, Gas, and Mining, studied the effects of underground coal mining and the resulting subsidence on the hydrologic system near the North Fork of the Right Fork of Miller Creek, Carbon County, Utah. The subsidence caused open fractures at land surface, debris slides, and rockfalls in the canyon above the mined area. Land surface subsided and moved several feet horizontally. The perennial stream and a tributary upstream from the mined area were diverted below the ground by surface fractures where the overburden thickness above the Wattis coal seam is 300 to 500 feet. The reach downstream was dry but flow resumed where the channel traversed the Star Point Sandstone, which forms the aquifer below the coal seams where ground-water discharge provides new base flow. Concentrations of dissolved constituents in the stream water sampled just downstream from the mined area increased from about 300 mg/L (milligrams per liter) to more than 1,500 mg/L, and the water changed from primarily a magnesium calcium bicarbonate to primarily a magnesium sulfate type. Monitored water levels in two wells completed in the perched aquifer(s) above the mine indicate that fractures from subsidence- related deformation drained the perched aquifer in the Blackhawk Formation. The deformation also could have contributed to the decrease in discharge of three springs above the mined area, but discharge from other springs in the area did not change ubstantially; thus, the relation between subsidence and spring discharge, if any, is not clear. No significant changes in the chemical character of water discharging from springs were detected, but the dissolved-solids concentration in water collected from a perched sandstone aquifer overlying the mined coal seams increased during mining activity.

  17. Differential regulation of the anti-crossover and replication fork regression activities of Mph1 by Mte1

    PubMed Central

    Xue, Xiaoyu; Papusha, Alma; Choi, Koyi; Bonner, Jaclyn N.; Kumar, Sandeep; Niu, Hengyao; Kaur, Hardeep; Zheng, Xiao-Feng; Donnianni, Roberto A.; Lu, Lucy; Lichten, Michael; Zhao, Xiaolan; Ira, Grzegorz; Sung, Patrick

    2016-01-01

    We identified Mte1 (Mph1-associated telomere maintenance protein 1) as a multifunctional regulator of Saccharomyces cerevisiae Mph1, a member of the FANCM family of DNA motor proteins important for DNA replication fork repair and crossover suppression during homologous recombination. We show that Mte1 interacts with Mph1 and DNA species that resemble a DNA replication fork and the D loop formed during recombination. Biochemically, Mte1 stimulates Mph1-mediated DNA replication fork regression and branch migration in a model substrate. Consistent with this activity, genetic analysis reveals that Mte1 functions with Mph1 and the associated MHF complex in replication fork repair. Surprisingly, Mte1 antagonizes the D-loop-dissociative activity of Mph1–MHF and exerts a procrossover role in mitotic recombination. We further show that the influence of Mte1 on Mph1 activities requires its binding to Mph1 and DNA. Thus, Mte1 differentially regulates Mph1 activities to achieve distinct outcomes in recombination and replication fork repair. PMID:26966246

  18. Simultaneous binding to the tracking strand, displaced strand and the duplex of a DNA fork enhances unwinding by Dda helicase.

    PubMed

    Aarattuthodiyil, Suja; Byrd, Alicia K; Raney, Kevin D

    2014-10-01

    Interactions between helicases and the tracking strand of a DNA substrate are well-characterized; however, the role of the displaced strand is a less understood characteristic of DNA unwinding. Dda helicase exhibited greater processivity when unwinding a DNA fork compared to a ss/ds DNA junction substrate. The lag phase in the unwinding progress curve was reduced for the forked DNA compared to the ss/ds junction. Fewer kinetic steps were required to unwind the fork compared to the ss/ds junction, suggesting that binding to the fork leads to disruption of the duplex. DNA footprinting confirmed that interaction of Dda with a fork leads to two base pairs being disrupted whereas no disruption of base pairing was observed with the ss/ds junction. Neutralization of the phosphodiester backbone resulted in a DNA-footprinting pattern similar to that observed with the ss/ds junction, consistent with disruption of the interaction between Dda and the displaced strand. Several basic residues in the 1A domain which were previously proposed to bind to the incoming duplex DNA were replaced with alanines, resulting in apparent loss of interaction with the duplex. Taken together, these results suggest that Dda interaction with the tracking strand, displaced strand and duplex coordinates DNA unwinding.

  19. Gas Phase Photoacoustic Sensor at 8.41 mu m Using Quartz Tuning Forks and Amplitude Modulated Quantum Cascade Lasers

    SciTech Connect

    Wojcik, Michael D.; Phillips, Mark C.; Cannon, Bret D.; Taubman, Matthew S.

    2006-10-01

    We demonstrate the performance of a novel long-wave infrared photoacoustic laser absorbance spectrometer for gas-phase species using an amplitude modulated (AM) quantum cascade (QC) laser and a quartz tuning fork microphone. Photoacoustic signal was generated by focusing the output of a Fabry-Perot QC laser operating at 8.41 ?m between the legs of a quartz tuning fork which served as a transducer for the transient acoustic pressure wave. The QC laser was modulated at the resonant frequency of the tuning fork (32.8 kHz) and delivered a modest 5.3 mW at the tuning fork. This spectrometer was calibrated using the infrared absorber Freon-134a by performing a simultaneous absorption measurement using a 35 cm absorption cell. The NEAS of this instrument was determined to be 2 x 10{sup -8} W cm-1 Hz{sup -1/2}. A corresponding theoretical analysis of the instrument sensitivity is presented and is capable of quantitatively reproducing the experimental NEAS, indicating that the fundamental sensitivity of this technique is limited by the noise floor of the tuning fork itself.

  20. Replication fork progression is paused in two large chromosomal zones flanking the DNA replication origin in Escherichia coli.

    PubMed

    Akiyama, Masahiro Tatsumi; Oshima, Taku; Chumsakul, Onuma; Ishikawa, Shu; Maki, Hisaji

    2016-08-01

    Although the speed of nascent DNA synthesis at individual replication forks is relatively uniform in bacterial cells, the dynamics of replication fork progression on the chromosome are hampered by a variety of natural impediments. Genome replication dynamics can be directly measured from an exponentially growing cell population by sequencing newly synthesized DNA strands that were specifically pulse-labeled with the thymidine analogue 5-bromo-2'-deoxyuridine (BrdU). However, a short pulse labeling with BrdU is impracticable for bacteria because of poor incorporation of BrdU into the cells, and thus, the genomewide dynamics of bacterial DNA replication remain undetermined. Using a new thymidine-requiring Escherichia coli strain, eCOMB, and high-throughput sequencing, we succeeded in determining the genomewide replication profile in bacterial cells. We also found that fork progression is paused in two ~200-kb chromosomal zones that flank the replication origin in the growing cells. This origin-proximal obstruction to fork progression was overcome by an increased thymidine concentration in the culture medium and enhanced by inhibition of transcription. These indicate that DNA replication near the origin is sensitive to the impediments to fork progression, namely a scarcity of the DNA precursor deoxythymidine triphosphate and probable conflicts between replication and transcription machineries.

  1. Water-quality trends and constituent-transport analysis for selected sampling sites in the Milltown Reservoir/Clark Fork River Superfund Site in the upper Clark Fork Basin, Montana, water years 1996–2015

    USGS Publications Warehouse

    Sando, Steven K.; Vecchia, Aldo V.

    2016-07-20

    During the extended history of mining in the upper Clark Fork Basin in Montana, large amounts of waste materials enriched with metallic contaminants (cadmium, copper, lead, and zinc) and the metalloid trace element arsenic were generated from mining operations near Butte and milling and smelting operations near Anaconda. Extensive deposition of mining wastes in the Silver Bow Creek and Clark Fork channels and flood plains had substantial effects on water quality. Federal Superfund remediation activities in the upper Clark Fork Basin began in 1983 and have included substantial remediation near Butte and removal of the former Milltown Dam near Missoula. To aid in evaluating the effects of remediation activities on water quality, the U.S. Geological Survey began collecting streamflow and water-quality data in the upper Clark Fork Basin in the 1980s.Trend analysis was done on specific conductance, selected trace elements (arsenic, copper, and zinc), and suspended sediment for seven sampling sites in the Milltown Reservoir/Clark Fork River Superfund Site for water years 1996–2015. The most upstream site included in trend analysis is Silver Bow Creek at Warm Springs, Montana (sampling site 8), and the most downstream site is Clark Fork above Missoula, Montana (sampling site 22), which is just downstream from the former Milltown Dam. Water year is the 12-month period from October 1 through September 30 and is designated by the year in which it ends. Trend analysis was done by using a joint time-series model for concentration and streamflow. To provide temporal resolution of changes in water quality, trend analysis was conducted for four sequential 5-year periods: period 1 (water years 1996–2000), period 2 (water years 2001–5), period 3 (water years 2006–10), and period 4 (water years 2011–15). Because of the substantial effect of the intentional breach of Milltown Dam on March 28, 2008, period 3 was subdivided into period 3A (October 1, 2005–March 27, 2008

  2. In-Field Performance Testing of the Fork Detector for Quantitative Spent Fuel Verification

    SciTech Connect

    Gauld, Ian C.; Hu, Jianwei; De Baere, P.; Vaccaro, S.; Schwalbach, P.; Liljenfeldt, Henrik; Tobin, Stephen

    2015-01-01

    Expanding spent fuel dry storage activities worldwide are increasing demands on safeguards authorities that perform inspections. The European Atomic Energy Community (EURATOM) and the International Atomic Energy Agency (IAEA) require measurements to verify declarations when spent fuel is transferred to difficult-to-access locations, such as dry storage casks and the repositories planned in Finland and Sweden. EURATOM makes routine use of the Fork detector to obtain gross gamma and total neutron measurements during spent fuel inspections. Data analysis is performed by modules in the integrated Review and Analysis Program (iRAP) software, developed jointly by EURATOM and the IAEA. Under the framework of the US Department of Energy–EURATOM cooperation agreement, a module for automated Fork detector data analysis has been developed by Oak Ridge National Laboratory (ORNL) using the ORIGEN code from the SCALE code system and implemented in iRAP. EURATOM and ORNL recently performed measurements on 30 spent fuel assemblies at the Swedish Central Interim Storage Facility for Spent Nuclear Fuel (Clab), operated by the Swedish Nuclear Fuel and Waste Management Company (SKB). The measured assemblies represent a broad range of fuel characteristics. Neutron count rates for 15 measured pressurized water reactor assemblies are predicted with an average relative standard deviation of 4.6%, and gamma signals are predicted on average within 2.6% of the measurement. The 15 measured boiling water reactor assemblies exhibit slightly larger deviations of 5.2% for the gamma signals and 5.7% for the neutron count rates, compared to measurements. These findings suggest that with improved analysis of the measurement data, existing instruments can provide increased verification of operator declarations of the spent fuel and thereby also provide greater ability to confirm integrity of an assembly. These results support the application of the Fork detector as a fully quantitative spent fuel

  3. Human brain factor 1, a new member of the fork head gene family

    SciTech Connect

    Murphy, D.B.; Wiese, S.; Burfeind, P.

    1994-06-01

    Analysis of cDNA clones that cross-hybridized with the fork head domain of the rat HNF-3 gene family revealed 10 cDNAs from human fetal brain and human testis cDNA libraries containing this highly conserved DNA-binding domain. Three of these cDNAs (HFK1, HFK2, and HFK3) were further analyzed. The cDNA HFK1 has a length of 2557 nucleotides and shows strong homology at the nucleotide level (91.2%) to brain factor 1 (BF-1) from rat. The HFK1 cDNA codes for a putative 476 amino acid protein. The homology to BF-1 from rat in the coding region at the amino acid level is 87.5%. The fork head homologous region includes 111 amino acids starting at amino acid 160 and has a 97.5% homology to BF-1. Southern hybridization revealed that HFK1 is highly conserved among mammalian species and possibly birds. Northern analysis with total RNA from human tissues and poly(A)-rich RNA from mouse revealed a 3.2-kb transcript that is present in human and mouse fetal brain and in adult mouse brain. In situ hybridization with sections of mouse embryo and human fetal brain reveals that HFK1 expression is restricted to the neuronal cells in the telencepthalon, with strong expression being observed in the developing dentate gyrus and hippocampus. HFK1 was chromosomally localized by in situ hybridization to 14q12. The cDNA clones HFK2 and HFK3 were analyzed by restriction analysis and sequencing. HFK2 and HFK3 were found to be closely related but different from HFK1. Therefore, it would appear that HFK1, HFK2, HFK3, and BF-1 form a new fork head related subfamily. 33 refs., 6 figs.

  4. Water quality of Fremont Lake and New Fork Lakes, western Wyoming: A progress report

    SciTech Connect

    Peterson, D.A.; Averett, R.C.; Mora, K.L.

    1987-01-01

    Fremont Lake and New Fork Lakes in the New Fork River drainage of western Wyoming were selected for a comprehensive study of hydrologic processes affecting mountain lakes in the Rocky Mountains. Information is needed about lakes in this area to assess their response to existing and planned development. The concerns include regional issues such as acid precipitation from gas-sweetening plants, coal-fired power plants, and smelters, as well as local issues, such as shoreline development and raising outlet control structures. Onsite measurements indicated strong thermal stratification in the lakes during the summer. Isothermal conditions occurred during December 1983 and May 1984. Mean phytoplankton concentrations were less than 5,000 cells/ml, and chlorophyll a concentrations were weakly correlated with phytoplankton concentrations. Zooplankton concentrations were small, less than 6 organisms/L. The numbers of benthic invertebrates/unit area in Fremont Lake were extremely small. The lake waters and inflow and outflow streams were chemically dilute solutions. Mean dissolved-solids concentrations were 13 mg/L in Fremont Lake and 24 mg/L in New Fork Lakes. Calcium and bicarbonate were the predominant ions. Concentrations of phosphorus and nitrogen usually were less than detection limits. Trace-metals concentrations in the lakes were similar to those in precipitation and generally were small. Dissolved organic-carbon concentrations were about 1 mg/L. Concentrations of fulvic and humic acids were relatively large in the inlet of Fremont Lake during the spring. Pine Creek has deposited 800 metric tons of sediment, on an annual average, to the delta of Fremont Lake. Most sediment is deposited during spring runoff. 32 refs., 33 figs., 9 tabs.

  5. Water quality of Fremont Lake and New Fork Lakes, western Wyoming; a progress report

    USGS Publications Warehouse

    Peterson, D.A.; Averett, R.C.; Mora, K.L.

    1987-01-01

    Fremont Lake and New Fork Lakes in the New Fork River drainage of western Wyoming were selected for a comprehensive study of hydrologic processes affecting mountain lakes in the Rocky Mountains. Information is needed about lakes in this area to assess their response to existing and planned development. The concerns include regional issues such as acid precipitation from gas-sweetening plants, coal-fired powerplants, and smelters, as well as local issues, such as shoreline development and raising outlet control structures. Onsite measurements indicated strong thermal stratification in the lakes during the summer. Isothermal conditions occurred during December 1983 and May 1984. Mean phytoplankton concentrations were less than 5,000 cells/ml, and chlorophyll a concentrations were weakly correlated with phytoplankton concentrations. Zooplankton concentrations were small, less than 6 organisms/L. The numbers of benthic invertebrates/unit area in Fremont Lake were extremely small. The lake waters and inflow and outflow streams were chemically dilute solutions. Mean dissolved-solids concentrations were 13 mg/L in Fremont Lake and 24 mg/L in New Fork Lakes. Calcium and bicarbonate were the predominant ions. Concentrations of phosphorus and nitrogen usually were less than detection limits. Trace-metals concentrations in the lakes were similar to those in precipitation and generally were small. Dissolved organic-carbon concentrations were about 1 mg/L. Concentrations of fulvic and humic acids were relatively large in the inlet of Fremont Lake during the spring. Pine Creek has deposited 800 metric tons of sediment, on an annual average, to the delta of Fremont Lake. Most sediment is deposited during spring runoff. (USGS)

  6. Holocene history of deep-seated landsliding in the North Fork Stillaguamish River valley from surface roughness analysis, radiocarbon dating, and numerical landscape evolution modeling

    NASA Astrophysics Data System (ADS)

    Booth, Adam M.; LaHusen, Sean R.; Duvall, Alison R.; Montgomery, David R.

    2017-02-01

    Documenting spatial and temporal patterns of past landsliding is a challenging step in quantifying the effect of landslides on landscape evolution. While landslide inventories can map spatial distributions, lack of dateable material, landslide reactivations, or time, access, and cost constraints generally limit dating large numbers of landslides to analyze temporal patterns. Here we quantify the record of the Holocene history of deep-seated landsliding along a 25 km stretch of the North Fork Stillaguamish River valley, Washington State, USA, including the 2014 Oso landslide, which killed 43 people. We estimate the ages of more than 200 deep-seated landslides in glacial sediment by defining an empirical relationship between landslide deposit age from radiocarbon dating and landslide deposit surface roughness. We show that roughness systematically decreases with age as a function of topographic wavelength, consistent with models of disturbance-driven soil transport. The age-roughness model predicts a peak in landslide frequency at 1000 calibrated (cal) years B.P., with very few landslide deposits older than 7000 cal years B.P. or younger than 100 cal years B.P., likely reflecting a combination of preservation bias and a complex history of changing climate, base level, and seismic shaking in the study area. Most recent landslides have occurred where channels actively interact with the toes of hillslopes composed of glacial sediments, suggesting that lateral channel migration is a primary control on the location of large deep-seated landslides in the valley.

  7. Best management practices plan for the Lower East Fork Poplar Creek Operable Unit, Oak Ridge, Tennessee

    SciTech Connect

    1996-04-01

    This plan was prepared in support of the Phase II Remedial Design Report (DOE/OR/01-1449&D1) and in accordance with requirements under CERCLA to present the plan for best management practices to be followed during the remediation. This document provides the Environmental Restoration Program with information about spill prevention and control, water quality monitoring, good housekeeping practices, sediment and erosion control measures, and inspections and environmental compliance practices to be used during Phase II of the remediation project for the Lower East Fork Poplar Creek Operable Unit.

  8. South Fork Zumbro River Stage 1B, Rochester, Minnesota. Design Memorandum Number 2, Flood Control Project

    DTIC Science & Technology

    1987-02-01

    Softb AMuchy, lack G M S, Very Dense, Block /00 Bo. 970 =_ Loose, Black-Gray 001, Very Dense, Tan -Gray 20 Very SofC Block TeO of Bedrock 2 , •MI P/a...Env cae,•,+,"’ epd ~-TaP ay. Dwq. 86 -1034e /0 May 49S6 :WS 9743 1 Water I To- of Bedrok -970 3 A/oaes: J .960 I/ ..Fork Zunbro River eev. 974.3: 2. ft

  9. Oxbow Conservation Area; Middle Fork John Day River, Annual Report 2001-2002.

    SciTech Connect

    Robertson, Shaun; Smith, Brent; Cochran, Brian

    2003-04-01

    In early 2001, the Confederated Tribes of Warm Springs, through their John Day Basin Office, concluded the acquisition of the Middle Fork Oxbow Ranch. Under a memorandum of agreement with the Bonneville Power Administration (BPA), the Tribes are required to provided BPA an 'annual written report generally describing the real property interests in the Project, HEP analyses undertaken or in progress, and management activities undertaken or in progress'. This report is to be provided to the BPA by 30 April of each year. This is the first annual report filed for the Oxbow Ranch property.

  10. South Fork of the Santa Clara River, Santa Clarita Valley, California. Supplement.

    DTIC Science & Technology

    1985-01-01

    designed as a broad - crested weir to pass the maximum probable flood (PF) with a peak of 24,500 ofs. The spillway crest length of 100 feet and the...California or the EPA. The Clean Water Act of 1977 requires a Federal agency to evaluate the effects of discharge of dredged or fill material into waters of...J42 THE EVALUATION OF THE EFFECTS OF THIE DISCHARGE OF DREDGED OR FILL MATERIAL INTO THE WATERS OF THE UNITED STATES SOUTH FORK, SANTA CLARA RIVER LOlS

  11. Hydrogeologic framework of the North Fork and surrounding areas, Long Island, New York

    USGS Publications Warehouse

    Schubert, Christopher E.; Bova, Richard G.; Misut, Paul E.

    2004-01-01

    Ground water on the North Fork of Long Island is the sole source of drinking water, but the supply is vulnerable to saltwater intrusion and upconing in response to heavy pumping. Information on the area's hydrogeologic framework is needed to analyze the effects of pumping and drought on ground-water levels and the position of the freshwater-saltwater interface. This will enable water-resource managers and water-supply purveyors to evaluate a wide range of water-supply scenarios to safely meet water-use demands. The extent and thickness of hydrogeologic units and position of the freshwater-saltwater interface were interpreted from previous work and from exploratory drilling during this study.The fresh ground-water reservoir on the North Fork consists of four principal freshwater flow systems (referred to as Long Island mainland, Cutchogue, Greenport, and Orient) within a sequence of unconsolidated Pleistocene and Late Cretaceous deposits. A thick glacial-lake-clay unit appears to truncate underlying deposits in three buried valleys beneath the northern shore of the North Fork. Similar glacial-lake deposits beneath eastern and east-central Long Island Sound previously were inferred to be younger than the surficial glacial deposits exposed along the northern shore of Long Island. Close similarities in thickness and upper-surface altitude between the glacial-lake-clay unit on the North Fork and the glacial-lake deposits in Long Island Sound indicate, however, that the two are correlated at least along the North Fork shore.The Matawan Group and Magothy Formation, undifferentiated, is the uppermost Cretaceous unit on the North Fork and constitutes the Magothy aquifer. The upper surface of this unit contains a series of prominent erosional features that can be traced beneath Long Island Sound and the North Fork. Northwest-trending buried ridges extend several miles offshore from areas southeast of Rocky Point and Horton Point. A promontory in the irregular, north

  12. Thermoelastic investigation of a quartz tuning fork used in infrared spectroscopy

    SciTech Connect

    Spajer, M. Cavallier, B.; Euphrasie, S.; Matten, G.; Vacheret, X.; Vairac, P.; Vernier, D.; Jalocha, A.

    2013-11-11

    The performances of quartz tuning forks (QTF) used in infrared spectroscopy for pollutant detection are investigated. The transduction between light and QTF vibration is elucidated, thanks to QTF encapsulation under vacuum. From the sensitivity enhancement which is obtained, we conclude that their interaction is photo-thermoelastic rather than photo-thermoacoustic. A mapping of the local sensitivity of the QTF is obtained by scanning its faces with the excitation probe beam. The comparison between the signal mapping and the theoretical strain mapping indicates that the most efficient areas of the QTF correspond to the areas where the strain or stress is the highest.

  13. Photo-thermal quartz tuning fork excitation for dynamic mode atomic force microscope

    SciTech Connect

    Bontempi, Alexia; Teyssieux, Damien; Thiery, Laurent; Hermelin, Damien; Vairac, Pascal; Friedt, Jean-Michel

    2014-10-13

    A photo-thermal excitation of a Quartz Tuning Fork (QTF) for topographic studies is introduced. The non-invasive photo-thermal excitation presents practical advantages compared to QTF mechanical and electrical excitations, including the absence of the anti-resonance and its associated phase rotation. Comparison between our theoretical model and experiments validate that the optical transduction mechanism is a photo-thermal rather than photo-thermoacoustic phenomenon. Topographic maps in the context of near-field microscopy distance control have been achieved to demonstrate the performance of the system.

  14. Autoimmune Pancreatitis Diagnosed with Core Biopsy Obtained from a Novel Fork-Tip EUS Needle

    PubMed Central

    Saini, Sameer D.; Chamberlain, Priscilla R.; Prabhu, Anoop

    2017-01-01

    The endoscopic diagnosis of autoimmune pancreatitis from histologic criteria remains challenging as it requires adequate architectural details rather than cytology alone. A 67-year-old man presented with progressive abdominal pain and weight loss. Cross-sectional imaging showed inflammatory changes of the pancreatic body and tail and periaortitis on abdominal computed tomography, but normal serum immunoglobulin G4. A mass-like lesion of the pancreatic body and tail was identified on endoscopic ultrasonography. A histologic diagnosis of autoimmune pancreatitis was accomplished through needle biopsy using a novel fork-tip needle. PMID:28144612

  15. Hydrogeologic framework of the North Fork and surrounding areas, Long Island, New York

    USGS Publications Warehouse

    Schubert, Christopher E.; Bova, Richard G.; Misut, Paul E.

    2004-01-01

    Ground water on the North Fork of Long Island is the sole source of drinking water, but the supply is vulnerable to saltwater intrusion and upconing in response to heavy pumping. Information on the area?s hydrogeologic framework is needed to analyze the effects of pumping and drought on ground-water levels and the position of the freshwater-saltwater interface. This will enable water-resource managers and water-supply purveyors to evaluate a wide range of water-supply scenarios to safely meet water-use demands. The extent and thickness of hydrogeologic units and position of the freshwater-saltwater interface were interpreted from previous work and from exploratory drilling during this study. The fresh ground-water reservoir on the North Fork consists of four principal freshwater flow systems (referred to as Long Island mainland, Cutchogue, Greenport, and Orient) within a sequence of unconsolidated Pleistocene and Late Cretaceous deposits. A thick glacial-lake-clay unit appears to truncate underlying deposits in three buried valleys beneath the northern shore of the North Fork. Similar glacial-lake deposits beneath eastern and east-central Long Island Sound previously were inferred to be younger than the surficial glacial deposits exposed along the northern shore of Long Island. Close similarities in thickness and upper-surface altitude between the glacial-lake-clay unit on the North Fork and the glacial-lake deposits in Long Island Sound indicate, however, that the two are correlated at least along the North Fork shore. The Matawan Group and Magothy Formation, undifferentiated, is the uppermost Cretaceous unit on the North Fork and constitutes the Magothy aquifer. The upper surface of this unit contains a series of prominent erosional features that can be traced beneath Long Island Sound and the North Fork. Northwest-trending buried ridges extend several miles offshore from areas southeast of Rocky Point and Horton Point. A promontory in the irregular, north

  16. Note: Wide band amplifier for quartz tuning fork sensors with digitally controlled stray capacitance compensation

    NASA Astrophysics Data System (ADS)

    Peng, Ping; Hao, Lifeng; Ding, Ning; Jiao, Weicheng; Wang, Qi; Zhang, Jian; Wang, Rongguo

    2015-11-01

    We presented a preamplifier design for quartz tuning fork (QTF) sensors in which the stray capacitance is digitally compensated. In this design, the manually controlled variable capacitor is replaced by a pair of varicap diodes, whose capacitance could be accurately tuned by a bias voltage. A tuning circuit including a single side low power operational amplifier, a digital-to-analog converter, and a microprocessor is also described, and the tuning process can be conveniently carried out on a personal computer. For the design, the noise level was investigated experimentally.

  17. Integrated Natural Resources Management Plan Grand Forks Air Force Base, North Dakota. 2004-2008

    DTIC Science & Technology

    2005-12-01

    Instruction 32-7064. t.L~~ t .-󈧏 ~~..,c...- I’ CIL- William J. Bender, Colonel, USAF Commander, 319 Air Refueling Wing Grand Forks Air Force Base...Prairie egion US Fish and Wildlife Service PO Box 25486, DFC Denver, CO 80225 Date I 2004·2008 UPDATE FOR INTEGRATED NATURAL RESOURCES...io omv;r<: ~ • -1e conservation and n:’labll! t ?-~~;)𔃻 of r.aturai rr?sources on n::!i~ary installatic:·ls • -~1e sustamable multipurpose use cf

  18. Monitoring the spatiotemporal dynamics of proteins at replication forks and in assembled chromatin using isolation of proteins on nascent DNA.

    PubMed

    Sirbu, Bianca M; Couch, Frank B; Cortez, David

    2012-03-01

    Understanding the processes of DNA replication, chromatin assembly and maturation, and the replication stress response requires the ability to monitor protein dynamics at active and damaged replication forks. Detecting protein accumulation at replication forks or damaged sites has primarily relied on immunofluorescence imaging, which is limited in resolution and antibody sensitivity. Here we describe a procedure to isolate proteins on nascent DNA (iPOND) that permits a high-resolution spatiotemporal analysis of proteins at replication forks or on chromatin following DNA replication in cultured cells. iPOND relies on labeling of nascent DNA with the nucleoside analog 5-ethynyl-2'-deoxyuridine (EdU). Biotin conjugation to EdU-labeled DNA using click chemistry facilitates a single-step streptavidin purification of proteins bound to the nascent DNA. iPOND permits an interrogation of any cellular process linked to DNA synthesis using a 3- to 4-d protocol.

  19. The Influence of Humidity on the Shear Force Between Tip and Sample in Nsom Using Piezoelectric Fork

    NASA Astrophysics Data System (ADS)

    Zhang, Tianhao; Fang, Zheyu; Zheng, Jianya; Gao, Limo; Yang, Haidong; Yin, Meirong; Yang, Jia; Lu, Yanzhen; Kang, Huizhen; Yang, Dapeng; Yang, Huizhan

    The distance between tip and sample can be regulated using piezoelectric quartz fork glued with micro optic fiber probe. A biquadrate vibration equation for the fork-probe-sample system is established to theoretically analyze the relations of the electric current flow through fork versus tip-sample (T-S) distance (I-d). The I-d curve and the action distance for shear force are influenced by environmental humidity. The results reinforce the opinions in the earlier works by other researches that the physical origin of the shear force is due to a material filling the tip-sample gap. Furthermore, the intrinsic reasons for shear force damping between tip and sample have been confirmed and developed, i.e. the water and hydrocarbon coupled between optic fiber probe and sample due to the capillary cohesion force.

  20. Qualitative Assessment: Evaluating the Impacts of Climate Change on Endangered Species Act Recovery Actions for the South Fork Nooksack River, WA

    EPA Science Inventory

    The South Fork Nooksack River (South Fork) is located in northwest Washington State and is home to nine species of Pacific salmon, including Nooksack early Chinook (aka, spring Chinook salmon), an iconic species for the Nooksack Indian Tribe. The quantity of salmon in the South F...

  1. Stream-Sediment Geochemistry in Mining-Impacted Drainages of the Yankee Fork of the Salmon River, Custer County, Idaho

    USGS Publications Warehouse

    Frost, Thomas P.; Box, Stephen E.

    2009-01-01

    This reconnaissance study was undertaken at the request of the USDA Forest Service, Region 4, to assess the geochemistry, in particular the mercury and selenium contents, of mining-impacted sediments in the Yankee Fork of the Salmon River in Custer County Idaho. The Yankee Fork has been the site of hard-rock and placer mining, primarily for gold and silver, starting in the 1880s. Major dredge placer mining from the 1930s to 1950s in the Yankee Fork disturbed about a 10-kilometer reach. Mercury was commonly used in early hard-rock mining and placer operations for amalgamation and recovery of gold. During the late 1970s, feasibility studies were done on cyanide-heap leach recovery of gold from low-grade ores of the Sunbeam and related deposits. In the mid-1990s a major open-pit bulk-vat leach operation was started at the Grouse Creek Mine. This operation shut down when gold values proved to be lower than expected. Mercury in stream sediments in the Yankee Fork ranges from below 0.02 ppm to 7 ppm, with the highest values associated with old mill locations and lode and placer mines. Selenium ranges from below the detection limit for this study of 0.2 ppm to 4 ppm in Yankee Fork sediment samples. The generally elevated selenium content in the sediment samples reflect the generally high selenium contents in the volcanic rocks that underlie the Yankee Fork and the presence of gold and silver selenides in some of the veins that were exploited in the early phases of mining.

  2. Native Aging Visions: A Resource for Native Elders. Volume 1, 1994-97.

    ERIC Educational Resources Information Center

    Native Aging Visions, 1997

    1997-01-01

    This volume of newsletters reports on the activities and research projects of the National Resource Center on Native American Aging located at the University of North Dakota, Grand Forks. The Center studies health issues and access problems facing American Indian, Alaska Native, and Native Hawaiian elders. Specifically, the resource center was…

  3. Anadronous Fish Habitat Enhancement for the Middle Fork and Upper Salmon River, 1988 Annual Report.

    SciTech Connect

    Andrews, John

    1990-01-01

    The wild and natural salmon and steelhead populations in the Middle Fork and Upper Salmon River are at a critical low. Habitat enhancement through decreasing sediment loads, increasing vegetative cover, removing passage barriers, and providing habitat diversity is imperative to the survival of these specially adapted fish, until passage problems over the Columbia River dams are solved. Personnel from the Boise and Sawtooth National Forests completed all construction work planned for 1988. In Bear Valley, 1573 feet of juniper revetment was constructed at eleven sites, cattle were excluded from 1291 feet of streambanks to prevent bank breakdown, and a small ephemeral gully was filled with juniper trees. Work in the Upper Salmon Drainage consisted of constructing nine rock sills/weirs, two rock deflectors, placing riprap along forty feet of streambank, construction of 2.1 miles of fence on private lands, and opening up the original Valley Creek channel to provide spring chinook passage to the upper watershed. A detailed stream survey of anadromous fish habitat covering 72.0 miles of streams in the Middle Fork Sub-basin was completed.

  4. RNA polymerase II contributes to preventing transcription-mediated replication fork stalls.

    PubMed

    Felipe-Abrio, Irene; Lafuente-Barquero, Juan; García-Rubio, María L; Aguilera, Andrés

    2015-01-13

    Transcription is a major contributor to genome instability. A main cause of transcription-associated instability relies on the capacity of transcription to stall replication. However, we know little of the possible role, if any, of the RNA polymerase (RNAP) in this process. Here, we analyzed 4 specific yeast RNAPII mutants that show different phenotypes of genetic instability including hyper-recombination, DNA damage sensitivity and/or a strong dependency on double-strand break repair functions for viability. Three specific alleles of the RNAPII core, rpb1-1, rpb1-S751F and rpb9∆, cause a defect in replication fork progression, compensated for by additional origin firing, as the main action responsible for instability. The transcription elongation defects of rpb1-S751F and rpb9∆ plus our observation that rpb1-1 causes RNAPII retention on chromatin suggest that RNAPII could participate in facilitating fork progression upon a transcription-replication encounter. Our results imply that the RNAPII or ancillary factors actively help prevent transcription-associated genome instability.

  5. Histone H2B mono-ubiquitylation maintains genomic integrity at stalled replication forks

    PubMed Central

    Northam, Matthew R.; Trujillo, Kelly M.

    2016-01-01

    Histone modifications play an important role in regulating access to DNA for transcription, DNA repair and DNA replication. A central player in these events is the mono-ubiquitylation of histone H2B (H2Bub1), which has been shown to regulate nucleosome dynamics. Previously, it was shown that H2Bub1 was important for nucleosome assembly onto nascent DNA at active replication forks. In the absence of H2Bub1, incomplete chromatin structures resulted in several replication defects. Here, we report new evidence, which shows that loss of H2Bub1 contributes to genomic instability in yeast. Specifically, we demonstrate that H2Bub1-deficient yeast accumulate mutations at a high frequency under conditions of replicative stress. This phenotype is due to an aberrant DNA Damage Tolerance (DDT) response upon fork stalling. We show that H2Bub1 normally functions to promote error-free translesion synthesis (TLS) mediated by DNA polymerase eta (Polη). Without H2Bub1, DNA polymerase zeta (Polζ) is responsible for a highly mutagenic alternative mechanism. While H2Bub1 does not appear to regulate other DDT pathways, error-free DDT mechanisms are employed by H2Bub1-deficient cells as another means for survival. However, in these instances, the anti-recombinase, Srs2, is essential to prevent the accumulation of toxic HR intermediates that arise in an unconstrained chromatin environment. PMID:27458205

  6. FANCD2 influences replication fork processes and genome stability in response to clustered DSBs.

    PubMed

    Zhu, Jiayun; Su, Fengtao; Mukherjee, Shibani; Mori, Eiichiro; Hu, Burong; Asaithamby, Aroumougame

    2015-01-01

    Fanconi Anemia (FA) is a cancer predisposition syndrome and the factors defective in FA are involved in DNA replication, DNA damage repair and tumor suppression. Here, we show that FANCD2 is critical for genome stability maintenance in response to high-linear energy transfer (LET) radiation. We found that FANCD2 is monoubiquitinated and recruited to the sites of clustered DNA double-stranded breaks (DSBs) specifically in S/G2 cells after high-LET radiation. Further, FANCD2 facilitated the repair of clustered DSBs in S/G2 cells and proper progression of S-phase. Furthermore, lack of FANCD2 led to a reduced rate of replication fork progression and elevated levels of both replication fork stalling and new origin firing in response to high-LET radiation. Mechanistically, FANCD2 is required for correct recruitment of RPA2 and Rad51 to the sites of clustered DSBs and that is critical for proper processing of clustered DSBs. Significantly, FANCD2-decifient cells exhibited defective chromosome segregation, elevated levels of chromosomal aberrations, and anchorage-independent growth in response to high-LET radiation. These findings establish FANCD2 as a key factor in genome stability maintenance in response to high-LET radiation and as a promising target to improve cancer therapy.

  7. The forked tongue and edge detection in snakes (Crotalus oreganus): an experimental test.

    PubMed

    Parker, M Rockwell; Young, Bruce A; Kardong, Kenneth V

    2008-02-01

    Many stimulus-detection systems are lateralized to allow for simultaneous comparison of paired stimuli. It has been hypothesized that the deeply forked tongue of snakes and some derived lizards functions as a chemical edge detector where cues gathered by each tine are kept separate to provide two points of lateral odor assessment by the central nervous system via vomeronasal input. While following a chemical trail, one time can be on the trail, the other off, and such differential information prompts the snake to turn back to the trail. The authors tested this hypothesis in rattlesnakes within a predatory context by unilaterally severing the vomeronasal nerves. If edge detection is used by snakes during prey trailing, then unilateral denervation should disrupt trailing ability. The authors found no change in the seven separate trailing parameters measured. Therefore, they found no support for the edge detection hypothesis as it applies to prey trailing behavior. Instead, the deeply forked tongue may represent a chemosensory specialization to increase odor-sampling area, with snakes and derived lizards detecting only the concentration of chemical trails.

  8. An investigation of shallow ground-water quality near East Fork Poplar Creek, Oak Ridge, Tennessee

    USGS Publications Warehouse

    Carmichael, J.K.

    1989-01-01

    Alluvial soils of the flood plain of East Fork Poplar Creek in Oak Ridge, Tennessee, are contaminated with mercury and other metals, organic compounds, and radio-nuclides originating from the Y-12 Plant, a nuclear-processing facility located within the U.S. Department of Energy 's Oak Ridge Reservation. Observation wells were installed in the shallow aquifer of the flood plain, and water quality samples were collected to determine if contaminants are present in the shallow groundwater. Groundwater in the shallow aquifer occurs under water-table conditions. Recharge is primarily from precipitation and discharge is to East Fork Poplar Creek. Groundwater levels fluctuate seasonally in response to variations in recharge and evapotranspiration. During extremely dry periods, the water table drops below the base of the shallow aquifer in some flood-plain areas. Contaminants found in water samples from several of the wells in concentrations which equaled or exceeded drinking-water standards established by the U.S. Environmental Protection Agency are antimony, chromium, lead, mercury, selenium, phenols, and strontium-90. Total and dissolved uranium concentrations exceeded the analytical detection limit in nearly 70% of the wells in the flood plain. The results of water quality determinations demonstrate that elevated concentrations of most trace metals (and possibly organic compounds and radionuclides) were caused by contaminated sediments in the samples. The presence of contaminated sediment in samples is suspected to be the result of borehole contamination during well installation. (USGS)

  9. Quartz Tuning Fork Pressure Gauge for High-Pressure Liquid Helium

    NASA Astrophysics Data System (ADS)

    Botimer, J.; Velasco, A.; Taborek, P.

    2017-01-01

    We have measured the quality factor Q and the frequency f of a 32-kHz quartz tuning fork immersed in liquid ^4He between 0.9 and 3.0 K, over pressures ranging from the saturated vapor pressure to ≈ 25 atm. At constant pressure, as a function of temperature, the quality factor and frequency have strong features related to the temperature dependence of the superfluid fraction. At constant temperature, Q depends on the superfluid fraction, while the frequency is a smooth function of pressure. The behavior is explained using a simple hydrodynamic model. The liquid helium viscosity is obtained from measured values of Q, and together with tabulated values of the helium density as a function of pressure and temperature, the frequency shift can be parameterized as a function of temperature and pressure. The observed sensitivity is ≈ 7.8 Hz/atm. The quartz tuning fork provides a compact low power method of measuring the pressure in the bulk liquid.

  10. RNA polymerase II contributes to preventing transcription-mediated replication fork stalls

    PubMed Central

    Felipe-Abrio, Irene; Lafuente-Barquero, Juan; García-Rubio, María L; Aguilera, Andrés

    2015-01-01

    Transcription is a major contributor to genome instability. A main cause of transcription-associated instability relies on the capacity of transcription to stall replication. However, we know little of the possible role, if any, of the RNA polymerase (RNAP) in this process. Here, we analyzed 4 specific yeast RNAPII mutants that show different phenotypes of genetic instability including hyper-recombination, DNA damage sensitivity and/or a strong dependency on double-strand break repair functions for viability. Three specific alleles of the RNAPII core, rpb1-1, rpb1-S751F and rpb9Δ, cause a defect in replication fork progression, compensated for by additional origin firing, as the main action responsible for instability. The transcription elongation defects of rpb1-S751F and rpb9Δ plus our observation that rpb1-1 causes RNAPII retention on chromatin suggest that RNAPII could participate in facilitating fork progression upon a transcription-replication encounter. Our results imply that the RNAPII or ancillary factors actively help prevent transcription-associated genome instability. PMID:25452497

  11. The Oak Ridge Y-12 Plant biological monitoring and abatement program for East Fork Poplar Creek

    SciTech Connect

    Loar, J.M.; Adams, S.M.; Allison, L.J.; Giddings, J.M.; McCarthy, J.F.; Southworth, G.R.; Smith, J.G.; Stewart, A.J.; Springborn Bionomics, Inc., Wareham, MA; Oak Ridge National Lab., TN )

    1989-10-01

    In May 1985, a National Pollutant Discharge Elimination System permit was issued for the Oak Ridge Y-12 Plant, a nuclear weapons components production facility located in Oak Ridge, Tennessee, and operated by Martin Marietta Energy Systems, Inc., for the US Department of Energy. As a condition of the permit, a Biological Monitoring and Abatement Program (BMAP) was developed to demonstrate that the effluent limitations established for the Oak Ridge Y-12 Plant protect the classified uses of the receiving stream (East Fork Poplar Creek), in particular, the growth and propagation of fish and aquatic life, as designated by the Tennessee Department of Health and Environment. A second purpose for the BMAP is to document the ecological effects resulting from implementation of a water pollution control program that will include construction of nine new wastewater treatment facilities over the next 4 years. Because of the complex nature of the effluent discharged to East Fork Poplar Creek and the temporal and spatial variability in the composition of the effluent (i.e., temporal variability related to various pollution abatement measures that will be implemented over the next several years and spatial variability caused by pollutant inputs downstream of the Oak Ridge Y-12 Plant), a comprehensive, integrated approach to biological monitoring was developed for the BMAP. 39 refs., 5 figs., 8 tabs.

  12. Ground motions from the 2002 Au Sable Forks, New York earthquake of M5.0

    NASA Astrophysics Data System (ADS)

    Sonley, E.; Atkinson, G. M.

    2002-12-01

    The moment magnitude (M) 5.0 earthquake that occurred near Au Sable Forks, New York on April 20, 2002 is the first moderate event in eastern North America to be well recorded on modern regional broadband seismographic stations, and is thus important in refining our understanding of source and propagation processes of moderate ENA earthquakes. We analyze the available seismographic recordings to obtain the source spectrum of the Au Sable Forks earthquake, comparing the results obtained using two methods. In the Direct Method, the Fourier spectra of the records from each station are corrected back to the source by using an empirical regional attenuation model for ENA. In the Empirical Green's Function Method, aftershocks are used as empirical Green's Functions to remove path and site effects. Results from these two methods agree closely, and are in agreement with a two-corner source model for ENA. A pronounced sag in the source spectrum at a frequency near 2 Hz is suggestive of significant source complexity. Observed response spectral amplitudes agree well with the predictions of several ground-motion relations for ENA for an event of M 5.0. It is concluded that ground motions from this earthquake were 'typical' for ENA earthquakes of this magnitude.

  13. Resonance frequency-retuned quartz tuning fork as a force sensor for noncontact atomic force microscopy

    SciTech Connect

    Ooe, Hiroaki; Sakuishi, Tatsuya; Arai, Toyoko; Nogami, Makoto; Tomitori, Masahiko

    2014-07-28

    Based on a two-prong type quartz tuning fork, a force sensor with a high Q factor, which we call a retuned fork sensor, was developed for non-contact atomic force microscopy (nc-AFM) with atomic resolution. By cutting a small notch and attaching an AFM tip to one prong, its resonance frequency can be retuned to that of the other intact prong. In balancing the two prongs in this manner, a high Q factor (>50 000 in ultrahigh vacuum) is obtained for the sensor. An atomic resolution image of the Si(111)-7 × 7 surface was demonstrated using an nc-AFM with the sensor. The dependence of the Q factor on resonance frequency of the sensor and the long-range force between tip and sample were measured and analyzed in view of the various dissipation channels. Dissipation in the signal detection circuit turned out to be mainly limited by the total Q factor of the nc-AFM system.

  14. Histone H2B mono-ubiquitylation maintains genomic integrity at stalled replication forks.

    PubMed

    Northam, Matthew R; Trujillo, Kelly M

    2016-11-02

    Histone modifications play an important role in regulating access to DNA for transcription, DNA repair and DNA replication. A central player in these events is the mono-ubiquitylation of histone H2B (H2Bub1), which has been shown to regulate nucleosome dynamics. Previously, it was shown that H2Bub1 was important for nucleosome assembly onto nascent DNA at active replication forks. In the absence of H2Bub1, incomplete chromatin structures resulted in several replication defects. Here, we report new evidence, which shows that loss of H2Bub1 contributes to genomic instability in yeast. Specifically, we demonstrate that H2Bub1-deficient yeast accumulate mutations at a high frequency under conditions of replicative stress. This phenotype is due to an aberrant DNA Damage Tolerance (DDT) response upon fork stalling. We show that H2Bub1 normally functions to promote error-free translesion synthesis (TLS) mediated by DNA polymerase eta (Polη). Without H2Bub1, DNA polymerase zeta (Polζ) is responsible for a highly mutagenic alternative mechanism. While H2Bub1 does not appear to regulate other DDT pathways, error-free DDT mechanisms are employed by H2Bub1-deficient cells as another means for survival. However, in these instances, the anti-recombinase, Srs2, is essential to prevent the accumulation of toxic HR intermediates that arise in an unconstrained chromatin environment.

  15. Middle Fork Holston River watershed biological assessment, summers of 1986 and 1987

    SciTech Connect

    Saylor, C.F.; Hill, D.M.; Ahlstedt, S.A.; Brown, A.M.

    1988-05-01

    Fish and macroinvertebrates were collected to obtain a qualitative and quantitative determination relating the impacts of land use activities on aquatic fauna and water quality in watersheds of the Middle Fork Holston River. Samples were compared to historical data, used for calculating an Index of Biological Integrity (IBI), and examined for diversity and abundance of macroinvertebrates. Most IBI's determined for subwatersheds of the Middle Fork Holston River (MFHR) supported land use inventories and soil loss estimates previously completed by TVA in 1985. These inventories targeted streams likely to be impacted by siltation, agricultural runoff, and other nonpoint pollution sources. Findings indicated that siltation and enrichment had increased in the mainstream of MFHR since 1969. Several sites exhibited characteristics implying additional forms of pollution which were impacting the fauna. Benthic macroinvertebrate samples were helpful in documenting degradation but did not always support IBI's and land use inventory and soil loss estimates. Macroinvertebrate fauna are typically more resilient and recover faster than fish fauna, offering a partial explanation for this phenomenon. 6 refs., 3 figs., 12 tabs.

  16. Fresnel and Fraunhofer diffraction of a Gaussian laser beam by fork-shaped gratings.

    PubMed

    Janicijevic, Ljiljana; Topuzoski, Suzana

    2008-11-01

    Expressions describing the vortex beams that are generated by the process of Fresnel diffraction of a Gaussian beam incident out of waist on fork-shaped gratings of arbitrary integer charge p, and vortex spots in the case of Fraunhofer diffraction by these gratings, are deduced. The common general transmission function of the gratings is defined and specialized for the cases of amplitude holograms, binary amplitude gratings, and their phase versions. Optical vortex beams, or carriers of phase singularity with charges mp and -mp, are the higher negative and positive diffraction-order beams. The radial part of their wave amplitudes is described by the product of the mpth-order Gauss-doughnut function and a Kummer function, or by the first-order Gauss-doughnut function and the difference of two modified Bessel functions whose orders do not match the singularity charge value. The wave amplitude and the intensity distributions are discussed for the near and far fields in the focal plane of a convergent lens, as well as the specialization of the results when the grating charge p=0; i.e., the grating turns from forked into rectilinear. The analytical expressions for the vortex radii are also discussed.

  17. Mussels: the forgotten fauna of regulated rivers: a case study of the Caney Fork River

    USGS Publications Warehouse

    Layzer, James B.; Gordon, Mark E.; Anderson, Robert M.

    1993-01-01

    During the past century freshwater mussel populations have declined precipitously throughout North America. Much of this loss has resulted from the construction of dams. In the Cumberland River system, 23% (22 species) of the historic mussel fauna is extinct or listed as endangered. Several additional species have either been extirpated from the Cumberland River or exist only in small, non-reproducing populations. Mussels of headwater streams have been severely affected by coal mining and poor land use practices. An intensive survey was conducted in the Caney Fork River, a major tributary to the Cumberland River, to determine the historic and extant mussel fauna. The results indicate that at least 37 species of mussels have been extirpated from the Caney Fork River, mainly as a result of the construction and operation of the Center Hill Dam. Among the species extirpated, two are now extinct, five are endangered and five are candidates for listing as threatened or endangered. Effects associated with this dam include the inundation of 102 km of riverine habitat, the discharge of hypolimnetic water (which limits mussel reproduction) and an alternating pattern of stream bed scouring and dewatering. The recognition of mussel life history requirements during preconstruction could have reduced many of these effects.

  18. Water Quality and Biological Characteristics of the Middle Fork of the Saline River, Arkansas, 2003-06

    USGS Publications Warehouse

    Galloway, Joel M.; Petersen, James C.; Shelby, Erica L.; Wise, Jim A.

    2008-01-01

    The Middle Fork of the Saline River has many qualities that have been recognized by State and Federal agencies. The Middle Fork provides habitat for several rare aquatic species and is part of a larger stream system (the Upper Saline River) that is known for relatively high levels of species richness and relatively high numbers of species of concern. Water-quality samples were collected and streamflow was measured by the U.S. Geological Survey at three sites in the Middle Fork Basin between October 2003 and October 2006. The Arkansas Department of Environmental Quality collected discrete synoptic water-quality samples from eight sites between January 2004 and October 2006. The Arkansas Department of Environmental Quality also sampled fish (September-October 2003) and benthic macroinvertebrate communities (September 2003-December 2005) at five sites. Streamflow varied annually among the three streamflow sites from October 2003 to October 2006. The mean annual streamflow for Brushy Creek near Jessieville (MFS06) was 0.72 cubic meters per second for water years 2004-2006. The Middle Fork below Jessieville (MFS05) had a mean annual streamflow of 1.11 cubic meters per second for water years 2004-2006. The Middle Fork near Owensville (MFS02), the most downstream site, had a mean annual streamflow of 3.01 cubic meters per second. The greatest streamflows at the three sites generally occurred in the winter and spring and the least in the summer. Nutrient dynamics in the Middle Fork are controlled by activities in the basin and processes that occur in the stream. Point sources and nonpoint sources of nutrients occur in the Middle Fork Basin that could affect the water-quality. Nitrogen and phosphorus concentrations generally were greatest in Mill Creek (MFS04E) and in the Middle Fork immediately downstream from the confluence with Mill Creek (MFS04) with decreasing concentrations at sites farther downstream in Middle Fork. The site in Mill Creek is located downstream from a

  19. Ground-water aspects of the lower Henrys Fork region, eastern Idaho

    USGS Publications Warehouse

    Crosthwaite, E.G.; Mundorff, Maurice John; Walker, Eugene H.

    1970-01-01

    The lower Henrys Fork region in eastern Idaho includes the plains and low benches between Ashton and the junction of Henrys Fork and Snake River. The northwestern and western parts of the area are part of the Snake River basalt plain. The central part of the area is occupied by alluvial plains of the Snake, Teton, and Falls Rivers and of Henrys Fork. The alluvial deposits are underlain by basalt. The southeastern part of the area is a bench (Rexburg Bench), chiefly on silicic and basaltic volcanic rocks, which rises gradually to mountain peaks (Big Hole Mountains) southeast of the area. Irrigation wells open to the basalt under the Snake River Plain and the basalt and sands and gravels under the alluvial plains yield large amounts of water with small drawdowns. Irrigation wells in the silicic volcanic rocks and the interbedded ash, pyroclastics, and sedimentary deposits beneath the Rexburg Bench generally yield much less water. The regional water table slopes southwestward beneath the basalt and alluvial plains. It is recharged by precipitation that infiltrates into the ground in the headwaters of Henrys Fork and Falls, and Teton Rivers and by water that moves downward from an extensive perched water body caused by seepage from stream channels and surface-water irrigation. The perched water in part moves vertically down to the regional water table and in part laterally to the streams. Ground water beneath the Rexburg Bench moves generally northwestward to join the regional ground-water body beneath the alluvia,1 and basalt plain, but this area contributes very little recharge to the main aquifer body. Recharge to the regional water table is estimated to average 725,000 acre-feet annually. The regional water table is below the level of the streams in the area, and ground water in the main aquifer, therefore, is not tributary to the streams. Pumping from the regional ground-water reservoir for irrigation or other uses would have no effect on streamflow or surface

  20. A short G1 phase imposes constitutive replication stress and fork remodelling in mouse embryonic stem cells

    PubMed Central

    Ahuja, Akshay K.; Jodkowska, Karolina; Teloni, Federico; Bizard, Anna H.; Zellweger, Ralph; Herrador, Raquel; Ortega, Sagrario; Hickson, Ian D.; Altmeyer, Matthias; Mendez, Juan; Lopes, Massimo

    2016-01-01

    Embryonic stem cells (ESCs) represent a transient biological state, where pluripotency is coupled with fast proliferation. ESCs display a constitutively active DNA damage response (DDR), but its molecular determinants have remained elusive. Here we show in cultured ESCs and mouse embryos that H2AX phosphorylation is dependent on Ataxia telangiectasia and Rad3 related (ATR) and is associated with chromatin loading of the ssDNA-binding proteins RPA and RAD51. Single-molecule analysis of replication intermediates reveals massive ssDNA gap accumulation, reduced fork speed and frequent fork reversal. All these marks of replication stress do not impair the mitotic process and are rapidly lost at differentiation onset. Delaying the G1/S transition in ESCs allows formation of 53BP1 nuclear bodies and suppresses ssDNA accumulation, fork slowing and reversal in the following S-phase. Genetic inactivation of fork slowing and reversal leads to chromosomal breakage in unperturbed ESCs. We propose that rapid cell cycle progression makes ESCs dependent on effective replication-coupled mechanisms to protect genome integrity. PMID:26876348

  1. Monitoring, Modeling, and Emergent Toxicology in the East Fork Watershed: Developing a Test Bed for Water Quality Management.

    EPA Science Inventory

    Overarching objectives for the development of the East Fork Watershed Test Bed in Southwestern Ohio include: 1) providing research infrastructure for integrating risk assessment and management research on the scale of a large multi-use watershed (1295 km2); 2) Focusing on process...

  2. Reactive Transport Modeling Of Remedial Scenarios To Predict Cadmium, Copper, And Zinc In North Fork of Clear Creek, Colorado

    EPA Science Inventory

    The North Fork of Clear Creek (NFCC), Colorado is an acid-mine-drainage-impacted stream typical of many mountain surface waters affected by historic metal mining in the western United States. The stream is devoid of fish primarily because of high metal concentrations in the wate...

  3. A COMPREHENSIVE NONPOINT SOURCE FIELD STUDY FOR SEDIMENT, NUTRIENTS AND PATHOGENS IN THE SOUTH FORK BROAD RIVER WATERSHED, GEORGIA

    EPA Science Inventory

    There is an urgent need for EPA to develop protocols for establishing Total Maximum Daily Loads (TMDLs) in streams, lakes and estuaries. A cooperative TMDL field data collection project between ORD and Region 4 is ongoing in the South Fork Broad River Watershed (SFBR), a 245.18 ...

  4. 76 FR 35009 - Draft Oil and Gas Management Plan/Environmental Impact Statement for Big South Fork National...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-15

    ... designation of ``Special Management Areas'' to provide protection for areas where park resources and values... National Park Service Draft Oil and Gas Management Plan/Environmental Impact Statement for Big South Fork.... ACTION: Notice of Availability of a Draft Oil and Gas Management Plan/ Environmental Impact Statement...

  5. Spatial Variations In The Fate And Transport Of Metals In A Mining-Influenced Stream, North Fork Clear Creek, Colorado

    EPA Science Inventory

    North Fork Clear Creek (NFCC) receives acid-mine drainage (AMD) from multiple abandoned mines in the Clear Creek Watershed. Point sources of AMD originate In the Black Hawk/Central City region of the stream. Water chemistry also is influenced by several non-point sources of AMD,...

  6. Histone H3K56 Acetylation, CAF1, and Rtt106 Coordinate Nucleosome Assembly and Stability of Advancing Replication Forks

    PubMed Central

    Clemente-Ruiz, Marta; González-Prieto, Román; Prado, Félix

    2011-01-01

    Chromatin assembly mutants accumulate recombinogenic DNA damage and are sensitive to genotoxic agents. Here we have analyzed why impairment of the H3K56 acetylation-dependent CAF1 and Rtt106 chromatin assembly pathways, which have redundant roles in H3/H4 deposition during DNA replication, leads to genetic instability. We show that the absence of H3K56 acetylation or the simultaneous knock out of CAF1 and Rtt106 increases homologous recombination by affecting the integrity of advancing replication forks, while they have a minor effect on stalled replication fork stability in response to the replication inhibitor hydroxyurea. This defect in replication fork integrity is not due to defective checkpoints. In contrast, H3K56 acetylation protects against replicative DNA damaging agents by DNA repair/tolerance mechanisms that do not require CAF1/Rtt106 and are likely subsequent to the process of replication-coupled nucleosome deposition. We propose that the tight connection between DNA synthesis and histone deposition during DNA replication mediated by H3K56ac/CAF1/Rtt106 provides a mechanism for the stabilization of advancing replication forks and the maintenance of genome integrity, while H3K56 acetylation has an additional, CAF1/Rtt106-independent function in the response to replicative DNA damage. PMID:22102830

  7. Swimming capability of the remopleuridid trilobite Hypodicranotus striatus: hydrodynamic functions of the exoskeleton and the long, forked hypostome.

    PubMed

    Shiino, Yuta; Kuwazuru, Osamu; Suzuki, Yutaro; Ono, Satoshi

    2012-05-07

    The sophisticated hydrodynamic performance achieved by the exoskeleton and the long, forked hypostome of the remopleuridid trilobite Hypodicranotus striatus was demonstrated using image-based modelling and computational fluid dynamics simulation techniques. To understand the function of the long, forked hypostome, we examined two types of exoskeletal models, one with and one without the hypostome. We simulated the flow structures around the exoskeletal models under several ambient flow velocities to evaluate the shapes of the streamlines, the values of the drag and lift forces and the relevant coefficients acting on the models. The simulation results showed that the long, forked hypostome prevents the formation of a ventral vortex; thus, it stabilises the flow structure under all of the ambient velocities tested. Moreover, the hypostome functions to create positive lift, with stable lift coefficients observed under a wide range of velocities, and to reduce the drag coefficient as velocity increases. These results imply that the hypostome can reduce viscous drag with a modest lift force, which is an essential requirement for actively swimming animals. We conclude that the long, forked hypostome evolved to provide an active and stable swimming system, and we therefore hypothesise that Hypodicranotus exoskeletal morphology resulted from the adaptation to be a high-performance swimmer.

  8. 75 FR 41237 - Public Land Order No. 7746; Withdrawal of Public Lands, South Fork of the American River; California

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-15

    ... mining laws for the Bureau of Land Management to protect the unique natural, scenic, cultural, and... this order does not alter the applicability of the public land laws other than under the mining laws. 3... Bureau of Land Management Public Land Order No. 7746; Withdrawal of Public Lands, South Fork of...

  9. Microsatellite diversity in sympatric reproductive ecotypes of pacific steelhead (Oncorhynchus mykiss) from the Middle Fork Eel River, California

    USGS Publications Warehouse

    Nielsen, J.L.; Fountain, Monique C.

    1999-01-01

    Genetic differentiation between two reproductive ecotypes of anadromous steelhead found in the Middle Fork Eel River in northern California was tested using 16 microsatellite loci. Twelve of these loci showed significant differences in allelic frequency between the two Middle Fork Eel River steelhead populations (Fisher's exact P<0.05). Fisher's combined test for independence also supported significant genetic separation between the two reproductive ecotype (P<0.001). Analysis of molecular variance indicated that only 1% of the overall microsatellite allelic variation contributed to differences between summer- and winter-run steelhead in the Middle Fork Eel River. Variation found among individuals within the two runs equaled 18.2%. Analyses showed less genetic distance between the two populations of steelhead in the Middle Fork Eel River than in comparisons made with geographically proximate coastal winter-run fish. Divergence time based on genetic distance for the two within-basin reproductive ecotypes was estimated to be 16,000-28,000 years ago.

  10. Map showing geochemical summary for the Bald Rock and Middle Fork Feather River Roadless Areas, Butte and Plumas counties, California

    USGS Publications Warehouse

    Peterson, Jocelyn A.; Sorensen, Martin L.

    1985-01-01

    The Bald Rock Roadless Area consists of 3,850 acres in Butte County, Calif. The Middle Rock Feather River Roadless Area consists of 29,300 acres ub Butte and Plumas Counties, Calif. Both roadless areas are in the Plumas National Forest and are on the west slope of the northern Sierra Nevada southwest of Quincy, Calif. (fig. 1). The two roadless areas are alined along the Middle Fork of the Feather River where they include the narrow canyon bottoms and precipitous sidewalls of the Middle Fork and several tributary drainages. Altitudes range from 800 ft in the canyon of the Middle Fork to approximately 6,600 ft at the northwest corner of the map area. The geology of the roadless areas has been briefly summarized by Sorenson and Pietropaoll (1982). This paper summarizes and interprets the semiquantitative emission spectrographic analyses of 106 rock sample and 165 samples of nonmagnetics heavy-mineral stream-sediment concentrates from the Blad Rock and Middle Fork Feather River Roadless Area (Sorenson and others, 1982).

  11. Gas Phase Photoacoustic Spectroscopy in the long-wave IR using Quartz Tuning Forks and Amplitude Modulated Quantum Cascade Lasers

    SciTech Connect

    Wojcik, Michael D.; Phillips, Mark C.; Cannon, Bret D.

    2006-12-31

    A paper to accompany a 20 minute talk about the progress of a DARPA funded project called LPAS. ABSTRACT: We demonstrate the performance of a novel long-wave infrared photoacoustic laser absorbance spectrometer for gas-phase species using an amplitude modulated (AM) quantum cascade (QC) laser and a quartz tuning fork microphone. Photoacoustic signal was generated by focusing the output of a Fabry-Perot QC laser operating at 8.41 micron between the legs of a quartz tuning fork which served as a transducer for the transient acoustic pressure wave. The QC laser was modulated at the resonant frequency of the tuning fork (32.8 kHz). This sensor was calibrated using the infrared absorber Freon-134a by performing a simultanious absorption measurement using a 35 cm absorption cell. The NEAS of this instrument was determined to be 2 x 10^-8 W cm^-1 /Hz^1/2 and the fundamental sensitivity of this technique is limited by the noise floor of the tuning fork itself.

  12. Bull Trout Population and Habitat Surveys in the Middle Fork Willamette and McKenzie Rivers, Annual Report 2002.

    SciTech Connect

    Seals, Jason; Reis, Kelly

    2003-10-01

    Bull trout in the Willamette River Basin were historically distributed throughout major tributaries including the Middle Fork Willamette and McKenzie rivers. Habitat degradation, over-harvest, passage barriers, fish removal by rotenone, and hybridization and competition with non-native brook trout are all likely factors that have led to the decline of bull trout in the Willamette Basin (Ratliff and Howell 1992). The U.S. Fish and Wildlife Service listed the Columbia River bull trout population segment as Threatened under the federal Endangered Species Act in 1998. Four bull trout populations were isolated in the upper Willamette River following the construction of flood control dams on the South Fork McKenzie River, McKenzie River, and Middle Fork Willamette River that created Cougar, Trail Bridge, and Hills Creek reservoirs. Buchanan et al. (1997) described the population in the main stem McKenzie as 'of special concern', the South Fork McKenzie population as 'high risk of extinction', the population above Trail Bridge Reservoir as 'high risk of extinction', and bull trout in the Middle Fork Willamette as 'probably extinct'. Various management efforts such as strict angling regulations and passage improvement projects have been implemented to stabilize and rehabilitate bull trout habitat and populations in the McKenzie River over the past 10 years. Since 1997, bull trout fry from Anderson Creek on the upper McKenzie River have been transferred to the Middle Fork Willamette basin above Hills Creek Reservoir in an attempt to re-establish a reproducing bull trout population. This project was developed in response to concerns over the population status and management of bull trout in the McKenzie and Middle Fork Willamette Rivers by the Oregon Department of Fish and Wildlife during the early 1990s. The project was conducted under measure 9.3G(2) of the Columbia Basin Fish and Wildlife Program to monitor the status, life history, habitat needs, and limiting factors for

  13. Hydrologic and hydraulic analyses for the Black Fork Mohican River Basin in and near Shelby, Ohio

    USGS Publications Warehouse

    Huitger, Carrie A.; Ostheimer, Chad J.; Koltun, G.F.

    2016-05-06

    Hydrologic and hydraulic analyses were done for selected reaches of five streams in and near Shelby, Richland County, Ohio. The U.S. Geological Survey (USGS), in cooperation with the Muskingum Watershed Conservancy District, conducted these analyses on the Black Fork Mohican River and four tributaries: Seltzer Park Creek, Seltzer Park Tributary, Tuby Run, and West Branch. Drainage areas of the four stream reaches studied range from 0.51 to 60.3 square miles. The analyses included estimation of the 10-, 2-, 1-, and 0.2-percent annual-exceedance probability (AEP) flood-peak discharges using the USGS Ohio StreamStats application. Peak discharge estimates, along with cross-sectional and hydraulic structure geometries, and estimates of channel roughness coefficients were used as input to step-backwater models. The step-backwater water models were used to determine water-surface elevation profiles of four flood-peak discharges and a regulatory floodway. This study involved the installation of, and data collection at, a streamflow-gaging station (Black Fork Mohican River at Shelby, Ohio, 03129197), precipitation gage (Rain gage at Reservoir Number Two at Shelby, Ohio, 405209082393200), and seven submersible pressure transducers on six selected river reaches. Two precipitation-runoff models, one for the winter events and one for nonwinter events for the headwaters of the Black Fork Mohican River, were developed and calibrated using the data collected. With the exception of the runoff curve numbers, all other parameters used in the two precipitation-runoff models were identical. The Nash-Sutcliffe model efficiency coefficients were 0.737, 0.899, and 0.544 for the nonwinter events and 0.850 and 0.671 for the winter events. Both of the precipitation-runoff models underestimated the total volume of water, with residual runoff ranging from -0.27 inches to -1.53 inches. The results of this study can be used to assess possible mitigation options and define flood hazard areas that

  14. Water-quality synoptic sampling, July 1999: North Fork Shenandoah River, Virginia

    USGS Publications Warehouse

    Krstolic, Jennifer L.; Hayes, Donald C.

    2004-01-01

    A study was conducted of water-quality conditions that may affect aquatic life during periods of low streamflow on the North Fork Shenandoah River, Va. Monthly mean streamflows in July 1999 at three streamflow-gaging stations were the lowest measured during the historical record on the river. Daily extremes of dissolved-oxygen concentrations were measured, along with pH, specific conductance, and water-temperature values, at 52 sites along 80 mi of the North Fork Shenandoah River from Cootes Store, Va., to its confluence with Passage Creek, near Strasburg, Va. Dissolved-oxygen concentrations ranged from 2.1 to 16.4 milligrams per liter (mg/L). Dissolved-oxygen concentrations were equal to or less than the State water-quality minimum of 4.0 mg/L at 18 of 52 monitoring sites; all 18 sites were in the upper and middle portions of the river, where more than half of the first 34 sites had minimum dissolved-oxygen concentrations equal to or less than 4.0 mg/L. There were large variations from minimum to maximum dissolved-oxygen concentrations, with concentrations fluctuating as much as 10 mg/L per day; and typically 5 mg/L per day during the study period. pH ranged from 7.6 to 9.6, with pH values frequently greater than 9.0 in the downstream portion of the river. Specific-conductance values ranged from 178 to 856 microsiemens per centimeter (?S/cm), with values greater than 600 ?S/cm only measured at a group of five sites in the upstream portion of the river. Air temperatures ranged from 21.0 to 37.0 degrees Celsius (?C), and water temperatures ranged from 17.00 to 30.14?C. Along the length of the North Fork Shenandoah River, longitudinal variation in water-quality parameters was small. Groups of sites that differed from the general pattern define reaches where increased monitoring may help determine the factors that affect water quality at those sites.

  15. Why is SMOS Drier than the South Fork In-situ Soil Moisture Network?

    NASA Astrophysics Data System (ADS)

    Walker, V. A.; Hornbuckle, B. K.; Cosh, M. H.

    2014-12-01

    Global maps of near-surface soil moisture are currently being produced by the European Space Agency's Soil Moisture and Ocean Salinity (SMOS) satellite mission at 40 km. Within the next few months NASA's Soil Moisture Active Passive (SMAP) satellite mission will begin producing observations of near-surface soil moisture at 10 km. Near-surface soil moisture is the water content of the first 3 to 5 cm of the soil. Observations of near-surface soil moisture are expected to improve weather and climate forecasts. These satellite observations must be validated. We define validation as determining the space/time statistical characteristics of the uncertainty. A standard that has been used for satellite validation is in-situ measurements of near-surface soil moisture made with a network of sensors spanning the extent of a satellite footprint. Such a network of sensors has been established in the South Fork of the Iowa River in Central Iowa by the USDA ARS. Our analysis of data in 2013 indicates that SMOS has a dry bias: SMOS near-surface soil moisture is between 0.05 to 0.10 m^3m^{-3} lower than what is observed by the South Fork network. A dry bias in SMOS observations has also been observed in other regions of North America. There are many possible explanations for this difference: underestimation of vegetation, or soil surface roughness; undetected radio frequency interference (RFI); a retrieval model that is not appropriate for agricultural areas; or the use of an incorrect surface temperature in the retrieval process. We will begin our investigation by testing this last possibility: that SMOS is using a surface temperature that is too low which results in a drier soil moisture that compensates for this error. We will present a comparison of surface temperatures from the European Center for Medium-range Weather Forecasting (ECMWF) used to retrieve near-surface soil moisture from SMOS measurements of brightness temperature, and surface temperatures in the South Fork

  16. Cooperation of the N-terminal Helicase and C-terminal endonuclease activities of Archaeal Hef protein in processing stalled replication forks.

    PubMed

    Komori, Kayoko; Hidaka, Masumi; Horiuchi, Takashi; Fujikane, Ryosuke; Shinagawa, Hideo; Ishino, Yoshizumi

    2004-12-17

    Blockage of replication fork progression often occurs during DNA replication, and repairing and restarting stalled replication forks are essential events in all organisms for the maintenance of genome integrity. The repair system employs processing enzymes to restore the stalled fork. In Archaea Hef is a well conserved protein that specifically cleaves nicked, flapped, and fork-structured DNAs. This enzyme contains two distinct domains that are similar to the DEAH helicase family and XPF nuclease superfamily proteins. Analyses of truncated mutant proteins consisting of each domain revealed that the C-terminal nuclease domain independently recognized and incised fork-structured DNA. The N-terminal helicase domain also specifically unwound fork-structured DNA and Holliday junction DNA in the presence of ATP. Moreover, the endonuclease activity of the whole Hef protein was clearly stimulated by ATP hydrolysis catalyzed by the N-terminal domain. These enzymatic properties suggest that Hef efficiently resolves stalled replication forks by two steps, which are branch point transfer to the 5'-end of the nascent lagging strand by the N-terminal helicase followed by template strand incision for leading strand synthesis by the C-terminal endonuclease.

  17. FANCD2, FANCJ and BRCA2 cooperate to promote replication fork recovery independently of the Fanconi Anemia core complex.

    PubMed

    Raghunandan, Maya; Chaudhury, Indrajit; Kelich, Stephanie L; Hanenberg, Helmut; Sobeck, Alexandra

    2015-01-01

    Fanconi Anemia (FA) is an inherited multi-gene cancer predisposition syndrome that is characterized on the cellular level by a hypersensitivity to DNA interstrand crosslinks (ICLs). To repair these lesions, the FA pathway proteins are thought to act in a linear hierarchy: Following ICL detection, an upstream FA core complex monoubiquitinates the central FA pathway members FANCD2 and FANCI, followed by their recruitment to chromatin. Chromatin-bound monoubiquitinated FANCD2 and FANCI subsequently coordinate DNA repair factors including the downstream FA pathway members FANCJ and FANCD1/BRCA2 to repair the DNA ICL. Importantly, we recently showed that FANCD2 has additional independent roles: it binds chromatin and acts in concert with the BLM helicase complex to promote the restart of aphidicolin (APH)-stalled replication forks, while suppressing the firing of new replication origins. Here, we show that FANCD2 fulfills these roles independently of the FA core complex-mediated monoubiquitination step. Following APH treatment, nonubiquitinated FANCD2 accumulates on chromatin, recruits the BLM complex, and promotes robust replication fork recovery regardless of the absence or presence of a functional FA core complex. In contrast, the downstream FA pathway members FANCJ and BRCA2 share FANCD2's role in replication fork restart and the suppression of new origin firing. Our results support a non-linear FA pathway model at stalled replication forks, where the nonubiquitinated FANCD2 isoform - in concert with FANCJ and BRCA2 - fulfills a specific function in promoting efficient replication fork recovery independently of the FA core complex.

  18. West Nile virus in host-seeking mosquitoes within a residential neighborhood in Grand Forks, North Dakota.

    PubMed

    Bell, Jeffrey A; Mickelson, Nathan J; Vaughan, Jefferson A

    2005-01-01

    West Nile virus (WNV) was first recovered in North Dakota near the city of Grand Forks in June 2002. During 2002, 2003, and 2004, we collected mosquitoes from Grand Forks using Mosquito Magnet traps and tested them for WNV. The seasonal abundance, species composition, and reproductive status of female mosquitoes were correlated with local environmental temperature and state surveillance data on WNV to determine the factors affecting local transmission of WNV. Over 90% of the mosquitoes collected were Aedes vexans, Ochlerotatus dorsalis, and Culex tarsalis, but WNV was detected only in Cx. tarsalis. Average summertime temperatures and relative abundance of mosquitoes were highest in 2002 but no WNV-positive mosquitoes were detected until the following summer. In 2003, nulliparous Cx. tarsalis appeared in mid-June (first summer brood), and parous Cx. tarsalis appeared in mid-July. The first WNV-positive pool occurred 21 July, and minimum daily infections rates increased thereafter until 27 August. The minimum infection rate (MIR) for Cx. tarsalis during the season was 5.7 infected mosquitoes per 1,000 tested, with the highest infection rates occurring at the end of the season as Cx. tarsalis populations started to decline. Mid-to-late August was identified as the period of highest risk for being bitten by a WNV-infected mosquito in Grand Forks during 2003. In 2004, viral activity in Grand Forks was low, due to very cool temperatures throughout the summer. To examine the genetic diversity of the 2003 WNV isolates from Grand Forks, we sequenced a 366-nucleotide region of the capsid and premembrane gene. Thirteen (46%) of the 28 WNV isolates contained at least one nucleotide substitution when compared to the homologous region of the progenitor WN NY-99 strain, and seven of these 13 substitutions coded for amino acid changes. Thus, WNV is established in North Dakota, it appears to be evolving and it is vectored primarily by Cx. tarsalis.

  19. Frequency shift, damping, and tunneling current coupling with quartz tuning forks in noncontact atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Nony, Laurent; Bocquet, Franck; Para, Franck; Loppacher, Christian

    2016-09-01

    A combined experimental and theoretical approach to the coupling between frequency-shift (Δ f ) , damping, and tunneling current (It) in combined noncontact atomic force microscopy/scanning tunneling microscopy using quartz tuning forks (QTF)-based probes is reported. When brought into oscillating tunneling conditions, the tip located at the QTF prong's end radiates an electromagnetic field which couples to the QTF prong motion via its piezoelectric tensor and loads its electrodes by induction. Our approach explains how those It-related effects ultimately modify the Δ f and the damping measurements. This paradigm to the origin of the coupling between It and the nc-AFM regular signals relies on both the intrinsic piezoelectric nature of the quartz constituting the QTF and its electrodes design.

  20. Influence of tectonic folding on rockfall susceptibility, American Fork Canyon, Utah, USA

    USGS Publications Warehouse

    Coe, J.A.; Harp, E.L.

    2007-01-01

    We examine rockfall susceptibility of folded strata in the Sevier fold-thrust belt exposed in American Fork Canyon in north-central Utah. Large-scale geologic mapping, talus production data, rock-mass-quality measurements, and historical rockfall data indicate that rockfall susceptibility is correlated with limb dip and curvature of the folded, cliff-forming Mississippian limestones. On fold limbs, rockfall susceptibility increases as dip increases. This relation is controlled by several factors, including an increase in adverse dip conditions and apertures of discontinuities, and shearing by flexural slip during folding that has reduced the friction angles of discontinuities by smoothing surface asperities. Susceptibility is greater in fold hinge zones than on adjacent limbs primarily because there are greater numbers of discontinuities in hinge zones. We speculate that susceptibility increases in hinge zones as fold curvature becomes tighter.

  1. Mercury Remediation Technology Development for Lower East Fork Poplar Creek - FY 2015 Progress Report

    SciTech Connect

    Peterson, Mark J.; Brooks, Scott C.; Mathews, Teresa J.; Mayes, Melanie; Johs, Alexander; Watson, David B.; Poteat, Monica D.; Smith, John; Mehlhorn, Tonia; Lester, Brian; Morris, Jesse; Lowe, Kenneth; Dickson, Johnbull O.; Eller, Virginia; DeRolph, Christopher R.

    2016-04-01

    Mercury remediation is a high priority for the US Department of Energy (DOE) Oak Ridge Office of Environmental Management (OREM) because of large historical losses of mercury within buildings and to soils and surface waters at the Y-12 National Security Complex (Y-12). Because of the extent of mercury losses and the complexities of mercury transport and fate in the downstream environment, the success of conventional options for mercury remediation in lower East Fork Poplar Creek (EFPC) is uncertain. A phased, adaptive management approach to remediation of surface water includes mercury treatment actions at Y-12 in the short-term and research and technology development (TD) to evaluate longer-term solutions in the downstream environment (US Department of Energy 2014b).

  2. Flood of July 5-7, 1978, on the South Fork Zumbro River at Rochester, Minnesota

    USGS Publications Warehouse

    Latkovich, V.J.

    1979-01-01

    The intense thunderstorm of July 5-6, 1978, caused record flooding on the South Fork Zumbro River at Rochester, Minnesota. The peak discharge on July 6 was 30,500 cubic feet per second compared with 19,600 cubic feet per second for the flood of March 1965, which was the largest previously known. The 1965 flood had a recurrence interval of about 30 years, whereas the 1978 flood had a recurrence interval exceeding 100 years. The flood waters claimed at least 5 lives and 5,000 people were forced to leave their homes. Millions of dollars in flood damage was reported, and this report summarizes some of the flood data and a photomosaic map shows the inundated area.

  3. South Fork Salmon River Watershed Restoration, 2008-2009 Annual Report.

    SciTech Connect

    Reaney, Mark D.

    2009-04-15

    The watershed restoration work elements within the project area, the South Fork Salmon River Watershed, follow the watershed restoration approach adopted by the Nez Perce Tribe Department of Fisheries Resource Management (DFRM) - Watershed Division. The vision of the Nez Perce Tribe DFRM-Watershed Division focuses on protecting, restoring, and enhancing watersheds and treaty resources within the ceded territory of the Nez Perce Tribe under the Treaty of 1855 with the United States Federal Government. The program uses a holistic approach, which encompasses entire watersheds, ridge top to ridge top, emphasizing all cultural aspects and strategies that rely on natural fish production and healthy river ecosystems. The Nez Perce Tribe DFRM-Watershed Division strives towards maximizing historic ecosystem productivity and health for the restoration of anadromous and resident fish populations and the habitat on which all depend on for future generations Originally, this project was funded to create a step/pool stream channel that was appropriate to restore fish passage where the 'Glory Hole Cascade' is currently located at the Stibnite Mine. Due to unforeseen circumstances at the time, the project is unable to move forward as planned and a request for a change in scope of the project and an expansion of the geographic area in which to complete project work was submitted. No additional funds were being requested. The ultimate goal of this project is to work with the holistic, ridge top to ridge top approach to protect and restore the ecological and biological functions of the South Fork Salmon River Watershed to assist in the recovery of threatened and endangered anadromous and resident fish species. FY 2008 Work Elements included two aquatic organism passage (AOP) projects to restore habitat connectivity to two fish-bearing tributaries to the East Fork South Fork Salmon River, Salt and Profile Creeks. The Work Elements also included road survey and assessment activities

  4. Quartz enhanced photoacoustic spectroscopy based trace gas sensors using different quartz tuning forks.

    PubMed

    Ma, Yufei; Yu, Guang; Zhang, Jingbo; Yu, Xin; Sun, Rui; Tittel, Frank K

    2015-03-27

    A sensitive trace gas sensor platform based on quartz-enhanced photoacoustic spectroscopy (QEPAS) is reported. A 1.395 μm continuous wave (CW), distributed feedback pigtailed diode laser was used as the excitation source and H2O was selected as the target analyte. Two kinds of quartz tuning forks (QTFs) with a resonant frequency (f0) of 30.72 kHz and 38 kHz were employed for the first time as an acoustic wave transducer, respectively for QEPAS instead of a standard QTF with a f0 of 32.768 kHz. The QEPAS sensor performance using the three different QTFs was experimentally investigated and theoretically analyzed. A minimum detection limit of 5.9 ppmv and 4.3 ppmv was achieved for f0 of 32.768 kHz and 30.72 kHz, respectively.

  5. Optimizing Data Locality for Fork/Join Programs Using Constrained Work Stealing

    SciTech Connect

    Lifflander, Jonathan; Krishnamoorthy, Sriram; Kale, Laxmikant

    2014-11-16

    We present an approach to improving data locality across different phases of fork/join programs scheduled using work stealing. The approach consists of: (1) user-specified and automated approaches to constructing a steal tree, the schedule of steal operations and (2) constrained work stealing algorithms that constrain the actions of the scheduler to mirror a given steal tree. These are combined to construct work stealing schedules that maximize data locality across computation phases while ensuring load balance within each phase. These algorithms are also used to demonstrate dynamic coarsening, an optimization to improve spatial locality and sequential overheads by combining many finer-grained tasks into coarser tasks while ensuring sufficient concurrency for locality-optimized load balance. Implementation and evaluation in Cilk demonstrate performance improvements of up to 2.5x on 80 cores. We also demonstrate that dynamic coarsening can combine the performance benefits of coarse task specification with the adaptability of finer tasks.

  6. Modulation of mutagenesis in eukaryotes by DNA replication fork dynamics and quality of nucleotide pools

    PubMed Central

    Waisertreiger, Irina S.-R.; Liston, Victoria G.; Menezes, Miriam R.; Kim, Hyun-Min; Lobachev, Kirill S.; Stepchenkova, Elena I.; Tahirov, Tahir H.; Rogozin, Igor B.; Pavlov, Youri. I.

    2014-01-01

    The rate of mutations in eukaryotes depends on a plethora of factors and is not immediately derived from the fidelity of DNA polymerases (Pols). Replication of chromosomes containing the anti-parallel strands of duplex DNA occurs through the copying of leading and lagging strand templates by a trio of Pols α, δ and ε, with the assistance of Pol ζ and Y-family Pols at difficult DNA template structures or sites of DNA damage. The parameters of the synthesis at a given location are dictated by the quality and quantity of nucleotides in the pools, replication fork architecture, transcription status, regulation of Pol switches, and structure of chromatin. The result of these transactions is a subject of survey and editing by DNA repair. PMID:23055184

  7. High-spatial-resolution scanning capacitance microscope using all-metal probe with quartz tuning fork

    NASA Astrophysics Data System (ADS)

    Naitou, Yuichi; Ookubo, Norio

    2004-09-01

    The scanning capacitance microscope (SCM) reported here uses a frequency modulation (FM) technique to control the distance between the sample and an all-metal probe. The probe was attached to a quartz tuning fork in a configuration minimizing the perturbation due to the probe. The FM-SCM yields two images of ∂C/∂V and ∂C/∂Z signals, where C is capacitance sensed by the probe, Z the probe-sample distance, and V a bias voltage, respectively. On a cross section of a field effect transistor, the two-dimensional p -n junction locus was observed with a spatial resolution better than 5nm in the ∂C/∂V image. The ∂C/∂Z images of polysilicon gate electrodes and highly doped source/drain regions have higher contrast than the ∂C/∂V images.

  8. Nanocharacterization of Soft Biological Samples in Shear Mode with Quartz Tuning Fork Probes

    PubMed Central

    Otero, Jorge; Gonzalez, Laura; Puig-Vidal, Manel

    2012-01-01

    Quartz tuning forks are extremely good resonators and their use is growing in scanning probe microscopy. Nevertheless, only a few studies on soft biological samples have been reported using these probes. In this work, we present the methodology to develop and use these nanosensors to properly work with biological samples. The working principles, fabrication and experimental setup are presented. The results in the nanocharacterization of different samples in different ambients are presented by using different working modes: amplitude modulation with and without the use of a Phase-Locked Loop (PLL) and frequency modulation. Pseudomonas aeruginosa bacteria are imaged in nitrogen using amplitude modulation. Microcontact printed antibodies are imaged in buffer using amplitude modulation with a PLL. Finally, metastatic cells are imaged in air using frequency modulation. PMID:22666059

  9. Nanocharacterization of soft biological samples in shear mode with quartz tuning fork probes.

    PubMed

    Otero, Jorge; Gonzalez, Laura; Puig-Vidal, Manel

    2012-01-01

    Quartz tuning forks are extremely good resonators and their use is growing in scanning probe microscopy. Nevertheless, only a few studies on soft biological samples have been reported using these probes. In this work, we present the methodology to develop and use these nanosensors to properly work with biological samples. The working principles, fabrication and experimental setup are presented. The results in the nanocharacterization of different samples in different ambients are presented by using different working modes: amplitude modulation with and without the use of a Phase-Locked Loop (PLL) and frequency modulation. Pseudomonas aeruginosa bacteria are imaged in nitrogen using amplitude modulation. Microcontact printed antibodies are imaged in buffer using amplitude modulation with a PLL. Finally, metastatic cells are imaged in air using frequency modulation.

  10. Brca2, Rad51 and Mre11: performing balancing acts on replication forks.

    PubMed

    Costanzo, Vincenzo

    2011-10-10

    Homologous recombination (HR) is required for faithful repair of double strand breaks (DSBs) and is believed to be important for DNA replication under stressful conditions in unicellular organisms. However, its role during DNA replication in high eukaryotes has always been elusive. In particular, due to the essential nature of its main players it has been difficult to dissect the direct role of HR in DNA replication. Recent studies revealed that some key HR factors such as Rad51 and BRCA2 play unexpected functions during DNA replication by protecting nascent DNA from Mre11 mediated degradation, which takes place at stalled replication forks. These novel functions appear to be essential to ensure smooth progression of DNA replication and to promote maintenance of genome stability.

  11. Water quality and streamflow data for the West Fork Trinity River in Forth Worth, Texas

    USGS Publications Warehouse

    McCutcheon, S.C.

    1985-01-01

    Water-quality data were collected on a 13.6-mile reach of the West Fork Trinity River in Fort Worth, Texas to test a dynamic Lagrangian model. Flow was steady. Loads of dissolved constituents varied with time at the beginning of the study reach and in the reach, primarily because of photosynthesis. River quality was fairly good despite low dissolved oxygen measured in the headwaters and the significant sewage load from the tributaries. Diel and longitudinal trends were defined by sampling at fixed sites and by following dyed parcels of water. Nitrification, deoxygenation, reaeration, and photosynthesis affected the dissolved oxygen balance. Independent estimates of some of the rate coefficients were 0.1 to 0.2, 0.8, and 0 to 3.6 , all per day, for deoxygenation, nitrification, and reaeration, respectively. (USGS)

  12. Piezoelectric tuning fork biosensors for the quantitative measurement of biomolecular interactions

    NASA Astrophysics Data System (ADS)

    Gonzalez, Laura; Rodrigues, Mafalda; Benito, Angel Maria; Pérez-García, Lluïsa; Puig-Vidal, Manel; Otero, Jorge

    2015-12-01

    The quantitative measurement of biomolecular interactions is of great interest in molecular biology. Atomic force microscopy (AFM) has proved its capacity to act as a biosensor and determine the affinity between biomolecules of interest. Nevertheless, the detection scheme presents certain limitations when it comes to developing a compact biosensor. Recently, piezoelectric quartz tuning forks (QTFs) have been used as laser-free detection sensors for AFM. However, only a few studies along these lines have considered soft biological samples, and even fewer constitute quantified molecular recognition experiments. Here, we demonstrate the capacity of QTF probes to perform specific interaction measurements between biotin-streptavidin complexes in buffer solution. We propose in this paper a variant of dynamic force spectroscopy based on representing adhesion energies E (aJ) against pulling rates v (nm s-1). Our results are compared with conventional AFM measurements and show the great potential of these sensors in molecular interaction studies.

  13. Assessing and Understanding Trail Degradation: Results from Big South Fork National River and Recreational Area

    USGS Publications Warehouse

    Marion, J.L.; Olive, N.

    2006-01-01

    This report describes results from a comprehensive assessment of resource conditions on a large (24%) sample of the trail system within Big South Fork National River and Recreational Area (BSF). Components include research to develop state-of-knowledge trail impact assessment and monitoring methods, application of survey methods to BSF trails, analysis and summary of results, and recommendations for trail management decision making and future monitoring. Findings reveal a trail system with some substantial degradation, particularly soil erosion, which additionally threatens water quality in areas adjacent to streams and rivers. Factors that contribute to or influence these problems are analyzed and described. Principal among these are trail design factors (trail topographic position, soil texture, grade and slope alignment angle), use-related factors (type and amount of use), and maintenance factors (water drainage). Recommendations are offered to assist managers in improving the sustainability of the trails system to accommodate visitation while enhancing natural resource protection.

  14. Eigenmodes of a quartz tuning fork and their application to photoinduced force microscopy

    NASA Astrophysics Data System (ADS)

    Kim, Bongsu; Jahng, Junghoon; Khan, Ryan Muhammad; Park, Sung; Potma, Eric O.

    2017-02-01

    We examine the mechanical eigenmodes of a quartz tuning fork (QTF) for the purpose of facilitating its use as a probe for multifrequency atomic force microscopy (AFM). We perform simulations based on the three-dimensional finite element method and compare the observed motions of the beams with experimentally measured resonance frequencies of two QTF systems. The comparison enabled us to assign the first seven asymmetric eigenmodes of the QTF. We also find that a modified version of single beam theory can be used to guide the assignment of mechanical eigenmodes of QTFs. The usefulness of the QTF for multifrequency AFM measurements is demonstrated through photoinduced force microscopy measurements. By using the QTF in different configurations, we show that the vectorial components of the photoinduced force can be independently assessed and that lateral forces can be probed in true noncontact mode.

  15. Stimulation techniques in the Red Fork Formation in the Anadarko Basin

    SciTech Connect

    Burnette, P.T.

    1983-02-01

    This paper presents the results of fracture stimulation treatments on the Red Fork formation in the Anadarko Basin. All wells studied are located in Roger Mills and Custer counties of Oklahoma. Only data for which valid production information was available are included. Fracturing techniques and their results using five different stimulation fluids are examined; cross-linked water base, gelled water (non cross-linked), gelled diesel, gelled carbon dioxide, and foamed carbon dioxide with water as the liquid phase. Three types of propping agents have been used in various grades in conjunction with the above stimulation fluids; sand, intermediate strength proppant and high strength sintered bauxite. A discussion of various treatment parameters and their possible overall effect on the production results is presented.

  16. Tectonic controls on large landslide complex: Williams Fork Mountains near Dillon, Colorado

    USGS Publications Warehouse

    Kellogg, K.S.

    2001-01-01

    An extensive (~ 25 km2) landslide complex covers a large area on the west side of the Williams Fork Mountains in central Colorado. The complex is deeply weathered and incised, and in most places geomorphic evidence of sliding (breakaways, hummocky topography, transverse ridges, and lobate distal zones) are no longer visible, indicating that the main mass of the slide has long been inactive. However, localized Holocene reactivation of the landslide deposits is common above the timberline (at about 3300 m) and locally at lower elevations. Clasts within the complex, as long as several tens of meters, are entirely of crystalline basement (Proterozoic gneiss and granitic rocks) from the hanging wall of the Laramide (Late Cretaceous to Early Tertiary), west-directed Williams Range thrust, which forms the western structural boundary of the Colorado Front Range. Late Cretaceous shale and sandstone compose most footwall rocks. The crystalline hanging-wall rocks are pervasively fractured or shattered, and alteration to clay minerals is locally well developed. Sackung structures (trenches or small-scale grabens and upslope-facing scarps) are common near the rounded crest of the range, suggesting gravitational spreading of the fractured rocks and oversteepening of the mountain flanks. Late Tertiary and Quaternary incision of the Blue River Valley, just west of the Williams Fork Mountains, contributed to the oversteepening. Major landslide movement is suspected during periods of deglaciation when abundant meltwater increased pore-water pressure in bedrock fractures. A fault-flexure model for the development of the widespread fracturing and weakening of the Proterozoic basement proposes that the surface of the Williams Range thrust contains a concave-downward flexure, the axis of which coincides approximately with the contact in the footwall between Proterozoic basement and mostly Cretaceous rocks. Movement of brittle, hanging-wall rocks through the flexure during Laramide

  17. Characterization of ecological risks at the Milltown Reservoir-Clark Fork River Sediments Superfund Site, Montana

    USGS Publications Warehouse

    Pascoe, Gary A.; Blanchet, Richard J.; Linder, Greg L.; Palawski, Don; Brumbaugh, William G.; Canfield, Tim J.; Kemble, Nile E.; Ingersoll, Chris G.; Farag, Aida M.; DalSoglio, Julie A.

    1994-01-01

    A comprehensive field and laboratory approach to the ecological risk assessment for the Milltown Reservoir-Clark Fork River Sediments Site, a Superfund site in the Rocky Mountains of Montana, has been described in the preceding reports of this series. The risk assessment addresses concerns over the ecological impacts of upstream releases of mining wastes to fisheries of the upper Clark Fork River (CFR) and the benthic and terrestrial habitats further downstream in Milltown Reservoir. The risk characterization component of the process integrated results from a triad of information sources: (a) chemistry studies of environmental media to identify and quantify exposures of terrestrial and aquatic organisms to site-related contaminants; (b) ecological or population studies of terrestrial vegetation, birds, benthic communities, and fish; and (c) in situ and laboratory toxicity studies with terrestrial and aquatic invertebrates and plants, small mammals, amphibians, and fish exposed to contaminated surface water, sediments, wetland soils, and food sources. Trophic transfer studies were performed on waterfowl, mammals, and predatory birds using field measurement data on metals concentrations in environmental media and lower trophic food sources. Studies with sediment exposures were incorporated into the Sediment Quality Triad approach to evaluate risks to benthic ecology. Overall results of the wetland and terrestrial studies suggested that acute adverse biological effects were largely absent from the wetland; however, adverse effects to reproductive, growth, and physiological end points of various terrestrial and aquatic species were related to metals exposures in more highly contaminated depositional areas. Feeding studies with contaminated diet collected from the upper CFR indicated that trout are at high risk from elevated metals concentrations in surface water, sediment, and aquatic invertebrates. Integration of chemical analyses with toxicological and ecological

  18. Constraints to microbial food safety policy: opinions from stakeholder groups along the farm to fork continuum.

    PubMed

    Sargeant, J M; Ramsingh, B; Wilkins, A; Travis, R G; Gavrus, D; Snelgrove, J W

    2007-01-01

    This exploratory qualitative study was conducted to identify constraints to microbial food safety policy in Canada and the USA from the perspective of stakeholder groups along the farm to fork continuum. Thirty-seven stakeholders participated in interviews or a focus group where semi-structured questions were used to facilitate discussion about constraints to policy development and implementation. An emergent grounded theory approach was used to determine themes and concepts that arose from the data (versus fitting the data to a hypothesis or a priori classification). Despite the plurality of stakeholders and the range of content expertise, participant perceptions emerged into five common themes, although, there were often disagreements as to the positive or negative attributes of specific concepts. The five themes included challenges related to measurement and objectives of microbial food safety policy goals, challenges arising from lack of knowledge, or problems with communication of knowledge coupled with current practices, beliefs and traditions; the complexity of the food system and the plurality of stakeholders; the economics of producing safe food and the limited resources to address the problem; and, issues related to decision-making and policy, including ownership of the problem and inappropriate inputs to the decision-making process. Responsibilities for food safety and for food policy failure were attributed to all stakeholders along the farm to fork continuum. While challenges regarding the biology of food safety were identified as constraints, a broader range of policy inputs encompassing social, economic and political considerations were also highlighted as critical to the development and implementation of effective food safety policy. Strategies to address these other inputs may require new, transdisciplinary approaches as an adjunct to the traditional science-based risk assessment model.

  19. Tennessee's East Fork Poplar Creek: A biological monitoring and abatement program

    SciTech Connect

    Halbrook, R.S. ); Loar, J.M.; Adams, S.M.; Black, M.C.; Boston, H.L.; Greeley, M.S. Jr.; Hill, W.R.; Hinzman, R.L.; McCarthy, J.F.; Peterson, M.J.; Ryon, M.G.; Schilling, E.M.; Smith, J.G.; Southworth, G.R.; Stewart, A.J. ); Gatz, A.J. )

    1991-01-01

    On May 1985, a Biological Monitoring Program was developed for East Fork Poplar Creek (EFPC) in eastern Tennessee, United States. This stream originates within the Oak Ridge Y-12 Plant that produces nuclear weapons components for the Department of Energy. Water and sediment in the stream contain metals, organic chemicals, and radionuclides from releases that have occurred over the past 45 years. The creek also receives urban and some agricultural runoff and effluent from the City of Oak Ridge's Wastewater Treatment Facility (WTF). The biological monitoring program includes four major tasks: (1) ambient toxicity testing: (2) bioaccumulation studies; (3) biological indicator studies; and (4) ecological monitoring of stream communities, including periphyton, benthic macroinvertebrates, and fish. Biological conditions are monitored at six sites on EFPC ranging from kilometer 24.4 near the headwaters to kilometer 6.3 near the month. A site on Brushy Fork, A stream just north of Oak Ridge, is used as reference. Ambient (instream) toxicity was monitored through the use of 7-day static-renewal tests that measured the survival and growth of fathead minnow (Pimephales promelas) larvae and the survival and reproduction of a microstrustacean (Ceriodaphnia dubia). Full-strength water from EFPC within the Y-12 Plant boundary was frequently toxic to Ceriodaphnia, but less frequently toxic to the minnow larvae. Chlorine has been identified as an important toxicant in upper EFPC. Water samples from six sites in EFPC downstream from the Y-12 Plant boundary were tested eight times with both species during a 2-year period (October, 1986 through October, 1988). These sites were ranked by the number of times they were best'' or worst'' for each species. Water samples collected for use in the ambient toxicity tests were routinely analyzed for conductivity, pH, alkalinity, hardness, total residual and free chlorine, and temperature.

  20. Tennessee`s East Fork Poplar Creek: A biological monitoring and abatement program

    SciTech Connect

    Halbrook, R.S.; Loar, J.M.; Adams, S.M.; Black, M.C.; Boston, H.L.; Greeley, M.S. Jr.; Hill, W.R.; Hinzman, R.L.; McCarthy, J.F.; Peterson, M.J.; Ryon, M.G.; Schilling, E.M.; Smith, J.G.; Southworth, G.R.; Stewart, A.J.; Gatz, A.J.

    1991-12-31

    On May 1985, a Biological Monitoring Program was developed for East Fork Poplar Creek (EFPC) in eastern Tennessee, United States. This stream originates within the Oak Ridge Y-12 Plant that produces nuclear weapons components for the Department of Energy. Water and sediment in the stream contain metals, organic chemicals, and radionuclides from releases that have occurred over the past 45 years. The creek also receives urban and some agricultural runoff and effluent from the City of Oak Ridge`s Wastewater Treatment Facility (WTF). The biological monitoring program includes four major tasks: (1) ambient toxicity testing: (2) bioaccumulation studies; (3) biological indicator studies; and (4) ecological monitoring of stream communities, including periphyton, benthic macroinvertebrates, and fish. Biological conditions are monitored at six sites on EFPC ranging from kilometer 24.4 near the headwaters to kilometer 6.3 near the month. A site on Brushy Fork, A stream just north of Oak Ridge, is used as reference. Ambient (instream) toxicity was monitored through the use of 7-day static-renewal tests that measured the survival and growth of fathead minnow (Pimephales promelas) larvae and the survival and reproduction of a microstrustacean (Ceriodaphnia dubia). Full-strength water from EFPC within the Y-12 Plant boundary was frequently toxic to Ceriodaphnia, but less frequently toxic to the minnow larvae. Chlorine has been identified as an important toxicant in upper EFPC. Water samples from six sites in EFPC downstream from the Y-12 Plant boundary were tested eight times with both species during a 2-year period (October, 1986 through October, 1988). These sites were ranked by the number of times they were ``best`` or ``worst`` for each species. Water samples collected for use in the ambient toxicity tests were routinely analyzed for conductivity, pH, alkalinity, hardness, total residual and free chlorine, and temperature.

  1. Spatial Patterns of Mercury Bioaccumulation in the Upper Clark Fork River Basin, MT

    NASA Astrophysics Data System (ADS)

    Staats, M. F.; Langner, H.; Moore, J. N.

    2010-12-01

    The Upper Clark Fork River Basin (UCFRB) in Montana has a legacy of historic gold/silver mine waste that contributes large quantities of mercury into the watershed. Mercury bioaccumulation at higher levels of the aquatic food chain, such as the mercury concentration in the blood of pre-fledge osprey, exhibit an irregular spatial signature based on the location of the nests throughout the river basin. Here we identify regions with a high concentration of bioavailable mercury and the major factors that allow the mercury to bioaccumulate within trophic levels. This identification is based on the abundance of mercury sources and the potential for mercury methylation. To address the source term, we did a survey of total mercury in fine sediments along selected UCFRB reaches, along with the assessment of environmental river conditions (percentage of backwaters/wetlands, water temperature and pH, etc). In addition, we analyzed the mercury levels of a representative number of macroinvertebrates and fish from key locations. The concentration of total mercury in sediment, which varies from reach to reach (tributaries of the Clark Fork River, <0.05 mg/kg to the main stem of the river, >5mg/kg) affects the concentration of mercury found at various trophic levels. However, reaches with a low supply of mine waste-derived mercury can also yield substantial concentrations of mercury in the biota, due to highly favorable conditions for mercury methylation. We identify that the major environmental factor that affects the methylation potential in the UCFRB is the proximity and connectivity of wetland areas to the river.

  2. Specific Shrinkage of Carotid Forks in Moyamoya Disease: A Novel Key Finding for Diagnosis

    PubMed Central

    KURODA, Satoshi; KASHIWAZAKI, Daina; AKIOKA, Naoki; KOH, Masaki; HORI, Emiko; NISHIKATA, Manabu; UMEMURA, Kimiko; HORIE, Yukio; NOGUCHI, Kyo; KUWAYAMA, Naoya

    2015-01-01

    This study was aimed to analyze the outer diameter of the involved arteries in moyamoya disease, using three-dimensional (3D) constructive interference in steady state (CISS) and direct surgical inspection. Radiological evaluation was performed in 64 patients with moyamoya disease. As the controls, six patients with severe middle cerebral artery (MCA) stenosis and 17 healthy subjects were also recruited. On 3D-CISS, the outer diameter was quantified in the supraclinoid portion of internal carotid artery (C1), the horizontal portions of MCA (M1) and anterior cerebral artery (A1), and basilar artery. The involved carotid fork was directly observed during surgery in another series of three adult patients with moyamoya disease. In 53 adult patients with moyamoya disease, the outer diameters of C1, M1, and A1 segments were 2.3 ± 0.7 mm, 1.3 ± 0.5 mm, and 1.0 ± 0.4 mm in the involved side (n = 91), being significantly smaller than the control (n = 17), severe M1 stenosis (n = 6), and non-involved side in moyamoya disease (n = 15, P < 0.01). There were significant correlations between Suzuki’s angiographical stage and the outer diameters of C1, M1, and A1 (P < 0.001). The laterality ratio of C1 and M1 was significantly smaller in unilateral moyamoya disease (n = 20) than the controls and severe MCA stenosis (P < 0.01). Direct observations revealed a marked decrease in the outer diameter of the carotid fork (n = 3). These findings strongly suggest specific shrinkage of the involved arteries in moyamoya disease, which may provide essential information to distinguish moyamoya disease from other intracranial arterial stenosis and shed light on the etiology and novel diagnosis cue of moyamoya disease. PMID:26369872

  3. Earthquake Source Scaling and Wave Propagation in Eastern North America: The Au Sable Forks, NY, Earthquake

    NASA Astrophysics Data System (ADS)

    Viegas, G.; Abercrombie, R.; Baise, L.; Kim, W.

    2005-12-01

    The 2002, M5 Au Sable Forks, NY earthquake and aftershocks are the best recorded sequence in the North Eastern USA. We use the local and regional recordings to investigate the characteristics of intraplate seismicity, focusing on source scaling relationships and regional wave propagation. A portable local network of 11 stations, recorded 74 aftershocks of M<3.2. We relocate the mainshock and early aftershocks using a master event technique. We then use the double-difference relocation method using differential travel times measured from waveform cross-correlation to relocate the aftershocks recorded by the local network. Both the master-event and double-difference location methods produce consistent results suggesting complex conjugate faulting during the sequence. We identify a number of highly clustered groups of earthquakes suitable for EGF analysis. We use the EGF method to calculate the stress drop and radiated energy of the larger aftershocks to determine how they compare to moderate magnitude earthquakes, and also whether they differ significantly from interplate earthquakes. We consider the 9 largest aftershocks (M3.7 to M2), which were recorded on the regional network, as potential EGFs for the mainshock, but they have focal mechanisms and locations that are sufficiently different that we cannot resolve the mainshock source time function well. They are good enough to enable us to place constraints on the shape and duration of the source pulse to use in modeling the regional waveforms. We investigate the crustal structure in New York (Grenville) and New England (Appalachian) through forward modeling of the Au Sable Forks regional broadband records. We compute synthetic records of wave propagation in a layered medium, using published crustal models of the two regions as a starting point. We identify differences between the recorded data and synthetics for the Grenville and the Appalachian regions and improve the crustal models to better fit the recorded

  4. An approach to monitor food and nutrition from ‘Factory to Fork.’

    PubMed Central

    Slining, Meghan; Yoon, Emily Ford; Davis, Jessica; Hollingsworth, Bridget; Miles, Donna; Ng, Shu Wen

    2014-01-01

    Background Accurate, adequate, and timely food and nutrition information is necessary in order to monitor changes in the US food supply and assess their impact on individual dietary intake. Objective Develop an approach that links time-specific purchase and consumption data to provide updated, market representative nutrient information. Data and Methods We utilized household purchase data (Nielsen Homescan, 2007–2008), self-reported dietary intake data [What We Eat in America (WWEIA), 2007–2008], and two sources of nutritional composition data. This factory to fork Crosswalk approach connected each of the items reported to have been obtained from stores from the 2007–2008 cycle of the WWEIA dietary intake survey to corresponding food and beverage products that were purchased by US households during the equivalent time period. Using nutrition composition information and purchase data, an alternate Crosswalk-based nutrient profile for each WWEIA intake code was created weighted by purchase volume of all corresponding items. Mean intakes of daily calories, total sugars, sodium, and saturated fat were estimated. Results Differences were observed in the average daily calories, sodium and total sugars reported consumed from beverages, yogurts and cheeses, depending on whether the FNDDS 4.1 or the alternate nutrient profiles were used. Conclusions The Crosswalk approach augments national nutrition surveys with commercial food and beverage purchases and nutrient databases to capture changes in the US food supply from factory to fork. The Crosswalk provides a comprehensive and representative measurement of the types, amounts, prices, locations and nutrient composition of CPG foods and beverages consumed in the US. This system has potential to be a major step forward in understanding the CPG sector of the US food system and the impacts of the changing food environment on human health. PMID:25441958

  5. DNA repair and replication fork helicases are differentially affected by alkyl phosphotriester lesion.

    PubMed

    Suhasini, Avvaru N; Sommers, Joshua A; Yu, Stephen; Wu, Yuliang; Xu, Ting; Kelman, Zvi; Kaplan, Daniel L; Brosh, Robert M

    2012-06-01

    DNA helicases are directly responsible for catalytically unwinding duplex DNA in an ATP-dependent and directionally specific manner and play essential roles in cellular nucleic acid metabolism. It has been conventionally thought that DNA helicases are inhibited by bulky covalent DNA adducts in a strand-specific manner. However, the effects of highly stable alkyl phosphotriester (PTE) lesions that are induced by chemical mutagens and refractory to DNA repair have not been previously studied for their effects on helicases. In this study, DNA repair and replication helicases were examined for unwinding a forked duplex DNA substrate harboring a single isopropyl PTE specifically positioned in the helicase-translocating or -nontranslocating strand within the double-stranded region. A comparison of SF2 helicases (RecQ, RECQ1, WRN, BLM, FANCJ, and ChlR1) with a SF1 DNA repair helicase (UvrD) and two replicative helicases (MCM and DnaB) demonstrates unique differences in the effect of the PTE on the DNA unwinding reactions catalyzed by these enzymes. All of the SF2 helicases tested were inhibited by the PTE lesion, whereas UvrD and the replication fork helicases were fully tolerant of the isopropyl backbone modification, irrespective of strand. Sequestration studies demonstrated that RECQ1 helicase was trapped by the PTE lesion only when it resided in the helicase-translocating strand. Our results are discussed in light of the current models for DNA unwinding by helicases that are likely to encounter sugar phosphate backbone damage during biological DNA transactions.

  6. Mass loading of selected major and trace elements in Lake Fork Creek near Leadville, Colorado, September-October 2001

    USGS Publications Warehouse

    Walton-Day, Katherine; Flynn, Jennifer L.; Kimball, Briant A.; Runkel, Robert L.

    2005-01-01

    A mass-loading study of Lake Fork Creek of the Arkansas River between Sugarloaf Dam and the mouth was completed in September-October 2001 to help ascertain the following: (1) variation of pH and aqueous constituent concentrations (calcium, sulfate, alkalinity, aluminum, cadmium, copper, iron, manganese, lead, and zinc) and their relation to toxicity standards along the study reach; (2) location and magnitude of sources of metal loading to Lake Fork Creek; (3) amount and locations of metal attenuation; (4) the effect of streamside wetlands on metal transport from contributing mine tunnels; and (5) the effect of organic-rich inflow from the Leadville National Fish Hatchery on water quality in Lake Fork Creek. The study was done in cooperation with the Bureau of Land Management, U.S. Department of Agriculture Forest Service, and U.S. Fish and Wildlife Service. Constituent concentrations and pH showed variable patterns over the study reach. Hardness-based acute and chronic toxicity standards were exceeded for some inflows and some constituents. However, stream concentrations did not exceed standards except for zinc starting in the upper parts of the study reach and extending to just downstream from the inflow from the Leadville National Fish Hatchery. Dilution from that inflow lowered stream zinc concentrations to less than acute and chronic toxicity standards. The uppermost 800 meters of the study reach that contained inflow from the Bartlett, Dinero, and Nelson mine tunnels and the Dinero wetland was the greatest source of loading for manganese and zinc. A middle section of the study reach that extended approximately 2 kilometers upstream from the National Fish Hatchery inflow to just downstream from that inflow was the largest source of aluminum, copper, iron, and lead loading. The loading was partially from the National Fish Hatchery inflow but also from unknown sources upstream from that inflow, possibly ground water. The largest sources for calcium and sulfate

  7. Water-quality trends for selected sampling sites in the upper Clark Fork Basin, Montana, water years 1996-2010

    USGS Publications Warehouse

    Sando, Steven K.; Vecchia, Aldo V.; Lorenz, David L.; Barnhart, Elliott P.

    2014-01-01

    A large-scale trend analysis was done on specific conductance, selected trace elements (arsenic, cadmium, copper, iron, lead, manganese, and zinc), and suspended-sediment data for 22 sites in the upper Clark Fork Basin for water years 1996–2010. Trend analysis was conducted by using two parametric methods: a time-series model (TSM) and multiple linear regression on time, streamflow, and season (MLR). Trend results for 1996–2010 indicate moderate to large decreases in flow-adjusted concentrations (FACs) and loads of copper (and other metallic elements) and suspended sediment in Silver Bow Creek upstream from Warm Springs. Deposition of metallic elements and suspended sediment within Warm Springs Ponds substantially reduces the downstream transport of those constituents. However, mobilization of copper and suspended sediment from floodplain tailings and stream banks in the Clark Fork reach from Galen to Deer Lodge is a large source of metallic elements and suspended sediment, which also affects downstream transport of those constituents. Copper and suspended-sediment loads mobilized from within this reach accounted for about 40 and 20 percent, respectively, of the loads for Clark Fork at Turah Bridge (site 20); whereas, streamflow contributed from within this reach only accounted for about 8 percent of the streamflow at Turah Bridge. Minor changes in FACs and loads of copper and suspended sediment are indicated for this reach during 1996–2010. Clark Fork reaches downstream from Deer Lodge are relatively smaller sources of metallic elements than the reach from Galen to Deer Lodge. In general, small decreases in loads and FACs of copper and suspended sediment are indicated for Clark Fork sites downstream from Deer Lodge during 1996–2010. Thus, although large decreases in FACs and loads of copper and suspended sediment are indicated for Silver Bow Creek upstream from Warm Springs, those large decreases are not translated to the more downstream reaches largely

  8. RecQ helicases: suppressors of tumorigenesis and premature aging.

    PubMed Central

    Bachrati, Csanád Z; Hickson, Ian D

    2003-01-01

    The RecQ helicases represent a subfamily of DNA helicases that are highly conserved in evolution. Loss of RecQ helicase function leads to a breakdown in the maintenance of genome integrity, in particular hyper-recombination. Germ-line defects in three of the five known human RecQ helicases give rise to defined genetic disorders associated with cancer predisposition and/or premature aging. These are Bloom's syndrome, Werner's syndrome and Rothmund-Thomson syndrome, which are caused by defects in the genes BLM, WRN and RECQ4 respectively. Here we review the properties of RecQ helicases in organisms from bacteria to humans, with an emphasis on the biochemical functions of these enzymes and the range of protein partners that they operate with. We will discuss models in which RecQ helicases are required to protect against replication fork demise, either through prevention of fork breakdown or restoration of productive DNA synthesis. PMID:12803543

  9. Final report from VFL Technologies for the pilot-scale thermal treatment of lower East Fork Poplar Creek floodplain soils. LEFPC appendices, Volume 4, Appendix V-C

    SciTech Connect

    1994-09-01

    This is the the final verification run data package for pilot scale thermal treatment of lower East Fork Poplar Creek floodplain soils. Included are data on volatiles, semivolatiles, and TCLP volatiles.

  10. A COMPREHENSIVE NONPOINT SOURCE FIELD STUDY FOR SEDIMENT, NUTRIENTS, AND PATHOGENS IN THE SOUTH FORK BROAD RIVER WATERSHED IN NORTHEAST GEORGIA

    EPA Science Inventory

    This technical report provides a description of the field project design, quality control, the sampling protocols and analysis methodology used, and standard operating procedures for the South Fork Broad River Watershed (SFBR) Total Maximum Daily Load (TMDL) project. This watersh...

  11. Final report from VFL technologies for the pilot-scale thermal treatment of Lower East Fork Poplar Creek floodplain soils: LEFPC appendices, volume 1, appendix I-IV

    SciTech Connect

    1994-09-01

    This document contains Appendix I-IV for the pilot-scale thermal treatment of lower East Fork Poplar Creek floodplain soils. Included are calibration records; quality assurance; soils characterization; pilot scale trial runs.

  12. Vacuum properties of high quality value tuning fork in high magnetic field up to 8 Tesla and at mK temperatures

    NASA Astrophysics Data System (ADS)

    Človečko, M.; Kupka, M.; Skyba, P.; Vavrek, F.

    2014-12-01

    Tuning forks are very popular experimental tools widely applied in low and ultra low temperature physics as mechanical resonators and cantilevers in the study of quantum liquids, STM and AFM techniques, etc. As an added benefit, these forks being cooled, have very high Q-value, typically 106 and their properties seems to be magnetic field independent. We present preliminary vacuum measurements of a commercial tuning fork oscillating at frequency 32 kHz conducted in magnetic fields up to 8 T and at temperature ~ 10 mK. We found an additional weak damping of the tuning fork motion depending on magnetic field magnitude and we discuss physical nature of the observed phenomena.

  13. Differences in survival and growth in hatchery and stream environments, and in maturation of residuls in a stream, between progeny of hatchery and wild steelhead (Study sites: Brushy Fork Creek and Dworshak Hatchery; Stocks:Dworshak hatchery and Fish Creek wild; Year classes: 1992 and 1993): Chapter 1

    USGS Publications Warehouse

    Rubin, Stephen P.; Reisenbichler, Reginald R.; Wetzel, Lisa A.; Hensleigh, Jay E.; Leonetti,; Rubin, Stephen P.; Reisenbichler, Reginald R.; Wetzel, Lisa A.; Hayes, Michael C.

    2012-01-01

    Freshwater survival in hatchery and natural rearing environments was compared between progeny of hatchery (H) and wild (W) steelhead Oncorhynchus mykiss from the Clearwater River drainage in Idaho. Adults from Dworshak National Fish Hatchery and wild adults from Fish Creek fish were artificially spawned, and their progeny were genetically marked at the PEPA allozyme locus and released together as unfed fry in production facilities at the hatchery and in Brushy Fork Creek, also in the Clearwater River drainage, in a common garden design. Survival was higher for H than for W progeny at the hatchery but lower for H than for W progeny in Brushy Fork, indicating reduced fitness of the hatchery population for natural rearing and suggesting domestication as the cause. Survival at the hatchery was lower than is typical due to disease outbreaks. Survival of the first year-class of experimental fish to smolt release was only 18%. Survival of H fish was 3.8 times that of W fish under these poor survival conditions. All fish from the second year-class died halfway through the scheduled 10 month rearing period. Survival of H fish was 5.2 times that of W fish to when 1% of the initial fry were still alive indicating that W fish succumbed to the epizootic sooner than did H fish. Emigrants from the Brushy Fork study reach were sampled for three years and fish residing in the study reach were sampled for six years following fry release. Most emigrants were one or two years old and too small to be smolts (mean fork length at age-2 = 93 mm). Survival in Brushy Fork was lower for H than for W fish of the first year-class. Survival of the second year-class was higher for H than for W fish during the first two months in the stream but was lower for H than for W fish thereafter, and net survival from release to ages 3 and older was also lower for H than for W fish if our emigrant samples were representative (periods of inoperative emigrant traps prevented certainty about this

  14. EFFECTS OF RESOURCE DEVELOPMENT ON WATER QUALITY IN THE BIG SOUTH FORK NATIONAL RIVER AND RECREATION AREA, TENNESSEE AND KENTUCKY.

    USGS Publications Warehouse

    Carey, William P.; ,

    1984-01-01

    The South Fork Cumberland River begins in Tennessee at the confluence of the New River and Clear Fork. Strip mining for coal in the New River basin has been ongoing for decades with little reclamation prior to 1977. Water-quality data show that suspended-sediment and dissolved-constituent loads from the New River dominate the water quality in the National River and Recreation Area. The suspended sediment can impart a highly turbid and aesthetically displeasing appearance to the water during low-flow periods which are times of maximum recreational use. High suspended-sediment concentrations are also potentially harmful to the aquatic habitat in the Recreation Area. In addition to the suspended-sediment load, a large supply of coarse material is slowly moving through the channels of the New River basin toward the Recreation Area.

  15. Piezoelectric tuning fork probe for atomic force microscopy imaging and specific recognition force spectroscopy of an enzyme and its ligand.

    PubMed

    Makky, Ali; Viel, Pascal; Chen, Shu-wen Wendy; Berthelot, Thomas; Pellequer, Jean-Luc; Polesel-Maris, Jérôme

    2013-11-01

    Piezoelectric quartz tuning fork has drawn the attention of many researchers for the development of new atomic force microscopy (AFM) self-sensing probes. However, only few works have been done for soft biological materials imaging in air or aqueous conditions. The aim of this work was to demonstrate the efficiency of the AFM tuning fork probe to perform high-resolution imaging of proteins and to study the specific interaction between a ligand and its receptor in aqueous media. Thus, a new kind of self-sensing AFM sensor was introduced to realize imaging and biochemical specific recognition spectroscopy of glucose oxidase enzyme using a new chemical functionalization procedure of the metallic tips based on the electrochemical reduction of diazonium salt. This scanning probe as well as the functionalization strategy proved to be efficient respectively for the topography and force spectroscopy of soft biological materials in buffer conditions.

  16. Environmental settings of the South Fork Iowa River basin, Iowa, and the Bogue Phalia basin, Mississippi, 2006-10

    USGS Publications Warehouse

    McCarthy, Kathleen A.; Rose, Claire E.; Kalkhoff, Stephen J.

    2012-01-01

    Studies of the transport and fate of agricultural chemicals in different environmental settings were conducted by the U.S. Geological Survey (USGS) National Water-Quality Assessment (NAWQA) Program's Agricultural Chemicals Team (ACT) at seven sites across the Nation, including the South Fork Iowa River basin in central Iowa and the Bogue Phalia basin in northwestern Mississippi. The South Fork Iowa River basin is representative of midwestern agriculture, where corn and soybeans are the predominant crops and a large percentage of the cultivated land is underlain by artificial drainage. The Bogue Phalia basin is representative of corn, soybean, cotton, and rice cropping in the humid, subtropical southeastern United States. Details of the environmental settings of these basins and the data-collection activities conducted by the USGS ACT over the 2006-10 study period are described in this report.

  17. Bed-material entrainment potential, Roaring Fork River at Basalt, Colorado

    USGS Publications Warehouse

    Elliott, John G.

    2002-01-01

    The Roaring Fork River at Basalt, Colorado, has a frequently mobile streambed composed of gravel, cobbles, and boulders. Recent urban and highway development on the flood plain, earlier attempts to realign and confine the channel, and flow obstructions such as bridge openings and piers have altered the hydrology, hydraulics, sediment transport, and sediment deposition areas of the Roaring Fork. Entrainment and deposition of coarse sediment on the streambed and in large alluvial bars have reduced the flood-conveying capacity of the river. Previous engineering studies have identified flood-prone areas and hazards related to inundation and high streamflow velocity, but those studies have not evaluated the potential response of the channel to discharges that entrain the coarse streambed. This study builds upon the results of earlier flood studies and identifies some potential areas of concern associated with bed-material entrainment. Cross-section surveys and simulated water-surface elevations from a previously run HEC?RAS model were used to calculate the boundary shear stress on the mean streambed, in the thalweg, and on the tops of adjacent alluvial bars for four reference streamflows. Sediment-size characteristics were determined for surficial material on the streambed, on large alluvial bars, and on a streambank. The median particle size (d50) for the streambed samples was 165 millimeters and for the alluvial bars and bank samples was 107 millimeters. Shear stresses generated by the 10-, 50-, and 100-year floods, and by a more common flow that just inundated most of the alluvial bars in the study reach were calculated at 14 of the cross sections used in the Roaring Fork River HEC?RAS model. The Shields equation was used with a Shields parameter of 0.030 to estimate the critical shear stress for entrainment of the median sediment particle size on the mean streambed, in the thalweg, and on adjacent alluvial bar surfaces at the 14 cross sections. Sediment

  18. Final Environmental Assessment: Installation of Digital Airport Surveillance Radar at Grand Forks Air Force Base, North Dakota

    DTIC Science & Technology

    2011-05-11

    northern pike (Esox lucius), white sucker (Catostomus commersonii), rock bass (Ambloplites sp.), black bullhead (Ameiurus melas), and channel...sedimentary sandstones, siltstones, and shales (Paleozoic and Mesozoic era) overlying igneous and metamorphic granites, schists, and greenstones (Precambrian...Air Base Wing 460 Steen Blvd Grand Forks AFB, ND 58205 Charles W. Murphy, Chairman Standing Rock Sioux Tribe POBoxD Fort Yates, ND 58538 Dear

  19. Spatially detailed quantification of metal loading for decision making: Metal mass loading to American fork and Mary Ellen Gulch, Utah

    USGS Publications Warehouse

    Kimball, B.A.; Runkel, R.L.

    2009-01-01

    Effective remediation requires an understanding of the relative contributions of metals from all sources in a catchment, and that understanding must be based on a spatially detailed quantification of metal loading. A traditional approach to quantifying metal loading has been to measure discharge and chemistry at a catchment outlet. This approach can quantify annual loading and the temporal changes in load, but does not provide the needed spatial detail to evaluate specific sources, which is needed to support remediation decisions. A catchment or massloading approach provides spatial detail by combining tracer-injection and synoptic-sampling methods to quantify loading. Examples of studies in American Fork, Utah, and its tributary Mary Ellen Gulch illustrate this different approach. The mass-loading study in American Fork treated Mary Ellen Gulch as a single inflow. From that point of view, Mary Ellen Gulch was one of the greatest sources of Fe, Mn, Zn, and colloidal Pb loads to American Fork. But when Mary Ellen Gulch was evaluated in a separate catchment study, the detailed locations of metal loading were identified, and the extent of metal attenuation upstream from the mouth of Mary Ellen Gulch was quantified. The net, instantaneous load measured at the mouth of Mary Ellen Gulch for remediation planning would greatly underestimate the contributions of principal sources within the catchment. Extending the detailed sampling downstream from Mary Ellen Gulch indicated the possibility of diffuse groundwater inflow from Mary Ellen Gulch to American Fork. Comparing loads for Mary Ellen Gulch in the two studies indicates that metal loads could be substantially underestimated for planning purposes without the detailed catchment approach for the low-flow conditions in these studies. A mass-loading approach provides both the needed quantification of metal loading and the spatial detail to guide remediation decisions that would be the most effective in the catchments

  20. Major complications associated with fork-based and screw-based tibial tuberosity advancement implants: 438 cases

    PubMed Central

    Edwards, George A.; Hosgood, Giselle; Hancock, Robert B.; Stubbs, W. Preston; Jackson, Andrew H.

    2016-01-01

    This study reports major complications in a large cohort of dogs following tibial tuberosity advancement using either a fork-based or a screw-based implant system. Four hundred thirty-eight stifles were included in the study and major complications occurred in 51 stifles. Explanatory variables evaluated included implant type and body weight. No variables evaluated were associated with major complications. PMID:27041760

  1. Confirmatory Sampling and Analysis Plan for the Lower East Fork Poplar Creek Operable Unit, Oak Ridge, Tennessee

    SciTech Connect

    1996-12-01

    This document describes the organization, strategy, and procedures to be used to confirm that mercury concentrations in soils in the remediated areas are statistically less than, or equal to, the cleanup standard of 400 ppm. It focuses on confirming the cleanup of the stretch of the Lower East Fork Popular Creed flowing from Lake Reality at the Y-12 Plant, through the City of Oak Ridge, to Poplar Creek on the Oak Ridge Reservation and its associated flood plain.

  2. Low-flow hydrology of the Sulphur Fork Red River basin, Robertson County, north-central Tennessee

    USGS Publications Warehouse

    Robbins, Clarence H.

    1979-01-01

    The objectives of this study were to define (1) the average 3-day natural low-flow with a 20-year recurrence interval for five low-flow partial-record sites and one continuous record station, (2) losing and gaining reaches of the main stem of the Sulphur Fork Red River and major tributaries, and (3) the quality of water during low-flow. An additional objective was the collection of continuous streamflow and temperature data at selected sites for development of a thermal model for use as a guide in design and management of a small reservoir. The quantity of surface water during low-flow varies considerably throughout the basin. Streamflow during periods of drought is groundwater discharging through numerous springs and seeps. The average 3-day, 20-year low-flow of the six study sites range from 0.1 to 2.2 cubic feet per second. Seepage investigations in October 1976 show that as much as 4.4 cubic feet per second are lost from the Sulphur Fork Red River within a reach of 1.7 miles between river mile 30.8 and 29.1. Seepage investigations in July 1977 show that as much as 3.7 cubic feet per second are gained in the Sulphur Fork Red River within a reach of 0.8 miles between river mile 42.6 and 41.8. Measured discharges from the 12 major springs in the basin ranged from less than 1 to 1660 gallons per minute during low-flow. Water quality of streams varies in time and space. Specific conductance ranged from 200 to 1,800 micromhos per centimeter at 25O centigrade during the 1976 seepage investigation on the Sulphur Fork Red River. During the two-year study the specific conductance of water from the springs ranged from 230 to 675 micromhos per centimeter at 25O centigrade.

  3. Debris Flow Control on Fluvial Hanging Valley Formation in the South Fork Eel River, CA

    NASA Astrophysics Data System (ADS)

    Deshpande, N.; Perkins, J.; Finnegan, N. J.

    2012-12-01

    An understanding of how base level signals are transmitted into landscapes is fundamental to interpreting river long profiles in tectonically active settings. Fluvial hanging valleys, locations where waves of incision have apparently arrested at tributary junctions, suggest that base level propagation is an unsteady process in many settings. A recent hypothesis (Wobus et al., 2006) explains the formation of fluvial hanging valleys via an instability in the saltation abrasion model of Sklar and Dietrich (2004). At locations where small steep tributaries join trunk streams, tributary incision rates can actually decrease with increasing channel slope when subjected to downstream base-level fall. However, we note that in mountainous river networks steep tributaries also commonly convey debris flows into trunk channels. Since these tributary junctions mark the upstream limit of channels whose beds are mobilized on a regular basis during flood events, here we hypothesize that transitions from fluvial to debris flow channels control the location of fluvial hanging valleys. To test our hypothesis, we exploit a natural experiment in base level fall and landscape evolution along the South Fork Eel River, which is argued to be responding to an increase in rock uplift rate associated with the passage of the Mendocino Triple Junction. In order to separate debris flow channels from fluvial channels, we use airborne laser swath mapping (ALSM) to quantify channel slopes and concavities. In our analysis, concavity data are noisy and represent a poor metric for determination of debris flow channels. In lieu of this, we choose a more straightforward metric of channel slope to discriminate where debris flows occur on the landscape. We find that, on average, fluvial hanging valleys are only present in tributaries with average gradients above 0.10, consistent with empirical determinations of the gradient at which debris flow channels transition to fluvial channels (0.03-0.10). Field

  4. South Fork Flathead Watershed Westslope Cutthroat Trout Conservation Program, Annual Report 2002.

    SciTech Connect

    Grisak, Grant; Marotz, Brian

    2003-06-01

    In 1999, Montana Fish, Wildlife & Parks (MFWP) began a program aimed at conserving the genetically pure populations of westslope cutthroat trout in the South Fork Flathead River drainage. The objective of this program is to eliminate all of the exotic and hybrid trout that threaten the genetically pure westslope cutthroat populations in the South Fork Flathead. The exotic and hybrid trout populations occur in several headwater lakes and their outflow streams. In 2001 MFWP released a draft environmental assessment, pursuant to the Montana Environmental Policy Act (MEPA), that addressed the use of motorized equipment to deliver personnel and materials to some of these lakes in the Bob Marshall and Great Bear Wildernesses (Grisak 2001). After a 30-day public comment period, MFWP determined that the complexity of issues was too great and warranted a more detailed analysis. These issues included transportation options for personnel, equipment and materials, the use of motorized equipment in wilderness, fish removal methods, fish stocking, and the status and distribution of amphibian populations in the project area. Because the program also involves the U.S. Forest Service (USFS) and Bonneville Power Administration (BPA), the environmental analysis needs to comply with the National Environmental Policy Act (NEPA). In October 2001, pursuant to NEPA, MFWP, along with the USFS and BPA initiated an environmental assessment to address these issues. In June 2002, the three agencies determined that the scope of these issues warranted an Environmental Impact Statement. This specialist report describes the logistical, technical and biological issues associated with this project and provides an analysis of options for fish removal, transportation and fish stocking. It further analyzes issues and concerns associated with amphibian populations and creating new domesticated stocks of westslope cutthroat trout. Finally, this document provides a description of each lake, the best

  5. Quarterly Progress Report - Biological Monitoring Program for East Fork Poplar Creek

    SciTech Connect

    Adams, S.M.; Christensen, S.W.; Greeley, M.S.jr; Hill, W.R.; McCarthy, J.F.; Peterson, M.J.; Ryon, M.G.; Smith, J.G.; Southworth, G.R.; Stewart, A.J.

    2000-04-18

    In May 1985, a National Pollutant Discharge Elimination System (NPDES) permit was issued for the Oak Ridge Y-12 Plant. As a condition of the permit, a Biological Monitoring and Abatement Program (BMAP) was developed to demonstrate that the effluent limitations established for the Y-12 Plant protect the classified uses of the receiving stream (East Fork Poplar Creek; EFPC), in particular, the growth and propagation of aquatic life (Loar et al. 1989). A second objective of the BMAP is to document the ecological effects resulting from the implementation of a water pollution control program designed to eliminate direct discharges of wastewaters to EFPC and to minimize the inadvertent release of pollutants to the environment. Because of the complex nature of the discharges to EFPC and the temporal and spatial variability in the composition of the discharges, a comprehensive, integrated approach to biological monitoring was developed. A new permit was issued to the Y-12 Plant on April 28, 1995 and became effective on July 1, 1995. Biological monitoring continues to be required under the new permit. The BMAP consists of four major tasks that reflect different but complementary approaches to evaluating the effects of the Y-12 Plant discharges on the aquatic integrity of EFPC. These tasks are (1) toxicity monitoring, (2) biological indicator studies, (3) bioaccumulation studies, and (4) ecological surveys of the periphyton, benthic macroinvertebrate, and fish communities. Monitoring is currently being conducted at five primary EFPC sites, although sites may be excluded or added depending upon the specific objectives of the various tasks. Criteria used in selecting the sites include: (1) location of sampling sites used in other studies, (2) known or suspected sources of downstream impacts, (3) proximity to U.S. Department of Energy (DOE) Oak Ridge Reservation (ORR) boundaries, (4) concentration of mercury in the adjacent floodplain, (5) appropriate habitat distribution, and

  6. Quarterly Progress Report - Biological Monitoring Program for East Fork Poplar Creek

    SciTech Connect

    Adams, S.M.; Christensen, S.W.; Greeley, M.S. jr; Hill, W.R.; McCarthy, J.F.; Peterson, M.J.; Ryon, M.G.; Smith, J.G.; Southworth, G.R.; Stewart, A.J.

    2000-07-18

    In May 1985, a National Pollutant Discharge Elimination System (NPDES) permit was issued for the Oak Ridge Y-12 Plant. As a condition of the permit, a Biological Monitoring and Abatement Program (BMAP) was developed to demonstrate that the effluent limitations established for the Y-12 Plant protect the classified uses of the receiving stream (East Fork Poplar Creek; EFPC), in particular, the growth and propagation of aquatic life (Loar et al. 1989). A second objective of the BMAP is to document the ecological effects resulting from the implementation of a water pollution control program designed to eliminate direct discharges of wastewaters to EFPC and to minimize the inadvertent release of pollutants to the environment. Because of the complex nature of the discharges to EFPC and the temporal and spatial variability in the composition of the discharges, a comprehensive, integrated approach to biological monitoring was developed. A new permit was issued to the Y-12 Plant on April 28, 1995 and became effective on July 1, 1995. Biological monitoring continues to be required under the new permit. The BMAP consists of four major tasks that reflect different but complementary approaches to evaluating the effects of the Y-12 Plant discharges on the aquatic integrity of EFPC. These tasks are (1) toxicity monitoring, (2) biological indicator studies, (3) bioaccumulation studies, and (4) ecological surveys of the periphyton, benthic macroinvertebrate, and fish communities. Monitoring is currently being conducted at five primary EFPC sites, although sites may be excluded or added depending upon the specific objectives of the various tasks. Criteria used in selecting the sites include: (1) location of sampling sites used in other studies, (2) known or suspected sources of downstream impacts, (3) proximity to U.S. Department of Energy (DOE) Oak Ridge Reservation (ORR) boundaries, (4) concentration of mercury in the adjacent floodplain, (5) appropriate habitat distribution, and

  7. Quarterly Progress Report - Biological Monitoring Program for East Fork Poplar Creek

    SciTech Connect

    Adams, S.M.; Christensen, S.W.; Greeley, M.S.jr; Hill, W.R.; McCarthy, J.F.; Peterson, M.J.; Ryon, M.G.; Smith, J.G.; Southworth, G.R.; Stewart, A.J.

    2000-10-18

    In May 1985, a National Pollutant Discharge Elimination System (NPDES) permit was issued for the Oak Ridge Y-12 Plant. As a condition of the permit, a Biological Monitoring and Abatement Program (BMAP) was developed to demonstrate that the effluent limitations established for the Y-12 Plant protect the classified uses of the receiving stream (East Fork Poplar Creek; EFPC), in particular, the growth and propagation of aquatic life (Loar et al. 1989). A second objective of the BMAP is to document the ecological effects resulting from the implementation of a water pollution control program designed to eliminate direct discharges of wastewaters to EFPC and to minimize the inadvertent release of pollutants to the environment. Because of the complex nature of the discharges to EFPC and the temporal and spatial variability in the composition of the discharges, a comprehensive, integrated approach to biological monitoring was developed. A new permit was issued to the Y-12 Plant on April 28, 1995 and became effective on July 1, 1995. Biological monitoring continues to be required under the new permit. The BMAP consists of four major tasks that reflect different but complementary approaches to evaluating the effects of the Y-12 Plant discharges on the aquatic integrity of EFPC. These tasks are (1) toxicity monitoring, (2) biological indicator studies, (3) bioaccumulation studies, and (4) ecological surveys of the periphyton, benthic macroinvertebrate, and fish communities. Monitoring is currently being conducted at five primary EFPC sites, although sites may be excluded or added depending upon the specific objectives of the various tasks. Criteria used in selecting the sites include: (1) location of sampling sites used in other studies, (2) known or suspected sources of downstream impacts, (3) proximity to U.S. Department of Energy (DOE) Oak Ridge Reservation (ORR) boundaries, (4) concentration of mercury in the adjacent floodplain, (5) appropriate habitat distribution, and

  8. Vibration Sensitivity Reduction of Micromachined Tuning Fork Gyroscopes through Stiffness Match Method with Negative Electrostatic Spring Effect

    PubMed Central

    Guan, Yanwei; Gao, Shiqiao; Liu, Haipeng; Jin, Lei; Zhang, Yaping

    2016-01-01

    In this paper, a stiffness match method is proposed to reduce the vibration sensitivity of micromachined tuning fork gyroscopes. Taking advantage of the coordinate transformation method, a theoretical model is established to analyze the anti-phase vibration output caused by the stiffness mismatch due to the fabrication imperfections. The analytical solutions demonstrate that the stiffness mismatch is proportional to the output induced by the external linear vibration from the sense direction in the anti-phase mode frequency. In order to verify the proposed stiffness match method, a tuning fork gyroscope (TFG) with the stiffness match electrodes is designed and implemented using the micromachining technology and the experimental study is carried out. The experimental tests illustrate that the vibration output can be reduced by 73.8% through the stiffness match method than the structure without the stiffness match. Therefore, the proposed stiffness match method is experimentally validated to be applicable to vibration sensitivity reduction in the Micro-Electro-Mechanical-Systems (MEMS) tuning fork gyroscopes without sacrificing the scale factor. PMID:27455272

  9. Contrasting roles of checkpoint proteins as recombination modulators at Fob1-Ter complexes with or without fork arrest.

    PubMed

    Mohanty, Bidyut K; Bairwa, Narendra K; Bastia, Deepak

    2009-04-01

    The replication terminator protein Fob1 of Saccharomyces cerevisiae specifically interacts with two tandem Ter sites (replication fork barriers) located in the nontranscribed spacer of ribosomal DNA (rDNA) to cause polar fork arrest. The Fob1-Ter complex is multifunctional and controls other DNA transactions such as recombination by multiple mechanisms. Here, we report on the regulatory roles of the checkpoint proteins in the initiation and progression of recombination at Fob1-Ter complexes. The checkpoint adapter proteins Tof1 and Csm3 either positively or negatively controlled recombination depending on whether it was provoked by polar fork arrest or by transcription, respectively. The absolute requirements for these proteins for inducing recombination at an active replication terminus most likely masked their negative modulatory role at a later step of the process. Other checkpoint proteins of the checkpoint adapter/mediator class such as Mrc1 and Rad9, which channel signals from the sensor to the effector kinase, tended to suppress recombination at Fob1-Ter complexes regardless of how it was initiated. We have also discovered that the checkpoint sensor kinase Mec1 and the effector Rad53 were positive modulators of recombination initiated by transcription but had little effect on recombination at Ter. The work also showed that the two pathways were Rad52 dependent but Rad51 independent. Since Ter sites occur in the intergenic spacer of rDNA from yeast to humans, the mechanism is likely to be of widespread occurrence.

  10. Vibration Sensitivity Reduction of Micromachined Tuning Fork Gyroscopes through Stiffness Match Method with Negative Electrostatic Spring Effect.

    PubMed

    Guan, Yanwei; Gao, Shiqiao; Liu, Haipeng; Jin, Lei; Zhang, Yaping

    2016-07-22

    In this paper, a stiffness match method is proposed to reduce the vibration sensitivity of micromachined tuning fork gyroscopes. Taking advantage of the coordinate transformation method, a theoretical model is established to analyze the anti-phase vibration output caused by the stiffness mismatch due to the fabrication imperfections. The analytical solutions demonstrate that the stiffness mismatch is proportional to the output induced by the external linear vibration from the sense direction in the anti-phase mode frequency. In order to verify the proposed stiffness match method, a tuning fork gyroscope (TFG) with the stiffness match electrodes is designed and implemented using the micromachining technology and the experimental study is carried out. The experimental tests illustrate that the vibration output can be reduced by 73.8% through the stiffness match method than the structure without the stiffness match. Therefore, the proposed stiffness match method is experimentally validated to be applicable to vibration sensitivity reduction in the Micro-Electro-Mechanical-Systems (MEMS) tuning fork gyroscopes without sacrificing the scale factor.

  11. Integrated tuning fork nanocavity optomechanical transducers with high f M Q M product and stress-engineered frequency tuning

    NASA Astrophysics Data System (ADS)

    Zhang, R.; Ti, C.; Davanço, M. I.; Ren, Y.; Aksyuk, V.; Liu, Y.; Srinivasan, K.

    2015-09-01

    Cavity optomechanical systems are being widely developed for precision force and displacement measurements. For nanomechanical transducers, there is usually a trade-off between the frequency (fM) and quality factor (QM), which limits temporal resolution and sensitivity. Here, we present a monolithic cavity optomechanical transducer supporting both high fM and high QM. By replacing the common doubly clamped, Si3N4 nanobeam with a tuning fork geometry, we demonstrate devices with the fundamental f M ≈ 29 MHz and Q M ≈ 2.2 × 10 5 , corresponding to an fMQM product of 6.35 × 10 12 Hz , comparable to the highest values previously demonstrated for room temperature operation. This high fMQM product is partly achieved by engineering the stress of the tuning fork to be 3 times the residual film stress through clamp design, which results in an increase of fM up to 1.5 times. Simulations reveal that the tuning fork design simultaneously reduces the clamping, thermoelastic dissipation, and intrinsic material damping contributions to mechanical loss. This work may find application when both high temporal and force resolution are important, such as in compact sensors for atomic force microscopy.

  12. Bloom syndrome complex promotes FANCM recruitment to stalled replication forks and facilitates both repair and traverse of DNA interstrand crosslinks

    PubMed Central

    Ling, Chen; Huang, Jing; Yan, Zhijiang; Li, Yongjiang; Ohzeki, Mioko; Ishiai, Masamichi; Xu, Dongyi; Takata, Minoru; Seidman, Michael; Wang, Weidong

    2016-01-01

    The recruitment of FANCM, a conserved DNA translocase and key component of several DNA repair protein complexes, to replication forks stalled by DNA interstrand crosslinks (ICLs) is a step upstream of the Fanconi anemia (FA) repair and replication traverse pathways of ICLs. However, detection of the FANCM recruitment has been technically challenging so that its mechanism remains exclusive. Here, we successfully observed recruitment of FANCM at stalled forks using a newly developed protocol. We report that the FANCM recruitment depends upon its intrinsic DNA translocase activity, and its DNA-binding partner FAAP24. Moreover, it is dependent on the replication checkpoint kinase, ATR; but is independent of the FA core and FANCD2–FANCI complexes, two essential components of the FA pathway, indicating that the FANCM recruitment occurs downstream of ATR but upstream of the FA pathway. Interestingly, the recruitment of FANCM requires its direct interaction with Bloom syndrome complex composed of BLM helicase, Topoisomerase 3α, RMI1 and RMI2; as well as the helicase activity of BLM. We further show that the FANCM–BLM complex interaction is critical for replication stress-induced FANCM hyperphosphorylation, for normal activation of the FA pathway in response to ICLs, and for efficient traverse of ICLs by the replication machinery. Epistasis studies demonstrate that FANCM and BLM work in the same pathway to promote replication traverse of ICLs. We conclude that FANCM and BLM complex work together at stalled forks to promote both FA repair and replication traverse pathways of ICLs. PMID:28058110

  13. Bioaccumulation of metals by Hyalella azteca exposed to contaminated sediments from the upper Clark Fork River, Montana

    SciTech Connect

    Ingersoll, C.G.; Brumbaugh, W.G.; Dwyer, F.J.; Kemble, N.E. . Midwest Science Center)

    1994-12-01

    Macroinvertebrate contaminated with metals in the Clark Fork River of Montana have been demonstrated to be a potentially toxic component in the diet of trout. Because sediment was the suspected source of metals to these invertebrates, bioaccumulation of As, Cd, Cu, Pb, and Zn from sediment was evaluated by exposing the amphipod Hyalella azteca for 28 d in the laboratory to samples of sediment collected from depositional areas of the Clark Fork River. Benthic invertebrates collected from riffles adjacent to the depositional areas were also analyzed for metals. The pattern of metal accumulation between laboratory-exposed and field-collected animals was similar; however, the concentrations of metals in laboratory-exposed amphipods were often 50 to 75% less than were the concentrations of metals in the field-collected invertebrates. These findings indicate that sediment is a significant source of metals to invertebrates in the Clark Fork River. Additional studies should be conducted to determine threshold concentrations for effects of dietary metals on fish. Long-term monitoring of the river should include sampling benthic invertebrates for metal accumulation.

  14. Hypermutagenesis in mutA cells is mediated by mistranslational corruption of polymerase, and is accompanied by replication fork collapse.

    PubMed

    Al Mamun, Abu Amar M; Gautam, Satyendra; Humayun, M Zafri

    2006-12-01

    Elevated mistranslation induces a mutator response termed translational stress-induced mutagenesis (TSM) that is mediated by an unidentified modification of DNA polymerase III. Here we address two questions: (i) does TSM result from direct polymerase corruption, or from an indirect pathway triggered by increased protein turnover? (ii) Why are homologous recombination functions required for the expression of TSM under certain conditions, but not others? We show that replication of bacteriophage T4 in cells expressing the mutA allele of the glyVtRNA gene (Asp-Gly mistranslation), leads to both increased mutagenesis, and to an altered mutational specificity, results that strongly support mistranslational corruption of DNA polymerase. We also show that expression of mutA, which confers a recA-dependent mutator phenotype, leads to increased lambdoid prophage induction (selectable in vivo expression technology assay), suggesting that replication fork collapse occurs more frequently in mutA cells relative to control cells. No such increase in prophage induction is seen in cells expressing alaVGlu tRNA (Glu-->Ala mistranslation), in which the mutator phenotype is recA-independent. We propose that replication fork collapse accompanies episodic hypermutagenic replication cycles in mutA cells, requiring homologous recombination functions for fork recovery, and therefore, for mutation recovery. These findings highlight hitherto under-appreciated links among translation, replication and recombination, and suggest that translational fidelity, which is affected by genetic and environmental signals, is a key modulator of replication fidelity.

  15. Bloom syndrome complex promotes FANCM recruitment to stalled replication forks and facilitates both repair and traverse of DNA interstrand crosslinks.

    PubMed

    Ling, Chen; Huang, Jing; Yan, Zhijiang; Li, Yongjiang; Ohzeki, Mioko; Ishiai, Masamichi; Xu, Dongyi; Takata, Minoru; Seidman, Michael; Wang, Weidong

    2016-01-01

    The recruitment of FANCM, a conserved DNA translocase and key component of several DNA repair protein complexes, to replication forks stalled by DNA interstrand crosslinks (ICLs) is a step upstream of the Fanconi anemia (FA) repair and replication traverse pathways of ICLs. However, detection of the FANCM recruitment has been technically challenging so that its mechanism remains exclusive. Here, we successfully observed recruitment of FANCM at stalled forks using a newly developed protocol. We report that the FANCM recruitment depends upon its intrinsic DNA translocase activity, and its DNA-binding partner FAAP24. Moreover, it is dependent on the replication checkpoint kinase, ATR; but is independent of the FA core and FANCD2-FANCI complexes, two essential components of the FA pathway, indicating that the FANCM recruitment occurs downstream of ATR but upstream of the FA pathway. Interestingly, the recruitment of FANCM requires its direct interaction with Bloom syndrome complex composed of BLM helicase, Topoisomerase 3α, RMI1 and RMI2; as well as the helicase activity of BLM. We further show that the FANCM-BLM complex interaction is critical for replication stress-induced FANCM hyperphosphorylation, for normal activation of the FA pathway in response to ICLs, and for efficient traverse of ICLs by the replication machinery. Epistasis studies demonstrate that FANCM and BLM work in the same pathway to promote replication traverse of ICLs. We conclude that FANCM and BLM complex work together at stalled forks to promote both FA repair and replication traverse pathways of ICLs.

  16. DNA damage tolerance pathway involving DNA polymerase ι and the tumor suppressor p53 regulates DNA replication fork progression

    PubMed Central

    Hampp, Stephanie; Kiessling, Tina; Buechle, Kerstin; Mansilla, Sabrina F.; Thomale, Jürgen; Rall, Melanie; Ahn, Jinwoo; Pospiech, Helmut; Gottifredi, Vanesa; Wiesmüller, Lisa

    2016-01-01

    DNA damage tolerance facilitates the progression of replication forks that have encountered obstacles on the template strands. It involves either translesion DNA synthesis initiated by proliferating cell nuclear antigen monoubiquitination or less well-characterized fork reversal and template switch mechanisms. Herein, we characterize a novel tolerance pathway requiring the tumor suppressor p53, the translesion polymerase ι (POLι), the ubiquitin ligase Rad5-related helicase-like transcription factor (HLTF), and the SWI/SNF catalytic subunit (SNF2) translocase zinc finger ran-binding domain containing 3 (ZRANB3). This novel p53 activity is lost in the exonuclease-deficient but transcriptionally active p53(H115N) mutant. Wild-type p53, but not p53(H115N), associates with POLι in vivo. Strikingly, the concerted action of p53 and POLι decelerates nascent DNA elongation and promotes HLTF/ZRANB3-dependent recombination during unperturbed DNA replication. Particularly after cross-linker–induced replication stress, p53 and POLι also act together to promote meiotic recombination enzyme 11 (MRE11)-dependent accumulation of (phospho-)replication protein A (RPA)-coated ssDNA. These results implicate a direct role of p53 in the processing of replication forks encountering obstacles on the template strand. Our findings define an unprecedented function of p53 and POLι in the DNA damage response to endogenous or exogenous replication stress. PMID:27407148

  17. Bioaccumulation of metals by Hyalella azteca exposed to contaminated sediments from the upper Clark Fork River, Montana

    USGS Publications Warehouse

    Ingersoll, Christopher G.; Brumbaugh, William G.; Dwyer, F. James; Kemble, Nile E.

    1994-01-01

    Macroinvertebrates contaminated with metals in the Clark Fork River of Montana have been demonstrated to be a potentially toxic component in the diet of trout Because sediment was the suspected source of metals to these invertebrates, bioaccumulation of As, Cd, Cu, Pb, and Zn from sediment was evaluated by exposing the amphipod Hyalella azteca for 28 d in the laboratory to samples of sediment collected from depositional areas of the Clark Fork River Benthic invertebrates collected from riffles adjacent to the depositional areas were also analyzed for metals The pattern of metal accumulation between laboratory-exposed and field-collected animals was similar, however, the concentrations of metals in laboratory exposed amphipods were often 50 to 75% less than were the concentrations of metals in the field collected invertebrates These findings indicate that sediment is a significant source of metals to invertebrates in the Clark Fork River Additional studies should be conducted to determine threshold concentrations for effects of dietary metals on fish Long-term monitoring of the river should include sampling benthic invertebrates for metal accumulation.

  18. Fork-tailed drongos use deceptive mimicked alarm calls to steal food.

    PubMed

    Flower, Tom

    2011-05-22

    Despite the prevalence of vocal mimicry in animals, few functions for this behaviour have been shown. I propose a novel hypothesis that false mimicked alarm calls could be used deceptively to scare other species and steal their food. Studies have previously suggested that animals use their own species-specific alarm calls to steal food. However none have shown conclusively that these false alarms are deceptive, or that mimicked alarm calls are used in this manner. Here, I show that wild fork-tailed drongos (Dicrurus adsimilis) make both drongo-specific and mimicked false alarm calls when watching target species handling food, in response to which targets flee to cover abandoning their food. The drongo-specific and mimicked calls made in false alarms were structurally indistinguishable from calls made during true alarms at predators by drongos and other species. Furthermore, I demonstrate by playback experiments that two of these species, meerkats (Suricata suricatta) and pied babblers (Turdoides bicolor), are deceived by both drongo-specific and mimicked false alarm calls. These results provide the first conclusive evidence that false alarm calls are deceptive and demonstrate a novel function for vocal mimicry. This work also provides valuable insight into the benefits of deploying variable mimetic signals in deceptive communication.

  19. A z-axis quartz cross-fork micromachined gyroscope based on shear stress detection.

    PubMed

    Xie, Liqiang; Wu, Xuezhong; Li, Shengyi; Wang, Haoxu; Su, Jianbin; Dong, Peitao

    2010-01-01

    Here we propose a novel quartz micromachined gyroscope. The sensor has a simple cross-fork structure in the x-y plane of quartz crystal. Shear stress rather than normal stress is utilized to sense Coriolis' force generated by the input angular rate signal. Compared to traditional quartz gyroscopes, which have two separate sense electrodes on each sidewall, there is only one electrode on each sidewall of the sense beam. As a result, the fabrication of the electrodes is simplified and the structure can be easily miniaturized. In order to increase sensitivity, a pair of proof masses is attached to the ends of the drive beam, and the sense beam has a tapered design. The structure is etched from a z-cut quartz wafer and the electrodes are realized by direct evaporation using the aperture mask method. The drive mode frequency of the prototype is 13.38 kHz, and the quality factor is approximately 1,000 in air. Therefore, the gyroscope can work properly without a vacuum package. The measurement ability of the shear stress detection design scheme is validated by the Coriolis' force test. The performance of the sensor is characterized on a precision rate table using a specially designed readout circuit. The experimentally obtained scale factor is 1.45 mV/°/s and the nonlinearity is 3.6% in range of ± 200 °/s.

  20. Rock fall simulation at Timpanogos Cave National Monument, American Fork Canyon, Utah, USA

    USGS Publications Warehouse

    Harp, E.L.; Dart, R.L.; Reichenbach, P.

    2011-01-01

    Rock fall from limestone cliffs at Timpanogos Cave National Monument in American Fork Canyon east of Provo, Utah, is a common occurrence. The cave is located in limestone cliffs high on the southern side of the canyon. One fatality in 1933 led to the construction of rock fall shelters at the cave entrance and exit in 1976. Numerous rock fall incidents, including a near miss in 2000 in the vicinity of the trail below the cave exit, have led to a decision to extend the shelter at the cave exit to protect visitors from these ongoing rock fall events initiating from cliffs immediately above the cave exit. Three-dimensional rock fall simulations from sources at the top of these cliffs have provided data from which to assess the spatial frequencies and velocities of rock falls from the cliffs and to constrain the design of protective measures to reduce the rock fall hazard. Results from the rock fall simulations are consistent with the spatial patterns of rock fall impacts that have been observed at the cave exit site. ?? 2011 Springer-Verlag.

  1. Rock fall simulation at Timpanogos Cave National Monument, American Fork Canyon, Utah, USA

    USGS Publications Warehouse

    Harp, Edwin L.; Dart, Richard L.; Reichenbach, Paola

    2011-01-01

    Rock fall from limestone cliffs at Timpanogos Cave National Monument in American Fork Canyon east of Provo, Utah, is a common occurrence. The cave is located in limestone cliffs high on the southern side of the canyon. One fatality in 1933 led to the construction of rock fall shelters at the cave entrance and exit in 1976. Numerous rock fall incidents, including a near miss in 2000 in the vicinity of the trail below the cave exit, have led to a decision to extend the shelter at the cave exit to protect visitors from these ongoing rock fall events initiating from cliffs immediately above the cave exit. Three-dimensional rock fall simulations from sources at the top of these cliffs have provided data from which to assess the spatial frequencies and velocities of rock falls from the cliffs and to constrain the design of protective measures to reduce the rock fall hazard. Results from the rock fall simulations are consistent with the spatial patterns of rock fall impacts that have been observed at the cave exit site.

  2. Chronic toxicity of Clark Fork River invertebrates to rainbow trout when administered via the diet

    SciTech Connect

    Barth, A.; Cohen, A.; Stubblefield, W.

    1995-12-31

    A 46-day exposure examined the effects of metals contamination in a live natural freshwater diet on rainbow trout fry. Survival, growth, and whole-body tissue metals were compared among groups of trout fed live planktonic invertebrates (primarily Daphnia pulex) collected from the Clark Fork River (CFR), Montana and trout fed live laboratory-reared D. pulex. Metals of interest in the diets were As, Cu, Cd, Pb, and Zn. In addition to dietary exposure, treatments included simultaneous exposure to a mixture of waterborne metals (Cu, Cd, Pb, and Zn) at sublethal concentrations. Trout showed no statistically significant effects on survival or growth from mean CFR invertebrate metal concentrations of 20.1 mg As/kg dwt, 60.7 mg Cu/kg dwt, 4.0 mg Cd/kg dwt, 4.9 mg Pb/kg dwt, and 249 mg Zn/kg dwt. Waterborne and dietary Cd and Pb appeared to result in increased tissue concentrations of these metals, while only dietary As resulted in increased tissue As. Neither dietary nor waterborne copper or zinc had a substantial effect on tissue levels of these metals. Results were consistent, in terms of the lack of statistically significant growth and survival effects, with those of previous in-house studies exposing rainbow trout to metals-enriched Artemia sp. (brine shrimp) diets.

  3. The Drosophila fork head domain protein crocodile is required for the establishment of head structures.

    PubMed Central

    Häcker, U; Kaufmann, E; Hartmann, C; Jürgens, G; Knöchel, W; Jäckle, H

    1995-01-01

    The fork head (fkh) domain defines the DNA-binding region of a family of transcription factors which has been implicated in regulating cell fate decisions across species lines. We have cloned and molecularly characterized the crocodile (croc) gene which encodes a new family member from Drosophila. croc is expressed in the head anlagen of the blastoderm embryo under the control of the anterior, the dorsoventral and the terminal maternal organizer systems. The croc mutant phenotype indicates that the croc wild-type gene is required to function as an early patterning gene in the anterior-most blastoderm head segment anlage and for the establishment of a specific head skeletal structure that derives from the non-adjacent intercalary segment at a later stage of embryogenesis. As an early patterning gene, croc exerts unusual properties which do not allow it to be grouped among the established segmentation genes. A single-site mutation within the croc fkh domain, which causes a replacement of the first out of four conserved amino acid residues thought to be involved in the coordinate binding of Mg2+, abolishes the DNA binding of the protein in vitro. In view of the resulting lack-of-function mutant phenotype, it appears likely that metal binding by the affected region of the fkh domain is crucial for proper folding of the DNA-binding structure. Images PMID:7489720

  4. Xenopus Mcm10 is a CDK-substrate required for replication fork stability

    PubMed Central

    Chadha, Gaganmeet Singh; Gambus, Agnieszka; Gillespie, Peter J.; Blow, J. Julian

    2016-01-01

    ABSTRACT During S phase, following activation of the S phase CDKs and the DBF4-dependent kinases (DDK), double hexamers of Mcm2-7 at licensed replication origins are activated to form the core replicative helicase. Mcm10 is one of several proteins that have been implicated from work in yeasts to play a role in forming a mature replisome during the initiation process. Mcm10 has also been proposed to play a role in promoting replisome stability after initiation has taken place. The role of Mcm10 is particularly unclear in metazoans, where conflicting data has been presented. Here, we investigate the role and regulation of Mcm10 in Xenopus egg extracts. We show that Xenopus Mcm10 is recruited to chromatin late in the process of replication initiation and this requires prior action of DDKs and CDKs. We also provide evidence that Mcm10 is a CDK substrate but does not need to be phosphorylated in order to associate with chromatin. We show that in extracts depleted of more than 99% of Mcm10, the bulk of DNA replication still occurs, suggesting that Mcm10 is not required for the process of replication initiation. However, in extracts depleted of Mcm10, the replication fork elongation rate is reduced. Furthermore, the absence of Mcm10 or its phosphorylation by CDK results in instability of replisome proteins on DNA, which is particularly important under conditions of replication stress. PMID:27327991

  5. Research on the Sensing Performance of the Tuning Fork-Probe as a Micro Interaction Sensor.

    PubMed

    Gao, Fengli; Li, Xide

    2015-09-23

    The shear force position system has been widely used in scanning near-field optical microscopy (SNOM) and recently extended into the force sensing area. The dynamic properties of a tuning fork (TF), the core component of this system, directly determine the sensing performance of the shear positioning system. Here, we combine experimental results and finite element method (FEM) analysis to investigate the dynamic behavior of the TF probe assembled structure (TF-probe). Results from experiments under varying atmospheric pressures illustrate that the oscillation amplitude of the TF-probe is linearly related to the quality factor, suggesting that decreasing the pressure will dramatically increase the quality factor. The results from FEM analysis reveal the influences of various parameters on the resonant performance of the TF-probe. We compared numerical results of the frequency spectrum with the experimental data collected by our recently developed laser Doppler vibrometer system. Then, we investigated the parameters affecting spatial resolution of the SNOM and the dynamic response of the TF-probe under longitudinal and transverse interactions. It is found that the interactions in transverse direction is much more sensitive than that in the longitudinal direction. Finally, the TF-probe was used to measure the friction coefficient of a silica-silica interface.

  6. Design of a Compact Tuning Fork-Shaped Notched Ultrawideband Antenna for Wireless Communication Application

    PubMed Central

    Shakib, M. N.; Moghavvemi, M.; Mahadi, W. N. L.

    2014-01-01

    A new compact planar notched ultrawideband (UWB) antenna is designed for wireless communication application. The proposed antenna has a compact size of 0.182λ × 0.228λ × 0.018λ where λ is the wavelength of the lowest operating frequency. The antenna is comprised of rectangular radiating patch, ground plane, and an arc-shaped strip in between radiating patch and feed line. By introducing a new Tuning Fork-shaped notch in the radiating plane, a stopband is obtained. The antenna is tested and measured. The measured result indicated that fabricated antenna has achieved a wide bandwidth of 4.33–13.8 GHz (at −10 dB return loss) with a rejection frequency band of 5.28–6.97 GHz (WiMAX, WLAN, and C-band). The effects of the parameters of the antenna are discussed. The experiment results demonstrate that the proposed antenna can well meet the requirement for the UWB communication in spite of its compactness and small size. PMID:24723835

  7. Borehole seismic monitoring of seismic stimulation at OccidentalPermian Ltd's -- South Wason Clear Fork Unit

    SciTech Connect

    Daley, Tom; Majer, Ernie

    2007-04-30

    Seismic stimulation is a proposed enhanced oil recovery(EOR) technique which uses seismic energy to increase oil production. Aspart of an integrated research effort (theory, lab and field studies),LBNL has been measuring the seismic amplitude of various stimulationsources in various oil fields (Majer, et al., 2006, Roberts,et al.,2001, Daley et al., 1999). The amplitude of the seismic waves generatedby a stimulation source is an important parameter for increased oilmobility in both theoretical models and laboratory core studies. Theseismic amplitude, typically in units of seismic strain, can be measuredin-situ by use of a borehole seismometer (geophone). Measuring thedistribution of amplitudes within a reservoir could allow improved designof stimulation source deployment. In March, 2007, we provided in-fieldmonitoring of two stimulation sources operating in Occidental (Oxy)Permian Ltd's South Wasson Clear Fork (SWCU) unit, located near DenverCity, Tx. The stimulation source is a downhole fluid pulsation devicedeveloped by Applied Seismic Research Corp. (ASR). Our monitoring used aborehole wall-locking 3-component geophone operating in two nearbywells.

  8. Solar project description for Design Construction Association single family dwelling, Big Fork, Montana

    NASA Astrophysics Data System (ADS)

    1980-04-01

    A solar energy system was installed in a 2100 sq ft house located in Big Fork, Montana. The system is designed to provide solar energy for heating and domestic hot water. Solar energy is collected by flat plate collectors with a gross area of 792 square feet. The collector banks are mounted on the roof of the house and face due south at an angle of 45 deg to the horizontal optimizing solar energy collection. Solar energy is transferred from the collector array to a 1500 gallon storage tank. Water is used as the heat collection, transfer and storage medium. Freeze protection is provided by use of a drain down system. Space heating demands are met by circulating hot water from storage through baseboard units in the distribution system of the house. Auxiliary space heating is provided by an electrical heating element in the boiler. Similarly, an electrical heating element in the DHW tank provides energy for water heating. The dwelling was fully instrumented for performance evaluation since October 1977 and the data is integrated into the National Solar Data Network.

  9. North Fork John Day Dredge Tailings Restoration Project Final Report 1997-2002.

    SciTech Connect

    Sanchez, John A.

    2002-12-01

    The USDA Forest Service (USFS) and the Confederated Tribes of the Umatilla Indian Reservation (CTUIR) worked together to rehabilitate 2.1 miles of Clear Creek floodplain, a tributary of the North Fork John Day River Basin. Dredge tailing were deposited from mining operations on Clear Creek's floodplain from the 1930's to the 1950's. These tailing confined the stream channel and degraded the floodplain. The work was completed by moving dredge tailing piles adjacent to the Clear Creek channel, using track-mounted excavators and dump trucks. A caterpillar tractor was used to contour the material placed outside the immediate floodplain, blending it into the hillside. The restored floodplain was very near channel bankfull level following excavation and contoured to accept future flood flows. Monitoring was initiated through pre and post-project photo points and cross-section measurements. Work was completed in two efforts. In 1997 and 1998 floodplain restoration was adjacent to the reconstruction of Road 13 from the junction with Road 10 from Clear Creek River Mile 1.9 to 3.1 for a distance of 1.2 miles. In 1999 the Environmental Assessment for Lower Clear Creek--Granite Creek Floodplain Restoration Project was completed for work proposed on Clear Creek from the mouth up to River mile 1.9 and the Granite Creek floodplain from River miles 5.9 to 7.7. Restoration proposed in the 1999 Environmental Assessment is the subject of this report.

  10. Comparison between Measured and Calculated Sediment Transport Rates in North Fork Caspar Creek, California

    NASA Astrophysics Data System (ADS)

    Kim, T. W.; Yarnell, S. M.; Yager, E.; Leidman, S. Z.

    2015-12-01

    Caspar Creek is a gravel-bedded stream located in the Jackson Demonstration State Forest in the coast range of California. The Caspar Creek Experimental Watershed has been actively monitored and studied by the Pacific Southwest Research Station and California Department of Forestry and Fire Protection for over five decades. Although total annual sediment yield has been monitored through time, sediment transport during individual storm events is less certain. At a study site on North Fork Caspar Creek, cross-section averaged sediment flux was collected throughout two storm events in December 2014 and February 2015 to determine if two commonly used sediment transport equations—Meyer-Peter-Müller and Wilcock—approximated observed bedload transport. Cross-section averaged bedload samples were collected approximately every hour during each storm event using a Helley-Smith bedload sampler. Five-minute composite samples were collected at five equally spaced locations along a cross-section and then sieved to half-phi sizes to determine the grain size distribution. The measured sediment flux values varied widely throughout the storm hydrographs and were consistently less than two orders of magnitude in value in comparison to the calculated values. Armored bed conditions, changing hydraulic conditions during each storm and variable sediment supply may have contributed to the observed differences.

  11. Oxbow Conservation Area; Middle Fork John Day River, Annual Report 2003-2004.

    SciTech Connect

    Cochran, Brian

    2004-02-01

    In early 2001, the Confederated Tribes of Warm Springs, through their John Day Basin Office, concluded the acquisition of the Oxbow Ranch, now know as the Oxbow Conservation Area (OCA). Under a memorandum of agreement with the Bonneville Power Administration (BPA), the Tribes are required to provided BPA an 'annual written report generally describing the real property interests in the Project, HEP analyses undertaken or in progress, and management activities undertaken or in progress'. The project during 2003 was crippled due to the aftermath of the BPA budget crisis. Some objectives were not completed during the first half of this contract because of limited funds in the 2003 fiscal year. The success of this property purchase can be seen on a daily basis. Water rights were utilized only in the early, high water season and only from diversion points with functional fish screens. After July 1, all of the OCA water rights were put instream. Riparian fences on the river, Ruby and Granite Boulder creeks continued to promote important vegetation to provide shade and bank stabilization. Hundreds of willow, dogwood, Douglas-fir, and cottonwood were planted along the Middle Fork John Day River. Livestock grazing on the property was carefully managed to ensure the protection of fish and wildlife habitat, while promoting meadow vigor and producing revenue for property taxes. Monitoring of property populations, resources, and management activities continued in 2003 to build a database for future management of this and other properties in the region.

  12. Mining-related metals in terrestrial food webs of the upper Clark Fork River basin

    SciTech Connect

    Pastorok, R.A.; LaTier, A.J.; Butcher, M.K.; Ginn, T.C.

    1994-12-31

    Fluvial deposits of tailings and other mining-related waste in selected riparian habitats of the Upper Clark Fork River basin (Montana) have resulted in metals enriched soils. The significance of metals exposure to selected wildlife species was evaluated by measuring tissue residues of metals (arsenic, cadmium, copper, lead, zinc) in key dietary species, including dominant grasses (tufted hair grass and redtop), willows, alfalfa, barley, invertebrates (grasshoppers, spiders, and beetles), and deer mice. Average metals concentrations in grasses, invertebrates, and deer mice collected from tailings-affected sites were elevated relative to reference to reference levels. Soil-tissue bioconcentration factors for grasses and invertebrates were generally lower than expected based on the range of values in the literature, indicating the reduced bioavailability of metals from mining waste. In general, metals concentrations in willows, alfalfa, and barley were not elevated above reference levels. Using these data and plausible assumptions for other exposure parameters for white-tailed deer, red fox, and American kestrel, metals intake was estimated for soil and diet ingestion pathways. Comparisons of exposure estimates with toxicity reference values indicated that the elevated concentrations of metals in key food web species do not pose a significant risk to wildlife.

  13. An inventory of wetlands in the East Fork Poplar Creek floodplain, Anderson and Roane Counties, Tennessee

    SciTech Connect

    1992-12-01

    An inventory of wetlands within the floodplain of East Fork Poplar Creek (EFPC) in Anderson and Roane Counties, Tennessee was conducted during October, 1991 through May, 1992 for the US Department of Energy (DOE) by the US Army Corps of Engineers, Nashville District. About 15 miles of EFPC channel and 500 acres of its floodplain are contaminated with mercury and other contaminants released from the Y-12 Plant on the DOE Oak Ridge Reservation. The wetland inventory will serve as baseline information for DOE`s remedial action planning and National Environmental Policy Act compliance efforts related to the contamination. In order to provide broad wetland determinations beyond which future wetland definitions are unlikely to expand, the 1989 Federal Manual for Identifying And Delineating Jurisdictional Wetlands was utilized. Using the manual`s methodology in a contaminated system under the approved health and safety plan presented some unique problems, resulting in intrusive sampling for field indicators of hydric soils being accomplished separately from observation of other criteria. Beginning with wetland areas identified on National Wetland Inventory Maps, the entire floodplain was examined for presence of wetland criteria, and 17 wetlands were identified ranging from 0.01 to 2.81 acres in size. The majority of wetlands identified were sized under 1 acre. Some of the wetlands identified were not delineated on the National Wetland Inventory Maps, and much of the wetland area delineated on the maps did not meet the criteria under the 1989 manual.

  14. Quarterly Progress Report on the Biological Monitoring Program for East Fork Poplar Creek

    SciTech Connect

    Adams, S.M.; Ashwood, T.L.; Cicerone, D.S.; Greeley, M.S. Jr.; Hill, W.R.; Kszos, L.A.

    1996-12-30

    In May 1985, a National Pollutant Discharge Elimination System (NPDES) permit was issued for the Oak Ridge Y-12 Plant. As a condition of the permit, a Biological Monitoring and Abatement Program ( BMAP) was developed to demonstrate that the effluent limitations established for the Y-12 Plant protect the classified uses of the receiving stream (East Fork Poplar Creek; EFPC), in particular, the growth and propagation of aquatic life (Lear et al. 1989). A second objective of the BMAP is to document the ecological effects resulting from the implementation of a water pollution control program designed to eliminate direct discharges of wastewaters to EFPC and to minimize the inadvertent release of pollutants to the environment. Because of the complex nature of the discharges to EFPC and the temporal and spatial variability in the composition of the discharges, a comprehensive, integrated approach to biological monitoring was developed. A new permit was issued to the Y-12 Plant on April 28, 1995 and became effective on July 1, 1995. Biological monitoring continues to be required under the new permit. The BMAP consists of four major tasks that reflect different but complementary approaches to evaluating the effects of the Y-12 Plant discharges on the aquatic integrity of EFPC. These tasks are (1) toxicity monitoring, (2) biological indicator studies, (3) bioaccumulation studies, and (4) ecological surveys of the periphyton, benthic macroinvertebrate, and fish communities.

  15. Mercury contamination in the riparian zones along the East Fork Poplar Creek at Oak Ridge.

    PubMed

    Pant, P; Allen, M; Tansel, B

    2011-03-01

    Oak Ridge (Tennessee, USA) has a history of mercury (Hg) contamination in its aquatic and soil environment associated with past nuclear-weapons production activities at its Department of Energy (DOE) sites. Three different riparian zones along the Lower East Fork Poplar Creek were investigated in order to study Hg distribution and transformation in surface soils. The surface soil samples collected from these areas showed higher total Hg on an average (129.08 mg/kg) and higher total organic carbon (5.50%) in the upstream soils compared to the other two downstream locations that contained only 31.78 and 19.98 mg/kg total Hg and 2.88% and 1.65% of TOC on average, respectively. Further, methyl Hg concentrations were also comparatively higher in case of the upstream soils (30.10 μg/kg) than that of the downstream sites (5.69 and 4.05 μg/kg). The study showed a plume-like dispersion of Hg in the terrestrial environment along the creek, with decreasing Hg concentrations with distance from the Hg source zone. Also, the transformation of Hg in the soils was found to have been influenced by the soil TOC contents.

  16. Design of a compact tuning fork-shaped notched ultrawideband antenna for wireless communication application.

    PubMed

    Shakib, M N; Moghavvemi, M; Mahadi, W N L

    2014-01-01

    A new compact planar notched ultrawideband (UWB) antenna is designed for wireless communication application. The proposed antenna has a compact size of 0.182λ × 0.228λ × 0.018λ where λ is the wavelength of the lowest operating frequency. The antenna is comprised of rectangular radiating patch, ground plane, and an arc-shaped strip in between radiating patch and feed line. By introducing a new Tuning Fork-shaped notch in the radiating plane, a stopband is obtained. The antenna is tested and measured. The measured result indicated that fabricated antenna has achieved a wide bandwidth of 4.33-13.8 GHz (at -10 dB return loss) with a rejection frequency band of 5.28-6.97 GHz (WiMAX, WLAN, and C-band). The effects of the parameters of the antenna are discussed. The experiment results demonstrate that the proposed antenna can well meet the requirement for the UWB communication in spite of its compactness and small size.

  17. Water resources of the Big Fork River watershed, north-central Minnesota

    USGS Publications Warehouse

    Lindholm, Gerald F.; Helgesen, John O.; Ericson, Donald W.

    1976-01-01

    The Big Fork River watershed is one of 39 watershed units designated by the Minnesota Department of Natural Resources for evaluation of the State 's water resources. Included is an appraisal of the occurrence, quantity, quality, and availability of ground and surface waters. Water resources are not intensively developed anywhere in the watershed. Most development is in the southern half, as much of the northern half is peat-covered wetlands. Essentially all water used is withdrawn from ground-water sources, mainly glacial drift, which ranges from 0 to 250 feet in thickness. Most ground water is of the calcium or sodium bicarbonated type. The degree of mineralization increases down-gradient in the flow system. Groundwater is typically very hard and high in iron and manganese. Lakes and large areas of wetlands have a natural regulating effect on streamflow. Water in streams is of the calcium bicarbonate type. The amount of mineralization at a given time reflects surficial geology, being greatest in streams draining till areas and least in streams draining peatlands. Water drained from peatlands is commonly higher in color and iron and lower in pH than water from areas of mineral soil.

  18. Waste Management Plan for the Lower East Fork Poplar Creek Remedial Action Project Oak Ridge, Tennessee

    SciTech Connect

    1996-08-01

    The Lower East Fork Poplar Creek (LEFPC) Remedial Action project will remove mercury-contaminated soils from the floodplain of LEFPC, dispose of these soils at the Y-12 Landfill V, and restore the affected floodplain upon completion of remediation activities. This effort will be conducted in accordance with the Record of Decision (ROD) for LEFPC as a Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) action. The Waste Management Plan addresses management and disposition of all wastes generated during the remedial action for the LEFPC Project Most of the solid wastes will be considered to be sanitary or construction/demolition wastes and will be disposed of at existing Y-12 facilities for those types of waste. Some small amounts of hazardous waste are anticipated, and the possibility of low- level or mixed waste exists (greater than 35 pCi/g), although these are not expected. Liquid wastes will be generated which will be sanitary in nature and which will be capable of being disposed 0214 of at the Oak Ridge Sewage Treatment Plant.

  19. Research on the Sensing Performance of the Tuning Fork-Probe as a Micro Interaction Sensor

    PubMed Central

    Gao, Fengli; Li, Xide

    2015-01-01

    The shear force position system has been widely used in scanning near-field optical microscopy (SNOM) and recently extended into the force sensing area. The dynamic properties of a tuning fork (TF), the core component of this system, directly determine the sensing performance of the shear positioning system. Here, we combine experimental results and finite element method (FEM) analysis to investigate the dynamic behavior of the TF probe assembled structure (TF-probe). Results from experiments under varying atmospheric pressures illustrate that the oscillation amplitude of the TF-probe is linearly related to the quality factor, suggesting that decreasing the pressure will dramatically increase the quality factor. The results from FEM analysis reveal the influences of various parameters on the resonant performance of the TF-probe. We compared numerical results of the frequency spectrum with the experimental data collected by our recently developed laser Doppler vibrometer system. Then, we investigated the parameters affecting spatial resolution of the SNOM and the dynamic response of the TF-probe under longitudinal and transverse interactions. It is found that the interactions in transverse direction is much more sensitive than that in the longitudinal direction. Finally, the TF-probe was used to measure the friction coefficient of a silica–silica interface. PMID:26404310

  20. Middle Fork and Upper Salmon River Habitat Improvement Implementation Plan, FY 1988-1992.

    SciTech Connect

    Andrews, John; Everson, Larry B.

    1988-02-01

    This document presents an implementation plan for completing the phase II portion of the Middle Fork and Upper Salmon River Habitat Improvement Agreement. Underseeding of spawning adult salmon and steelhead, high instream sediment levels, a lack of habitat diversity in the form of overhanging riparian vegetation and edge, and barriers to both adult and juvenile anadromous fish migration were identified as the principal factors limiting anadromous fish production in the project area. Underseeding is being addressed in other projects sponsored and funded by the Bonneville Power Administration while this implementation plan lays out a schedule for resolving the other identified limiting factors. The primary goal of this program is to increase the quality and quantity of anadromous fish habitat (spring chinook and summer steelhead) with an emphasis on the survival of the wild stocks. This goal will be achieved by reducing the impact of sediment loading, improving riparian vegetation, eliminating passage barriers, and increasing habitat diversity. Meeting the above goal will provide off-site mitigation under the manadate of the pacific northwest electric power planning and conservation act of 1980. Project implementation will follow measures in the Northwest Power Council's Columbia River Fish and Wildlife Program. 9 refs., 3 figs., 5 tabs.

  1. DNA damage response pathway and replication fork stress during oligonucleotide directed gene editing.

    PubMed

    Bonner, Melissa; Strouse, Bryan; Applegate, Mindy; Livingston, Paula; Kmiec, Eric B

    2012-04-03

    Single-stranded DNA oligonucleotides (ODNs) can be used to direct the exchange of nucleotides in the genome of mammalian cells in a process known as gene editing. Once refined, gene editing should become a viable option for gene therapy and molecular medicine. Gene editing is regulated by a number of DNA recombination and repair pathways whose natural activities often lead to single- and double-stranded DNA breaks. It has been previously shown that introduction of a phosphorotioated ODN, designed to direct a gene-editing event, into cells results in the activation of γH2AX, a well-recognized protein biomarker for double-stranded DNA breakage. Using a single copy, integrated mutant enhanced green fluorescent protein (eGFP) gene as our target, we now demonstrate that several types of ODNs, capable of directing gene editing, also activate the DNA damage response and the post-translational modification of proliferating cell nuclear antigen (PCNA), a signature modification of replication stress. We find that the gene editing reaction itself leads to transient DNA breakage, perhaps through replication fork collapse. Unmodified specific ODNs elicit a lesser degree of replication stress than their chemically modified counterparts, but are also less active in gene editing. Modified phosphothioate oligonucleotides (PTOs) are detrimental irrespective of the DNA sequence. Such collateral damage may prove problematic for proliferation of human cells genetically modified by gene editing.

  2. U.S. Geological Survey 2013 assessment of undiscovered resources in the Bakken and Three Forks Formations of the U.S. Williston Basin Province

    USGS Publications Warehouse

    Gaswirth, Stephanie B.; Marra, Kristen R.

    2014-01-01

    The Upper Devonian Three Forks and Upper Devonian to Lower Mississippian Bakken Formations comprise a major United States continuous oil resource. Current exploitation of oil is from horizontal drilling and hydraulic fracturing of the Middle Member of the Bakken and upper Three Forks, with ongoing exploration of the lower Three Forks, and the Upper, Lower, and Pronghorn Members of the Bakken Formation. In 2008, the U.S. Geological Survey (USGS) estimated a mean of 3.65 billion bbl of undiscovered, technically recoverable oil resource within the Bakken Formation. The USGS recently reassessed the Bakken Formation, which included an assessment of the underlying Three Forks Formation. The Pronghorn Member of the Bakken Formation, where present, was included as part of the Three Forks assessment due to probable fluid communication between reservoirs. For the Bakken Formation, five continuous and one conventional assessment units (AUs) were defined. These AUs are modified from the 2008 AU boundaries to incorporate expanded geologic and production information. The Three Forks Formation was defined with one continuous and one conventional AU. Within the continuous AUs, optimal regions of hydrocarbon recovery, or “sweet spots,” were delineated and estimated ultimate recoveries were calculated for each continuous AU. Resulting undiscovered, technically recoverable resource estimates were 3.65 billion bbl for the five Bakken continuous oil AUs and 3.73 billion bbl for the Three Forks Continuous Oil AU, generating a total mean resource estimate of 7.38 billion bbl. The two conventional AUs are hypothetical and represent a negligible component of the total estimated resource (8 million barrels of oil).

  3. Transcription Termination Factor reb1p Causes Two Replication Fork Barriers at Its Cognate Sites in Fission Yeast Ribosomal DNA In Vivo

    PubMed Central

    Sánchez-Gorostiaga, Alicia; López-Estraño, Carlos; Krimer, Dora B.; Schvartzman, Jorge B.; Hernández, Pablo

    2004-01-01

    Polar replication fork barriers (RFBs) near the 3′ end of the rRNA transcriptional unit are a conserved feature of ribosomal DNA (rDNA) replication in eukaryotes. In the mouse, in vivo studies indicate that the cis-acting Sal boxes required for rRNA transcription termination are also involved in replication fork blockage. On the contrary, in the budding yeast Saccharomyces cerevisiae, the rRNA transcription termination factors are not required for RFBs. Here we characterized the rDNA RFBs in the fission yeast Schizosaccharomyces pombe. S. pombe rDNA contains three closely spaced polar replication barriers named RFB1, RFB2, and RFB3 in the 3′ to 5′ order. The transcription termination protein reb1 and its two binding sites, present at the 3′ end of the coding region, were required for fork arrest at RFB2 and RFB3 in vivo. On the other hand, fork arrest at the strongest RFB1 barrier was independent of the above transcription termination factors. Therefore, RFB2 and RFB3 resemble the barriers present in the mouse rDNA, whereas RFB1 is similar to the budding yeast RFBs. These results suggest that during evolution, cis- and trans-acting factors required for rRNA transcription termination became involved in replication fork blockage also. S. pombe is suggested to be a transitional species in which both mechanisms coexist. PMID:14673172

  4. Recombinase and translesion DNA polymerase decrease the speed of replication fork progression during the DNA damage response in Escherichia coli cells.

    PubMed

    Tan, Kang Wei; Pham, Tuan Minh; Furukohri, Asako; Maki, Hisaji; Akiyama, Masahiro Tatsumi

    2015-02-18

    The SOS response is a DNA damage response pathway that serves as a general safeguard of genome integrity in bacteria. Extensive studies of the SOS response in Escherichia coli have contributed to establishing the key concepts of cellular responses to DNA damage. However, how the SOS response impacts on the dynamics of DNA replication fork movement remains unknown. We found that inducing the SOS response decreases the mean speed of individual replication forks by 30-50% in E. coli cells, leading to a 20-30% reduction in overall DNA synthesis. dinB and recA belong to a group of genes that are upregulated during the SOS response, and encode the highly conserved proteins DinB (also known as DNA polymerase IV) and RecA, which, respectively, specializes in translesion DNA synthesis and functions as the central recombination protein. Both genes were independently responsible for the SOS-dependent slowdown of replication fork progression. Furthermore, fork speed was reduced when each gene was ectopically expressed in SOS-uninduced cells to the levels at which they are expressed in SOS-induced cells. These results clearly indicate that the increased expression of dinB and recA performs a novel role in restraining the progression of an unperturbed replication fork during the SOS response.

  5. Bedload and river hydraulics - Inferences from the East Fork River, Wyoming

    USGS Publications Warehouse

    Leopold, Luna Bergere; Emmett, William W.

    1997-01-01

    During 1973-79, bedload data were collected in a sophisticated trap on a river of moderate size, the East Fork. The transport rate was measured most days through a full snowmelt season, and the rate was determined separately for eight zones across the channel width. The quantitative data are unique and unlikely to be repeated. Nor need they be, because as a result of this effort a practical bedload sampler was adequately tested against full river measurement.It was shown that bedload moves sporadically and randomly on the river bed. Therefore, transport rate is highly variable in short periods of time. There is also a wide variance from day to day. Yet, different rivers have transport rates, which are functions of discharge, depth, and sediment size, that are clearly distinct. Comparison of computed and measured transport rates indicates that a major problem remains: What grain size is representative of the bedload when there is a wide or heterogeneous particle-size distribution? Size of the bedload in motion may be very different from the size of bed material obtained from samples of the streambed.For general computation, the river channel slope may be averaged, and it may be assumed that water-surface slope does not change materially with changing discharge. Indeed, this generality is correct, in that, compared with depth, velocity, and width, slope is conservative at-a-station. However, in more detail, slope changes importantly with discharge in short reaches of channel, and those changes are very different in pool and riffle.These local changes in slope are not merely an aspect of a detailed longitudinal profile but involve cross-channel as well as down-channel components. The pool and riffle sequence involves not only undulation of bed elevation and bar formation on alternate sides of the channel, but alternation of the zone of superovulation of the water surface, and changing relation of watersurface slope to discharge. These details can be seen only in the

  6. Quarterly Progress Report - Biological Monitoring Program for East Fork Poplar Creek

    SciTech Connect

    Adams, S. M.; Christensen, S. W.; Greeley, M.S. jr; McCracken, M.K.; Peterson, M.J.; Ryon, M.G.; Smith, J.G.; Southworth G. R.; Stewart, A. J.

    2001-01-19

    In May 1985, a National Pollutant Discharge Elimination System (NPDES) permit was issued for the Oak Ridge Y-12 National Security Complex (formerly the Oak Ridge Y-12 Plant). As a condition of the permit, a Biological Monitoring and Abatement Program (BMAP) was developed to demonstrate that the effluent limitations established for the Y-12 Complex protect the classified uses of the receiving stream (East Fork Poplar Creek; EFPC), in particular, the growth and propagation of aquatic life (Loar et al. 1989). A second objective of the BMAP is to document the ecological effects resulting from the implementation of a water pollution control program designed to eliminate direct discharges of wastewaters to EFPC and to minimize the inadvertent release of pollutants to the environment. Because of the complex nature of the discharges to EFPC and the temporal and spatial variability in the composition of the discharges, a comprehensive, integrated approach to biological monitoring was developed. A new permit was issued to the Y-12 Complex on April 28, 1995 and became effective on July 1, 1995. Biological monitoring continues to be required under the new permit. The BMAP consists of four major tasks that reflect different but complementary approaches to evaluating the effects of the Y-12 Complex discharges on the aquatic integrity of EFPC. These tasks are (1) toxicity monitoring, (2) biological indicator studies, (3) bioaccumulation studies, and (4) ecological surveys of the periphyton, benthic macroinvertebrate, and fish communities. Monitoring is currently being conducted at five primary EFPC sites, although sites may be excluded or added depending upon the specific objectives of the various tasks. Criteria used in selecting the sites include: (1) location of sampling sites used in other studies, (2) known or suspected sources of downstream impacts, (3) proximity to U.S. Department of Energy (DOE) Oak Ridge Reservation (ORR) boundaries, (4) concentration of mercury in the

  7. Comparing effects of active and passive restoration on the Middle Fork John Day River, NE Oregon

    NASA Astrophysics Data System (ADS)

    McDowell, P. F.; Goslin, M.

    2015-12-01

    Since 2000, cattle grazing has been eliminated on over 14 km of the upper Middle Fork John Day. Starting in 2008, active restoration (log structures with dug pools, woody vegetation planting, and modifications to increase channel-floodplain hydrologic connectivity) was implemented on nearly 6 km within the cattle exclosure length. Implementation of active and passive restoration strategies in the same and adjacent reaches allows comparison of these two approaches. We have been monitoring these reaches since 2008. Unexpectedly in response to grazing exclosure, a native sedge, Carex nudata (torrent sedge), has exploded in population. C. nudata grows in the active channel, anchoring itself tightly to the gravel-cobble river bed with a dense root network. As a result, C. nudata has changed erosion and sedimentation patterns including bank erosion, channel bed scour, and island formation. We present data on fish cover increases due to C. nudata and log structures, and on channel complexity before and after restoration. Both active and passive restorations are increasing channel complexity and juvenile fish cover, although in different ways. Fish cover provided by active and passive restoration are similar in area but different in depth and position, with C. nudata fish cover generally shallower and partly mid-channel. Residual pool depth is larger in log structure pools than in C. nudata scour pools, but C. nudata pools are more numerous in some reaches. By producing frequent, small scour features and small islands, it can be argued that C. nudata is increasing hydraulic complexity more than the large, meander-bend pools at log structures, but this is hard to quantify. C. nudata has also stabilized active bars, perhaps changing the bedload sediment budget. Positive habitat benefits of active restoration appear to be greater in the short term, but over the long term (20 years or more) effects of C. nudata may be comparable or greater.

  8. Geomorphic Effects of Engineered Log Jams in River Restoration, Middle Fork John Day River

    NASA Astrophysics Data System (ADS)

    Duffin, J.; McDowell, P. F.

    2014-12-01

    The Middle Fork of the John Day River (MFJD) Intensively Monitored Watershed in eastern Oregon is a multi-phase restoration implementation and monitoring project. MFJD is a tributary to the Colombia and is part of one of the longest free flowing rivers systems in the continental United States. It is a gravel and cobble bed river with a drainage area of 2,100 km2. The river has endured extensive channel and floodplain degradation from years of channel alteration and straightening due to human influences including dredge mining, ranching, and farming. As part of the river restoration project on the MFJD, engineered log jams have been constructed to address many of the restoration goals including creating scour pools, inhibiting bank erosion, creating and maintaining a sinuous river planform, and increasing complexity of fish habitat. There is a need for more detailed understanding on ELJ channel morphologic effects and how site-specific characteristics and differences in log jam infrastructure interact to create the in-channel features over timescales longer than a few years. This study uses detailed channel bed topographic surveys collected either with a total station or RTK-GPS technology. Geomorphic change detection techniques are utilized to monitor topographic change under and around the 26 log structures in two different river reaches over a six to seven year period The log structures are often associated with deepening of pools as desired, but also some structures show sedimentation under the structure. Differences in the patterns will be assessed based on the design, location, and specific characteristics of the log structures; variables include number and placement of logs, volume of structure, location on meander bend, and sediment sizes.

  9. The 2002 M5 Au Sable Forks, NY, earthquake sequence: Source scaling relationships and energy budget

    NASA Astrophysics Data System (ADS)

    Viegas, Gisela; Abercrombie, Rachel E.; Kim, Won-Young

    2010-07-01

    We find invariant high stress drops and radiated energies for a sequence of intraplate earthquakes. We estimate source parameters of the Au Sable Forks, NY, earthquake (M5, 2002) and aftershocks. This intraplate earthquake was the largest to occur in Eastern North America since 1988 and the largest to be recorded by regional broadband networks. We use the empirical Green's function (EGF) method and define a set of qualitative and quantitative rules for the selection of EGF earthquake pairs and for the quality verification of the obtained EGF spectral ratio. We use a multitaper code that performs the complex spectral division with minimum frequency leakage and allows transformation back to the time domain to check the validity of the EGF event. We estimate source parameters for 22 earthquakes (M1-M5) in the sequence. The median stress drop of 104 MPa (using Madariaga source model, and 19 MPa for a Brune model) is significantly larger than estimates for interplate earthquakes. The lower crustal strain rates, and longer fault healing times in intraplate environments, may be responsible for this high average value. We find constant stress drop between M2 and M5, up to the bandwidth resolution limit (80 Hz) of the study, and no evidence of stress drop breakdown for M2 to M1 earthquakes. We find consistently high radiated seismic energy and apparent stress, and a median radiated energy to seismic moment ratio of 9 × 10-5. This is significantly larger than estimates for interplate earthquakes (˜2 × 10-5) and consistent with higher stress drops and stronger faults.

  10. Quality control mechanisms exclude incorrect polymerases from the eukaryotic replication fork

    PubMed Central

    Schauer, Grant D.; O’Donnell, Michael E.

    2017-01-01

    The eukaryotic genome is primarily replicated by two DNA polymerases, Pol ε and Pol δ, that function on the leading and lagging strands, respectively. Previous studies have established recruitment mechanisms whereby Cdc45-Mcm2-7-GINS (CMG) helicase binds Pol ε and tethers it to the leading strand, and PCNA (proliferating cell nuclear antigen) binds tightly to Pol δ and recruits it to the lagging strand. The current report identifies quality control mechanisms that exclude the improper polymerase from a particular strand. We find that the replication factor C (RFC) clamp loader specifically inhibits Pol ε on the lagging strand, and CMG protects Pol ε against RFC inhibition on the leading strand. Previous studies show that Pol δ is slow and distributive with CMG on the leading strand. However, Saccharomyces cerevisiae Pol δ–PCNA is a rapid and processive enzyme, suggesting that CMG may bind and alter Pol δ activity or position it on the lagging strand. Measurements of polymerase binding to CMG demonstrate Pol ε binds CMG with a Kd value of 12 nM, but Pol δ binding CMG is undetectable. Pol δ, like bacterial replicases, undergoes collision release upon completing replication, and we propose Pol δ–PCNA collides with the slower CMG, and in the absence of a stabilizing Pol δ–CMG interaction, the collision release process is triggered, ejecting Pol δ on the leading strand. Hence, by eviction of incorrect polymerases at the fork, the clamp machinery directs quality control on the lagging strand and CMG enforces quality control on the leading strand. PMID:28069954

  11. Computed and estimated pollutant loads, West Fork Trinity River, Fort Worth, Texas, 1997

    USGS Publications Warehouse

    McKee, Paul W.; McWreath, Harry C.

    2001-01-01

    In 1998 the U.S. Geological Survey, in cooperation with the Trinity River Authority, did a study to estimate storm-runoff pollutant loads using two models—a deterministic model and a statistical model; the estimated loads were compared to loads computed from measured data for a large (118,000 acres) basin in the Dallas-Fort Worth, Texas, metropolitan area. Loads were computed and estimated for 12 properties and constituents in runoff from two 1997 storms at streamflow-gaging station 08048543 West Fork Trinity River at Beach Street in Fort Worth. Each model uses rainfall as a primary variable to estimate pollutant load. In addition to using point rainfall at the Beach Street station to estimate pollutant loads, areal-averaged rainfall for the basin was computed to obtain a more representative estimate of rainfall over the basin. Loads estimated by the models for the two storms, using both point and areal-averaged rainfall, generally did not compare closely to computed loads for the 12 water-quality properties and constituents. Both models overestimated loads more frequently than they underestimated loads. The models tended to yield similar estimates for the same property or constituent. In general, areal-averaged rainfall data yielded better estimates of loads than point rainfall data for both models. Neither the deterministic model nor the statistical model (both using areal-averaged rainfall) was consistently better at estimating loads. Several factors could account for the inability of the models to estimate loads closer to computed loads. Chief among them is the fact that neither model was designed for the specific application of this study.

  12. Groundwater and climate change: a sensitivity analysis for the Grand Forks aquifer, southern British Columbia, Canada

    NASA Astrophysics Data System (ADS)

    Allen, D. M.; Mackie, D. C.; Wei, M.

    The Grand Forks aquifer, located in south-central British Columbia, Canada was used as a case study area for modeling the sensitivity of an aquifer to changes in recharge and river stage consistent with projected climate-change scenarios for the region. Results suggest that variations in recharge to the aquifer under the different climate-change scenarios, modeled under steady-state conditions, have a much smaller impact on the groundwater system than changes in river-stage elevation of the Kettle and Granby Rivers, which flow through the valley. All simulations showed relatively small changes in the overall configuration of the water table and general direction of groundwater flow. High-recharge and low-recharge simulations resulted in approximately a +0.05 m increase and a -0.025 m decrease, respectively, in water-table elevations throughout the aquifer. Simulated changes in river-stage elevation, to reflect higher-than-peak-flow levels (by 20 and 50%), resulted in average changes in the water-table elevation of 2.72 and 3.45 m, respectively. Simulated changes in river-stage elevation, to reflect lower-than-baseflow levels (by 20 and 50%), resulted in average changes in the water-table elevation of -0.48 and -2.10 m, respectively. Current observed water-table elevations in the valley are consistent with an average river-stage elevation (between current baseflow and peak-flow stages). L'aquifère de Grand Forks, situé en Colombie britannique (Canada), a été utilisé comme zone d'étude pour modéliser la sensibilité d'un aquifère à des modifications de la recharge et du niveau de la rivière, correspondant à des scénarios envisagés de changement climatique dans cette région. Les résultats font apparaître que les variations de recharge de l'aquifère pour différents scénarios de changement climatique, modélisées pour des conditions de régime permanent, ont un impact sur le système aquifère beaucoup plus faible que les changements du niveau des

  13. A ruthenium polypyridyl intercalator stalls DNA replication forks, radiosensitizes human cancer cells and is enhanced by Chk1 inhibition

    PubMed Central

    Gill, Martin R.; Harun, Siti Norain; Halder, Swagata; Boghozian, Ramon A.; Ramadan, Kristijan; Ahmad, Haslina; Vallis, Katherine A.

    2016-01-01

    Ruthenium(II) polypyridyl complexes can intercalate DNA with high affinity and prevent cell proliferation; however, the direct impact of ruthenium-based intercalation on cellular DNA replication remains unknown. Here we show the multi-intercalator [Ru(dppz)2(PIP)]2+ (dppz = dipyridophenazine, PIP = 2-(phenyl)imidazo[4,5-f][1,10]phenanthroline) immediately stalls replication fork progression in HeLa human cervical cancer cells. In response to this replication blockade, the DNA damage response (DDR) cell signalling network is activated, with checkpoint kinase 1 (Chk1) activation indicating prolonged replication-associated DNA damage, and cell proliferation is inhibited by G1-S cell-cycle arrest. Co-incubation with a Chk1 inhibitor achieves synergistic apoptosis in cancer cells, with a significant increase in phospho(Ser139) histone H2AX (γ-H2AX) levels and foci indicating increased conversion of stalled replication forks to double-strand breaks (DSBs). Normal human epithelial cells remain unaffected by this concurrent treatment. Furthermore, pre-treatment of HeLa cells with [Ru(dppz)2(PIP)]2+ before external beam ionising radiation results in a supra-additive decrease in cell survival accompanied by increased γ-H2AX expression, indicating the compound functions as a radiosensitizer. Together, these results indicate ruthenium-based intercalation can block replication fork progression and demonstrate how these DNA-binding agents may be combined with DDR inhibitors or ionising radiation to achieve more efficient cancer cell killing. PMID:27558808

  14. A ruthenium polypyridyl intercalator stalls DNA replication forks, radiosensitizes human cancer cells and is enhanced by Chk1 inhibition

    NASA Astrophysics Data System (ADS)

    Gill, Martin R.; Harun, Siti Norain; Halder, Swagata; Boghozian, Ramon A.; Ramadan, Kristijan; Ahmad, Haslina; Vallis, Katherine A.

    2016-08-01

    Ruthenium(II) polypyridyl complexes can intercalate DNA with high affinity and prevent cell proliferation; however, the direct impact of ruthenium-based intercalation on cellular DNA replication remains unknown. Here we show the multi-intercalator [Ru(dppz)2(PIP)]2+ (dppz = dipyridophenazine, PIP = 2-(phenyl)imidazo[4,5-f][1,10]phenanthroline) immediately stalls replication fork progression in HeLa human cervical cancer cells. In response to this replication blockade, the DNA damage response (DDR) cell signalling network is activated, with checkpoint kinase 1 (Chk1) activation indicating prolonged replication-associated DNA damage, and cell proliferation is inhibited by G1-S cell-cycle arrest. Co-incubation with a Chk1 inhibitor achieves synergistic apoptosis in cancer cells, with a significant increase in phospho(Ser139) histone H2AX (γ-H2AX) levels and foci indicating increased conversion of stalled replication forks to double-strand breaks (DSBs). Normal human epithelial cells remain unaffected by this concurrent treatment. Furthermore, pre-treatment of HeLa cells with [Ru(dppz)2(PIP)]2+ before external beam ionising radiation results in a supra-additive decrease in cell survival accompanied by increased γ-H2AX expression, indicating the compound functions as a radiosensitizer. Together, these results indicate ruthenium-based intercalation can block replication fork progression and demonstrate how these DNA-binding agents may be combined with DDR inhibitors or ionising radiation to achieve more efficient cancer cell killing.

  15. Development of an empirical nonlinear model for mercury bioaccumulation in the South and South Fork Shenandoah rivers of Virginia.

    PubMed

    Brent, Robert N; Kain, Donald G

    2011-11-01

    Mercury is a globally distributed pollutant that biomagnifies in aquatic food webs. In the United States, 3781 water bodies fail to meet criteria for safe fish consumption due to mercury bioaccumulation. In the risk assessment and management of these impairments (through the total maximum daily load program), an important step is evaluating the relationship between aqueous mercury and mercury in fish tissue. Often, this relationship is simplified to a bioaccumulation factor (BAF): the ratio of fish tissue mercury to aqueous mercury. This article evaluates the relationship between aqueous mercury and fish tissue mercury across a contamination gradient in the South and South Fork Shenandoah rivers of Virginia. The relationship was found to be nonlinear, with BAFs decreasing as the level of contamination increased. This means that protective water column mercury concentration targets established from site-specific BAFs will be overestimated in contaminated areas and will not be sufficiently protective. To avoid this over-prediction in the South and South Fork Shenandoah rivers, an empirical nonlinear Michaelis-Menten model was used to establish a protective water-quality target. Among other models and variables, the Michaelis-Menten model, relating total mercury in the water column to methylmercury in fish tissue, achieved the best empirical fit (r(2) = 0.9562). The resulting water-quality targets using this model were 3.8 and 3.2 ng/l for the South and South Fork Shenandoah rivers, respectively. These values are 2.1-2.5 times lower than the water-quality target developed using a site-specific BAF. These findings demonstrate the need to consider nonlinear BAF relationships in mercury-contaminated areas.

  16. E. coli mismatch repair acts downstream of replication fork stalling to stabilize the expanded (GAA·TTC)n sequence

    PubMed Central

    Bourn, Rebecka L.; Rindler, Paul M.; Pollard, Laura M.; Bidichandani, Sanjay I.

    2008-01-01

    Expanded triplet repeat sequences are known to cause at least 16 inherited neuromuscular diseases. In addition to short length changes, expanded triplet repeat tracts frequently undergo large changes, often amounting to hundreds of base-pairs. Such changes might occur when template or primer slipping creates insertion/deletion loops (IDLs), which are normally repaired by the mismatch repair system (MMR). However, in prokaryotes and eukaryotes, MMR promotes large changes in the length of (CTG·CAG)n sequences, the motif most commonly associated with human disease. We tested the effect of MMR on instability of the expanded (GAA·TTC)n sequence, which causes Friedreich ataxia, by comparing repeat instability in wild-type and MMR-deficient strains of E. coli. As expected, the prevalence of small mutations increased in the MMR-deficient strains. However, the prevalence of large contractions increased in the MMR mutants specifically when GAA was the lagging strand template, the orientation in which replication fork stalling is known to occur. After hydroxyurea-induced stalling, both orientations of replication showed significantly more large contractions in MMR mutants than in the wild-type, suggesting that fork stalling may be responsible for the large contractions. Deficiency of MMR promoted large contractions independently of RecA status, a known determinant of (GAA·TTC)n instability. These data suggest that two independent mechanisms act in response to replication stalling to prevent instability of the (GAA·TTC)n sequence in E. coli, when GAA serves as the lagging strand template: one that is dependent on RecA-mediated restart of stalled forks, and another that is dependent on MMR-mediated repair of IDLs. While MMR destabilizes the (CTG·CAG)n sequence, it is involved in stabilization of the (GAA·TTC)n sequence. The role of MMR in triplet repeat instability therefore depends on the repeat sequence and the orientation of replication. PMID:19046977

  17. Sediment Transport and Deposition Resulting from a Dam-Removal Sediment Pulse: Milltown Dam, Clark Fork River, MT

    NASA Astrophysics Data System (ADS)

    Wilcox, A. C.

    2010-12-01

    The removal of Milltown Dam in 2008 from the Clark Fork River, Montana, USA, lowered base level at the dam site by 9 m and triggered erosion of nearly 600,000 metric tons of predominantly fine reservoir sediment. Bedload and bed-material sampling, repeat topographic surveys, sediment transport modeling, geochemical fingerprinting of downstream sediments, and Lidar analysis have all been applied to study the upstream and downstream effects of the dam removal. In the years since dam breaching, successive years with similar peak flows (3-year recurrence interval) were followed by a third year with below-average runoff. Nearly all of the documented reservoir erosion occurred in the first year, when sand and silt was eroded and transported downstream. In subsequent years, minimal reservoir erosion occurred, in part as a result of active management to prevent further reservoir erosion, but coarse material eroded from the reservoir has dispersed downstream. Upstream responses in this system have been strongly mediated by Superfund remediation activities in Milltown Reservoir, in which over two million metric tons of contaminated sediments have been mechanically excavated. Downstream aggradation has been limited in the main channel but was initially substantial in bars and side channels of a multi-thread reach 21 to 25 km downstream of the dam site, suggesting that channel change has been influenced far more by the antecedent depositional environment than by proximity to the source of the sediment pulse. Comparison of observed erosion with pre-removal modeling shows that reservoir erosion exceeded model predictions by two orders of magnitude in the unconfined Clark Fork arm of the reservoir. In addition, fine reservoir sediments predicted to move exclusively in suspension traveled as bedload at lower transport stages. The resulting fine sediment deposition in substrate interstices, on bars, and in side channels of the gravel- and cobble-bed Clark Fork River is the most

  18. The Escherichia coli GTPase ObgE modulates hydroxyl radical levels in response to DNA replication fork arrest.

    PubMed

    Kint, Cyrielle I; Verstraeten, Natalie; Wens, Inez; Liebens, Veerle R; Hofkens, Johan; Versées, Wim; Fauvart, Maarten; Michiels, Jan

    2012-10-01

    Obg proteins are universally conserved GTP-binding proteins that are essential for viability in bacteria. Homologs in different organisms are involved in various cellular processes, including DNA replication. The goal of this study was to analyse the structure-function relationship of Escherichia coli ObgE with regard to DNA replication in general and sensitivity to stalled replication forks in particular. Defined C-terminal chromosomal deletion mutants of obgE were constructed and tested for sensitivity to the replication inhibitor hydroxyurea. The ObgE C-terminal domain was shown to be dispensable for normal growth of E.coli. However, a region within this domain is involved in the cellular response to replication fork stress. In addition, a mutant obgE over-expression library was constructed by error-prone PCR and screened for increased hydroxyurea sensitivity. ObgE proteins with substitutions L159Q, G163V, P168V, G216A or R237C, located within distinct domains of ObgE, display dominant-negative effects leading to hydroxyurea hypersensitivity when over-expressed. These effects are abolished in strains with a single deletion of the iron transporter TonB or combined deletions the toxin/antitoxin modules RelBE/MazEF, strains both of which have been shown to be involved in a pathway that stimulates hydroxyl radical formation following hydroxyurea treatment. Moreover, the observed dominant-negative effects are lost in the presence of the hydroxyl radical scavenger thiourea. Together, these results indicate involvement of hydroxyl radical toxicity in ObgE-mediated protection against replication fork stress.

  19. Flood-inundation maps for an 8.9-mile reach of the South Fork Little River at Hopkinsville, Kentucky

    USGS Publications Warehouse

    Lant, Jeremiah G.

    2013-01-01

    Digital flood-inundation maps for an 8.9-mile reach of South Fork Little River at Hopkinsville, Kentucky, were created by the U.S. Geological Survey (USGS) in cooperation with the City of Hopkinsville Community Development Services. The inundation maps, which can be accessed through the USGS Flood Inundation Mapping Science Web site at http://water.usgs.gov/osw/flood_inundation/ depict estimates of the areal extent and depth of flooding corresponding to selected water levels (stages) at the USGS streamgage at South Fork Little River at Highway 68 By-Pass at Hopkinsville, Kentucky (station no. 03437495). Current conditions for the USGS streamgage may be obtained online at the USGS National Water Information System site (http://waterdata.usgs.gov/nwis/inventory?agency_code=USGS&site_no=03437495). In addition, the information has been provided to the National Weather Service (NWS) for incorporation into their Advanced Hydrologic Prediction Service flood warning system (http://water.weather.gov/ahps/). The NWS forecasts flood hydrographs at many places that are often co-located at USGS streamgages. The forecasted peak-stage information, also available on the Internet, may be used in conjunction with the maps developed in this study to show predicted areas of flood inundation. In this study, flood profiles were computed for the South Fork Little River reach by using HEC-RAS, a one-dimensional step-backwater model developed by the U.S. Army Corps of Engineers. The hydraulic model was calibrated by using the most current (2012) stage-discharge relation at the South Fork Little River at Highway 68 By-Pass at Hopkinsville, Kentucky, streamgage and measurements collected during recent flood events. The calibrated model was then used to calculate 13 water-surface profiles for a sequence of flood stages, most at 1-foot intervals, referenced to the streamgage datum and ranging from a stage near bank full to the estimated elevation of the 1.0-percent annual exceedance

  20. Storm-water characterization and lagoon sediment analysis, Grand Forks Air Force Base, North Dakota. Final report

    SciTech Connect

    Garland, J.G.; Vaughn, R.W.; Scott, P.T.

    1990-08-01

    Sampling was conducted in the wastewater treatment lagoons and stormwater runoff at Grand Forks AFB. The base was concerned about whether the unlined lagoons were creating a potential groundwater contamination problem and whether their stormwater runoff met North Dakota state stream standards. Lagoon sediment did not contain Extraction Procedure hazardous chemicals. Stormwater runoff exceeded state standards for boron, phosphates, and phenols and contained trace levels of methylene chloride. Characterization of lagoon influent showed it to be generally representative of domestic sewage, but also contained trace levels of boron, phenols, toluene, cyanide, chloroform, methylene chloride and ethyl benzene.

  1. Research on the influence of transparent vacuum encapsulation quartz tuning fork on the photo-thermoelastic spectroscopy of acetylene

    NASA Astrophysics Data System (ADS)

    Zhang, Zhouqiang; Jia, Shuhai; Wang, Yonglin; Tang, Zhenhua; Wang, Fei

    2016-10-01

    In this paper, a transparent vacuum-encapsulated quartz tuning fork (QTF) is proposed for the first time to improve the quality factor and sensitivity of QTF sensors. Increasing the vacuum considerably improved the quality factor of QTF, and the resonance frequency was also shifted to higher values to 10 Hz. Subsequently, the spectroscopy detection of acetylene gas using an exposed QTF and a transparent vacuum-encapsulated QTF was investigated. The sensitivity of the detection system improved in the presence of the transparent vacuum-sealed QTF. The current findings represent a gateway to subsequent research in photo-thermoelastic spectroscopy.

  2. Flood-inundation map library for the Licking River and South Fork Licking River near Falmouth, Kentucky

    USGS Publications Warehouse

    Lant, Jeremiah G.

    2016-09-19

    Digital flood inundation maps for a 17-mile reach of Licking River and 4-mile reach of South Fork Licking River near Falmouth, Kentucky, were created by the U.S. Geological Survey (USGS) in cooperation with Pendleton County and the U.S. Army Corps of Engineers–Louisville District. The inundation maps, which can be accessed through the USGS Flood Inundation Mapping Science Web site at http://wim.usgs.gov/FIMI/FloodInundationMapper.html, depict estimates of the areal extent and depth of flooding corresponding to selected water levels (stages) at the USGS streamgage on the Licking River at Catawba, Ky., (station 03253500) and the USGS streamgage on the South Fork Licking River at Hayes, Ky., (station 03253000). Current conditions (2015) for the USGS streamgages may be obtained online at the USGS National Water Information System site (http://waterdata.usgs.gov/nwis). In addition, the streamgage information has been provided to the National Weather Service (NWS) for incorporation into their Advanced Hydrologic Prediction Service (AHPS) flood warning system (http:/water.weather.gov/ahps/). The flood hydrograph forecasts provided by the NWS are usually collocated with USGS streamgages. The forecasted peak-stage information, also available on the NWS Web site, may be used in conjunction with the maps developed in this study to show predicted areas of flood inundation.In this study, flood profiles were computed for the Licking River reach and South Fork Licking River reach by using a one-dimensional step-backwater model. The hydraulic model was calibrated by using the most current (2015) stage-discharge relations for the Licking River at Catawba, Ky., and the South Fork Licking River at Hayes, Ky., USGS streamgages. The calibrated model was then used to calculate 60 water-surface profiles for a sequence of flood stages, at 2-foot intervals, referenced to the streamgage datum and ranging from an elevation near bankfull to the elevation associated with a major flood that

  3. Baseline and Postremediation Monitoring Program Plan for the Lower East Fork Poplar Creek operable unit, Oak Ridge, Tennessee

    SciTech Connect

    1996-04-01

    This report was prepared in accordance with CERCLA requirements to present the plan for baseline and postremediation monitoring as part of the selected remedy. It provides the Environmental Restoration Program with information about the requirements to monitor for soil and terrestrial biota in the Lower East Fork Poplar Creek (LEFPC) floodplain; sediment, surface water, and aquatic biota in LEFPC; wetland restoration in the LEFPC floodplain; and human use of shallow groundwater wells in the LEFPC floodplain for drinking water. This document describes the monitoring program that will ensure that actions taken under Phases I and II of the LEFPC remedial action are protective of human health and the environment.

  4. Measurement of the reaeration coefficients of the North Fork Licking River at Utica, Ohio by radioactive tracers

    USGS Publications Warehouse

    Hren, Janet

    1983-01-01

    Reaeration coefficients of the North Fork Licking River at Utica, Ohio were measured by the radioactive-tracer method. The tests were conducted on a 2.1-mile reach on September 23 and October 7, 1981, during low-flow conditions. Krypton-85 gas and tritium were the radioopactive tracers, which were used in conjunction with rhodamine-WT dye. The reaertion coefficients determined on September 23 were 3.09 days-1 (subreach 1-2) and 3.32 days-1 (subreach 2-3). On October 7, the values were 2.04 days -1 and 2.23 days-1 respectively.

  5. Scanning thermal microscopy based on a quartz tuning fork and a micro-thermocouple in active mode (2ω method).

    PubMed

    Bontempi, Alexia; Nguyen, Tran Phong; Salut, Roland; Thiery, Laurent; Teyssieux, Damien; Vairac, Pascal

    2016-06-01

    A novel probe for scanning thermal microscope using a micro-thermocouple probe placed on a Quartz Tuning Fork (QTF) is presented. Instead of using an external deflection with a cantilever beam for contact detection, an original combination of piezoelectric resonator and thermal probe is employed. Due to a non-contact photothermal excitation principle, the high quality factor of the QTF allows the probe-to-surface contact detection. Topographic and thermal scanning images obtained on a specific sample points out the interest of our system as an alternative to cantilevered resistive probe systems which are the most spread.

  6. Log-derived evaluation of gas-bearing Cherokee, Red Fork, and Morrow formations, Custer County, OK

    SciTech Connect

    Busch, E.A.; Fertl, W.H.; Neill, B.E.; Sinha, A.K.; Sobkowich, K.N.

    1985-03-01

    Medium to low porosity and rather tight Cherokee, Red Fork and Morrow sands, located in Oklahoma, contain significant hydrocarbon resources. To evaluate the commercial importance of wells drilled in Custer County, Oklahoma, an innovative digital shaly sand analysis approach (CLASS - Epilog) has been applied, which provides information on total and effective reservoir porosity, total and effective fluid distribution based on the Waxman-Smits equation, shaliness, clay typing, and reservoir productivity. Several field case examples are presented and discussed based on (1) open hole logging suite, consisting of induction, compensated density/neutron and Spectralog, (2) CLASS analysis, (3) well completion and stimulation data, and (4) the resulting production test results.

  7. South Fork Tolt River Hydroelectric Project : Adopted Portions of a 1987 Federal Energy Regulatory Commission`s Final Environmental Impact Statement.

    SciTech Connect

    United States. Bonneville Power Administration.

    1992-07-01

    The South Fork Tolt River Hydroelectric Project that world produce 6.55 average megawatts of firm energy per year and would be sited in the Snohomish River Basin, Washington, was evaluated by the Federal Energy Regulatory commission (FERC) along with six other proposed projects for environmental effects and economic feasibility Based on its economic analysis and environmental evaluation of the project, the FERC staff found that the South Fork Tolt River Project would be economically feasible and would result in insignificant Impacts if sedimentation issues could be resolved. Upon review, the BPA is adopting portions of the 1987 FERC FEIS that concern the South Fork Tolt River Hydroelectric Project and updating specific sections in an Attachment.

  8. Topography and near-field image measurement of soft biological samples in liquid by using a tuning fork based bent optical-fiber sensor.

    PubMed

    Kwon, Sangjin; Jeong, Sungho; Kang, Yongseok

    2011-04-01

    The fabrication of a tuning fork based bent optical-fiber sensor and its application for topography and near-field image measurement of soft biological samples in physiological solution are reported. By adopting the bent optical fiber and tuning fork feedback scheme, the possibility of signal interference with stray light is minimized, which is especially important for near-field applications. From the measured tuning fork amplitude and its calibration with the preamplifier output voltage, it was determined that the interaction force between the fiber tip and a soft sample in liquid needs to be controlled within approximately 10 nN level and that the image quality depends sensitively to the interaction force. The results of topography measurements of fixed COS-7 and MCF-7 cells in phosphate buffered saline and of the near-field imaging of red blood cell also in phosphate buffered saline with a resolution of about 100 nm are presented.

  9. Twelve Years of Monitoring Phosphorus and Suspended-Solids Concentrations and Yields in the North Fork Ninnescah River above Cheney Reservoir, South-Central Kansas 1997-2008

    USGS Publications Warehouse

    Stone, Mandy L.; Graham, Jennifer L.; Ziegler, Andrew C.

    2009-01-01

    Cheney Reservoir, located on the North Fork Ninnescah River in south-central Kansas, is the primary water supply for the city of Wichita and an important recreational resource. Concerns about taste-and-odor occurrences in Cheney Reservoir have drawn attention to potential pollutants, including total phosphorus (TP) and total suspended solids (TSS). July 2009 was the 15th anniversary of the establishment of the Cheney Reservoir Watershed pollution management plan. The U.S. Geological Survey (USGS), in cooperation with the city of Wichita, has collected water-quality data in the basin since 1996, and has monitored water quality continuously on the North Fork Ninnescah River since 1998. This fact sheet describes 12 years (1997-2008) of computed TP and TSS data and compares these data with water-quality goals for the North Fork Ninnescah River, the main tributary to Cheney Reservoir.

  10. Assessment of possible sources of microbiological contamination in the water column and streambed sediment of the Jacks Fork, Ozark National Scenic Riverways, Missouri - Phase III

    USGS Publications Warehouse

    Davis, Jerri V.; Barr, Miya N.

    2006-01-01

    In 1998, a 5 river-mile reach of the Jacks Fork was included on Missouri's list of impaired waters as required by Section 303(d) of the Federal Clean Water Act. The identified pollutant on the Jacks Fork was fecal coliform bacteria. The length of the impaired reach was changed to 7 miles on the Missouri 2002 303(d) list because of data indicating the fecal coliform bacteria problem existed over a broader area. The U.S. Geological Survey, in cooperation with the National Park Service, conducted a study to better understand the extent and sources of microbiological contamination within the Jacks Fork from Alley Spring to the mouth, which includes the 7-mile 303(d) reach. Ten sites were sampled from June 2003 through October 2003 and from June 2004 through October 2004. Water-column and streambed sediment samples were collected from main-stem and tributary sites mostly during base-flow conditions during a variety of recreational season river uses and analyzed for fecal coliform and Escherichia coli bacteria. Isolates of Escherichia coli obtained from water samples collected at five sites were submitted for rep-PCR analysis to identify presumptive sources of fecal indicator bacteria in the Jacks Fork. Results indicate that recreational users (including boaters and swimmers) are not the primary source of fecal coliform bacteria in the Jacks Fork; rather, the presence of fecal coliform bacteria is associated with other animals, of which horses are the primary source. Increases in fecal coliform bacteria densities in the Jacks Fork are associated with cross-country horseback trail-riding events.

  11. Gestational age

    MedlinePlus

    Fetal age - gestational age; Gestation; Neonatal gestational age; Newborn gestational age ... Gestational age can be determined before or after birth. Before birth, your health care provider will use ultrasound to ...

  12. Aging Skin

    MedlinePlus

    ... email address Submit Home > Healthy Aging > Wellness Healthy Aging Aging skin More information on aging skin When it ... treated early. Return to top More information on Aging skin Read more from womenshealth.gov Varicose Veins ...

  13. Calendar year 1996 annual groundwater monitoring report for the Upper East Fork Poplar Creek Hydrogeologic Regime at the U.S. Department of Energy Y-12 Plant, Oak Ridge, Tennessee

    SciTech Connect

    1997-02-01

    This annual monitoring report contains groundwater and surface water monitoring data obtained in the Upper East Fork Poplar Creek Hydrogeologic Regime (East Fork Regime) during calendar year (CY) 1996. The East Fork Regime encompasses several confirmed and suspected sources of groundwater contamination within industrialized areas of the US Department of Energy (DOE) Oak Ridge Y-12 Plant in Bear Creek Valley (BCV) southeast of Oak Ridge, Tennessee. Groundwater and surface water monitoring in the East Fork Regime are performed under the auspices of the Y-12 Plant Groundwater Protection Program (GWPP). Included are the groundwater monitoring data obtained in compliance with the Resource Conservation and Recovery Act (RCRA) post-closure permit for the East Fork Regime issued by the Tennessee Department of Environment and Conservation (TDEC) on August 30, 1996. The post-closure permit addresses post-closure monitoring requirements for two closed RCRA-regulated surface impoundments: the S-3 Ponds and New Hope Pond.

  14. [Nutrition, aging, old age].

    PubMed

    Iván, L

    1998-12-06

    In humans there is evidence that the restriction of total caloric intake appears to be more important than the restriction of any particular macronutrient. Today the mechanism of the effect of caloric restriction is unknown. With advancing age and the occurrence of concomitant illness there is an increased risk of developing nutritional deficiencies. Altered nutritional status is associated with the pathogenesis of a number of common diseases of the elderly, thus it would appear that nutritional modulation and manipulation represents one possible approach to successful aging and a healthy longevity. The conceptual framework of the paper suggests the need of a newer light of the aging processes namely by a holistic human-gero-ecological model and a personality oriented geriatry. There are accentuated the role of the nutrients and vitamins, the food intake and drug-nutrients interactions and the meanings of the differences between the normal and pathological aging.

  15. Evaluating the effectiveness of floodplain restoration on the North Fork John Day River, Northeast Oregon, USA

    NASA Astrophysics Data System (ADS)

    Clifton, C. F.; Blanton, P.; Long, W.; Walterman, M. T.; McDowell, P. F.; Maus, P.

    2007-12-01

    Over the last decade hundreds of river restoration projects intended to maintain, protect, and restore watersheds, rivers, and habitat for native species in the Pacific Northwest have been implemented. By some counts, investment in watershed restoration exceeds hundreds of millions of dollars annually yet the effectiveness of these efforts remains an elusive question (Roni, 2005). Remote sensing and GIS technologies show great promise for large-scale river monitoring, however most natural resource organizations who implement these projects have limited budget and staff and would benefit from simple, low cost monitoring techniques that use readily available imagery. We used 1:24000 digitized orthorectified resource imagery from 1995, and National Agriculture Imagery Program (NAIP) digital orthophotography from 2005 to assess the effectiveness of floodplain restoration on a 16 km reach of the North Fork John Day River. Between 1993 and 1997 this section was restored by mechanically removing, reshaping, and revegetating cobble-boulder tailings piles left from dredge mining. The project was intended to directly improve floodplain function (i.e. inundation, riparian habitat) and indirectly improve instream habitat (pools, spawning) by reconnecting the active river channel with a reconstructed floodplain surface. Project effectiveness was not well documented initially in terms of quantifying floodplain functional area improvement or channel condition and response at the river-reach scale. Our objectives were to field-verify remote sensing measurements of response variables to test the applicability of available remote sensing imagery for project effectiveness monitoring, and to quantify adjustment in river response variables, using a "before-after" case study approach. Bracketing restoration activities with 1995 and 2000 imagery, we developed and tested methods for acquisition and processing of digital imagery and identified a core set of response variables to sample

  16. [Age identification and growth characteristics of Katsuwonus pelamis in western and central Pacific Ocean].

    PubMed

    Wang, Xue-Fang; Xu, Liu-Xiong; Zhu, Guo-Ping; Wang, Chun-Lei

    2010-03-01

    Fish age and growth are the important biological parameters for the assessment of fishery resources. With the help of purse seiners, 262 individuals of skipjack tuna (Katsuwonus pelamis) were sampled from western and central Pacific Ocean in October 2007 - January 2008. The measurements in situ showed that the fork length of the samples ranged from 278 to 746 mm, and their body mass ranged from 345 to 9905 g. The first dorsal spine of each individual was collected for age identification and growth parameters estimation. The relationship between fork length (L, mm) and body mass (M, g) was expressed as M = 3.612 x 10(-6) L3.278 (R2 = 0.9782), and no significant difference was found for the males and females (F = 2.002, P > 0.05). A comparison with Akaike information criterion (AIC) suggested that among power regression equation, linear regression equation, and exponential regression equation, linear regression equation was most suitable for describing the relationship between fork length and spine radius (AIC = 2257.4). The mean back-calculated fork lengths of K. pelamis with the ages of 1-5 estimated by Fraser-Lee's method were 398.4, 494.2, 555.4, 636.8, and 728.8 mm, respectively. Residual analyses indicated that there was no significant difference in the growth of male and female K. pelamis (F = 0.670; df = 182; P > 0.05). The sex-combined von Bertalanffy growth equation of K. pelamis was L(t) = 706.51 (1 - e(-0.64(t + 0.037))).

  17. Oligodeoxynucleotide binding to (CTG) · (CAG) microsatellite repeats inhibits replication fork stalling, hairpin formation, and genome instability.

    PubMed

    Liu, Guoqi; Chen, Xiaomi; Leffak, Michael

    2013-02-01

    (CTG)(n) · (CAG)(n) trinucleotide repeat (TNR) expansion in the 3' untranslated region of the dystrophia myotonica protein kinase (DMPK) gene causes myotonic dystrophy type 1. However, a direct link between TNR instability, the formation of noncanonical (CTG)(n) · (CAG)(n) structures, and replication stress has not been demonstrated. In a human cell model, we found that (CTG)(45) · (CAG)(45) causes local replication fork stalling, DNA hairpin formation, and TNR instability. Oligodeoxynucleotides (ODNs) complementary to the (CTG)(45) · (CAG)(45) lagging-strand template eliminated DNA hairpin formation on leading- and lagging-strand templates and relieved fork stalling. Prolonged cell culture, emetine inhibition of lagging-strand synthesis, or slowing of DNA synthesis by low-dose aphidicolin induced (CTG)(45) · (CAG)(45) expansions and contractions. ODNs targeting the lagging-strand template blocked the time-dependent or emetine-induced instability but did not eliminate aphidicolin-induced instability. These results show directly that TNR replication stalling, replication stress, hairpin formation, and instability are mechanistically linked in vivo.

  18. Comparison of Stream Restoration and Vegetation Restoration on Stream Temperature in the Middle Fork John Day River, Oregon

    NASA Astrophysics Data System (ADS)

    Diabat, M.; Wondzell, S. M.; Haggerty, R.

    2013-12-01

    Stream temperature is an important component of aquatic ecosystems. During the past century, various anthropogenic activities (such as timber harvest, mining, and agriculture) reduced riparian vegetation and channel complexity along many streams around the world. As a result, stream temperature increased and suitable habitat for cool- and cold-water organisms declined. Stream temperatures are expected to increase even more under future climate. The effects of warmer climate and anthropogenic activities are proposed to be mitigated by restoration projects aimed to reduce stream temperatures. Common restoration practices are replanting natural vegetation along stream banks and restoring channel complexity. The Middle Fork John Day River, in northeastern Oregon, USA is an example of such a process. We modeled stream temperature along a 37-km section of the Middle Fork John Day River for current and projected conditions of climate, restored riparian vegetation along 6.6-km, and restored channel meanders along 1.5 km. Preliminary simulations suggest that if current riparian vegetation remains unchanged, an average summertime air warming of 4°C increased the 7-day average daily maximum (7DADM) by about 1.3°C. However, restored riparian vegetation reduced the 7DADM by about 0.7°C relative to the current temperature. Restored channel meanders reduced the 7DADM by less than 0.05°C relative to the current temperature. These preliminary simulations assume no hyporheic exchange and riparian vegetation that is 10 m tall and has 30% canopy density.

  19. Fragmentation of riverine systems: the genetic effects of dams on bull trout (Salvelinus confluentus) in the Clark Fork River system.

    PubMed

    Neraas, L P; Spruell, P

    2001-05-01

    Migratory bull trout (Salvelinus confluentus) historically spawned in tributaries of the Clark Fork River, Montana and inhabited Lake Pend Oreille as subadult and adult fish. However, in 1952 Cabinet Gorge Dam was constructed without fish passage facilities disrupting the connectivity of this system. Since the construction of this dam, bull trout populations in upstream tributaries have been in decline. Each year adult bull trout return to the base of Cabinet Gorge Dam when most migratory bull trout begin their spawning migration. However, the origin of these fish is uncertain. We used eight microsatellite loci to compare bull trout collected at the base of Cabinet Gorge Dam to fish sampled from both above and further downstream from the dam. Our data indicate that Cabinet Gorge bull trout are most likely individuals that hatched in above-dam tributaries, reared in Lake Pend Oreille, and could not return to their natal tributaries to spawn. This suggests that the risk of outbreeding depression associated with passing adults over dams in the Clark Fork system is minimal compared to the potential genetic and demographic benefits to populations located above the dams.

  20. The Replication Initiation Protein Sld3/Treslin Orchestrates the Assembly of the Replication Fork Helicase during S Phase*

    PubMed Central

    Bruck, Irina; Kaplan, Daniel L.

    2015-01-01

    The initiation of DNA replication is a highly regulated process in eukaryotic cells, and central to the process of initiation is the assembly and activation of the replication fork helicase. The replication fork helicase is comprised of CMG (Cdc45, Mcm2–7, and GINS) in eukaryotic cells, and the mechanism underlying assembly of the CMG during S phase was studied in this article. We identified a point mutation of Sld3 that is specifically defective for Mcm3 and Mcm5 interaction (sld3-m10), and also identified a point mutation of Sld3 that is specifically defective for single-stranded DNA (ssDNA) interaction (sld3-m9). Expression of wild-type levels of sld3-m9 resulted in a severe DNA replication defect with no recruitment of GINS to Mcm2–7, whereas expression of wild-type levels of sld3-m10 resulted in a severe replication defect with no Cdc45 recruitment to Mcm2–7. We propose a model for Sld3-mediated control of replication initiation, wherein Sld3 manages the proper assembly of the CMG during S phase. We also find that the biochemical functions identified for Sld3 are conserved in human Treslin, suggesting that Treslin orchestrates assembly of the CMG in human cells. PMID:26405041

  1. Replication of the Escherichia coli chromosome in RNase HI-deficient cells: multiple initiation regions and fork dynamics.

    PubMed

    Maduike, Nkabuije Z; Tehranchi, Ashley K; Wang, Jue D; Kreuzer, Kenneth N

    2014-01-01

    DNA replication in Escherichia coli is normally initiated at a single origin, oriC, dependent on initiation protein DnaA. However, replication can be initiated elsewhere on the chromosome at multiple ectopic oriK sites. Genetic evidence indicates that initiation from oriK depends on RNA-DNA hybrids (R-loops), which are normally removed by enzymes such as RNase HI to prevent oriK from misfiring during normal growth. Initiation from oriK sites occurs in RNase HI-deficient mutants, and possibly in wild-type cells under certain unusual conditions. Despite previous work, the locations of oriK and their impact on genome stability remain unclear. We combined 2D gel electrophoresis and whole genome approaches to map genome-wide oriK locations. The DNA copy number profiles of various RNase HI-deficient strains contained multiple peaks, often in consistent locations, identifying candidate oriK sites. Removal of RNase HI protein also leads to global alterations of replication fork migration patterns, often opposite to normal replication directions, and presumably eukaryote-like replication fork merging. Our results have implications for genome stability, offering a new understanding of how RNase HI deficiency results in R-loop-mediated transcription-replication conflict, as well as inappropriate replication stalling or blockage at Ter sites outside of the terminus trap region and at ribosomal operons.

  2. Roles of Replication Protein-a Subunits 2 and 3 in DNA Replication Fork Movement in Saccharomyces Cerevisiae

    PubMed Central

    Maniar, H. S.; Wilson, R.; Brill, S. J.

    1997-01-01

    Replication Protein-A, the eukaryotic SSB, consists of a large subunit (RPA1) with strong ssDNA binding activity and two smaller subunits (RPA2 and 3) that may cooperate with RPA1 to bind ssDNA in a higher-order mode. To determine the in vivo function of the two smaller subunits and the potential role of higher-order ssDNA binding, we isolated an assortment of heat-lethal mutations in the genes encoding RPA2 and RPA3. At the permissive temperature, the mutants show a range of effects on DNA replication fidelity and sensitivities to UV and MMS. At the nonpermissive temperature, four out of five RPA2 mutants show a fast-stop DNA synthesis phenotype typical of a replication fork block. In contrast, the fifth RPA2 mutant and all RPA3 mutants are able to complete at least one round of DNA replication at the nonpermissive temperature. The effect of these mutations on the stability of the RPA complex was tested using a coprecipitation assay. At the nonpermissive temperature, we find that RPA1 and RPA2 are dissociated in the fast-stop mutants, but not in the slow-stop mutants. Thus, replication fork movement in vivo requires the association of at least two subunits of RPA. This result is consistent with the hypothesis that RPA functions in vivo by binding ssDNA in a higher-order mode. PMID:9093844

  3. Best management practices plan for the Lower East Fork Poplar Creek remedial action project, Oak Ridge, Tennessee

    SciTech Connect

    1996-08-01

    The U.S. Department of Energy (DOE) has three major operating facilities on the DOE Oak Ridge Reservation (ORR) in Oak Ridge, Tennessee: the Oak Ridge Y-12 Plant, the K-25 Site, and the Oak Ridge National Laboratory (ORNL) managed by Lockheed Martin Environmental Research Corporation. All facilities are managed by Lockheed Martin Energy Systems, Incorporated (Energy Systems) for the DOE. The Y-12 Plant is adjacent to the city of Oak Ridge and is also upstream from Oak Ridge along East Fork Poplar Creek. The portion of the creek downstream from the Y-12 Plant is Lower East Fork Poplar Creek (LEFPC). This project will remove mercury-contaminated soils from the LEFPC floodplain, transport the soils to Industrial Landfill V (ILF-V), and restore any affected areas. This project contains areas that were designated in 1989 as a Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) site. The site includes DOE property and portions of commercial, residential, agricultural, and miscellaneous areas within the city of Oak Ridge.

  4. A water-quality assessment of the Muddy Fork Silver Creek watershed, Clark, Floyd, and Washington Counties, Indiana

    USGS Publications Warehouse

    Hardy, Mark A.

    1978-01-01

    Data collected for a wide range of flow conditions from September 8, 1975, to July 13, 1976, reveal that human and animal waste loading of streams and pesticides use in the Muddy Fork Silver Creek watershed, Indiana, are probably the most significant water-quality problems. Generally, the type(s) of water in tributary streams in the south and southwest parts of the watershed was calcium bicarbonate and in other tributaries were calcium sulfate and magnesium sulfate. Dissolved-solids concentrations of discharge from top-spill reservoirs were lower and more consistent over a range of flows than concentrations from uncontrolled streams. Concentrations of fecal coliform bacteria and fecal streptococcal bacteria ranged from 5 to 65 ,000 colonies per 100 milliliters and from 5 to 14,000 colonies per 100 milliliters, respectively. Data on periphyton, phytoplankton, and benthic communities collected during low flow in September 1975 indicate organic loading of Muddy Fork downstream from the town of Speed. Phytoplankton community structures varied temporally and spatially. Ranges of concentration (In micrograms per kilogram) of various chlorinated hydrocarbons in samples of bed materials were: chlordane, from 0 to 14; DDT, from 0 to 19; and PCB's, from 0 to 11. Concentrations of aldrin, DDD, DDE, heptachlor, and heptachlor epoxide of 5.1 micrograms per kilogram or less were also detected. The presence of these compounds makes them potentially available for accumulation in the biological food chain. (Woodard-USGS)

  5. Impairment of lagging strand synthesis triggers the formation of a RuvABC substrate at replication forks

    PubMed Central

    Flores, Maria-Jose; Bierne, Hélène; Ehrlich, S.Dusko; Michel, Bénédicte

    2001-01-01

    The holD gene codes for the ψ subunit of the Escherichia coli DNA polymerase III holoenzyme, a component of the γ complex clamp loader. A holD mutant was isolated for the first time in a screen for mutations that increase the frequency of tandem repeat deletions. In contrast to tandem repeat deletions in wild-type strains, deletion events stimulated by the holD mutation require RecA. They do not require RecF, and hence do not result from the recombinational repair of gaps, arguing against uncoupling of the leading and lagging strand polymerases in the holD mutant. The holD recBC combination of mutations is lethal and holD recBts recCts strains suffer DNA double-strand breaks (DSBs) at restrictive temperature. DSBs require the presence of the Holliday junction-specific enzymes RuvABC and are prevented in the presence of RecBCD. We propose that impairment of replication due to the holD mutation causes the arrest of the entire replisome; consequently, Holliday junctions are formed by replication fork reversal, and unequal crossing over during RecA- and RecBCD-mediated re-incorporation of reversed forks causes the hyper-recombination phenotype. PMID:11157768

  6. The role of psychological determinants and demographic factors in consumer demand for farm-to-fork traceability systems.

    PubMed

    Myae, Aye Chan; Goddard, Ellen; Aubeeluck, Ashwina

    2011-01-01

    Traceability systems are an important tool (1) for tracking, monitoring, and managing product flows through the supply chain for better efficiency and profitability of suppliers, and (2) to improve consumer confidence in the face of serious food safety incidents. After the global bovine spongiform encephalopathy (BSE) crisis affected producers, consumers, trade, and the health status of animals and humans, new systems to help confirm the status of cattle products along the supply chain from farm to fork were implemented in many countries (Trautman et al. 2008 ). In this study, people's overall food safety beliefs are explored with the main objective of measuring the link between their food safety beliefs and their attitudes toward traceability. A comparison is made among English-speaking Canadians, French-speaking Canadians, and Japanese consumers. In the study, an Internet-based survey was used to collect data from nationally representative samples of the population in Canada-English (1275), Canada-French (343), and Japanese (1940) in the summer of 2009. Respondents' interests in traceability systems are clearly linked to their sense that the industry is primarily responsible for any food safety outbreaks. Moreover, it is clear that certain segments of the population in all samples feel strongly about the importance of farm to fork traceability in beef; thus, policymakers may wish to consider extending traceability beyond the point of slaughter as a way of encouraging beef sales in Canada.

  7. Determination of instream metal loads using tracer-injection and synoptic-sampling techniques, Wightman Fork, southwestern Colorado, July 1999

    USGS Publications Warehouse

    Ortiz, Roderick F.

    2001-01-01

    In July 1999, a tracer-injection study was conducted concurrently with synoptic sampling to generate mass-load profiles in Wightman Fork near the Summitville Mine site. The mine site is located in the San Juan Mountains of southwestern Colorado at an elevation of about 3,500 meters above sea level. Metal loads increased substantially along the 2,815-meter study reach along the boundary of the mine site. Spatial determinations of dissolved aluminum, copper, iron, manganese, and zinc loads were used to identify potential source areas to the stream. Overall, four source areas appeared to contribute most of the specific load at the end of the study reach. One source area was along a 60-meter reach downgradient from the toe of the North Waste Dump that generally corresponded to a region of radial faults. Another source area was a short reach that included inputs from the Summitville Water Treatment Facility and the Pump House Fault. In July 1999, seepage from the Summitville Dam Impoundment was a substantial contributor of metal load at the end of the study reach. Finally, the metal load contributed along a 60-meter reach that included Cropsy Creek is considered a substantial source of metal load to Wightman Fork.

  8. DNA polymerase η modulates replication fork progression and DNA damage responses in platinum-treated human cells

    NASA Astrophysics Data System (ADS)

    Sokol, Anna M.; Cruet-Hennequart, Séverine; Pasero, Philippe; Carty, Michael P.

    2013-11-01

    Human cells lacking DNA polymerase η (polη) are sensitive to platinum-based cancer chemotherapeutic agents. Using DNA combing to directly investigate the role of polη in bypass of platinum-induced DNA lesions in vivo, we demonstrate that nascent DNA strands are up to 39% shorter in human cells lacking polη than in cells expressing polη. This provides the first direct evidence that polη modulates replication fork progression in vivo following cisplatin and carboplatin treatment. Severe replication inhibition in individual platinum-treated polη-deficient cells correlates with enhanced phosphorylation of the RPA2 subunit of replication protein A on serines 4 and 8, as determined using EdU labelling and immunofluorescence, consistent with formation of DNA strand breaks at arrested forks in the absence of polη. Polη-mediated bypass of platinum-induced DNA lesions may therefore represent one mechanism by which cancer cells can tolerate platinum-based chemotherapy.

  9. Arsenic Removal from Drinking Water by Coagulation/Filtration U.S. EPA Demonstration Project at City of Three Forks, MT, Final Performance Evaluation Report

    EPA Science Inventory

    This report documents the activities performed during and the results obtained from the arsenic removal treatment technology demonstration project at the City of Three Forks, MT facility. The objectives of the project were to evaluate: 1) the effectiveness of Kinetico’s FM-248-A...

  10. Water-quality, bed-sediment, and biological data (October 2011 through September 2012) and statistical summaries of data for streams in the Clark Fork Basin, Montana

    USGS Publications Warehouse

    Dodge, Kent A.; Hornberger, Michelle I.; Dyke, Jessica

    2014-01-01

    Water, bed sediment, and biota were sampled in streams from Butte to near Missoula, Montana, as part of a monitoring program in the upper Clark Fork Basin of western Montana. The sampling program was conducted by the U.S. Geological Survey in cooperation with the U.S. Environmental Protection Agency to characterize aquatic resources in the Clark Fork Basin, with emphasis on trace elements associated with historic mining and smelting activities. Sampling sites were located on the Clark Fork and selected tributaries. Water samples were collected periodically at 20 sites from October 2011 through September 2012. Bed-sediment and biota samples were collected once at 13 sites during August 2012. This report presents the analytical results and quality-assurance data for water-quality, bed-sediment, and biota samples collected at sites from October 2011 through September 2012. Water-quality data include concentrations of selected major ions, trace elements, and suspended sediment. Turbidity was analyzed for water samples collected at the four sites where seasonal daily values of turbidity were being determined. Daily values of suspended-sediment concentration and suspended-sediment discharge were determined for four sites. Bed-sediment data include trace-element concentrations in the fine-grained fraction. Biological data include trace-element concentrations in whole-body tissue of aquatic benthic insects. Statistical summaries of water-quality, bed-sediment, and biological data for sites in the upper Clark Fork Basin are provided for the period of record since 1985.

  11. Final report from VFL technologies for the pilot-scale thermal treatment of Lower East Fork Poplar Creek floodplain soils. LEFPC Appendices, Volume 2, Appendix V-A

    SciTech Connect

    1994-09-01

    This document contains information concerning validation of analytical data for the pilot-scale thermal treatment of Lower East Fork Poplar Creek Floodplain soils located at the Y-12 Plant site. This volume is an appendix of compiled data from this validation process.

  12. Sampling and analysis plan for treatment water and creek water for the Lower East Fork Poplar Creek Operable Unit, Oak Ridge, Tennessee

    SciTech Connect

    1996-04-01

    This document provides the Environmental Restoration Program with information about the methodology, organizational structure, quality assurance and health and safety practices to be employed during the water sampling and analysis activities associated with the remediation of the Lower East Fork Poplar Creek Operable Unit during remediation of the National Oceanic and Atmospheric Administration and Bruner sites.

  13. GENE EXPRESSION ALTERATIONS OBSERVED IN PRIMARY CULTURED RAT HEPATOCYTES AFTER TREATMENT WITH CHLORINATED OR CHLORINATED AND OZONATED DRINKING WATER FROM EAST FORK LAKE, OHIO

    EPA Science Inventory

    Drinking water from East Fork Lake was spiked with iodide and bromide, disinfected with chlorine or ozone + chlorine, concentrated ~100-fold using reverse osmosis, and volatile disinfection by-products (DBPs) added back. Primary rat hepatocytes were exposed to full-strength, 1:10...

  14. A COMPREHENISVE NONPOINT SOURCE FIELD STUDY FOR SEDIMENT, NUTRIENTS AND PATHOGENS IN THE SOUTH FORK BROAD RIVER WATERSHED IN NORTHEAST GEORGIA

    EPA Science Inventory

    There is an urgent need for EPA to develop protocols for establishing Total Maximum Daily Loads (TMDLs) in streams, lakes and estuaries. A cooperative TMDL field data collection project between ORD and Region 4 is ongoing in the South Fork Broad River Watershed (SFBR), a 245.18 ...

  15. Free-ranging Rocky Mountain bighorn sheep and an outbreak of inflammatory bowel disease along the Clark Fork River in Plains, Montana.

    PubMed

    Pierce, Ellen S

    2012-10-01

    Nine individuals with ulcerative colitis or Crohn disease grew up or lived in Plains, Montana, a 1,200-person community adjacent to the Clark Fork River near herds of free ranging Rocky Mountain bighorn sheep. This inflammatory bowel disease outbreak is similar to others that have occurred along rivers contaminated by animal feces.

  16. Use of a rainfall-runoff model for simulating effects of forest management on streamflow in the east Fork Lobster Creek Basin, Oregon. Water resources investigation

    SciTech Connect

    Nakama, L.Y.; Risley, J.C.

    1993-12-31

    The report describes the results of model calibration and validation, and evaluates the extent to which runoff response to timber harvesting and increased road densities in East Fork Lobster Creek Basin can be simulated, using Precipitation-Runoff Modeling System (PRMS), a deterministic, destributed-parameter-modeling system.

  17. Genome-wide localization of Rrm3 and Pif1 DNA helicases at stalled active and inactive DNA replication forks of Saccharomyces cerevisiae

    PubMed Central

    Rossi, Silvia Emma; Carotenuto, Walter; Giannattasio, Michele

    2015-01-01

    The genome of the budding yeast Saccharomyces cerevisiae is sequenced and the location and dynamic of activation of DNA replication origins are known. G1 synchronized yeast cells can be released into S-phase in the presence of hydroxyurea (HU) (1), which slows down DNA replication and retains replication forks in proximity of DNA replication origins. In this condition, the Chromatin Immuno-Precipitation on chip (ChIP on chip) (2–4) of replisome components allows the precise localization of all active DNA replication forks. This analysis can be coupled with the ssDNA-BromodeoxyUridine (ssDNA-BrdU) Immuno-Precipitation on chip (ssDNA-BrdU IP on chip) technique (5–7), which detects the location of newly synthesized DNA. Comparison of binding and BrdU incorporation profiles allows to locate a factor of interest at DNA replication forks genome wide. We present datasets deposited in the gene expression omnibus (GEO) database under accession number GSE68214, which show how the DNA helicases Rrm3 and Pif1 (8) associate to active and inactive DNA replication forks. PMID:26981397

  18. Water-quality, bed-sediment, and biological data (October 2009 through September 2010) and statistical summaries of data for streams in the Clark Fork basin, Montana

    USGS Publications Warehouse

    Dodge, Kent A.; Hornberger, Michelle I.; Dyke, Jessica

    2012-01-01

    Water, bed sediment, and biota were sampled in streams from Butte to near Missoula, Montana, as part of a monitoring program in the upper Clark Fork basin. The sampling program was conducted by the U.S. Geological Survey in cooperation with the U.S. Environmental Protection Agency to characterize aquatic resources in the Clark Fork basin of western Montana, with emphasis on trace elements associated with historic mining and smelting activities. Sampling sites were located on the Clark Fork and selected tributaries. Water samples were collected periodically at 20 sites from October 2009 through September 2010. Bed-sediment and biota samples were collected once at 13 sites during August 2010. This report presents the analytical results and quality-assurance data for water-quality, bed-sediment, and biota samples collected at sites from October 2009 through September 2010. Water-quality data include concentrations of selected major ions, trace elements, and suspended sediment. Turbidity was analyzed for water samples collected at the four sites where seasonal daily values of turbidity were being determined. Daily values of suspended-sediment concentration and suspended-sediment discharge were determined for four sites. Bed-sediment data include trace-element concentrations in the fine-grained fraction. Biological data include trace-element concentrations in whole-body tissue of aquatic benthic insects. Statistical summaries of water-quality, bed-sediment, and biological data for sites in the upper Clark Fork basin are provided for the period of record since 1985.

  19. Habitat selection influences sex distribution, morphology, tissue biochemistry, and parasite load of juvenile coho salmon in the West Fork Smith River, Oregon

    EPA Science Inventory

    Given the strong influence of water temperature on salmonid physiology and behavior, in the summers of 2004 and 2005 we studied juvenile male and female coho salmon Oncorhynchus kisutch in two reaches of Oregon’s West Fork Smith River with different thermal profiles. Our goals we...

  20. Final report from VFL Technologies for the pilot-scale thermal treatment of Lower East Fork Poplar Creek floodplain soils. LEFPC appendices. Volume 5. Appendix V-D

    SciTech Connect

    1994-09-01

    This final report from VFL Technologies for the pilot-scale thermal treatment of lower East Fork Poplar Creek floodplain soils dated September 1994 contains LEFPC Appendices, Volume 5, Appendix V - D. This appendix includes the final verification run data package (PAH, TCLP herbicides, TCLP pesticides).