WorldWideScience

Sample records for harboring ad-36 dna

  1. Cold Spring Harbor symposia on quantitative biology. Volume XLVII, Part 1. Structures of DNA

    International Nuclear Information System (INIS)

    Anon.

    1983-01-01

    The proceedings for the 47th Annual Cold Spring Harbor Symposia on Quantitative Biology are presented. This symposium focused on the Structure of DNA. Topics presented covered research in the handedness of DNA, conformational analysis, chemically modified DNA, chemical synthesis of DNA, DNA-protein interactions, DNA within nucleosomes, DNA methylation, DNA replication, gyrases and topoisomerases, recombining and mutating DNA, transcription of DNA and its regulation, the organization of genes along DNA, repetitive DNA and pseudogenes, and origins of replication, centromeres, and teleomeres

  2. Abstracts of papers presented at the LVIII Cold Spring Harbor Symposium on quantitative Biology: DNA and chromosomes

    Energy Technology Data Exchange (ETDEWEB)

    1993-12-31

    This volume contains the abstracts of oral and poster presentations made at the LVIII Cold Spring Harbor Symposium on Quantitative Biology entitles DNA & Chromosomes. The meeting was held June 2--June 9, 1993 at Cold Spring Harbor, New York.

  3. Cold Spring Harbor symposia on quantitative biology: Volume 49, Recombination at the DNA level

    International Nuclear Information System (INIS)

    1984-01-01

    This volume contains full papers prepared by the participants to the 1984 Cold Springs Harbor Symposia on Quantitative Biology. This year's theme is entitled Recombination at the DNA level. The volume consists of 93 articles grouped into subject areas entitled chromosome mechanics, yeast systems, mammalian homologous recombination, transposons, mu, plant transposons/T4 recombination, topoisomerase, resolvase and gyrase, Escherichia coli general recombination, RecA, repair, leukaryotic enzymes, integration and excision of bacteriophage, site-specific recombination, and recombination in vitro

  4. Cloning and Sequencing of Protein Kinase cDNA from Harbor Seal (Phoca vitulina Lymphocytes

    Directory of Open Access Journals (Sweden)

    Jennifer C. C. Neale

    2004-01-01

    Full Text Available Protein kinases (PKs play critical roles in signal transduction and activation of lymphocytes. The identification of PK genes provides a tool for understanding mechanisms of immunotoxic xenobiotics. As part of a larger study investigating persistent organic pollutants in the harbor seal and their possible immunomodulatory actions, we sequenced harbor seal cDNA fragments encoding PKs. The procedure, using degenerate primers based on conserved motifs of human protein tyrosine kinases (PTKs, successfully amplified nine phocid PK gene fragments with high homology to human and rodent orthologs. We identified eight PTKs and one dual (serine/threonine and tyrosine kinase. Among these were several PKs important in early signaling events through the B- and T-cell receptors (FYN, LYN, ITK and SYK and a MAP kinase involved in downstream signal transduction. V-FGR, RET and DDR2 were also expressed. Sequential activation of protein kinases ultimately induces gene transcription leading to the proliferation and differentiation of lymphocytes critical to adaptive immunity. PKs are potential targets of bioactive xenobiotics, including persistent organic pollutants of the marine environment; characterization of these molecules in the harbor seal provides a foundation for further research illuminating mechanisms of action of contaminants speculated to contribute to large-scale die-offs of marine mammals via immunosuppression.

  5. The role of Ad-36 as a risk factor in males with gynecomastia.

    Science.gov (United States)

    Kocazeybek, Bekir; Saribas, Suat; Ergin, Sevgi

    2015-12-01

    Gynecomastia is highly prevalent worldwide and Adenovirus-36 (Ad-36), recently implicated in increased adipose tissue deposition due to its affinity for adipose tissue, is a potential etiological agent in the development of obesity and therefore we hypothesized that Ad-36 may also play a role in the development of gynecomastia by possibly accompanying increased regional adiposity. To support our hypothesis, we conducted a study that included 33 adult males with gynecomastia (PG) and 15 adult males as the patient control group (HCG). Leptin and adiponectin levels were monitored using ELISA. A significant difference in Ad-36 antibody positivity was found between the groups (pgynecomastia may develop following an increase in aromatase enzyme activity, by which more oestrogen is produced and the estrogen-androgen balance disrupted. Also, regional adipose tissue enlargements may cause the excessive production of estrogens leading to gynecomastia. Adipose tissue has been recognized as a major endocrine organ in recent years. Another plausible explanation is excessive aromatization of androgens to estrogens by peripheral adipose tissue may promote gynecomastia in males. Moreover, our results suggest that there might be a relationship between Ad-36 and gynecomastia. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Adipogenic human adenovirus Ad-36 induces commitment, differentiation, and lipid accumulation in human adipose-derived stem cells

    DEFF Research Database (Denmark)

    Pasarica, Magdalena; Mashtalir, Nazar; McAllister, Emily J

    2008-01-01

    Human adenovirus Ad-36 is causatively and correlatively linked with animal and human obesity, respectively. Ad-36 enhances differentiation of rodent preadipocytes, but its effect on adipogenesis in humans is unknown. To indirectly assess the role of Ad-36-induced adipogenesis in human obesity......, the effect of the virus on commitment, differentiation, and lipid accumulation was investigated in vitro in primary human adipose-derived stem/stromal cells (hASC). Ad-36 infected hASC in a time- and dose-dependent manner. Even in the presence of osteogenic media, Ad-36-infected hASC showed significantly...... greater lipid accumulation, suggestive of their commitment to the adipocyte lineage. Even in the absence of adipogenic inducers, Ad-36 significantly increased hASC differentiation, as indicated by a time-dependent expression of genes within the adipogenic cascade-CCAAT/Enhancer binding protein...

  7. Rapid molecular detection of invasive species in ballast and harbor water by integrating environmental DNA and light transmission spectroscopy.

    Science.gov (United States)

    Egan, Scott P; Grey, Erin; Olds, Brett; Feder, Jeffery L; Ruggiero, Steven T; Tanner, Carol E; Lodge, David M

    2015-04-07

    Invasive species introduced via the ballast water of commercial ships cause enormous environmental and economic damage worldwide. Accurate monitoring for these often microscopic and morphologically indistinguishable species is challenging but critical for mitigating damages. We apply eDNA sampling, which involves the filtering and subsequent DNA extraction of microscopic bits of tissue suspended in water, to ballast and harbor water sampled during a commercial ship's 1400 km voyage through the North American Great Lakes. Using a lab-based gel electrophoresis assay and a rapid, field-ready light transmission spectroscopy (LTS) assay, we test for the presence of two invasive species: quagga (Dreissena bugensis) and zebra (D. polymorpha) mussels. Furthermore, we spiked a set of uninfested ballast and harbor samples with zebra mussel tissue to further test each assay's detection capabilities. In unmanipulated samples, zebra mussel was not detected, while quagga mussel was detected in all samples at a rate of 85% for the gel assay and 100% for the LTS assay. In the spiked experimental samples, both assays detected zebra mussel in 94% of spiked samples and 0% of negative controls. Overall, these results demonstrate that eDNA sampling is effective for monitoring ballast-mediated invasions and that LTS has the potential for rapid, field-based detection.

  8. [Pearl Harbor.

    Science.gov (United States)

    Johnson, Jennifer, Ed.

    1992-01-01

    This issue of "Loblolly Magazine" was written in observance of the 50th anniversary of the U.S. entrance into World War II. The publication features interviews conducted by East Texas high school students with Clarence Otterman, one of the few survivors of the crew of the USS Arizona, which was bombed during the attack on Pearl Harbor,…

  9. Human adenovirus Ad36 and its E4orf1 gene enhance cellular glucose uptake even in the presence of inflammatory cytokines.

    Science.gov (United States)

    Na, Ha-Na; Dubuisson, Olga; Hegde, Vijay; Nam, Jae-Hwan; Dhurandhar, Nikhil V

    2016-05-01

    Aging and obesity are associated with elevated pro-inflammatory cytokines such as monocyte chemoattractant protein (MCP)-1 and tumor necrosis factor (TNF)α, which are linked to insulin resistance. Anti-inflammatory agents have marginal effect in improving insulin resistance. Hence, agents are needed to improve glycemic control despite the inflammation. Ad36, a human adenovirus, increases TNFα and MCP1 mRNA in adipose tissue, yet improves glycemic control in mice. Ad36 via its E4orf1 gene, up-regulates AKT/glucose transporter (Glut)-4 signaling to enhance cellular glucose uptake. Directly test a role of Ad36, or E4orf1 in enhancing cellular glucose uptake in presence of inflammatory cytokines. Experiment 1: 3T3-L1 preadipocytes were treated with 0, 10 or 100 ng/mL lipopolysaccharides (LPS), and infected with 0 or 5 plaque forming units (PFU) of Ad36/cell. 3T3-L1 cells that stably and inducibly express E4orf1 or a null vector (pTRE-E4orf1 or pTRE-null cells), were similarly treated with LPS and then with doxycycline, to induce E4orf1. Experiment 2: 3T3L1 preadipocytes were treated with 25 nM MCP1 or 20 nM TNFα for 16 h, followed by infection with 0 or 5 PFU of Ad36/cell. Experiment 3: pTRE-E4orf1 or -null cells were similarly treated with MCP1 or TNFα followed by doxycycline to induce E4orf1. Cellular glucose uptake and cellular signaling were determined 72 h post-Ad36 infection or E4orf1-induction, in continued presence of MCP1 or TNFα. In 3T3-L1 preadipocytes, Ad36, but not E4orf1, increased MCP1 and TNFα mRNA, in presence of LPS stimulation. Ad36 or E4orf1 up-regulated AKT-phosphorylation and Glut4 and increased glucose uptake (P E4orf1 does not appear to stimulate inflammatory response. Ad36 and E4orf1 both enhance cellular glucose uptake even in presence of inflammation. Further research is needed to harness this novel and beneficial property of E4orf1 to improve hyperglycemia despite chronic inflammation that is commonly present in aging and

  10. Hydroxyurea enhances the activity of acyclovir and cidofovir against herpes simplex virus type 1 resistant strains harboring mutations in the thymidine kinase and/or the DNA polymerase genes.

    Science.gov (United States)

    Sergerie, Yan; Boivin, Guy

    2008-01-01

    Drug-resistant herpes simplex virus type 1 (HSV-1) recombinant strains harboring mutations in the thymidine kinase and/or the DNA polymerase genes were evaluated for their susceptibility to various antivirals in the presence of 25 microg/ml of hydroxyurea (HyU). The latter compound decreased the 50% inhibitory concentrations of acyclovir by 1.5-3.8-fold and that of cidofovir by 2.7-14.4-fold. However, HyU did not affect the susceptibilities of the various recombinant mutants to foscarnet. Hydroxyurea, a ribonucleotide reductase inhibitor, can increase the activity of nucleoside/nucleotide analogues against drug-resistant viruses.

  11. Coastal Harbors Modeling Facility

    Data.gov (United States)

    Federal Laboratory Consortium — The Coastal Harbors Modeling Facility is used to aid in the planning of harbor development and in the design and layout of breakwaters, absorbers, etc.. The goal is...

  12. Extrachromosomal deoxyribonucleic acid in R factor-harboring Enterobacteriaceae

    DEFF Research Database (Denmark)

    Møller, JK; Bak, AL; Christiansen, C

    1976-01-01

    Extrachromosomal deoxyribonucleic acid (DNA) from 24 different R factor-harboring Enterobacteriaceae was isolated and characterized by analytical ultracentrifugation and electron microscopy. The R factors represented 15 different patterns of transferable drug resistance found in enterobacteria from...

  13. Pearl Harbor Biological Survey

    Science.gov (United States)

    1974-08-30

    Pearl Harbor also receives Irrigation tailgate waters from the Oahu Sug- ar Company, Industrial waste waters from the Prlmo Brewery , and heated waters...34Observations of the Cell Structure of Salt Fingers", J. Fluid Mech. 41:4, pp 707-719. ~) 3.3-79 ,’:•.-. ^ IV s’V- EFFECTS OF SHIP ACTIVITY Paul L...anticyclonic) death assemblage - in this report, an assemblage (q.v.) of remains (such as shells or bones ) from a naturally occurring association of living

  14. Extrachromosomal deoxyribonucleic acid in R factor-harboring Enterobacteriaceae

    DEFF Research Database (Denmark)

    Møller, JK; Bak, AL; Christiansen, C

    1976-01-01

    Extrachromosomal deoxyribonucleic acid (DNA) from 24 different R factor-harboring Enterobacteriaceae was isolated and characterized by analytical ultracentrifugation and electron microscopy. The R factors represented 15 different patterns of transferable drug resistance found in enterobacteria from...... from 1.700 to 1.720 g/cm3. The majority of the bacteria contained extrachromosomal DNAs of various densities. Three-fourths of the R factors were classified as fi+. The investigation illustrates the extensive variability in the physical characteristics of plasmid DNA from R factor-harboring strains....

  15. Grays Harbor Paper

    Energy Technology Data Exchange (ETDEWEB)

    Quigg, B. [Grays Harbor Paper, Hoquiam, WA (United States)

    2009-07-01

    Wood waste biomass boilers are used at Grays Harbor Paper in Hoquiam, Washington. This presentation showed that large volumes of biomass are left after a traditional clearcut. The opportunities and challenges of collecting branches, tops and stumps from this wet coastal climate were outlined. The paper described some of the low-tech methods for picking up branches, stumps and woody debris. It included several photographs of custom logging machines for timber harvest, including a brush grapple slasher, a shearer shovel, chippers, grinders, slicesaws, trucks, trailers and caterpillar log loaders for handling slash. The slash recovery program relies on innovative harvesting machines that convert scattered logging slash into bundles that can be easily collected, transported, and stored for use in existing facilities that utilize wood fiber for fuel. figs.

  16. Rhizosphere of rice plants harbor bacteria with multiple plant growth ...

    African Journals Online (AJOL)

    Rhizosphere of rice plants harbor bacteria with multiple plant growth promoting features. ... 45 (39.46%) isolates were capable of producing siderophore, the range of production being 4.50 to 223.26 μg mg-1 protein. Analysis of molecular diversity was made by amplified ribosomal DNA restriction analysis (ARDRA) and ...

  17. Alaska Harbor Seal Glacial Surveys

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Floating glacial ice serves as a haul-out substrate for a significant number (10-15%) of Alaskan harbor seals, and thus surveying tidewater glacial fjords is an...

  18. Geoscience rediscovers Phoenicia's buried harbors

    Science.gov (United States)

    Marriner, Nick; Morhange, Christophe; Doumet-Serhal, Claude; Carbonel, Pierre

    2006-01-01

    After centuries of archaeological debate, the harbors of Phoenicia's two most important city states, Tyre and Sidon, have been rediscovered, and including new geoarcheological results reveal how, where, and when they evolved after their Bronze Age foundations. The early ports lie beneath their present urban centers, and we have indentified four harbor phases. (1) During the Bronze Age, Tyre and Sidon were characterized by semi-open marine coves that served as protoharbors. (2) Biostratigraphic and lithostratigraphic data indicate the presence of early artificial basins after the first millennium B.C. (3) The harbors reached their apogees during the Greco-Roman and Byzantine periods. (4) Silting up and coastal progradation led to burial of the medieval basins, lost until now.

  19. 77 FR 19967 - Safety Zone, Port of Dutch Harbor; Dutch Harbor, AK

    Science.gov (United States)

    2012-04-03

    ...-AA00 Safety Zone, Port of Dutch Harbor; Dutch Harbor, AK AGENCY: Coast Guard, DHS. ACTION: Notice of proposed rulemaking. SUMMARY: The Coast Guard proposes temporary safety zones in the Port of Dutch Harbor... Dutch Harbor, Alaska, and the adjacent territorial sea due to additional vessel traffic associated with...

  20. Army Engineers at Pearl Harbor

    Science.gov (United States)

    2011-01-01

    siblings, he was the grandson of David Belden Lyman—a Christian missionary from New England who settled in the Hilo , Hawaii area—and the descendent of...of Hawaii appeared over Oahu. Some headed for Ameri- can warships at Pearl Harbor and the planes on the ground at nearby Hickam Field; oth- ers...hit Schofield Barracks, Wheeler Field, and Bellows Field. USACE in Hawaii con- sisted of Soldier-engineers in the Army’s Hawaiian Depart- ment and

  1. 33 CFR 125.15 - Access to waterfront facilities, and port and harbor areas, including vessels and harbor craft...

    Science.gov (United States)

    2010-07-01

    ..., and port and harbor areas, including vessels and harbor craft therein. 125.15 Section 125.15....15 Access to waterfront facilities, and port and harbor areas, including vessels and harbor craft....09 to those waterfront facilities, and port and harbor areas, including vessels and harbor craft...

  2. CRSMP Potential Harbor Borrow Sites 2012

    Data.gov (United States)

    California Natural Resource Agency — Harbor locations as identified originally in the California Shoreline Database compiled by Noble Consultants (Jon Moore) for California Department of Boating and...

  3. 33 CFR 100.109 - Winter Harbor Lobster Boat Race, Winter Harbor, ME.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Winter Harbor Lobster Boat Race, Winter Harbor, ME. 100.109 Section 100.109 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY REGATTAS AND MARINE PARADES SAFETY OF LIFE ON NAVIGABLE WATERS § 100.109 Winter Harbor...

  4. The Suez Canal and the petroleum harbors

    International Nuclear Information System (INIS)

    Anon.

    1997-01-01

    The Suez Canal is the second longest channel in the world and allows to save 60% of the travel time between the petroleum harbors of the Arabic peninsula and Europe. This short paper gives a summary of the main petroleum harbors activity along the channel from the Red sea to the Mediterranean sea. (J.S.)

  5. DNA replication and cancer

    DEFF Research Database (Denmark)

    Boyer, Anne-Sophie; Walter, David; Sørensen, Claus Storgaard

    2016-01-01

    A dividing cell has to duplicate its DNA precisely once during the cell cycle to preserve genome integrity avoiding the accumulation of genetic aberrations that promote diseases such as cancer. A large number of endogenous impacts can challenge DNA replication and cells harbor a battery of pathways...... causing DNA replication stress and genome instability. Further, we describe cellular and systemic responses to these insults with a focus on DNA replication restart pathways. Finally, we discuss the therapeutic potential of exploiting intrinsic replicative stress in cancer cells for targeted therapy....

  6. Genetics Home Reference: Floating-Harbor syndrome

    Science.gov (United States)

    ... Patton MA, Hurst J, Donnai D, McKeown CM, Cole T, Goodship J. Floating-Harbor syndrome. J Med ... medicine? What is newborn screening? New Pages Lyme disease Fibromyalgia White-Sutton syndrome All New & Updated Pages ...

  7. Madaket Harbor, Nantucket, Massachusetts. Water Resources Improvement.

    Science.gov (United States)

    1977-07-01

    will continue to be, important increases in the recreational use of land and water. The harbor area is an important arena for commercial shellfishing...an important arena for commercial shell fishing. The past few years have seen a rather rapid increase in residential land use. Construction has...beamc. Tnis material will be re-deposited,, viaj troio it 1-apfro1inr ox prior location. j, MADAKET HARBOR NANTUCKET, MASSACHUSETTS FEASIBILITY

  8. 76 FR 8653 - Drawbridge Operation Regulation; Gulf Intracoastal Waterway, New Orleans Harbor, Inner Harbor...

    Science.gov (United States)

    2011-02-15

    ... Operation Regulation; Gulf Intracoastal Waterway, New Orleans Harbor, Inner Harbor Navigation Canal, New Orleans, Orleans Parish, LA AGENCY: Coast Guard, DHS. ACTION: Notice of temporary deviation from... Lock), at New Orleans, Orleans Parish, Louisiana. This deviation is necessary to replace all of the...

  9. 75 FR 78601 - Drawbridge Operation Regulation; Gulf Intracoastal Waterway, New Orleans Harbor, Inner Harbor...

    Science.gov (United States)

    2010-12-16

    ... Operation Regulation; Gulf Intracoastal Waterway, New Orleans Harbor, Inner Harbor Navigation Canal, New Orleans, Orleans Parish, LA AGENCY: Coast Guard, DHS. ACTION: Notice of temporary deviation from... Harvey Lock), at New Orleans, Orleans Parish, Louisiana. This deviation is necessary to adjust the...

  10. The yeast Saccharomyces cerevisiae DNA polymerase IV: possible involvement in double strand break DNA repair.

    OpenAIRE

    Leem, S H; Ropp, P A; Sugino, A

    1994-01-01

    We identified and purified a new DNA polymerase (DNA polymerase IV), which is similar to mammalian DNA polymerase beta, from Saccharomyces cerevisiae and suggested that it is encoded by YCR14C (POLX) on chromosome III. Here, we provided a direct evidence that the purified DNA polymerase IV is indeed encoded by POLX. Strains harboring a pol4 deletion mutation exhibit neither mitotic growth defect nor a meiosis defect, suggesting that DNA polymerase IV participates in nonessential functions in ...

  11. New Harbor in Kangerlussuaq, Western Greenland

    DEFF Research Database (Denmark)

    Stenstad, Jaran Gjerlandj; Eppeland, Kjetil Grødal; Ingeman-Nielsen, Thomas

    2015-01-01

    transported by rivers from the inland ice to the inner parts of the fjord. These sediment layers reduce the water depth and prevent container- and cruiseships to dock, imposing large additional maintenance costs, and inefficient operability. Through engineering geological field and lab investigations......, a possible new harbor location around 10 km further out the fjord near Hancock Pynt, has been investigated. The onshore area was found to be highly suitable for a harbor support area, where a sub-base thickness of 1.8 m with gravel cover-layer was found adequate for the calculated design loads. Existing...

  12. Evaluation of Sediment Contamination in Pearl Harbor

    Science.gov (United States)

    1992-06-01

    ancient Hawaiians, was a large natural inland lagoon. Numerous walled fishponds located inside the harbor were used to cultivate various species of fishes... Ecotoxicology , Commission on Natural Resources, National Academy Press, Washington, D.C., 103 pp. National Research Council, 1989. Contaminated Marine

  13. Modeling of Tsunami Currents in Harbors

    Science.gov (United States)

    Lynett, P. J.

    2010-12-01

    Extreme events, such as large wind waves and tsunamis, are well recognized as a damaging hazard to port and harbor facilities. Wind wave events, particularly those with long period spectral components or infragravity wave generation, can excite resonance inside harbors leading to both large vertical motions and strong currents. Tsunamis can cause great damage as well. The geometric amplification of these very long waves can create large vertical motions in the interior of a harbor. Additionally, if the tsunami is composed of a train of long waves, which it often is, resonance can be easily excited. These long wave motions create strong currents near the node locations of resonant motions, and when interacting with harbor structures such as breakwaters, can create intense turbulent rotational structures, typical in the form of large eddies or gyres. These gyres have tremendous transport potential, and have been observed to break mooring lines, and even cause ships to be trapped inside the rotation, moving helplessly with the flow until collision, grounding, or dissipation of the eddy (e.g. Okal et al., 2006). This presentation will introduce the traditional theory used to predict wave impacts on harbors, discussing both how these models are practically useful and in what types of situations require a more accurate tool. State-of-the-art numerical models will be introduced, with a focus on recent developments in Boussinesq-type modeling. The Boussinesq equations model can account the dispersive, turbulent and rotational flow properties frequently observed in nature. Also they have the ability to coupling currents and waves and can predict nonlinear wave propagation over uneven bottom from deep (or intermediate) water area to shallow water area. However, during the derivation of a 2D-horizontal equation set, some 3D flow features, such those driven by as the dispersive stresses and the effects of the unresolved small scale 3D turbulence, are excluded. Consequently

  14. 32 CFR 765.6 - Regulations for Pearl Harbor, Hawaii.

    Science.gov (United States)

    2010-07-01

    ... 32 National Defense 5 2010-07-01 2010-07-01 false Regulations for Pearl Harbor, Hawaii. 765.6... RULES RULES APPLICABLE TO THE PUBLIC § 765.6 Regulations for Pearl Harbor, Hawaii. The Commander, U.S. Naval Base, Pearl Harbor, Hawaii, is responsible for prescribing and enforcing such rules and...

  15. Teaching about Pearl Harbor. Curriculum Enhancement Series #1.

    Science.gov (United States)

    Shields, Anna Marshall

    These materials consist of sample lesson plans for teaching about the Japanese attack on Pearl Harbor on December 7, 1941, in both U.S. and world history classes. The lesson plans challenge students to examine how current attitudes toward the Japanese may be rooted in World War II and Pearl Harbor. Selected bibliographies on Pearl Harbor, World…

  16. Remembering Pearl Harbor at 75 Years.

    Science.gov (United States)

    Liehr, Patricia; Sopcheck, Janet; Milbrath, Gwyneth

    2016-12-01

    : On December 7, 1941, the Sunday-morning quiet of the U.S. naval base in Pearl Harbor, Hawaii, was shattered by dive-bombing Japanese fighter planes. The planes came in two waves-and when it was all over, more than 2,400 were killed and more than 1,100 were injured.Nurses were stationed at U.S. Naval Hospital Pearl Harbor, Tripler General Hospital (now Tripler Army Medical Center), Hickam Field Hospital, Schofield Barracks Station Hospital, and aboard the USS Solace, and witnessed the devastation. But they also did what nurses do in emergencies-they responded and provided care to those in need. Here are the stories of a few of those nurses.

  17. Old Harbor Scammon Bay Hydro Feasibility

    Energy Technology Data Exchange (ETDEWEB)

    Brent Petrie

    2007-06-27

    The grantee, Alaska Village Electric Cooperative (AVEC), is a non-profit member owned rural electric generation and distribution cooperative. The proposed Project is located near the community of Old Harbor, Alaska. Old Harbor is on the southeastern coast of Kodiak Island, approximately 70 miles southwest of the City of Kodiak and 320 miles southwest of Anchorage. In 1998 sufficient information had been developed to apply for a license to construct the project and the cost was estimated to be $2,445,000 for a 500 KW project on Lagoon Creek. Major features of the project included an eight-foot high diversion dam on Mountain Creek, a desander box, a 9,800-foot long penstock to the powerhouse on Lagoon Creek, and a 5,500-foot long access road. It was also anticipated that the project could provide an additional source of water to Old Harbor. The report details the history and lessons learned in designing and permiting the proposed hydroelectric facility.

  18. Rapid identification of DNA-binding proteins by mass spectrometry

    DEFF Research Database (Denmark)

    Nordhoff, E.; Korgsdam, A.-M.; Jørgensen, H.F.

    1999-01-01

    We report a protocol for the rapid identification of DNA-binding proteins. Immobilized DNA probes harboring a specific sequence motif are incubated with cell or nuclear extract. Proteins are analyzed directly off the solid support by matrix-assisted laser desorption/ionization time-of-flight mass...... was validated by the identification of known prokaryotic and eukaryotic DNA-binding proteins, and its use provided evidence that poly(ADP-ribose) polymerase exhibits DNA sequence-specific binding to DNA....

  19. Cultural Resources Survey of Mobile Harbor, Alabama.

    Science.gov (United States)

    1983-01-01

    improvement from the point of view of supply and communication with other European settlements, since it cut the lightering distance to the capital in half...order to cut the costs of building (Bathe 1978:08.00-02; Millar 1978:15-29). 32 6e The sharing of ship builders, the borrowing of vessel lines and the... Eslava Street Mobile. Burned to water’s edge during overhaul. Notes: Served as HINGHAM in Boston Harbor; served as ORIENT in Long Island Sound. Operated

  20. 77 FR 50916 - Safety Zone; Boston Harbor's Rock Removal Project, Boston Inner Harbor, Boston, MA

    Science.gov (United States)

    2012-08-23

    ... operation on the navigable waters of Boston Inner Harbor, in the main ship channel near Castle Island. This... operations in support of the U.S. Army Corps of Engineers rock removal project. Entering into, transiting... before the start date of the project. The U.S. Army Corps of Engineers also discussed the rock removal...

  1. Synanthropic Cockroaches (Blattidae: Periplaneta spp.) Harbor Pathogenic Leptospira in Colombia.

    Science.gov (United States)

    Gonzalez-Astudillo, Viviana; Bustamante-Rengifo, Javier A; Bonilla, Álvaro; Lehmicke, Anna Joy J; Castillo, Andrés; Astudillo-Hernández, Miryam

    2016-01-01

    Leptospirosis cases in Colombia are typically linked to peridomestic rodents; however, empirical data suggest that Leptospira-infected patients with no apparent exposure to these reservoirs are common. Cockroaches (Periplaneta spp.) have equal or greater interaction with humans than rodents, yet their potential role as carriers of Leptospira has not been assessed. We determined if pathogenic Leptospira is harbored by Periplaneta spp. in Cali (Colombia) and the variables influencing this relationship. Fifty-nine cockroaches were captured from seven sites and DNA was extracted from the body surface and digestive tract for a multiplex polymerase chain reaction, targeting genes secY and flaB. Logistic regression models and proportion tests showed a higher likelihood for Leptospira to be isolated from body surfaces (P > 0.001) and from individuals inside houses (six times more likely). These findings are the first to demonstrate an association between Periplaneta spp. and Leptospira, suggesting the need to investigate the potential for cockroaches to serve as reservoirs or transport hosts for Leptospira. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  2. Ancient DNA

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair......ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair...

  3. Vibration-based structural health monitoring of harbor caisson structure

    Science.gov (United States)

    Lee, So-Young; Lee, So-Ra; Kim, Jeong-Tae

    2011-04-01

    This study presents vibration-based structural health monitoring method in foundation-structure interface of harbor caisson structure. In order to achieve the objective, the following approaches are implemented. Firstly, vibration-based response analysis method is selected and structural health monitoring (SHM) technique is designed for harbor caisson structure. Secondly, the performance of designed SHM technique for harbor structure is examined by FE analysis. Finally, the applicability of designed SHM technique for harbor structure is evaluated by dynamic tests on a lab-scaled caisson structure.

  4. Hazardous substances shipping at inland water harbors

    International Nuclear Information System (INIS)

    Benkovic, Z.

    2009-01-01

    Safety measures and regulations system covering the aspects of fire protection, professional and ecological safety are aimed to create a safe working environment, by detection and remedy of conditions that are potentially hazardous for the well-being of the employees or are leading to certain undesired events. Such unwanted incidents may result in different consequences: operating person's injury, environment pollution or material damage. This study attempts to illustrate the organization of work during hazardous matter loading and unloading at inland water harbors, based on legal provisions and decrees involving safety precautions, and in order to achieve constant enhancement of operating procedure, decreasing thereby the number of work-related injuries and various accidental situations. Fundamental precondition required to prevent possible accidents and to optimize general safety policy is to recognize and control any danger or potential hazard, as well as to be familiar with the legal provisions covering the inland waterway transport of harmful substances.(author)

  5. Tumor‐associated DNA mutation detection in individuals undergoing colonoscopy

    OpenAIRE

    Fleshner, Phillip; Braunstein, Glenn D.; Ovsepyan, Gayane; Tonozzi, Theresa R.; Kammesheidt, Anja

    2017-01-01

    Abstract The majority of colorectal cancers (CRC) harbor somatic mutations and epigenetic modifications in the tumor tissue, and some of these mutations can be detected in plasma as circulating tumor DNA (ctDNA). Precancerous colorectal lesions also contain many of these same mutations. This study examined plasma for ctDNA from patients undergoing a screening or diagnostic colonoscopy to determine the sensitivity and specificity of the ctDNA panel for detecting CRC and precancerous lesions. T...

  6. 33 CFR 80.1460 - Kahului Harbor, Maui, HI.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Kahului Harbor, Maui, HI. 80.1460 Section 80.1460 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1460 Kahului Harbor, Maui, HI. A line drawn...

  7. 33 CFR 80.1450 - Nawiliwili Harbor, Kauai, HI.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Nawiliwili Harbor, Kauai, HI. 80.1450 Section 80.1450 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1450 Nawiliwili Harbor, Kauai, HI...

  8. 33 CFR 110.238 - Apra Harbor, Guam.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Apra Harbor, Guam. 110.238 Section 110.238 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.238 Apra Harbor, Guam. (a) The anchorage grounds (Datum: WGS...

  9. 33 CFR 80.1470 - Kawaihae Harbor, Hawaii, HI.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Kawaihae Harbor, Hawaii, HI. 80.1470 Section 80.1470 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1470 Kawaihae Harbor, Hawaii, HI...

  10. 33 CFR 80.1480 - Hilo Harbor, Hawaii, HI.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Hilo Harbor, Hawaii, HI. 80.1480 Section 80.1480 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1480 Hilo Harbor, Hawaii, HI. A line drawn...

  11. 33 CFR 110.208 - Buffalo Harbor, N.Y.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Buffalo Harbor, N.Y. 110.208 Section 110.208 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.208 Buffalo Harbor, N.Y. (a) The anchorage grounds—(1...

  12. 32 CFR 705.31 - USS Arizona Memorial, Pearl Harbor.

    Science.gov (United States)

    2010-07-01

    ... 32 National Defense 5 2010-07-01 2010-07-01 false USS Arizona Memorial, Pearl Harbor. 705.31... NAVY REGULATIONS AND OFFICIAL RECORDS PUBLIC AFFAIRS REGULATIONS § 705.31 USS Arizona Memorial, Pearl Harbor. (a) Limited space and the desirability of keeping the Memorial simple and dignified require the...

  13. 76 FR 50489 - Agency Information Collection Activities: Harbor Maintenance Fee

    Science.gov (United States)

    2011-08-15

    ... Activities: Harbor Maintenance Fee AGENCY: U.S. Customs and Border Protection, Department of Homeland... Fee (CBP Forms 349 and 350). This is a proposed extension of an information collection that was... Fee. OMB Number: 1651-0055. Form Number: CBP Forms 349 and 350. Abstract: The Harbor Maintenance Fee...

  14. 33 CFR 165.904 - Lake Michigan at Chicago Harbor & Burnham Park Harbor-Safety and Security Zone.

    Science.gov (United States)

    2010-07-01

    ... & Burnham Park Harbor-Safety and Security Zone. 165.904 Section 165.904 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) PORTS AND WATERWAYS SAFETY REGULATED NAVIGATION... Guard District § 165.904 Lake Michigan at Chicago Harbor & Burnham Park Harbor—Safety and Security Zone...

  15. 77 FR 59551 - Safety Zone, Changes to Original Rule; Boston Harbor's Rock Removal Project, Boston Inner Harbor...

    Science.gov (United States)

    2012-09-28

    ... DEPARTMENT OF HOMELAND SECURITY Coast Guard 33 CFR Part 165 [Docket No. USCG-2012-0767] RIN 1625-AA00 Safety Zone, Changes to Original Rule; Boston Harbor's Rock Removal Project, Boston Inner Harbor... original provisions of that temporary final rule, but adds two additional safety zones necessary for the...

  16. Wave Climate and Wave Response, 2025 Plan, Kahului Harbor, Maui, Hawaii

    National Research Council Canada - National Science Library

    Thompson, Edward

    2002-01-01

    ... (wind waves and swell) and long waves (harbor oscillations), was used to evaluate the technical feasibility of three alternative modifications to the harbor, including the Kahului Commercial Harbor 2025 Master Plan...

  17. Harbor porpoise Phocoena phocoena strandings on the Dutch coast: No genetic structure, but evidence of inbreeding

    Science.gov (United States)

    van der Plas-Duivesteijn, Suzanne J.; Smit, Femmie J. L.; van Alphen, Jacques J. M.; Kraaijeveld, Ken

    2015-03-01

    Conservation management in the North Sea is often motivated by the population size of marine mammals, like harbor porpoises Phocoena phocoena. In the Dutch part of the North Sea, sighting and stranding data are used to estimate population sizes, but these data give little insight into genetic structuring of the population. In this study we investigated genetic structure among animals stranded at different locations and times of year. We also tested whether there is a link between stranding and necropsy data, and genetic diversity. We made use of both mitochondrial (mtDNA) and microsatellite DNA analysis of samples from dead stranded porpoises along the Dutch coast during 2007. mtDNA analysis showed 6 variable positions in the control region, defining 3 different haplotypes. mtDNA haplotypes were not randomly distributed along the Dutch coastline. However, microsatellite analysis showed that these mtDNA haplotypes did not represent separate groups on a nuclear level. Furthermore, microsatellite analysis revealed no genotypic differences between seasons, locations or genders. The results of this study indicate that the Dutch population is panmictic. In contrast, heterozygosity levels were low, indicating some level of inbreeding in this population. However, this was not corroborated by other indices of inbreeding. This research provided insight into genetic structuring of stranded porpoises in 2007, but data from multiple years should be included to be able to help estimate population sizes.

  18. Raw Sewage Harbors Diverse Viral Populations

    Science.gov (United States)

    Cantalupo, Paul G.; Calgua, Byron; Zhao, Guoyan; Hundesa, Ayalkibet; Wier, Adam D.; Katz, Josh P.; Grabe, Michael; Hendrix, Roger W.; Girones, Rosina; Wang, David; Pipas, James M.

    2011-01-01

    ABSTRACT At this time, about 3,000 different viruses are recognized, but metagenomic studies suggest that these viruses are a small fraction of the viruses that exist in nature. We have explored viral diversity by deep sequencing nucleic acids obtained from virion populations enriched from raw sewage. We identified 234 known viruses, including 17 that infect humans. Plant, insect, and algal viruses as well as bacteriophages were also present. These viruses represented 26 taxonomic families and included viruses with single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), positive-sense ssRNA [ssRNA(+)], and dsRNA genomes. Novel viruses that could be placed in specific taxa represented 51 different families, making untreated wastewater the most diverse viral metagenome (genetic material recovered directly from environmental samples) examined thus far. However, the vast majority of sequence reads bore little or no sequence relation to known viruses and thus could not be placed into specific taxa. These results show that the vast majority of the viruses on Earth have not yet been characterized. Untreated wastewater provides a rich matrix for identifying novel viruses and for studying virus diversity. Importance At this time, virology is focused on the study of a relatively small number of viral species. Specific viruses are studied either because they are easily propagated in the laboratory or because they are associated with disease. The lack of knowledge of the size and characteristics of the viral universe and the diversity of viral genomes is a roadblock to understanding important issues, such as the origin of emerging pathogens and the extent of gene exchange among viruses. Untreated wastewater is an ideal system for assessing viral diversity because virion populations from large numbers of individuals are deposited and because raw sewage itself provides a rich environment for the growth of diverse host species and thus their viruses. These studies suggest that

  19. Analysis of in vivo binding of yeast heat shock factor to promoter DNA

    African Journals Online (AJOL)

    SERVER

    2008-04-17

    Apr 17, 2008 ... The baker's yeast, Saccharomyces cerevisiae, harbors only a single HSF ... ethanol. The resulting DNA was dissolved in 20 µl TE. PCR. 3% of each .... tolerance oxidant stress, and involve in other biochemical pathways.

  20. Bar Harbor, ME Tsunami Forecast Grids for MOST Model

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Bar Harbor, Maine Forecast Model Grids provides bathymetric data strictly for tsunami inundation modeling with the Method of Splitting Tsunami (MOST) model. MOST...

  1. Hydrocarbon pollutants shape bacterial community assembly of harbor sediments

    KAUST Repository

    Barbato, Marta; Mapelli, Francesca; Magagnini, Mirko; Chouaia, Bessem; Armeni, Monica; Marasco, Ramona; Crotti, Elena; Daffonchio, Daniele; Borin, Sara

    2016-01-01

    Petroleum pollution results in co-contamination by different classes of molecules, entailing the occurrence of marine sediments difficult to remediate, as in the case of the Ancona harbor (Mediterranean Sea, Italy). Autochthonous bioaugmentation

  2. 75 FR 76613 - National Pearl Harbor Remembrance Day, 2010

    Science.gov (United States)

    2010-12-09

    .... The deadly attack on Pearl Harbor did not accomplish its mission of breaking the American spirit..., aiding the war effort by working in manufacturing plants, participating in rationing programs, or...

  3. Apra Harbor, Guam Tsunami Forecast Grids for MOST Model

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Apra Harbor, Guam Forecast Model Grids provides bathymetric data strictly for tsunami inundation modeling with the Method of Splitting Tsunami (MOST) model. MOST...

  4. Pearl Harbor, Hawaii 1 arc-second DEM

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The 1/3-second Pearl Harbor Hawaii Elevation Grid provides bathymetric data in ASCII raster format of 1/3-second resolution in geographic coordinates. This grid is...

  5. Submarine Biofouling Control- Chlorination DATS Study at Pearl Harbor

    National Research Council Canada - National Science Library

    Wegand, John

    2001-01-01

    The intent of this document is to sumarize the chlorination studies performed at Naval Station, Pearl Harbor in support of biofouling control initiatives for the submarine community, as requested by NAVSEA 92T...

  6. Ground-water status report, Pearl Harbor area, Hawaii, 1978

    Science.gov (United States)

    Soroos, Ronald L.; Ewart, Charles J.

    1979-01-01

    Increasing demand for freshwater in Hawaii has placed heavy stress on many of the State 's basal aquifer systems. The most heavily stressed of these systems is the Pearl Harbor on Oahu. The Pearl Harbor basal aquifer supplies as much as 277 million gallons per day. Since early in this century, spring discharge has been declining while pumpage has been increasing. Total ground-water discharge has remained steady despite short-term fluctuations. Some wells show general increases in chloride concentration while others remain steady. Chloride concentrations throughout the area show no apparent increase since 1970. Basal water head maps of the Pearl Harbor area clearly reflect the natural discharge points, which are the springs located along the shore near the center of Pearl Harbor. Basal-water hydrographs show a general decline of about 0.09 foot per year. This implies depletion of storage at a rate of about 25 million gallons per day. (USGS).

  7. Pearl Harbor, Hawaii Tsunami Forecast Grids for MOST Model

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Pearl Harbor, Hawaii Forecast Model Grids provides bathymetric data strictly for tsunami inundation modeling with the Method of Splitting Tsunami (MOST) model....

  8. Harbor seal vibrissa morphology suppresses vortex-induced vibrations

    OpenAIRE

    Hanke, Wolf; Witte, Mathias; Miersch, Lars; Brede, Martin; Oeffner, Johannes; Michael, Mark; Hanke, Frederike; Leder, Alfred; Dehnhardt, Guido

    2010-01-01

    Harbor seals (Phoca vitulina) often live in dark and turbid waters, where their mystacial vibrissae, or whiskers, play an important role in orientation. Besides detecting and discriminating objects by direct touch, harbor seals use their whiskers to analyze water movements, for example those generated by prey fish or by conspecifics. Even the weak water movements left behind by objects that have passed by earlier can be sensed and followed accurately (hydrodynamic trail following). While scan...

  9. Satellite Monitoring of Boston Harbor Water Quality: Initial Investigations

    Science.gov (United States)

    Sheldon, P.; Chen, R. F.; Schaaf, C.; Pahlevan, N.; Lee, Z.

    2016-02-01

    The transformation of Boston Harbor from the "dirtiest in America" to a National Park Area is one of the most remarkable estuarine recoveries in the world. A long-term water quality dataset from 1991 to present exists in Boston Harbor due to a $3. 8 billion lawsuit requiring the harbor clean-up. This project uses discrete water sampling and underway transects with a towed vehicle coordinated with Landsat 7 and Landsat 8 to create surface maps of chlorophyll a (Chl a), dissolved organic matter (CDOM and DOC), total suspended solids (TSS), diffuse attenuation coefficient (Kd_490), and photic depth in Boston Harbor. In addition, 3 buoys have been designed, constructed, and deployed in Boston Harbor that measure Chl a and CDOM fluorescence, optical backscatter, salinity, temperature, and meteorological parameters. We are initially using summer and fall of 2015 to develop atmospheric corrections for conditions in Boston Harbor and develop algorithms for Landsat 8 data to estimate in water photic depth, TSS, Chl a, Kd_490, and CDOM. We will report on initial buoy and cruise data and show 2015 Landsat-derived distributions of water quality parameters. It is our hope that once algorithms for present Landsat imagery can be developed, historical maps of water quality can be constructed using in water data back to 1991.

  10. Replication and Transcription of Eukaryotic DNA in Esherichia coli

    Science.gov (United States)

    Morrow, John F.; Cohen, Stanley N.; Chang, Annie C. Y.; Boyer, Herbert W.; Goodman, Howard M.; Helling, Robert B.

    1974-01-01

    Fragments of amplified Xenopus laevis DNA, coding for 18S and 28S ribosomal RNA and generated by EcoRI restriction endonuclease, have been linked in vitro to the bacterial plasmid pSC101; and the recombinant molecular species have been introduced into E. coli by transformation. These recombinant plasmids, containing both eukaryotic and prokaryotic DNA, replicate stably in E. coli. RNA isolated from E. coli minicells harboring the plasmids hybridizes to amplified X. laevis rDNA. Images PMID:4600264

  11. Tech Talk for Social Studies Teachers Lest We Forget: Remembering Pearl Harbor.

    Science.gov (United States)

    Green, Tim

    2001-01-01

    Presents an annotated bibliography that provides Web sites about Pearl Harbor (Hawaii). Includes Web sites that cover Pearl Harbor history, a live view of Pearl Harbor, stories from people who remember where they were during the attack, information on the naval station at Pearl Harbor, and a virtual tour of the USS Arizona. (CMK)

  12. The creation of cybrids harboring mitochondrial haplogroups in the Taiwanese population of ethnic Chinese background: an extensive in vitro tool for the study of mitochondrial genomic variations.

    Science.gov (United States)

    Lin, Tsu-Kung; Lin, Hung-Yu; Chen, Shang-Der; Chuang, Yao-Chung; Chuang, Jiin-Haur; Wang, Pei-Wen; Huang, Sheng-Teng; Tiao, Mao-Meng; Chen, Jin-Bor; Liou, Chia-Wei

    2012-01-01

    Mitochondrial DNA (mtDNA) haplogroups may contribute to the development of aging-related diseases. A reliable in vitro cellular system for investigating the physiologic significance of mtDNA haplogroups is essential. This study aims to construct and characterize a series of cybrid cell lines harboring variant mtDNA haplogroups collected from healthy Taiwanese volunteers. Cybrid cells harboring different mtDNA haplogroups like B4a, B4b, B4c, B4d, B5, R, F1a, F2, D4e, D4a, D5b, D5a, E, M8, C, and N9a were prepared. Luminex 1000 and full-length mtDNA sequencing were used to confirm that mtDNA haplogroups of transmitochondrial cybrids were identical to their original donors. Cybrid B4b had a significantly lower oxygen consumption rate and higher mitochondrial membrane potential compared to F1a, B5, D5a, D4a, and N9a but had more susceptibility to H(2)O(2)-induced oxidative stress than cybrid F1a, D4a, and N9a. Cybrid N9a had better oxygen consumption and H(2)O(2)-challenged viability compared to B4b, F1a, B5, D5a, and D4a. A series of cybrid cells harboring the main haplogroups of the Taiwanese population with ethnic Chinese background has been developed in vitro. With this mtDNA haplogroup population, the underlying mechanisms of aging-related diseases may be better understood, and therapeutic interventions can be accelerated.

  13. 33 CFR 207.610 - St. Lawrence River, Cape Vincent Harbor, N.Y.; use, administration, and navigation of the harbor...

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false St. Lawrence River, Cape Vincent Harbor, N.Y.; use, administration, and navigation of the harbor and U.S. breakwater. 207.610 Section 207... NAVIGATION REGULATIONS § 207.610 St. Lawrence River, Cape Vincent Harbor, N.Y.; use, administration, and...

  14. Colorimetric DNAzyme Biosensor for Convenience Detection of Enterotoxin B Harboring Staphylococcus aureus from Food Samples.

    Science.gov (United States)

    Mondal, Bhairab; N, Bhavanashri; Ramlal, Shylaja; Kingston, Joseph

    2018-02-14

    In the present study, a colorimetric DNAzymes biosensor strategy was devised in combination with immunomagnetic separation for rapid and easy detection of enterotoxin B harboring Staphylococcus aureus from food and clinical samples. The method employs immunocapture of S. aureus and amplification of seb gene by DNAzyme complementary sequence integrated forward primer and with specific reverse primer. The DNAzyme sequence integrated dsDNA PCR products when treated with hemin and TMB (3,3',5,5'-tetramethylbenzidine) in the presence of H 2 O 2 produce colorimetric signal. A linear relationship of optical signal with the initial template of seb was obtained which could be monitored by visually or spectrophotrometrically for qualitative and quantitative detection. The limit of detection for the assay was approximately 10 2 CFU/mL of seb gene harboring target. This method is convenient compared to gel based and ELISA systems. Further, spiking studies and analysis on natural samples emphasized the robustness and applicability of developed method. Altogether, the established assay could be a reliable alternative, low-cost, viable detection tool for the routine investigation of seb from food and clinical sources.

  15. Littoral cells and harbor dredging along the California coast

    Science.gov (United States)

    Griggs, Gary B.

    1987-02-01

    Beach compartments or littoral cells form the framework for our understanding of the sources, transport, and sinks of sand in the nearshore zone. In general, along the California coast, beach sand is derived from rivers or clifferosion, moves alongshore under the influence of the prevailing waver conditions, and ultimately is lost either to a submarine canyon or a dune field. Marinas or harbors built either between or at the upcoast ends of beach compartments have been relatively maintenance-free, because of a lack of significant littoral drift at these locations. On the other hand, those harbors built in the middle reaches or at the downcoast ends of littoral cells have had expensive annual dredging problems, because of the interruption of large volumes of littoral drift. Although engineers have labored for years on various breakwater, jetty, or entrance channel configurations, the actual design utilized is of secondary importance. The critical factors are harbor location within a littoral cell and annual litoral drift volume.

  16. Respiratory properties of blood in the harbor porpoise, Phocoena phocoena

    DEFF Research Database (Denmark)

    Soegaard, Lisette B; Hansen, Marie N; van Elk, Cornelis

    2012-01-01

    Harbor porpoises are active divers that exchange O(2) and CO(2) with the environment during a fast single breath upon surfacing. We investigated blood O(2)-transporting properties, buffer characteristics, Cl(-) transport via the erythrocyte anion exchanger (AE1), circulating nitric oxide metaboli......Harbor porpoises are active divers that exchange O(2) and CO(2) with the environment during a fast single breath upon surfacing. We investigated blood O(2)-transporting properties, buffer characteristics, Cl(-) transport via the erythrocyte anion exchanger (AE1), circulating nitric oxide....... The true plasma non-bicarbonate buffer value was moderately higher than in terrestrial mammals and increased upon deoxygenation. Plasma bicarbonate was also relatively high, contributing to increase the overall buffer capacity. The apparent Cl(-) permeability of harbor porpoise erythrocytes was similar......, plasma nitrate and hemoglobin-mediated nitrite reduction were elevated compared with mammalian standards, suggesting that increased nitric oxide bioavailability and nitrite-derived nitric oxide could play important roles in diving physiology....

  17. 33 CFR 110.87 - Henderson Harbor, N.Y.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Henderson Harbor, N.Y. 110.87... ANCHORAGE REGULATIONS Special Anchorage Areas § 110.87 Henderson Harbor, N.Y. (a) Area A. The area in the... latitude 43°51′08.8″ N, longitude 76°12′08.9″ W, thence to latitude 43°51′09.0″ N, longitude 76°12′19.0″ W...

  18. Oral keratinocytes support non-replicative infection and transfer of harbored HIV-1 to permissive cells.

    Science.gov (United States)

    Vacharaksa, Anjalee; Asrani, Anil C; Gebhard, Kristin H; Fasching, Claudine E; Giacaman, Rodrigo A; Janoff, Edward N; Ross, Karen F; Herzberg, Mark C

    2008-07-17

    Oral keratinocytes on the mucosal surface are frequently exposed to HIV-1 through contact with infected sexual partners or nursing mothers. To determine the plausibility that oral keratinocytes are primary targets of HIV-1, we tested the hypothesis that HIV-1 infects oral keratinocytes in a restricted manner. To study the fate of HIV-1, immortalized oral keratinocytes (OKF6/TERT-2; TERT-2 cells) were characterized for the fate of HIV-specific RNA and DNA. At 6 h post inoculation with X4 or R5-tropic HIV-1, HIV-1gag RNA was detected maximally within TERT-2 cells. Reverse transcriptase activity in TERT-2 cells was confirmed by VSV-G-mediated infection with HIV-NL4-3Deltaenv-EGFP. AZT inhibited EGFP expression in a dose-dependent manner, suggesting that viral replication can be supported if receptors are bypassed. Within 3 h post inoculation, integrated HIV-1 DNA was detected in TERT-2 cell nuclei and persisted after subculture. Multiply spliced and unspliced HIV-1 mRNAs were not detectable up to 72 h post inoculation, suggesting that HIV replication may abort and that infection is non-productive. Within 48 h post inoculation, however, virus harbored by CD4 negative TERT-2 cells trans infected co-cultured peripheral blood mononuclear cells (PBMCs) or MOLT4 cells (CD4+ CCR5+) by direct cell-to-cell transfer or by releasing low levels of infectious virions. Primary tonsil epithelial cells also trans infected HIV-1 to permissive cells in a donor-specific manner. Oral keratinocytes appear, therefore, to support stable non-replicative integration, while harboring and transmitting infectious X4- or R5-tropic HIV-1 to permissive cells for up to 48 h.

  19. Oral keratinocytes support non-replicative infection and transfer of harbored HIV-1 to permissive cells

    Directory of Open Access Journals (Sweden)

    Giacaman Rodrigo A

    2008-07-01

    Full Text Available Abstract Background Oral keratinocytes on the mucosal surface are frequently exposed to HIV-1 through contact with infected sexual partners or nursing mothers. To determine the plausibility that oral keratinocytes are primary targets of HIV-1, we tested the hypothesis that HIV-1 infects oral keratinocytes in a restricted manner. Results To study the fate of HIV-1, immortalized oral keratinocytes (OKF6/TERT-2; TERT-2 cells were characterized for the fate of HIV-specific RNA and DNA. At 6 h post inoculation with X4 or R5-tropic HIV-1, HIV-1gag RNA was detected maximally within TERT-2 cells. Reverse transcriptase activity in TERT-2 cells was confirmed by VSV-G-mediated infection with HIV-NL4-3Δenv-EGFP. AZT inhibited EGFP expression in a dose-dependent manner, suggesting that viral replication can be supported if receptors are bypassed. Within 3 h post inoculation, integrated HIV-1 DNA was detected in TERT-2 cell nuclei and persisted after subculture. Multiply spliced and unspliced HIV-1 mRNAs were not detectable up to 72 h post inoculation, suggesting that HIV replication may abort and that infection is non-productive. Within 48 h post inoculation, however, virus harbored by CD4 negative TERT-2 cells trans infected co-cultured peripheral blood mononuclear cells (PBMCs or MOLT4 cells (CD4+ CCR5+ by direct cell-to-cell transfer or by releasing low levels of infectious virions. Primary tonsil epithelial cells also trans infected HIV-1 to permissive cells in a donor-specific manner. Conclusion Oral keratinocytes appear, therefore, to support stable non-replicative integration, while harboring and transmitting infectious X4- or R5-tropic HIV-1 to permissive cells for up to 48 h.

  20. Isolation of Shiga toxin-producing Escherichia coli harboring variant Shiga toxin genes from seafood

    Directory of Open Access Journals (Sweden)

    Sreepriya Prakasan

    2018-03-01

    Full Text Available Background and Aim: Shiga toxin-producing Escherichia coli (STEC are important pathogens of global significance. STEC are responsible for numerous food-borne outbreaks worldwide and their presence in food is a potential health hazard. The objective of the present study was to determine the incidence of STEC in fresh seafood in Mumbai, India, and to characterize STEC with respect to their virulence determinants. Materials and Methods: A total of 368 E. coli were isolated from 39 fresh seafood samples (18 finfish and 21 shellfish using culture-based methods. The isolates were screened by polymerase chain reaction (PCR for the genes commonly associated with STEC. The variant Shiga toxin genes were confirmed by Southern blotting and hybridization followed by DNA sequencing. Results: One or more Shiga toxins genes were detected in 61 isolates. Of 39 samples analyzed, 10 (25.64% samples harbored STEC. Other virulence genes, namely, eaeA (coding for an intimin and hlyA (hemolysin A were detected in 43 and 15 seafood isolates, respectively. The variant stx1 genes from 6 isolates were sequenced, five of which were found to be stx1d variants, while one sequence varied considerably from known stx1 sequences. Southern hybridization and DNA sequence analysis suggested putative Shiga toxin variant genes (stx2 in at least 3 other isolates. Conclusion: The results of this study showed the occurrence of STEC in seafood harboring one or more Shiga toxin genes. The detection of STEC by PCR may be hampered due to the presence of variant genes such as the stx1d in STEC. This is the first report of stx1d gene in STEC isolated from Indian seafood.

  1. Fidelity of DNA Replication in Normal and Malignant Human Breast Cells.

    Science.gov (United States)

    1997-08-01

    enzyme) into the multiple cloning site (MCS). This template will not only replicate inside a mammalian cell (utilizing the E-B virus origin), and...Maniatis, T. Commonly used techniques in molecular cloning . In: Molecular cloning : REFERENCES a laboratory manual, 2nd edition. Cold Spring Harbor...A vatit"Y Of DNA synthesis and the typt of DNA replica~tion Products " celular prca including DNA rsplicatlon. DNA repsair. R~NA formed in experiments

  2. Harbor seal vibrissa morphology suppresses vortex-induced vibrations.

    Science.gov (United States)

    Hanke, Wolf; Witte, Matthias; Miersch, Lars; Brede, Martin; Oeffner, Johannes; Michael, Mark; Hanke, Frederike; Leder, Alfred; Dehnhardt, Guido

    2010-08-01

    Harbor seals (Phoca vitulina) often live in dark and turbid waters, where their mystacial vibrissae, or whiskers, play an important role in orientation. Besides detecting and discriminating objects by direct touch, harbor seals use their whiskers to analyze water movements, for example those generated by prey fish or by conspecifics. Even the weak water movements left behind by objects that have passed by earlier can be sensed and followed accurately (hydrodynamic trail following). While scanning the water for these hydrodynamic signals at a swimming speed in the order of meters per second, the seal keeps its long and flexible whiskers in an abducted position, largely perpendicular to the swimming direction. Remarkably, the whiskers of harbor seals possess a specialized undulated surface structure, the function of which was, up to now, unknown. Here, we show that this structure effectively changes the vortex street behind the whiskers and reduces the vibrations that would otherwise be induced by the shedding of vortices from the whiskers (vortex-induced vibrations). Using force measurements, flow measurements and numerical simulations, we find that the dynamic forces on harbor seal whiskers are, by at least an order of magnitude, lower than those on sea lion (Zalophus californianus) whiskers, which do not share the undulated structure. The results are discussed in the light of pinniped sensory biology and potential biomimetic applications.

  3. Integrated approach to assess ecosystem health in harbor areas.

    Science.gov (United States)

    Bebianno, M J; Pereira, C G; Rey, F; Cravo, A; Duarte, D; D'Errico, G; Regoli, F

    2015-05-01

    Harbors are critical environments with strategic economic importance but with potential environmental impact: health assessment criteria are a key issue. An ecosystem health status approach was carried out in Portimão harbor as a case-study. Priority and specific chemical levels in sediments along with their bioavailability in mussels, bioassays and a wide array of biomarkers were integrated in a biomarker index (IBR index) and the overall data in a weight of evidence (WOE) model. Metals, PAHs, PCBs and HCB were not particularly high compared with sediment guidelines and standards for dredging. Bioavailability was evident for Cd, Cu and Zn. Biomarkers proved more sensitive namely changes of antioxidant responses, metallothioneins and vittellogenin-like proteins. IBR index indicated that site 4 was the most impacted area. Assessment of the health status by WOE approach highlighted the importance of integrating sediment chemistry, bioaccumulation, biomarkers and bioassays and revealed that despite some disturbance in the harbor area, there was also an impact of urban effluents from upstream. Environmental quality assessment in harbors. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. 78 FR 63381 - Safety Zones; Hawaiian Island Commercial Harbors, HI

    Science.gov (United States)

    2013-10-24

    ...; Kaumalapau, Lanai; Kahului, Maui and Kawaihae and Hilo on the Island of Hawaii). The purpose of these safety... the piers faces. (9) All waters of Hilo Harbor, Hawaii immediately adjacent to commercial piers 1 and.... SUMMARY: The Coast Guard is establishing nine (9) permanent safety zones encompassing Hawaii's commercial...

  5. 33 CFR 117.181 - Oakland Inner Harbor Tidal Canal.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Oakland Inner Harbor Tidal Canal. 117.181 Section 117.181 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY... Tidal Canal. The draws of the Alameda County highway drawbridges at Park Street, mile 5.2; Fruitvale...

  6. 78 FR 21597 - Marine Mammals: Alaska Harbor Seal Habitats

    Science.gov (United States)

    2013-04-11

    ... seek input as to whether management measures are needed, and if so, what types of measures should be... proposed rulemaking (ANPR) on potential management measures to protect glacially-associated harbor seal... need for regulations; (2) the geographic scope and time horizon of regulations; (3) management options...

  7. Quantitative Measures of Anthropogenic Noise on Harbor Porpoises

    DEFF Research Database (Denmark)

    Wisniewska, Danuta Maria; Teilmann, Jonas; Hermannsen, Line

    2016-01-01

    -animal recordings as proxies for actual exposure. Here, we quantify sound exposure levels recorded with a DTAG-3 tag on a captive harbor porpoise exposed to vessel noise in a controlled acoustic environment. Results show that fl ow noise is limiting onboard noise recordings, whereas no evidence of body shading has...

  8. U.S. Department of Defense - Pearl Harbor Special

    Science.gov (United States)

    Hawaii saw that seminal moment in history, and those that were there vividly remember that Sunday morning this noise," he said in an oral history on the Pearl Harbor Survivors' Association Web site. " seeing was an attack. "It didn't mean anything to us until a large group of planes came near the

  9. Incidence of plasmid-linked antibiotic-heavy metal resistant enterics in water-sediment from agricultural and harbor sites

    Energy Technology Data Exchange (ETDEWEB)

    Mietz, J.A.; Sjorgren, R.E.

    1983-01-01

    This study assesses the impact of antibiotics used in clinical and veterinary practices on the incidence of antibiotic-heavy metal resistant enterics in fresh water and sediment from agricultural and harbor sample sites. A total of 848 bacterial strains of the family Enterobacteriaceae was isolated from agricultural and lake harbor samples. These were examined for anitbiotic-heavy metal resistance. A select smaller number of these isolates were also examined for the presence of plasmids and ability to transfer antibiotic resistance via conjugation or transformation. More than 85% of the 848 isolates from all four sites were resistant to Pb, Zn, and Co while 5.6% to 16% were resistant to Te and 2.4% to 5.7% to Hg. Of the total isolates tested, 87% were resistant to six or more antibiotics and 74% were also simultaneously resistant to Co, Zn, and Pb. Testing the resistance of the water isolates to antibiotics used solely in animal husbandry-veterinary medicine indicated that 55.6% of the agricultural isolates possessed resistance to these antibiotics while only 31.9% of the isolates from harbor water showed resistance to the same antibiotics. Of 41 ampicillin resistant isolates examined, 16 (39%) were capable of transferring antibiotic-heavy resistance markers via conjugation. From this same group, plasmid DNA preparations were made. Of these latter preparations, 67% transformed recipient E. coli cells while 58% possessed discernible, often multiple plasmids when examined by gel electrophoresis.

  10. Underwater noise from three types of offshore wind turbines: estimation of impact zones for harbor porpoises and harbor seals.

    Science.gov (United States)

    Tougaard, Jakob; Henriksen, Oluf Damsgaard; Miller, Lee A

    2009-06-01

    Underwater noise was recorded from three different types of wind turbines in Denmark and Sweden (Middelgrunden, Vindeby, and Bockstigen-Valar) during normal operation. Wind turbine noise was only measurable above ambient noise at frequencies below 500 Hz. Total sound pressure level was in the range 109-127 dB re 1 microPa rms, measured at distances between 14 and 20 m from the foundations. The 1/3-octave noise levels were compared with audiograms of harbor seals and harbor porpoises. Maximum 1/3-octave levels were in the range 106-126 dB re 1 microPa rms. Maximum range of audibility was estimated under two extreme assumptions on transmission loss (3 and 9 dB per doubling of distance, respectively). Audibility was low for harbor porpoises extending 20-70 m from the foundation, whereas audibility for harbor seals ranged from less than 100 m to several kilometers. Behavioral reactions of porpoises to the noise appear unlikely except if they are very close to the foundations. However, behavioral reactions from seals cannot be excluded up to distances of a few hundred meters. It is unlikely that the noise reaches dangerous levels at any distance from the turbines and the noise is considered incapable of masking acoustic communication by seals and porpoises.

  11. Brain transcriptomes of harbor seals demonstrate gene expression patterns of animals undergoing a metabolic disease and a viral infection

    Directory of Open Access Journals (Sweden)

    Stephanie M. Rosales

    2016-12-01

    Full Text Available Diseases of marine mammals can be difficult to diagnose because of their life history and protected status. Stranded marine mammals have been a particularly useful resource to discover and comprehend the diseases that plague these top predators. Additionally, advancements in high-throughput sequencing (HTS has contributed to the discovery of novel pathogens in marine mammals. In this study, we use a combination of HTS and stranded harbor seals (Phoca vitulina to better understand a known and unknown brain disease. To do this, we used transcriptomics to evaluate brain tissues from seven neonatal harbor seals that expired from an unknown cause of death (UCD and compared them to four neonatal harbor seals that had confirmed phocine herpesvirus (PhV-1 infections in the brain. Comparing the two disease states we found that UCD animals showed a significant abundance of fatty acid metabolic transcripts in their brain tissue, thus we speculate that a fatty acid metabolic dysregulation contributed to the death of these animals. Furthermore, we were able to describe the response of four young harbor seals with PhV-1 infections in the brain. PhV-1 infected animals showed a significant ability to mount an innate and adaptive immune response, especially to combat viral infections. Our data also suggests that PhV-1 can hijack host pathways for DNA packaging and exocytosis. This is the first study to use transcriptomics in marine mammals to understand host and viral interactions and assess the death of stranded marine mammals with an unknown disease. Furthermore, we show the value of applying transcriptomics on stranded marine mammals for disease characterization.

  12. Detection of multidrug-resistant Pseudomonas aeruginosa harboring bla GES-1 and bla GES-11 in Recife, Brazil

    Directory of Open Access Journals (Sweden)

    Valdemir Vicente da Silva Júnior

    Full Text Available Abstract INTRODUCTION: Pseudomonas aeruginosa, an important pathogen globally, presents several resistance mechanisms. This study aimed to investigate the presence of bla GES in clinical isolates of Pseudomonas aeruginosa obtained from various clinical specimens from patients admitted to three different hospitals in Recife, Brazil. The Guiana extended spectrum beta-lactamase (GES enzymes are responsible for conferring broad spectrum resistance to beta-lactam drugs, including the carbapenems. METHODS: A total of 100 carbapenem-resistant P. aeruginosa isolates underwent polymerase chain reaction (PCR testing to identify bla GES, bla KPC, bla SPM-1, bla IMP, and bla VIM. Additionally, PCR products positive for bla GES were sequenced. The clonal profiles of these same isolates were then determined by means of enterobacterial repetitive intergenic consensus (ERIC-PCR analysis. RESULTS: PCR analysis revealed that four isolates harbored bla GES; DNA sequencing showed that two harbored bla GES-1 and two bla GES-11. Beta-lactamase genes bla SPM-1, bla IMP, bla VIM, and bla KPC were investigated; none of these genes was detected. Automated susceptibility testing methods (Vitek®2, bioMérieux showed that the bla GES-1-positive isolates were only susceptible to polymyxin B. The patterns obtained with ERIC-PCR methods showed clonal relationship between the two isolates that harbored bla GES-11, whereas different clonal profiles were found in the isolates harboring bla GES-1. CONCLUSIONS: We detected the presence of bacterial isolates positive for two different variants of the enzyme GES in three different hospitals from Recife, Brazil. These enzymes have a great capacity for dissemination among Gram-negative bacteria and confer broad-spectrum resistance to beta-lactam antibiotics and to the carbapenems.

  13. Aerial Survey Counts of Harbor Seals in Coastal Alaska (2003-2011)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This dataset supports efforts to estimate the abundance and trends in population size of Alaska harbor seals. Annual surveys of harbor seal populations are...

  14. Aerial Survey Counts of Harbor Seals in Coastal Alaska (1998-2002)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This dataset supports efforts to estimate the abundance and trends in population size of Alaska harbor seals. Annual surveys of harbor seal populations are...

  15. A Comprehensive Copper Compliance Strategy: Implementing Regulatory Guidance at Pearl Harbor Naval Shipyard & Intermediate Maintenance Facility

    National Research Council Canada - National Science Library

    Earley, P. J; Rosen, G; Rivera-Duarte, I; Gauthier, R. D; Arias-Thode, Y; Thompson, J; Swope, B

    2007-01-01

    Studies were performed to develop a new National Pollution Discharge Elimination Systems Permit for the discharge of effluents from the Pearl Harbor Naval Shipyard and Intermediate Maintenance Facility into Pearl Harbor...

  16. Telemetry data from satellite tags deployed on harbor seals in Cook Inlet, Alaska

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Between 2004 and 2006 we conducted four harbor seal tagging trips in Cook Inlet during the months of October and May. In total, we captured and released 93 harbor...

  17. cDNA, genomic sequence cloning and overexpression of ribosomal ...

    African Journals Online (AJOL)

    PRECIOUS

    2009-11-02

    Nov 2, 2009 ... basic machinery of protein synthesis and regulation, but also in various ... The genomic DNA was isolated from Giant Panda muscle tissue according to the ... for 45 s, 72°C for 2 min in the first cycle and the anneal temperature deceased 0.2°C ..... edition, Cold Spring Harbor aboratory Press. Cold Spring ...

  18. Isolating silkworm genomic DNA without liquid nitrogen suitable for ...

    African Journals Online (AJOL)

    Administrator

    2011-09-21

    Sep 21, 2011 ... *DNA diluted a thousand times to measure OD. silkworms are raised .... using gel extraction kit (Hi Media) and cloned into pGEMT easy vector (Promega) ..... Laboratory Press, Cold Spring Harbor, New York. Sharma J, Yadav ...

  19. DNA probe for strain typing of Cryptococcus neoformans.

    OpenAIRE

    Varma, A; Kwon-Chung, K J

    1992-01-01

    A 7-kb linear plasmid, harbored by a URA5 transformant, hybridized to all the chromosomes of Cryptococcus neoformans separated by contour-clamped homogeneous electric field electrophoresis. Its linear maintenance was determined to have been facilitated by the presence of telomere-like sequences at its free ends. Hybridization of this plasmid to AccI-digested genomic DNAs of 26 C. neoformans strains generated 21 unique DNA fingerprints. The DNA fingerprints of isolates within the same serotype...

  20. A smart ROV solution for ship hull and harbor inspection

    Science.gov (United States)

    Reed, Scott; Wood, Jon; Vazquez, Jose; Mignotte, Pierre-Yves; Privat, Benjamin

    2010-04-01

    Hull and harbor infrastructure inspections are frequently performed manually and involve quite a bit of risk and human and monetary resources. In any kind of threat and resource constrained environment, this involves unacceptable levels of risk and cost. Modern Remotely Operated Vehicles are highly refined machines that provide features and capabilities previously unavailable. Operations once carried out by divers can now be carried out more quickly, efficiently and safely by smart enabled ROVs. ROVs are rapidly deployable and capable of continuous, reliable operations in adverse conditions. They also provide a stable platform on which multiple sensors may be mounted and utilized to meet the harbor inspection problem. Automated Control software provides ROV's and their pilots with the capability to inspect complex, constrained environments such as those found in a harbor region. This application and the user interface allow the ROV to automatically conduct complex maneuvers relative to the area being inspected and relieves the training requirements and work load for the pilot, allowing he or she to focus on the primary task of survey, inspection and looking for possible threats (such as IEDs, Limpet Mines, signs of sabotage, etc). Real-time sensor processing tools can be integrated into the smart ROV solution to assist the operator. Automatic Target Recognition (ATR) algorithms are used to search through the sensor data collected by the ROV in real time. These algorithms provide immediate feedback on possible threats and notify the operator of regions that may require manual verification. Sensor data (sonar or video) is also mosaiced, providing the operator with real-time situational awareness and a coverage map of the hull or seafloor. Detected objects may also be placed in the context of the large scale characteristics of the hull (or bottom or pilings) and localized. Within the complex areas such as the harbor pier pilings and the running gear of the ship, real

  1. 33 CFR 334.1430 - Apra Inner Harbor, Island of Guam; restricted area.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Apra Inner Harbor, Island of Guam... THE ARMY, DEPARTMENT OF DEFENSE DANGER ZONE AND RESTRICTED AREA REGULATIONS § 334.1430 Apra Inner Harbor, Island of Guam; restricted area. (a) The restricted area. The waters within Apra Inner Harbor and...

  2. 33 CFR 165.1402 - Apra Outer Harbor, Guam-regulated navigation area.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Apra Outer Harbor, Guam-regulated....1402 Apra Outer Harbor, Guam—regulated navigation area. (a) The following is a regulated navigation area—The waters of the Pacific Ocean and Apra Outer Harbor enclosed by a line beginning at latitude 13...

  3. 77 FR 45239 - Amendment of Class E Airspace; Bar Harbor, ME

    Science.gov (United States)

    2012-07-31

    ...-1366; Airspace Docket No. 11-ANE-13] Amendment of Class E Airspace; Bar Harbor, ME AGENCY: Federal... area at Bar Harbor, ME, as the Surry Non-Directional Radio Beacon (NDB) has been decommissioned and new Standard Instrument Approach Procedures have been developed at Hancock County-Bar Harbor Airport. This...

  4. 77 FR 27666 - Proposed Amendment of Class E Airspace; Bar Harbor, ME

    Science.gov (United States)

    2012-05-11

    ...-1366; Airspace Docket No. 11-ANE-13] Proposed Amendment of Class E Airspace; Bar Harbor, ME AGENCY... action proposes to amend Class E Airspace at Bar Harbor, ME, as the Surry Non-Directional Radio Beacon... Hancock County-Bar Harbor Airport. This action would enhance the safety and airspace management of...

  5. 33 CFR 162.165 - Buffalo and Rochester Harbors, New York.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Buffalo and Rochester Harbors, New York. 162.165 Section 162.165 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND... and Rochester Harbors, New York. In Buffalo and Rochester Harbors, no vessel may exceed 6 miles per...

  6. 76 FR 32071 - Safety Zone; Conneaut Festival Fireworks, Conneaut Harbor, Conneaut, OH

    Science.gov (United States)

    2011-06-03

    ...-AA00 Safety Zone; Conneaut Festival Fireworks, Conneaut Harbor, Conneaut, OH AGENCY: Coast Guard, DHS... Conneaut Harbor, Conneaut, OH for the Conneaut Festival Fireworks. This zone is intended to restrict vessels from a portion of Conneaut Harbor, Conneaut, OH during the Conneaut Festival Fireworks on July 3...

  7. 78 FR 18479 - Drawbridge Operation Regulations; Inner Harbor Navigation Canal, New Orleans, LA

    Science.gov (United States)

    2013-03-27

    ... Operation Regulations; Inner Harbor Navigation Canal, New Orleans, LA AGENCY: Coast Guard, DHS. ACTION... across the Inner Harbor Navigation Canal, mile 4.6, at New Orleans, Louisiana. This deviation is... Seabrook Highway crossing the Inner Harbor Navigation Canal, mile 4.6, in New Orleans, Louisiana. The...

  8. 76 FR 38153 - California State Nonroad Engine Pollution Control Standards; Commercial Harbor Craft Regulations...

    Science.gov (United States)

    2011-06-29

    ... Standards; Commercial Harbor Craft Regulations; Opportunity for Public Hearing and Comment AGENCY... engines on commercial harbor craft. CARB has requested that EPA issue a new authorization under [email protected] . SUPPLEMENTARY INFORMATION: I. California's Commercial Harbor Craft Regulations In a...

  9. Hydrocarbon pollutants shape bacterial community assembly of harbor sediments

    KAUST Repository

    Barbato, Marta

    2016-02-02

    Petroleum pollution results in co-contamination by different classes of molecules, entailing the occurrence of marine sediments difficult to remediate, as in the case of the Ancona harbor (Mediterranean Sea, Italy). Autochthonous bioaugmentation (ABA), by exploiting the indigenous microbes of the environment to be treated, could represent a successful bioremediation strategy. In this perspective we aimed to i) identify the main drivers of the bacterial communities\\' richness in the sediments, ii) establish enrichment cultures with different hydrocarbon pollutants evaluating their effects on the bacterial communities\\' composition, and iii) obtain a collection of hydrocarbon degrading bacteria potentially exploitable in ABA. The correlation between the selection of different specialized bacterial populations and the type of pollutants was demonstrated by culture-independent analyses, and by establishing a collection of bacteria with different hydrocarbon degradation traits. Our observations indicate that pollution dictates the diversity of sediment bacterial communities and shapes the ABA potential in harbor sediments.

  10. Oral DNA Vaccine in Chickens

    Directory of Open Access Journals (Sweden)

    Seyed Davoud Jazayeri

    2012-01-01

    Full Text Available Attenuated Salmonella has been used as a carrier for DNA vaccine. However, in vitro and in vivo studies on the bacteria following transfection of plasmid DNA were poorly studied. In this paper, eukaryotic expression plasmids encoding avian influenza virus (AIV subtype H5N1 genes, pcDNA3.1/HA, NA, and NP, were transfected into an attenuated Salmonella enteric typhimurium SV4089. In vitro stability of the transfected plasmids into Salmonella were over 90% after 100 generations. The attenuated Salmonella were able to invade MCF-7 (1.2% and MCF-10A (0.5% human breast cancer cells. Newly hatched specific-pathogen-free (SPF chicks were inoculated once by oral gavage with 109 colony-forming unit (CFU of the attenuated Salmonella. No abnormal clinical signs or deaths were recorded after inoculation. Viable bacteria were detected 3 days after inoculation by plating from spleen, liver, and cecum. Fluorescent in situ hybridization (FISH and polymerase chain reaction (PCR were carried out for confirmation. Salmonella was not detected in blood cultures although serum antibody immune responses to Salmonella O antiserum group D1 factor 1, 9, and 12 antigens were observed in all the inoculated chickens after 7 days up to 35 days. Our results showed that live attenuated S. typhimurium SV4089 harboring pcDNA3.1/HA, NA, and NP may provide a unique alternative as a carrier for DNA oral vaccine in chickens.

  11. Buffalo Harbor Study. Preliminary Feasibility Report. Volume I. Main Report.

    Science.gov (United States)

    1983-04-01

    to usually narrow strips of riparian vegetation, which is composed of various trees and shrubs of the Salix genus (willow), sumac, aspen, boxelder...reptiles were found. Species included, leopard frogs, snapping turtles, painted turtle, and garter snakes (SUNY Brockport: 1982). (7) Endangered Species...vessel traffic on the Buffalo River causes interrupted truck service. Firms have also cited snow removal as a problem. The harbor area road service

  12. Army Engineer Divers: First In Port-Au-Prince Harbor

    Science.gov (United States)

    2010-12-01

    to the pile once the concrete was poured. This step was com- pleted in a few minutes for each pile. Last, a prefabricated wooden form was emplaced...September-December 201010 Engineer This prefabricated wooden form was emplaced around a rebar cage at the top of damaged piles to hold concrete until it...the mainland into the harbor. Waste from tugboats and sewage from the mainland compounded ecological hazards. The only alternative for the Army and

  13. Environmental Assessment for Boston Harbor Maintenance Dredging, Boston, Massachusetts.

    Science.gov (United States)

    1981-12-01

    Harbor was developed by Jerome et al (1966), Chesmore et al (1971) and Iwanowicz et al. (1973). The studies on the Lower Mystic River were concentrated in... Iwanowicz et al. (1973) and this data should be referred to for detailed information. Waters overlying the shellfish beds are contaminated by wastes...DMRP Technical Report DS-78-5, Environmental Laboratory, U.S. Army Engineer Waterways Experiment Station, Vicksburg, Mississippi. Iwanowicz , H. R., R D

  14. An Evaluation of the Acquisition Streamlining Methods at the Fleet and Industrial Supply Center Pearl Harbor Hawaii

    National Research Council Canada - National Science Library

    Henry, Mark

    1999-01-01

    ...) Pearl Harbor's implementation of acquisition streamlining initiatives and recommends viable methods of streamlining the acquisition process at FISC Pearl Harbor and other Naval Supply Systems Command...

  15. Towards an ethics safe harbor for global biomedical research

    Science.gov (United States)

    Dove, Edward S.; Knoppers, Bartha M.; Zawati, Ma'n H.

    2014-01-01

    Although increasingly global, data-driven genomics and other ‘omics’-focused research hold great promise for health discoveries, current research ethics review systems around the world challenge potential improvements in human health from such research. To overcome this challenge, we propose a ‘Safe Harbor Framework for International Ethics Equivalency’ that facilitates the harmonization of ethics review of specific types of data-driven international research projects while respecting globally transposable research ethics norms and principles. The Safe Harbor would consist in part of an agency supporting an International Federation for Ethics Review (IFER), formed by a voluntary compact among countries, granting agencies, philanthropies, institutions, and healthcare, patient advocacy, and research organizations. IFER would be both a central ethics review body, and also a forum for review and follow-up of policies concerning ethics norms for international research projects. It would be built on five principle elements: (1) registration, (2) compliance review, (3) recognition, (4) monitoring and enforcement, and (5) public participation. The Safe Harbor would create many benefits for researchers, countries, and the general public, and may eventually have application beyond (gen)omics to other areas of biomedical research that increasingly engage in secondary use of data and present only negligible risks. PMID:27774154

  16. Pearl Harbor: lessons for the dam safety community

    Energy Technology Data Exchange (ETDEWEB)

    Martin, T.E. [AMEC Earth and Environmental Ltd., Burnaby, BC (Canada)

    2001-10-01

    Every good dam safety program must be based on surveillance and emergency response planning. The same principles apply to the gathering of information for military intelligence and the planning of defence tactics. Lessons learned from failure have spurred the advancement of dam engineering. Dam safety experts can benefit from the inadequacies encountered by the military community, with the most famous occurring on December 7, 1941 in Pearl Harbor. Both intelligence gathering and contingency response planning failed miserably. The data was not properly disseminated, interpreted, analysed. The proper response to the situation was not initiated. Human error and failure to communicate are the two main reasons that explain the debacle. The inquiries into the tragedy at Pearl Harbor provided valuable lessons, related to individual and organizational failures, which the authors shared in this presentation. The relevance to dam safety was made. All Federal Bureau of Investigation (FBI) agents must read the lessons drawn from Pearl Harbor, as they have responsibility for dam safety. 4 refs.

  17. Modeling DNA

    Science.gov (United States)

    Robertson, Carol

    2016-01-01

    Deoxyribonucleic acid (DNA) is life's most amazing molecule. It carries the genetic instructions that almost every organism needs to develop and reproduce. In the human genome alone, there are some three billion DNA base pairs. The most difficult part of teaching DNA structure, however, may be getting students to visualize something as small as a…

  18. Cladophora (Chlorophyta) spp. Harbor Human Bacterial Pathogens in Nearshore Water of Lake Michigan†

    Science.gov (United States)

    Ishii, Satoshi; Yan, Tao; Shively, Dawn A.; Byappanahalli, Muruleedhara N.; Whitman, Richard L.; Sadowsky, Michael J.

    2006-01-01

    Cladophora glomerata, a macrophytic green alga, is commonly found in the Great Lakes, and significant accumulations occur along shorelines during the summer months. Recently, Cladophora has been shown to harbor high densities of the fecal indicator bacteria Escherichia coli and enterococci. Cladophora may also harbor human pathogens; however, until now, no studies to address this question have been performed. In the present study, we determined whether attached Cladophora, obtained from the Lake Michigan and Burns Ditch (Little Calumet River, Indiana) sides of a breakwater during the summers of 2004 and 2005, harbored the bacterial pathogens Shiga toxin-producing Escherichia coli (STEC), Salmonella, Shigella, and Campylobacter. The presence of potential pathogens and numbers of organisms were determined by using cultural methods and by using conventional PCR, most-probable-number PCR (MPN-PCR), and quantitative PCR (QPCR) performed with genus- and toxin-specific primers and probes. While Shigella and STEC were detected in 100% and 25%, respectively, of the algal samples obtained near Burns Ditch in 2004, the same pathogens were not detected in samples collected in 2005. MPN-PCR and QPCR allowed enumeration of Salmonella in 40 to 80% of the ditch- and lakeside samples, respectively, and the densities were up to 1.6 × 103 cells per g Cladophora. Similarly, these PCR methods allowed enumeration of up to 5.4 × 102 Campylobacter cells/g Cladophora in 60 to 100% of lake- and ditchside samples. The Campylobacter densities were significantly higher (P Cladophora samples than in the ditchside Cladophora samples. DNA fingerprint analyses indicated that genotypically identical Salmonella isolates were associated with geographically and temporally distinct Cladophora samples. However, Campylobacter isolates were genetically diverse. Since animal hosts are thought to be the primary habitat for Campylobacter and Salmonella species, our results suggest that Cladophora is a

  19. Cladophora (Chlorophyta) spp. harbor human bacterial pathogens in nearshore water of Lake Michigan.

    Science.gov (United States)

    Ishii, Satoshi; Yan, Tao; Shively, Dawn A; Byappanahalli, Muruleedhara N; Whitman, Richard L; Sadowsky, Michael J

    2006-07-01

    Cladophora glomerata, a macrophytic green alga, is commonly found in the Great Lakes, and significant accumulations occur along shorelines during the summer months. Recently, Cladophora has been shown to harbor high densities of the fecal indicator bacteria Escherichia coli and enterococci. Cladophora may also harbor human pathogens; however, until now, no studies to address this question have been performed. In the present study, we determined whether attached Cladophora, obtained from the Lake Michigan and Burns Ditch (Little Calumet River, Indiana) sides of a breakwater during the summers of 2004 and 2005, harbored the bacterial pathogens Shiga toxin-producing Escherichia coli (STEC), Salmonella, Shigella, and Campylobacter. The presence of potential pathogens and numbers of organisms were determined by using cultural methods and by using conventional PCR, most-probable-number PCR (MPN-PCR), and quantitative PCR (QPCR) performed with genus- and toxin-specific primers and probes. While Shigella and STEC were detected in 100% and 25%, respectively, of the algal samples obtained near Burns Ditch in 2004, the same pathogens were not detected in samples collected in 2005. MPN-PCR and QPCR allowed enumeration of Salmonella in 40 to 80% of the ditch- and lakeside samples, respectively, and the densities were up to 1.6 x 10(3) cells per g Cladophora. Similarly, these PCR methods allowed enumeration of up to 5.4 x 10(2) Campylobacter cells/g Cladophora in 60 to 100% of lake- and ditchside samples. The Campylobacter densities were significantly higher (P Cladophora samples than in the ditchside Cladophora samples. DNA fingerprint analyses indicated that genotypically identical Salmonella isolates were associated with geographically and temporally distinct Cladophora samples. However, Campylobacter isolates were genetically diverse. Since animal hosts are thought to be the primary habitat for Campylobacter and Salmonella species, our results suggest that Cladophora is a

  20. C-5 Propynyl Modifications Enhance the Mechanical Stability of DNA.

    Science.gov (United States)

    Aschenbrenner, Daniela; Baumann, Fabian; Milles, Lukas F; Pippig, Diana A; Gaub, Hermann E

    2015-07-20

    Increased thermal or mechanical stability of DNA duplexes is desired for many applications in nanotechnology or -medicine where DNA is used as a programmable building block. Modifications of pyrimidine bases are known to enhance thermal stability and have the advantage of standard base-pairing and easy integration during chemical DNA synthesis. Through single-molecule force spectroscopy experiments with atomic force microscopy and the molecular force assay we investigated the effect of pyrimidines harboring C-5 propynyl modifications on the mechanical stability of double-stranded DNA. Utilizing these complementary techniques, we show that propynyl bases significantly increase the mechanical stability if the DNA is annealed at high temperature. In contrast, modified DNA complexes formed at room temperature and short incubation times display the same stability as non-modified DNA duplexes. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. From structure to mechanism-understanding initiation of DNA replication.

    Science.gov (United States)

    Riera, Alberto; Barbon, Marta; Noguchi, Yasunori; Reuter, L Maximilian; Schneider, Sarah; Speck, Christian

    2017-06-01

    DNA replication results in the doubling of the genome prior to cell division. This process requires the assembly of 50 or more protein factors into a replication fork. Here, we review recent structural and biochemical insights that start to explain how specific proteins recognize DNA replication origins, load the replicative helicase on DNA, unwind DNA, synthesize new DNA strands, and reassemble chromatin. We focus on the minichromosome maintenance (MCM2-7) proteins, which form the core of the eukaryotic replication fork, as this complex undergoes major structural rearrangements in order to engage with DNA, regulate its DNA-unwinding activity, and maintain genome stability. © 2017 Riera et al.; Published by Cold Spring Harbor Laboratory Press.

  2. Investigating the potential use of environmental DNA (eDNA for genetic monitoring of marine mammals.

    Directory of Open Access Journals (Sweden)

    Andrew D Foote

    Full Text Available The exploitation of non-invasive samples has been widely used in genetic monitoring of terrestrial species. In aquatic ecosystems, non-invasive samples such as feces, shed hair or skin, are less accessible. However, the use of environmental DNA (eDNA has recently been shown to be an effective tool for genetic monitoring of species presence in freshwater ecosystems. Detecting species in the marine environment using eDNA potentially offers a greater challenge due to the greater dilution, amount of mixing and salinity compared with most freshwater ecosystems. To determine the potential use of eDNA for genetic monitoring we used specific primers that amplify short mitochondrial DNA sequences to detect the presence of a marine mammal, the harbor porpoise, Phocoena phocoena, in a controlled environment and in natural marine locations. The reliability of the genetic detections was investigated by comparing with detections of harbor porpoise echolocation clicks by static acoustic monitoring devices. While we were able to consistently genetically detect the target species under controlled conditions, the results from natural locations were less consistent and detection by eDNA was less successful than acoustic detections. However, at one site we detected long-finned pilot whale, Globicephala melas, a species rarely sighted in the Baltic. Therefore, with optimization aimed towards processing larger volumes of seawater this method has the potential to compliment current visual and acoustic methods of species detection of marine mammals.

  3. Effects of Harbor Modification on Crescent City, California's Tsunami Vulnerability

    Science.gov (United States)

    Dengler, Lori; Uslu, Burak

    2011-06-01

    More damaging tsunamis have impacted Crescent City, California in historic times than any other location on the West Coast of the USA. Crescent City's harbor has undergone significant modification since the early 20th century, including construction of several breakwaters, dredging, and a 200 × 300 m2 small boat basin. In 2006, a M w 8.3 earthquake in the Kuril Islands generated a moderate Pacific-wide tsunami. Crescent City recorded the highest amplitudes of any tide gauge in the Pacific and was the only location to experience structural damage. Strong currents damaged docks and boats within the small boat basin, causing more than US 20 million in damage and replacement costs. We examine how modifications to Crescent City's harbor may have affected its vulnerability to moderate tsunamis such as the 2006 event. A bathymetric grid of the basin was constructed based on US Army Corps of Engineers soundings in 1964 and 1965 before the construction of the small boat basin. The method of splitting tsunamis was used to estimate tsunami water heights and current velocities at several locations in the harbor using both the 1964-1965 grid and the 2006 bathymetric grid for the 2006 Kuril event and a similar-sized source along the Sanriku coast of Japan. Model velocity outputs are compared for the two different bathymetries at the tide gauge location and at six additional computational sites in the harbor. The largest difference between the two grids is at the small boat basin entrance, where the 2006 bathymetry produces currents over three times the strength of the currents produced by the 1965 bathymetry. Peak currents from a Sanriku event are comparable to those produced by the 2006 event, and within the boat basin may have been higher. The modifications of the harbor, and in particular the addition of the small boat basin, appear to have contributed to the high current velocities and resulting damage in 2006 and help to explain why the 1933 M w 8.4-8.7 Sanriku tsunami

  4. Grays Harbor and Chehalis River Improvements to Navigation Environmental Studies. Wildlife Studies at Proposed Disposal Sites in Grays Harbor, Washington,

    Science.gov (United States)

    1982-01-01

    sltand. T 𔃼~P i’ W 210 three times VtwCerI November IOC’C -nd ~co l.Etls ~ ec!,!zervc-o betxwe H -gF 12 Th -ind hl rway u- 7Plie Sicuobh. E. Cumin -s 1... stress imposed by dredge dsosal ;ictivities on these species. It is difficult to rredict the effects of establishing a salt marsh in Grays Harbor on

  5. Thymidine kinase 2 (H126N) knockin mice show the essential role of balanced deoxynucleotide pools for mitochondrial DNA maintenance

    OpenAIRE

    Akman, Hasan O.; Dorado, Beatriz; López, Luis C.; García-Cazorla, Ángeles; Vilà, Maya R.; Tanabe, Lauren M.; Dauer, William T.; Bonilla, Eduardo; Tanji, Kurenai; Hirano, Michio

    2008-01-01

    Mitochondrial DNA (mtDNA) depletion syndrome (MDS), an autosomal recessive condition, is characterized by variable organ involvement with decreased mtDNA copy number and activities of respiratory chain enzymes in affected tissues. MtDNA depletion has been associated with mutations in nine autosomal genes, including thymidine kinase (TK2), which encodes a ubiquitous mitochondrial protein. To study the pathogenesis of TK2-deficiency, we generated mice harboring an H126N Tk2 mutation. Homozygous...

  6. Caffeine in Boston Harbor past and present, assessing its utility as a tracer of wastewater contamination in an urban estuary

    Science.gov (United States)

    Sites throughout Boston Harbor were analyzed for caffeine to assess its utility as a tracer in identifying sources of sanitary wastewater. Caffeine ranged from 15 ng/L in the outer harbor to a high of 185 ng/L in the inner harbor. Inner harbor concentrations were a result of comb...

  7. Heat from harbor to city; Warmte van haven naar stad

    Energy Technology Data Exchange (ETDEWEB)

    Roggen, M. (ed.)

    2004-09-01

    The Rotterdam harbor area is perfect for an industrial heat distribution network. Numerous major heat producers and many potential consumers of all sizes group together in this industrial area. The new Heat Company ('Warmtebedrijf') is making a detailed business plan to build a heat distribution system. [Dutch] Als er een regio is waar een industrieel warmtenet voor de hand ligt, is het het Rotterdamse havengebied wel. Tal van grote warmteproducenten en een woud aan kleinere en grotere afnemers zijn praktisch buren. Om handen en voeten te geven aan dit op papier mooie idee, stelt het kersverse Warmtebedrijf io een gedetailleerd businessplan op.

  8. DNA Camouflage

    Science.gov (United States)

    2016-01-08

    1 DNA Camouflage Supplementary Information Bijan Zakeri1,2*, Timothy K. Lu1,2*, Peter A. Carr2,3* 1Department of Electrical Engineering and...ll.mit.edu). Distribution A: Public Release   2 Supplementary Figure 1 DNA camouflage with the 2-state device. (a) In the presence of Cre, DSD-2[α...10 1 + Cre 1 500 1,000 length (bp) chromatogram alignment template − Cre   4 Supplementary Figure 3 DNA camouflage with a switchable

  9. Hydraulic modeling of stream channels and structures in Harbor and Crow Hollow Brooks, Meriden, Connecticut

    Science.gov (United States)

    Weiss, Lawrence A.; Sears, Michael P.; Cervione, Michael A.

    1994-01-01

    Effects of urbanization have increased the frequency and size of floods along certain reaches of Harbor Brook and Crow Hollow Brook in Meriden, Conn. A floodprofile-modeling study was conducted to model the effects of selected channel and structural modifications on flood elevations and inundated areas. The study covered the reach of Harbor Brook downstream from Interstate 691 and the reach of Crow Hollow Brook downstream from Johnson Avenue. Proposed modifications, which include changes to bank heights, channel geometry, structural geometry, and streambed armoring on Harbor Brook and changes to bank heights on Crow Hollow Brook, significantly lower flood elevations. Results of the modeling indicate a significant reduction of flood elevations for the 10-year, 25-year, 35-year, 50-year, and 100-year flood frequencies using proposed modifications to (1 ) bank heights between Harbor Brook Towers and Interstate 691 on Harbor Brook, and between Centennial Avenue and Johnson Avenue on Crow Hollow Brook; (2) channel geometry between Coe Avenue and Interstate 69 1 on Harbor Brook; (3) bridge and culvert opening geometry between Harbor Brook Towers and Interstate 691 on Harbor Brook; and (4) channel streambed armoring between Harbor Brook Towers and Interstate 691 on Harbor Brook. The proposed modifications were developed without consideration of cost-benefit ratios.

  10. Dose-response relationships in gene expression profiles in a harbor seal B lymphoma cell line exposed to 17α-ethinyl estradiol

    Directory of Open Access Journals (Sweden)

    Christine Kleinert

    2017-05-01

    Full Text Available The determination of changes in gene expression profiles with xenobiotic dose will allow identifying biomarkers and modes of toxicant action. The harbor seal (Phoca vitulina 11B7501 B lymphoma cell line was exposed to 1, 10, 100, 1000, 10,000, or 25,000 μg/L 17α-ethinyl estradiol (EE2, the active compound of the contraceptive pill for 24 h. Following exposure, RNA was extracted and transformed into cDNA. Transcript expression in exposed vs. control lymphocytes was analyzed via RT-qPCR to identify genes with altered expression. Our analysis indicates that gene expression for all but the reference gene varied with dose, suggesting that different doses induce distinct physiological responses. These findings demonstrate that RT-qPCR could be used to identify immunotoxicity and relative dose in harbor seal leukocytes.

  11. Bluff evolution along coastal drumlins: Boston Harbor Islands, Massachusetts

    Science.gov (United States)

    Himmelstoss, E.A.; FitzGerald, D.M.; Rosen, P.S.; Allen, J.R.

    2006-01-01

    A series of partially drowned drumlins forms the backbone of the inner islands within Boston Harbor. The shoreline of these rounded glacial deposits is composed of actively retreating bluffs formed by continual wave attack. Comparisons of bluffs reveal variability in their height and lateral extent, as well as in the dominant mechanism causing their retreat. Two processes are responsible for bluff erosion and yield distinct bluff morphologies: (1) wave attack undercuts the bluff and causes episodic slumping, yielding planar bluff slopes, and (2) subaerial processes such as rainfall create irregular slopes characterized by rills and gullies. We propose a model of drumlin bluff evolution that is based on processes of erosion and physical characteristics such as bluff height, slope morphology, and the orientation of the bluff with respect to the long axis of the drumlin and its topographic crest. The four phases of drumlin bluff evolution consist of (1) initial formation of bluff, with retreat dominated by wave notching and slumping processes; (2) rill and gully development as bluff heights exceed 10 m and slumped sediment at bluff base inhibits wave attack; (3) return of wave notching and slumping as bluff heights decrease; and (4) final development of boulder retreat lag as last remnants of drumlin are eroded by wave action. These phases capture the important physical processes of drumlin evolution in Boston Harbor and could apply to other eroding coastal drumlin deposits.

  12. New world bats harbor diverse influenza A viruses.

    Directory of Open Access Journals (Sweden)

    Suxiang Tong

    Full Text Available Aquatic birds harbor diverse influenza A viruses and are a major viral reservoir in nature. The recent discovery of influenza viruses of a new H17N10 subtype in Central American fruit bats suggests that other New World species may similarly carry divergent influenza viruses. Using consensus degenerate RT-PCR, we identified a novel influenza A virus, designated as H18N11, in a flat-faced fruit bat (Artibeus planirostris from Peru. Serologic studies with the recombinant H18 protein indicated that several Peruvian bat species were infected by this virus. Phylogenetic analyses demonstrate that, in some gene segments, New World bats harbor more influenza virus genetic diversity than all other mammalian and avian species combined, indicative of a long-standing host-virus association. Structural and functional analyses of the hemagglutinin and neuraminidase indicate that sialic acid is not a ligand for virus attachment nor a substrate for release, suggesting a unique mode of influenza A virus attachment and activation of membrane fusion for entry into host cells. Taken together, these findings indicate that bats constitute a potentially important and likely ancient reservoir for a diverse pool of influenza viruses.

  13. Grace Under Fire: The Army Nurses of Pearl Harbor, 1941.

    Science.gov (United States)

    Milbrath, Gwyneth R

    2016-01-01

    Much has been written about the military events of December 7, 1941; however, little has been documented about the nurses' work and experience at Pearl Harbor, Hawaii. The aerial assault on Pearl Harbor was the first time in US history that Army nurses had been on the front line of battle. Nurses quickly triaged and stabilized those who could be saved, and provided compassion and comfort to those who were dying, in an environment where the nurses were unsure of their own survival. Traditional historical methods and a social history framework were used in this investigation. Primary sources included oral histories from the US Army Medical Department Center of History and Heritage and the State of Hawaii's website, Hawaii Aviation. Secondary sources included published books, newspaper articles, military websites, and history texts. Due to the limited bed capacity, Hickam Field Hospital converted to an evacuation hospital. Nurses, physicians, and medical corpsman triaged, stabilized, and transported those likely to survive, while staging the dead behind the building. The emergency room at Tripler Hospital was quickly flooded with patients from the battlefield, but the staff was able to sort patients appropriately to the wards, to the operating room, or provide comfort care as they died. At Schofield Hospital, collaboration between tireless doctors, nurses, and corpsmen was key to providing life-saving surgery and care.

  14. The historical significance of anaesthesia events at Pearl Harbor.

    Science.gov (United States)

    Crowhurst, Ja

    2014-07-01

    Up to the end of World War II, less than 10% of the general anaesthetics administered was with intravenous barbiturates. The remaining 90% of anaesthetics given in the USA were with diethyl ether. In the United Kingdom and elsewhere, chloroform was also popular. Diethyl ether administration was a relatively safe and simple procedure, often delegated to nurses or junior doctors with little or no specific training in anaesthesia. During the Japanese attack on the US bases at Pearl Harbor, with reduced stocks of diethyl ether available, intravenous Sodium Pentothal(®), a most 'sophisticated and complex' drug, was used with devastating effects in many of those hypovolaemic, anaemic and septic patients. The hazards of spinal anaesthesia too were realised very quickly. These effects were compounded by the dearth of trained anaesthetists. This paper presents the significance of the anaesthesia tragedies at Pearl Harbor, and the discovery in the next few years of many other superior drugs that caused medical and other health professionals to realise that anaesthesia needed to be a specialist medical discipline in its own right. Specialist recognition, aided by the foundation of the National Health Service in the UK, the establishment of Faculties of Anaesthesia and appropriate training in pharmacology, physiology and other sciences soon followed. Modern anaesthesiology, as we understand it today, was born and a century or more of ether anaesthesia finally ceased.

  15. Emergence of fatal avian influenza in New England harbor seals

    Science.gov (United States)

    Anthony, S.J.; St. Leger, J. A.; Pugliares, K.; Ip, Hon S.; Chan, J.M.; Carpenter, Z.W.; Navarrete-Macias, I.; Sanchez-Leon, M.; Saliki, J.T.; Pedersen, J.; Karesh, W.; Daszak, P.; Rabadan, R.; Rowles, T.; Lipkin, W.I.

    2012-01-01

    From September to December 2011, 162 New England harbor seals died in an outbreak of pneumonia. Sequence analysis of postmortem samples revealed the presence of an avian H3N8 influenza A virus, similar to a virus circulating in North American waterfowl since at least 2002 but with mutations that indicate recent adaption to mammalian hosts. These include a D701N mutation in the viral PB2 protein, previously reported in highly pathogenic H5N1 avian influenza viruses infecting people. Lectin staining and agglutination assays indicated the presence of the avian-preferred SAα-2,3 and mammalian SAα-2,6 receptors in seal respiratory tract, and the ability of the virus to agglutinate erythrocytes bearing either the SAα-2,3 or the SAα-2,6 receptor. The emergence of this A/harbor seal/Massachusetts/1/2011 virus may herald the appearance of an H3N8 influenza clade with potential for persistence and cross-species transmission.

  16. DNA glue

    DEFF Research Database (Denmark)

    Filichev, Vyacheslav V; Astakhova, Irina V.; Malakhov, Andrei D.

    2008-01-01

    Significant alterations in thermal stability of parallel DNA triplexes and antiparallel duplexes were observed upon changing the attachment of ethynylpyrenes from para to ortho in the structure of phenylmethylglycerol inserted as a bulge into DNA (TINA). Insertions of two ortho-TINAs as a pseudo...

  17. Hyperstretching DNA

    NARCIS (Netherlands)

    Schakenraad, Koen; Biebricher, Andreas S.; Sebregts, Maarten; Ten Bensel, Brian; Peterman, Erwin J.G.; Wuite, Gijs J L; Heller, Iddo; Storm, Cornelis; Van Der Schoot, Paul

    2017-01-01

    The three-dimensional structure of DNA is highly susceptible to changes by mechanical and biochemical cues in vivo and in vitro. In particular, large increases in base pair spacing compared to regular B-DNA are effected by mechanical (over)stretching and by intercalation of compounds that are widely

  18. Polycyclic aromatic hydrocarbons and trace elements bounded to airborne PM10 in the harbor of Volos, Greece: Implications for the impact of harbor activities

    Science.gov (United States)

    Manoli, E.; Chelioti-Chatzidimitriou, A.; Karageorgou, K.; Kouras, A.; Voutsa, D.; Samara, C.; Kampanos, I.

    2017-10-01

    Harbors are often characterized by high levels of air pollutants that are emitted from ship traffic and other harbor activities. In the present study, the concentrations of Polycyclic Aromatic Hydrocarbons (PAHs) and trace elements (As, Cd, Ni, Pb, Cr, Mn, Zn, and Fe) bounded to the inhalable particulate matter PM10 were studied in the harbor of Volos, central Greece, during a 2-year period (2014-2015). Seasonal and daily variations were investigated. Moreover, total carcinogenic and mutagenic activities of PAHs were calculated. The effect of major wind sectors (sea, city, industrial, harbor) was estimated to assess the potential contribution of ship traffic and harbor activities, such as scrap metal handling operations. Results showed that the harbor sector (calm winds ≤ 0.5 m s-1) was associated with the highest concentrations of PM10. The harbor sector was also associated with relatively increased levels of trace elements (As, Fe, Cr, Mn, Ni), however the effect of this sector was lower than the corresponding effect of the industrial wind sector. The sea sector showed only a slight increase in B[a]Py and Σ12PAHs, whereas the highest increasing effect for PAHs and traffic-related elements, such as Pb and Zn, was evidenced for the city sector.

  19. A marked response to icotinib in a patient with large cell neuroendocrine carcinoma harboring an EGFR mutation: A case report.

    Science.gov (United States)

    Wang, Yuehong; Shen, Yi Hong; Ma, Shanni; Zhou, Jianying

    2015-09-01

    The present study reports the case of an 84-year-old male with primary pulmonary large cell neuroendocrine carcinoma (LCNEC) harboring an epidermal growth factor receptor (EGFR) gene mutation that exhibited a long-lasting response to the EGFR-tyrosine kinase inhibitor (EGFR-TKI) icotinib. The patient had an extensive smoking history, a poor performance status, and presented with an irregular mass in the middle lobe of the right lung on computed tomography (CT) and an enlarged left supraclavicular lymph node on physical examination. Right middle lobe bronchial brushing during fiberoptic bronchoscopy identified poorly-differentiated cancer cells. The left supraclavicular lymph node was biopsied and a diagnosis of metastatic LCNEC was determined. Furthermore, an EGFR exon 19 deletion was identified by DNA sequencing. Following diagnosis, icotinib was administered at a dose of 125 mg three times a day. Chest CT scans were performed after 1 month of treatment, which indicated that the tumor was in partial remission. This marked response to icotinib lasted for 8 months. Thus, the present case illustrates the possibility of identifying EGFR mutations in LCNEC and indicates that EGFR-tyrosine kinase inhibitors may be an alternative treatment strategy for patients with LCNEC harboring activating EGFR mutations.

  20. Extraction of Chromosomal DNA from Schizosaccharomyces pombe.

    Science.gov (United States)

    Murray, Johanne M; Watson, Adam T; Carr, Antony M

    2016-05-02

    Extraction of DNA from Schizosaccharomyces pombe cells is required for various uses, including templating polymerase chain reactions (PCRs), Southern blotting, library construction, and high-throughput sequencing. To purify high-quality DNA, the cell wall is removed by digestion with Zymolyase or Lyticase and the resulting spheroplasts lysed using sodium dodecyl sulfate (SDS). Cell debris, SDS, and SDS-protein complexes are subsequently precipitated by the addition of potassium acetate and removed by centrifugation. Finally, DNA is precipitated using isopropanol. At this stage, purity is usually sufficient for PCR. However, for more sensitive procedures, such as restriction enzyme digestion, additional purification steps, including proteinase K digestion and phenol-chloroform extraction, are recommended. All of these steps are described in detail here. © 2016 Cold Spring Harbor Laboratory Press.

  1. Fanconi anemia core complex gene promoters harbor conserved transcription regulatory elements.

    Science.gov (United States)

    Meier, Daniel; Schindler, Detlev

    2011-01-01

    The Fanconi anemia (FA) gene family is a recent addition to the complex network of proteins that respond to and repair certain types of DNA damage in the human genome. Since little is known about the regulation of this novel group of genes at the DNA level, we characterized the promoters of the eight genes (FANCA, B, C, E, F, G, L and M) that compose the FA core complex. The promoters of these genes show the characteristic attributes of housekeeping genes, such as a high GC content and CpG islands, a lack of TATA boxes and a low conservation. The promoters functioned in a monodirectional way and were, in their most active regions, comparable in strength to the SV40 promoter in our reporter plasmids. They were also marked by a distinctive transcriptional start site (TSS). In the 5' region of each promoter, we identified a region that was able to negatively regulate the promoter activity in HeLa and HEK 293 cells in isolation. The central and 3' regions of the promoter sequences harbor binding sites for several common and rare transcription factors, including STAT, SMAD, E2F, AP1 and YY1, which indicates that there may be cross-connections to several established regulatory pathways. Electrophoretic mobility shift assays and siRNA experiments confirmed the shared regulatory responses between the prominent members of the TGF-β and JAK/STAT pathways and members of the FA core complex. Although the promoters are not well conserved, they share region and sequence specific regulatory motifs and transcription factor binding sites (TBFs), and we identified a bi-partite nature to these promoters. These results support a hypothesis based on the co-evolution of the FA core complex genes that was expanded to include their promoters.

  2. Fanconi anemia core complex gene promoters harbor conserved transcription regulatory elements.

    Directory of Open Access Journals (Sweden)

    Daniel Meier

    Full Text Available The Fanconi anemia (FA gene family is a recent addition to the complex network of proteins that respond to and repair certain types of DNA damage in the human genome. Since little is known about the regulation of this novel group of genes at the DNA level, we characterized the promoters of the eight genes (FANCA, B, C, E, F, G, L and M that compose the FA core complex. The promoters of these genes show the characteristic attributes of housekeeping genes, such as a high GC content and CpG islands, a lack of TATA boxes and a low conservation. The promoters functioned in a monodirectional way and were, in their most active regions, comparable in strength to the SV40 promoter in our reporter plasmids. They were also marked by a distinctive transcriptional start site (TSS. In the 5' region of each promoter, we identified a region that was able to negatively regulate the promoter activity in HeLa and HEK 293 cells in isolation. The central and 3' regions of the promoter sequences harbor binding sites for several common and rare transcription factors, including STAT, SMAD, E2F, AP1 and YY1, which indicates that there may be cross-connections to several established regulatory pathways. Electrophoretic mobility shift assays and siRNA experiments confirmed the shared regulatory responses between the prominent members of the TGF-β and JAK/STAT pathways and members of the FA core complex. Although the promoters are not well conserved, they share region and sequence specific regulatory motifs and transcription factor binding sites (TBFs, and we identified a bi-partite nature to these promoters. These results support a hypothesis based on the co-evolution of the FA core complex genes that was expanded to include their promoters.

  3. Influenza A(H10N7) Virus in Dead Harbor Seals, Denmark

    DEFF Research Database (Denmark)

    Krog, Jesper Schak; Hansen, Mette Sif; Holm, Elisabeth

    2015-01-01

    Since April 2014, an outbreak of influenza in harbor seals has been ongoing in northern Europe. In Denmark during June-August, 152 harbor seals on the island of Anholt were found dead from severe pneumonia. We detected influenza A(H10N7) virus in 2 of 4 seals examined.......Since April 2014, an outbreak of influenza in harbor seals has been ongoing in northern Europe. In Denmark during June-August, 152 harbor seals on the island of Anholt were found dead from severe pneumonia. We detected influenza A(H10N7) virus in 2 of 4 seals examined....

  4. DNA probes

    International Nuclear Information System (INIS)

    Castelino, J.

    1992-01-01

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with 32 P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism's genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens

  5. DNA probes

    Energy Technology Data Exchange (ETDEWEB)

    Castelino, J

    1993-12-31

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with {sup 32}P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism`s genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens 10 figs, 2 tabs

  6. Ecological evaluation of proposed dredged material from Richmond Harbor

    Energy Technology Data Exchange (ETDEWEB)

    Pinza, M R; Ward, J A; Mayhew, H L; Word, J Q; Niyogi, D K; Kohn, N P [Battelle/Marine Sciences Lab., Sequim, WA (United States)

    1992-10-01

    During the summer of 1991, Battelle/Marine Sciences Laboratory (MSL) was contracted to conduct sampling and testing of sediments proposed for dredging of Richmond Harbor, California. The MSL collected sediment cores to a depth of [minus]40 ft MLLW ([minus]38 ft + 2 ft overdepth) from 28 (12-in. core) and 30 (4-in. core) stations. The sediment cores were allocated to six composite samples referred to as sediment treatments, which were then subjected to physical, chemical, toxicological, and bioaccumulation testing. Physical and chemical parameters included grain size, total organic carbon (TOC), total volatile solids (TVS), oil and grease, total petroleum hydrocarbons (TPH), polynuclear aromatic hydrocarbons (PAH), chlorinated pesticides, polychlorinated biphenyis (PCBs), priority pollutant metals, and butyltins. The results from the test treatments were compared to results from five reference treatments representative of potential in-bay and offshore disposal sites.

  7. Ecological evaluation of proposed dredged material from Richmond Harbor

    International Nuclear Information System (INIS)

    Pinza, M.R.; Ward, J.A.; Mayhew, H.L.; Word, J.Q.; Niyogi, D.K.; Kohn, N.P.

    1992-10-01

    During the summer of 1991, Battelle/Marine Sciences Laboratory (MSL) was contracted to conduct sampling and testing of sediments proposed for dredging of Richmond Harbor, California. The MSL collected sediment cores to a depth of -40 ft MLLW (-38 ft + 2 ft overdepth) from 28 (12-in. core) and 30 (4-in. core) stations. The sediment cores were allocated to six composite samples referred to as sediment treatments, which were then subjected to physical, chemical, toxicological, and bioaccumulation testing. Physical and chemical parameters included grain size, total organic carbon (TOC), total volatile solids (TVS), oil and grease, total petroleum hydrocarbons (TPH), polynuclear aromatic hydrocarbons (PAH), chlorinated pesticides, polychlorinated biphenyis (PCBs), priority pollutant metals, and butyltins. The results from the test treatments were compared to results from five reference treatments representative of potential in-bay and offshore disposal sites

  8. West Nile Flavivirus Polioencephalomyelitis in a harbor seal (Phoca vitulina).

    Science.gov (United States)

    Del Piero, F; Stremme, D W; Habecker, P L; Cantile, C

    2006-01-01

    A 12-year-old male harbor seal presented with progressive signs of neurologic dysfunction including head tremors, muzzle twitching, clonic spasms, and weakness. Lesions included polioencephalomyelitis with glial nodules, spheroids, neuronophagia, ring hemorrhages, and a few neutrophils. Neurons, fibers, and glial nodules were multifocally colonized with intracytoplasmic West Nile flavivirus antigens that were demonstrated using indirect immunohistochemical analysis. Flavivirus on cultured cells also was isolated and was identified by use of monoclonal antibodies and reverse transcriptase-polymerase chain reaction analysis. Clinical signs of disease and lesion morphology and distribution were similar to those of equine West Nile virus infection. Similar to horses, alpacas, humans, dogs, and reptiles, seals can be dead-end hosts of West Nile virus.

  9. Structural damage monitoring of harbor caissons with interlocking condition

    Energy Technology Data Exchange (ETDEWEB)

    Huynh, Thanh Canh; Lee, So Young; Nauyen, Khac Duy; Kim, Jeong Tae [Pukyong National Univ., Busan (Korea, Republic of)

    2012-12-15

    The objective of this study is to monitor the health status of harbor caissons which have potential foundation damage. To obtain the objective, the following approaches are performed. Firstly, a structural damage monitoring(SDM) method is designed for interlocked multiple caisson structures. The SDM method utilizes the change in modal strain energy to monitor the foundation damage in a target caisson unit. Secondly, a finite element model of a caisson system which consists of three caisson units is established to verify the feasibility of the proposed method. In the finite element simulation, the caisson units are constrained each other by shear key connections. The health status of the caisson system against various levels of foundation damage is monitored by measuring relative modal displacements between the adjacent caissons.

  10. Structural damage monitoring of harbor caissons with interlocking condition

    International Nuclear Information System (INIS)

    Huynh, Thanh Canh; Lee, So Young; Nauyen, Khac Duy; Kim, Jeong Tae

    2012-01-01

    The objective of this study is to monitor the health status of harbor caissons which have potential foundation damage. To obtain the objective, the following approaches are performed. Firstly, a structural damage monitoring(SDM) method is designed for interlocked multiple caisson structures. The SDM method utilizes the change in modal strain energy to monitor the foundation damage in a target caisson unit. Secondly, a finite element model of a caisson system which consists of three caisson units is established to verify the feasibility of the proposed method. In the finite element simulation, the caisson units are constrained each other by shear key connections. The health status of the caisson system against various levels of foundation damage is monitored by measuring relative modal displacements between the adjacent caissons

  11. Jam Formation of Traffic Flow in Harbor Tunnel

    International Nuclear Information System (INIS)

    He Hongdi; Lu Weizhen; Dong Liyun

    2011-01-01

    This paper reports a study concerning occurrence and growth of traffic jam in a harbor tunnel. The single-lane with three sections (downgrade, flat, and upgrade) is taken into account and they are characterized with different velocity limit. At the low density, the traffic current increases linearly with density and saturates at some values of immediately density. As the density increases, the traffic jam appears firstly before the upgrade section and then extends to the downgrade section. Additionally, the relationships of the velocity and headway against position in different densities are obtained from simulation. These results clearly clarify where and when the traffic jam appears. Finally, the critical densities are derived via the theoretical analysis before and after the discontinuous fronts and the theoretical results are consistent with the critical values of simulation results. (interdisciplinary physics and related areas of science and technology)

  12. Geographic, seasonal, and diurnal surface behavior of harbor porpoises

    DEFF Research Database (Denmark)

    Teilmann, Jonas; Christiansen, C.T.; Kjellerup, Sanne

    2013-01-01

    are essential information on the status and management of the species. Thirty-five free-ranging harbor porpoises (Phocoena phocoena) were tracked in the region between the Baltic and the North Sea for 25-349 d using Argos satellite transmitters. No differences were found in surface behavior between geographical...... areas or the size of the animals. Slight differences were found between the two sexes and time of day. Surface time peaked in April, where 6% was spent with the transmitter above surface and 61.5% between 0 and 2 m depth, while the minimum values occurred in February (3.4% and 42.5%, respectively......). The analyses reveal that individual variation among porpoises is the most important factor in explaining variation in surface rates. However, the large number of animals documented in the present study covering a wide range of age and sex groups justifies the use of the seasonal average surface times...

  13. Anthropogenic inputs of dissolved organic matter in New York Harbor

    Science.gov (United States)

    Gardner, G. B.; Chen, R. F.; Olavasen, J.; Peri, F.

    2016-02-01

    The Hudson River flows into the Atlantic Ocean through a highly urbanized region which includes New York City to the east and Newark, New Jersey to the west. As a result, the export of Dissolved Organic Carbon (DOC) from the Hudson to the Atlantic Ocean includes a significant anthropogenic component. A series of high resolution studies of the DOC dynamics of this system were conducted between 2003 and 2010. These included both the Hudson and adjacent large waterways (East River, Newark Bay, Kill Van Kull and Arthur Kill) using coastal research vessels and smaller tributaries (Hackensack, Pasaic and Raritan rivers) using a 25' boat. In both cases measurements were made using towed instrument packages which could be cycled from near surface to near bottom depths with horizontal resolution of approximately 20 to 200 meters depending on depth and deployment strategy. Sensors on the instrument packages included a CTD to provide depth and salinity information and a chromophoric dissolved organic matter(CDOM) fluorometer to measure the fluorescent fraction of the DOC. Discrete samples allowed calibration of the fluorometer and the CDOM data to be related to DOC. The combined data set from these cruises identified multiple scales of source and transport processes for DOC within the Hudson River/New York Harbor region. The Hudson carries a substantial amount of natural DOC from its 230 km inland stretch. Additional sources exist in fringing salt marshes adjacent to the Hackensack and Raritan rivers. However the lower Hudson/New Harbor region receives a large input of DOC from multiple publically owned treatment works (POTW) discharges. The high resolution surveys allowed us to elucidate the distribution of these sources and the manner in which they are rapidly mixed to create the total export. We estimate that anthropogenic sources account for up to 2.5 times the DOC flux contributed by natural processes.

  14. DNA methylation

    DEFF Research Database (Denmark)

    Williams, Kristine; Christensen, Jesper; Helin, Kristian

    2012-01-01

    DNA methylation is involved in key cellular processes, including X-chromosome inactivation, imprinting and transcriptional silencing of specific genes and repetitive elements. DNA methylation patterns are frequently perturbed in human diseases such as imprinting disorders and cancer. The recent...... discovery that the three members of the TET protein family can convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) has provided a potential mechanism leading to DNA demethylation. Moreover, the demonstration that TET2 is frequently mutated in haematopoietic tumours suggests that the TET...... proteins are important regulators of cellular identity. Here, we review the current knowledge regarding the function of the TET proteins, and discuss various mechanisms by which they contribute to transcriptional control. We propose that the TET proteins have an important role in regulating DNA methylation...

  15. DNA data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Raw DNA chromatogram data produced by the ABI 373, 377, 3130 and 3730 automated sequencing machines in ABI format. These are from fish (primarily Sebastes spp.,...

  16. DNA nanotechnology

    Science.gov (United States)

    Seeman, Nadrian C.; Sleiman, Hanadi F.

    2018-01-01

    DNA is the molecule that stores and transmits genetic information in biological systems. The field of DNA nanotechnology takes this molecule out of its biological context and uses its information to assemble structural motifs and then to connect them together. This field has had a remarkable impact on nanoscience and nanotechnology, and has been revolutionary in our ability to control molecular self-assembly. In this Review, we summarize the approaches used to assemble DNA nanostructures and examine their emerging applications in areas such as biophysics, diagnostics, nanoparticle and protein assembly, biomolecule structure determination, drug delivery and synthetic biology. The introduction of orthogonal interactions into DNA nanostructures is discussed, and finally, a perspective on the future directions of this field is presented.

  17. DNA expressions - A formal notation for DNA

    NARCIS (Netherlands)

    Vliet, Rudy van

    2015-01-01

    We describe a formal notation for DNA molecules that may contain nicks and gaps. The resulting DNA expressions denote formal DNA molecules. Different DNA expressions may denote the same molecule. Such DNA expressions are called equivalent. We examine which DNA expressions are minimal, which

  18. Thymidine Kinase 2 Deficiency-Induced mtDNA Depletion in Mouse Liver Leads to Defect beta-Oxidation

    OpenAIRE

    Zhou, Xiaoshan; Kannisto, Kristina; Curbo, Sophie; von Dobeln, Ulrika; Hultenby, Kjell; Isetun, Sindra; Gåfvels, Mats; Karlsson, Anna

    2013-01-01

    Thymidine kinase 2 (TK2) deficiency in humans causes mitochondrial DNA (mtDNA) depletion syndrome. To study the molecular mechanisms underlying the disease and search for treatment options, we previously generated and described a TK2 deficient mouse strain (TK2(-/-)) that progressively loses its mtDNA. The TK2(-/-) mouse model displays symptoms similar to humans harboring TK2 deficient infantile fatal encephalomyopathy. Here, we have studied the TK2(-/-) mouse model to clarify the pathologica...

  19. The hearing threshold of a harbor porpoise (Phocoena phocoena) for impulsive sounds (L)

    NARCIS (Netherlands)

    Kastelein, R.A.; Gransier, R.; Hoek, L.; Jong, C.A.F. de

    2012-01-01

    The distance at which harbor porpoises can hear underwater detonation sounds is unknown, but depends, among other factors, on the hearing threshold of the species for impulsive sounds. Therefore, the underwater hearing threshold of a young harbor porpoise for an impulsive sound, designed to mimic a

  20. 76 FR 38302 - Safety Zone; Cape Charles Fireworks, Cape Charles Harbor, Cape Charles, VA

    Science.gov (United States)

    2011-06-30

    ... the Town of Cape Charles will sponsor a fireworks display on the shoreline of the navigable waters of...-AA00 Safety Zone; Cape Charles Fireworks, Cape Charles Harbor, Cape Charles, VA AGENCY: Coast Guard... navigable waters of Cape Charles City Harbor in Cape Charles, VA in support of the Fourth of July Fireworks...

  1. 77 FR 29929 - Safety Zone; Town of Cape Charles Fireworks, Cape Charles Harbor, Cape Charles, VA

    Science.gov (United States)

    2012-05-21

    ... section of this notice. Basis and Purpose On July 4, 2012 the Town of Cape Charles will sponsor a...-AA00 Safety Zone; Town of Cape Charles Fireworks, Cape Charles Harbor, Cape Charles, VA AGENCY: Coast... temporary safety zone on the waters of Cape Charles City Harbor in Cape Charles, VA in support of the Fourth...

  2. 76 FR 71598 - Pearl Harbor National Wildlife Refuge, Honolulu County, HI; Final Comprehensive Conservation Plan...

    Science.gov (United States)

    2011-11-18

    ...] Pearl Harbor National Wildlife Refuge, Honolulu County, HI; Final Comprehensive Conservation Plan and.../docs/HI-PI/docsjcpearl.htm . Email: [email protected] . Include ``Pearl Harbor final CCP'' in...`iwa, HI 96712. FOR FURTHER INFORMATION CONTACT: David Ellis, Project Leader, (808) 637-6330...

  3. 33 CFR 110.129a - Apra Harbor, Guam. (Datum: WGS 84)

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Apra Harbor, Guam. (Datum: WGS 84) 110.129a Section 110.129a Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.129a Apra Harbor, Guam. (Datum: WGS 84) (a...

  4. 33 CFR 80.1490 - Apra Harbor, U.S. Territory of Guam.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Apra Harbor, U.S. Territory of Guam. 80.1490 Section 80.1490 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1490 Apra Harbor, U...

  5. 76 FR 34865 - Safety Zone; Rochester Harbor Festival, Genesee River, Rochester, NY

    Science.gov (United States)

    2011-06-15

    ...-AA00 Safety Zone; Rochester Harbor Festival, Genesee River, Rochester, NY AGENCY: Coast Guard, DHS. ACTION: Temporary final rule. SUMMARY: The Coast Guard is establishing a temporary safety zone on the Genesee River, Rochester, NY for the Rochester Harbor Festival fireworks. This zone is intended to...

  6. 33 CFR 110.31 - Hull Bay and Allerton Harbor at Hull, Mass.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Hull Bay and Allerton Harbor at Hull, Mass. 110.31 Section 110.31 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.31 Hull Bay and Allerton Harbor at...

  7. 76 FR 81904 - Solicitation of New Safe Harbors and Special Fraud Alerts

    Science.gov (United States)

    2011-12-29

    ... Medicaid Patient and Program Protection Act of 1987, Public Law 100-93 Sec. 14, the Act, Sec. 1128B(b), 42...-called ``safe harbor'' provisions, specifying various payment and business practices that, although... basis for administrative sanctions. OIG safe harbor provisions have been developed ``to limit the reach...

  8. 33 CFR 117.753 - Ship Channel, Great Egg Harbor Bay.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Ship Channel, Great Egg Harbor Bay. 117.753 Section 117.753 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements New Jersey § 117.753 Ship Channel, Great Egg Harbor Bay. The draw of the S52 (Ship...

  9. 33 CFR 117.458 - Inner Harbor Navigation Canal, New Orleans.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Inner Harbor Navigation Canal, New Orleans. 117.458 Section 117.458 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF... Harbor Navigation Canal, New Orleans. (a) The draws of the SR 46 (St. Claude Avenue) bridge, mile 0.5...

  10. 77 FR 46285 - Drawbridge Operation Regulation; Inner Harbor Navigational Canal, New Orleans, LA

    Science.gov (United States)

    2012-08-03

    ... Operation Regulation; Inner Harbor Navigational Canal, New Orleans, LA AGENCY: Coast Guard, DHS. ACTION... Navigational Canal, mile 3.1, at New Orleans, LA. The deviation is necessary to replace the wire rope lifting... of the US 90 (Danzinger) Bridge across the Inner Harbor Navigational Canal, mile 3.1, at New Orleans...

  11. 75 FR 4693 - Drawbridge Operation Regulation; Inner Harbor Navigational Canal, New Orleans, LA

    Science.gov (United States)

    2010-01-29

    ... Operation Regulation; Inner Harbor Navigational Canal, New Orleans, LA AGENCY: Coast Guard, DHS. ACTION... C. Simon) Bascule Bridge across the Inner Harbor Navigational Canal, mile 4.6, at New Orleans, LA... Ochsner Ironman 70.3 New Orleans event. This deviation allows the bridge to remain closed during the event...

  12. Frequency Domain Response at Pacific Coast Harbors to Major Tsunamis of 2005-2011

    Science.gov (United States)

    Xing, Xiuying; Kou, Zhiqing; Huang, Ziyi; Lee, Jiin-Jen

    2013-06-01

    Tsunamis waves caused by submarine earthquake or landslide might contain large wave energy, which could cause significant human loss and property damage locally as well as in distant region. The response of three harbors located at the Pacific coast (i.e. Crescent City Harbor, Los Angeles/Long Beach Port, and San Diego Harbor) to six well-known tsunamis events generated (both near-field and far-field) between 2005 and 2011 are examined and simulated using a hybrid finite element numerical model in frequency domain. The model incorporated the effects of wave refraction, wave diffraction, partial wave reflection from boundaries, entrance and bottom energy dissipation. It can be applied to harbor regions with arbitrary shapes and variable water depth. The computed resonant periods or modes of oscillation for three harbors are in good agreement with the energy spectral analysis of the time series of water surface elevations recorded at tide gauge stations inside three harbors during the six tsunamis events. The computed wave induced currents based on the present model are also in qualitative agreement with some of the reported eye-witness accounts absence of reliable current data. The simulated results show that each harbor responded differently and significantly amplified certain wave period(s) of incident wave trains according to the shape, topography, characteristic dimensions and water depth of the harbor basins.

  13. 76 FR 37005 - Safety Zone; Fan Pier Yacht Club Fireworks, Boston Harbor, Boston, MA

    Science.gov (United States)

    2011-06-24

    ...-AA00 Safety Zone; Fan Pier Yacht Club Fireworks, Boston Harbor, Boston, MA AGENCY: Coast Guard, DHS... Sector Boston Captain of the Port (COTP) Zone for the Fan Pier Yacht Club Fireworks display. This safety... Safety Zone; Fan Pier Yacht Club Fireworks, Boston Harbor, Boston, Massachusetts. (a) General. A...

  14. 33 CFR 110.27 - Lynn Harbor in Broad Sound, Mass.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Lynn Harbor in Broad Sound, Mass. 110.27 Section 110.27 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.27 Lynn Harbor in Broad Sound, Mass. North of...

  15. Analyzing Approaches to Internet Jurisdiction Based on Model of Harbors and the High Seas

    NARCIS (Netherlands)

    Jiménez, W.G.; Lodder, A.R.

    2015-01-01

    The inherent cross-border nature of the internet has challenged the legal system for over two decades. In this paper we introduce a model in which the internet is approached as if it were the high seas, the harbor of origin, the harbor of destination, or a combination of these. This model is used to

  16. 33 CFR 165.754 - Safety Zone: San Juan Harbor, San Juan, PR.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Safety Zone: San Juan Harbor, San Juan, PR. 165.754 Section 165.754 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND... Zone: San Juan Harbor, San Juan, PR. (a) Regulated area. A moving safety zone is established in the...

  17. Genetic characterization of blaNDM-harboring plasmids in carbapenem-resistant Escherichia coli from Myanmar.

    Directory of Open Access Journals (Sweden)

    Yo Sugawara

    Full Text Available The bacterial enzyme New Delhi metallo-β-lactamase hydrolyzes almost all β-lactam antibiotics, including carbapenems, which are drugs of last resort for severe bacterial infections. The spread of carbapenem-resistant Enterobacteriaceae that carry the New Delhi metallo-β-lactamase gene, blaNDM, poses a serious threat to public health. In this study, we genetically characterized eight carbapenem-resistant Escherichia coli isolates from a tertiary care hospital in Yangon, Myanmar. The eight isolates belonged to five multilocus-sequence types and harbored multiple antimicrobial-resistance genes, resulting in resistance against nearly all of the antimicrobial agents tested, except colistin and fosfomycin. Nine plasmids harboring blaNDM genes were identified from these isolates. Multiple blaNDM genes were found in the distinct Inc-replicon types of the following plasmids: an IncA/C2 plasmid harboring blaNDM-1 (n = 1, IncX3 plasmids harboring blaNDM-4 (n = 2 or blaNDM-7 (n = 1, IncFII plasmids harboring blaNDM-4 (n = 1 or blaNDM-5 (n = 3, and a multireplicon F plasmid harboring blaNDM-5 (n = 1. Comparative analysis highlighted the diversity of the blaNDM-harboring plasmids and their distinct characteristics, which depended on plasmid replicon types. The results indicate circulation of phylogenetically distinct strains of carbapenem-resistant E. coli with various plasmids harboring blaNDM genes in the hospital.

  18. 77 FR 2019 - Security Zone; Passenger Vessel SAFARI EXPLORER Arrival/Departure, Kaunakakai Harbor, Molokai, HI

    Science.gov (United States)

    2012-01-13

    ...-AA87 Security Zone; Passenger Vessel SAFARI EXPLORER Arrival/ Departure, Kaunakakai Harbor, Molokai, HI... vessel SAFARI EXPLORER to its intended berth in the harbor. Entry into the temporary security zone is... operation of the SAFARI EXPLORER into Molokai has been voluntarily suspended by the operating company...

  19. 77 FR 24381 - Security Zone; Passenger Vessel SAFARI EXPLORER Arrival/Departure, Kaunakakai Harbor, Molokai, HI

    Science.gov (United States)

    2012-04-24

    ...-AA87 Security Zone; Passenger Vessel SAFARI EXPLORER Arrival/ Departure, Kaunakakai Harbor, Molokai, HI... channel's entrance during the arrival and departure of the Passenger Vessel Safari Explorer in Kaunakakai... entrance during the arrival and departure of the Passenger Vessel Safari Explorer in Kaunakakai Harbor...

  20. 33 CFR 110.235 - Pacific Ocean (Mamala Bay), Honolulu Harbor, Hawaii (Datum: NAD 83).

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Pacific Ocean (Mamala Bay), Honolulu Harbor, Hawaii (Datum: NAD 83). 110.235 Section 110.235 Navigation and Navigable Waters COAST... Pacific Ocean (Mamala Bay), Honolulu Harbor, Hawaii (Datum: NAD 83). (a) The anchorage grounds—(1...

  1. Environmental space management in the harbor of Amsterdam, Netherlands; Milieuruimtemanagement haven Amsterdam

    Energy Technology Data Exchange (ETDEWEB)

    Klok, L.; Hulskotte, J. [TNO Built Environment and Geosciences, Den Haag (Netherlands); Van Breemen, T. [Haven Amsterdam, Amsterdam (Netherlands)

    2012-02-15

    A new calculation tool will quickly offer the Harbor of Amsterdam insight in the effect of activities in the harbor on the air quality and hence the available environmental space. [Dutch] Een nieuw rekeninstrument geeft Haven Amsterdam snel inzicht in het effect van alle activiteiten in de haven op de luchtkwaliteit en daarmee in de beschikbare milieuruimte.

  2. 75 FR 81556 - Solicitation of New Safe Harbors and Special Fraud Alerts

    Science.gov (United States)

    2010-12-28

    ... statute (section 1128B(b) of the Social Security Act), as well as developing new OIG Special Fraud Alerts... of New Safe Harbors and Special Fraud Alerts AGENCY: Office of Inspector General (OIG), HHS. ACTION... the public on recommendations for developing new or revised safe harbors and Special Fraud Alerts...

  3. 77 FR 76434 - Solicitation of New Safe Harbors and Special Fraud Alerts

    Science.gov (United States)

    2012-12-28

    ... statute (section 1128B(b) of the Social Security Act), as well as developing new OIG Special Fraud Alerts... of New Safe Harbors and Special Fraud Alerts AGENCY: Office of Inspector General (OIG), HHS. ACTION... revised safe harbors and Special Fraud Alerts. Please assist us by referencing the file code OIG-121-N...

  4. 78 FR 78807 - Solicitation of New Safe Harbors and Special Fraud Alerts

    Science.gov (United States)

    2013-12-27

    ... statute (section 1128B(b) of the Social Security Act), as well as developing new OIG Special Fraud Alerts... of New Safe Harbors and Special Fraud Alerts AGENCY: Office of Inspector General (OIG), HHS. ACTION... revised safe harbors and Special Fraud Alerts. Please assist us by referencing the file code OIG-122-N...

  5. 33 CFR 207.600 - Rochester (Charlotte) Harbor, N.Y.; use, administration, and navigation.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Rochester (Charlotte) Harbor, N.Y.; use, administration, and navigation. 207.600 Section 207.600 Navigation and Navigable Waters CORPS OF... (Charlotte) Harbor, N.Y.; use, administration, and navigation. (a)-(b) [Reserved] (c) No vessel shall moor or...

  6. 33 CFR 207.580 - Buffalo Harbor, N.Y.; use, administration, and navigation.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Buffalo Harbor, N.Y.; use, administration, and navigation. 207.580 Section 207.580 Navigation and Navigable Waters CORPS OF ENGINEERS, DEPARTMENT OF THE ARMY, DEPARTMENT OF DEFENSE NAVIGATION REGULATIONS § 207.580 Buffalo Harbor, N.Y.; use...

  7. 78 FR 13479 - Drawbridge Operation Regulation; New Haven Harbor, Quinnipiac and Mill Rivers, CT

    Science.gov (United States)

    2013-02-28

    ...-AA09 Drawbridge Operation Regulation; New Haven Harbor, Quinnipiac and Mill Rivers, CT AGENCY: Coast... regulations that govern the operation of three bridges across the Quinnipiac and Mill Rivers at New Haven...) entitled ``Drawbridge Operation Regulations New Haven Harbor, Quinnipiac and Mill Rivers,'' in the Federal...

  8. Congress Investigates: Pearl Harbor and 9/11 Congressional Hearing Exhibits

    Science.gov (United States)

    Blackerby, Christine

    2011-01-01

    On the morning of December 7, 1941, Japanese bombers staged a surprise attack on U.S. military forces at Pearl Harbor in Hawaii. Sixty years after the attack on Pearl Harbor, the United States was attacked again. On the morning of September 11, 2001, four commercial airplanes hijacked by 19 terrorists killed nearly 3,000 people when they crashed…

  9. Pearl Harbor bombing attack: a contamination legacy revealed in the sedimentary record

    International Nuclear Information System (INIS)

    Ashwood, T.L.; Olsen, C.R.

    1988-01-01

    Sediment cores collected from Middle Loch and West Loch of Pearl Harbor were dated using fallout 137 Cs and excess 210 Pb and analysed for several major elements and trace metals. Results indicate that sediment deposited immediately following the 7 December, 1941, bombing attack on Pearl Harbor contained elevated levels of several trace metals. (author)

  10. Pearl Harbor bombing attack: a contamination legacy revealed in the sedimentary record

    Energy Technology Data Exchange (ETDEWEB)

    Ashwood, T.L.; Olsen, C.R.

    1988-02-01

    Sediment cores collected from Middle Loch and West Loch of Pearl Harbor were dated using fallout /sup 137/Cs and excess /sup 210/Pb and analysed for several major elements and trace metals. Results indicate that sediment deposited immediately following the 7 December, 1941, bombing attack on Pearl Harbor contained elevated levels of several trace metals.

  11. 77 FR 38490 - Safety Zone; Mentor Harbor Yachting Club Fireworks, Lake Erie, Mentor, OH

    Science.gov (United States)

    2012-06-28

    ...-AA00 Safety Zone; Mentor Harbor Yachting Club Fireworks, Lake Erie, Mentor, OH AGENCY: Coast Guard, DHS... Erie, Mentor, OH. This safety zone is intended to restrict vessels from a portion of Lake Erie during the Mentor Harbor Yachting Club fireworks display. This temporary safety zone is necessary to protect...

  12. Are federal sustained yield units equitable? A case study of the Grays Harbor unit.

    Science.gov (United States)

    Con H Schallau; Wilbur R. Maki

    1986-01-01

    The Grays Harbor Federal Sustained Yield Unit (U.S. Department of Agriculture, Forest Service) was established in 1949 to enhance the economic stability of the forest products industry and dependent communities in Grays Harbor County, Washington. Provisions of the unit's charter require that all logs harvested from the Quinault Ranger District of the Olympic...

  13. 78 FR 19632 - Special Local Regulations; St. Thomas Carnival Watersport Activities, Charlotte Amalie Harbor; St...

    Science.gov (United States)

    2013-04-02

    ...-AA08 Special Local Regulations; St. Thomas Carnival Watersport Activities, Charlotte Amalie Harbor; St... proposes to establish a special local regulation on the waters of Charlotte Amalie Harbor in St Thomas, USVI during the St. Thomas Carnival Watersport Activities, a high speed boat race. The event is...

  14. 33 CFR 110.214 - Los Angeles and Long Beach harbors, California.

    Science.gov (United States)

    2010-07-01

    ... Angeles Harbor). A circular area with a radius of 400 yards (approximately 366 meters), centered in... 400 Transportation Corridor. (C) Outer Harbor: The western boundary of Commercial Anchorage B. (2... Thence along a line described as an arc, radius of 460 meters (approximately 1509 feet) centered on 33...

  15. 77 FR 60109 - Takes of Marine Mammals Incidental to Specified Activities; Harbor Activities Related to the...

    Science.gov (United States)

    2012-10-02

    ...; and Northern elephant seals by Level B harassment only. To date, we have issued nine, 1-year... numbers of marine mammals, incidental to conducting Delta Mariner harbor operations for one year. We... California sea lions (Zalophus californianus), Pacific harbor seals (Phoca vitulina), and Northern elephant...

  16. 78 FR 28492 - Special Local Regulation; Low Country Splash, Wando River, Cooper River, and Charleston Harbor...

    Science.gov (United States)

    2013-05-15

    ...-AA08 Special Local Regulation; Low Country Splash, Wando River, Cooper River, and Charleston Harbor... establishing a special local regulation on the waters of the Wando River, Cooper River, and Charleston Harbor... rulemaking (NPRM) entitled, ``Special Local Regulation; Low Country Splash, Wando River, Cooper River, and...

  17. 33 CFR 165.708 - Safety/Security Zone; Charleston Harbor and Cooper River, Charleston, SC.

    Science.gov (United States)

    2010-07-01

    ... Harbor and Cooper River, Charleston, SC. 165.708 Section 165.708 Navigation and Navigable Waters COAST... Guard District § 165.708 Safety/Security Zone; Charleston Harbor and Cooper River, Charleston, SC. (a... Cooper River. All coordinates referenced use datum: NAD 1983. (2) All waters within 100 yards of the...

  18. 33 CFR 110.250 - St. Thomas Harbor, Charlotte Amalie, V.I.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false St. Thomas Harbor, Charlotte... SECURITY ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.250 St. Thomas Harbor, Charlotte Amalie.... Thomas, V.I. of the United States and approaches thereto, including all waters under its jurisdiction, as...

  19. What Is Mitochondrial DNA?

    Science.gov (United States)

    ... DNA What is mitochondrial DNA? What is mitochondrial DNA? Although most DNA is packaged in chromosomes within ... proteins. For more information about mitochondria and mitochondrial DNA: Molecular Expressions, a web site from the Florida ...

  20. The yeast Saccharomyces cerevisiae DNA polymerase IV: possible involvement in double strand break DNA repair.

    Science.gov (United States)

    Leem, S H; Ropp, P A; Sugino, A

    1994-08-11

    We identified and purified a new DNA polymerase (DNA polymerase IV), which is similar to mammalian DNA polymerase beta, from Saccharomyces cerevisiae and suggested that it is encoded by YCR14C (POLX) on chromosome III. Here, we provided a direct evidence that the purified DNA polymerase IV is indeed encoded by POLX. Strains harboring a pol4 deletion mutation exhibit neither mitotic growth defect nor a meiosis defect, suggesting that DNA polymerase IV participates in nonessential functions in DNA metabolism. The deletion strains did not exhibit UV-sensitivity. However, they did show weak sensitivity to MMS-treatment and exhibited a hyper-recombination phenotype when intragenic recombination was measured during meiosis. Furthermore, MAT alpha pol4 delta segregants had a higher frequency of illegitimate mating with a MAT alpha tester strain than that of wild-type cells. These results suggest that DNA polymerase IV participates in a double-strand break repair pathway. A 3.2kb of the POL4 transcript was weakly expressed in mitotically growing cells. During meiosis, a 2.2 kb POL4 transcript was greatly induced, while the 3.2 kb transcript stayed at constant levels. This induction was delayed in a swi4 delta strain during meiosis, while no effect was observed in a swi6 delta strain.

  1. Comparison of Methods of Extracting Salmonella enterica Serovar Enteritidis DNA from Environmental Substrates and Quantification of Organisms by Using a General Internal Procedural Control

    NARCIS (Netherlands)

    Klerks, M.M.; Bruggen, van A.H.C.; Zijlstra, C.; Donnikov, M.; Vos, de R.

    2006-01-01

    This paper compares five commercially available DNA extraction methods with respect to DNA extraction efficiency of Salmonella enterica serovar Enteritidis from soil, manure, and compost and uses an Escherichia coli strain harboring a plasmid expressing green fluorescent protein as a general

  2. Function of Junk: Pericentromeric Satellite DNA in Chromosome Maintenance.

    Science.gov (United States)

    Jagannathan, Madhav; Yamashita, Yukiko M

    2018-04-02

    Satellite DNAs are simple tandem repeats that exist at centromeric and pericentromeric regions on eukaryotic chromosomes. Unlike the centromeric satellite DNA that comprises the vast majority of natural centromeres, function(s) for the much more abundant pericentromeric satellite repeats are poorly understood. In fact, the lack of coding potential allied with rapid divergence of repeat sequences across eukaryotes has led to their dismissal as "junk DNA" or "selfish parasites." Although implicated in various biological processes, a conserved function for pericentromeric satellite DNA remains unidentified. We have addressed the role of satellite DNA through studying chromocenters, a cytological aggregation of pericentromeric satellite DNA from multiple chromosomes into DNA-dense nuclear foci. We have shown that multivalent satellite DNA-binding proteins cross-link pericentromeric satellite DNA on chromosomes into chromocenters. Disruption of chromocenters results in the formation of micronuclei, which arise by budding off the nucleus during interphase. We propose a model that satellite DNAs are critical chromosome elements that are recognized by satellite DNA-binding proteins and incorporated into chromocenters. We suggest that chromocenters function to preserve the entire chromosomal complement in a single nucleus, a fundamental and unquestioned feature of eukaryotic genomes. We speculate that the rapid divergence of satellite DNA sequences between closely related species results in discordant chromocenter function and may underlie speciation and hybrid incompatibility. © 2017 Jagannathan and Yamashita; Published by Cold Spring Harbor Laboratory Press.

  3. A Qualitative and Quantitative Assay to Study DNA/Drug Interaction ...

    African Journals Online (AJOL)

    Purpose: To explore the use of restriction inhibition assay (RIA) to study the binding specificity of some anticancer drugs. Methods: A 448 bp DNA fragment derived from pBCKS+ plasmid (harboring the polylinker region with multiple restriction endonuclease sites) was used as a template for sequence selective inhibition of ...

  4. Biochemical characterization of cells transformed via transfection by feline sarcoma virus proviral DNA.

    OpenAIRE

    Rosenberg, Z F; Sahagan, B G; Snyder, H W; Worley, M B; Essex, M; Haseltine, W A

    1981-01-01

    Murine fibroblasts transformed by transfection with DNA from mink cells infected with the Snyder-Theilen strain of feline sarcoma virus and subgroup B feline leukemia virus were analyzed for the presence of integrated proviral DNA and the expression of feline leukemia virus- and feline sarcoma virus-specific proteins. The transformed murine cells harbored at least one intact feline sarcoma virus provirus, but did not contain feline leukemia virus provirus. The transformed murine cells express...

  5. Critical threshold levels of DNA methyltransferase 1 are required to maintain DNA methylation across the genome in human cancer cells.

    Science.gov (United States)

    Cai, Yi; Tsai, Hsing-Chen; Yen, Ray-Whay Chiu; Zhang, Yang W; Kong, Xiangqian; Wang, Wei; Xia, Limin; Baylin, Stephen B

    2017-04-01

    Reversing DNA methylation abnormalities and associated gene silencing, through inhibiting DNA methyltransferases (DNMTs) is an important potential cancer therapy paradigm. Maximizing this potential requires defining precisely how these enzymes maintain genome-wide, cancer-specific DNA methylation. To date, there is incomplete understanding of precisely how the three DNMTs, 1, 3A, and 3B, interact for maintaining DNA methylation abnormalities in cancer. By combining genetic and shRNA depletion strategies, we define not only a dominant role for DNA methyltransferase 1 (DNMT1) but also distinct roles of 3A and 3B in genome-wide DNA methylation maintenance. Lowering DNMT1 below a threshold level is required for maximal loss of DNA methylation at all genomic regions, including gene body and enhancer regions, and for maximally reversing abnormal promoter DNA hypermethylation and associated gene silencing to reexpress key genes. It is difficult to reach this threshold with patient-tolerable doses of current DNMT inhibitors (DNMTIs). We show that new approaches, like decreasing the DNMT targeting protein, UHRF1, can augment the DNA demethylation capacities of existing DNA methylation inhibitors for fully realizing their therapeutic potential. © 2017 Cai et al.; Published by Cold Spring Harbor Laboratory Press.

  6. Strategies for Overcoming Resistance in Tumours Harboring BRAF Mutations

    Directory of Open Access Journals (Sweden)

    Nourah Mohammad Obaid

    2017-03-01

    Full Text Available The development of resistance to previously effective treatments has been a challenge for health care providers and a fear for patients undergoing cancer therapy. This is an unfortunately frequent occurrence for patients undergoing targeted therapy for tumours harboring the activating V600E mutation of the BRAF gene. Since the initial identification of the BRAF mutation in 2002, a series of small molecular inhibitors that target the BRAFV600E have been developed, but intrinsic and acquired resistance to these drugs has presented an ongoing challenge. More recently, improvements in therapy have been achieved by combining the use of BRAF inhibitors with other drugs, such as inhibitors of the downstream effector mitogen activated protein kinase (MAPK/extracellular-signal regulated kinase (ERK kinase (MEK. Despite improved success in response rates and in delaying resistance using combination therapy, ultimately, the acquisition of resistance remains a concern. Recent research articles have shed light on some of the underlying mechanisms of this resistance and have proposed numerous strategies that might be employed to overcome or avoid resistance to targeted therapies. This review will explore some of the resistance mechanisms, compare what is known in melanoma cancer to colorectal cancer, and discuss strategies under development to manage the development of resistance.

  7. Evaluation of older bay mud sediment from Richmond Harbor, California

    Energy Technology Data Exchange (ETDEWEB)

    Pinza, M.R.; Mayhew, H.L.; Word, J.Q.

    1996-09-01

    The older, bay mud (OBM) unit predates modem man and could act as a barrier to the downward transport of contaminants from the younger bay mud (YBM) because of its hard-packed consistency. However, its chemical and biological nature have not been well characterized. Battelle/Marine Sciences Laboratory (MSL) conducted three independent studies of OBM sediment in January 1993, January 1994, and October 1994. These studies evaluated potential chemical contamination and biological effects of OBM that could occur as a result of dredging and disposal activities. These evaluations were performed by conducting chemical analysis, solid-phase toxicity tests, suspended- particulate-phase (SPP) toxicity tests, and bioaccumulation tests on the OBM sediment. If the sediment chemistry and toxicity results showed no or minimal contamination and toxicological responses, then either the OBM could be left exposed in Richmond Harbor after dredging the YBM without leaving a source of contamination, or if the project depths necessitate, the OBM would be acceptable for disposal at an appropriate disposal site.

  8. The yeast genome may harbor hypoxia response elements (HRE).

    Science.gov (United States)

    Ferreira, Túlio César; Hertzberg, Libi; Gassmann, Max; Campos, Elida Geralda

    2007-01-01

    The hypoxia-inducible factor-1 (HIF-1) is a heterodimeric transcription factor activated when cells are submitted to hypoxia. The heterodimer is composed of two subunits, HIF-1alpha and the constitutively expressed HIF-1beta. During normoxia, HIF-1alpha is degraded by the 26S proteasome, but hypoxia causes HIF-1alpha to be stabilized, enter the nucleus and bind to HIF-1beta, thus forming the active complex. The complex then binds to the regulatory sequences of various genes involved in physiological and pathological processes. The specific regulatory sequence recognized by HIF-1 is the hypoxia response element (HRE) that has the consensus sequence 5'BRCGTGVBBB3'. Although the basic transcriptional regulation machinery is conserved between yeast and mammals, Saccharomyces cerevisiae does not express HIF-1 subunits. However, we hypothesized that baker's yeast has a protein analogous to HIF-1 which participates in the response to changes in oxygen levels by binding to HRE sequences. In this study we screened the yeast genome for HREs using probabilistic motif search tools. We described 24 yeast genes containing motifs with high probability of being HREs (p-value<0.1) and classified them according to biological function. Our results show that S. cerevisiae may harbor HREs and indicate that a transcription factor analogous to HIF-1 may exist in this organism.

  9. Foraminiferal proxies for pollution monitoring in moderately polluted harbors

    International Nuclear Information System (INIS)

    Armynot du Chatelet, E.; Debenay, J.-P.; Soulard, R.

    2004-01-01

    Foraminiferal density and species richness that decrease with an increase in heavy metal and PAH concentration may be used as pollution indicators. - Benthic foraminifera are increasingly used as environmental bio-indicators, especially in polluted environments where their sensitivity to pollutants may be expressed by a modification of the assemblages. Eighteen sediment samples were collected in September 2000 in five harbors located in moderately polluted estuaries on the coast of Vendee (France) for the study of foraminiferal assemblages. Ten heavy metals and 13 PAH have been analyzed from the sediments. The marine to continental estuarine gradient has a prevalent influence on the foraminiferal distribution. However, the results show that foraminiferal density and species richness of the assemblages decrease with an increase in heavy metal and PAH concentration, and therefore may be used as pollution indicators. Moreover, the more polluted areas are dominated by the tolerant pioneer species Haynesina germanica that may be used as bio-indicator of pollution, mainly in the uppermost areas

  10. DNA Vaccines

    Indian Academy of Sciences (India)

    diseases. Keywords. DNA vaccine, immune response, antibodies, infectious diseases. GENERAL .... tein vaccines require expensive virus/protein purification tech- niques as ... sphere continue to remain major health hazards in developing nations. ... significance since it can be produced at a very low cost and can be stored ...

  11. DNA Investigations.

    Science.gov (United States)

    Mayo, Ellen S.; Bertino, Anthony J.

    1991-01-01

    Presents a simulation activity that allow students to work through the exercise of DNA profiling and to grapple with some analytical and ethical questions involving a couple arranging with a surrogate mother to have a baby. Can be used to teach the principles of restriction enzyme digestion, gel electrophoresis, and probe hybridization. (MDH)

  12. 77 FR 42076 - Notice of Opportunity for Public Comment on Surplus Property Release at Hancock County-Bar Harbor...

    Science.gov (United States)

    2012-07-17

    ... Comment on Surplus Property Release at Hancock County-Bar Harbor Airport, Trenton, ME AGENCY: Federal... located at Hancock County-Bar Harbor Airport, Trenton, Maine. DATES: Comments must be received on or... INFORMATION: The Federal Aviation Administration is reviewing a request by Hancock County-Bar Harbor Airport...

  13. 33 CFR 165.T14-204 - Safety Zone; fixed mooring balls, south of Barbers Pt Harbor Channel, Oahu, Hawaii.

    Science.gov (United States)

    2010-07-01

    ..., south of Barbers Pt Harbor Channel, Oahu, Hawaii. 165.T14-204 Section 165.T14-204 Navigation and... Pt Harbor Channel, Oahu, Hawaii. (a) Location. The following area is a safety zone: All waters... position is approximately 2,500 yards south of Barbers Point Harbor channel buoy #2, Oahu, Hawaii. This...

  14. 77 FR 67563 - Regulated Navigation Area-New Haven Harbor, Quinnipiac River, Mill River, New Haven, CT; Pearl...

    Science.gov (United States)

    2012-11-13

    ... 1625-AA11 Regulated Navigation Area--New Haven Harbor, Quinnipiac River, Mill River, New Haven, CT... Haven Harbor, Quinnipiac River and Mill River. The current RNA pertains only to the operation of tugs...) entitled Regulated Navigation Area--New Haven Harbor, Quinnipiac River, Mill River, New Haven, CT; Pearl...

  15. Transcription and recombination: when RNA meets DNA.

    Science.gov (United States)

    Aguilera, Andrés; Gaillard, Hélène

    2014-08-01

    A particularly relevant phenomenon in cell physiology and proliferation is the fact that spontaneous mitotic recombination is strongly enhanced by transcription. The most accepted view is that transcription increases the occurrence of double-strand breaks and/or single-stranded DNA gaps that are repaired by recombination. Most breaks would arise as a consequence of the impact that transcription has on replication fork progression, provoking its stalling and/or breakage. Here, we discuss the mechanisms responsible for the cross talk between transcription and recombination, with emphasis on (1) the transcription-replication conflicts as the main source of recombinogenic DNA breaks, and (2) the formation of cotranscriptional R-loops as a major cause of such breaks. The new emerging questions and perspectives are discussed on the basis of the interference between transcription and replication, as well as the way RNA influences genome dynamics. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

  16. A lifelong journey of moving beyond wartime trauma for survivors from Hiroshima and Pearl Harbor.

    Science.gov (United States)

    Liehr, Patricia; Nishimura, Chie; Ito, Mio; Wands, Lisa Marie; Takahashi, Ryutaro

    2011-01-01

    This study examines 51 stories of health, shared by people who survived the wartime trauma of Hiroshima and Pearl Harbor, seeking to identify turning points that moved participants along over their lifetime. The central turning point for Hiroshima survivors was "becoming Hibabusha (A-bomb survivor)" and for Pearl Harbor survivors was "honoring the memory and setting it aside." Wartime trauma was permanently integrated into survivors' histories, surfacing steadily over decades for Hiroshima survivors and intermittently over decades for Pearl Harbor survivors. Regardless of experience or nationality, participants moved through wartime trauma by connecting with others, pursuing personal and global peace.

  17. Temporal and spatial variation in harbor seal (Phoca vitulina L.) roar calls from southern Scandinavia

    DEFF Research Database (Denmark)

    Sabinsky, Puk Faxe; Larsen, Ole Næsbye; Wahlberg, Magnus

    2017-01-01

    Male harbor seals gather around breeding sites for competitive mating displays. Here, they produce underwater vocalizations possibly to attract females and/or scare off other males. These calls offer prospects for passive acoustic monitoring. Acoustic monitoring requires a good understanding...... of natural variation in calling behavior both temporally and among geographically separate sites. Such variation in call structure and calling patterns were studied in harbor seal vocalizations recorded at three locations in Danish and Swedish waters. There was a strong seasonality in the calls from end...... biological differences when comparing harbor seal roars among recording sites and between years....

  18. Mitochondrial DNA variation, but not nuclear DNA, sharply divides morphologically identical chameleons along an ancient geographic barrier.

    Directory of Open Access Journals (Sweden)

    Dan Bar Yaacov

    Full Text Available The Levant is an important migration bridge, harboring border-zones between Afrotropical and palearctic species. Accordingly, Chameleo chameleon, a common species throughout the Mediterranean basin, is morphologically divided in the southern Levant (Israel into two subspecies, Chamaeleo chamaeleon recticrista (CCR and C. c. musae (CCM. CCR mostly inhabits the Mediterranean climate (northern Israel, while CCM inhabits the sands of the north-western Negev Desert (southern Israel. AFLP analysis of 94 geographically well dispersed specimens indicated moderate genetic differentiation (PhiPT = 0.097, consistent with the classical division into the two subspecies, CCR and CCM. In contrast, sequence analysis of a 637 bp coding mitochondrial DNA (mtDNA fragment revealed two distinct phylogenetic clusters which were not consistent with the morphological division: one mtDNA cluster consisted of CCR specimens collected in regions northern of the Jezreel Valley and another mtDNA cluster harboring specimens pertaining to both the CCR and CCM subspecies but collected southern of the Jezreel Valley. AMOVA indicated clear mtDNA differentiation between specimens collected northern and southern to the Jezreel Valley (PhiPT = 0.79, which was further supported by a very low coalescent-based estimate of effective migration rates. Whole chameleon mtDNA sequencing (∼17,400 bp generated from 11 well dispersed geographic locations revealed 325 mutations sharply differentiating the two mtDNA clusters, suggesting a long allopatric history further supported by BEAST. This separation correlated temporally with the existence of an at least 1 million year old marine barrier at the Jezreel Valley exactly where the mtDNA clusters meet. We discuss possible involvement of gender-dependent life history differences in maintaining such mtDNA genetic differentiation and suggest that it reflects (ancient local adaptation to mitochondrial-related traits.

  19. Mnemiopsis leidyi Gut Harbors Seasonally Variant and Commensal Microbial Assemblages

    Science.gov (United States)

    Mariita, R. M.; Hossain, M. J.; Liles, M. R.; Moss, A.

    2016-02-01

    Studies have shown that with widespread use of antibiotics in human and domestic animal populations, antibiotic resistance becomes increasingly common in the environment. Estuaries provide ideal conditions for acquisition and dissemination of drug resistance genes because they serve as sinks for pollution. This study aimed to identify M. leidyi microbial diversity and richness and their potential to act as vectors for antibiotic resistance determinants (ARDs). M. leidyi, although native to study area are highly invasive. Metagenomic analyses indicate that there are temporal variations of bacterioplankton assemblages in M. leidyi gut. Overall, Proteobacteria and Actinobacteria are the most abundant phyla. Despite the temporal dynamics in the microbial assemblages in M. leidyi gut, they seem to retain Propionibacterium acnes (gut microbiota in some insects) and select proteobacteria across all seasons. The results contradict previous studies that suggest that M. leidyi does not have constant a microbiota, but only seasonally variant microbial assemblages. Here we reveal the presence of M. leidyi gut ARDs in winter and summer, probably because of the ctenophores' positive geotaxis during rough surface conditions. Genes responsible for resistance to fluoroquinolones, multidrug resistance efflux pumps, mercuric reductase, copper homeostasis and blaR1 genes were observed. This is the first study to demonstrate that M. leidyi harbors constant microbiota and provides a baseline for understanding M. leidyi gut microbial and ARDs ecology. It also suggests that M. leidyi bacterial taxonomic and functional dynamics is influenced by season. Funding: Alabama EPSCoR GRSP fellowship, AU-CMB fellowship, NSF EPS-1158862, USDA-Hatch 370225-310100 (AGM, ML).

  20. A Look into the Melting Pot: The mecC-Harboring Region Is a Recombination Hot Spot in Staphylococcus stepanovicii.

    Directory of Open Access Journals (Sweden)

    Torsten Semmler

    Full Text Available Horizontal gene transfer (HGT is an important driver for resistance- and virulence factor accumulation in pathogenic bacteria such as Staphylococcus aureus.Here, we have investigated the downstream region of the bacterial chromosomal attachment site (attB for the staphylococcal cassette chromosome mec (SCCmec element of a commensal mecC-positive Staphylococcus stepanovicii strain (IMT28705; ODD4 with respect to genetic composition and indications of HGT. S. stepanovicii IMT28705 was isolated from a fecal sample of a trapped wild bank vole (Myodes glareolus during a screening study (National Network on "Rodent-Borne Pathogens" in Germany. Whole genome sequencing (WGS of IMT28705 together with the mecC-negative type strain CM7717 was conducted in order to comparatively investigate the genomic region downstream of attB (GenBank accession no. KR732654 and KR732653.The bank vole isolate (IMT28705 harbors a mecC gene which shares 99.2% nucleotide (and 98.5% amino acid sequence identity with mecC of MRSA_LGA251. In addition, the mecC-encoding region harbors the typical blaZ-mecC-mecR1-mecI structure, corresponding with the class E mec complex. While the sequences downstream of attB in both S. stepanovicii isolates (IMT28705 and CM7717 are partitioned by 15 bp direct repeats, further comparison revealed a remarkable low concordance of gene content, indicating a chromosomal "hot spot" for foreign DNA integration and exchange.Our data highlight the necessity for further research on transmission routes of resistance encoding factors from the environmental and wildlife resistome.

  1. Settlement of the USS Arizona, Pearl Harbor, Hawaii

    Science.gov (United States)

    Carkin, Brad A.; Kayen, Robert E.

    2013-01-01

    The U.S. Geological Survey, in collaboration with the National Park Service Submerged Resources Center, undertook investigations at the USS Arizona Memorial at Pearl Harbor, Hawaii, in 2002, 2003, and 2005 to characterize geological factors affecting the deterioration and movement of the hull of the USS Arizona. Since sinking on the morning of December 7, 1941, the hull of the USS Arizona has been slowly but steadily disappearing below the surface of Pearl Harbor. Continuous sediment coring at three of four locations around the hull of the Arizona was only partially successful, but it was sufficient to identify a varied sedimentary substrate beneath the hull. A boring near the stern reveals a thick, continuous sequence of soft, gray clay to the bottom of the boring. In contrast, borings near the bow and starboard side, below about 5 meters subbottom depth, indicate the presence of very stiff, brown clay and coral debris and an absence of soft clay. Multisensor core logger scanning of the recovered cores distinguishes the lower density of the soft, gray clay at the stern from the higher density of the stiff, brown clays and coral debris at the bow and starboard side. Uniaxial consolidation testing of the soft gray clay indicates a normally consolidated sequence, whereas the stiff, brown clay and coral debris are overconsolidated. Profiles of shear wave velocity vs. depth obtained through spectral analysis of interface wave testing around the perimeter of the hull in 2005 identified areas of higher velocity, stiffer sediment at the bow and starboard side, which correspond to the dense, stiff clay recovered near the bow and starboard borings. Low shear-wave velocities at the port midship and quarter of the hull correlate with the lower density, softer sediment recovered from the boring at the stern. Cross sections of the subbottom of the Memorial combine results from the sediment borings and geophysical surveys and depict a wedge of soft clay unconformably overlying

  2. DNA repair

    International Nuclear Information System (INIS)

    Setlow, R.

    1978-01-01

    Some topics discussed are as follows: difficulty in extrapolating data from E. coli to mammalian systems; mutations caused by UV-induced changes in DNA; mutants deficient in excision repair; other postreplication mechanisms; kinds of excision repair systems; detection of repair by biochemical or biophysical means; human mutants deficient in repair; mutagenic effects of UV on XP cells; and detection of UV-repair defects among XP individuals

  3. Onondaga Lake Inner Harbor Dredging Design Project, Syracuse, New York: Final Design Memorandum

    National Research Council Canada - National Science Library

    1997-01-01

    .... The sponsor is the New York State Canal Corporation. The design includes deepening the Inner Harbor channel and a portion of the terminal slip area to a depth of 10 feet below Low Water Datum (LWD...

  4. Aerial Survey Trend Counts of Harbor Seals in Coastal Alaska (1984-2006) - ADF&G

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Aerial surveys were conducted during 1983–2006 in the Ketchikan, Sitka, Kodiak, and Bristol Bay areas of Alaska to estimate trends in abundance of harbor seals.

  5. Aerial Survey Counts of Harbor Seals in Lake Iliamna, Alaska, 1984-2013 (NODC Accession 0123188)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This dataset provides counts of harbor seals from aerial surveys over Lake Iliamna, Alaska, USA. The data have been collated from three previously published sources...

  6. Sedimentation and chronology of heavy metal pollution in Oslo harbor, Norway

    International Nuclear Information System (INIS)

    Lepland, Aivo; Andersen, Thorbjorn J.; Lepland, Aave; Arp, Hans Peter H.; Alve, Elisabeth; Breedveld, Gijs D.; Rindby, Anders

    2010-01-01

    Stratigraphic profiles of Cu, Cd and Hg in ten sediment cores from the Oslo harbor, Norway, combined with results of radiometric dating demonstrate that pollution by these metals peaked between 1940 and 1970. Dating results indicate that Hg discharges peaked between 1940 and 1950, Cd reached maximum ca. 1955-1960, and Cu has the highest concentration in sediment interval corresponding to ca. 1970. Geochemical profiles and maxima of Cu, Cd and Hg concentrations can be used as chronostratigraphic markers for sediment cores from the Oslo harbor. Acoustic backscatter and sediment core data indicate that propeller wash affects the seabed in the Oslo harbor. The propeller-induced turbulence causes erosion, and in places exposes and remobilizes contaminated sediments that accumulated in the harbor during previous decades. Such re-exposure of contaminated sediments could be detrimental to local ecosystems and offset remediation efforts, warranting further impact studies and potential mitigation strategies to prevent redistribution.

  7. Wave Climate and Wave Response, Kawaihae Deep Draft Harbor, Island of Hawaii, Hawaii

    National Research Council Canada - National Science Library

    Thompson, Edward F; Demirbilek, Zeki; Briggs, Michael J

    2006-01-01

    Present and projected commercial activities in Kawaihae Deep Draft Harbor, Island of Hawaii, HI, indicate that a deeper basin and entrance channel and better protected berthing areas will be needed. The U.S...

  8. DEPOT MAINTENANCE: Key Financial Issues for Consolidations at Pearl Harbor and Elsewhere Are Still Unresolved

    National Research Council Canada - National Science Library

    2001-01-01

    .... In September 1999, we reported that the preliminary results of the ongoing Pearl Harbor pilot were mixed and recommended that the Departments of Defense and the Navy address unresolved issues related...

  9. Inshore Survey Results: Approaches to New York Harbor, Fall 1955 (NODC Accession 7000294)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A current survey in the approaches to New York Harbor was initiated 06 September 1955 and continued through 04 November 1955. This survey was conducted in accordance...

  10. Environmental Assessment for Building 88 Interior Demolition, Pearl Harbor Naval Complex, O'ahu, Hawaii

    National Research Council Canada - National Science Library

    2005-01-01

    ...) and ancillary equipment from the interior of Building 88, a former lubricating oil storage facility, and the related exposed piping underneath Mike wharves M3 and M4 at Merry Point, Pearl Harbor Naval Complex...

  11. Defense Infrastructure: General and Flag Officer Quarters at Pearl Harbor, Hawaii

    National Research Council Canada - National Science Library

    2002-01-01

    .... We reviewed 17 GFOQs at Pearl Harbor, Hawaii, with budgeted maintenance and repair costs of $1,247,300, to determine whether the Navy had properly classified interior shutter costs as maintenance and repair...

  12. Environmental Assessment for Waterfront Facilities Maintenance and Improvements, Pearl Harbor Naval Complex, Oahu, Hawaii

    National Research Council Canada - National Science Library

    2005-01-01

    Commander, Navy Region Hawaii (CNRH) proposes to repair, maintain, and improve waterfront berthing and maintenance facilities for ships and submarines on an as-needed basis within the Pearl Harbor Naval Complex (PHNC...

  13. Gridded multibeam bathymetry of Apra Harbor, Guam U.S. Territory

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Gridded bathymetry from Apra Harbor, Guam U.S. Territory. The netCDF and Arc ASCII grids include multibeam bathymetry from the Reson SeaBat 8125 multibeam sonar...

  14. DefenseLink Special: Attack on Pearl Harbor, 65th Anniversary

    Science.gov (United States)

    Japanese raid on Pearl Harbor has been called a defining moment in U.S. history. It caught the country by Hawaii-based combat planes, were heavily damaged. By crippling the U.S. Pacific Fleet, Japan hoped to

  15. MODELING HOW A HURRICANE BARRIER IN NEW BEDFORD HARBOR, MASSACHUSETTS, AFFECTS THE HYDRODYNAMICS AND RESIDENCE TIMES

    Science.gov (United States)

    Two-dimensional hydrodynamic and transport models were used to simulate tidal and subtidal circulation, residence times, and the longitudinal distributions of conservative constituents in New Bedford Harbor, Massachusetts, before and after a hurricane barrier was constructed. The...

  16. Aerial Survey Effort for Harbor Seals in Coastal Alaska (2004-2015)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The most feasible approach to determining harbor seal distribution and abundance in Alaska coastal habitats is to use aircraft to count seals when they haul out of...

  17. A Dataset of Aerial Survey Counts of Harbor Seals in Iliamna Lake, Alaska: 1984-2013

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This dataset provides counts of harbor seals from aerial surveys over Iliamna Lake, Alaska, USA. The data have been collated from three previously published sources...

  18. Ice Harbor Spillway Dissolved Gas Field Studies: Before and After Spillway Deflectors

    Science.gov (United States)

    2016-07-01

    Steven C. Wilhelms Coastal And Hydraulics Laboratory U.S. Army Engineer Research and Development Center 3909 Halls Ferry Road Vicksburg, Mississippi...Harbor as a measure to reduce the total dissolved gas (TDG) production during spill operations. Three field studies were conducted at the Ice Harbor...significantly reduced for nearly all spill operations with deflectors in place. TDG near the stilling basin was reduced from approximately 150% to

  19. Emergence of colistin-resistant Escherichia coli clinical isolates harboring mcr-1 in Vietnam.

    Science.gov (United States)

    Tada, Tatsuya; Nhung, Pham Hong; Shimada, Kayo; Tsuchiya, Mitsuhiro; Phuong, Doan Mai; Anh, Nguyen Quoc; Ohmagari, Norio; Kirikae, Teruo

    2017-10-01

    The mcr-1 was first detected on a plasmid in colistin-resistant Escherichia coli from livestock and patients in China. We described here the emergence of colistin-resistant E. coli clinical isolates harboring mcr-1 on the chromosomes in Vietnam. To our knowledge, this is the first report of hospital-acquired E. coli isolates harboring mcr-1 in a medical setting in Vietnam. Copyright © 2017. Published by Elsevier Ltd.

  20. Analysis of Protection Measures for Naval Vessels Berthed at Harbor Against Terrorist Attacks

    Science.gov (United States)

    2016-06-01

    of discriminating neutral vessels from threats. A naval vessel berthed at harbor is more susceptible to attack than a vessel in open seas. The...discriminating neutral vessels from threats. A naval vessel berthed at harbor is more susceptible to attack than a vessel in open seas. The chances of...this thesis. He was a source of inspiration, encouragement, and reassurance. Captain Jeffery E. Kline, I am really thankful to you for your ideas

  1. Charleston Harbor, SC, Regional Sediment Management Study: Beneficial Use of Dredged Material through Nearshore Placement

    Science.gov (United States)

    2017-05-01

    Modeling System (CMS) that were developed and applied previously for the Charleston Harbor numerical modeling study (Kashlan 2013) were used in...Particle Tracking Model; Report 1: Model theory, implementation, and example applications. ERDC/CHL TR-6-20. Vicksburg, MS: U.S. Army Engineer Research ...ER D C/ CH L TR -1 7- 7 Regional Sediment Management (RSM) Program Charleston Harbor, SC, Regional Sediment Management Study

  2. Charleston Harbor, SC, Regional Sediment Management Study; Beneficial Use of Dredged Material through Nearshore Placement

    Science.gov (United States)

    2017-05-01

    Modeling System (CMS) that were developed and applied previously for the Charleston Harbor numerical modeling study (Kashlan 2013) were used in...Particle Tracking Model; Report 1: Model theory, implementation, and example applications. ERDC/CHL TR-6-20. Vicksburg, MS: U.S. Army Engineer Research ...ER D C/ CH L TR -1 7- 7 Regional Sediment Management (RSM) Program Charleston Harbor, SC, Regional Sediment Management Study

  3. Cladophora (Chlorophyta) spp. Harbor Human Bacterial Pathogens in Nearshore Water of Lake Michigan†

    OpenAIRE

    Ishii, Satoshi; Yan, Tao; Shively, Dawn A.; Byappanahalli, Muruleedhara N.; Whitman, Richard L.; Sadowsky, Michael J.

    2006-01-01

    Cladophora glomerata, a macrophytic green alga, is commonly found in the Great Lakes, and significant accumulations occur along shorelines during the summer months. Recently, Cladophora has been shown to harbor high densities of the fecal indicator bacteria Escherichia coli and enterococci. Cladophora may also harbor human pathogens; however, until now, no studies to address this question have been performed. In the present study, we determined whether attached Cladophora, obtained from the L...

  4. 75 FR 43823 - Safety Zone; He'eia Kea Small Boat Harbor, Kaneohe Bay, Oahu, HI

    Science.gov (United States)

    2010-07-27

    ...The Coast Guard is establishing a temporary safety zone in He'eia Kea Small Boat Harbor located in Kaneohe Bay, Oahu, Hawaii. The safety zone is necessary to protect watercraft and the general public from hazards associated with five vessels moored for approximately 3- weeks off the boat harbor's main pier. Vessels desiring to transit through the zone can request permission by contacting the Captain of the Port Honolulu.

  5. A solitary hyperfunctioning thyroid nodule harboring thyroid carcinoma: review of the literature

    OpenAIRE

    Mirfakhraee, Sasan; Mathews, Dana; Peng, Lan; Woodruff, Stacey; Zigman, Jeffrey M

    2013-01-01

    Hyperfunctioning nodules of the thyroid are thought to only rarely harbor thyroid cancer, and thus are infrequently biopsied. Here, we present the case of a patient with a hyperfunctioning thyroid nodule harboring thyroid carcinoma and, using MEDLINE literature searches, set out to determine the prevalence of and characteristics of malignant ?hot? nodules as a group. Historical, biochemical and radiologic characteristics of the case subjects and their nodules were compared to those in cases o...

  6. Numerical Modeling of Wave Overtopping of Buffalo Harbor Confined Disposal Facility (CDF4)

    Science.gov (United States)

    2017-10-01

    navigation channel , and harbor complex. Though there are anecdotal claims and debris indicating possible sediment movement, there has been no evidence of...littoral sediments inside the disposal area, into the channel and harbor, and other adjacent areas to the CDF4. 1.4 Study plan 1.4.1 Purpose There...locations. 2.4 Maintenance dredging data The need for maintenance dredging arises from sedimentation in the navigation channels , which impedes

  7. Impact of Geomorphological Changes to Harbor Resonance During Meteotsunamis: The Vela Luka Bay Test Case

    Science.gov (United States)

    Denamiel, Cléa; Šepić, Jadranka; Vilibić, Ivica

    2018-05-01

    In engineering studies, harbor resonance, including quality and amplification factors, is typically computed for swell and waves with periods shorter than 10 min. However, in various locations around the world, such as Vela Luka Bay in Croatia, meteotsunami waves of periods greater than 10 min can excite the bay or harbor natural modes and produce substantial structural damages. In this theoretical study, the impact of some geomorphological changes of Vela Luka Bay—i.e. deepening of the bay, dredging the harbor, adding a pier or a marina—to the amplification of the meteotsunami waves are presented for a set of 6401 idealized pressure wave field forcing used to derive robust statistics. The most substantial increase in maximum elevation is found when the Vela Luka harbor is dredged to a 5 m depth, which is in contradiction with the calculation of the quality factor showing a decrease of the harbor natural resonance. It has been shown that the forcing energy content at different frequency bands should also be taken into account when estimating the quality and amplification factors, as their typical definitions derived from the peak frequency of the sea level spectrum fail to represent the harbor response during meteotsunami events. New definitions of these factors are proposed in this study and are shown to be in good agreement with the results of the statistical analysis of the Vela Luka Bay maximum elevation results. In addition, the presented methodology can easily be applicable to any other location in the world where meteotsunamis occur.

  8. DNA repair

    International Nuclear Information System (INIS)

    Van Zeeland, A.A.

    1984-01-01

    In this chapter a series of DNA repair pathways are discussed which are available to the cell to cope with the problem of DNA damaged by chemical or physical agents. In the case of microorganisms our knowledge about the precise mechanism of each DNA repair pathway and the regulation of it has been improved considerably when mutants deficient in these repair mechanisms became available. In the case of mammalian cells in culture, until recently there were very little repair deficient mutants available, because in almost all mammalian cells in culture at least the diploid number of chromosomes is present. Therefore the frequency of repair deficient mutants in such populations is very low. Nevertheless because replica plating techniques are improving some mutants from Chinese hamsters ovary cells and L5178Y mouse lymphoma cells are now available. In the case of human cells, cultures obtained from patients with certain genetic diseases are available. A number of cells appear to be sensitive to some chemical or physical mutagens. These include cells from patients suffering from xeroderma pigmentosum, Ataxia telangiectasia, Fanconi's anemia, Cockayne's syndrome. However, only in the case of xeroderma pigmentosum cells, has the sensitivity to ultraviolet light been clearly correlated with a deficiency in excision repair of pyrimidine dimers. Furthermore the work with strains obtained from biopsies from man is difficult because these cells generally have low cloning efficiencies and also have a limited lifespan in vitro. It is therefore very important that more repair deficient mutants will become available from established cell lines from human or animal origin

  9. DNA repair is indispensable for survival after acute inflammation

    Science.gov (United States)

    Calvo, Jennifer A.; Meira, Lisiane B.; Lee, Chun-Yue I.; Moroski-Erkul, Catherine A.; Abolhassani, Nona; Taghizadeh, Koli; Eichinger, Lindsey W.; Muthupalani, Sureshkumar; Nordstrand, Line M.; Klungland, Arne; Samson, Leona D.

    2012-01-01

    More than 15% of cancer deaths worldwide are associated with underlying infections or inflammatory conditions, therefore understanding how inflammation contributes to cancer etiology is important for both cancer prevention and treatment. Inflamed tissues are known to harbor elevated etheno-base (ε-base) DNA lesions induced by the lipid peroxidation that is stimulated by reactive oxygen and nitrogen species (RONS) released from activated neutrophils and macrophages. Inflammation contributes to carcinogenesis in part via RONS-induced cytotoxic and mutagenic DNA lesions, including ε-base lesions. The mouse alkyl adenine DNA glycosylase (AAG, also known as MPG) recognizes such base lesions, thus protecting against inflammation-associated colon cancer. Two other DNA repair enzymes are known to repair ε-base lesions, namely ALKBH2 and ALKBH3; thus, we sought to determine whether these DNA dioxygenase enzymes could protect against chronic inflammation-mediated colon carcinogenesis. Using established chemically induced colitis and colon cancer models in mice, we show here that ALKBH2 and ALKBH3 provide cancer protection similar to that of the DNA glycosylase AAG. Moreover, Alkbh2 and Alkbh3 each display apparent epistasis with Aag. Surprisingly, deficiency in all 3 DNA repair enzymes confers a massively synergistic phenotype, such that animals lacking all 3 DNA repair enzymes cannot survive even a single bout of chemically induced colitis. PMID:22684101

  10. Mitochondrial DNA single nucleotide polymorphism associated with weight estimated breeding values in Nelore cattle (Bos indicus

    Directory of Open Access Journals (Sweden)

    Fernando Henrique Biase

    2007-01-01

    Full Text Available We sampled 119 Nelore cattle (Bos indicus, 69 harboring B. indicus mtDNA plus 50 carrying Bos taurus mtDNA, to estimate the frequencies of putative mtDNA single nucleotide polymorphisms (SNPs and investigate their association with Nelore weight and scrotal circumference estimated breeding values (EBVs. The PCR restriction fragment length polymorphism (PCR-RFLP method was used to detect polymorphisms in the mitochondrial asparagine, cysteine, glycine, leucine and proline transporter RNA (tRNA genes (tRNAasn, tRNAcys, tRNAgly, tRNAleu and tRNApro. The 50 cattle carrying B. taurus mtDNA were monomorphic for all the tRNA gene SNPs analyzed, suggesting that they are specific to mtDNA from B. indicus cattle. No tRNAcys or tRNAgly polymorphisms were detected in any of the cattle but we did detect polymorphic SNPs in the tRNAasn, tRNAleu and tRNApro genes in the cattle harboring B. indicus mtDNA, with the same allele observed in the B. taurus sequence being present in the following percentage of cattle harboring B. indicus mtDNA: 72.46% for tRNAasn, 95.23% for tRNAleu and 90.62% for tRNApro. Analyses of variance using the tRNAasn SNP as the independent variable and EBVs as the dependent variable showed that the G -> T SNP was significantly associated (p < 0.05 with maternal EBVs for weight at 120 and 210 days (p < 0.05 and animal's EBVs for weight at 210, 365 and 455 days. There was no association of the tRNAasn SNP with the scrotal circumference EBVs. These results confirm that mtDNA can affect weight and that mtDNA polymorphisms can be a source of genetic variation for quantitative traits.

  11. The genome of Chelonid herpesvirus 5 harbors atypical genes

    Science.gov (United States)

    Ackermann, Mathias; Koriabine, Maxim; Hartmann-Fritsch, Fabienne; de Jong, Pieter J.; Lewis, Teresa D.; Schetle, Nelli; Work, Thierry M.; Dagenais, Julie; Balazs, George H.; Leong, Jo-Ann C.

    2012-01-01

    The Chelonid fibropapilloma-associated herpesvirus (CFPHV; ChHV5) is believed to be the causative agent of fibropapillomatosis (FP), a neoplastic disease of marine turtles. While clinical signs and pathology of FP are well known, research on ChHV5 has been impeded because no cell culture system for its propagation exists. We have cloned a BAC containing ChHV5 in pTARBAC2.1 and determined its nucleotide sequence. Accordingly, ChHV5 has a type D genome and its predominant gene order is typical for the varicellovirus genus within thealphaherpesvirinae. However, at least four genes that are atypical for an alphaherpesvirus genome were also detected, i.e. two members of the C-type lectin-like domain superfamily (F-lec1, F-lec2), an orthologue to the mouse cytomegalovirus M04 (F-M04) and a viral sialyltransferase (F-sial). Four lines of evidence suggest that these atypical genes are truly part of the ChHV5 genome: (1) the pTARBAC insertion interrupted the UL52 ORF, leaving parts of the gene to either side of the insertion and suggesting that an intact molecule had been cloned. (2) Using FP-associated UL52 (F-UL52) as an anchor and the BAC-derived sequences as a means to generate primers, overlapping PCR was performed with tumor-derived DNA as template, which confirmed the presence of the same stretch of “atypical” DNA in independent FP cases. (3) Pyrosequencing of DNA from independent tumors did not reveal previously undetected viral sequences, suggesting that no apparent loss of viral sequence had happened due to the cloning strategy. (4) The simultaneous presence of previously known ChHV5 sequences and F-sial as well as F-M04 sequences was also confirmed in geographically distinct Australian cases of FP. Finally, transcripts of F-sial and F-M04 but not transcripts of lytic viral genes were detected in tumors from Hawaiian FP-cases. Therefore, we suggest that F-sial and F-M04 may play a role in FP pathogenesis

  12. DNA replication and cancer: From dysfunctional replication origin activities to therapeutic opportunities.

    Science.gov (United States)

    Boyer, Anne-Sophie; Walter, David; Sørensen, Claus Storgaard

    2016-06-01

    A dividing cell has to duplicate its DNA precisely once during the cell cycle to preserve genome integrity avoiding the accumulation of genetic aberrations that promote diseases such as cancer. A large number of endogenous impacts can challenge DNA replication and cells harbor a battery of pathways to promote genome integrity during DNA replication. This includes suppressing new replication origin firing, stabilization of replicating forks, and the safe restart of forks to prevent any loss of genetic information. Here, we describe mechanisms by which oncogenes can interfere with DNA replication thereby causing DNA replication stress and genome instability. Further, we describe cellular and systemic responses to these insults with a focus on DNA replication restart pathways. Finally, we discuss the therapeutic potential of exploiting intrinsic replicative stress in cancer cells for targeted therapy. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Linkage of DNA Methylation Quantitative Trait Loci to Human Cancer Risk

    Directory of Open Access Journals (Sweden)

    Holger Heyn

    2014-04-01

    Full Text Available Epigenetic regulation and, in particular, DNA methylation have been linked to the underlying genetic sequence. DNA methylation quantitative trait loci (meQTL have been identified through significant associations between the genetic and epigenetic codes in physiological and pathological contexts. We propose that interrogating the interplay between polymorphic alleles and DNA methylation is a powerful method for improving our interpretation of risk alleles identified in genome-wide association studies that otherwise lack mechanistic explanation. We integrated patient cancer risk genotype data and genome-scale DNA methylation profiles of 3,649 primary human tumors, representing 13 solid cancer types. We provide a comprehensive meQTL catalog containing DNA methylation associations for 21% of interrogated cancer risk polymorphisms. Differentially methylated loci harbor previously reported and as-yet-unidentified cancer genes. We suggest that such regulation at the DNA level can provide a considerable amount of new information about the biology of cancer-risk alleles.

  14. Specific and Efficient Regression of Cancers Harboring KRAS Mutation by Targeted RNA Replacement.

    Science.gov (United States)

    Kim, Sung Jin; Kim, Ju Hyun; Yang, Bitna; Jeong, Jin-Sook; Lee, Seong-Wook

    2017-02-01

    Mutations in the KRAS gene, which persistently activate RAS function, are most frequently found in many types of human cancers. Here, we proposed and verified a new approach against cancers harboring the KRAS mutation with high cancer selectivity and efficient anti-cancer effects based on targeted RNA replacement. To this end, trans-splicing ribozymes from Tetrahymena group I intron were developed, which can specifically target and reprogram the mutant KRAS G12V transcript to induce therapeutic gene activity in cells. Adenoviral vectors containing the specific ribozymes with downstream suicide gene were constructed and then infection with the adenoviruses specifically downregulated KRAS G12V expression and killed KRAS G12V-harboring cancer cells additively upon pro-drug treatment, but it did not affect the growth of wild-type KRAS-expressing cells. Minimal liver toxicity was noted when the adenoviruses were administered systemically in vivo. Importantly, intratumoral injection of the adenoviruses with pro-drug treatment specifically and significantly impeded the growth of xenografted tumors harboring KRAS G12V through a trans-splicing reaction with the target RNA. In contrast, xenografted tumors harboring wild-type KRAS were not affected by the adenoviruses. Therefore, RNA replacement with a mutant KRAS-targeting trans-splicing ribozyme is a potentially useful therapeutic strategy to combat tumors harboring KRAS mutation. Copyright © 2017 The American Society of Gene and Cell Therapy. Published by Elsevier Inc. All rights reserved.

  15. Reducing Vulnerability of Ports and Harbors to Earthquake and Tsunami Hazards

    Science.gov (United States)

    Wood, Nathan J.; Good, James W.; Goodwin, Robert F.

    2002-01-01

    Recent scientific research suggests the Pacific Northwest could experience catastrophic earthquakes in the near future, both from distant and local sources, posing a significant threat to coastal communities. Damage could result from numerous earthquake-related hazards, such as severe ground shaking, soil liquefaction, landslides, land subsidence/uplift, and tsunami inundation. Because of their geographic location, ports and harbors are especially vulnerable to these hazards. Ports and harbors, however, are important components of many coastal communities, supporting numerous activities critical to the local and regional economy and possibly serving as vital post-event, response-recovery transportation links. A collaborative, multi-year initiative is underway to increase the resiliency of Pacific Northwest ports and harbors to earthquake and tsunami hazards, involving Oregon Sea Grant (OSG), Washington Sea Grant (WSG), the National Oceanic and Atmospheric Administration Coastal Services Center (CSC), and the U.S. Geological Survey Center for Science Policy (CSP). Specific products of this research, planning, and outreach initiative include a regional stakeholder issues and needs assessment, a community-based mitigation planning process, a Geographic Information System (GIS) — based vulnerability assessment methodology, an educational web-site and a regional data archive. This paper summarizes these efforts, including results of two pilot port-harbor community projects, one in Yaquina Bay, Oregon and the other in Sinclair Inlet, Washington. Finally, plans are outlined for outreach to other port and harbor communities in the Pacific Northwest and beyond, using "getting started" workshops and a web-based tutorial.

  16. Stabilization and in situ management of radioactive contaminated sediments of Port Hope harbor

    International Nuclear Information System (INIS)

    Dolinar, G.M.; Killey, R.W.D.; Philipase, K.E.

    1991-01-01

    This paper presents the findings of laboratory and field studies undertaken to assess the feasibility of in situ management of contaminated sediments in Port Hope harbor. The contaminated sediments stem from historic releases from an adjacent radium and uranium refinery, and uranium, arsenic, and radium are the most abundant contaminants. With improved emission controls, currently accumulating sediments have much lower levels of contamination, and the harbor waters currently meet water quality limits for the contaminants of concern. Within a few years, however, the continuing sedimentation will render the harbor unusable. Field tests have confirmed the dredging will result in incomplete removal of the contaminated sediments and that sediment suspension and the release of pores waters during dredging will produce harbor water contaminant concentrations that would require the treatment of large volumes of water. In addition, no remedial work can start until a site for the dredged material can be found. The local community inquired whether in situ burial of the sediments and abandonment of the harbor would provide safe disposal

  17. Pediatric fecal microbiota harbor diverse and novel antibiotic resistance genes.

    Directory of Open Access Journals (Sweden)

    Aimée M Moore

    Full Text Available Emerging antibiotic resistance threatens human health. Gut microbes are an epidemiologically important reservoir of resistance genes (resistome, yet prior studies indicate that the true diversity of gut-associated resistomes has been underestimated. To deeply characterize the pediatric gut-associated resistome, we created metagenomic recombinant libraries in an Escherichia coli host using fecal DNA from 22 healthy infants and children (most without recent antibiotic exposure, and performed functional selections for resistance to 18 antibiotics from eight drug classes. Resistance-conferring DNA fragments were sequenced (Illumina HiSeq 2000, and reads assembled and annotated with the PARFuMS computational pipeline. Resistance to 14 of the 18 antibiotics was found in stools of infants and children. Recovered genes included chloramphenicol acetyltransferases, drug-resistant dihydrofolate reductases, rRNA methyltransferases, transcriptional regulators, multidrug efflux pumps, and every major class of beta-lactamase, aminoglycoside-modifying enzyme, and tetracycline resistance protein. Many resistance-conferring sequences were mobilizable; some had low identity to any known organism, emphasizing cryptic organisms as potentially important resistance reservoirs. We functionally confirmed three novel resistance genes, including a 16S rRNA methylase conferring aminoglycoside resistance, and two tetracycline-resistance proteins nearly identical to a bifidobacterial MFS transporter (B. longum s. longum JDM301. We provide the first report to our knowledge of resistance to folate-synthesis inhibitors conferred by a predicted Nudix hydrolase (part of the folate synthesis pathway. This functional metagenomic survey of gut-associated resistomes, the largest of its kind to date, demonstrates that fecal resistomes of healthy children are far more diverse than previously suspected, that clinically relevant resistance genes are present even without recent selective

  18. Persistence of Multidrug-Resistant Acinetobacter baumannii Isolates Harboring blaOXA-23 and bap for 5 Years.

    Science.gov (United States)

    Sung, Ji Youn; Koo, Sun Hoe; Kim, Semi; Kwon, Gye Cheol

    2016-08-28

    The emergence and dissemination of carbapenemase-producing Acinetobacter baumannii isolates have been reported worldwide, and A. baumannii isolates harboring blaOXA-23 are often resistant to various antimicrobial agents. Antimicrobial resistance can be particularly strong for biofilm-forming A. baumannii isolates. We investigated the genetic basis for carbapenem resistance and biofilm-forming ability of multidrug-resistant (MDR) clinical isolates. Ninety-two MDR A. baumannii isolates were collected from one university hospital located in the Chungcheong area of Korea over a 5-year period. Multiplex PCR and DNA sequencing were performed to characterize carbapenemase and bap genes. Clonal characteristics were analyzed using REP-PCR. In addition, imaging and quantification of biofilms were performed using a crystal violet assay. All 92 MDR A. baumannii isolates involved in our study contained the blaOXA-23 and bap genes. The average absorbance of biomass in Bap-producing strains was much greater than that in non-Bap-producing strains. In our study, only three REP-PCR types were found, and the isolates showing type A or type B were found more than 60 times among unique patients during the 5 years of surveillance. These results suggest that the isolates have persisted and colonized for 5 years, and biofilm formation ability has been responsible for their persistence and colonization.

  19. Optimized Mitochondrial Targeting of Proteins Encoded by Modified mRNAs Rescues Cells Harboring Mutations in mtATP6

    Directory of Open Access Journals (Sweden)

    Randall Marcelo Chin

    2018-03-01

    Full Text Available Summary: Mitochondrial disease may be caused by mutations in the protein-coding genes of the mitochondrial genome. A promising strategy for treating such diseases is allotopic expression—the translation of wild-type copies of these proteins in the cytosol, with subsequent translocation into the mitochondria, resulting in rescue of mitochondrial function. In this paper, we develop an automated, quantitative, and unbiased screening platform to evaluate protein localization and mitochondrial morphology. This platform was used to compare 31 mitochondrial targeting sequences and 15 3′ UTRs in their ability to localize up to 9 allotopically expressed proteins to the mitochondria and their subsequent impact on mitochondrial morphology. Taking these two factors together, we synthesized chemically modified mRNAs that encode for an optimized allotopic expression construct for mtATP6. These mRNAs were able to functionally rescue a cell line harboring the 8993T > G point mutation in the mtATP6 gene. : Allotopic expression of proteins normally encoded by mtDNA is a promising therapy for mitochondrial disease. Chin et al. use an unbiased and high-content imaging-based screening platform to optimize allotopic expression. Modified mRNAs encoding for the optimized allotopic expression constructs rescued the respiration and growth of mtATP6-deficient cells. Keywords: mitochondria, mitochondrial disease, mRNA, modified mRNA, ATP6, allotopic expression, rare disease, gene therapy, screening, high content imaging

  20. The regulation of transactivator of transcription on the activity of DNA-PKcs promoter

    International Nuclear Information System (INIS)

    Yang Tianyi; Zhang Shimeng; Qin Xia; Li Bing; Liu Xiaodan; Zhou Pingkun

    2012-01-01

    Objective: To explore the influence of human immunodeficiency virus transactivator of transcription (TAT) on the promoter activity of DNA dependent protein kinase catalytic subunit (DNA-PKcs). Methods: The truncated promoters of DNA-PKcs were cloned by PCR from the template DNA from HeLa genomic DNA, and the pGL3-basic-DNA-PKcs promoter reporter plasmids were constructed. The activity of DNA-PKcs promoters was detected by dual-luciferase reporter assay system. A Lac-repressor and Lacoperator based green fluorescent protein imaging system was used to assay the chromatin remodeling activity. Results: A series of reporter plasmids harboring the truncated promoters of DNA-PKcs from -939 bp to -1 bp were constructed. The sequence of -64 bp to-1 bp was identified as a critical element for the activity of DNA-PKes promoter. TAT can suppress the activity of DNA-PKcs promoter. TAT participates in the regulation of the large scale chromatin relaxation. Ionizing radiation attenuates the activity of TAT played in the chromatin remodeling. Conclusion: TAT represses the promoter activity of DNA repair protein DNA-PKcs, and also play a role of large scale chromatin remodeling which can te attenuated by ionizing radiation. (authors)

  1. Mitochondrial DNA deletion mutations in adult mouse cardiac side population cells

    International Nuclear Information System (INIS)

    Lushaj, Entela B.; Lozonschi, Lucian; Barnes, Maria; Anstadt, Emily; Kohmoto, Takushi

    2012-01-01

    We investigated the presence and potential role of mitochondrial DNA (mtDNA) deletion mutations in adult cardiac stem cells. Cardiac side population (SP) cells were isolated from 12-week-old mice. Standard polymerase chain reaction (PCR) was used to screen for the presence of mtDNA deletion mutations in (a) freshly isolated SP cells and (b) SP cells cultured to passage 10. When present, the abundance of mtDNA deletion mutation was analyzed in single cell colonies. The effect of different levels of deletion mutations on SP cell growth and differentiation was determined. MtDNA deletion mutations were found in both freshly isolated and cultured cells from 12-week-old mice. While there was no significant difference in the number of single cell colonies with mtDNA deletion mutations from any of the groups mentioned above, the abundance of mtDNA deletion mutations was significantly higher in the cultured cells, as determined by quantitative PCR. Within a single clonal cell population, the detectable mtDNA deletion mutations were the same in all cells and unique when compared to deletions of other colonies. We also found that cells harboring high levels of mtDNA deletion mutations (i.e. where deleted mtDNA comprised more than 60% of total mtDNA) had slower proliferation rates and decreased differentiation capacities. Screening cultured adult stem cells for mtDNA deletion mutations as a routine assessment will benefit the biomedical application of adult stem cells.

  2. Yeast transformation mediated by Agrobacterium strains harboring an Ri plasmid: comparative study between GALLS of an Ri plasmid and virE of a Ti plasmid.

    Science.gov (United States)

    Kiyokawa, Kazuya; Yamamoto, Shinji; Sato, Yukari; Momota, Naoto; Tanaka, Katsuyuki; Moriguchi, Kazuki; Suzuki, Katsunori

    2012-07-01

    Agrobacterium strains containing a Ti plasmid can transfer T-DNA not only to plants but also to fungi, including the yeast Saccharomyces cerevisiae. However, no Agrobacterium strain harboring an Ri plasmid has been evaluated in fungal transformation. Some Ri plasmids have GALLS , instead of virE1 and virE2. GALLS protein can functionally substitute in plant transformation for a structurally different protein VirE2. In this study, we compared the yeast transformation ability among Agrobacterium donors: a strain containing a Ti plasmid, strains harboring either an agropine-type or a mikimopine-type Ri plasmid, and a strain having a modified Ri plasmid supplemented with a Ti plasmid type virE operon. Agrobacterium strains possessing GALLS transformed yeast cells far less efficiently than the strain containing virE operon. Production of GALLS in recipient yeast cells improved the yeast transformation mediated by an Agrobacterium strain lacking neither GALLS nor virE operon. A reporter assay to detect mobilization of the proteins fused with Cre recombinase revealed that VirE2 protein is much more abundant in yeast cells than GALLS. Based on these results, we concluded that the low yeast transformability mediated by Agrobacterium strains having the Ri plasmid is because of low amount of mobilized GALLS in yeast cells. © 2012 The Authors Journal compilation © 2012 by the Molecular Biology Society of Japan/Blackwell Publishing Ltd.

  3. A nuclear-encoded chloroplast protein harboring a single CRM domain plays an important role in the Arabidopsis growth and stress response.

    Science.gov (United States)

    Lee, Kwanuk; Lee, Hwa Jung; Kim, Dong Hyun; Jeon, Young; Pai, Hyun-Sook; Kang, Hunseung

    2014-04-16

    Although several chloroplast RNA splicing and ribosome maturation (CRM) domain-containing proteins have been characterized for intron splicing and rRNA processing during chloroplast gene expression, the functional role of a majority of CRM domain proteins in plant growth and development as well as chloroplast RNA metabolism remains largely unknown. Here, we characterized the developmental and stress response roles of a nuclear-encoded chloroplast protein harboring a single CRM domain (At4g39040), designated CFM4, in Arabidopsis thaliana. Analysis of CFM4-GFP fusion proteins revealed that CFM4 is localized to chloroplasts. The loss-of-function T-DNA insertion mutants for CFM4 (cfm4) displayed retarded growth and delayed senescence, suggesting that CFM4 plays a role in growth and development of plants under normal growth conditions. In addition, cfm4 mutants showed retarded seed germination and seedling growth under stress conditions. No alteration in the splicing patterns of intron-containing chloroplast genes was observed in the mutant plants, but the processing of 16S and 4.5S rRNAs was abnormal in the mutant plants. Importantly, CFM4 was determined to possess RNA chaperone activity. These results suggest that the chloroplast-targeted CFM4, one of two Arabidopsis genes encoding a single CRM domain-containing protein, harbors RNA chaperone activity and plays a role in the Arabidopsis growth and stress response by affecting rRNA processing in chloroplasts.

  4. Ancient mtDNA genetic variants modulate mtDNA transcription and replication.

    Directory of Open Access Journals (Sweden)

    Sarit Suissa

    2009-05-01

    Full Text Available Although the functional consequences of mitochondrial DNA (mtDNA genetic backgrounds (haplotypes, haplogroups have been demonstrated by both disease association studies and cell culture experiments, it is not clear which of the mutations within the haplogroup carry functional implications and which are "evolutionary silent hitchhikers". We set forth to study the functionality of haplogroup-defining mutations within the mtDNA transcription/replication regulatory region by in vitro transcription, hypothesizing that haplogroup-defining mutations occurring within regulatory motifs of mtDNA could affect these processes. We thus screened >2500 complete human mtDNAs representing all major populations worldwide for natural variation in experimentally established protein binding sites and regulatory regions comprising a total of 241 bp in each mtDNA. Our screen revealed 77/241 sites showing point mutations that could be divided into non-fixed (57/77, 74% and haplogroup/sub-haplogroup-defining changes (i.e., population fixed changes, 20/77, 26%. The variant defining Caucasian haplogroup J (C295T increased the binding of TFAM (Electro Mobility Shift Assay and the capacity of in vitro L-strand transcription, especially of a shorter transcript that maps immediately upstream of conserved sequence block 1 (CSB1, a region associated with RNA priming of mtDNA replication. Consistent with this finding, cybrids (i.e., cells sharing the same nuclear genetic background but differing in their mtDNA backgrounds harboring haplogroup J mtDNA had a >2 fold increase in mtDNA copy number, as compared to cybrids containing haplogroup H, with no apparent differences in steady state levels of mtDNA-encoded transcripts. Hence, a haplogroup J regulatory region mutation affects mtDNA replication or stability, which may partially account for the phenotypic impact of this haplogroup. Our analysis thus demonstrates, for the first time, the functional impact of particular mtDNA

  5. DNA Repair Systems

    Indian Academy of Sciences (India)

    DNA molecule which makes it ideal for storage and propagation of genetic information. ... of these errors are broadly referred to as DNA repair. DNA can ... changes occur in the human genome per day. ..... nails, frequent physical and mental.

  6. Multivariate analysis of heavy metal contaminations in seawater and sediments from a heavily industrialized harbor in Southern Taiwan

    International Nuclear Information System (INIS)

    Lin, Yung-Chang; Chang-Chien, Guo-Ping; Chiang, Pen-Chi; Chen, Wei-Hsiang; Lin, Yuan-Chung

    2013-01-01

    Highlights: • Kaohsiung Harbor is the largest international commercial port in Taiwan. • The metal distributions in the seawater and sediments were investigated. • Many metals exhibited higher levels of enrichment inside the harbor. • Multivariate statistical analysis was used to characterize the metal pollutions. • Two complex arrays of contamination behaviors exist inside and outside the harbor. -- Abstract: Heavy metal pollution, including chromium, zinc, arsenic, cadmium, mercury, copper, lead, and aluminum, in the largest industrial harbor in southern Taiwan was investigated. Increasing metal contamination was observed by monitoring heavy metal concentrations in seawater and sediments and estimating the enrichment factors, particularly those inside the harbor. Compared to other metal-polluted harbors worldwide, the presence of chromium in the sediments was relatively high. Excluding the background contribution, the harbor area was polluted by outflows from river mouths, wastewater discharging pipes, and point sources near industrial activities within the harbor. It is shown by principal component and cluster analyses that metal contamination was affected by a wide range of different and complex contamination mechanisms inside and outside the harbor, suggesting managing the pollution using straightforward strategies, i.e., solutions that only consider a single source or single pathway of metal emissions, is problematic

  7. A neurological comparative study of the harp seal (Pagophilus groenlandicus) and harbor porpoise (Phocoena phocoena) brain

    DEFF Research Database (Denmark)

    Walløe, Solveig; Eriksen, Nina; Dabelsteen, Torben

    2010-01-01

    The cetacean brain is well studied. However, few comparisons have been done with other marine mammals. In this study, we compared the harp seal (Pagophilus groenlandicus) and the harbor porpoise brain (Phocoena phocoena). Stereological methods were applied to compare three areas of interest...... cells, whereas the harp seal have 6.1 × 10(9) neocortical neurons and 17.5 × 10(9) neocortical glial cells. The harbor porpoise have significantly more neurons and glial cells in the auditory cortex than in the visual cortex, whereas the pattern was opposite for the harp seal. These results...... are the first to provide estimates of the number of neurons and glial cells in the neocortex of the harp seal and harbor porpoise brain and offer new data to the comparative field of mammalian brain evolution....

  8. Synthesis of DNA

    Science.gov (United States)

    Mariella, Jr., Raymond P.

    2008-11-18

    A method of synthesizing a desired double-stranded DNA of a predetermined length and of a predetermined sequence. Preselected sequence segments that will complete the desired double-stranded DNA are determined. Preselected segment sequences of DNA that will be used to complete the desired double-stranded DNA are provided. The preselected segment sequences of DNA are assembled to produce the desired double-stranded DNA.

  9. C-terminal phenylalanine of bacteriophage T7 single-stranded DNA-binding protein is essential for strand displacement synthesis by T7 DNA polymerase at a nick in DNA.

    Science.gov (United States)

    Ghosh, Sharmistha; Marintcheva, Boriana; Takahashi, Masateru; Richardson, Charles C

    2009-10-30

    Single-stranded DNA-binding protein (gp2.5), encoded by gene 2.5 of bacteriophage T7, plays an essential role in DNA replication. Not only does it remove impediments of secondary structure in the DNA, it also modulates the activities of the other replication proteins. The acidic C-terminal tail of gp2.5, bearing a C-terminal phenylalanine, physically and functionally interacts with the helicase and DNA polymerase. Deletion of the phenylalanine or substitution with a nonaromatic amino acid gives rise to a dominant lethal phenotype, and the altered gp2.5 has reduced affinity for T7 DNA polymerase. Suppressors of the dominant lethal phenotype have led to the identification of mutations in gene 5 that encodes the T7 DNA polymerase. The altered residues in the polymerase are solvent-exposed and lie in regions that are adjacent to the bound DNA. gp2.5 lacking the C-terminal phenylalanine has a lower affinity for gp5-thioredoxin relative to the wild-type gp2.5, and this affinity is partially restored by the suppressor mutations in DNA polymerase. gp2.5 enables T7 DNA polymerase to catalyze strand displacement DNA synthesis at a nick in DNA. The resulting 5'-single-stranded DNA tail provides a loading site for T7 DNA helicase. gp2.5 lacking the C-terminal phenylalanine does not support this event with wild-type DNA polymerase but does to a limited extent with T7 DNA polymerase harboring the suppressor mutations.

  10. C-terminal Phenylalanine of Bacteriophage T7 Single-stranded DNA-binding Protein Is Essential for Strand Displacement Synthesis by T7 DNA Polymerase at a Nick in DNA*

    Science.gov (United States)

    Ghosh, Sharmistha; Marintcheva, Boriana; Takahashi, Masateru; Richardson, Charles C.

    2009-01-01

    Single-stranded DNA-binding protein (gp2.5), encoded by gene 2.5 of bacteriophage T7, plays an essential role in DNA replication. Not only does it remove impediments of secondary structure in the DNA, it also modulates the activities of the other replication proteins. The acidic C-terminal tail of gp2.5, bearing a C-terminal phenylalanine, physically and functionally interacts with the helicase and DNA polymerase. Deletion of the phenylalanine or substitution with a nonaromatic amino acid gives rise to a dominant lethal phenotype, and the altered gp2.5 has reduced affinity for T7 DNA polymerase. Suppressors of the dominant lethal phenotype have led to the identification of mutations in gene 5 that encodes the T7 DNA polymerase. The altered residues in the polymerase are solvent-exposed and lie in regions that are adjacent to the bound DNA. gp2.5 lacking the C-terminal phenylalanine has a lower affinity for gp5-thioredoxin relative to the wild-type gp2.5, and this affinity is partially restored by the suppressor mutations in DNA polymerase. gp2.5 enables T7 DNA polymerase to catalyze strand displacement DNA synthesis at a nick in DNA. The resulting 5′-single-stranded DNA tail provides a loading site for T7 DNA helicase. gp2.5 lacking the C-terminal phenylalanine does not support this event with wild-type DNA polymerase but does to a limited extent with T7 DNA polymerase harboring the suppressor mutations. PMID:19726688

  11. Safe Harbor Legislation for Juvenile Victims of Sex Trafficking: A Myopic View of Improvements in Practice

    Directory of Open Access Journals (Sweden)

    Kimberly Mehlman-Orozco

    2015-02-01

    Full Text Available Current social and political realties have focused attention on human trafficking in the United States. Although new mechanisms for criminalizing offenders and protecting victims are increasingly funded and implemented across the country, empirical exploration into the efficacy of these interventions is lacking. This article uses yearly count data on juvenile prostitution arrests aggregated at the state level to explore the criminalization of commercial sexually exploited children post safe harbor policy implementation. Preliminary data from four states suggests that the passage of safe harbor laws may not reduce the number of juveniles arrested for prostitution crimes. Implications for future research are discussed.

  12. Phaeobacter inhibens from the Roseobacter clade has an environmental niche as a surface colonizer in harbors

    DEFF Research Database (Denmark)

    Gram, Lone; Rasmussen, Bastian Barker; Wemheuer, Bernd

    2015-01-01

    in the environment is to date unknown. Here, we report on the repeated isolation of Phaeobacter inhibens strains from a marine environment (harbors) not related to aquaculture. Based on phenotype and 16S rRNA gene sequence similarity, a total of 64 P. inhibens strains were identified from 35 samples (eukaryotic...... and used for amplification of 16S rRNA. P. inhibens was detected in five of these samples, all of which were biofilm samples, by pyrotag-sequencing at a prevalence of 0.02–0.68% of the prokaryotic community. The results indicated that P. inhibens had a niche in biofilms of fouled surfaces in harbor areas...

  13. Harbor Seal (Phoca vitulina) Reproductive Advertisement Behavior and the Effects of Vessel Noise

    Science.gov (United States)

    Matthews, Leanna P.

    Harbor seals (Phoca vitulina) are a widely distributed pinniped species that mate underwater. Similar to other aquatically mating pinnipeds, male harbor seals produce vocalizations during the breeding season that function in male-male interactions and possibly as an attractant for females. I investigated multiple aspects of these reproductive advertisement displays in a population of harbor seals in Glacier Bay National Park and Preserve, Alaska. First, I looked at vocal production as a function of environmental variables, including season, daylight, and tidal state. Vocalizations were highly seasonal and detection of these vocalizations peaked in June and July, which correspond with the estimated time of breeding. Vocalizations also varied with light, with the lowest probability of detection during the day and the highest probability of detection at night. The high probability of detection corresponded to when females are known to forage. These results are similar to the vocal behavior of previously studied populations. However, unlike previously studied populations, the detection of harbor seal breeding vocalizations did not vary with tidal state. This is likely due to the location of the hydrophone, as it was not near the haul out and depth was therefore not significantly influenced by changes in tidal height. I also investigated the source levels and call parameters of vocalizations, as well as call rate and territoriality. The average source level of harbor seal breeding vocalizations was 144 dB re 1 ?Pa at 1 m and measurements ranged from 129 to 149 dB re 1 ?Pa. Analysis of call parameters indicated that vocalizations of harbor seals in Glacier Bay were similar in duration to other populations, but were much lower in frequency. During the breeding season, there were two discrete calling areas that likely represent two individual males; the average call rate in these display areas was approximately 1 call per minute. The harbor seal breeding season also

  14. New genomic resources for switchgrass: a BAC library and comparative analysis of homoeologous genomic regions harboring bioenergy traits

    Directory of Open Access Journals (Sweden)

    Feltus Frank A

    2011-07-01

    Full Text Available Abstract Background Switchgrass, a C4 species and a warm-season grass native to the prairies of North America, has been targeted for development into an herbaceous biomass fuel crop. Genetic improvement of switchgrass feedstock traits through marker-assisted breeding and biotechnology approaches calls for genomic tools development. Establishment of integrated physical and genetic maps for switchgrass will accelerate mapping of value added traits useful to breeding programs and to isolate important target genes using map based cloning. The reported polyploidy series in switchgrass ranges from diploid (2X = 18 to duodecaploid (12X = 108. Like in other large, repeat-rich plant genomes, this genomic complexity will hinder whole genome sequencing efforts. An extensive physical map providing enough information to resolve the homoeologous genomes would provide the necessary framework for accurate assembly of the switchgrass genome. Results A switchgrass BAC library constructed by partial digestion of nuclear DNA with EcoRI contains 147,456 clones covering the effective genome approximately 10 times based on a genome size of 3.2 Gigabases (~1.6 Gb effective. Restriction digestion and PFGE analysis of 234 randomly chosen BACs indicated that 95% of the clones contained inserts, ranging from 60 to 180 kb with an average of 120 kb. Comparative sequence analysis of two homoeologous genomic regions harboring orthologs of the rice OsBRI1 locus, a low-copy gene encoding a putative protein kinase and associated with biomass, revealed that orthologous clones from homoeologous chromosomes can be unambiguously distinguished from each other and correctly assembled to respective fingerprint contigs. Thus, the data obtained not only provide genomic resources for further analysis of switchgrass genome, but also improve efforts for an accurate genome sequencing strategy. Conclusions The construction of the first switchgrass BAC library and comparative analysis of

  15. Manila clams from Hg polluted sediments of Marano and Grado lagoons (Italy) harbor detoxifying Hg resistant bacteria in soft tissues

    International Nuclear Information System (INIS)

    Baldi, Franco; Gallo, Michele; Marchetto, Davide; Faleri, Claudia; Maida, Isabel; Fani, Renato

    2013-01-01

    A mechanism of mercury detoxification has been suggested by a previous study on Hg bioaccumulation in Manila clams (Ruditapes philippinarum) in the polluted Marano and Grado lagoons and in this study we demonstrate that this event could be partly related to the detoxifying activities of Hg-resistant bacteria (MRB) harbored in clam soft tissues. Therefore, natural clams were collected in six stations during two different periods (winter and spring) from Marano and Grado Lagoons. Siphons, gills and hepatopancreas from acclimatized clams were sterile dissected to isolate MRB. These anatomical parts were glass homogenized or used for whole, and they were lying on a solid medium containing 5 mg l −1 HgCl 2 and incubated at 30 °C. A total of fourteen bacterial strains were isolated and were identified by 16S rDNA sequencing and analysis, revealing that strains were representative of eight bacterial genera, four of which were Gram-positive (Enterococcus, Bacillus, Jeotgalicoccus and Staphylococcus) and other four were Gram-negative (Stenotrophomonas, Vibrio, Raoultella and Enterobacter). Plasmids and merA genes were found and their sequences determined. Fluorescence in situ hybridization (FISH) technique shows the presence of Firmicutes, Actinobacteria and Gammaproteobacteria by using different molecular probes in siphon and gills. Bacterial clumps inside clam flesh were observed and even a Gram-negative endosymbiont was disclosed by transmission electronic microscope inside clam cells. Bacteria harbored in cavities of soft tissue have mercury detoxifying activity. This feature was confirmed by the determination of mercuric reductase in glass-homogenized siphons and gills. -- Highlights: ► We isolated Gram-positive and Gram-negative Hg resistant strains from soft tissues of Ruditapes philippinarum. ► We identify 14 mercury resistant strains by 16S rRNA gene sequences. ► Bacteria in siphon and gill tissues of clams were observed by TEM and identified with

  16. Manila clams from Hg polluted sediments of Marano and Grado lagoons (Italy) harbor detoxifying Hg resistant bacteria in soft tissues

    Energy Technology Data Exchange (ETDEWEB)

    Baldi, Franco [Dipartimento di Scienze Molecolari e Nanosistemi, Cà Foscari University of Venice, Dorsoduro 2137, 30123 Venice (Italy); Gallo, Michele; Marchetto, Davide [Dipartimento di Scienze Molecolari e Nanosistemi, Cà Foscari University of Venice, Dorsoduro 2137, 30123 Venice (Italy); Faleri, Claudia [Department of Environmental Science ‘G. Sarfatti’, University of Siena, 53100 Siena (Italy); Maida, Isabel; Fani, Renato [Dipartimento di Biologia Evoluzionistica, Via Romana, 17, University of Florence, 50125 Florence (Italy)

    2013-08-15

    A mechanism of mercury detoxification has been suggested by a previous study on Hg bioaccumulation in Manila clams (Ruditapes philippinarum) in the polluted Marano and Grado lagoons and in this study we demonstrate that this event could be partly related to the detoxifying activities of Hg-resistant bacteria (MRB) harbored in clam soft tissues. Therefore, natural clams were collected in six stations during two different periods (winter and spring) from Marano and Grado Lagoons. Siphons, gills and hepatopancreas from acclimatized clams were sterile dissected to isolate MRB. These anatomical parts were glass homogenized or used for whole, and they were lying on a solid medium containing 5 mg l{sup −1} HgCl{sub 2} and incubated at 30 °C. A total of fourteen bacterial strains were isolated and were identified by 16S rDNA sequencing and analysis, revealing that strains were representative of eight bacterial genera, four of which were Gram-positive (Enterococcus, Bacillus, Jeotgalicoccus and Staphylococcus) and other four were Gram-negative (Stenotrophomonas, Vibrio, Raoultella and Enterobacter). Plasmids and merA genes were found and their sequences determined. Fluorescence in situ hybridization (FISH) technique shows the presence of Firmicutes, Actinobacteria and Gammaproteobacteria by using different molecular probes in siphon and gills. Bacterial clumps inside clam flesh were observed and even a Gram-negative endosymbiont was disclosed by transmission electronic microscope inside clam cells. Bacteria harbored in cavities of soft tissue have mercury detoxifying activity. This feature was confirmed by the determination of mercuric reductase in glass-homogenized siphons and gills. -- Highlights: ► We isolated Gram-positive and Gram-negative Hg resistant strains from soft tissues of Ruditapes philippinarum. ► We identify 14 mercury resistant strains by 16S rRNA gene sequences. ► Bacteria in siphon and gill tissues of clams were observed by TEM and identified

  17. Brown-headed cowbirds (Molothrus ater) harbor Sarcocystis neurona and act as intermediate hosts.

    Science.gov (United States)

    Mansfield, L S; Mehler, S; Nelson, K; Elsheikha, H M; Murphy, A J; Knust, B; Tanhauser, S M; Gearhart, P M; Rossano, M G; Bowman, D D; Schott, H C; Patterson, J S

    2008-05-06

    We tested the hypothesis that brown-headed cowbirds (Molothrus ater) harbor Sarcocystis neurona, the agent of equine protozoal myeloencephalitis (EPM), and act as intermediate hosts for this parasite. In summer 1999, wild caught brown-headed cowbirds were collected and necropsied to determine infection rate with Sarcocystis spp. by macroscopic inspection. Seven of 381 (1.8%) birds had grossly visible sarcocysts in leg muscles with none in breast muscles. Histopathology revealed two classes of sarcocysts in leg muscles, thin-walled and thick-walled suggesting two species. Electron microscopy showed that thick-walled cysts had characteristics of S. falcatula and thin-walled cysts had characteristics of S. neurona. Thereafter, several experiments were conducted to confirm that cowbirds had viable S. neurona that could be transmitted to an intermediate host and cause disease. Specific-pathogen-free opossums fed cowbird leg muscle that was enriched for muscle either with or without visible sarcocysts all shed high numbers of sporocysts by 4 weeks after infection, while the control opossum fed cowbird breast muscle was negative. These sporocysts were apparently of two size classes, 11.4+/-0.7 microm by 7.6+/-0.4 microm (n=25) and 12.6+/-0.6 microm by 8.0+/-0 microm (n=25). When these sporocysts were excysted and introduced into equine dermal cell tissue culture, schizogony occurred, most merozoites survived and replicated long term and merozoites sampled from the cultures with long-term growth were indistinguishable from known S. neurona isolates. A cowbird Sarcocystis isolate, Michigan Cowbird 1 (MICB1), derived from thin-walled sarcocysts from cowbirds that was passaged in SPF opossums and tissue culture went on to produce neurological disease in IFNgamma knockout mice indistinguishable from that of the positive control inoculated with S. neurona. This, together with the knowledge that S. falcatula does not cause lesions in IFNgamma knockout mice, showed that cowbird

  18. 76 FR 27970 - Safety Zone; Cape Charles Fireworks, Cape Charles Harbor, Cape Charles, VA.

    Science.gov (United States)

    2011-05-13

    ... Charles will sponsor a fireworks display on the shoreline of the navigable waters of Cape Charles City...[deg]01'30'' W (NAD 1983). This safety zone will be established in the vicinity of Cape Charles, VA...-AA00 Safety Zone; Cape Charles Fireworks, Cape Charles Harbor, Cape Charles, VA. AGENCY: Coast Guard...

  19. 75 FR 38019 - Safety Zone; Fixed Mooring Balls, South of Barbers Pt. Harbor Channel, Oahu, HI

    Science.gov (United States)

    2010-07-01

    ... DEPARTMENT OF HOMELAND SECURITY Coast Guard 33 CFR Part 165 [Docket No. USCG-2010-0457] RIN 1625-AA00 Safety Zone; Fixed Mooring Balls, South of Barbers Pt. Harbor Channel, Oahu, HI AGENCY: Coast Guard, DHS. ACTION: Temporary final rule. SUMMARY: Due to the placement of six fixed mooring balls in an...

  20. 75 FR 56130 - Pearl Harbor National Wildlife Refuge, Honolulu County, HI; Comprehensive Conservation Plan and...

    Science.gov (United States)

    2010-09-15

    ... DEPARTMENT OF THE INTERIOR Fish and Wildlife Service [FWS-R1-R-2010-N160; 1265-0000-10137-S3] Pearl Harbor National Wildlife Refuge, Honolulu County, HI; Comprehensive Conservation Plan and... Kamehameha Highway, Room 2C, Hale`iwa, HI 96712. Alternatively, you may fax comments to the refuge at (808...

  1. Side-scan imagery of Apra Harbor, Guam U.S. Territory

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Gridded side-scan imagery collected in Apra Harbor, Guam U.S. Territory, USA. The GeoTIFF and Arc ASCII file includes data that were collected using a Klein 3000...

  2. Evaluation of Proposed Dredged Material Disposal Alternatives for New York/New Jersey Harbor. Phase 1

    Science.gov (United States)

    1988-08-01

    been developed ( Westerdahl and Skogerboe 1981) and is being used x..-’. to predict surface runoff water quality from dredged material as part of the...Islands in New York Harbor," Miscellaneous Paper D-88-3, US Army Engineer Waterways Experiment Station, Vicksburg, MS. Westerdahl , H. E., and Skogerboe

  3. Application of heterogeneous multiple camera system with panoramic capabilities in a harbor environment

    NARCIS (Netherlands)

    Schwering, P.B.W.; Lensen, H.A.; Broek, S.P. van den; Hollander, R.J.M. den; Mark, W. van der; Bouma, H.; Kemp, R.A.W.

    2009-01-01

    In a harbor environment threats like explosives-packed rubber boats, mine-carrying swimmers and divers must be detected in an early stage. This paper describes the integration and use of a heterogeneous multiple camera system with panoramic observation capabilities for detecting these small vessels

  4. Cold Spring Harbor symposia on quantitative biology: Volume 51, Molecular biology of /ital Homo sapiens/

    International Nuclear Information System (INIS)

    1986-01-01

    This volume is the second part of a collection of papers submitted by the participants to the 1986 Cold Spring Harbor Symposium on Quantitative Biology entitled Molecular Biology of /ital Homo sapiens/. The 49 papers included in this volume are grouped by subject into receptors, human cancer genes, and gene therapy. (DT)

  5. Mitigation of Shore Damage Attributed to the Federal Navigation Structures at Port Sanilac Harbor, Michigan.

    Science.gov (United States)

    1975-09-01

    produces waves with nealioible wace heights (i.e., 0.5 feet); (b) all waves were deep water waves with no correction for shallow water; and, (c) the...at that harbor. This would re- sult in a loss to the local economy . Ini addition, littoral drift would resume southward thus affecting the littoral

  6. Factors Contributing to Corrosion of Steel Pilings in Duluth-Superior Harbor

    Science.gov (United States)

    2009-11-01

    1226 Office of Counsel,Code 1008.3 ADOR/Director NCST E. R. Franchi , 7000 Public Affairs (Unclassified/ Unlimited Only), Code 703o 4...Great Lakes. Accelerated corrosion of CS pilings in estua- rine and marine harbors is a global phenomenon.9 The term "accelerated low water corrosion

  7. 78 FR 18481 - Drawbridge Operation Regulations; Inner Harbor Navigation Canal, LA

    Science.gov (United States)

    2013-03-27

    ... regulation governing the operation of the US 90 (Danzinger) vertical lift span drawbridge across the Inner... Lift Span Bridge across the Inner Harbor Navigation Canal, mile 3.10 at New Orleans, Orleans Parish, Louisiana. The bridge has a vertical clearance of 50 feet above mean high water, elevation 5.0 feet Mean Sea...

  8. 77 FR 42640 - Safety Zone; Can-Am Festival Fireworks, Black River Bay, Sackets Harbor, NY

    Science.gov (United States)

    2012-07-20

    ...-AA00 Safety Zone; Can-Am Festival Fireworks, Black River Bay, Sackets Harbor, NY AGENCY: Coast Guard... Black River Bay during the Can-Am Festival Fireworks display. This temporary safety zone is necessary to... Can-Am Festival Fireworks. This zone will be effective and enforced from 9:15 p.m. until 10:45 p.m. on...

  9. 33 CFR 110.190 - Tortugas Harbor, in vicinity of Garden Key, Dry Tortugas, Fla.

    Science.gov (United States)

    2010-07-01

    ... Garden Key, Dry Tortugas, Fla. 110.190 Section 110.190 Navigation and Navigable Waters COAST GUARD..., in vicinity of Garden Key, Dry Tortugas, Fla. (a) The anchorage grounds. All of Bird Key Harbor, southwest of Garden Key, bounded by the surrounding reefs and shoals and, on the northeast, by a line...

  10. 78 FR 62439 - Drawbridge Operation Regulation; Inner Harbor Navigational Canal, New Orleans, LA

    Science.gov (United States)

    2013-10-22

    ... Operation Regulation; Inner Harbor Navigational Canal, New Orleans, LA AGENCY: Coast Guard, DHS. ACTION..../Seabrook) bridge across the IHNC, mile 4.6, both at New Orleans, LA. This deviation will test changes to... Intra-Costal Waterway (GIWW). The US 90 (Danzinger) Bridge across the IHNC, mile 3.1, at New Orleans...

  11. 75 FR 8486 - Drawbridge Operation Regulation; Inner Harbor Navigational Canal, New Orleans, LA

    Science.gov (United States)

    2010-02-25

    ... Operation Regulation; Inner Harbor Navigational Canal, New Orleans, LA AGENCY: Coast Guard, DHS. ACTION... EHL), at New Orleans, LA. The deviation is necessary to replace the counterweight wire ropes on the... Building Ground Floor, Room W12-140, 1200 New Jersey Avenue, SE., Washington, DC 20590, between 9 a.m. and...

  12. 78 FR 63136 - Drawbridge Operation Regulation; Inner Harbor Navigational Canal, New Orleans, LA

    Science.gov (United States)

    2013-10-23

    ...-AA09 Drawbridge Operation Regulation; Inner Harbor Navigational Canal, New Orleans, LA AGENCY: Coast... 4.6, both at New Orleans, LA. This proposed change would allow for the safe navigation of vessels... Department of Transportation and Development (LDOTD) (representing the New Orleans Levee District which is...

  13. 3 CFR 8463 - Proclamation 8463 of December 4, 2009. National Pearl Harbor Remembrance Day, 2009

    Science.gov (United States)

    2010-01-01

    ... who selflessly served our Nation at home and abroad during World War II. On a tranquil Sunday morning, as war raged around the globe, the attack on Pearl Harbor effectively ended American isolation... have hereunto set my hand this fourth day of December, in the year of our Lord two thousand nine, and...

  14. 76 FR 4574 - Drawbridge Operation Regulations; Oakland Inner Harbor Tidal Canal, Oakland/Alameda, CA, Schedule...

    Science.gov (United States)

    2011-01-26

    ... Boating Federation, Hanson Aggregates, Power Engineering, Harbor Bay Maritime, Dutra Group, Oakland Yacht... Association, Aeolian Yacht Club, Briar Rose Yacht Charters, Baytech Marine Service, Heinold's First and Last... Outboard Motor Shop, Waterfront Hotel-Miss Pearl's Restaurant, Encinal Yacht Club, Marina Village Inn...

  15. 78 FR 24069 - Safety Zone; 12th Annual Saltwater Classic; Port Canaveral Harbor; Port Canaveral, FL

    Science.gov (United States)

    2013-04-24

    ... under Executive Order 13045, Protection of Children from Environmental Health Risks and Safety Risks. This rule is not an economically significant rule and does not create an environmental risk to health...-AA00 Safety Zone; 12th Annual Saltwater Classic; Port Canaveral Harbor; Port Canaveral, FL AGENCY...

  16. 78 FR 27304 - Safety Zone; Melrose Pyrotechnics Fireworks Display; Chicago Harbor, Chicago, IL

    Science.gov (United States)

    2013-05-10

    ... environmental risk to health or risk to safety that may disproportionately affect children. 11. Indian Tribal... Pier in Chicago Harbor, Chicago, IL. The Captain of the Port, Lake Michigan, has determined that these fireworks displays will pose a significant risk to public safety and property. Such hazards include falling...

  17. 78 FR 52753 - Taking of Marine Mammals Incidental to Commercial Fishing Operations; Harbor Porpoise Take...

    Science.gov (United States)

    2013-08-26

    ... strategy enacted in 2010 based on deliberations by the Harbor Porpoise Take Reduction Team. This action is... information (e.g., name, address, etc.), confidential business information, or otherwise sensitive information... Protection Act (MMPA) to reduce the level of serious injury and mortality of the Gulf of Maine/Bay of Fundy...

  18. 75 FR 18887 - Division of Longshore and Harbor Workers' Compensation; Proposed Collection; Comment Request

    Science.gov (United States)

    2010-04-13

    ... can be provided in the desired format, reporting burden (time and financial resources) is minimized... comment on proposed and/or continuing collections of information in accordance with the paperwork... concerning the proposed collection: Securing Financial Obligations under the Longshore and Harbor Workers...

  19. Observations and modeling of tsunami-induced currents in ports and harbors

    Science.gov (United States)

    Lynett, Patrick J.; Borrero, Jose C.; Weiss, Robert; Son, Sangyoung; Greer, Dougal; Renteria, Willington

    2012-04-01

    Tsunamis, or "harbor waves" in Japanese, are so-named due to common observations of enhanced wave heights, currents and damage in harbors and ports. However, dynamic currents induced by these waves, while regularly observed and known to cause significant damage, are poorly understood. Observations and modeling of the currents induced by the 2011 Tohoku and 2004 Indian Ocean tsunamis allows us to show that the strongest flows in harbor basins are governed by horizontally sheared and rotational shallow features, such as jets and large eddies. When examining currents in harbors, this conclusion will generally require a simulation approach that both includes the relevant physical processes in the governing equations and uses a numerical scheme that does not artificially damp these features. Without proper representation of the physics associated with these phenomena, predictive models may provide drag force estimates that are an order of magnitude or more in error. The immediate implementation of this type of analysis into tsunami hazard studies can mean the difference between an unaffected port and one in which 300 m long container vessels are detached from their moorings and drift chaotically.

  20. Surveillance for zoonotic and selected pathogens in harbor seals Phoca vitulina from central California

    Science.gov (United States)

    Greig, Denise J.; Ip, Hon S.; Gulland, Frances M. D.; Miller, Woutrina A.; Conrad, Patricia A.; Field, Cara L.; Fleetwood, Michelle; Harvey, James T.; Jang, Spencer; Packham, Andrea; Wheeler, Elizabeth; Hall, Ailsa J.

    2014-01-01

    The infection status of harbor seals Phoca vitulina in central California, USA, was evaluated through broad surveillance for pathogens in stranded and wild-caught animals from 2001 to 2008, with most samples collected in 2007 and 2008. Stranded animals from Mendocino County to San Luis Obispo County were sampled at a rehabilitation facility: The Marine Mammal Center (TMMC, n = 175); wild-caught animals were sampled at 2 locations: San Francisco Bay (SF, n = 78) and Tomales Bay (TB, n = 97), that differed in degree of urbanization. Low prevalences of Salmonella, Campylobacter, Giardia, and Cryptosporidium were detected in the feces of stranded and wild-caught seals. Clostridium perfringens and Escherichia coli were more prevalent in the feces of stranded (58% [78 out of 135] and 76% [102 out of 135]) than wild-caught (42% [45 out of 106] and 66% [68 out of 106]) seals, whereas Vibrio spp. were 16 times more likely to be cultured from the feces of seals from SF than TB or TMMC (p neurona, and type A influenza was only detected in the wild-caught harbor seals (post-weaning age classes), whereas antibody titers to Leptospira spp. were detected in stranded and wild-caught seals. No stranded (n = 109) or wild-caught (n = 217) harbor seals had antibodies to phocine distemper virus, although a single low titer to canine distemper virus was detected. These results highlight the role of harbor seals as sentinel species for zoonotic and terrestrial pathogens in the marine environment.

  1. Influenza A (H10N7) Virus Causes Respiratory Tract Disease in Harbor Seals and Ferrets

    NARCIS (Netherlands)

    van den Brand, Judith M A; Wohlsein, Peter; Herfst, Sander; Bodewes, Rogier; Pfankuche, Vanessa M; van de Bildt, Marco W G; Seehusen, Frauke; Puff, Christina; Richard, Mathilde; Siebert, Ursula; Lehnert, Kristina; Bestebroer, Theo; Lexmond, Pascal; Fouchier, Ron A M; Prenger-Berninghoff, Ellen; Herbst, Werner; Koopmans, Marion; Osterhaus, Albert D M E; Kuiken, Thijs; Baumgärtner, Wolfgang

    2016-01-01

    Avian influenza viruses sporadically cross the species barrier to mammals, including humans, in which they may cause epidemic disease. Recently such an epidemic occurred due to the emergence of avian influenza virus of the subtype H10N7 (Seal/H10N7) in harbor seals (Phoca vitulina). This epidemic

  2. Sedimentation and chronology of heavy metal pollution in Oslo harbor, Norway

    DEFF Research Database (Denmark)

    Lepland, Aivo; Andersen, Thorbjørn Joest; Lepland, Aave

    2010-01-01

    Stratigraphic profiles of Cu, Cd and Hg in ten sediment cores from the Oslo harbor, Norway, combined with results of radiometric dating demonstrate that pollution by these metals peaked between 1940 and 1970. Dating results indicate that Hg discharges peaked between 1940 and 1950, Cd reached...

  3. Seroprevalence of Brucella antibodies in harbor seals in Alaska, USA, with age, regional, and reproductive comparisons.

    Science.gov (United States)

    Hoover-Miller, A; Dunn, J L; Field, C L; Blundell, G; Atkinson, S

    2017-09-20

    Populations of harbor seal Phoca vitulina in the Gulf of Alaska have dramatically declined during the past 4 decades. Numbers of seals in Glacier Bay, in southeast Alaska, USA, have also declined despite extensive protection. Causes of the declines and slow recovery are poorly understood. Brucellosis is a zoonotic disease that adversely affects reproduction in many domestic species. We measured the seroprevalence of Brucella antibodies in 554 harbor seals in 3 Alaska locations: Prince William Sound (PWS), Glacier Bay (GB), and Tracy Arm Fords Terror (TAFT) Wilderness Area. Objectives included testing for regional, sex, age, and female reproductive state differences in Brucella antibody seroprevalence, persistence in titers in recaptured seals, and differences in titers between mother seals and their pups. Overall, 52% of adults (AD), 53% of subadults (SA), 77% of yearlings (YRL), and 26% of Brucella. Results show higher seroprevalence (64%) for AD and SA seals in the depressed and declining populations in PWS and GB than in TAFT (29%). Lactating females were less likely to be seropositive than other AD females, including pregnant females. Further research is needed to seek evidence of Brucella infection in Alaskan harbor seals, identify effects on neonatal viability, and assess zoonotic implications for Alaska Natives who rely on harbor seals for food.

  4. 33 CFR 117.213 - New Haven Harbor, Quinnipiac and Mill Rivers.

    Science.gov (United States)

    2010-07-01

    ... Mill Rivers. 117.213 Section 117.213 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF... Haven Harbor, Quinnipiac and Mill Rivers. The draws of the Tomlinson bridge, mile 0.0, the Ferry Street... bridge, mile 0.4 across Mill River, shall operate as follows: (a) The draws shall open on signal; except...

  5. 75 FR 1738 - Drawbridge Operation Regulation; New Haven Harbor, Quinnipiac and Mill Rivers, CT

    Science.gov (United States)

    2010-01-13

    ...-AA09 Drawbridge Operation Regulation; New Haven Harbor, Quinnipiac and Mill Rivers, CT AGENCY: Coast... regulation governing the operation of three bridges across the Quinnipiac and Mill Rivers at New Haven... and 15 feet at mean low water. The Chapel Street Bridge at mile 0.4, across the Mill River has a...

  6. 77 FR 75917 - Drawbridge Operation Regulation; New Haven Harbor, Quinnipiac and Mill Rivers, CT

    Science.gov (United States)

    2012-12-26

    ...-AA09 Drawbridge Operation Regulation; New Haven Harbor, Quinnipiac and Mill Rivers, CT AGENCY: Coast..., mile 1.3, across the Quinnipiac River, and the Chapel Street Bridge, mile 0.4, across the Mill River..., across the Quinnipiac River, and the Chapel Street Bridge, mile 0.4, across the Mill River, to reduce the...

  7. 76 FR 12 - Drawbridge Operation Regulations; New Haven Harbor, Quinnipiac and Mill Rivers, New Haven, CT

    Science.gov (United States)

    2011-01-03

    ... DEPARTMENT OF HOMELAND SECURITY Coast Guard 33 CFR Part 117 [Docket No. USCG-2010-1096] Drawbridge Operation Regulations; New Haven Harbor, Quinnipiac and Mill Rivers, New Haven, CT AGENCY: Coast Guard, DHS. ACTION: Notice of temporary deviation from regulations. SUMMARY: The Commander, First Coast Guard...

  8. Space Threat Warning: Foundation for Space Superiority, Avoiding a Space Pearl Harbor

    National Research Council Canada - National Science Library

    Burke, Alan W

    2006-01-01

    ... have stated the US must avoid a space Pearl Harbor. This concern is due to the idea that a decrease in the perceived threat to space assets after the demise of the Soviet Union coupled with a competition for space resources has resulted...

  9. Radiological survey of the Pearl Harbor Naval Shipyard and Environs, Honolulu, Hawaii. Final report

    International Nuclear Information System (INIS)

    Callis, R.S.

    1987-06-01

    This report presents results of the survey conducted by the Eastern Environmental Radiation Facility personnel to assess levels of environmental radioactivity resulting from maintenance and operation of nuclear-powered warships at the Pearl Harbor Naval Shipyard and Environs on the Hawaiian Island of Oahu

  10. Remembering Pearl Harbor: The USS Arizona Memorial. Teaching with Historic Places.

    Science.gov (United States)

    Vierra, John, Jr.

    This lesson describes and discusses the submerged remains of the battleship USS Arizona which rests on the silt of Pearl Harbor (Hawaii), just as it had settled on December 7, 1941, the day Japan attacked the U.S. fleet and began the Pacific battles of World War II. The lesson is based on the National Register of Historic Places registration file,…

  11. One surgeon's Army experience with "wound shock" from Pearl Harbor to the present.

    Science.gov (United States)

    Hardaway, Robert M

    2009-09-01

    The Army has had extensive experience in the study and treatment of shock, beginning with the American Civil War and continuing to the present. This is the story of one Army surgeon's experience, both in research and treatment of shock, from Pearl Harbor to the present.

  12. Japan's Monroe Doctrine?: Re-Framing the Story of Pearl Harbor

    Science.gov (United States)

    Murnane, John R.

    2007-01-01

    Ever since War Department propaganda films set the mold, historians have pretty much followed: the road to Pearl Harbor began in 1931 with Japanese aggression in Manchuria. Any "revision" regarding the War in the Pacific has its own set of problems--engendering controversy, often running up against patriotic sentiments and the tendency…

  13. Revisiting "Pearl Harbor": Resistance to Reel and Real Events in an English Language Classroom

    Science.gov (United States)

    Mackie, Ardiss; Norton, Bonny

    2006-01-01

    In this article, we draw on disruptive scenes in a postsecondary classroom to examine a critical incident concerning conflicting readings of the film "Pearl Harbor" (2001). We raise crucial questions for pedagogical work with popular film: Who speaks for whom about the meaning of a given film? Under what conditions do students resist…

  14. 78 FR 46855 - Safety Zone; East End Maritime Foundation Fireworks Display, Greenport Harbor, Greenport, NY

    Science.gov (United States)

    2013-08-02

    ... 1625-AA00 Safety Zone; East End Maritime Foundation Fireworks Display, Greenport Harbor, Greenport, NY... temporary rule proposes to establish a safety zone for the East End Maritime Foundation fireworks display....1. 0 2. Add Sec. 165.T01-0600 to read as follows: Sec. 165.T01-0600 Safety Zone; East End Maritime...

  15. 75 FR 18056 - Safety Zone; Fireworks Display, Patuxent River, Solomons Island Harbor, MD

    Science.gov (United States)

    2010-04-09

    ... the event, and enhancing public and maritime safety. Basis and Purpose Fireworks displays are... promote public and maritime safety during a fireworks display, and to protect mariners transiting the area...-AA00 Safety Zone; Fireworks Display, Patuxent River, Solomons Island Harbor, MD AGENCY: Coast Guard...

  16. 76 FR 57087 - Stone Harbor Investment Partners LP, et al.; Notice of Application

    Science.gov (United States)

    2011-09-15

    ... SECURITIES AND EXCHANGE COMMISSION [Investment Company Act Release No. 29784; File No. 812-13931] Stone Harbor Investment Partners LP, et al.; Notice of Application September 7, 2011. AGENCY: Securities..., or cause more than 10% of the acquired company's voting stock to be owned by investment companies and...

  17. 33 CFR 165.116 - Safety and Security Zones; Salem and Boston Harbors, Massachusetts.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Safety and Security Zones; Salem..., DEPARTMENT OF HOMELAND SECURITY (CONTINUED) PORTS AND WATERWAYS SAFETY REGULATED NAVIGATION AREAS AND LIMITED... § 165.116 Safety and Security Zones; Salem and Boston Harbors, Massachusetts. (a) Location. The...

  18. 33 CFR 165.114 - Safety and Security Zones: Escorted Vessels-Boston Harbor, Massachusetts.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Safety and Security Zones... COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) PORTS AND WATERWAYS SAFETY REGULATED NAVIGATION... Guard District § 165.114 Safety and Security Zones: Escorted Vessels—Boston Harbor, Massachusetts. (a...

  19. 78 FR 19158 - Safety Zone; USA Triathlon, Milwaukee Harbor, Milwaukee, WI

    Science.gov (United States)

    2013-03-29

    ... have minimal impact on the economy, will not interfere with other agencies, will not adversely alter... Milwaukee Harbor due to the 2013 and 2014 Olympic and Sprint Distance National Championships. This proposed... the 2013 and 2014 Olympic and Sprint Distance National Championships. DATES: Comments and related...

  20. Beyond Parasitism: Hepatic Lesions in Stranded Harbor Porpoises (Phocoena phocoena) Without Trematode (Campula oblonga) Infections

    NARCIS (Netherlands)

    S. Hiemstra; L. Harkema (Liesbeth); L.C.M. Wiersma (Lidewij); R.I. Keesler

    2015-01-01

    textabstractThe liver can be an indicator of the health of an individual or of a group, which can be especially important to identify agents that can cause disease in multiple species. To better characterize hepatic lesions in stranded harbor porpoises (Phocoena phocoena), we analyzed the livers

  1. Synergistic growth inhibition of cancer cells harboring the RET/PTC1 ...

    Indian Academy of Sciences (India)

    Synergistic growth inhibition of cancer cells harboring the RET/PTC1 oncogene by staurosporine and rotenone involves enhanced cell death. ANTÓNIO PEDRO GONÇALVES, ARNALDO VIDEIRA, VALDEMAR MÁXIMO and PAULA SOARES. J. Biosci. 36(4), September 2011, 639-648, © Indian Academy of Sciences.

  2. 33 CFR 117.669 - St. Louis River (Duluth Superior Harbor).

    Science.gov (United States)

    2010-07-01

    ... SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements Minnesota § 117.669 St. Louis River (Duluth Superior Harbor). (a) The draws of the Burlington Northern railroad bridge, mile 5.7, shall open... Missabe and Iron Range Railway bridge, mile 16.3, need not be opened for the passage of vessels. The owner...

  3. 33 CFR 117.1083 - Duluth-Superior Harbor (St. Louis River).

    Science.gov (United States)

    2010-07-01

    ... SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements Wisconsin § 117.1083 Duluth-Superior Harbor (St. Louis River). (a) The draws of the Burlington Northern railroad bridge, mile 5.7 at... blasts. (c) The draw of the Duluth, Missabe and Iron Range Railway bridge, mile 16.3 at Duluth, need not...

  4. 76 FR 33721 - Takes of Marine Mammals Incidental to Specified Activities; Harbor Activities Related to the...

    Science.gov (United States)

    2011-06-09

    ..., incidental to conducting Delta Mariner harbor operations for one year. NMFS reviewed the ULA application and... vitulina), and Northern elephant seals (Mirounga angustirostris) hauled out on Small Haul-out Site 1 to... lions; and 43 Northern elephant seals by Level B harassment only. Description of the Specified...

  5. 76 FR 21862 - Takes of Marine Mammals Incidental to Specified Activities; Harbor Activities Related to the...

    Science.gov (United States)

    2011-04-19

    ...; and 43 Northern elephant seals by Level B harassment only. To date, NMFS has issued eight, 1-year... elephant seals spend much of the year, generally about nine months, in the ocean. They are usually... Mariner harbor operations for one year. After addressing comments from NMFS, ULA modified its application...

  6. 77 FR 38587 - Takes of Marine Mammals Incidental to Specified Activities; Harbor Activities Related to the...

    Science.gov (United States)

    2012-06-28

    ... Northern elephant seals by Level B harassment only. To date, we have issued nine, one-year, Incidental... as far north as Alaska and as far south as Mexico. Northern elephant seals spend much of the year... numbers of marine mammals, incidental to conducting Delta Mariner harbor operations for one year. We...

  7. 78 FR 36662 - Safety Zone; Fairport Harbor Mardi Gras, Lake Erie, Fairport, OH

    Science.gov (United States)

    2013-06-19

    ... the Fairport Harbor Mardi Gras Fireworks display. This temporary safety zone is necessary to protect spectators and vessels from the hazards associated with a fireworks display. DATES: This rule is effective...: Temporary final rule. SUMMARY: The Coast Guard is establishing a temporary safety zone on Lake Erie...

  8. 33 CFR 334.470 - Cooper River and Charleston Harbor, S.C.; restricted areas.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Cooper River and Charleston....470 Cooper River and Charleston Harbor, S.C.; restricted areas. (a) The restricted areas. (1) Area No. 1 is that portion of the Cooper River beginning near the westerly shore north of Shipyard Creek at...

  9. 78 FR 18277 - Special Local Regulation; Low Country Splash, Wando River, Cooper River, and Charleston Harbor...

    Science.gov (United States)

    2013-03-26

    ...-AA08 Special Local Regulation; Low Country Splash, Wando River, Cooper River, and Charleston Harbor... proposes to issue a special local regulation on the waters of the Wando River, Cooper River, and Charleston... Country Splash is scheduled to take place on the waters of the Wando River, Cooper River, and Charleston...

  10. 33 CFR 165.709 - Security Zone; Charleston Harbor, Cooper River, South Carolina.

    Science.gov (United States)

    2010-07-01

    ..., Cooper River, South Carolina. 165.709 Section 165.709 Navigation and Navigable Waters COAST GUARD... § 165.709 Security Zone; Charleston Harbor, Cooper River, South Carolina. (a) Regulated area. The Coast Guard is establishing a fixed security zone on all waters of the Cooper River, bank-to-bank and surface...

  11. Novel B19-like parvovirus in the brain of a harbor seal

    NARCIS (Netherlands)

    R. Bodewes (Rogier); A.R. García (Ana Rubio); L.C.M. Wiersma (Lidewij); S. Getu (Sarah); M. Beukers (Martijn); C.M.E. Schapendonk (Claudia); P.R.W.A. van Run (Peter); M.W.G. van de Bildt (Marco); M.J. Poen (Marjolein); N. Osinga (Nynke); G.J. Sánchez Contreras (Guillermo); T. Kuiken (Thijs); S.L. Smits (Saskia); A.D.M.E. Osterhaus (Albert)

    2013-01-01

    textabstractUsing random PCR in combination with next-generation sequencing, a novel parvovirus was detected in the brain of a young harbor seal (Phoca vitulina) with chronic non-suppurative meningo-encephalitis that was rehabilitated at the Seal Rehabilitation and Research Centre (SRRC) in the

  12. The isolation and partial characterization of a highly pathogenic herpesvirus from the harbor seal (Phoca vitulina).

    NARCIS (Netherlands)

    A.D.M.E. Osterhaus (Albert); H. Yang (Hong); H.E.M. Spijkers (Ine); J. Groen (Jan); J.S. Teppema; G. van Steenis (Bert)

    1985-01-01

    textabstractThis report describes the first isolation and partial characterization of a herpesvirus from the harbor seal (Phoca vitulina). The virus was isolated during a disease outbreak in a group of young seals nursed in a seal orphanage in The Netherlands. Almost half of the seals died with

  13. 76 FR 82117 - Regulations Implementing the Longshore and Harbor Workers' Compensation Act: Recreational Vessels

    Science.gov (United States)

    2011-12-30

    ... activity, and whether it falls within the Coast Guard definition of a non- recreational vessel less than 20... recreational vessel work, the employee will be eligible for benefits based on the covered work. The last... Regulations Implementing the Longshore and Harbor Workers' Compensation Act: Recreational Vessels AGENCY...

  14. 75 FR 53574 - Safety Zone; Fireworks Displays, Potomac River, National Harbor, MD

    Science.gov (United States)

    2010-09-01

    ...-AA00 Safety Zone; Fireworks Displays, Potomac River, National Harbor, MD AGENCY: Coast Guard, DHS... safety of life on navigable waters during five fireworks displays launched from a discharge barge located... necessary to protect persons and vessels against the hazards associated with a fireworks display on...

  15. 78 FR 68002 - Safety Zone for Fireworks Display, Baltimore Harbor, Baltimore, MD

    Science.gov (United States)

    2013-11-13

    ... 1625-AA00 Safety Zone for Fireworks Display, Baltimore Harbor, Baltimore, MD AGENCY: Coast Guard, DHS... safety of life on navigable waters during a fireworks display launched from a barge located in Baltimore... rule involves a fireworks display associated with a New Year's Eve event that will take place in...

  16. 33 CFR 110.197 - Galveston Harbor, Bolivar Roads Channel, Texas.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Galveston Harbor, Bolivar Roads Channel, Texas. 110.197 Section 110.197 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF... Roads Channel, Texas. (a)(1) Anchorage area (A). The water bounded by a line connecting the following...

  17. 78 FR 57319 - Children's Online Privacy Protection Rule Safe Harbor Proposed Self-Regulatory Guidelines...

    Science.gov (United States)

    2013-09-18

    ...-AB20 Children's Online Privacy Protection Rule Safe Harbor Proposed Self-Regulatory Guidelines; kidSAFE... proposed self-regulatory guidelines submitted by the kidSAFE Seal Program (``kidSAFE''), owned and operated... enabling industry groups or others to submit to the Commission for approval self-regulatory guidelines that...

  18. 77 FR 11434 - Safety Zone; Patapsco River, Northwest and Inner Harbors, Baltimore, MD

    Science.gov (United States)

    2012-02-27

    ...-AA00 Safety Zone; Patapsco River, Northwest and Inner Harbors, Baltimore, MD AGENCY: Coast Guard, DHS... intended route immediately prior to, during, and following the scheduled towing evolution, vessel traffic... made to the maritime community via marine information broadcasts so mariners may adjust their plans...

  19. 75 FR 5907 - Safety Zone; Dive Platform, Pago Pago Harbor, American Samoa

    Science.gov (United States)

    2010-02-05

    ... platform vessel in Pago Pago Harbor, American Samoa, while diving operations are under way in and around the CHEHALIS wreck. The safety zone is necessary to protect other vessels and the general public from... Pago, American Samoa. Today, the CHEHALIS wreck remains a potential pollution threat to the environment...

  20. 33 CFR 334.1420 - Pacific Ocean off Orote Point, Apra Harbor, Island of Guam, Marianas Islands; small arms firing...

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Pacific Ocean off Orote Point, Apra Harbor, Island of Guam, Marianas Islands; small arms firing range. 334.1420 Section 334.1420... AND RESTRICTED AREA REGULATIONS § 334.1420 Pacific Ocean off Orote Point, Apra Harbor, Island of Guam...

  1. 33 CFR 334.85 - New York Harbor, adjacent to the Stapleton Naval Station, Staten Island, New York; restricted area.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false New York Harbor, adjacent to the Stapleton Naval Station, Staten Island, New York; restricted area. 334.85 Section 334.85 Navigation and... RESTRICTED AREA REGULATIONS § 334.85 New York Harbor, adjacent to the Stapleton Naval Station, Staten Island...

  2. 33 CFR 165.776 - Security Zone; Coast Guard Base San Juan, San Juan Harbor, Puerto Rico

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Security Zone; Coast Guard Base San Juan, San Juan Harbor, Puerto Rico 165.776 Section 165.776 Navigation and Navigable Waters COAST... Guard District § 165.776 Security Zone; Coast Guard Base San Juan, San Juan Harbor, Puerto Rico (a...

  3. 33 CFR 334.840 - Waters of Lake Michigan south of Northerly Island at entrance to Burnham Park Yacht Harbor...

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Waters of Lake Michigan south of Northerly Island at entrance to Burnham Park Yacht Harbor, Chicago, Ill.; danger zone adjacent to airport on... Michigan south of Northerly Island at entrance to Burnham Park Yacht Harbor, Chicago, Ill.; danger zone...

  4. 78 FR 16208 - Safety Zone; V. I. Carnival Finale; St. Thomas Harbor; St. Thomas, U.S. Virgin Islands

    Science.gov (United States)

    2013-03-14

    ... 1625-AA00 Safety Zone; V. I. Carnival Finale; St. Thomas Harbor; St. Thomas, U.S. Virgin Islands AGENCY... establish a safety zone on the waters of St. Thomas Harbor in St. Thomas, U. S. Virgin Islands during the V... between 9 a.m. and 5 p.m., Monday through Friday, except federal holidays. The telephone number is 202-366...

  5. 78 FR 16211 - Safety Zone, Corp. Event Finale UHC, St. Thomas Harbor; St. Thomas, U.S. Virgin Islands

    Science.gov (United States)

    2013-03-14

    ... 1625-AA00 Safety Zone, Corp. Event Finale UHC, St. Thomas Harbor; St. Thomas, U.S. Virgin Islands... establish a temporary safety zone on the waters of St. Thomas Harbor in St. Thomas, U.S. Virgin Islands... through Friday, except federal holidays. The telephone number is 202-366-9329. See the ``Public...

  6. 78 FR 23489 - Safety Zone; V.I. Carnival Finale, St. Thomas Harbor; St. Thomas, U.S.V.I.

    Science.gov (United States)

    2013-04-19

    ... waters of St. Thomas Harbor in St. Thomas, U.S. Virgin Islands during the V.I. Carnival Finale, a... through Friday, except Federal holidays. FOR FURTHER INFORMATION CONTACT: If you have questions on this... event. The event will be held on the waters of St. Thomas Harbor, St. Thomas, U. S. Virgin Islands...

  7. 78 FR 7663 - SLR; 2013 International Rolex Regatta; St. Thomas Harbor; St. Thomas, U.S. Virgin Islands

    Science.gov (United States)

    2013-02-04

    ... 1625-AA08 SLR; 2013 International Rolex Regatta; St. Thomas Harbor; St. Thomas, U.S. Virgin Islands... special local regulations on the waters of St. Thomas Harbor in St. Thomas, U. S. Virgin Islands during... 5 p.m., Monday through Friday, except federal holidays. The telephone number is 202-366-9329. See...

  8. Summary of oceanographic and water–quality measurements in West Falmouth Harbor and Buzzards Bay, Massachusetts, 2009–2010

    Science.gov (United States)

    Ganju, Neil K.; Dickhudt, Patrick J.; Thomas, Jennifer A.; Borden, Jonathan; Sherwood, Christopher R.; Montgomery, Ellyn T.; Twomey, Erin R.; Martini, Marinna A.

    2011-01-01

    This data report presents oceanographic and water-quality observations made at six locations in West Falmouth Harbor and Buzzards Bay, Massachusetts, from August 2009 to September 2010. Both Buzzards Bay and West Falmouth Harbor are estuarine embayments; the input of freshwater on the eastern margin of Buzzards Bay adjacent to Cape Cod and West Falmouth Harbor is largely due to groundwater. In West Falmouth Harbor, the groundwater that seeps into the harbor is characterized by relatively high levels of nitrate. This high nitrate load has modified the ecology of the harbor (Howes and others, 2006) and may be a significant source of nitrate to Buzzards Bay during seasons with low biological nitrate uptake. The U.S. Geological Survey undertook these measurements to improve understanding of circulation, residence time, and water quality in the harbor and bay. We set up and monitored multiple sites in both Buzzards Bay and West Falmouth Harbor, measuring depth, water velocity,salinity, pH, dissolved oxygen, chlorophyll-a, and nitrate concentration. In this report we present the processed time-series data at these locations and provide access to the data and metadata. The results will be used to understand circulation mechanisms and verify numerical models of hydrodynamics and biogeochemistry.

  9. 77 FR 60319 - Harbor Porpoise Take Reduction Plan; Coastal Gulf of Maine Closure Area Established With a...

    Science.gov (United States)

    2012-10-03

    ...-XC099 Harbor Porpoise Take Reduction Plan; Coastal Gulf of Maine Closure Area Established With a... Atmospheric Administration (NOAA), Commerce. ACTION: Establishment of the Coastal Gulf of Maine Closure Area... Service (NMFS) announces the establishment of the Coastal Gulf of Maine Closure Area under the Harbor...

  10. 77 FR 47331 - Regulated Navigation Area-New Haven Harbor, Quinnipiac River, Mill River, New Haven, CT; Pearl...

    Science.gov (United States)

    2012-08-08

    ...-AA11 Regulated Navigation Area--New Haven Harbor, Quinnipiac River, Mill River, New Haven, CT; Pearl... navigable waters of New Haven Harbor, Quinnipiac River and Mill River. The current RNA pertains only to the..., Quinnipiac River, and Mill River RNA. The proposed amendment would give the Captain of the Port Sector Long...

  11. 33 CFR 162.260 - Channel leading to San Juan Harbor, P.R.; use, administration, and navigation.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Channel leading to San Juan Harbor, P.R.; use, administration, and navigation. 162.260 Section 162.260 Navigation and Navigable... WATERWAYS NAVIGATION REGULATIONS § 162.260 Channel leading to San Juan Harbor, P.R.; use, administration...

  12. Recombinant methods for screening human DNA excision repair proficiency

    International Nuclear Information System (INIS)

    Athas, W.F.

    1988-01-01

    A method for measuring DNA excision repair in response to ultraviolet radiation (UV)-induced DNA damage has been developed, validated, and field-tested in cultured human lymphocytes. The methodology is amenable to population-based screening and should facilitate future epidemiologic studies seeking to investigate associations between excision repair proficiency and cancer susceptibility. The impetus for such endeavors derives from the belief that the high incidence of skin cancer in the genetic disorder xeroderma pigmentosum (XP) primarily is a result of the reduced capacity of patients cells to repair UV-induced DNA damage. For assay, UV-irradiated non-replicating recombinant plasmid DNA harboring a chloramphenicol acetyltransferase (CAT) indicator gene is introduced into lymphocytes using DEAE-dextran short-term transfection conditions. Exposure to UV induces transcriptionally-inactivating DNA photoproducts in the plasmid DNA which inactivate CAT gene expression. Excision repair of the damaged CAT gene is monitored indirectly as a function of reactivated CAT enzyme activity following a 40 hour repair/expression incubation period

  13. A Comparison of Microbial Water Quality and Diversity for Ballast and Tropical Harbor Waters.

    Science.gov (United States)

    Ng, Charmaine; Le, Thai-Hoang; Goh, Shin Giek; Liang, Liang; Kim, Yiseul; Rose, Joan B; Yew-Hoong, Karina Gin

    2015-01-01

    Indicator organisms and antibiotic resistance were used as a proxy to measure microbial water quality of ballast tanks of ships, and surface waters in a tropical harbor. The survival of marine bacteria in ballast tanks appeared to diminish over longer water retention time, with a reduction of cell viability observed after a week based on heterotrophic plate counts. Pyrosequencing of 16S rRNA genes showed distinct differences in microbial composition of ballast and harbor waters. The harbor waters had a higher abundance of operational taxonomic units (OTUs) assigned to Cyanobacteria (Synechococcus spp.) and α-proteobacteria (SAR11 members), while marine hydrocarbon degraders such as γ-proteobacteria (Ocenspirillaes spp., Thiotrchales spp.) and Bacteroidetes (Flavobacteriales spp.) dominated the ballast water samples. Screening of indicator organisms found Escherichia coli (E. coli), Enterococcus and Pseudomonas aeruginosa (P. aeruginosa) in two or more of the ballast and harbor water samples tested. Vibrio spp. and Salmonella spp. were detected exclusively in harbor water samples. Using quantitative PCR (qPCR), we screened for 13 antibiotic resistant gene (ARG) targets and found higher abundances of sul1 (4.13-3.44 x 102 copies/mL), dfrA (0.77-1.80 x10 copies/mL) and cfr (2.00-5.21 copies/mL) genes compared to the other ARG targets selected for this survey. These genes encode for resistance to sulfonamides, trimethoprim and chloramphenicol-florfenicol antibiotics, which are also known to persist in sediments of aquaculture farms and coastal environments. Among the ARGs screened, we found significant correlations (Pwater quality survey, quantitatively assessing indicators of antibiotic resistance, potentially pathogenic organisms and a broad-brush description of difference in microbial composition and diversity between open oceans and tropical coastal environments through the use of next generation sequencing technology.

  14. Distribution and contamination status of chromium in surface sediments of northern Kaohsiung Harbor, Taiwan.

    Science.gov (United States)

    Dong, Cheng-Di; Chen, Chiu-Wen; Chen, Chih-Feng

    2013-07-01

    The distribution, enrichment, accumulation, and potential ecological risk of chromium (Cr) in the surface sediments of northern Kaohsiung Harbor, Taiwan, China were investigated. Sediment samples from ten locations located between the river mouths and harbor entrance of northern Kaohsiung Harbor were collected quarterly in 2011 and characterized for Cr, aluminum, water content, organic matter, total nitrogen, total phosphorous, total grease, and grain size. Results showed that the Cr concentrations varied from 27.0 to 361.9 mg/kg with an average of (113.5 +/- 87.0) mg/kg. High Cr concentration was observed near the Jen-Gen River mouth. The mean Cr concentration was high at 255.5 mg/kg, which was at least 2 to 7 times than that of other sites. This might imply significant Cr contribution from upstream receiving tanneries wastewater into the Jen-Gen River. The spatial distribution of Cr reveals relatively high in the river mouth region, especially in Jen-Gen River, and gradually diminishes toward the harbor entrance region. This indicates that the major sources of Cr pollution from upstream industrial and municipal wastewaters discharged along the river bank; and Cr may drift with sea current and be dispersed into open sea. Moreover, Cr concentrations correlated closely to the physical-chemical properties of the sediments, which suggested the influence of industrial and municipal wastewaters discharged from the neighboring industrial parks and river basins. Results from the enrichment factor and geo-accumulation index analyses imply that the Jen-Gen River sediments can be characterized as moderate enrichment and none to medium accumulation of Cr, respectively. However, results of potential ecological risk index indicate that the sediment has low ecological potential risk. The results can provide valuable information to developing future strategies for the management of river mouth and harbor.

  15. Current and historic mercury deposition to New Haven Harbor (CT, USA): Implications for industrial coastal environments

    International Nuclear Information System (INIS)

    Clark, Heather F.; Benoit, Gaboury

    2009-01-01

    This study quantifies historic and current mercury contamination in New Haven Harbor (New Haven, Connecticut, USA) through the analysis of sediment cores. The mercury concentration measured in surface sediment ranged from 320 to 1640 μg kg -1 with an average of 530 μg kg -1 . The harbor is relatively small in area (6.6 km 2 ) but displays a large range in concentrations, illustrating the important methodological issue that a large number of samples may be necessary to capture the variability in even a small area. Depth profiles of mercury reflect sedimentation over a range of 20 to 200 years and indicate a complex history of contamination. Mercury depth profiles were compared with lead, copper, cadmium, and silver concentrations and the metals generally covary. This trend indicates that the sources of mercury and heavy metals are linked and that regionally specific sources dominate the historic input of metals rather than large-scale atmospheric deposition patterns. Results also show there are large differences in absolute concentrations of metals among sites in the harbor. Differences in the abundance of Fe-rich, fine-grained sediment likely control the level of metals in various parts of the harbor. Proximity to current sources and the long, diverse industrial history of the harbor also influence the distribution pattern. All of the cores can be modeled as mixing between pre-industrial sediments and either one or two pollution endmembers. This study demonstrates the importance of riverine sources in the mass balance of mercury delivered to coastal areas and of watershed management to preserve coastal ecosystems.

  16. A germline FANCA alteration that is associated with increased sensitivity to DNA damaging agents.

    OpenAIRE

    Wilkes, David C; Sailer, Verena; Xue, Hui; Cheng, Hongwei; Collins, Colin C; Gleave, Martin; Wang, Yuzhuo; Demichelis, Francesca; Beltran, Himisha; Rubin, Mark Andrew; Rickman, David S

    2017-01-01

    Defects in genes involved in DNA damage repair (DDR) pathway are emerging as novel biomarkers and targets for new prostate cancer drug therapies. A previous report revealed an association between an exceptional response to cisplatin treatment and a somatic loss of heterozygosity (LOH) of FANCA in a patient with metastatic prostate cancer who also harbored a germline FANCA variant (S1088F). Although germline FANCA mutations are the most frequent alterations in patients with Fanconi anemia, ger...

  17. Cluster analysis of Helicobacter pylori genomic DNA fingerprints suggests gastroduodenal disease-specific associations.

    Science.gov (United States)

    Go, M F; Chan, K Y; Versalovic, J; Koeuth, T; Graham, D Y; Lupski, J R

    1995-07-01

    Helicobacter pylori infection is now accepted as the most common cause of chronic active gastritis and peptic ulcer disease. The etiologies of many infectious diseases have been attributed to specific or clonal strains of bacterial pathogens. Polymerase chain reaction (PCR) amplification of DNA between repetitive DNA sequences, REP elements (REP-PCR), has been utilized to generate DNA fingerprints to examine similarity among strains within a bacterial species. Genomic DNA from H. pylori isolates obtained from 70 individuals (39 duodenal ulcers and 31 simple gastritis) was PCR-amplified using consensus probes to repetitive DNA elements. The H. pylori DNA fingerprints were analyzed for similarity and correlated with disease presentation using the NTSYS-pc computer program. Each H. pylori strain had a distinct DNA fingerprint except for two pairs. Single-colony DNA fingerprints of H. pylori from the same patient were identical, suggesting that each patient harbors a single strain. Computer-assisted cluster analysis of the REP-PCR DNA fingerprints showed two large clusters of isolates, one associated with simple gastritis and the other with duodenal ulcer disease. Cluster analysis of REP-PCR DNA fingerprints of H. pylori strains suggests that duodenal ulcer isolates, as a group, are more similar to one another and different from gastritis isolates. These results suggest that disease-specific strains may exist.

  18. Nonindigenous Marine Species Introductions in the harbors of the South and West Shores of Oahu, Hawaii 1997-1998 (NODC Accession 0000324)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Despite the potential importance of Honolulu Harbor or other commercial harbors on Oahu as potential gateways for nonindigenous marine species to enter the Hawaiian...

  19. A Probabilistic and Observation Based Methodology to Estimate Small Craft Harbor Vulnerability to Tsunami Events

    Science.gov (United States)

    Keen, A. S.; Lynett, P. J.; Ayca, A.

    2016-12-01

    Because of the damage resulting from the 2010 Chile and 2011 Japanese tele-tsunamis, the tsunami risk to the small craft marinas in California has become an important concern. The talk will outline an assessment tool which can be used to assess the tsunami hazard to small craft harbors. The methodology is based on the demand and structural capacity of the floating dock system, composed of floating docks/fingers and moored vessels. The structural demand is determined using a Monte Carlo methodology. Monte Carlo methodology is a probabilistic computational tool where the governing might be well known, but the independent variables of the input (demand) as well as the resisting structural components (capacity) may not be completely known. The Monte Carlo approach uses a distribution of each variable, and then uses that random variable within the described parameters, to generate a single computation. The process then repeats hundreds or thousands of times. The numerical model "Method of Splitting Tsunamis" (MOST) has been used to determine the inputs for the small craft harbors within California. Hydrodynamic model results of current speed, direction and surface elevation were incorporated via the drag equations to provide the bases of the demand term. To determine the capacities, an inspection program was developed to identify common features of structural components. A total of six harbors have been inspected ranging from Crescent City in Northern California to Oceanside Harbor in Southern California. Results from the inspection program were used to develop component capacity tables which incorporated the basic specifications of each component (e.g. bolt size and configuration) and a reduction factor (which accounts for the component reduction in capacity with age) to estimate in situ capacities. Like the demand term, these capacities are added probabilistically into the model. To date the model has been applied to Santa Cruz Harbor as well as Noyo River. Once

  20. Optimized mtDNA Control Region Primer Extension Capture Analysis for Forensically Relevant Samples and Highly Compromised mtDNA of Different Age and Origin

    Directory of Open Access Journals (Sweden)

    Mayra Eduardoff

    2017-09-01

    Full Text Available The analysis of mitochondrial DNA (mtDNA has proven useful in forensic genetics and ancient DNA (aDNA studies, where specimens are often highly compromised and DNA quality and quantity are low. In forensic genetics, the mtDNA control region (CR is commonly sequenced using established Sanger-type Sequencing (STS protocols involving fragment sizes down to approximately 150 base pairs (bp. Recent developments include Massively Parallel Sequencing (MPS of (multiplex PCR-generated libraries using the same amplicon sizes. Molecular genetic studies on archaeological remains that harbor more degraded aDNA have pioneered alternative approaches to target mtDNA, such as capture hybridization and primer extension capture (PEC methods followed by MPS. These assays target smaller mtDNA fragment sizes (down to 50 bp or less, and have proven to be substantially more successful in obtaining useful mtDNA sequences from these samples compared to electrophoretic methods. Here, we present the modification and optimization of a PEC method, earlier developed for sequencing the Neanderthal mitochondrial genome, with forensic applications in mind. Our approach was designed for a more sensitive enrichment of the mtDNA CR in a single tube assay and short laboratory turnaround times, thus complying with forensic practices. We characterized the method using sheared, high quantity mtDNA (six samples, and tested challenging forensic samples (n = 2 as well as compromised solid tissue samples (n = 15 up to 8 kyrs of age. The PEC MPS method produced reliable and plausible mtDNA haplotypes that were useful in the forensic context. It yielded plausible data in samples that did not provide results with STS and other MPS techniques. We addressed the issue of contamination by including four generations of negative controls, and discuss the results in the forensic context. We finally offer perspectives for future research to enable the validation and accreditation of the PEC MPS

  1. DNA preservation in silk.

    Science.gov (United States)

    Liu, Yawen; Zheng, Zhaozhu; Gong, He; Liu, Meng; Guo, Shaozhe; Li, Gang; Wang, Xiaoqin; Kaplan, David L

    2017-06-27

    The structure of DNA is susceptible to alterations at high temperature and on changing pH, irradiation and exposure to DNase. Options to protect and preserve DNA during storage are important for applications in genetic diagnosis, identity authentication, drug development and bioresearch. In the present study, the stability of total DNA purified from human dermal fibroblast cells, as well as that of plasmid DNA, was studied in silk protein materials. The DNA/silk mixtures were stabilized on filter paper (silk/DNA + filter) or filter paper pre-coated with silk and treated with methanol (silk/DNA + PT-filter) as a route to practical utility. After air-drying and water extraction, 50-70% of the DNA and silk could be retrieved and showed a single band on electrophoretic gels. 6% silk/DNA + PT-filter samples provided improved stability in comparison with 3% silk/DNA + filter samples and DNA + filter samples for DNA preservation, with ∼40% of the band intensity remaining at 37 °C after 40 days and ∼10% after exposure to UV light for 10 hours. Quantitative analysis using the PicoGreen assay confirmed the results. The use of Tris/borate/EDTA (TBE) buffer enhanced the preservation and/or extraction of the DNA. The DNA extracted after storage maintained integrity and function based on serving as a functional template for PCR amplification of the gene for zinc finger protein 750 (ZNF750) and for transgene expression of red fluorescence protein (dsRed) in HEK293 cells. The high molecular weight and high content of a crystalline beta-sheet structure formed on the coated surfaces likely accounted for the preservation effects observed for the silk/DNA + PT-filter samples. Although similar preservation effects were also obtained for lyophilized silk/DNA samples, the rapid and simple processing available with the silk-DNA-filter membrane system makes it appealing for future applications.

  2. Force induced DNA melting

    International Nuclear Information System (INIS)

    Santosh, Mogurampelly; Maiti, Prabal K

    2009-01-01

    When pulled along the axis, double-strand DNA undergoes a large conformational change and elongates by roughly twice its initial contour length at a pulling force of about 70 pN. The transition to this highly overstretched form of DNA is very cooperative. Applying a force perpendicular to the DNA axis (unzipping), double-strand DNA can also be separated into two single-stranded DNA, this being a fundamental process in DNA replication. We study the DNA overstretching and unzipping transition using fully atomistic molecular dynamics (MD) simulations and argue that the conformational changes of double-strand DNA associated with either of the above mentioned processes can be viewed as force induced DNA melting. As the force at one end of the DNA is increased the DNA starts melting abruptly/smoothly above a critical force depending on the pulling direction. The critical force f m , at which DNA melts completely decreases as the temperature of the system is increased. The melting force in the case of unzipping is smaller compared to the melting force when the DNA is pulled along the helical axis. In the case of melting through unzipping, the double-strand separation has jumps which correspond to the different energy minima arising due to sequence of different base pairs. The fraction of Watson-Crick base pair hydrogen bond breaking as a function of force does not show smooth and continuous behavior and consists of plateaus followed by sharp jumps.

  3. DNA damage and autophagy

    International Nuclear Information System (INIS)

    Rodriguez-Rocha, Humberto; Garcia-Garcia, Aracely; Panayiotidis, Mihalis I.; Franco, Rodrigo

    2011-01-01

    Both exogenous and endogenous agents are a threat to DNA integrity. Exogenous environmental agents such as ultraviolet (UV) and ionizing radiation, genotoxic chemicals and endogenous byproducts of metabolism including reactive oxygen species can cause alterations in DNA structure (DNA damage). Unrepaired DNA damage has been linked to a variety of human disorders including cancer and neurodegenerative disease. Thus, efficient mechanisms to detect DNA lesions, signal their presence and promote their repair have been evolved in cells. If DNA is effectively repaired, DNA damage response is inactivated and normal cell functioning resumes. In contrast, when DNA lesions cannot be removed, chronic DNA damage triggers specific cell responses such as cell death and senescence. Recently, DNA damage has been shown to induce autophagy, a cellular catabolic process that maintains a balance between synthesis, degradation, and recycling of cellular components. But the exact mechanisms by which DNA damage triggers autophagy are unclear. More importantly, the role of autophagy in the DNA damage response and cellular fate is unknown. In this review we analyze evidence that supports a role for autophagy as an integral part of the DNA damage response.

  4. DNA Open states and DNA hydratation

    International Nuclear Information System (INIS)

    Lema-Larre, B. de; Martin-Landrove, M

    1995-01-01

    It is a very well-known fact that an protonic exchange exists among natural DNA filaments and synthetic polynucleotides with the solvent (1--2). The existence of DNA open states, that is to say states for which the interior of the DNA molecule is exposed to the external environment, it has been demonstrated by means of proton-deuterium exchange (3). This work has carried out experiments measuring the dispersion of the traverse relaxation rate (4), as a pulsation rate function in a Carr-Purcell-Meiboom-Gill (CPMG) pulses sequence rate, to determine changes in the moist layer of the DNA molecule. The experiments were carried out under different experimental conditions in order to vary the probability that open states occurs, such as temperature or the exposure to electromagnetic fields. Some theoretical models were supposed to adjust the experimental results including those related to DNA non linear dynamic [es

  5. The human vascular endothelial cell line HUV-EC-C harbors the integrated HHV-6B genome which remains stable in long term culture.

    Science.gov (United States)

    Shioda, Setsuko; Kasai, Fumio; Ozawa, Midori; Hirayama, Noriko; Satoh, Motonobu; Kameoka, Yousuke; Watanabe, Ken; Shimizu, Norio; Tang, Huamin; Mori, Yasuko; Kohara, Arihiro

    2018-02-01

    Human herpes virus 6 (HHV-6) is a common human pathogen that is most often detected in hematopoietic cells. Although human cells harboring chromosomally integrated HHV-6 can be generated in vitro, the availability of such cell lines originating from in vivo tissues is limited. In this study, chromosomally integrated HHV-6B has been identified in a human vascular endothelial cell line, HUV-EC-C (IFO50271), derived from normal umbilical cord tissue. Sequence analysis revealed that the viral genome was similar to the HHV-6B HST strain. FISH analysis using a HHV-6 DNA probe showed one signal in each cell, detected at the distal end of the long arm of chromosome 9. This was consistent with a digital PCR assay, validating one copy of the viral DNA. Because exposure of HUV-EC-C to chemicals did not cause viral reactivation, long term cell culture of HUV-EC-C was carried out to assess the stability of viral integration. The growth rate was altered depending on passage numbers, and morphology also changed during culture. SNP microarray profiles showed some differences between low and high passages, implying that the HUV-EC-C genome had changed during culture. However, no detectable change was observed in chromosome 9, where HHV-6B integration and the viral copy number remained unchanged. Our results suggest that integrated HHV-6B is stable in HUV-EC-C despite genome instability.

  6. Hydraulic experiment on flow and topography change in harbor due to tsunami and its numerical simulation

    International Nuclear Information System (INIS)

    Fujii, Naoki; Ikeno, Masaaki; Sakakiyama, Tsutomu; Matsuyama, Masafumi; Takao, Makoto; Mukohara, Takeshi

    2009-01-01

    Numerical model of topography change is important to examine collapse of the harbor facilities by sand transport due to tsunami. Problems for evaluation of sand transport due to tsunami with topography change model are in precision of the numerical model and topography change data. Therefore, we installed the harbor in large-scaled wave tank and carried out experiment about tsunami flow and topography change to get those detailed data. For results provided by experimental test, we applied the topography change model of Ikeno et al. (2009a) and evaluated it about the reproduction characteristics. As a result, it was confirmed that reproduction of an experiment improved by using new pickup rate formula proposed by Ikeno et al. (2009a). (author)

  7. Bacterial Communities in Polluted Seabed Sediments: A Molecular Biology Assay in Leghorn Harbor

    Directory of Open Access Journals (Sweden)

    Carolina Chiellini

    2013-01-01

    Full Text Available Seabed sediments of commercial ports are often characterized by high pollution levels. Differences in number and distribution of bacteria in such areas can be related to distribution of pollutants in the port and to sediment conditions. In this study, the bacterial communities of five sites from Leghorn Harbor seabed were characterized, and the main bacterial groups were identified. T-RFLP was used for all samples; two 16S rRNA libraries and in silico digestion of clones were used to identify fingerprint profiles. Library data, phylogenetic analysis, and T-RFLP coupled with in silico digestion of the obtained sequences evidenced the dominance of Proteobacteria and the high percentage of Bacteroidetes in all sites. The approach highlighted similar bacterial communities between samples coming from the five sites, suggesting a modest differentiation among bacterial communities of different harbor seabed sediments and hence the capacity of bacterial communities to adapt to different levels and types of pollution.

  8. Assay dependence of Brucella antibody prevalence in a declining Alaskan harbor seal (Phoca vitulina population

    Directory of Open Access Journals (Sweden)

    Hueffer Karsten

    2013-01-01

    Full Text Available Abstract Background Brucella is a group of bacteria that causes brucellosis, which can affect population health and reproductive success in many marine mammals. We investigated the serological prevalence of antibodies against Brucella bacteria in a declining harbor seal population in Glacier Bay National Park, Alaska. Results Prevalence ranged from 16 to 74 percent for those tests detecting antibodies, indicating that harbor seals in Glacier Bay have been exposed to Brucella bacteria. However, the actual level of serological prevalence could not be determined because results were strongly assay-dependent. Conclusions This study reinforces the need to carefully consider assay choice when comparing different studies on the prevalence of anti–Brucella antibodies in pinnipeds and further highlights the need for species- or taxon-specific assay validation for both pathogen and host species.

  9. Immunoassay of DNA damage

    International Nuclear Information System (INIS)

    Gasparro, F.P.; Santella, R.M.

    1988-01-01

    The direct photomodification of DNA by ultraviolet light or the photo-induced addition of exogenous compounds to DNA components results in alterations of DNA structure ranging from subtle to profound. There are two consequences of these conformational changes. First, cells in which the DNA has been damaged are capable of executing repair steps. Second, the DNA which is usually of very low immunogenicity now becomes highly antigenic. This latter property has allowed the production of a series of monoclonal antibodies that recognize photo-induced DNA damage. Monoclonal antibodies have been generated that recognize the 4',5'-monoadduct and the crosslink of 8-methoxypsoralen in DNA. In addition, another antibody has been prepared which recognizes the furan-side monoadduct of 6,4,4'-trimethylangelicin in DNA. These monoclonal antibodies have been characterized as to sensitivity and specificity using non-competitive and competitive enzyme-linked-immunosorbent assays (ELISA). (author)

  10. Immunoassay of DNA damage

    Energy Technology Data Exchange (ETDEWEB)

    Gasparro, F P; Santella, R M

    1988-09-01

    The direct photomodification of DNA by ultraviolet light or the photo-induced addition of exogenous compounds to DNA components results in alterations of DNA structure ranging from subtle to profound. There are two consequences of these conformational changes. First, cells in which the DNA has been damaged are capable of executing repair steps. Second, the DNA which is usually of very low immunogenicity now becomes highly antigenic. This latter property has allowed the production of a series of monoclonal antibodies that recognize photo-induced DNA damage. Monoclonal antibodies have been generated that recognize the 4',5'-monoadduct and the crosslink of 8-methoxypsoralen in DNA. In addition, another antibody has been prepared which recognizes the furan-side monoadduct of 6,4,4'-trimethylangelicin in DNA. These monoclonal antibodies have been characterized as to sensitivity and specificity using non-competitive and competitive enzyme-linked-immunosorbent assays (ELISA).

  11. DNA computing models

    CERN Document Server

    Ignatova, Zoya; Zimmermann, Karl-Heinz

    2008-01-01

    In this excellent text, the reader is given a comprehensive introduction to the field of DNA computing. The book emphasizes computational methods to tackle central problems of DNA computing, such as controlling living cells, building patterns, and generating nanomachines.

  12. DNA tagged microparticles

    Science.gov (United States)

    Farquar, George Roy; Leif, Roald N; Wheeler, Elizabeth

    2015-05-05

    A simulant that includes a carrier and DNA encapsulated in the carrier. Also a method of making a simulant including the steps of providing a carrier and encapsulating DNA in the carrier to produce the simulant.

  13. Modeling DNA Replication.

    Science.gov (United States)

    Bennett, Joan

    1998-01-01

    Recommends the use of a model of DNA made out of Velcro to help students visualize the steps of DNA replication. Includes a materials list, construction directions, and details of the demonstration using the model parts. (DDR)

  14. A Review of Circulating Tumor DNA in Hepatobiliary Malignancies

    Directory of Open Access Journals (Sweden)

    Kabir Mody

    2018-06-01

    Full Text Available Circulating tumor DNA (ctDNA is released into circulation (blood specifically from tumor cells undergoing metabolic secretion, apoptosis, or necrosis, carries tumor-specific genetic or epigenetic alterations. Technologies enabling clinical evaluation of ctDNA continue to advance rapidly and allow for the assessment of patient-specific tumoral genetic and epigenetic alterations. This holds great potential for earlier detection of disease, serial monitoring of tumor heterogeneity, identification of therapeutic targets, and evaluation of treatment response and mechanisms of resistance. Hepatobiliary malignancies are often diagnosed late, recur commonly, yield limited available tumor on biopsy, and harbor several genomic alterations with potential therapeutic impacts. Patients suffering from or at risk for these diseases thus stand to benefit immensely from this technology. Herein, we review the limited literature pertaining to the potential for ctDNA technologies in such patients. Patients with these cancers stand to benefit greatly from the application of ctDNA technologies, and concerted efforts at further investigation of such are ongoing and greatly needed.

  15. Re-alimentation in harbor seal pups: effects on the somatotropic axis and growth rate.

    Science.gov (United States)

    Richmond, Julie P; Norris, Tenaya; Zinn, Steven A

    2010-01-15

    The metabolic hormones, growth hormone (GH) and insulin-like growth factor (IGF)-I, together with IGF binding proteins (IGFBP), have been well studied in domestic species and are the primary components of the somatotropic axis. This hormone axis is responsive to nutrient intake, associated with growth rate, and accretion of protein and adipose. However, this relationship has not been evaluated in species that rely heavily on adipose stores for survival, such as pinnipeds. The primary objectives of this research were to investigate the response of the somatotropic axis to reduced nutrient intake and re-alimentation in rehabilitated harbor seal pups, and to assess if these hormones are related to nutritional status and growth rate in harbor seals. Stranded harbor seal pups (n=24) arrived at the rehabilitation facility very thin after fasting for several days (nutritional nadir). Throughout rehabilitation nutrient intake increased and pups gained mass and body condition. Concentrations of GH and IGFBP-2 decreased with re-alimentation, while IGF-I and IGFBP-3 concentrations increased. Overall, GH and IGFBP-2 were negatively associated and IGF-I and IGFBP-3 were positively associated with growth rate and increased body condition of harbor sea pups. Further, the magnitude of the growth response was related to the magnitude in response of the somatotropic axis to varied levels of intake. These data suggest that multiple components of the somatotropic axis may be used to assess the energy status of individuals and may also provide information on the level of feed intake that is predictive of growth rate.

  16. Female harbor seal (Phoca vitulina) behavioral response to playbacks of underwater male acoustic advertisement displays.

    Science.gov (United States)

    Matthews, Leanna P; Blades, Brittany; Parks, Susan E

    2018-01-01

    During the breeding season, male harbor seals ( Phoca vitulina ) make underwater acoustic displays using vocalizations known as roars. These roars have been shown to function in territory establishment in some breeding areas and have been hypothesized to be important for female choice, but the function of these sounds remains unresolved. This study consisted of a series of playback experiments in which captive female harbor seals were exposed to recordings of male roars to determine if females respond to recordings of male vocalizations and whether or not they respond differently to roars from categories with different acoustic characteristics. The categories included roars with characteristics of dominant males (longest duration, lowest frequency), subordinate males (shortest duration, highest frequency), combinations of call parameters from dominant and subordinate males (long duration, high frequency and short duration, low frequency), and control playbacks of water noise and water noise with tonal signals in the same frequency range as male signals. Results indicate that overall females have a significantly higher level of response to playbacks that imitate male vocalizations when compared to control playbacks of water noise. Specifically, there was a higher level of response to playbacks representing dominant male vocalization when compared to the control playbacks. For most individuals, there was a greater response to playbacks representing dominant male vocalizations compared to playbacks representing subordinate male vocalizations; however, there was no statistical difference between those two playback types. Additionally, there was no difference between the playbacks of call parameter combinations and the controls. Investigating female preference for male harbor seal vocalizations is a critical step in understanding the harbor seal mating system and further studies expanding on this captive study will help shed light on this important issue.

  17. Calculating background levels for ecological risk parameters in toxic harbor sediment

    Science.gov (United States)

    Leadon, C.J.; McDonnell, T.R.; Lear, J.; Barclift, D.

    2007-01-01

    Establishing background levels for biological parameters is necessary in assessing the ecological risks from harbor sediment contaminated with toxic chemicals. For chemicals in sediment, the term contaminated is defined as having concentrations above background and significant human health or ecological risk levels. For biological parameters, a site could be considered contaminated if levels of the parameter are either more or less than the background level, depending on the specific parameter. Biological parameters can include tissue chemical concentrations in ecological receptors, bioassay responses, bioaccumulation levels, and benthic community metrics. Chemical parameters can include sediment concentrations of a variety of potentially toxic chemicals. Indirectly, contaminated harbor sediment can impact shellfish, fish, birds, and marine mammals, and human populations. This paper summarizes the methods used to define background levels for chemical and biological parameters from a survey of ecological risk investigations of marine harbor sediment at California Navy bases. Background levels for regional biological indices used to quantify ecological risks for benthic communities are also described. Generally, background stations are positioned in relatively clean areas exhibiting the same physical and general chemical characteristics as nearby areas with contaminated harbor sediment. The number of background stations and the number of sample replicates per background station depend on the statistical design of the sediment ecological risk investigation, developed through the data quality objective (DQO) process. Biological data from the background stations can be compared to data from a contaminated site by using minimum or maximum background levels or comparative statistics. In Navy ecological risk assessments (ERA's), calculated background levels and appropriate ecological risk screening criteria are used to identify sampling stations and sites with contaminated

  18. The War on Cancer: Cold Spring Harbor Laboratory Is Fighting the Good Fight.

    Science.gov (United States)

    Mertz, Leslie

    2017-01-01

    Located on the north shore of Long Island in New York, Cold Spring Harbor Laboratory (Figure 1) started out with a marine biology emphasis at the end of the 19th century, but it soon established itself as a prominent cancer research facility. That strong emphasis on cancer work continues today as this private, not-for-profit research institution enters its 127th year (Figure 2).

  19. 33 CFR 165.150 - New Haven Harbor, Quinnipiac River, Mill River.

    Science.gov (United States)

    2010-07-01

    ... River, Mill River. 165.150 Section 165.150 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF... New Haven Harbor, Quinnipiac River, Mill River. (a) The following is a regulated navigation area: The... 303°T to point D at the west bank of the mouth of the Mill River 41°18′05″ N, 72°54′23″ W thence south...

  20. The Secant Rate of Corrosion: Correlating Observations of the USS Arizona Submerged in Pearl Harbor

    Science.gov (United States)

    Johnson, Donald L.; DeAngelis, Robert J.; Medlin, Dana J.; Johnson, Jon E.; Carr, James D.; Conlin, David L.

    2018-03-01

    Contrary to previous linear projections of steel corrosion in seawater, analysis of an inert marker embedded in USS Arizona concretion since the 7 December 1941 attack on Pearl Harbor reveals evidence that the effective corrosion rate decreases with time. The secant rate of corrosion, or SRC correlation, derived from this discovery could have a significant impact on failure analysis investigations for concreted shipwrecks or underwater structures. The correlation yields a lower rate of metal thinning than predicted. Development of the correlation is described.

  1. A Comprehensive Copper Compliance Strategy: Implementing Regulatory Guidance at Pearl Harbor Naval Shipyard & Intermediate Maintenance Facility

    Science.gov (United States)

    2007-01-01

    species was not listed in the PHLP database (Bishop Museum, 1998). Personal observations by John Zardus (Kewalo Marine Laboratory, Honolulu, Hawaii...Ringwood, 1992). Specimens collected from an open coastal site by the University of Hawaii ( John Zardus ), did not survive the shipment (less than 24... John Ornellas, Randy Kido, and Rich Anderson from Code 106.3. The Shipyard Pearl Harbor Regional Dive Locker, Code 760, provided professional, high

  2. Covalently bound DNA on naked iron oxide nanoparticles: Intelligent colloidal nano-vector for cell transfection.

    Science.gov (United States)

    Magro, Massimiliano; Martinello, Tiziana; Bonaiuto, Emanuela; Gomiero, Chiara; Baratella, Davide; Zoppellaro, Giorgio; Cozza, Giorgio; Patruno, Marco; Zboril, Radek; Vianello, Fabio

    2017-11-01

    Conversely to common coated iron oxide nanoparticles, novel naked surface active maghemite nanoparticles (SAMNs) can covalently bind DNA. Plasmid (pDNA) harboring the coding gene for GFP was directly chemisorbed onto SAMNs, leading to a novel DNA nanovector (SAMN@pDNA). The spontaneous internalization of SAMN@pDNA into cells was compared with an extensively studied fluorescent SAMN derivative (SAMN@RITC). Moreover, the transfection efficiency of SAMN@pDNA was evaluated and explained by computational model. SAMN@pDNA was prepared and characterized by spectroscopic and computational methods, and molecular dynamic simulation. The size and hydrodynamic properties of SAMN@pDNA and SAMN@RITC were studied by electron transmission microscopy, light scattering and zeta-potential. The two nanomaterials were tested by confocal scanning microscopy on equine peripheral blood-derived mesenchymal stem cells (ePB-MSCs) and GFP expression by SAMN@pDNA was determined. Nanomaterials characterized by similar hydrodynamic properties were successfully internalized and stored into mesenchymal stem cells. Transfection by SAMN@pDNA occurred and GFP expression was higher than lipofectamine procedure, even in the absence of an external magnetic field. A computational model clarified that transfection efficiency can be ascribed to DNA availability inside cells. Direct covalent binding of DNA on naked magnetic nanoparticles led to an extremely robust gene delivery tool. Hydrodynamic and chemical-physical properties of SAMN@pDNA were responsible of the successful uptake by cells and of the efficiency of GFP gene transfection. SAMNs are characterized by colloidal stability, excellent cell uptake, persistence in the host cells, low toxicity and are proposed as novel intelligent DNA nanovectors for efficient cell transfection. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. The Plurality of Harbors at Caesarea: The Southern Anchorage in Late Antiquity

    Science.gov (United States)

    Ratzlaff, Alexandra; Galili, Ehud; Waiman-Barak, Paula; Yasur-Landau, Assaf

    2017-08-01

    The engineering marvel of Sebastos, or Portus Augusti as it was called in Late Antiquity (284-638 CE), dominated Caesarea's harbor center along modern Israel's central coast but it was only one part of a larger maritime complex. The Southern Anchorage provides a case study as one portion of the Caesarea complex, as well as a node within the regional network of anchorages and small harbors. Ceramics recovered from here show a high percentage of locally, and provincially, produced storage jars engaged in maritime trade. The ceramic evidence points towards an intensified regional trade or cabotage rather than favouring long distance trade from large port to port. Working out of these small harbors, opportunities arose for greater flexibility in specialization of commodities and materials passing through the network of subsidiary ports, contributing to a more diversified market economy. This analysis provides another example in the growing focus on how these simple and semi-modified anchorages in the Eastern Mediterranean were often the predominant economic networks connecting hinterland and coastal trade.

  4. Faunal and vegetation monitoring in response to harbor dredging in the Port of Miami

    Science.gov (United States)

    Daniels, Andre; Stevenson, Rachael; Smith, Erin; Robblee, Michael

    2018-04-11

    Seagrasses are highly productive ecosystems. A before-after-control-impact (BACI) design was used to examine effects of dredging on seagrasses and the animals that inhabit them. The control site North Biscayne Bay and the affected site Port of Miami had seagrass densities decrease during both the before, Fish and Invertebrate Assessment Network 2006-2011, and after, Faunal Monitoring in Response to Harbor Dredging 2014-2016, studies. Turbidity levels increased at North Biscayne Bay and Port of Miami basins during the Faunal Monitoring in Response to Harbor Dredging study, especially in 2016. Animal populations decreased significantly in North Biscayne Bay and Port of Miami in the Faunal Monitoring in Response to Harbor Dredging study compared to the Fish and Invertebrate Assessment Network study. Predictive modeling shows that numbers of animal populations will likely continue to decrease if the negative trends in seagrass densities continue unabated. There could be effects on several fisheries vital to the south Florida economy. Additional research could determine if animal populations and seagrass densities have rebounded or continued to decrease.

  5. Characteristics and management of Enterobacteriaceae harboring IMP-4 or IMP-8 carbapenemase in a tertiary hospital.

    Science.gov (United States)

    Pang, Feng; Jia, Xiu-Qin; Song, Zhen-Zhu; Li, Yan-Hua; Wang, Bin; Zhao, Qi-Gang; Wang, Chuan-Xin; Zhang, Yi; Wang, Le-Xin

    2016-03-01

    The emergence of Enterobacteriaceae harboring IMP-4 or IMP-8 carbapenemases is rare. We report an occurrence of Enterobacteriaceae harboring IMP-4 or IMP-8 carbapenemases in a Chinese tertiary care hospital from November 2010 to December 2012. The clinical characteristics of 30 patients were described. The genetic relationship of isolates was determined by pulsed-field gel electrophoresis (PFGE). Carbapenemases were detected by modified Hodge test (MHT) and polymerase chain reactions (PCRs). Amplicons were sequenced and blasted to determine the genotype. Most infected patients were from intensive care unit and had complex and serious underlying illnesses requiring mechanical ventilation. PFGE revealed that Klebsiella pneumoniae showed two major PFGE types. Two Klebsiella oxytoca had an indistinguishable PFGE pattern, while four Enterobacter cloacae were different strains. The sequencing studies showed Enterobacteriaceae harboring IMP-4 or IMP-8 carbapenemase in the 23 infected patients. The majority of patients had infections with the carbapenemase-producing Enterobacteriaceae (CPE) strain, most were successfully treated with a range of antibiotics and discharged. It is important to maintain a high index of suspicion to screen for carbapenemase-producing Enterobacteriaceae strains. Rapid identification of these strains and implementation of stringent procedures are the key to prevent major outbreaks in a hospital setting.

  6. Organochlorines in harbor seal (Phoca vitulina) tissues from the northern Gulf of Alaska

    International Nuclear Information System (INIS)

    Wang Dongli; Atkinson, Shannon; Hoover-Miller, Anne; Lee, Sung-Eun; Li, Qing X.

    2007-01-01

    Polychlorinated biphenyls (PCBs), dichlorodiphenyltrichloroethane (DDT) and its metabolites, heptachlor and hexachlorocyclohexanes (HCHs) were analyzed in the harbor seal (Phoca vitulina) tissues collected from the Gulf of Alaska during 2000-2001. ΣPCBs (16-728 ng/g lw) and ΣDDTs (14-368 ng/g lw) were the predominant pollutants followed by ΣHCHs (0.56-93 ng/g lw) and heptachlor (≤0.068-6.0 ng/g lw). Concentrations of the above organochlorines (OCs) in the liver, kidney and blubber tissues correlated with ages, sex, body weight and blubber thickness of the harbor seals. The OC concentrations were similar between the samples collected from two different regions - Prince William Sound, and Kodiak Island and Southern Alaska Peninsula. Mean levels of OCs in nursing female adults were much lower than those in male adults, which indicate that lactation transfer OCs from mother seals to newborns. - Σ28 PCB congeners, p,p'-DDE, p,p'-DDD and p,p'-DDT, α-, β-, γ-, and δ-HCH and heptachlor in harbor seal tissues from the northern Gulf of Alaska are reported

  7. Length-weight relationship of northern pike, Esox lucius, from East Harbor, Ohio

    Science.gov (United States)

    Brown, Edward H.; Clark, Clarence F.

    1965-01-01

    The northern pike is one of Ohio's largest game fish but is well known to comparatively few anglers. Large numbers of the big fish spawn in the Ohio marshes adjacent to Lake Erie. Movements related to spawning reach a peak in late March or early April. Later the spawning population disperses and is seldom represented in catches by experimental gear or by anglers. The short period of availability was used to obtain life history information in March of 1951 through 1953. No comprehensive length-weight data for this species have previously been published from this area. East Harbor is a sandspit pond separated from Lake Erie by a large sand bar. Waters and fish populations of the harbor and lake can mix freely through a permanent connecting channel. The larger part of the 850 surface acres of the harbor is normally less than 8 feet deep. The male northern pike averaged 20.5 inches in length and ranged from 13.5 to 28.5 inches. The conspicuously larger females averaged 26.0 inches and ranged from 15.5 to 37.5 inches.

  8. Composition and source of butyltins in sediments of Kaohsiung Harbor, Taiwan

    Science.gov (United States)

    Dong, Cheng-Di; Chen, Chih-Feng; Chen, Chiu-Wen

    2015-04-01

    Fifty-eight sediment samples were collected from the Kaohsiung Harbor (Taiwan) for analyses of monobutyltin (MBT), dibutyltin (DBT) and tributyltin (TBT), using gas chromatography/flame photometric detector (GC/FPD). The concentration of total butyltins (ΣBTs), sum of MBT, DBT, and TBT, varied from 3.9 to 158.5 ng Sn/g dw in sediment samples with TBT being the major component of the sediment samples, except for the vicinity of the Love River mouth where MBT was the most abundant BT compound (a proportion of over 57%). Based on the BTs concentration, distribution, composition and correlations, the sources of BTs found in harbor sediments are shipping activities, and TBT is the main pollutant; the estuary (i.e. Love River) has been the anthropogenic source of MBT from upstream inputs. Influences of TBT on aquatic organisms are evaluated using the toxicity guidelines proposed by the US EPA (US Environmental Protection Agency) and the ACCI (assessment class criterion for imposex) proposed by OSPAR (Oslo and Paris Commission). The evaluation shows that the TBT contained in the sediment at Kaohsiung Harbor is likely to have a negative influence at ACCI class C because gastropods present imposex and TBT levels are above ecotoxicological assessment criteria (EAC) limits.

  9. DNA: Structure and function

    DEFF Research Database (Denmark)

    Sinden, Richard R.; E. Pearson, Christopher; N. Potaman, Vladimir

    1998-01-01

    This chapter discusses the structure and function of DNA. DNA occupies a critical role in cells, because it is the source of all intrinsic genetic information. Chemically, DNA is a very stable molecule, a characteristic important for a macromolecule that may have to persist in an intact form...

  10. Replicating animal mitochondrial DNA

    Directory of Open Access Journals (Sweden)

    Emily A. McKinney

    2013-01-01

    Full Text Available The field of mitochondrial DNA (mtDNA replication has been experiencing incredible progress in recent years, and yet little is certain about the mechanism(s used by animal cells to replicate this plasmid-like genome. The long-standing strand-displacement model of mammalian mtDNA replication (for which single-stranded DNA intermediates are a hallmark has been intensively challenged by a new set of data, which suggests that replication proceeds via coupled leading-and lagging-strand synthesis (resembling bacterial genome replication and/or via long stretches of RNA intermediates laid on the mtDNA lagging-strand (the so called RITOLS. The set of proteins required for mtDNA replication is small and includes the catalytic and accessory subunits of DNA polymerase y, the mtDNA helicase Twinkle, the mitochondrial single-stranded DNA-binding protein, and the mitochondrial RNA polymerase (which most likely functions as the mtDNA primase. Mutations in the genes coding for the first three proteins are associated with human diseases and premature aging, justifying the research interest in the genetic, biochemical and structural properties of the mtDNA replication machinery. Here we summarize these properties and discuss the current models of mtDNA replication in animal cells.

  11. A DNA Mini-Barcoding System for Authentication of Processed Fish Products.

    Science.gov (United States)

    Shokralla, Shadi; Hellberg, Rosalee S; Handy, Sara M; King, Ian; Hajibabaei, Mehrdad

    2015-10-30

    Species substitution is a form of seafood fraud for the purpose of economic gain. DNA barcoding utilizes species-specific DNA sequence information for specimen identification. Previous work has established the usability of short DNA sequences-mini-barcodes-for identification of specimens harboring degraded DNA. This study aims at establishing a DNA mini-barcoding system for all fish species commonly used in processed fish products in North America. Six mini-barcode primer pairs targeting short (127-314 bp) fragments of the cytochrome c oxidase I (CO1) DNA barcode region were developed by examining over 8,000 DNA barcodes from species in the U.S. Food and Drug Administration (FDA) Seafood List. The mini-barcode primer pairs were then tested against 44 processed fish products representing a range of species and product types. Of the 44 products, 41 (93.2%) could be identified at the species or genus level. The greatest mini-barcoding success rate found with an individual primer pair was 88.6% compared to 20.5% success rate achieved by the full-length DNA barcode primers. Overall, this study presents a mini-barcoding system that can be used to identify a wide range of fish species in commercial products and may be utilized in high throughput DNA sequencing for authentication of heavily processed fish products.

  12. The Ku80 carboxy terminus stimulates joining and artemis-mediated processing of DNA ends.

    Science.gov (United States)

    Weterings, Eric; Verkaik, Nicole S; Keijzers, Guido; Florea, Bogdan I; Wang, Shih-Ya; Ortega, Laura G; Uematsu, Naoya; Chen, David J; van Gent, Dik C

    2009-03-01

    Repair of DNA double-strand breaks (DSBs) is predominantly mediated by nonhomologous end joining (NHEJ) in mammalian cells. NHEJ requires binding of the Ku70-Ku80 heterodimer (Ku70/80) to the DNA ends and subsequent recruitment of the DNA-dependent protein kinase catalytic subunit (DNA-PK(CS)) and the XRCC4/ligase IV complex. Activation of the DNA-PK(CS) serine/threonine kinase requires an interaction with Ku70/80 and is essential for NHEJ-mediated DSB repair. In contrast to previous models, we found that the carboxy terminus of Ku80 is not absolutely required for the recruitment and activation of DNA-PK(CS) at DSBs, although cells that harbored a carboxy-terminal deletion in the Ku80 gene were sensitive to ionizing radiation and showed reduced end-joining capacity. More detailed analysis of this repair defect showed that DNA-PK(CS) autophosphorylation at Thr2647 was diminished, while Ser2056 was phosphorylated to normal levels. This resulted in severely reduced levels of Artemis nuclease activity in vivo and in vitro. We therefore conclude that the Ku80 carboxy terminus is important to support DNA-PK(CS) autophosphorylation at specific sites, which facilitates DNA end processing by the Artemis endonuclease and the subsequent joining reaction.

  13. The Ku80 Carboxy Terminus Stimulates Joining and Artemis-Mediated Processing of DNA Ends▿

    Science.gov (United States)

    Weterings, Eric; Verkaik, Nicole S.; Keijzers, Guido; Florea, Bogdan I.; Wang, Shih-Ya; Ortega, Laura G.; Uematsu, Naoya; Chen, David J.; van Gent, Dik C.

    2009-01-01

    Repair of DNA double-strand breaks (DSBs) is predominantly mediated by nonhomologous end joining (NHEJ) in mammalian cells. NHEJ requires binding of the Ku70-Ku80 heterodimer (Ku70/80) to the DNA ends and subsequent recruitment of the DNA-dependent protein kinase catalytic subunit (DNA-PKCS) and the XRCC4/ligase IV complex. Activation of the DNA-PKCS serine/threonine kinase requires an interaction with Ku70/80 and is essential for NHEJ-mediated DSB repair. In contrast to previous models, we found that the carboxy terminus of Ku80 is not absolutely required for the recruitment and activation of DNA-PKCS at DSBs, although cells that harbored a carboxy-terminal deletion in the Ku80 gene were sensitive to ionizing radiation and showed reduced end-joining capacity. More detailed analysis of this repair defect showed that DNA-PKCS autophosphorylation at Thr2647 was diminished, while Ser2056 was phosphorylated to normal levels. This resulted in severely reduced levels of Artemis nuclease activity in vivo and in vitro. We therefore conclude that the Ku80 carboxy terminus is important to support DNA-PKCS autophosphorylation at specific sites, which facilitates DNA end processing by the Artemis endonuclease and the subsequent joining reaction. PMID:19103741

  14. A Comparison of Microbial Water Quality and Diversity for Ballast and Tropical Harbor Waters.

    Directory of Open Access Journals (Sweden)

    Charmaine Ng

    Full Text Available Indicator organisms and antibiotic resistance were used as a proxy to measure microbial water quality of ballast tanks of ships, and surface waters in a tropical harbor. The survival of marine bacteria in ballast tanks appeared to diminish over longer water retention time, with a reduction of cell viability observed after a week based on heterotrophic plate counts. Pyrosequencing of 16S rRNA genes showed distinct differences in microbial composition of ballast and harbor waters. The harbor waters had a higher abundance of operational taxonomic units (OTUs assigned to Cyanobacteria (Synechococcus spp. and α-proteobacteria (SAR11 members, while marine hydrocarbon degraders such as γ-proteobacteria (Ocenspirillaes spp., Thiotrchales spp. and Bacteroidetes (Flavobacteriales spp. dominated the ballast water samples. Screening of indicator organisms found Escherichia coli (E. coli, Enterococcus and Pseudomonas aeruginosa (P. aeruginosa in two or more of the ballast and harbor water samples tested. Vibrio spp. and Salmonella spp. were detected exclusively in harbor water samples. Using quantitative PCR (qPCR, we screened for 13 antibiotic resistant gene (ARG targets and found higher abundances of sul1 (4.13-3.44 x 102 copies/mL, dfrA (0.77-1.80 x10 copies/mL and cfr (2.00-5.21 copies/mL genes compared to the other ARG targets selected for this survey. These genes encode for resistance to sulfonamides, trimethoprim and chloramphenicol-florfenicol antibiotics, which are also known to persist in sediments of aquaculture farms and coastal environments. Among the ARGs screened, we found significant correlations (P<0.05 between ereA, ermG, cfr and tetO genes to one or more of the indicator organisms detected in this study, which may suggest that these members contribute to the environmental resistome. This study provides a baseline water quality survey, quantitatively assessing indicators of antibiotic resistance, potentially pathogenic organisms and a

  15. Fast phylogenetic DNA barcoding

    DEFF Research Database (Denmark)

    Terkelsen, Kasper Munch; Boomsma, Wouter Krogh; Willerslev, Eske

    2008-01-01

    We present a heuristic approach to the DNA assignment problem based on phylogenetic inferences using constrained neighbour joining and non-parametric bootstrapping. We show that this method performs as well as the more computationally intensive full Bayesian approach in an analysis of 500 insect...... DNA sequences obtained from GenBank. We also analyse a previously published dataset of environmental DNA sequences from soil from New Zealand and Siberia, and use these data to illustrate the fact that statistical approaches to the DNA assignment problem allow for more appropriate criteria...... for determining the taxonomic level at which a particular DNA sequence can be assigned....

  16. Radiation and DNA

    Energy Technology Data Exchange (ETDEWEB)

    Riabchenko, N I

    1979-01-01

    Consideration is given to the effects of ionizing radiation on the structure of DNA. Physical and chemical methods of determining radiation damage to the primary (polynucleotide chain and nitrogenous base) and secondary (helical) structure of DNA are discussed, and the effects of ionizing radiation on deoxyribonucleoprotein complexes are considered. The radiolysis of DNA in vitro and in bacterial and mammalian cells is examined and cellular mechanisms for the repair of radiation-damaged DNA are considered, taking into account single-strand and double-strand breaks, gamma-radiation damage and deoxyribonucleoprotein-membrane complex damage. Postradiation DNA degradation in bacteria and lymphatic cells is also discussed.

  17. DNA-Mediated Electrochemistry

    Science.gov (United States)

    Gorodetsky, Alon A.; Buzzeo, Marisa C.

    2009-01-01

    The base pair stack of DNA has been demonstrated as a medium for long range charge transport chemistry both in solution and at DNA-modified surfaces. This chemistry is exquisitely sensitive to structural perturbations in the base pair stack as occur with lesions, single base mismatches, and protein binding. We have exploited this sensitivity for the development of reliable electrochemical assays based on DNA charge transport at self-assembled DNA monolayers. Here we discuss the characteristic features, applications, and advantages of DNA-mediated electrochemistry. PMID:18980370

  18. Selenium and mercury concentrations in harbor seals (Phoca vitulina) from central California: Health implications in an urbanized estuary

    Science.gov (United States)

    McHuron, Elizabeth A.; Harvey, James T.; Castellini, J. Margaret; Stricker, Craig A.; O'Hara, Todd M.

    2014-01-01

    We measured total selenium and total mercury concentrations ([TSe] and [THg]) in hair (n = 138) and blood (n = 73) of harbor seals (Phoca vitulina) from California to assess variation by geography and sex, and inferred feeding relationships based on carbon, nitrogen, and sulfur stable isotopes. Harbor seals from Hg-contaminated sites had significantly greater [THg], and lesser [TSe] and TSe:THg molar ratios than seals from a relatively uncontaminated site. Males had significantly greater [THg] than females at all locations. Sulfur stable isotope values explained approximately 25% of the variability in [THg], indicating increased Hg exposure for seals with a greater use of estuarine prey species. Decreased [TSe] in harbor seals from Hg-contaminated regions may indicate a relative Se deficiency to mitigate the toxic effects of Hg. Further investigation into the Se status and the potential negative impact of Hg on harbor seals from Hg-contaminated sites is warranted.

  19. Comparative account of macrofouling ecology at Vijaydurg Harbor and Musakazi-Jaitapur Bay, central western coast of India

    Digital Repository Service at National Institute of Oceanography (India)

    Sawant, S.S.; Wagh, A.B.

    The extent and the nature of fouling were studied on mild steel, aluminum, and stainless steel panels at the Vijaydurg Harbor and Musakazi-Jaitapur Bay on the central western coast of India. In addition, cathodically protected and unprotected panels...

  20. Biodiversity of marine communities in Pearl Harbor, Oahu, Hawaii with observations in 1996 on introduced exotic species (NODC Accession 0000330)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The marine and estuarine invertebrate and fish communities in Pearl Harbor, Oahu, Hawaii were surveyed between January and October, 1996. Samples were taken and...

  1. Benthic grab data from October 1994 in the Lower Bay of New York/New Jersey Harbor

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Benthic grab samples were collected using a Shipek grab at pre-determined locations in the harbor. Taxonomic enumerations and biological community parameters were...

  2. Directional wave and temperature data from nine buoys in Gray's Harbor, Washington, 1994-2002 (NODC Accession 0000756)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Wave data were collected from 9 buoys in Grays Harbor, Washington, from 01 January 1994 to 24 July 2002. Data were collected as part of the Coastal Data Information...

  3. Central nervous system disease and genital disease in harbor porpoises (Phocoena phocoena) are associated with different herpesviruses

    NARCIS (Netherlands)

    C.E. van Elk; M.W.G. van de Bildt (Marco); P.R.W.A. van Run (Peter); De Jong, A. (Anton); S. Getu (Sarah); G.M.G.M. Verjans (George); A.D.M.E. Osterhaus (Albert); T. Kuiken (Thijs)

    2016-01-01

    textabstractHerpesvirus infection causes disease of variable severity in many species, including cetaceans. However, little is known about herpesvirus infection in harbor porpoises (Phocoena phocoena), despite being widespread in temperate coastal waters of the Northern Hemisphere. Therefore, we

  4. Case study of small harbor excitation under storm and tsunami conditions

    Science.gov (United States)

    Synolakis, Costas; Maravelakis, Nikos; Kalligeris, Nikos; Skanavis, Vassilios; Kanoglu, Utku; Yalciner, Ahmet; Lynett, Pat

    2016-04-01

    Simultaneous nearshore and interior-to-ports wave and current measurements for small ports are not common, and few, if any, benchmarking cases at sufficient resolution exist to help validate numerical model of intermediate waves, or even long waves. The wave conditions inside the old Venetian harbor of Chania, Greece and offshore were measured and studied from 2012 to 2015. The construction of this harbor began in the 14th century, and since then, its layout has been modified to adapt to different social and to economic conditions. It is divided into a western and an eastern basin. The eastern basin is used by recreational vessels and fishing boats throughout the year. The western basin has an exposed entrance to the north, and it is essentially functional half of the year, because of the severe overtopping and flooding that occur during the northern winter storms. Our work is motivated by the necessity to protect the monument from severe winter storm conditions and allow safe mooring and all other recreational activities that take place in the exposed western basin. Two earlier studies had proposed the construction of a low crested breakwater near the harbor entrance. The first design has been partially constructed, while the second never materialized. The main disadvantage of both studies was the lack of any wave field measurements. At the same time, second order or complimentary phenomena such as harbor resonance had not been considered. To address the lack of field data, the offshore wave climate has been monitored since October 2012 using an AWAC 600kHz instrument, deployed at 23m depth. The response of the western and eastern basins of the harbor was measured with a TWR-2050 (deployed at 5.5m depth) and an RBRDuet T.D./wave (deployed at 2m depth) pressure gauges respectively. Significant wave heights ranging up to 5.8 m with significant periods of up to 10 sec were measured. The harbor pressure gauges are now being re-deployed in other locations to collect

  5. Sediment quality in Burlington Harbor, Lake Champlain, U.S.A.

    Science.gov (United States)

    Lacey, E.M.; King, J.W.; Quinn, J.G.; Mecray, E.L.; Appleby, P.G.; Hunt, A.S.

    2001-01-01

    Surface samples and cores were collected in 1993 from the Burlington Harbor region of Lake Champlain. Sediment samples were analyzed for trace metals (cadmium, copper, lead, nickel, silver and zinc), simultaneously extracted metal/acid volatile sulfide (SEM-AVS), grain size, nutrients (carbon and nitrogen) and organic contaminants (polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs)). The concentrations of cadmium, copper, silver and zinc from the partial sediment digestion of the surface samples correlated well with each other (r2 > 0.60) indicating that either a common process, or group of processes determined the sediment concentrations of these metals. In an analysis of the spatial distribution of the trace metals and PAHs, high surficial concentrations were present in the southern portion of the Harbor. The trace metal trend was strengthened when the concentrations were normalized by grain size. A sewage treatment plant outfall discharge was present in the southeastern portion of the Harbor at the time of this study and is the major source of trace metal and PAH contamination. Evaluation of sediment cores provides a proxy record of historical trace metal and organic inputs. The peak accumulation rate for copper, cadmium, lead, and zinc was in the late 1960s and the peak silver accumulation rate was later. The greatest accumulation of trace metals occurred in the late 1960s after discharges from the STP began. Subsequent declines in trace metal concentrations may be attributed to increased water and air regulations. The potential toxicity of trace metals and organic contaminants was predicted by comparing contaminant concentrations to benchmark concentrations and potential trace metal bioavailability was predicted with SEM-AVS results. Surface sample results indicate lead, silver, ???PAHs and ???PCBs are potentially toxic and/or bioavailable. These predictions were supported by studies of biota in the Burlington Harbor watershed. There

  6. DNA fragmentation in spermatozoa

    DEFF Research Database (Denmark)

    Rex, A S; Aagaard, J.; Fedder, J

    2017-01-01

    Sperm DNA Fragmentation has been extensively studied for more than a decade. In the 1940s the uniqueness of the spermatozoa protein complex which stabilizes the DNA was discovered. In the fifties and sixties, the association between unstable chromatin structure and subfertility was investigated....... In the seventies, the impact of induced DNA damage was investigated. In the 1980s the concept of sperm DNA fragmentation as related to infertility was introduced as well as the first DNA fragmentation test: the Sperm Chromatin Structure Assay (SCSA). The terminal deoxynucleotidyl transferase nick end labelling...... (TUNEL) test followed by others was introduced in the nineties. The association between DNA fragmentation in spermatozoa and pregnancy loss has been extensively investigated spurring the need for a therapeutic tool for these patients. This gave rise to an increased interest in the aetiology of DNA damage...

  7. Biophysics of DNA

    CERN Document Server

    Vologodskii, Alexander

    2015-01-01

    Surveying the last sixty years of research, this book describes the physical properties of DNA in the context of its biological functioning. It is designed to enable both students and researchers of molecular biology, biochemistry and physics to better understand the biophysics of DNA, addressing key questions and facilitating further research. The chapters integrate theoretical and experimental approaches, emphasising throughout the importance of a quantitative knowledge of physical properties in building and analysing models of DNA functioning. For example, the book shows how the relationship between DNA mechanical properties and the sequence specificity of DNA-protein binding can be analyzed quantitatively by using our current knowledge of the physical and structural properties of DNA. Theoretical models and experimental methods in the field are critically considered to enable the reader to engage effectively with the current scientific literature on the physical properties of DNA.

  8. An investigation of the feasibility of building a harbor on the West coast of South America using explosive power of nuclear weapons, a preliminary report

    Energy Technology Data Exchange (ETDEWEB)

    Zodtner, H. H.

    1971-12-31

    There is an interest in discovering the various peace time uses of nuclear explosives. One of the proposals is the building of harbors. There are several ports along the west coast of South America where lighterage is necessary. This implies a need for expanded harbor facilities. The problem is to find a good location for creating a harbor, and the feasibility of accomplishing this with the use of nuclear force. Feasibility includes blast effects, radiation hazards, the number of weapons needed, and economic considerations. Economic considerations include the cost of treating a harbor of sufficient depth and area, the building of harbor facilities, and the estimated savings and advantages of the new harbor. Several meetings were held with naval personnel of the Military Liaison group at UCRL to discuss the general problems of harbors. Thirty-three different ports were given a preliminary investigation.

  9. Interim Feasibility Report and Draft Environmental Impact Statement, Grays Harbor, Chehalis and Hoquiam Rivers, Washington, Channel Improvements for Navigation.

    Science.gov (United States)

    1982-06-01

    community depends on the continued descent of organic materials from the overlying waters for nourishment. The Dungeness crab ( Cancer magister) is an...immediately north and south of Grays Harbor. EIS-34 o Crabs. Dungeness crabs ( Cancer magister) are abundant in Grays Harbor, though most are smaller...Cooper Cultural Resources Mama Seattle District, Evaluation Corps of Engineers Endangered Species Brunner Seattle District, Evaluation Corps of Engineers

  10. Benthic foraminifera distribution in high polluted sediments from Niterói Harbor (Guanabara Bay), Rio de Janeiro, Brazil

    OpenAIRE

    Claudia G. Vilela; Daniele S. Batista; José A. Batista-Neto; Mirian Crapez; John J. Mcallister

    2004-01-01

    Dockyards and harbors are recognized as being important locations where sediment-associated pollutants can accumulate, which constitutes an environmental risk to aquatic life due to potential uptake and accumulation of heavy metals in the biota. The aim of this paper is to assess the concentrations and the effects of some heavy metals in the benthic foraminifera assemblage in Niterói Harbor. Low concentrations in the benthic foraminifera as well as the dominance of indicative species such as ...

  11. Genomic and Functional Characterization of the Unusual pLOCK 0919 Plasmid Harboring the spaCBA Pili Cluster in Lactobacillus casei LOCK 0919

    Science.gov (United States)

    Aleksandrzak-Piekarczyk, Tamara; Koryszewska-Bagińska, Anna; Grynberg, Marcin; Nowak, Adriana; Cukrowska, Bożena; Kozakova, Hana; Bardowski, Jacek

    2016-01-01

    Here, we report the extensive bioinformatic and functional analyses of the unusual pLOCK 0919, a plasmid originating from the probiotic Lactobacillus casei LOCK 0919 strain. This plasmid is atypical because it harbors the spaCBA-srtC gene cluster encoding SpaCBA pili. We show that all other spaCBA-srtC sequences of the Lactobacillus genus that have been previously described and deposited in GenBank are present in the chromosomal DNA. Another important observation for pLOCK 0919 is that the spaCBA-srtC gene cluster and its surrounding genes are highly similar to the respective DNA region that is present in the most well-known and active SpaCBA pili producer, the probiotic Lactobacillus rhamnosus GG strain. Our results demonstrate that the spaCBA-srtC clusters of pLOCK 0919 and L. rhamnosus GG are genealogically similar, located in DNA regions that are rich in transposase genes and are poorly conserved among the publicly available sequences of Lactobacillus sp. In contrast to chromosomally localized pilus gene clusters from L. casei and Lactobacillus paracasei, the plasmidic spaC of L. casei LOCK 0919 is expressed and undergoes a slight glucose-induced repression. Moreover, results of series of in vitro tests demonstrate that L. casei LOCK 0919 has an adhesion potential, which is largely determined by the presence of the pLOCK 0919 plasmid. In particular, the plasmid occurrence positively influenced the hydrophobicity and aggregation abilities of L. casei LOCK 0919. Moreover, in vivo studies indicate that among the three Lactobacillus strains used to colonize the gastrointestinal tract of germ-free mice, already after 2 days of colonization, L. casei LOCK 0919 became the dominant strain and persisted there for at least 48 days. PMID:26637469

  12. Assessment of a combination between hard structures and sand nourishment eastern of Damietta harbor using numerical modeling

    Directory of Open Access Journals (Sweden)

    A.M. Khalifa

    2017-12-01

    Full Text Available Damietta harbor was constructed in 1982 as an inland harbor with its 15 m depth navigation channel and two jetties acting like an obstacle to not allow sediment deposition in the harbor. On the other hand, they significantly affect the northern coast shoreline and hinder the sediment circulation in Damietta promontory. Satellite images show that new headlands are being implemented in the coastal shores of As-senaneyah. The proposed project consists of implementation of four headlands with length of 160 m, spacing of 400 m and using 150,000 m3 nourishment in those spacing between the hard structures only once during the construction time. Litpack 1D-model is used to predict shoreline responses to number of different five scenarios considered as combination between hard structures such as headlands and sand nourishment. A total number of 32 profiles were used to assess the shoreline changes along Gamasa, Damietta and Ras El-bar resort from 2010 to 2015. This study prevails a high erosion rate of the eastern and western shorelines of the proposed headlands. Nourishment of 200,000 m3/year is found to be a reasonable solution due to simplicity of being attained from Damietta harbor’s annual dredged materials which was reported to be average of 1 million m3/year. Keywords: Numerical modeling, Damietta harbor, Egyptian shoreline changes, Inland harbor

  13. Pathological mechanisms underlying single large‐scale mitochondrial DNA deletions

    Science.gov (United States)

    Rocha, Mariana C.; Rosa, Hannah S.; Grady, John P.; Blakely, Emma L.; He, Langping; Romain, Nadine; Haller, Ronald G.; Newman, Jane; McFarland, Robert; Ng, Yi Shiau; Gorman, Grainne S.; Schaefer, Andrew M.; Tuppen, Helen A.; Taylor, Robert W.

    2018-01-01

    Objective Single, large‐scale deletions in mitochondrial DNA (mtDNA) are a common cause of mitochondrial disease. This study aimed to investigate the relationship between the genetic defect and molecular phenotype to improve understanding of pathogenic mechanisms associated with single, large‐scale mtDNA deletions in skeletal muscle. Methods We investigated 23 muscle biopsies taken from adult patients (6 males/17 females with a mean age of 43 years) with characterized single, large‐scale mtDNA deletions. Mitochondrial respiratory chain deficiency in skeletal muscle biopsies was quantified by immunoreactivity levels for complex I and complex IV proteins. Single muscle fibers with varying degrees of deficiency were selected from 6 patient biopsies for determination of mtDNA deletion level and copy number by quantitative polymerase chain reaction. Results We have defined 3 “classes” of single, large‐scale deletion with distinct patterns of mitochondrial deficiency, determined by the size and location of the deletion. Single fiber analyses showed that fibers with greater respiratory chain deficiency harbored higher levels of mtDNA deletion with an increase in total mtDNA copy number. For the first time, we have demonstrated that threshold levels for complex I and complex IV deficiency differ based on deletion class. Interpretation Combining genetic and immunofluorescent assays, we conclude that thresholds for complex I and complex IV deficiency are modulated by the deletion of complex‐specific protein‐encoding genes. Furthermore, removal of mt‐tRNA genes impacts specific complexes only at high deletion levels, when complex‐specific protein‐encoding genes remain. These novel findings provide valuable insight into the pathogenic mechanisms associated with these mutations. Ann Neurol 2018;83:115–130 PMID:29283441

  14. “Infectobesity: viral infections (especially with human adenovirus-36: Ad-36) may be a cause of obesity

    NARCIS (Netherlands)

    Ginneken, van V.J.T.; Sitnyakowsky, L.; Jeffery, J.E.

    2009-01-01

    In recent years viral infections have been recognized as possible cause of obesity, alongside the traditionally recognized causes (genetic inheritance, and behaviour/environmental causes such as diet exercise, cultural practices and stress). Although four viruses have been reported to induce obesity

  15. A germline FANCA alteration that is associated with increased sensitivity to DNA damaging agents.

    Science.gov (United States)

    Wilkes, David C; Sailer, Verena; Xue, Hui; Cheng, Hongwei; Collins, Colin C; Gleave, Martin; Wang, Yuzhuo; Demichelis, Francesca; Beltran, Himisha; Rubin, Mark A; Rickman, David S

    2017-09-01

    Defects in genes involved in DNA damage repair (DDR) pathway are emerging as novel biomarkers and targets for new prostate cancer drug therapies. A previous report revealed an association between an exceptional response to cisplatin treatment and a somatic loss of heterozygosity (LOH) of FANCA in a patient with metastatic prostate cancer who also harbored a germline FANCA variant (S1088F). Although germline FANCA mutations are the most frequent alterations in patients with Fanconi anemia, germline alterations are less common in prostate cancer. We hypothesized that the germline S1088F FANCA variant in combination with FANCA LOH was deleterious for FANCA function and contributed to the patient's exceptional response to cisplatin. We show that although it properly localizes to the nucleus, the S1088F FANCA mutant protein disrupts the FANC protein complex resulting in increased sensitivity to DNA damaging agents. Because molecular stratification is emerging as a strategy for treating men with metastatic, castrate-resistant prostate cancer harboring specific DDR gene defects, our findings suggest that more biomarker studies are needed to better define clinically relevant germline and somatic alterations. © 2017 Wilkes et al.; Published by Cold Spring Harbor Laboratory Press.

  16. Beyond DNA repair: DNA-PK function in cancer

    OpenAIRE

    Goodwin, Jonathan F.; Knudsen, Karen E.

    2014-01-01

    The DNA-dependent protein kinase (DNA-PK) is a pivotal component of the DNA repair machinery that governs the response to DNA damage, serving to maintain genome integrity. However, the DNA-PK kinase component was initially isolated with transcriptional complexes, and recent findings have illuminated the impact of DNA-PK-mediated transcriptional regulation on tumor progression and therapeutic response. DNA-PK expression has also been correlated with poor outcome in selected tumor types, furthe...

  17. Comparison of DNA extraction methods for human gut microbial community profiling.

    Science.gov (United States)

    Lim, Mi Young; Song, Eun-Ji; Kim, Sang Ho; Lee, Jangwon; Nam, Young-Do

    2018-03-01

    The human gut harbors a vast range of microbes that have significant impact on health and disease. Therefore, gut microbiome profiling holds promise for use in early diagnosis and precision medicine development. Accurate profiling of the highly complex gut microbiome requires DNA extraction methods that provide sufficient coverage of the original community as well as adequate quality and quantity. We tested nine different DNA extraction methods using three commercial kits (TianLong Stool DNA/RNA Extraction Kit (TS), QIAamp DNA Stool Mini Kit (QS), and QIAamp PowerFecal DNA Kit (QP)) with or without additional bead-beating step using manual or automated methods and compared them in terms of DNA extraction ability from human fecal sample. All methods produced DNA in sufficient concentration and quality for use in sequencing, and the samples were clustered according to the DNA extraction method. Inclusion of bead-beating step especially resulted in higher degrees of microbial diversity and had the greatest effect on gut microbiome composition. Among the samples subjected to bead-beating method, TS kit samples were more similar to QP kit samples than QS kit samples. Our results emphasize the importance of mechanical disruption step for a more comprehensive profiling of the human gut microbiome. Copyright © 2017 The Authors. Published by Elsevier GmbH.. All rights reserved.

  18. DNA topology and transcription

    Science.gov (United States)

    Kouzine, Fedor; Levens, David; Baranello, Laura

    2014-01-01

    Chromatin is a complex assembly that compacts DNA inside the nucleus while providing the necessary level of accessibility to regulatory factors conscripted by cellular signaling systems. In this superstructure, DNA is the subject of mechanical forces applied by variety of molecular motors. Rather than being a rigid stick, DNA possesses dynamic structural variability that could be harnessed during critical steps of genome functioning. The strong relationship between DNA structure and key genomic processes necessitates the study of physical constrains acting on the double helix. Here we provide insight into the source, dynamics, and biology of DNA topological domains in the eukaryotic cells and summarize their possible involvement in gene transcription. We emphasize recent studies that might inspire and impact future experiments on the involvement of DNA topology in cellular functions. PMID:24755522

  19. Eukaryotic DNA Replication Fork.

    Science.gov (United States)

    Burgers, Peter M J; Kunkel, Thomas A

    2017-06-20

    This review focuses on the biogenesis and composition of the eukaryotic DNA replication fork, with an emphasis on the enzymes that synthesize DNA and repair discontinuities on the lagging strand of the replication fork. Physical and genetic methodologies aimed at understanding these processes are discussed. The preponderance of evidence supports a model in which DNA polymerase ε (Pol ε) carries out the bulk of leading strand DNA synthesis at an undisturbed replication fork. DNA polymerases α and δ carry out the initiation of Okazaki fragment synthesis and its elongation and maturation, respectively. This review also discusses alternative proposals, including cellular processes during which alternative forks may be utilized, and new biochemical studies with purified proteins that are aimed at reconstituting leading and lagging strand DNA synthesis separately and as an integrated replication fork.

  20. Assessment of the impact of oil spill on Mumbai harbor bay

    International Nuclear Information System (INIS)

    Pandit, G.G.; Saradhi, I.V.; Puranik, V.D.; Sharma, D.N.; Ghosh, A.K.

    2011-04-01

    On 7 th August, 2010 two cargo ships MSC Chitra and MV Khalijia collided off Mumbai coast causing an oil spill that spread quickly through Maharashtra's coastline. MSC Chitra ruptured its tank when it hit incoming MV Khalijia. MSC Chitra tilted to about 80 degrees soon after the collision, spilling an estimated 400 to 500 tonnes of oil. The ship was loaded with an estimated 2,600 tonnes of oil, 300 tonnes of diesel and 70 tonnes of lubricating oil at the time of the accident. The oil spill has spreaded over an area of 25 square kilometers. MSC Chitra was carrying 1219 containers out of which 31 had hazardous chemicals like organophosphate pesticides. After the collision about 400 containers fall off into to the sea from the deck of MSC Chitra. The oil spill has resulted in severe environmental damage along the Mumbai coastline as well as to the marine life. In order to assess the impact of oil spill on the marine environment daily monitoring of oil and grease levels has been carried out at CIRUS Jetty. Additionally three field surveys have been carried out along the coast line of Mumbai harbor bay from Vashi Jetty to Uran collecting sea water samples. The samples collected at CIRUS Jetty and Mumbai harbor bay are analyzed for various water quality parameters apart from oil and grease. The results indicate the oil and grease levels in sea water at CIRUS Jetty reduced to background levels within 15 days. The filed survey along Mumbai harbor bay also shows a decreasing trend in the oil and grease levels in seawater. (author)

  1. Movements and foraging effort of Steller's Eiders and Harlequin Ducks wintering near Dutch Harbor, Alaska

    Science.gov (United States)

    Reed, J.A.; Flint, Paul L.

    2007-01-01

    We studied the movements and foraging effort of radio-marked Steller's Eiders (Polysticta stelleri) and Harlequin Ducks (Histrionicus histrionicus) to evaluate habitat quality in an area impacted by industrial activity near Dutch Harbor, Alaska. Foraging effort was relatively low, with Steller's Eiders foraging only 2.7 ± 0.6 (SE) hours per day and Harlequin Ducks 4.1 ± 0.5 hours per day. Low-foraging effort during periods of high-energetic demand generally suggests high food availability, and high food availability frequently corresponds with reductions in home range size. However, the winter ranges of Harlequin Ducks did not appear to be smaller than usual, with the mean range size in our study (5.5 ± 1.1 km2) similar to that reported by previous investigators. The mean size of the winter ranges of Steller's Eiders was similar (5.1 ± 1.3 km2), but no comparable estimates are available. Eutrophication of the waters near Dutch Harbor caused by seafood processing and municipal sewage effluent may have increased populations of the invertebrate prey of these sea ducks and contributed to their low-foraging effort. The threat of predation by Bald Eagles (Haliaeetus leucocephalus) that winter near Dutch Harbor may cause Steller's Eiders and Harlequin Ducks to move further offshore when not foraging, contributing to an increase in range sizes. Thus, the movement patterns and foraging behavior of these ducks likely represent a balance between the cost and benefits of wintering in a human-influenced environment.

  2. Clinical and CT characteristics of surgically resected lung adenocarcinomas harboring ALK rearrangements or EGFR mutations

    International Nuclear Information System (INIS)

    Wang, Hua; Schabath, Matthew B.; Liu, Ying; Han, Ying; Li, Qi; Gillies, Robert J.; Ye, Zhaoxiang

    2016-01-01

    Purpose: To determine if clinical and CT characteristics of surgically resected lung adenocarcinomas can distinguish those harboring ALK rearrangements from EGFR mutations. Materials and methods: Patients who had surgical resection and histologically confirmed lung adenocarcinoma were enrolled, including 41 patients with ALK rearrangements and 66 patients with EGFR mutations. Eighteen categorical and six quantitative CT characteristics were used to evaluate the tumors. Differences in clinical and CT characteristics between the two groups were investigated. Results: Age (P = 0.003), histological subtypes (P < 0.001), pathological stage (P = 0.007), and five CT characteristics, including size (P < 0.001), GGO (P = 0.001), bubble-like lucency (P = 0.048), lymphadenopathy (P = 0.001), and tumor shadow disappearance rate (P = 0.005) were significantly different between patients harboring ALK rearrangements compared to patients with EGFR mutations. When we compared histologic components, a solid pattern was more common (P = 0.009) in tumors with ALK rearrangements, and lepidic and acinar patterns were more common (P < 0.001 and P = 0.040, respectively) in those with EGFR mutations. Backward elimination analyses revealed that age (OR = 0.93; 95% CI 0.89–0.98), GGO (OR = 0.14; 95% CI 0.03–0.67), and lymphadenopathy (OR = 4.15; 95% CI 1.49–11.60) were significantly associated with ALK rearrangement status. Conclusion: Our analyses revealed that clinical and CT characteristics of lung adenocarcinomas harboring ALK rearrangements were significantly different, compared with those with EGFR mutations. These differences may be related to the molecular pathology of these diseases.

  3. Influenza A (H10N7 Virus Causes Respiratory Tract Disease in Harbor Seals and Ferrets.

    Directory of Open Access Journals (Sweden)

    Judith M A van den Brand

    Full Text Available Avian influenza viruses sporadically cross the species barrier to mammals, including humans, in which they may cause epidemic disease. Recently such an epidemic occurred due to the emergence of avian influenza virus of the subtype H10N7 (Seal/H10N7 in harbor seals (Phoca vitulina. This epidemic caused high mortality in seals along the north-west coast of Europe and represented a potential risk for human health. To characterize the spectrum of lesions and to identify the target cells and viral distribution, findings in 16 harbor seals spontaneously infected with Seal/H10N7 are described. The seals had respiratory tract inflammation extending from the nasal cavity to bronchi associated with intralesional virus antigen in respiratory epithelial cells. Virus infection was restricted to the respiratory tract. The fatal outcome of the viral infection in seals was most likely caused by secondary bacterial infections. To investigate the pathogenic potential of H10N7 infection for humans, we inoculated the seal virus intratracheally into six ferrets and performed pathological and virological analyses at 3 and 7 days post inoculation. These experimentally inoculated ferrets displayed mild clinical signs, virus excretion from the pharynx and respiratory tract inflammation extending from bronchi to alveoli that was associated with virus antigen expression exclusively in the respiratory epithelium. Virus was isolated only from the respiratory tract. In conclusion, Seal/H10N7 infection in naturally infected harbor seals and experimentally infected ferrets shows that respiratory epithelial cells are the permissive cells for viral replication. Fatal outcome in seals was caused by secondary bacterial pneumonia similar to that in fatal human cases during influenza pandemics. Productive infection of ferrets indicates that seal/H10N7 may possess a zoonotic potential. This outbreak of LPAI from wild birds to seals demonstrates the risk of such occasions for mammals

  4. NifH- Harboring Bacterial Community Composition Across an Alaskan Permafrost Thaw Gradient

    Directory of Open Access Journals (Sweden)

    Christopher Ryan Penton

    2016-11-01

    Full Text Available Since nitrogen (N is often limiting in permafrost soils, we investigated the N2-fixing genetic potential and the inferred taxa harboring those genes by sequencing nifH gene fragments in samples taken along a permafrost thaw gradient in an Alaskan boreal soil. Samples from minimally, moderately and extensively thawed sites were taken to a depth of 79 cm to encompass zones above and below the depth of the water table. NifH reads were translated with frameshift correction and 112,476 sequences were clustered at 5% amino acid dissimilarity resulting in 1,631 OTUs. Sample depth in relation to water table depth was correlated to differences in the NifH sequence classes. NifH sequences most closely related to group I nifH-harboring Alpha- and Beta Proteobacteria were in higher abundance above water table depth while those related to group III nifH-harboring Delta and Gamma Proteobacteria were more abundant below. The most dominant below water table depth NifH sequences, comprising 1/3 of the total, were distantly related to Verrucomicrobia-Opitutaceae. Overall, these results suggest that permafrost thaw alters the class-level composition of N2-fixing communities in the thawed soil layers and that this distinction corresponds to the depth of the water table. These nifH data were also compared to nifH sequences obtained from a study at an Alaskan taiga site, and to those of other geographically distant, non-permafrost sites. The two Alaska sites were differentiated largely by changes in relative abundances of the same OTUs, whereas the non-Alaska sites were differentiated by the lack of many Alaskan OTUs, and the presence of unique halophilic, sulfate- and iron-reducing taxa in the Alaska sites.

  5. Characterization of differential gene expression in adrenocortical tumors harboring beta-catenin (CTNNB1) mutations.

    Science.gov (United States)

    Durand, Julien; Lampron, Antoine; Mazzuco, Tania L; Chapman, Audrey; Bourdeau, Isabelle

    2011-07-01

    Mutations of β-catenin gene (CTNNB1) are frequent in adrenocortical adenomas (AA) and adrenocortical carcinomas (ACC). However, the target genes of β-catenin have not yet been identified in adrenocortical tumors. Our objective was to identify genes deregulated in adrenocortical tumors harboring CTNNB1 genetic alterations and nuclear accumulation of β-catenin. Microarray analysis identified a dataset of genes that were differently expressed between AA with CTNNB1 mutations and wild-type (WT) tumors. Within this dataset, the expression profiles of five genes were validated by real time-PCR (RT-PCR) in a cohort of 34 adrenocortical tissues (six AA and one ACC with CTNNB1 mutations, 13 AA and four ACC with WT CTNNB1, and 10 normal adrenal glands) and two human ACC cell lines. We then studied the effects of suppressing β-catenin transcriptional activity with the T-cell factor/β-catenin inhibitors PKF115-584 and PNU74654 on gene expression in H295R and SW13 cells. RT-PCR analysis confirmed the overexpression of ISM1, RALBP1, and PDE2A and the down-regulation of PHYHIP in five of six AA harboring CTNNB1 mutations compared with WT AA (n = 13) and normal adrenal glands (n = 10). RALBP1 and PDE2A overexpression was also confirmed at the protein level by Western blotting analysis in mutated tumors. ENC1 was specifically overexpressed in three of three AA harboring CTNNB1 point mutations. mRNA expression and protein levels of RALBP1, PDE2A, and ENC1 were decreased in a dose-dependent manner in H295R cells after treatment with PKF115-584 or PNU74654. This study identified candidate genes deregulated in CTNNB1-mutated adrenocortical tumors that may lead to a better understanding of the role of the Wnt-β-catenin pathway in adrenocortical tumorigenesis.

  6. Clinical and CT characteristics of surgically resected lung adenocarcinomas harboring ALK rearrangements or EGFR mutations

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Hua [Department of Radiology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin (China); Schabath, Matthew B. [Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL (United States); Liu, Ying [Department of Radiology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin (China); Department of Cancer Imaging and Metabolism, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL (United States); Han, Ying [Department of Biotherapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin (China); Li, Qi [Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin (China); Gillies, Robert J. [Department of Cancer Imaging and Metabolism, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL (United States); Department of Radiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL (United States); Ye, Zhaoxiang, E-mail: yezhaoxiang@163.com [Department of Radiology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin (China)

    2016-11-15

    Purpose: To determine if clinical and CT characteristics of surgically resected lung adenocarcinomas can distinguish those harboring ALK rearrangements from EGFR mutations. Materials and methods: Patients who had surgical resection and histologically confirmed lung adenocarcinoma were enrolled, including 41 patients with ALK rearrangements and 66 patients with EGFR mutations. Eighteen categorical and six quantitative CT characteristics were used to evaluate the tumors. Differences in clinical and CT characteristics between the two groups were investigated. Results: Age (P = 0.003), histological subtypes (P < 0.001), pathological stage (P = 0.007), and five CT characteristics, including size (P < 0.001), GGO (P = 0.001), bubble-like lucency (P = 0.048), lymphadenopathy (P = 0.001), and tumor shadow disappearance rate (P = 0.005) were significantly different between patients harboring ALK rearrangements compared to patients with EGFR mutations. When we compared histologic components, a solid pattern was more common (P = 0.009) in tumors with ALK rearrangements, and lepidic and acinar patterns were more common (P < 0.001 and P = 0.040, respectively) in those with EGFR mutations. Backward elimination analyses revealed that age (OR = 0.93; 95% CI 0.89–0.98), GGO (OR = 0.14; 95% CI 0.03–0.67), and lymphadenopathy (OR = 4.15; 95% CI 1.49–11.60) were significantly associated with ALK rearrangement status. Conclusion: Our analyses revealed that clinical and CT characteristics of lung adenocarcinomas harboring ALK rearrangements were significantly different, compared with those with EGFR mutations. These differences may be related to the molecular pathology of these diseases.

  7. A solitary hyperfunctioning thyroid nodule harboring thyroid carcinoma: review of the literature.

    Science.gov (United States)

    Mirfakhraee, Sasan; Mathews, Dana; Peng, Lan; Woodruff, Stacey; Zigman, Jeffrey M

    2013-05-04

    Hyperfunctioning nodules of the thyroid are thought to only rarely harbor thyroid cancer, and thus are infrequently biopsied. Here, we present the case of a patient with a hyperfunctioning thyroid nodule harboring thyroid carcinoma and, using MEDLINE literature searches, set out to determine the prevalence of and characteristics of malignant "hot" nodules as a group. Historical, biochemical and radiologic characteristics of the case subjects and their nodules were compared to those in cases of benign hyperfunctioning nodules. A literature review of surgical patients with solitary hyperfunctioning thyroid nodules managed by thyroid resection revealed an estimated 3.1% prevalence of malignancy. A separate literature search uncovered 76 cases of reported malignant hot thyroid nodules, besides the present case. Of these, 78% were female and mean age at time of diagnosis was 47 years. Mean nodule size was 4.13 ± 1.68 cm. Laboratory assessment revealed T3 elevation in 76.5%, T4 elevation in 51.9%, and subclinical hyperthyroidism in 13% of patients. Histological diagnosis was papillary thyroid carcinoma (PTC) in 57.1%, follicular thyroid carcinoma (FTC) in 36.4%, and Hurthle cell carcinoma in 7.8% of patients. Thus, hot thyroid nodules harbor a low but non-trivial rate of malignancy. Compared to individuals with benign hyperfunctioning thyroid nodules, those with malignant hyperfunctioning nodules are younger and more predominantly female. Also, FTC and Hurthle cell carcinoma are found more frequently in hot nodules than in general. We were unable to find any specific characteristics that could be used to distinguish between malignant and benign hot nodules.

  8. DNA-based machines.

    Science.gov (United States)

    Wang, Fuan; Willner, Bilha; Willner, Itamar

    2014-01-01

    The base sequence in nucleic acids encodes substantial structural and functional information into the biopolymer. This encoded information provides the basis for the tailoring and assembly of DNA machines. A DNA machine is defined as a molecular device that exhibits the following fundamental features. (1) It performs a fuel-driven mechanical process that mimics macroscopic machines. (2) The mechanical process requires an energy input, "fuel." (3) The mechanical operation is accompanied by an energy consumption process that leads to "waste products." (4) The cyclic operation of the DNA devices, involves the use of "fuel" and "anti-fuel" ingredients. A variety of DNA-based machines are described, including the construction of "tweezers," "walkers," "robots," "cranes," "transporters," "springs," "gears," and interlocked cyclic DNA structures acting as reconfigurable catenanes, rotaxanes, and rotors. Different "fuels", such as nucleic acid strands, pH (H⁺/OH⁻), metal ions, and light, are used to trigger the mechanical functions of the DNA devices. The operation of the devices in solution and on surfaces is described, and a variety of optical, electrical, and photoelectrochemical methods to follow the operations of the DNA machines are presented. We further address the possible applications of DNA machines and the future perspectives of molecular DNA devices. These include the application of DNA machines as functional structures for the construction of logic gates and computing, for the programmed organization of metallic nanoparticle structures and the control of plasmonic properties, and for controlling chemical transformations by DNA machines. We further discuss the future applications of DNA machines for intracellular sensing, controlling intracellular metabolic pathways, and the use of the functional nanostructures for drug delivery and medical applications.

  9. DNA repair and cancer

    International Nuclear Information System (INIS)

    Rathore, Shakuntla; Joshi, Pankaj Kumar; Gaur, Sudha

    2012-01-01

    DNA repair refers to a collection of processes by which a cell identifies and corrects damage to the DNA molecule that encode it's genome. In human cells, both normal metabolic activities and environmental factors such as UV light and radiation can cause DNA damage, resulting in as many one million individual molecular lesions per day. Many of these lesions cause structural damage to the DNA molecule and can alter or eliminate the cell's ability to transcribe the gene that the affected DNA encodes. Other lesions include potentially harmful mutation in cell's genome which affect the survival of it's daughter cells after it undergoes mitosis. As a consequence, the DNA repair process is constantly active as it responds to damage in the DNA structure. Inherited mutation that affect DNA repair genes are strongly associated with high cancer risks in humans. Hereditary non polyposis colorectal cancer (HNPCC) is strongly associated with specific mutation in the DNA mismatch repair pathway. BRCA1, BRCA2 two famous mutation conferring a hugely increased risk of breast cancer on carrier, are both associated with a large number of DNA repair pathway, especially NHEJ and homologous recombination. Cancer therapy procedures such as chemotherapy and radiotherapy work by overwhelming the capacity of the cell to repair DNA damage, resulting in cell death. Cells that are most rapidly dividing most typically cancer cells are preferentially affected. The side effect is that other non-cancerous but rapidly dividing cells such as stem cells in the bone marrow are also affected. Modern cancer treatment attempt to localize the DNA damage to cells and tissue only associated with cancer, either by physical means (concentrating the therapeutic agent in the region of the tumor) or by biochemical means (exploiting a feature unique to cancer cells in the body). (author)

  10. Production of infectious chimeric hepatitis C virus genotype 2b harboring minimal regions of JFH-1.

    Science.gov (United States)

    Murayama, Asako; Kato, Takanobu; Akazawa, Daisuke; Sugiyama, Nao; Date, Tomoko; Masaki, Takahiro; Nakamoto, Shingo; Tanaka, Yasuhito; Mizokami, Masashi; Yokosuka, Osamu; Nomoto, Akio; Wakita, Takaji

    2012-02-01

    To establish a cell culture system for chimeric hepatitis C virus (HCV) genotype 2b, we prepared a chimeric construct harboring the 5' untranslated region (UTR) to the E2 region of the MA strain (genotype 2b) and the region of p7 to the 3' UTR of the JFH-1 strain (genotype 2a). This chimeric RNA (MA/JFH-1.1) replicated and produced infectious virus in Huh7.5.1 cells. Replacement of the 5' UTR of this chimera with that from JFH-1 (MA/JFH-1.2) enhanced virus production, but infectivity remained low. In a long-term follow-up study, we identified a cell culture-adaptive mutation in the core region (R167G) and found that it enhanced virus assembly. We previously reported that the NS3 helicase (N3H) and the region of NS5B to 3' X (N5BX) of JFH-1 enabled replication of the J6CF strain (genotype 2a), which could not replicate in cells. To reduce JFH-1 content in MA/JFH-1.2, we produced a chimeric viral genome for MA harboring the N3H and N5BX regions of JFH-1, combined with a JFH-1 5' UTR replacement and the R167G mutation (MA/N3H+N5BX-JFH1/R167G). This chimeric RNA replicated efficiently, but virus production was low. After the introduction of four additional cell culture-adaptive mutations, MA/N3H+N5BX-JFH1/5am produced infectious virus efficiently. Using this chimeric virus harboring minimal regions of JFH-1, we analyzed interferon sensitivity and found that this chimeric virus was more sensitive to interferon than JFH-1 and another chimeric virus containing more regions from JFH-1 (MA/JFH-1.2/R167G). In conclusion, we established an HCV genotype 2b cell culture system using a chimeric genome harboring minimal regions of JFH-1. This cell culture system may be useful for characterizing genotype 2b viruses and developing antiviral strategies.

  11. Physiological studies in aerobic batch cultivations of Saccharomyces cerevisiae strains harboring the MEL1 gene

    DEFF Research Database (Denmark)

    Østergaard, Simon; Roca, Christophe Francois Aime; Ronnow, B.

    2000-01-01

    Physiological studies of Saccharomyces cerevisiae strains harboring the MEL1 gene were carried out in aerobic batch cultivations on glucose-galactose mixtures and on the disaccharide melibiose, which is hydrolyzed by the enzyme melibiase (Mel1, EC 3.2.1.22) into a glucose and a galactose moiety...... rates were 2.5-3.3-fold higher on glucose than on galactose for all the strains examined, and hence, ethanol production was pronounced on glucose due to respiro-fermentative metabolism. The T256 strain and the T200 strain having the MEL1 gene inserted in the HXK2 locus and the LEU2 locus, respectively...

  12. Drug discovery and the impact of the safe harbor provision of the Hatch- Waxman Act.

    Science.gov (United States)

    Goodson, Susanne H

    2010-01-01

    Many facets of drug discovery involve the use of patented materials and methods, subjecting the researcher to potential liability from infringement of the underlying patents. Enacted in 1984, the Hatch-Waxman Act established a “safe harbor” for activities that would otherwise constitute infringement of a patented invention, if those activities were “solely for uses reasonably related to the development and submission of information under a Federal law which regulates the manufacture, use, or sale of drugs or veterinary biological products”. This article examines the major court decisions interpreting the scope of the safe harbor and their application to various activities in drug development.

  13. Clean Water Act (Section 404) and Rivers and Harbors Act (Sections 9 and 10)

    International Nuclear Information System (INIS)

    1992-01-01

    This Reference Book contains a current copy of the Clean Water Act (Section 404) and the Rivers and Harbors Act (Sections 9 and 10) and those regulations that implement those sections of the statutes and appear to be most relevant to DOE activities. The document is provided to DOE and contractor staff for informational purposes only and should not be interpreted as legal guidance. Updates that include important new requirements will be provided periodically. Questions concerning this Reference Book may be directed to Mark Petts, IH-231 (FTS 896-2609 or Commercial 202/586-2609)

  14. "Tugboat Annie:" nursing's hero of Pearl Harbor--Grace Lally (1897-1983).

    Science.gov (United States)

    Hawkins, J W; Matthews, I

    1991-01-01

    In 1991 we will mark the 50th anniversary of the Japanese attack on Pearl Harbor. Few nurses know that the Chief Nurse aboard the USS Solace, the only hospital ship in port on that fateful day, played a critical role in caring for the survivors. Grace Lally's calm, professional manner, along with her sensitivity to the needs of her patients, her 12 nurses, and the crew of the Solace made her a hero. This study is an investigation of her role on December 7, 1941, and her contributions as a career military nurse.

  15. Nonisotopic DNA probe techniques

    National Research Council Canada - National Science Library

    Kricka, Larry J

    1992-01-01

    The objective of this book is to bring together descriptions of the principal nonisotopic methods for DNA hybridization assays, together with experimental details of the methods, including labelling...

  16. Forensic DNA testing.

    Science.gov (United States)

    Butler, John M

    2011-12-01

    Forensic DNA testing has a number of applications, including parentage testing, identifying human remains from natural or man-made disasters or terrorist attacks, and solving crimes. This article provides background information followed by an overview of the process of forensic DNA testing, including sample collection, DNA extraction, PCR amplification, short tandem repeat (STR) allele separation and sizing, typing and profile interpretation, statistical analysis, and quality assurance. The article concludes with discussions of possible problems with the data and other forensic DNA testing techniques.

  17. Structure of DNA toroids and electrostatic attraction of DNA duplexes

    International Nuclear Information System (INIS)

    Cherstvy, A G

    2005-01-01

    DNA-DNA electrostatic attraction is considered as the driving force for the formation of DNA toroids in the presence of DNA condensing cations. This attraction comes from the DNA helical charge distribution and favours hexagonal toroidal cross-sections. The latter is in agreement with recent cryo-electron microscopy studies on DNA condensed with cobalt hexammine. We treat the DNA-DNA interactions within the modern theory of electrostatic interaction between helical macromolecules. The size and thickness of the toroids is calculated within a simple model; other models of stability of DNA toroids are discussed and compared

  18. H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells.

    Science.gov (United States)

    Fernández, Agustín F; Bayón, Gustavo F; Urdinguio, Rocío G; Toraño, Estela G; García, María G; Carella, Antonella; Petrus-Reurer, Sandra; Ferrero, Cecilia; Martinez-Camblor, Pablo; Cubillo, Isabel; García-Castro, Javier; Delgado-Calle, Jesús; Pérez-Campo, Flor M; Riancho, José A; Bueno, Clara; Menéndez, Pablo; Mentink, Anouk; Mareschi, Katia; Claire, Fabian; Fagnani, Corrado; Medda, Emanuela; Toccaceli, Virgilia; Brescianini, Sonia; Moran, Sebastián; Esteller, Manel; Stolzing, Alexandra; de Boer, Jan; Nisticò, Lorenza; Stazi, Maria A; Fraga, Mario F

    2015-01-01

    In differentiated cells, aging is associated with hypermethylation of DNA regions enriched in repressive histone post-translational modifications. However, the chromatin marks associated with changes in DNA methylation in adult stem cells during lifetime are still largely unknown. Here, DNA methylation profiling of mesenchymal stem cells (MSCs) obtained from individuals aged 2 to 92 yr identified 18,735 hypermethylated and 45,407 hypomethylated CpG sites associated with aging. As in differentiated cells, hypermethylated sequences were enriched in chromatin repressive marks. Most importantly, hypomethylated CpG sites were strongly enriched in the active chromatin mark H3K4me1 in stem and differentiated cells, suggesting this is a cell type-independent chromatin signature of DNA hypomethylation during aging. Analysis of scedasticity showed that interindividual variability of DNA methylation increased during aging in MSCs and differentiated cells, providing a new avenue for the identification of DNA methylation changes over time. DNA methylation profiling of genetically identical individuals showed that both the tendency of DNA methylation changes and scedasticity depended on nongenetic as well as genetic factors. Our results indicate that the dynamics of DNA methylation during aging depend on a complex mixture of factors that include the DNA sequence, cell type, and chromatin context involved and that, depending on the locus, the changes can be modulated by genetic and/or external factors. © 2015 Fernández et al.; Published by Cold Spring Harbor Laboratory Press.

  19. In situ assessment of two catfish species (pisces, Ariidae) to evaluate pollution in a harbor

    Science.gov (United States)

    Neta, Raimunda Nonata Fortes Carvalho; Junior, Audalio Rebelo Torres; Sousa, Débora Batista Pinheiro; de Sousa de Oliveira Mota Andrade, Ticianne; Torres, Hetty Salvino; da Silva Castro, Jonatas; da Silva de Almeida, Zafira; Santos, Débora Martins Silva; Tchaicka, Lígia

    2016-12-01

    A histopathological and biometric database for the catfish Sciades herzbergii and Bagre bagre from São Luís Island (Harbor area) and Caranguejos Island (reference area) in Brazil is presented. Branchial and hepatic lesions were classified into three reaction patterns: 1) circulatory or inflammatory disturbances; 2) regressive changes; 3) progressive changes. The total length (Lt), standard length (Ls), furcal length (Lf), total weight (Wt), and gonad weight (Wg) of each fish were recorded. As expected, most populations of catfish considered in this study are highly heterogeneous, with lengths and weights deviating from the reference sample. No histopathological lesions were observed in Sciades herzbergii examined at the reference site (Caranguejos Island). In contrast, 90% of the catfish S. herzbergii from sites located in the Harbor Area (São Luís Island) had one or more types of branchial and hepatic lesions. As opposed to what was observed in S. herzbergii, more than 86.33% of Bagre bagre individuals showed histopathological alterations in both areas. The utility of histopathological lesions and biometric data as sensitive indicators of the health of wild catfish populations has been demonstrated. Sciades herzbergii proved to be a better species for biomonitoring because it was able to differentiate one impacted site (Port Area/ São Luís Island) from a region relatively free of contaminants (Reference Area/ Caranguejos Island).

  20. Expansion of Adult Human Pancreatic Tissue Yields Organoids Harboring Progenitor Cells with Endocrine Differentiation Potential

    Directory of Open Access Journals (Sweden)

    Cindy J.M. Loomans

    2018-03-01

    Full Text Available Summary: Generating an unlimited source of human insulin-producing cells is a prerequisite to advance β cell replacement therapy for diabetes. Here, we describe a 3D culture system that supports the expansion of adult human pancreatic tissue and the generation of a cell subpopulation with progenitor characteristics. These cells display high aldehyde dehydrogenase activity (ALDHhi, express pancreatic progenitors markers (PDX1, PTF1A, CPA1, and MYC, and can form new organoids in contrast to ALDHlo cells. Interestingly, gene expression profiling revealed that ALDHhi cells are closer to human fetal pancreatic tissue compared with adult pancreatic tissue. Endocrine lineage markers were detected upon in vitro differentiation. Engrafted organoids differentiated toward insulin-positive (INS+ cells, and circulating human C-peptide was detected upon glucose challenge 1 month after transplantation. Engrafted ALDHhi cells formed INS+ cells. We conclude that adult human pancreatic tissue has potential for expansion into 3D structures harboring progenitor cells with endocrine differentiation potential. : In the context of β cell replacement therapy for diabetes, de Koning and colleagues describe a 3D culture platform that supports ex vivo expansion of human pancreatic tissue as organoids. These organoids harbor a subpopulation of ALDHhi cells that display proliferative capacity and can differentiate to an endocrine fate. Keywords: pancreas, organoid, human, ALDH, endocrine differentiation, beta cells, insulin, progenitor, fetal, diabetes

  1. Relation between PAH and black carbon contents in size fractions of Norwegian harbor sediments

    International Nuclear Information System (INIS)

    Oen, Amy M.P.; Cornelissen, Gerard; Breedveld, Gijs D.

    2006-01-01

    Distributions of total organic carbon (TOC), black carbon (BC), and polycyclic aromatic hydrocarbons (PAH) were investigated in different particle size fractions for four Norwegian harbor sediments. The total PAH (16-EPA) concentrations ranged from 2 to 113 mg/kg dry weight with the greatest fraction of PAH mass in the sand fraction for three of the four sediments. TOC contents ranged from 0.84% to 14.2% and BC contents from 0.085% to 1.7%. This corresponds to organic carbon (OC = TOC - BC) contents in the range of 0.81-14% and BC:TOC ratios of 1.3-18.1%. PAH isomer ratios suggested that the PAH in all four sediments were of pyrogenic origin. Furthermore, stronger correlations between PAH versus BC (r 2 = 0.85) than versus OC (r 2 = 0.15) were found. For all size fractions and bulk sediments, the PAH-to-BC ratios for the total PAHs were on average 6 ± 3 mg PAH/g BC. These results suggest that PAH distributions were dominated by the presence of BC, rather than OC. As sorption to BC is much stronger than sorption to OC, this may result in significantly lower dissolved concentrations of PAH than expected on the basis of organic carbon partitioning alone. - PAH contents correlated better with black carbon than organic carbon for four Norwegian harbor sediments

  2. Characteristics of trophic transfer of polychlorinated biphenyls in marine organisms in Incheon North Harbor, Korea.

    Science.gov (United States)

    Kim, Seung Kyu; Lee, Dong Soo; Oh, Jae Ryong

    2002-04-01

    The trophic transfer of polychlorinated biphenyls (PCBs) was characterized for zooplankton (primarily Paracalanus spp. and Acartia spp.), pacific oyster (Crassostrea gigas), shore crab (Hemigrapsus penicillatus), and goby (Acanthogobius hasta) in the aquatic system of Incheon North Harbor, Korea. The congener pattern in the species was clearly divided by the main PCB uptake route. Compared with zooplankton and oyster, the fraction of heavier homologues increased in crab and goby that take PCBs from food. Linear relationships were observed between log (fugacity in lipid/fugacity in seawater) and log Kow for all the species. For zooplankton and oyster, such an observation should not be regarded as a true absence of superhydrophobicity, because establishment of equilibrium with seawater was not evident. For crab and goby, the absence of superhydrophobicity was evidenced by the trophic transfer factor that continuously increased with Kow up to 10(7.8). These results suggest that superhydrophobicity might be species specific. The trophic transfer factors and the fugacity levels in the lipid phase indicated that bioaccumulation in crab and goby advanced beyond the level in equilibrium with seawater in the harbor basin.

  3. Dungeness crab survey for the Southwest Ocean Disposal Site off Grays Harbor, Washington, June 1990

    Energy Technology Data Exchange (ETDEWEB)

    Higgins, B.J.; Pearson, W.H. (Battelle/Marine Sciences Lab., Sequim, WA (United States))

    1991-09-01

    As part of the Grays Harbor Navigation Improvement Project, the Seattle District of the US Army Corps of Engineers has begun active use of the Southwest Ocean Disposal Site off Grays Harbor, Washington. This survey was to verify that the location of the area of high crab density observed during site selection surveys has not shifted into the Southeast Ocean Disposal Site. In June 1990, mean densities of juvenile Dungeness crab were 146 crab/ha within the disposal site and 609 crab/ha outside ad north of the disposal site. At nearshore locations outside the disposal site, juvenile crab density was 3275 crab/ha. Despite the low overall abundance, the spatial distribution of crab was such that the high crab densities in 1990 have remained outside the Southwest Ocean Disposal Site. The survey data have confirmed the appropriateness of the initial selection of the disposal site boundaries and indicated no need to move to the second monitoring tier. 8 refs., 9 figs., 2 tabs.

  4. Human case of bacteremia caused by Streptococcus canis sequence type 9 harboring the scm gene.

    Science.gov (United States)

    Taniyama, Daisuke; Abe, Yoshihiko; Sakai, Tetsuya; Kikuchi, Takahide; Takahashi, Takashi

    2017-01-01

    Streptococcus canis (Sc) is a zoonotic pathogen that is transferred mainly from companion animals to humans. One of the major virulence factors in Sc is the M-like protein encoded by the scm gene, which is involved in anti-phagocytic activities, as well as the recruitment of plasminogen to the bacterial surface in cooperation with enolase, and the consequent enhancement of bacterial transmigration and survival. This is the first reported human case of uncomplicated bacteremia following a dog bite, caused by Streptococcus canis harboring the scm gene. The similarity of the 16S rRNA from the infecting species to that of the Sc type strain, as well as the amplification of the species-specific cfg gene, encoding a co-hemolysin, was used to confirm the species identity. Furthermore, the isolate was confirmed as sequence type 9. The partial scm gene sequence harbored by the isolate was closely related to those of other two Sc strains. While this isolate did not possess the erm (A), erm (B), or mef (A), macrolide/lincosamide resistance genes, it was not susceptible to azithromycin: its susceptibility was intermediate. Even though human Sc bacteremia is rare, clinicians should be aware of this microorganism, as well as Pasteurella sp., Prevotella sp., and Capnocytophaga sp., when examining and treating patients with fever who maintain close contact with companion animals.

  5. A case of lung adenocarcinoma harboring EGFR mutation and EML4-ALK fusion gene

    International Nuclear Information System (INIS)

    Tanaka, Hisashi; Hayashi, Akihito; Morimoto, Takeshi; Taima, Kageaki; Tanaka, Yoshihito; Shimada, Michiko; Kurose, Akira; Takanashi, Shingo; Okumura, Ken

    2012-01-01

    Lung cancer is the leading cause of cancer-related death worldwide. Epidermal growth factor receptor (EGFR) - tyrosine kinase inhibitor (TKI) is used for the patients with EGFR-mutant lung cancer. Recently, phase III studies in the patients with EGFR-mutant demonstrated that EGFR-TKI monotherapy improved progression-free survival compared with platinum-doublet chemotherapy. The echinoderm microtubule-associated protein-like 4 (EML4) - anaplastic lymphoma kinase (ALK) fusion oncogene represents one of the newest molecular targets in non-small cell lung cancer (NSCLC). Patients who harbor EML4-ALK fusions have been associated with a lack of EGFR or KRAS mutations. We report a 39-year-old patient diagnosed as adenocarcinoma harboring EGFR mutation and EML4-ALK fusion gene. We treated this patient with erlotinib as the third line therapy, but no clinical benefit was obtained. We experienced a rare case with EGFR mutation and EML4-ALK. Any clinical benefit using EGFR-TKI was not obtained in our case. The therapeutic choice for the patients with more than one driver mutations is unclear. We needs further understanding of the lung cancer molecular biology and the biomarker infomation

  6. Numerical Simulation of Borehole Flow in Deep Monitor Wells, Pearl Harbor Aquifer, Oahu, Hawaii

    Science.gov (United States)

    Rotzoll, K.; Oki, D. S.; El-Kadi, A. I.

    2010-12-01

    Salinity profiles collected from uncased deep monitor wells are commonly used to monitor freshwater-lens thickness in coastal aquifers. However, vertical flow in these wells can cause the measured salinity to differ from salinity in the adjacent aquifer. Substantial borehole flow has been observed in uncased wells in the Pearl Harbor aquifer, Oahu, Hawaii. A numerical modeling approach, incorporating aquifer hydraulic characteristics and recharge rates representative of the Pearl Harbor aquifer, was used to evaluate the effects of borehole flow on measured salinity profiles from deep monitor wells. Borehole flow caused by vertical hydraulic gradients associated with the natural regional groundwater-flow system and local groundwater withdrawals was simulated. Model results were used to estimate differences between vertical salinity profiles in deep monitor wells and the adjacent aquifer in areas of downward, horizontal, and upward flow within the regional flow system—for cases with and without nearby pumped wells. Aquifer heterogeneity, represented in the model as layers of contrasting permeability, was incorporated in model scenarios. Results from this study provide insight into the magnitude of the differences between vertical salinity profiles from deep monitor wells and the salinity distributions in the aquifers. These insights are relevant and are critically needed for management and predictive modeling purposes.

  7. Seasonal Variation of Harbor Seal's Diet from the Wadden Sea in Relation to Prey Availability.

    Directory of Open Access Journals (Sweden)

    Camille de la Vega

    Full Text Available The Wadden Sea has an important role for marine mammals in terms of resting, nursing and foraging. Harbor seal is the most abundant marine mammal species in this area. The use of the food resources of the Wadden Sea by seals is not clear, and previous studies showed that this species can travel kilometers away from their haul-outs to forage in the North Sea. In this study, we analyzed the stable isotopes of vibrissae from 23 dead harbor seals found on the island of Sylt to investigate their diet. The predator´s carbon and nitrogen isotope compositions were compared to the compositions of different potential prey items from the Sylt-Rømø Bight and from the North Sea in order to study seasonal pattern in the diet and in the foraging location. In parallel, seasonal variation of abundance and biomass of the potential prey items from the Sylt-Rømø Bight were studied and compare to their contribution to the seal´s diet. The results revealed a change in the seal´s diet from pelagic sources in spring to a benthic based diet in summer, and an increasing use of the North Sea resources in fall and winter in accordance with the seasonal variation of the availability of prey in the Sylt-Rømø Bight.

  8. Novel B19-like parvovirus in the brain of a harbor seal.

    Directory of Open Access Journals (Sweden)

    Rogier Bodewes

    Full Text Available Using random PCR in combination with next-generation sequencing, a novel parvovirus was detected in the brain of a young harbor seal (Phoca vitulina with chronic non-suppurative meningo-encephalitis that was rehabilitated at the Seal Rehabilitation and Research Centre (SRRC in the Netherlands. In addition, two novel viruses belonging to the family Anelloviridae were detected in the lungs of this animal. Phylogenetic analysis of the coding sequence of the novel parvovirus, tentatively called Seal parvovirus, indicated that this virus belonged to the genus Erythrovirus, to which human parvovirus B19 also belongs. Although no other seals with similar signs were rehabilitated in SRRC in recent years, a prevalence study of tissues of seals from the same area collected in the period 2008-2012 indicated that the Seal parvovirus has circulated in the harbor seal population at least since 2008. The presence of the Seal parvovirus in the brain was confirmed by real-time PCR and in vitro replication. Using in situ hybridization, we showed for the first time that a parvovirus of the genus Erythrovirus was present in the Virchow-Robin space and in cerebral parenchyma adjacent to the meninges. These findings showed that a parvovirus of the genus Erythrovirus can be involved in central nervous system infection and inflammation, as has also been suspected but not proven for human parvovirus B19 infection.

  9. Novel B19-like parvovirus in the brain of a harbor seal.

    Science.gov (United States)

    Bodewes, Rogier; Rubio García, Ana; Wiersma, Lidewij C M; Getu, Sarah; Beukers, Martijn; Schapendonk, Claudia M E; van Run, Peter R W A; van de Bildt, Marco W G; Poen, Marjolein J; Osinga, Nynke; Sánchez Contreras, Guillermo J; Kuiken, Thijs; Smits, Saskia L; Osterhaus, Albert D M E

    2013-01-01

    Using random PCR in combination with next-generation sequencing, a novel parvovirus was detected in the brain of a young harbor seal (Phoca vitulina) with chronic non-suppurative meningo-encephalitis that was rehabilitated at the Seal Rehabilitation and Research Centre (SRRC) in the Netherlands. In addition, two novel viruses belonging to the family Anelloviridae were detected in the lungs of this animal. Phylogenetic analysis of the coding sequence of the novel parvovirus, tentatively called Seal parvovirus, indicated that this virus belonged to the genus Erythrovirus, to which human parvovirus B19 also belongs. Although no other seals with similar signs were rehabilitated in SRRC in recent years, a prevalence study of tissues of seals from the same area collected in the period 2008-2012 indicated that the Seal parvovirus has circulated in the harbor seal population at least since 2008. The presence of the Seal parvovirus in the brain was confirmed by real-time PCR and in vitro replication. Using in situ hybridization, we showed for the first time that a parvovirus of the genus Erythrovirus was present in the Virchow-Robin space and in cerebral parenchyma adjacent to the meninges. These findings showed that a parvovirus of the genus Erythrovirus can be involved in central nervous system infection and inflammation, as has also been suspected but not proven for human parvovirus B19 infection.

  10. Immunization with avian metapneumovirus harboring chicken Fc induces higher immune responses.

    Science.gov (United States)

    Paudel, Sarita; Easwaran, Maheswaran; Jang, Hyun; Jung, Ho-Kyoung; Kim, Joo-Hun; Shin, Hyun-Jin

    2016-07-15

    In this study, we evaluated the immune responses of avian metapneumovirus harboring chicken Fc molecule. Stable Vero cells expressing chicken Fc chimera on its surface (Vero-cFc) were established, and we confirmed that aMPV grown in Vero-cFc incorporated host derived chimera Fc into the aMPV virions. Immunization of chicken with aMPV-cFc induced higher level of antibodies and inflammatory cytokines; (Interferon (IFN)-γ and Interleukin (IL)-1β) compared to those of aMPV. The increased levels of antibodies and inflammatory cytokines in chicken immunized with aMPV-cFc were statistically significantly (p<0.05) to that of aMPV and control. The aMPV-cFc group also generated the highest neutralizing antibody response. After challenges, chickens immunized with aMPV-cFc showed much less pathological signs in nasal turbinates and trachea so that we could confirm aMPV-cFc induced higher protection than that of aMPV. The greater ability of aMPV harboring chicken Fc to that of aMPV presented it as a possible vaccine candidate. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Extended DNA Tile Actuators

    DEFF Research Database (Denmark)

    Kristiansen, Martin; Kryger, Mille; Zhang, Zhao

    2012-01-01

    A dynamic linear DNA tile actuator is expanded to three new structures of higher complexity. The original DNA actuator was constructed from a central roller strand which hybridizes with two piston strands by forming two half-crossover junctions. A linear expansion of the actuator is obtained...

  12. Dna fingerprinting - review paper

    OpenAIRE

    Blundell, Renald

    2006-01-01

    Before the Polymerase Chain Reaction (PCR) was established, DNA fingerprinting technology has relied for years on Restriction Fragment Length Polymorphism (RFLP) and Variable Number of Tandom Repeats (VNTR) analysis, a very efficient technique but quite laborious and not suitable for high throughput mapping. Since its, development, PCR has provided a new and powerful tool for DNA fingerprinting.

  13. DNA Repair Systems

    Indian Academy of Sciences (India)

    Thanks to the pioneering research work of Lindahl, Sancar, Modrich and their colleagues, we now have an holistic awareness of how DNA damage occurs and how the damage is rectified in bacteria as well as in higher organisms including human beings. A comprehensive understanding of DNA repair has proven crucial ...

  14. DNA repair genes

    International Nuclear Information System (INIS)

    Morimyo, Mitsuoki

    1995-01-01

    Fission yeast S. pombe is assumed to be a good model for cloning of human DNA repair genes, because human gene is normally expressed in S. pombe and has a very similar protein sequence to yeast protein. We have tried to elucidate the DNA repair mechanisms of S. pombe as a model system for those of mammals. (J.P.N.)

  15. DNA-cell conjugates

    Science.gov (United States)

    Hsiao, Shih-Chia; Francis, Matthew B.; Bertozzi, Carolyn; Mathies, Richard; Chandra, Ravi; Douglas, Erik; Twite, Amy; Toriello, Nicholas; Onoe, Hiroaki

    2018-05-15

    The present invention provides conjugates of DNA and cells by linking the DNA to a native functional group on the cell surface. The cells can be without cell walls or can have cell walls. The modified cells can be linked to a substrate surface and used in assay or bioreactors.

  16. Characterization of muntjac DNA

    International Nuclear Information System (INIS)

    Davis, R.C.

    1981-01-01

    Sister chromatid exchange (SCE) in muntjac chromosomes is generally proportional to the chromosomal DNA content, but the SCE frequency is reduced in the heterochromatic neck region of the X chromosome. The physical properties of muntjac DNA and the kinetics of repair of UV damage in muntjac heterochromatin and euchromatin were examined and compared with the distribution of sister chromatid exchange

  17. DNA-cell conjugates

    Science.gov (United States)

    Hsiao, Shih-Chia; Francis, Matthew B.; Bertozzi, Carolyn; Mathies, Richard; Chandra, Ravi; Douglas, Erik; Twite, Amy; Toriello, Nicholas; Onoe, Hiroaki

    2016-05-03

    The present invention provides conjugates of DNA and cells by linking the DNA to a native functional group on the cell surface. The cells can be without cell walls or can have cell walls. The modified cells can be linked to a substrate surface and used in assay or bioreactors.

  18. Characterization of muntjac DNA

    Energy Technology Data Exchange (ETDEWEB)

    Davis, R.C.

    1981-05-27

    Sister chromatid exchange (SCE) in muntjac chromosomes is generally proportional to the chromosomal DNA content, but the SCE frequency is reduced in the heterochromatic neck region of the X chromosome. The physical properties of muntjac DNA and the kinetics of repair of UV damage in muntjac heterochromatin and euchromatin were examined and compared with the distribution of sister chromatid exchange.

  19. The Decrease in Mitochondrial DNA Mutation Load Parallels Visual Recovery in a Leber Hereditary Optic Neuropathy Patient

    Directory of Open Access Journals (Sweden)

    Sonia Emperador

    2018-02-01

    Full Text Available The onset of Leber hereditary optic neuropathy is relatively rare in childhood and, interestingly, the rate of spontaneous visual recovery is very high in this group of patients. Here, we report a child harboring a rare pathological mitochondrial DNA mutation, present in heteroplasmy, associated with the disease. A patient follow-up showed a rapid recovery of the vision accompanied by a decrease of the percentage of mutated mtDNA. A retrospective study on the age of recovery of all childhood-onset Leber hereditary optic neuropathy patients reported in the literature suggested that this process was probably related with pubertal changes.

  20. Whose DNA is this?

    DEFF Research Database (Denmark)

    Taroni, Franco; Biedermann, Alex; Vuille, Joëlle

    2013-01-01

    This communication seeks to draw the attention of researchers and practitioners dealing with forensic DNA profiling analyses to the following question: is a scientist's report, offering support to a hypothesis according to which a particular individual is the source of DNA detected during...... evoked during the international conference "The hidden side of DNA profiles. Artifacts, errors and uncertain evidence" held in Rome (April 27th to 28th, 2012). Indeed, despite the fact that this conference brought together some of the world's leading forensic DNA specialists, it appeared clearly...... talk considerably different languages. It thus is fundamental to address this issue of communication about results of forensic DNA analyses, and open a dialogue with practicing non-scientists at large who need to make meaningful use of scientific results to approach and help solve judicial cases...

  1. DNA repair protocols

    DEFF Research Database (Denmark)

    Bjergbæk, Lotte

    In its 3rd edition, this Methods in Molecular Biology(TM) book covers the eukaryotic response to genomic insult including advanced protocols and standard techniques in the field of DNA repair. Offers expert guidance for DNA repair, recombination, and replication. Current knowledge of the mechanisms...... that regulate DNA repair has grown significantly over the past years with technology advances such as RNA interference, advanced proteomics and microscopy as well as high throughput screens. The third edition of DNA Repair Protocols covers various aspects of the eukaryotic response to genomic insult including...... recent advanced protocols as well as standard techniques used in the field of DNA repair. Both mammalian and non-mammalian model organisms are covered in the book, and many of the techniques can be applied with only minor modifications to other systems than the one described. Written in the highly...

  2. Racemic DNA crystallography.

    Science.gov (United States)

    Mandal, Pradeep K; Collie, Gavin W; Kauffmann, Brice; Huc, Ivan

    2014-12-22

    Racemates increase the chances of crystallization by allowing molecular contacts to be formed in a greater number of ways. With the advent of protein synthesis, the production of protein racemates and racemic-protein crystallography are now possible. Curiously, racemic DNA crystallography had not been investigated despite the commercial availability of L- and D-deoxyribo-oligonucleotides. Here, we report a study into racemic DNA crystallography showing the strong propensity of racemic DNA mixtures to form racemic crystals. We describe racemic crystal structures of various DNA sequences and folded conformations, including duplexes, quadruplexes, and a four-way junction, showing that the advantages of racemic crystallography should extend to DNA. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Identification and localization of a gene that specifies production of Escherichia coli DNA topoisomerase I

    International Nuclear Information System (INIS)

    Trucksis, M.; Depew, R.E.

    1981-01-01

    A gene that specifies production of Escherichia coli DNA topoisomerase I (ω protein) was identified with the aid of a radioimmunoassay for this protein. E. coli DNA topoisomerase I was produced by Salmonella typhimurium merodiploids that harbored E. coli plasmid F' 123, but not by strains that lost this plasmid. Analysis of strains with spontaneous deletions of F' 123 showed that the gene, topA, required for production of the E. coli ω protein was between the trp operon and the cysB gene. Deletions that eliminated topA also eliminated the supX gene. We suggest that topA is the structural gene of E. coli DNA topoisomerase I and that topA is identical to supX

  4. Bacteriomes of the corn leafhopper, Dalbulus maidis (DeLong & Wolcott, 1923) (Insecta, Hemiptera, Cicadellidae: Deltocephalinae) harbor Sulcia symbiont: molecular characterization, ultrastructure, and transovarial transmission.

    Science.gov (United States)

    Brentassi, María Eugenia; Franco, Ernesto; Balatti, Pedro; Medina, Rocío; Bernabei, Franco; Marino de Remes Lenicov, Ana M

    2017-05-01

    In this study, we surveyed the bacteriome-associated microbiota of the corn leafhopper Dalbulus maidis by means of histological, ultrastructural, and molecular analyses. Amplification and sequencing of 16S rDNA genes revealed that the endosymbiont "Candidatus Sulcia muelleri" (Phylum Bacteroidetes) resides in bacteriomes of D. maidis. Phylogenetic analysis showed that the sequence was closely allied to others found in representatives of the subfamily Deltocephalinae. We failed to amplify other sequences as "Candidatus Nasuia deltocephalinicola," a co-primary symbiont frequently associated to deltocephaline leafhoppers. In addition, a metagenetic analysis carried out in order to investigate the presence of other bacteriome-associated bacteria of D. maidis showed that the sequence of Sulcia accounted for 98.56 % of all the sequences. Histological and ultrastructural observations showed that microorganisms harbored in bacteriomes (central syncytium and cytoplasm of uninucleate bacteriocytes) look like others Sulcia described in hemipteran species and they were transovarially transmitted from mother to offspring which is typical of obligate endosymbionts. The only presence of Sulcia in the bacteriomes of D. maidis was discussed.

  5. LEDGF/p75 Deficiency Increases Deletions at the HIV-1 cDNA Ends.

    Science.gov (United States)

    Bueno, Murilo T D; Reyes, Daniel; Llano, Manuel

    2017-09-15

    Processing of unintegrated linear HIV-1 cDNA by the host DNA repair system results in its degradation and/or circularization. As a consequence, deficient viral cDNA integration generally leads to an increase in the levels of HIV-1 cDNA circles containing one or two long terminal repeats (LTRs). Intriguingly, impaired HIV-1 integration in LEDGF/p75-deficient cells does not result in a correspondent increase in viral cDNA circles. We postulate that increased degradation of unintegrated linear viral cDNA in cells lacking the lens epithelium-derived growth factor (LEDGF/p75) account for this inconsistency. To evaluate this hypothesis, we characterized the nucleotide sequence spanning 2-LTR junctions isolated from LEDGF/p75-deficient and control cells. LEDGF/p75 deficiency resulted in a significant increase in the frequency of 2-LTRs harboring large deletions. Of note, these deletions were dependent on the 3' processing activity of integrase and were not originated by aberrant reverse transcription. Our findings suggest a novel role of LEDGF/p75 in protecting the unintegrated 3' processed linear HIV-1 cDNA from exonucleolytic degradation.

  6. Mcm10 regulates DNA replication elongation by stimulating the CMG replicative helicase.

    Science.gov (United States)

    Lõoke, Marko; Maloney, Michael F; Bell, Stephen P

    2017-02-01

    Activation of the Mcm2-7 replicative DNA helicase is the committed step in eukaryotic DNA replication initiation. Although Mcm2-7 activation requires binding of the helicase-activating proteins Cdc45 and GINS (forming the CMG complex), an additional protein, Mcm10, drives initial origin DNA unwinding by an unknown mechanism. We show that Mcm10 binds a conserved motif located between the oligonucleotide/oligosaccharide fold (OB-fold) and A subdomain of Mcm2. Although buried in the interface between these domains in Mcm2-7 structures, mutations predicted to separate the domains and expose this motif restore growth to conditional-lethal MCM10 mutant cells. We found that, in addition to stimulating initial DNA unwinding, Mcm10 stabilizes Cdc45 and GINS association with Mcm2-7 and stimulates replication elongation in vivo and in vitro. Furthermore, we identified a lethal allele of MCM10 that stimulates initial DNA unwinding but is defective in replication elongation and CMG binding. Our findings expand the roles of Mcm10 during DNA replication and suggest a new model for Mcm10 function as an activator of the CMG complex throughout DNA replication. © 2017 Lõoke et al.; Published by Cold Spring Harbor Laboratory Press.

  7. A crisis in waste management, economic vitality, and a coastal marine environment: Boston Harbor and Massachusetts Bay

    Science.gov (United States)

    Manheim, F.T.; Butman, B.

    1994-01-01

    Discharge of sewage sludge and effluent from 43 communities in the greater Boston metropolitan area has helped make the harbor one of the most polluted in the nation. As part of a court-mandated plan to end pollution of the harbor, effluent will no longer be discharged into the harbor, but instead, by 1995 it will be discharged into Massachusetts Bay through a record-long 15.34 km tunnel. By the year 2000 all of the sewage is scheduled to recive full secondary treatment. The public is concerned about long-term effects of the new ocean outfall on the environment, including Cape Cod Bay and Stellwagen Bank, which is an important habitat for whales and a newly designated national marine sanctuary. The bay has been additionally stressed by dumping of low-level radioactive and other hazardous wastes during the 1950s and 1960s. -from Authors

  8. Nanostructures via DNA scaffold metallization

    OpenAIRE

    Ning, C.; Zinchenko, A.; Baigl, D.; Pyshkina, O.; Sergeyev, V.; Endo, Kazunaka; Yoshikawa, K.

    2005-01-01

    The critical role of polymers in process of noble metals nanostructures formation is well known, however, the use of DNA chain template in this process is yet largely unknown. In this study we demonstrate different ways of silver deposition on DNA template and report the influence of silver nanostructures formation on DNA conformational state. Metallization of DNA chain proceeds by two different scenarios depending on DNA conformation. If DNA chain is unfolded (elongated) chain, silver reduct...

  9. DNA damage and polyploidization.

    Science.gov (United States)

    Chow, Jeremy; Poon, Randy Y C

    2010-01-01

    A growing body of evidence indicates that polyploidization triggers chromosomal instability and contributes to tumorigenesis. DNA damage is increasingly being recognized for its roles in promoting polyploidization. Although elegant mechanisms known as the DNA damage checkpoints are responsible for halting the cell cycle after DNA damage, agents that uncouple the checkpoints can induce unscheduled entry into mitosis. Likewise, defects of the checkpoints in several disorders permit mitotic entry even in the presence of DNA damage. Forcing cells with damaged DNA into mitosis causes severe chromosome segregation defects, including lagging chromosomes, chromosomal fragments and chromosomal bridges. The presence of these lesions in the cleavage plane is believed to abort cytokinesis. It is postulated that if cytokinesis failure is coupled with defects of the p53-dependent postmitotic checkpoint pathway, cells can enter S phase and become polyploids. Progress in the past several years has unraveled some of the underlying principles of these pathways and underscored the important role of DNA damage in polyploidization. Furthermore, polyploidization per se may also be an important determinant of sensitivity to DNA damage, thereby may offer an opportunity for novel therapies.

  10. Quantitive DNA Fiber Mapping

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Chun-Mei; Wang, Mei; Greulich-Bode, Karin M.; Weier, Jingly F.; Weier, Heinz-Ulli G.

    2008-01-28

    Several hybridization-based methods used to delineate single copy or repeated DNA sequences in larger genomic intervals take advantage of the increased resolution and sensitivity of free chromatin, i.e., chromatin released from interphase cell nuclei. Quantitative DNA fiber mapping (QDFM) differs from the majority of these methods in that it applies FISH to purified, clonal DNA molecules which have been bound with at least one end to a solid substrate. The DNA molecules are then stretched by the action of a receding meniscus at the water-air interface resulting in DNA molecules stretched homogeneously to about 2.3 kb/{micro}m. When non-isotopically, multicolor-labeled probes are hybridized to these stretched DNA fibers, their respective binding sites are visualized in the fluorescence microscope, their relative distance can be measured and converted into kilobase pairs (kb). The QDFM technique has found useful applications ranging from the detection and delineation of deletions or overlap between linked clones to the construction of high-resolution physical maps to studies of stalled DNA replication and transcription.

  11. Regulating DNA Self-assembly by DNA-Surface Interactions.

    Science.gov (United States)

    Liu, Longfei; Li, Yulin; Wang, Yong; Zheng, Jianwei; Mao, Chengde

    2017-12-14

    DNA self-assembly provides a powerful approach for preparation of nanostructures. It is often studied in bulk solution and involves only DNA-DNA interactions. When confined to surfaces, DNA-surface interactions become an additional, important factor to DNA self-assembly. However, the way in which DNA-surface interactions influence DNA self-assembly is not well studied. In this study, we showed that weak DNA-DNA interactions could be stabilized by DNA-surface interactions to allow large DNA nanostructures to form. In addition, the assembly can be conducted isothermally at room temperature in as little as 5 seconds. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Chimeric proteins for detection and quantitation of DNA mutations, DNA sequence variations, DNA damage and DNA mismatches

    Science.gov (United States)

    McCutchen-Maloney, Sandra L.

    2002-01-01

    Chimeric proteins having both DNA mutation binding activity and nuclease activity are synthesized by recombinant technology. The proteins are of the general formula A-L-B and B-L-A where A is a peptide having DNA mutation binding activity, L is a linker and B is a peptide having nuclease activity. The chimeric proteins are useful for detection and identification of DNA sequence variations including DNA mutations (including DNA damage and mismatches) by binding to the DNA mutation and cutting the DNA once the DNA mutation is detected.

  13. Cladophora (Chlorophyta) spp. harbor human bacterial pathogens in nearshore water of Lake Michigan

    Science.gov (United States)

    Ishii, S.; Yan, T.; Shively, D.A.; Byappanahalli, M.N.; Whitman, R.L.; Sadowsky, M.J.

    2006-01-01

    Cladophora glomerata, a macrophytic green alga, is commonly found in the Great Lakes, and significant accumulations occur along shorelines during the summer months. Recently, Cladophora has been shown to harbor high densities of the fecal indicator bacteria Escherichia coli and enterococci. Cladophora may also harbor human pathogens; however, until now, no studies to address this question have been performed. In the present study, we determined whether attachedCladophora, obtained from the Lake Michigan and Burns Ditch (Little Calumet River, Indiana) sides of a breakwater during the summers of 2004 and 2005, harbored the bacterial pathogens Shiga toxin-producing Escherichia coli (STEC),Salmonella, Shigella, and Campylobacter. The presence of potential pathogens and numbers of organisms were determined by using cultural methods and by using conventional PCR, most-probable-number PCR (MPN-PCR), and quantitative PCR (QPCR) performed with genus- and toxin-specific primers and probes. WhileShigella and STEC were detected in 100% and 25%, respectively, of the algal samples obtained near Burns Ditch in 2004, the same pathogens were not detected in samples collected in 2005. MPN-PCR and QPCR allowed enumeration of Salmonella in 40 to 80% of the ditch- and lakeside samples, respectively, and the densities were up to 1.6 × 103 cells per g Cladophora. Similarly, these PCR methods allowed enumeration of up to 5.4 × 102 Campylobacter cells/gCladophora in 60 to 100% of lake- and ditchside samples. The Campylobacterdensities were significantly higher (P fingerprint analyses indicated that genotypically identical Salmonella isolates were associated with geographically and temporally distinct Cladophora samples. However, Campylobacter isolates were genetically diverse. Since animal hosts are thought to be the primary habitat forCampylobacter and Salmonella species, our results suggest that Cladophora is a likely secondary habitat for pathogenic

  14. Feeding kinematics, suction, and hydraulic jetting performance of harbor seals (Phoca vitulina.

    Directory of Open Access Journals (Sweden)

    Christopher D Marshall

    Full Text Available The feeding kinematics, suction and hydraulic jetting capabilities of captive harbor seals (Phoca vitulina were characterized during controlled feeding trials. Feeding trials were conducted using a feeding apparatus that allowed a choice between biting and suction, but also presented food that could be ingested only by suction. Subambient pressure exerted during suction feeding behaviors was directly measured using pressure transducers. The mean feeding cycle duration for suction-feeding events was significantly shorter (0.15±0.09 s; P<0.01 than biting feeding events (0.18±0.08 s. Subjects feeding in-water used both a suction and a biting feeding mode. Suction was the favored feeding mode (84% of all feeding events compared to biting, but biting comprised 16% of feeding events. In addition, seals occasionally alternated suction with hydraulic jetting, or used hydraulic jetting independently, to remove fish from the apparatus. Suction and biting feeding modes were kinematically distinct regardless of feeding location (in-water vs. on-land. Suction was characterized by a significantly smaller gape (1.3±0.23 cm; P<0.001 and gape angle (12.9±2.02°, pursing of the rostral lips to form a circular aperture, and pursing of the lateral lips to occlude lateral gape. Biting was characterized by a large gape (3.63±0.21 cm and gape angle (28.8±1.80°; P<0.001 and lip curling to expose teeth. The maximum subambient pressure recorded was 48.8 kPa. In addition, harbor seals were able to jet water at food items using suprambient pressure, also known as hydraulic jetting. The maximum hydraulic jetting force recorded was 53.9 kPa. Suction and hydraulic jetting where employed 90.5% and 9.5%, respectively, during underwater feeding events. Harbor seals displayed a wide repertoire of behaviorally flexible feeding strategies to ingest fish from the feeding apparatus. Such flexibility of feeding strategies and biomechanics likely forms the basis of their

  15. CC8 MRSA strains harboring SCCmec type IVc are predominant in Colombian hospitals.

    Directory of Open Access Journals (Sweden)

    J Natalia Jiménez

    Full Text Available BACKGROUND: Recent reports highlight the incursion of community-associated MRSA within healthcare settings. However, knowledge of this phenomenon remains limited in Latin America. The aim of this study was to evaluate the molecular epidemiology of MRSA in three tertiary-care hospitals in Medellín, Colombia. METHODS: An observational cross-sectional study was conducted from 2008-2010. MRSA infections were classified as either community-associated (CA-MRSA or healthcare-associated (HA-MRSA, with HA-MRSA further classified as hospital-onset (HAHO-MRSA or community-onset (HACO-MRSA according to standard epidemiological definitions established by the U.S. Centers for Disease Control and Prevention (CDC. Genotypic analysis included SCCmec typing, spa typing, PFGE and MLST. RESULTS: Out of 538 total MRSA isolates, 68 (12.6% were defined as CA-MRSA, 243 (45.2% as HACO-MRSA and 227 (42.2% as HAHO-MRSA. The majority harbored SCCmec type IVc (306, 58.7%, followed by SCCmec type I (174, 33.4%. The prevalence of type IVc among CA-, HACO- and HAHO-MRSA isolates was 92.4%, 65.1% and 43.6%, respectively. From 2008 to 2010, the prevalence of type IVc-bearing strains increased significantly, from 50.0% to 68.2% (p = 0.004. Strains harboring SCCmec IVc were mainly associated with spa types t1610, t008 and t024 (MLST clonal complex 8, while PFGE confirmed that the t008 and t1610 strains were closely related to the USA300-0114 CA-MRSA clone. Notably, strains belonging to these three spa types exhibited high levels of tetracycline resistance (45.9%. CONCLUSION: CC8 MRSA strains harboring SCCmec type IVc are becoming predominant in Medellín hospitals, displacing previously reported CC5 HA-MRSA clones. Based on shared characteristics including SCCmec IVc, absence of the ACME element and tetracycline resistance, the USA300-related isolates in this study are most likely related to USA300-LV, the recently-described 'Latin American variant' of USA300.

  16. Tales of some ancient harbors in the Aegean back-arc region: Earthquakes, coastal changes, historical impacts

    Science.gov (United States)

    Stiros, Stathis; Saltogianni, Vasso

    2017-04-01

    Tectonically active terrains are characterized by seismic transient ground motions (shaking) and by permanent ground motions in the vicinity of activated faults, with both effects occasionally leaving their signature on human constructions and the landscape. Especially in coastal areas marked by small tidal ranges and normal water salinity, as is the case with most parts of the Eastern Mediterranean, even small-amplitude tectonic motions can be derived from observations on coastal constructions, mainly harbors, but also on spring chambers in nearly arid environments, sewers, etc. Such observations, if coupled with well-dated observations of destructions and repairs and of changes in the occupation style of ancient sites can permit precious information conveyed from archaeology to tectonics/seismology and vice versa. A transect with harbor remains from Rhodes to the Gulf of Corinth and then till the Ionian Islands provides some excellent examples. The military harbor of Rhodes, in an area of long term uplift, a coded report of which seems to be provided by ancient poet Pindar, was subject to seismic subsidence and destruction, but with major international support, it was repaired, till renewed uplift brought it several meters above the water. In the Corinth area, the Kenchreai harbor was abruptly submerged during a major repair of a temple, as revealed by precious stained glass panels, ready to use but abandoned in shallow water beneath ruins, while radiometric dating of the uplift in the western Lechaion harbor, constrains its excavation in swampy environment not in Roman times, but to the period of flourishing of Corinth in circa 600BC and the colonization of Italy. Farther west, the sea-level mark of the harbor of Aigeira, at Mavra Litharia (Derveni/Akrata) indicates 4m uplift since the Roman period, at least partly seismic, correlating with an exposed reef and the abandonment of the repairs of the theatre of Aigeira. Seismic land uplift explains the demise of

  17. "Artifactual" arsenate DNA

    DEFF Research Database (Denmark)

    Nielsen, Peter E

    2012-01-01

    The recent claim by Wolfe-Simon et al. that the Halomonas bacterial strain GFAJ-1 when grown in arsenate-containing medium with limiting phosphate is able to substitute phosphate with arsenate in biomolecules including nucleic acids and in particular DNA(1) arose much skepticism, primarily due...... to the very limited chemical stability of arsenate esters (see ref. 2 and references therein). A major part of the criticisms was concerned with the insufficient (bio)chemical evidence in the Wolfe-Simon study for the actual chemical incorporation of arsenate in DNA (and/or RNA). Redfield et al. now present...... evidence that the identification of arsenate DNA was artifactual....

  18. Correction of the lack of commutability between plasmid DNA and genomic DNA for quantification of genetically modified organisms using pBSTopas as a model.

    Science.gov (United States)

    Zhang, Li; Wu, Yuhua; Wu, Gang; Cao, Yinglong; Lu, Changming

    2014-10-01

    Plasmid calibrators are increasingly applied for polymerase chain reaction (PCR) analysis of genetically modified organisms (GMOs). To evaluate the commutability between plasmid DNA (pDNA) and genomic DNA (gDNA) as calibrators, a plasmid molecule, pBSTopas, was constructed, harboring a Topas 19/2 event-specific sequence and a partial sequence of the rapeseed reference gene CruA. Assays of the pDNA showed similar limits of detection (five copies for Topas 19/2 and CruA) and quantification (40 copies for Topas 19/2 and 20 for CruA) as those for the gDNA. Comparisons of plasmid and genomic standard curves indicated that the slopes, intercepts, and PCR efficiency for pBSTopas were significantly different from CRM Topas 19/2 gDNA for quantitative analysis of GMOs. Three correction methods were used to calibrate the quantitative analysis of control samples using pDNA as calibrators: model a, or coefficient value a (Cva); model b, or coefficient value b (Cvb); and the novel model c or coefficient formula (Cf). Cva and Cvb gave similar estimated values for the control samples, and the quantitative bias of the low concentration sample exceeded the acceptable range within ±25% in two of the four repeats. Using Cfs to normalize the Ct values of test samples, the estimated values were very close to the reference values (bias -13.27 to 13.05%). In the validation of control samples, model c was more appropriate than Cva or Cvb. The application of Cf allowed pBSTopas to substitute for Topas 19/2 gDNA as a calibrator to accurately quantify the GMO.

  19. Working Conditions, Occupational Injuries, and Health Among Filipino Fish Processing Workers in Dutch Harbor, Alaska.

    Science.gov (United States)

    Garcia, Gabriel Macasiray; de Castro, Butch

    2017-05-01

    This study explored how unique environmental conditions in Alaska influenced occupational health and safety for Filipino fish processing workers, many of whom migrated from warm locations (e.g., the Philippines, California, and Nevada). In-depth interviews were conducted with 26 Filipino workers in one commercial fish processing company in Dutch Harbor. Results indicated that cold weather interferes with workers' job performance, increasing their risk for injury and illness, whereas the community's isolation and rural nature causes loneliness and boredom, resulting in more high-risk behaviors. Other non-environmental factors affecting worker health include roommate and supervisor concerns and culture-specific practices. Findings suggest the importance of job rotation to avoid long exposures to cold temperatures, the value of a designated individual to inform workers about company and community resources that promote healthy lifestyles, and the possible utility of a joint worker-management safety committee.

  20. Contamination of harbor sediments in the eastern Gulf of Finland (Neva Bay), Baltic Sea

    Energy Technology Data Exchange (ETDEWEB)

    Ussenkov, S.M. [Dept. of Lithology and Marine Geology, Faculty of Geology, St. Petersburg State Univ. (Russian Federation)

    1997-11-01

    The areal distribution of oil products and various trace metals have been studied in bottom surface deposits from the harbors of Neva Bay. The data of contents were normalized to natural background concentrations. Also the size and biomass of benthos groups were analyzed. The results show clearly that industrial discharges have elevated levels of contamination in the sediments. Few efficient measures against environmental contamination have been taken. The sediments contain very high concentrations of oil products and such heavy metals as Hg, Pb, Cu, and Zn. The benthic organisms most sensitive to heavy metal contamination are Chironomidae. The dredging and dumping of the contaminated deposits can lead to secondary contamination of the Gulf of Finland and the Baltic proper. (orig.)

  1. Environmental risk analysis of oil handling facilities in port areas. Application to Tarragona harbor (NE Spain).

    Science.gov (United States)

    Valdor, Paloma F; Gómez, Aina G; Puente, Araceli

    2015-01-15

    Diffuse pollution from oil spills is a widespread problem in port areas (as a result of fuel supply, navigation and loading/unloading activities). This article presents a method to assess the environmental risk of oil handling facilities in port areas. The method is based on (i) identification of environmental hazards, (ii) characterization of meteorological and oceanographic conditions, (iii) characterization of environmental risk scenarios, and (iv) assessment of environmental risk. The procedure has been tested by application to the Tarragona harbor. The results show that the method is capable of representing (i) specific local pollution cases (i.e., discriminating between products and quantities released by a discharge source), (ii) oceanographic and meteorological conditions (selecting a representative subset data), and (iii) potentially affected areas in probabilistic terms. Accordingly, it can inform the design of monitoring plans to study and control the environmental impact of these facilities, as well as the design of contingency plans. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Application of AE to evaluate deterioration of prt and harbor structures

    International Nuclear Information System (INIS)

    Matsuyama, Kimitoshi; Ishibashi, Akichika; Fujiwara, Tetsuro; Kanemoto, Yasuhiro; Hamada, Shigenori; Ohtsu, Masayasu

    1997-01-01

    The degree of concrete deterioration is normally evaluated by uniaxial compression tests of core samples taken from existing concrete structures. The uniaxial compression test can give details on concrete strength, elastic modulus and so forth. By using AE(acoustic emission) technique with uniaxial compression tests, we can get more useful information on interior failures of the core sample. The observation of AE activity was conducted during uniaxial compression tests of concrete specimens and samples. The specimens were cast with 5, 10, 15 and 20% air content. The samples were taken from 2 harbor sites in Japan. Generating behavior of AE was studied quantitatively on the basis of rate process theory. Distribution of pores in the concrete could be measured by the porosimeter. The relation between AE activity in the uniaxial compression test of core samples and concrete property is clarified.

  3. SPEECH ACTS EMPLOYED BY THE MAIN CHARACTERS OF PEARL HARBOR MOVIE

    Directory of Open Access Journals (Sweden)

    Nurul Khasanah

    2012-06-01

    Full Text Available Abstrak: Tindak tutur sangat penting dalam sebuah percakapan. Penelitian ini mengkaji tindak tutur dari ketiga pemeran utama sebuah film yang berjudul Pearl Harbor. Teori yang digunakan adalah teorinya Austin (1962 yang membagi tindak tutur menjadi tiga jenis, yaitu: tindak locutionary, tindak illocutionary, dan tindak perlocutionary. Data dibagi atas dialog-dialog berdasarkan scene yang ada dalam film, kemudian diidentifikasi tindak tutur yang terkandung dalam ujaran  para pemeran utama dalam film tersebut. Selanjutnya diklasifikasikan berdasarkan jenisnya. Hasil analisis, ditemukan bahwa ketiga pemeran utama tersebut menggunggunakan ketiga jenis tindak tutur. Hasil tindak locutionary menunjukkan bahwa sebagian besar yang digunakan oleh ketiga pemeran utama adalah kalimat deklaratif yaitu sebamyak 60.19%. hasil dari tindak illocutionary menunjukkan bahwa sebagian besar yang digunakan adalah assertive yaitu sebanyak 40.79%. dan hasil yang terakhir adalah tindak perlocutionary, menunjukkan bahwa pengaruh yang peling besar adalah “meminta pendengar untuk melakukan sesuatu” yaitu sebanyak 32 ujaran dari 55 dialog yang ada.

  4. Study of recent sediment accumulation rate using 210Pb around Mumbai Harbor Bay

    International Nuclear Information System (INIS)

    Chaudhury, Moushumi D.; Pulhani, Vandana; Jha, S.K.; Tripathi, R.M.

    2016-01-01

    The study of the coastal marine sediment of Mumbai harbor bay (MHB) provides a significant insight of the stress due to unprecedented increase of anthropogenic activities in and around the bay and climatic changes. This encourages archiving the sediments for characterizing the depositional environment of water system by examining the sediment accumulation rate (SAR) to understand thc annual deposition of chemical contaminants. The study of SAR evaluates the fate and potential effects of chemical contaminants which when discharged into aquatic environment quickly become attached to sediment particles at different exchange sites. The rate of sediment accumulation has a significant impact on many geochemical processes; it is also vital for the functioning of benthic organisms in this environment, particularly the seabed fauna. SAR is calculated from sedimentation rate, bulk density and porosity

  5. Use of the sea hare (Aplysia fasciata) in marine pollution biomonitoring of harbors and bays.

    Science.gov (United States)

    Dirrigl, Frank J; Badaoui, Zachariah; Tamez, Carlos; Vitek, Christopher J; Parsons, Jason G

    2017-10-27

    Our study evaluated heavy metal concentrations in soft tissues of sea hare, Aplysia fasciata, from the Lower Laguna Madre, Texas. Heavy metals in tissues followed Se>As>Pb>Cd. Concentrations ranged As (BDL-28.08), Cd (BDL-5.50), Pb (BDL-12.85) and Se (4.25-93.43ppm). Median As, Cd, Pb, and Se tissue levels exceeded exposure levels. Significant relationships occurred in metal-metal (AsCd, AsPb, CdPb, CdSe, and PbSe), metal-tissue (significant Se uptake by inhalant and exhalant siphons and As in the hepatopancreas), and metal-metal within tissue (AsPb in the hepatopancreas and CdPb in the digestive cecum) analyses (pmarine pollution in harbors and bays. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. DNA replication origins-where do we begin?

    Science.gov (United States)

    Prioleau, Marie-Noëlle; MacAlpine, David M

    2016-08-01

    For more than three decades, investigators have sought to identify the precise locations where DNA replication initiates in mammalian genomes. The development of molecular and biochemical approaches to identify start sites of DNA replication (origins) based on the presence of defining and characteristic replication intermediates at specific loci led to the identification of only a handful of mammalian replication origins. The limited number of identified origins prevented a comprehensive and exhaustive search for conserved genomic features that were capable of specifying origins of DNA replication. More recently, the adaptation of origin-mapping assays to genome-wide approaches has led to the identification of tens of thousands of replication origins throughout mammalian genomes, providing an unprecedented opportunity to identify both genetic and epigenetic features that define and regulate their distribution and utilization. Here we summarize recent advances in our understanding of how primary sequence, chromatin environment, and nuclear architecture contribute to the dynamic selection and activation of replication origins across diverse cell types and developmental stages. © 2016 Prioleau and MacAlpine; Published by Cold Spring Harbor Laboratory Press.

  7. Mitochondrial DNA sequence variation in human evolution and disease.

    Science.gov (United States)

    Wallace, D C

    1994-09-13

    Germ-line and somatic mtDNA mutations are hypothesized to act together to shape our history and our health. Germ-line mtDNA mutations, both ancient and recent, have been associated with a variety of degenerative diseases. Mildly to moderately deleterious germ-line mutations, like neutral polymorphisms, have become established in the distant past through genetic drift but now may predispose certain individuals to late-onset degenerative diseases. As an example, a homoplasmic, Caucasian, tRNA(Gln) mutation at nucleotide pair (np) 4336 has been observed in 5% of Alzheimer disease and Parkinson disease patients and may contribute to the multifactorial etiology of these diseases. Moderately to severely deleterious germ-line mutations, on the other hand, appear repeatedly but are eliminated by selection. Hence, all extant mutations of this class are recent and associated with more devastating diseases of young adults and children. Representative of these mutations is a heteroplasmic mutation in MTND6 at np 14459 whose clinical presentations range from adult-onset blindness to pediatric dystonia and basal ganglial degeneration. To the inherited mutations are added somatic mtDNA mutations which accumulate in random arrays within stable tissues. These mutations provide a molecular clock that measures our age and may cause a progressive decline in tissue energy output that could precipitate the onset of degenerative diseases in individuals harboring inherited deleterious mutations.

  8. Restoration Science in New York Harbor: It takes a (large, diverse and engaged) village

    Science.gov (United States)

    Newton, R.; Birney, L.; Janis, S.; Groome, M.; Palmer, M.; Bone, E.; O'Neil, J. M.; Hill, J.; Dennison, W.; Malinowski, P.; Kohne, L.; Molina, M.; Moore, G.; Woods, N.

    2015-12-01

    The Curriculum + Community Enterprise for Restoration Science (CCE-RS) facilitates partnerships between scientists and middle school educators on ecological restoration and environmental monitoring projects. The educational model is designed to wrap around the student, including classroom instruction, field science, after-school programs and engagement with the student's community. Its pillars include: a teacher training fellowship at Pace University, student curriculum, a digital platform, afterschool and summer mentoring, and community exhibits. The digital platform includes a tablet app tailored to the project's field protocols and linked to a database shared across schools and partnering institutions. Through the digital platform, data is integrated into a single citizen-science monitoring project, teachers share curriculum and best practices, and students link directly to their peers at other schools. Curriculum development has been collaborative between scientists, science education specialists, and secondary school teachers. The CCE-RS is rooted in project-based learning: the New York Harbor School has engaged high school students in environmental monitoring and oyster restoration in the Harbor for about the last decade. The science partners (U. of Maryland and Columbia) have been working with students and other citizen scientists in outdoor science over about the last decade. Local partners in outside-the-classroom education include the New York Academy of Sciences, The River Project, which will provide field education services, and Good Shepherd Services, which provides after-school programming in schools serving primarily poor families. Scientists on the project engage directly with teachers and informal educators in curriculum development and citizen-science outreach. We present the lessons learned from our first cohort of Fellows, the pedagogical model, and the digital platform, which is extensible to other ecological restoration settings.

  9. Impact of climate changes on the Santos Harbor, São Paulo State (Brazil

    Directory of Open Access Journals (Sweden)

    Paolo Alfredini

    2013-12-01

    Full Text Available Santos Harbor Area (SHA in Sao Paulo Coastline (Brazil is the most important marine cargo transfer terminal in the Southern Hemisphere. A long term relative tidal level variability assessment shows a consistent response to relative sea level rise. A wave data base Wave Watch III was compared with a long term wave data-base generated by the ERA40-ECMWF (2003, both local validated. The current bed level of SHA Outer Channel is -15.00 m (Chart Datum or, in abbreviation, CD, maintained by dredging. According to the cargo throughput forecast, in 2025, the Access Channel will have to be deepened to level of -17.00 m. The feasibility of that choice is discussed from a technical, economical and conceptual navigation point of view in that context. A data set found from a scale model of the whole area of Santos Bay, Estuary and nearby beaches, showed the impact of maritime climate changes upon the coastal area. In the previous researches developed by the authors, it was demonstrated that the wave climate, the tides and tidal currents affect harbor and coastal structures maintenance, beaches stability, tidal inlet, sediment transport, saline intrusion and wetlands. Considering the increasing of the sea hazards and the high values of the infrastructures in that coastline, it is necessary to mitigate the risks. Hence, based on the results obtained by the authors, are highlighted guidelines strategies suggested for Access Channels dimensions, wharves free-board, jetties dimensions, dredging rates, rigid and flexible littoral defenses and land protection against flooding (including wetlands.

  10. Genes of the unfolded protein response pathway harbor risk alleles for primary open angle glaucoma.

    Directory of Open Access Journals (Sweden)

    Mary Anna Carbone

    Full Text Available The statistical power of genome-wide association (GWA studies to detect risk alleles for human diseases is limited by the unfavorable ratio of SNPs to study subjects. This multiple testing problem can be surmounted with very large population sizes when common alleles of large effects give rise to disease status. However, GWA approaches fall short when many rare alleles may give rise to a common disease, or when the number of subjects that can be recruited is limited. Here, we demonstrate that this multiple testing problem can be overcome by a comparative genomics approach in which an initial genome-wide screen in a genetically amenable model organism is used to identify human orthologues that may harbor risk alleles for adult-onset primary open angle glaucoma (POAG. Glaucoma is a major cause of blindness, which affects over 60 million people worldwide. Several genes have been associated with juvenile onset glaucoma, but genetic factors that predispose to adult onset primary open angle glaucoma (POAG remain largely unknown. Previous genome-wide analysis in a Drosophila ocular hypertension model identified transcripts with altered regulation and showed induction of the unfolded protein response (UPR upon overexpression of transgenic human glaucoma-associated myocilin (MYOC. We selected 16 orthologous genes with 62 polymorphic markers and identified in two independent human populations two genes of the UPR that harbor POAG risk alleles, BIRC6 and PDIA5. Thus, effectiveness of the UPR in response to accumulation of misfolded or aggregated proteins may contribute to the pathogenesis of POAG and provide targets for early therapeutic intervention.

  11. Genes of the unfolded protein response pathway harbor risk alleles for primary open angle glaucoma.

    Science.gov (United States)

    Carbone, Mary Anna; Chen, Yuhong; Hughes, Guy A; Weinreb, Robert N; Zabriskie, Norman A; Zhang, Kang; Anholt, Robert R H

    2011-01-01

    The statistical power of genome-wide association (GWA) studies to detect risk alleles for human diseases is limited by the unfavorable ratio of SNPs to study subjects. This multiple testing problem can be surmounted with very large population sizes when common alleles of large effects give rise to disease status. However, GWA approaches fall short when many rare alleles may give rise to a common disease, or when the number of subjects that can be recruited is limited. Here, we demonstrate that this multiple testing problem can be overcome by a comparative genomics approach in which an initial genome-wide screen in a genetically amenable model organism is used to identify human orthologues that may harbor risk alleles for adult-onset primary open angle glaucoma (POAG). Glaucoma is a major cause of blindness, which affects over 60 million people worldwide. Several genes have been associated with juvenile onset glaucoma, but genetic factors that predispose to adult onset primary open angle glaucoma (POAG) remain largely unknown. Previous genome-wide analysis in a Drosophila ocular hypertension model identified transcripts with altered regulation and showed induction of the unfolded protein response (UPR) upon overexpression of transgenic human glaucoma-associated myocilin (MYOC). We selected 16 orthologous genes with 62 polymorphic markers and identified in two independent human populations two genes of the UPR that harbor POAG risk alleles, BIRC6 and PDIA5. Thus, effectiveness of the UPR in response to accumulation of misfolded or aggregated proteins may contribute to the pathogenesis of POAG and provide targets for early therapeutic intervention.

  12. Haul-out behavior of harbor seals (Phoca vitulina in Hood Canal, Washington.

    Directory of Open Access Journals (Sweden)

    Josh M London

    Full Text Available The goal of this study was to model haul-out behavior of harbor seals (Phoca vitulina in the Hood Canal region of Washington State with respect to changes in physiological, environmental, and temporal covariates. Previous research has provided a solid understanding of seal haul-out behavior. Here, we expand on that work using a generalized linear mixed model (GLMM with temporal autocorrelation and a large dataset. Our dataset included behavioral haul-out records from archival and VHF radio tag deployments on 25 individual seals representing 61,430 seal hours. A novel application for increased computational efficiency allowed us to examine this large dataset with a GLMM that appropriately accounts for temporal autocorellation. We found significant relationships with the covariates hour of day, day of year, minutes from high tide and year. Additionally, there was a significant effect of the interaction term hour of day : day of year. This interaction term demonstrated that seals are more likely to haul out during nighttime hours in August and September, but then switch to predominantly daylight haul-out patterns in October and November. We attribute this change in behavior to an effect of human disturbance levels. This study also examined a unique ecological event to determine the role of increased killer whale (Orcinus orca predation on haul-out behavior. In 2003 and 2005 these harbor seals were exposed to unprecedented levels of killer whale predation and results show an overall increase in haul-out probability after exposure to killer whales. The outcome of this study will be integral to understanding any changes in population abundance as a result of increased killer whale predation.

  13. Effect of infrared radiation A on photoaged hairless mice harboring eumelanin and pheomelanin in the epidermis.

    Science.gov (United States)

    Okazaki, Shizuka; Funasaka, Yoko; Wakamatsu, Kazumasa; Kawana, Seiji; Saeki, Hidehisa

    2015-04-01

    Infrared radiation A (IRA) is absorbed by melanin and generates heat. Therefore, the effect of IRA could be well analyzed using skin, which contains melanin in the epidermis. Hairless mice harboring epidermal melanocytes that produce eumelanin, pheomelanin, or non-melanin were generated by backcrossing K14-stem cell factor mice, recessive yellow mice, and then albino hairless mice. High-dose IRA was irradiated over 18 weeks after the establishment of photoaged mice by irradiation with ultraviolet B (UVB) three times a week for 14 weeks. Tumor formation was assessed every week. The formation of cyclobutane pyrimidine dimer and apoptotic cells by the irradiation of IRA and UVB was evaluated. Repetitive irradiation of IRA did not promote tumor formation in all types of mice. Pre-irradiation of IRA to UVB, but not post-irradiation, accelerated the elimination of cyclobutane pyrimidine dimers and enhanced apoptosis; these effects were most obvious in eumelanin-producing mice. Real-time polymerase chain reaction analysis showed downregulation of FLICE (cellular caspase 8)-like inhibitory protein and B-cell lymphoma-extra large and upregulation of Bcl-2-associated X protein by UVB, but further enhancement of these molecules by pre-irradiation of IRA was not observed. These results indicate that IRA does not confer the promotion of UVB-induced carcinogenesis in photoaged mice harboring epidermal melanocytes and that photochemical reaction between IRA and melanin might be involved in the induction of apoptosis and the elimination of cyclobutane pyrimidine dimers by UVB. The enhancement of apoptosis by pre-irradiation of IRA to UVB might be induced by mechanisms other than the modification of the mRNA expression of FLICE (cellular caspase 8)-like inhibitory protein, B-cell lymphoma-extra large, and Bcl-2-associated X. © 2015 Japanese Dermatological Association.

  14. DNA from keratinous tissue

    DEFF Research Database (Denmark)

    Bengtsson, Camilla F.; Olsen, Maja E.; Brandt, Luise Ørsted

    2011-01-01

    Keratinous tissues such as nail, hair, horn, scales and feather have been used as a source of DNA for over 20 years. Particular benefits of such tissues include the ease with which they can be sampled, the relative stability of DNA in such tissues once sampled, and, in the context of ancient...... genetic analyses, the fact that sampling generally causes minimal visual damage to valuable specimens. Even when freshly sampled, however, the DNA quantity and quality in the fully keratinized parts of such tissues is extremely poor in comparison to other tissues such as blood and muscle – although little...... systematic research has been undertaken to characterize how such degradation may relate to sample source. In this review paper we present the current understanding of the quality and limitations of DNA in two key keratinous tissues, nail and hair. The findings indicate that although some fragments of nuclear...

  15. DNA fusion gene vaccines

    DEFF Research Database (Denmark)

    Holst, Peter Johannes; Bassi, Maria Rosaria; Thomsen, Allan Randrup

    2010-01-01

    DNA vaccines are versatile and safe, but limited immunogenicity has prevented their use in the clinical setting. Experimentally, immunogenicity may be enhanced by the use of new delivery technologies, by coadministration of cytokines and pathogen-associated molecular patterns, or by fusion...... of antigens into molecular domains that enhance antigen presentation. More specifically, the immunogenicity of DNA vaccines may benefit from increased protein synthesis, increased T-cell help and MHC class I presentation, and the addition of a range of specific cytokines and pathogen-associated molecular...... with viral-vectored vaccines, various synergistic components may need to be incorporated into DNA vaccines. From the perspective of the future clinical use of DNA vaccines, it has been suggested that antigen presentation should be improved and cytokine coadministration attempted. However, even...

  16. DNA Sampling Hook

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The DNA Sampling Hook is a significant improvement on a method of obtaining a tissue sample from a live fish in situ from an aquatic environment. A tissue sample...

  17. Retroviral DNA Integration

    Science.gov (United States)

    2016-01-01

    The integration of a DNA copy of the viral RNA genome into host chromatin is the defining step of retroviral replication. This enzymatic process is catalyzed by the virus-encoded integrase protein, which is conserved among retroviruses and LTR-retrotransposons. Retroviral integration proceeds via two integrase activities: 3′-processing of the viral DNA ends, followed by the strand transfer of the processed ends into host cell chromosomal DNA. Herein we review the molecular mechanism of retroviral DNA integration, with an emphasis on reaction chemistries and architectures of the nucleoprotein complexes involved. We additionally discuss the latest advances on anti-integrase drug development for the treatment of AIDS and the utility of integrating retroviral vectors in gene therapy applications. PMID:27198982

  18. DNA damage and carcinogenesis

    International Nuclear Information System (INIS)

    Stelow, R.B.

    1980-01-01

    Although cancer may arise as a result of many different types of molecular changes, there is little reason to doubt that changes to DNA are one of the more important ones in cancer initiation. Although DNA repair mechanisms seem able to eliminate a very large fraction of deleterious changes to DNA, we not only have little insight into the molecular mechanisms involved in such repair, but have a negligible amount of information to permit us to estimate the shape of dose response relations at low doses. The case of skin cancer is a special one, in that the average population is exposed to sufficient solar uv so that the effects of small increments in uv dose may be estimated. An approximate 85% reduction in DNA repair increases skin cancer incidence 10 4 fold

  19. DNA-Origami

    DEFF Research Database (Denmark)

    Voigt, Niels Vinther; Tørring, Thomas; Gothelf, Kurt Vesterager

    2010-01-01

    DNA-nanostrukturer giver nye muligheder for studier af individuelle molekyler. Ved at udnytte DNAs unikke selvsamlende egenskaber kan man designe systemer, hvorpå der kan studeres kemiske reaktioner, fluoroforer og biiomolekyler på enkeltmolekyle-niveau....

  20. DNA Microarray Technology

    Science.gov (United States)

    Skip to main content DNA Microarray Technology Enter Search Term(s): Español Research Funding An Overview Bioinformatics Current Grants Education and Training Funding Extramural Research News Features Funding Divisions Funding ...