Science.gov

Sample records for nick kettridge andrew

  1. Andrew W. S. In

    ERIC Educational Resources Information Center

    Nishimoto, Warren

    2007-01-01

    This article presents an interview with Andrew W. S. In, professor and dean in the University of Hawai'i's College of Education from 1951 to 1984. Born and raised in Honolulu, In attended Royal Elementary, Central Junior High, and McKinley High schools, graduating from McKinley in 1938. He then attended the University of Hawai'i Teachers College…

  2. Christina's World: Andrew Wyeth.

    ERIC Educational Resources Information Center

    Niceley, H. T.

    1990-01-01

    Describes and illustrates "Christina's World" by Andrew Wyeth. Provides background information on Wyeth's life and compares "Christina's World" to Wyeth's "Siri." Suggests activities to help all levels of art students understand use of color, mood, and composition. Introduces related activities designed specifically for elementary school students.…

  3. Andrew: CMU's New Computing Environment.

    ERIC Educational Resources Information Center

    Zabowski, Susan

    1986-01-01

    Reviews the progress and problems associated with the development of Carnegie Mellon University's new computing and communications system, "Andrew." Describes the accomplishments and capacities of the system and provides examples of the programs developed for "Andrew." (ML)

  4. Stories Along the Way: Andrew

    ERIC Educational Resources Information Center

    Kittle, Penny

    2009-01-01

    Andrew is among the forgotten, the written-off, the hopeless...at least to many of the adults in his life--police, teachers, even family. But when you see that glimmer, that potential, you can't turn your back. Andrew stands as a person, but also a metaphor for believing that each student has a chance to succeed.

  5. Faces of Marshall: Erika Andrews

    NASA Video Gallery

    Several Marshall employees were interviewed as part of Marshall's 50th Anniversary activities. Human Resources Specialist Erika Andrews tells how she came to work at NASA as a specialist in organiz...

  6. Sequence-specific DNA nicking endonucleases.

    PubMed

    Xu, Shuang-yong

    2015-08-01

    A group of small HNH nicking endonucleases (NEases) was discovered recently from phage or prophage genomes that nick double-stranded DNA sites ranging from 3 to 5 bp in the presence of Mg2+ or Mn2+. The cosN site of phage HK97 contains a gp74 nicking site AC↑CGC, which is similar to AC↑CGR (R=A/G) of N.ϕGamma encoded by Bacillus phage Gamma. A minimal nicking domain of 76 amino acid residues from N.ϕGamma could be fused to other DNA binding partners to generate chimeric NEases with new specificities. The biological roles of a few small HNH endonucleases (HNHE, gp74 of HK97, gp37 of ϕSLT, ϕ12 HNHE) have been demonstrated in phage and pathogenicity island DNA packaging. Another group of NEases with 3- to 7-bp specificities are either natural components of restriction systems or engineered from type IIS restriction endonucleases. A phage group I intron-encoded HNH homing endonucleases, I-PfoP3I was found to nick DNA sites of 14-16 bp. I-TslI encoded by T7-like ΦI appeared to nick DNA sites with a 9-bp core sequence. DNA nicking and labeling have been applied to optical mapping to aid genome sequence assembly and detection of large insertion/deletion mutations in genomic DNA of cancer cells. Nicking enzyme-mediated amplification reaction has been applied to rapid diagnostic testing of influenza A and B in clinical setting and for construction of DNA-based Boolean logic gates. The clustered regularly interspaced short palindromic repeats-ribonucleoprotein complex consisting of engineered Cas9 nickases in conjunction with tracerRNA:crRNA or a single-guide RNA have been successfully used in genome modifications. PMID:26352356

  7. Benevolent Builder: Appraising Andrew Carnegie.

    ERIC Educational Resources Information Center

    Deitch, Joseph

    1984-01-01

    Discussion of Andrew Carnegie era in American public library history focuses on library buildings financed and built in Philadelphia, Pennsylvania. The building design which Carnegie developed, surviving Carnegie libraries in Philadelphia, procedures for obtaining a library, and comparison of architectural attractiveness of Carnegie libraries with…

  8. Libraries and Andrew Carnegie's Challenge.

    ERIC Educational Resources Information Center

    Gregorian, Vartan

    This essay by the president of the Carnegie Corporation of New York (reprinted from the 1998 annual report) opens by noting that the year 1999 marks the 100th anniversary of Andrew Carnegie's support for the planning and development of 65 branch libraries of the New York Public Library System, a gift that came to more than $5.2 million. Discussion…

  9. The McAndrews Leadership Lecture: Origins

    PubMed Central

    Hamm, Anthony W.; Burkhart, Lori A.

    2015-01-01

    Objective This article describes the origins and rationale for the McAndrews Leadership Lecture and explains why the American Chiropractic Association honors George and Jerome McAndrews. Discussion George and Jerome McAndrews’ backgrounds demonstrate their leadership contributions to the chiropractic profession. Jerome McAndrews, a chiropractor, held substantial leadership roles in the chiropractic profession. George McAndrews, a lawyer, administered a permanent injunction forbidding the American Medical Association’s restraint of trade toward the chiropractic profession. Conclusion The American Chiropractic Association has established the McAndrews Leadership Lecture to honor their contributions to the chiropractic profession. PMID:26770176

  10. Distinct genetic control of homologous recombination repair of Cas9-induced double-strand breaks, nicks and paired nicks

    PubMed Central

    Vriend, Lianne E.M.; Prakash, Rohit; Chen, Chun-Chin; Vanoli, Fabio; Cavallo, Francesca; Zhang, Yu; Jasin, Maria; Krawczyk, Przemek M.

    2016-01-01

    DNA double-strand breaks (DSBs) are known to be powerful inducers of homologous recombination (HR), but single-strand breaks (nicks) have also been shown to trigger HR. Both DSB- and nick-induced HR (nickHR) are exploited in advanced genome-engineering approaches based on the bacterial RNA-guided nuclease Cas9. However, the mechanisms of nickHR are largely unexplored. Here, we applied Cas9 nickases to study nickHR in mammalian cells. We find that nickHR is unaffected by inhibition of major damage signaling kinases and that it is not suppressed by nonhomologous end-joining (NHEJ) components, arguing that nick processing does not require a DSB intermediate to trigger HR. Relative to a single nick, nicking both strands enhances HR, consistent with a DSB intermediate, even when nicks are induced up to ∼1kb apart. Accordingly, HR and NHEJ compete for repair of these paired nicks, but, surprisingly, only when 5' overhangs or blunt ends can be generated. Our study advances the understanding of molecular mechanisms driving nick and paired-nick repair in mammalian cells and clarify phenomena associated with Cas9-mediated genome editing. PMID:27001513

  11. Engineering nicking enzymes that preferentially nick 5-methylcytosine-modified DNA

    PubMed Central

    Gutjahr, Alice; Xu, Shuang-yong

    2014-01-01

    N.ϕGamma is a strand-specific and site-specific DNA nicking enzyme (YCG↓GT or AC↑CGR). Here we describe the isolation of single and double mutants of N.ϕGamma with attenuated activity. The nicking domains (NDs) of E59A and 11 double mutants were fused to the 5mCG-binding domain of MBD2 and generated fusion enzymes that preferentially nick 5mCG-modified DNA. The CG dinucleotide can be modified by C5 methyltransferases (MTases) such as M.SssI, M.HhaI or M.HpaII to create composite sites AC↑YGG N(8–15) 5mCG. We also constructed a fusion enzyme 2xMBD2-ND(N.BceSVIII) targeting more frequent composite sites AS↑YS N(5–12) 5mCG in Mn2+ buffer. 5mCG-dependent nicking requires special digestion conditions in high salt (0.3 M KCl) or in Ni2+ buffer. The fusion enzyme can be used to nick and label 5mCG-modified plasmid and genomic DNAs with fluorescently labeled Cy3-dUTP and potentially be useful for diagnostic applications, DNA sequencing and optical mapping of epigenetic markers. The importance of the predicted catalytic residues D89, H90, N106 and H115 in N.ϕGamma was confirmed by mutagenesis. We found that the wild-type enzyme N.ϕGamma prefers to nick 5mCG-modified DNA in Ni2+ buffer even though the nicking activity is sub-optimal compared to the activity in Mg2+ buffer. PMID:24609382

  12. GEN1 promotes Holliday junction resolution by a coordinated nick and counter-nick mechanism

    PubMed Central

    Chan, Ying Wai; West, Stephen

    2015-01-01

    Holliday junctions (HJs) that physically link sister chromatids or homologous chromosomes are formed as intermediates during DNA repair by homologous recombination. Persistent recombination intermediates are acted upon by structure-selective endonucleases that are required for proper chromosome segregation at mitosis. Here, we have purified full-length human GEN1 protein and show that it promotes Holliday junction resolution by a mechanism that is analogous to that exhibited by the prototypic HJ resolvase E. coli RuvC. We find that GEN1 cleaves HJs by a nick and counter-nick mechanism involving dual co-ordinated incisions that lead to the formation of ligatable nicked duplex products. As observed with RuvC, cleavage of the first strand is rate limiting, while second strand cleavage is rapid. In contrast to RuvC, however, GEN1 is largely monomeric in solution, but dimerizes on the HJ. Using HJs containing non-cleavable phosphorothioate-containing linkages in one strand, we show that the two incisions can be uncoupled and that the first nick occurs upon GEN1 dimerization at the junction. These results indicate that the mechanism of HJ resolution is largely conserved from bacteria to man, despite a lack of sequence homology between the resolvases. PMID:26578604

  13. The Impeachment of Andrew Johnson. Web Lesson.

    ERIC Educational Resources Information Center

    Constitutional Rights Foundation, Los Angeles, CA.

    This lesson presents the historical background of Abraham Lincoln's selection of Andrew Johnson as his running mate in the election of 1864. The lesson considers the climate in the U.S. Congress after President Lincoln's assassination. The details of the impeachment and trial of President Andrew Johnson are given. The lesson presents three…

  14. Obituary: Andrew Stephen Wilson, 1947-2008

    NASA Astrophysics Data System (ADS)

    Veilleux, Sylvain

    2009-01-01

    On 24 May 2008, Andrew Stephen Wilson passed away at the age of 61, in his home in Silver Spring, Maryland, from complications resulting from a painful spinal illness. Andrew was arguably one of the first truly multi-wavelength astronomers of his generation. His scientific work on active galactic nuclei [AGN] spanned the entire electromagnetic spectrum from the radio to the X-rays. Andrew was born in Doncaster, Yorkshire, England, on 26 March 1947. He was the younger of two brothers whose births were separated by the Second World War. His father, Norman, came from a relatively affluent family who were coal merchants. His mother, Mary, came from a less comfortable background, one of seven children, daughter of a skilled cabinet maker/French polisher, who went through a very hard time during the depression. As a teacher, she placed enormous value on hard work and education as a way of gaining advancement in life. When Andrew was four, the family moved to Skipton, a nice market town in the Yorkshire dales. Andrew went to a small village school until age eleven when he entered Ermysted's Grammar School. He was an enthusiastic soccer and cricket player. He never lost his enthusiasm for soccer and supported the local soccer team, Leeds United, for all his life. Andrew also followed the Yorkshire county cricket team. Andrew's interest in astronomy stemmed from the fact that at Ermysted's Grammar School someone donated a four-inch refracting telescope, so he and his friends used to go back in the evenings to investigate the rings of Saturn, the moons of Jupiter, and various nebulae. While an undergraduate at Cambridge, Andrew joined the astronomy club and ground an 8-inch mirror by hand as a part of a telescope that he set up in the backyard of his parents' house. Andrew spent hours observing with this telescope, and it was the wonder of the family. At Cambridge, Andrew obtained his bachelor's degree with first-class honors in 1969. During a short visit in London with his

  15. Congruences for the Andrews spt function.

    PubMed

    Ono, Ken

    2011-01-11

    Ramanujan-type congruences for the Andrews spt(n) partition function have been found for prime moduli 5 ≤ ℓ ≤ 37 in the work of Andrews [Andrews GE, (2008) J Reine Angew Math 624:133-142] and Garvan [Garvan F, (2010) Int J Number Theory 6:1-29]. We exhibit unexpectedly simple congruences for all ℓ≥5. Confirming a conjecture of Garvan, we show that if ℓ≥5 is prime and (-δ/ℓ) = 1, then spt[(ℓ2(ℓn+δ)+1)/24] ≡ 0 (mod ℓ). This congruence gives (ℓ - 1)/2 arithmetic progressions modulo ℓ(3) which support a mod ℓ congruence. This result follows from the surprising fact that the reduction of a certain mock theta function modulo ℓ, for every ℓ≥5, is an eigenform of the Hecke operator T(ℓ(2)). PMID:21177432

  16. Obituary: Andrew Stephen Wilson, 1947-2008

    NASA Astrophysics Data System (ADS)

    Veilleux, Sylvain

    2009-01-01

    On 24 May 2008, Andrew Stephen Wilson passed away at the age of 61, in his home in Silver Spring, Maryland, from complications resulting from a painful spinal illness. Andrew was arguably one of the first truly multi-wavelength astronomers of his generation. His scientific work on active galactic nuclei [AGN] spanned the entire electromagnetic spectrum from the radio to the X-rays. Andrew was born in Doncaster, Yorkshire, England, on 26 March 1947. He was the younger of two brothers whose births were separated by the Second World War. His father, Norman, came from a relatively affluent family who were coal merchants. His mother, Mary, came from a less comfortable background, one of seven children, daughter of a skilled cabinet maker/French polisher, who went through a very hard time during the depression. As a teacher, she placed enormous value on hard work and education as a way of gaining advancement in life. When Andrew was four, the family moved to Skipton, a nice market town in the Yorkshire dales. Andrew went to a small village school until age eleven when he entered Ermysted's Grammar School. He was an enthusiastic soccer and cricket player. He never lost his enthusiasm for soccer and supported the local soccer team, Leeds United, for all his life. Andrew also followed the Yorkshire county cricket team. Andrew's interest in astronomy stemmed from the fact that at Ermysted's Grammar School someone donated a four-inch refracting telescope, so he and his friends used to go back in the evenings to investigate the rings of Saturn, the moons of Jupiter, and various nebulae. While an undergraduate at Cambridge, Andrew joined the astronomy club and ground an 8-inch mirror by hand as a part of a telescope that he set up in the backyard of his parents' house. Andrew spent hours observing with this telescope, and it was the wonder of the family. At Cambridge, Andrew obtained his bachelor's degree with first-class honors in 1969. During a short visit in London with his

  17. Obituary: Andrew Lange (1957-2010)

    NASA Astrophysics Data System (ADS)

    Kamionkowski, Marc

    2011-12-01

    The worlds of physics and astrophysics were stunned to learn on 22 January 2010 that Andrew Lange, the Marvin L. Goldberger Professor of Physics at Caltech, had taken his own life the night before. He had succumbed to the severe depression that he had suffered from for many years, unbeknownst to even his closest colleagues. Lange will perhaps be best remembered as the co-leader of Boomerang, the balloon-borne experiment that provided the first high-angular-resolution map of the cosmic microwave background (CMB). And while this was certainly his most notable achievement, Andrew amassed a record of accomplishment as an instrumentalist, leader, mentor, and communicator that extended much further. Andrew was born in Urbana, Illinois on July 23, 1957, the son of an architect and a librarian, and raised primarily in Connecticut. His family and early friends remember him as a serious and extremely intelligent child and young man. Andrew Lange's lifelong interest in the CMB was nurtured as an undergraduate at Princeton University by David Wilkinson, and he recalled fondly a summer spent working with John Mather at Goddard Space Flight Center. Andrew Lange went to graduate school in physics at Berkeley where he worked in Paul Richards' group. Although his thesis project, the Berkeley-Nagoya rocket experiment, showed an anomalous sub-millimeter excess in the CMB spectrum that was shortly thereafter shown by a later flight of the same rocket and COBE-FIRAS to be incorrect, Lange's talents were recognized by the physics department at Berkeley who appointed him shortly after his PhD (1987) to their faculty. While on the Berkeley faculty, Andrew obtained early detections of the Sunyaev-Zeldovich effect, upper limits to small-angle CMB fluctuations, and important infrared constraints to the interstellar medium. He also led a pioneering instrument operating 300 mK detectors for a small infrared satellite experiment. This early work showed high ambition and daring, and it pioneered

  18. A History of the Andrew File System

    SciTech Connect

    2011-02-22

    Derrick Brashear and Jeffrey Altman will present a technical history of the evolution of Andrew File System starting with the early days of the Andrew Project at Carnegie Mellon through the commercialization by Transarc Corporation and IBM and a decade of OpenAFS. The talk will be technical with a focus on the various decisions and implementation trade-offs that were made over the course of AFS versions 1 through 4, the development of the Distributed Computing Environment Distributed File System (DCE DFS), and the course of the OpenAFS development community. The speakers will also discuss the various AFS branches developed at the University of Michigan, Massachusetts Institute of Technology and Carnegie Mellon University.

  19. Andrew shortens lifetime of Louisiana Barrier Islands

    NASA Astrophysics Data System (ADS)

    Bush, Susan

    Because the Isles Dernieres, a series of four barrier islands off the coast of Louisiana, have one of the most rapidly eroding shorelines in the world, geologists at the U.S. Geological Survey and the Louisiana Geological Survey have been monitoring erosion activity over the last several years, said Jeff Williams of the USGS in Reston, Va. Hurricane Andrew, which struck the state on August 26, caused severe erosional damage to these islands that has shortened their lifetimes.Before Andrew struck, geologists projected that Raccoon Island would disappear below sea level by the year 2001 and that Whiskey Island would disappear by 2016. Now, due to the severe erosion from Hurricane Andrew, the scientists claim that the islands may disappear before the turn of the century, and the other islands in the Dernieres chain are expected to follow suit within 2 decades. Raccoon, Whiskey, Trinity, and East islands make up the Isles Dernieres, which existed as one island, known as the Isle Derniere, before an 1856 hurricane and subsequent erosion.

  20. Oxygen and Metastasis: A Conversation with Dr. Nick Restifo

    Cancer.gov

    Dr. Nick Restifo, a senior investigator in NCI’s Center for Cancer Research, discusses his recently published study finding that Oxygen, a molecule necessary for life, paradoxically aids cancer metastasis to the lung by impairing cancer-killing immune cells.

  1. Obituary: Andrew Lange (1957-2010)

    NASA Astrophysics Data System (ADS)

    Kamionkowski, Marc

    2011-12-01

    The worlds of physics and astrophysics were stunned to learn on 22 January 2010 that Andrew Lange, the Marvin L. Goldberger Professor of Physics at Caltech, had taken his own life the night before. He had succumbed to the severe depression that he had suffered from for many years, unbeknownst to even his closest colleagues. Lange will perhaps be best remembered as the co-leader of Boomerang, the balloon-borne experiment that provided the first high-angular-resolution map of the cosmic microwave background (CMB). And while this was certainly his most notable achievement, Andrew amassed a record of accomplishment as an instrumentalist, leader, mentor, and communicator that extended much further. Andrew was born in Urbana, Illinois on July 23, 1957, the son of an architect and a librarian, and raised primarily in Connecticut. His family and early friends remember him as a serious and extremely intelligent child and young man. Andrew Lange's lifelong interest in the CMB was nurtured as an undergraduate at Princeton University by David Wilkinson, and he recalled fondly a summer spent working with John Mather at Goddard Space Flight Center. Andrew Lange went to graduate school in physics at Berkeley where he worked in Paul Richards' group. Although his thesis project, the Berkeley-Nagoya rocket experiment, showed an anomalous sub-millimeter excess in the CMB spectrum that was shortly thereafter shown by a later flight of the same rocket and COBE-FIRAS to be incorrect, Lange's talents were recognized by the physics department at Berkeley who appointed him shortly after his PhD (1987) to their faculty. While on the Berkeley faculty, Andrew obtained early detections of the Sunyaev-Zeldovich effect, upper limits to small-angle CMB fluctuations, and important infrared constraints to the interstellar medium. He also led a pioneering instrument operating 300 mK detectors for a small infrared satellite experiment. This early work showed high ambition and daring, and it pioneered

  2. 76 FR 48168 - Andrew K. Choi: Debarment Order

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-08

    ... HUMAN SERVICES Food and Drug Administration Andrew K. Choi: Debarment Order AGENCY: Food and Drug... the Federal Food, Drug, and Cosmetic Act (the FD&C Act) debarring Andrew K. Choi, M.D. for 4 years... K. Choi has been convicted of a misdemeanor under Federal law for conduct relating to the...

  3. Introduction of Dr. Andrew V Schally

    PubMed Central

    Mendoza-Valdés, Arturo

    2015-01-01

    I first met Dr. Andrew V Schally (PhD, MDhc (Multi), DSc, Distinguished Medical Research Scientist, U.S. Department of Veterans Affairs Professor of Pathology and Department of Medicine,
Miller School of Medicine, University of Miami, Miami, Florida, USA) many years ago, probably around the beginning of the 1990's in one of his visits to Mexico City (Figure 1). He has many friends in my country since some of the investigations that led to the development of the LHRH agonists were made in a couple of Mexican hospitals in collaboration with some outstanding Mexican physicians that I will mention later. In that time, I was the head of the Department of Urology of the Mexican National Cancer Institute and our Director, Dr. Jaime de la Garza, invited him for a meeting. I was surprised by his humbleness, intelligence and easy going personality, in spite of being a Nobel Prize scientist. PMID:26112485

  4. Structural Basis for Nick Recognition by a Minimal Pluripotent DNA Ligase

    SciTech Connect

    Nair,P.; Nandakumar, J.; Smith, P.; Odell, M.; Lima, C.; Shuman, S.

    2007-01-01

    Chlorella virus DNA ligase, the smallest eukaryotic ligase known, has pluripotent biological activity and an intrinsic nick-sensing function, despite having none of the accessory domains found in cellular ligases. A 2.3-{angstrom} crystal structure of the Chlorella virus ligase-AMP intermediate bound to duplex DNA containing a 3'-OH-5'-PO{sub 4} nick reveals a new mode of DNA envelopment, in which a short surface loop emanating from the OB domain forms a {beta}-hairpin 'latch' that inserts into the DNA major groove flanking the nick. A network of interactions with the 3'-OH and 5'-PO{sub 4} termini in the active site illuminates the DNA adenylylation mechanism and the crucial roles of AMP in nick sensing and catalysis. Addition of a divalent cation triggered nick sealing in crystallo, establishing that the nick complex is a bona fide intermediate in the DNA repair pathway.

  5. Fred Plaut in conversation with Andrew Samuels. Interview by Andrew Samuels.

    PubMed

    Plaut, Fred

    2010-02-01

    This is a reprint of an interview of Fred Plaut (who died in June 2009) conducted by Andrew Samuels in mid-1988 and first published in April 1989 in the Journal, 34, 2, pp. 159-83. The interview covers Plaut's early life, his career, and historical observations of the development of the Society of Analytical Psychology from its beginnings, and of the wider community of Jungian analysis. Plaut reflects uninhibitedly on such topics as the role of leadership in analytical psychology, discussing the parts played by Michael Fordham in London and Hannes Dieckmann in Berlin. Plaut explains his thinking concerning individuation. PMID:20433496

  6. 1. Historic American Buildings Survey L. D. Andrew, Photographer Enlarged ...

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

    1. Historic American Buildings Survey L. D. Andrew, Photographer Enlarged Photographed by Harold Bush-Brown Nov. 14, 1936 GENERAL VIEW OF SLAVE CABINS - Bass Place (Slave Cabins), Columbus, Muscogee County, GA

  7. 2. Historic American Buildings Survey L. D. Andrew, Photographer, Enlarged ...

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

    2. Historic American Buildings Survey L. D. Andrew, Photographer, Enlarged Photographed by Harold Bush-Brown Nov. 14, 1936 VIEW OF EASTERN SLAVE CABIN - Bass Place (Slave Cabins), Columbus, Muscogee County, GA

  8. 15. Historic American Buildings Survey L. D. Andrew Photographer ...

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

    15. Historic American Buildings Survey L. D. Andrew - Photographer June, 19, 1936 DETAIL OF NICHE AND CORNICE (RIGHT FRONT ROOM) Parlour - Blount House, (moved to Newnan vicinity, GA), Haddock, Jones County, GA

  9. 16. Historic American Buildings Survey L. D. Andrew Photographer ...

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

    16. Historic American Buildings Survey L. D. Andrew - Photographer June, 19, 1936 DETAIL OF NICHE AND CORNICE (RIGHT FRONT ROOM) Parlour - Blount House, (moved to Newnan vicinity, GA), Haddock, Jones County, GA

  10. 7. Historic American Buildings Survey L. D. Andrew, Photographer Aug. ...

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

    7. Historic American Buildings Survey L. D. Andrew, Photographer Aug. 26, 1936 DETAIL OF NICHE AND ARCH OVER MANTEL IN EAST FRONT ROOM - MANTEL REMOVED - Boykin Hall, Milledgeville, Baldwin County, GA

  11. 2. Historic American Buildings Survey L. D. Andrew, Photographer Dec. ...

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

    2. Historic American Buildings Survey L. D. Andrew, Photographer Dec. 30, 1936 VIEW FROM MORRISON'S CAF? (CORNER OF WHITAKER & CONGRESS) SHOWING S. FACADE - Gibbons Block, Congress, Saint Julian, Barnard, Whitaker Streets, Savannah, Chatham County, GA

  12. 3. Historic American Buildings Survey L. D. Andrew, Photographer Dec. ...

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

    3. Historic American Buildings Survey L. D. Andrew, Photographer Dec. 30, 1936 VIEW FROM CORNER OF WHITAKER AND ST JULIAN SHOWING NORTH FACADE - Gibbons Block, Congress, Saint Julian, Barnard, Whitaker Streets, Savannah, Chatham County, GA

  13. 9. HISTORIC AMERICAN BUILDINGS SURVEY L. D. ANDREW PHOTOGRAPHER ...

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

    9. HISTORIC AMERICAN BUILDINGS SURVEY L. D. ANDREW - PHOTOGRAPHER SEPT. 7, 1936 BEAM, CORNICE, AND CEILING ORNAMENT IN FRONT HALL - Sorrel-Weed House, 6 West Harris Street, Savannah, Chatham County, GA

  14. 6. Historic American Buildings Survey L. D. Andrew, Photographer Dec. ...

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

    6. Historic American Buildings Survey L. D. Andrew, Photographer Dec. 1936 From Photographs from Misses Baber-Blackshear, Macon, Georgia ARCH AND STAIRHALL - Baber House, Walnut Street, Macon, Bibb County, GA

  15. 3. Historic American Buildings Survey L. D. Andrew, Photographer Aug. ...

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

    3. Historic American Buildings Survey L. D. Andrew, Photographer Aug. 2, 1936 PANELS AND VAULTED CEILING IN DRAWING ROOM, SECOND FLOOR - Emerson & Holmes Building, 556 Mulberry Street, Macon, Bibb County, GA

  16. 5. Historic American Buildings Survey L. D. Andrew, Photographer Aug. ...

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

    5. Historic American Buildings Survey L. D. Andrew, Photographer Aug. 2, 1936 DETAIL OF DOUBLE OPENING WITH IRON GRATING IN THIRD STORY REAR ROOM - Emerson & Holmes Building, 556 Mulberry Street, Macon, Bibb County, GA

  17. 4. Historic American Buildings Survey L. D. Andrew, Photographer Aug. ...

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

    4. Historic American Buildings Survey L. D. Andrew, Photographer Aug. 19, 1936 STAIRWAY AND REAR DOOR THROUGH OPENING Between NORTHEAST ROOM AND HALL - Ross Crane House, Pulaski & Washington Streets, Athens, Clarke County, GA

  18. 2. Historic American Buildings Survey L. D. Andrew, Photographer Dec. ...

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

    2. Historic American Buildings Survey L. D. Andrew, Photographer Dec. 1936 From Photograph furnished by W. Elliott Dunwody, Jr. Arch't., Macon, Ga. ENTRANCE STOOP AND DOORWAY - Baber House, Walnut Street, Macon, Bibb County, GA

  19. 1. Historic American Buildings Survey L. D. Andrew, Photographer (Enlarged ...

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

    1. Historic American Buildings Survey L. D. Andrew, Photographer (Enlarged by) Aug. 6, 1936 Photographed by Harold Bush-Brown SIDE VIEW - Covered Bridge, Spanning Soap Creek, Atlanta, Fulton County, GA

  20. 1. Historic American Buildings Survey L. D. Andrew, Photographer Enlarged ...

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

    1. Historic American Buildings Survey L. D. Andrew, Photographer Enlarged from picture photographed by Harold Bush-Brown Aug. 1936 VIEW OF FRONT AND RIGHT SIDE - Old Methodist Church, Roswell, Fulton County, GA

  1. 2. Historic American Buildings Survey L. D. Andrew, Photographer Enlarged ...

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

    2. Historic American Buildings Survey L. D. Andrew, Photographer Enlarged Photo From photo of Miss Edith Johnston, Savannah, Ga. 1936 VIEW OF FRONT AND RIGHT SIDE (Restoration 1936) - Wild Heron Plantation, Little Ogeechee River Vicinity, Savannah, Chatham County, GA

  2. 1. Historic American Buildings Survey L. D. Andrew, Photographer Enlarged ...

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

    1. Historic American Buildings Survey L. D. Andrew, Photographer Enlarged Photo From Photo of Miss Edith Johnston's, Savannah, Ga. 1936 VIEW OF FRONT AND SIDE (Before Restoration, 1936). - Wild Heron Plantation, Little Ogeechee River Vicinity, Savannah, Chatham County, GA

  3. The Andrews-Sellers family of partition congruences.

    PubMed

    Paule, Peter; Radu, Cristian-Silviu

    2012-06-20

    In 1994, James Sellers conjectured an infinite family of Ramanujan type congruences for 2-colored Frobenius partitions introduced by George E. Andrews. These congruences arise modulo powers of 5. In 2002 Dennis Eichhorn and Sellers were able to settle the conjecture for powers up to 4. In this article, we prove Sellers' conjecture for all powers of 5. In addition, we discuss why the Andrews-Sellers family is significantly different from classical congruences modulo powers of primes. PMID:23471147

  4. A ligation-independent cloning method using nicking DNA endonuclease.

    PubMed

    Yang, Jie; Zhang, Zhihong; Zhang, Xin A; Luo, Qingming

    2010-11-01

    Using nicking DNA endonuclease (NiDE), we developed a novel technique to clone DNA fragments into plasmids. We created a NiDE cassette consisting of two inverted NiDE substrate sites sandwiching an asymmetric four-base sequence, and NiDE cleavage resulted in 14-base single-stranded termini at both ends of the vector and insert. This method can therefore be used as a ligation-independent cloning strategy to generate recombinant constructs rapidly. In addition, we designed and constructed a simple and specific vector from an Escherichia coli plasmid back-bone to complement this cloning method. By cloning cDNAs into this modified vector, we confirmed the predicted feasibility and applicability of this cloning method. PMID:21091446

  5. NCYM promotes calpain-mediated Myc-nick production in human MYCN-amplified neuroblastoma cells

    SciTech Connect

    Shoji, Wataru; Suenaga, Yusuke; Kaneko, Yoshiki; Islam, S.M. Rafiqul; Alagu, Jennifer; Yokoi, Sana; Nio, Masaki; Nakagawara, Akira

    2015-06-05

    NCYM is a cis-antisense gene of MYCN and is amplified in human neuroblastomas. High NCYM expression is associated with poor prognoses, and the NCYM protein stabilizes MYCN to promote proliferation of neuroblastoma cells. However, the molecular mechanisms of NCYM in the regulation of cell survival have remained poorly characterized. Here we show that NCYM promotes cleavage of MYCN to produce the anti-apoptotic protein, Myc-nick, both in vitro and in vivo. NCYM and Myc-nick were induced at G2/M phase, and NCYM knockdown induced apoptotic cell death accompanied by Myc-nick downregulation. These results reveal a novel function of NCYM as a regulator of Myc-nick production in human neuroblastomas. - Highlights: • NCYM promotes cleavages of MYC and MYCN to produce Myc-nick in vitro. • NCYM increases Myc-nick production in MYCN-amplified neuroblastoma cells. • NCYM knockdown decreases Myc-nick production and induces apoptosis at G2/M phase.

  6. Nick Ransford: 'There is a job to do so let's get on with it'.

    PubMed

    Ransford, Nick; Doherty, Ruth

    2014-03-01

    Nick Ransford is a consultant in special care dentistry at Birmingham Community Healthcare NHS Trust. He has over 25 years' experience working with adults with disabilities and medical conditions across the spectrum. PMID:24603240

  7. PARP3 is a sensor of nicked nucleosomes and monoribosylates histone H2BGlu2

    PubMed Central

    Grundy, Gabrielle J.; Polo, Luis M.; Zeng, Zhihong; Rulten, Stuart L.; Hoch, Nicolas C.; Paomephan, Pathompong; Xu, Yingqi; Sweet, Steve M.; Thorne, Alan W.; Oliver, Antony W.; Matthews, Steve J.; Pearl, Laurence H.; Caldecott, Keith W.

    2016-01-01

    PARP3 is a member of the ADP-ribosyl transferase superfamily that we show accelerates the repair of chromosomal DNA single-strand breaks in avian DT40 cells. Two-dimensional nuclear magnetic resonance experiments reveal that PARP3 employs a conserved DNA-binding interface to detect and stably bind DNA breaks and to accumulate at sites of chromosome damage. PARP3 preferentially binds to and is activated by mononucleosomes containing nicked DNA and which target PARP3 trans-ribosylation activity to a single-histone substrate. Although nicks in naked DNA stimulate PARP3 autoribosylation, nicks in mononucleosomes promote the trans-ribosylation of histone H2B specifically at Glu2. These data identify PARP3 as a molecular sensor of nicked nucleosomes and demonstrate, for the first time, the ribosylation of chromatin at a site-specific DNA single-strand break. PMID:27530147

  8. Appreciating Unity in Diversity: An Interview with Andrew Solomon

    ERIC Educational Resources Information Center

    Peters, Dane L.

    2014-01-01

    The theme of the AMS 2014 Annual Conference is "Unity in Diversity," a concept that also describes the work of conference keynote speaker Andrew Solomon. Solomon is a writer and lecturer on psychology and politics; winner of the National Book Award; and an activist for LGBT [lesbian, gay, bisexual, and transgender] rights, mental health,…

  9. The isolation of strand-specific nicking endonucleases from a randomized SapI expression library

    PubMed Central

    Samuelson, James C.; Zhu, Zhenyu; Xu, Shuang-yong

    2004-01-01

    The Type IIS restriction endonuclease SapI recognizes the DNA sequence 5′-GCTCTTC-3′ (top strand by convention) and cleaves downstream (N1/N4) indicating top- and bottom-strand spacing, respectively. The asymmetric nature of DNA recognition presented the possibility that one, if not two, nicking variants might be created from SapI. To explore this possibility, two parallel selection procedures were designed to isolate either top-strand nicking or bottom-strand nicking variants from a randomly mutated SapI expression library. These procedures take advantage of a SapI substrate site designed into the expression plasmid, which allows for in vitro selection of plasmid clones possessing a site-specific and strand-specific nick. A procedure designed to isolate bottom-strand nicking enzymes yielded Nb.SapI-1 containing a critical R420I substitution near the end of the protein. The top-strand procedure yielded several SapI variants with a distinct preference for top-strand cleavage. Mutations present within the selected clones were segregated to confirm a top-strand nicking phenotype for single variants Q240R, E250K, G271R or K273R. The nature of the amino acid substitutions found in the selected variants provides evidence that SapI may possess two active sites per monomer. This work presents a framework for establishing the mechanism of SapI DNA cleavage. PMID:15247348

  10. Characterization of a novel eukaryal nick-sealing RNA ligase from Naegleria gruberi

    PubMed Central

    Unciuleac, Mihaela-Carmen; Shuman, Stewart

    2015-01-01

    The proteome of the amoebo-flagellate protozoan Naegleria gruberi is rich in candidate RNA repair enzymes, including 15 putative RNA ligases, one of which, NgrRnl, is a eukaryal homolog of Deinococcus radiodurans RNA ligase, DraRnl. Here we report that purified recombinant NgrRnl seals nicked 3′-OH/5′-PO4 duplexes in which the 3′-OH strand is RNA. It does so via the “classic” ligase pathway, entailing reaction with ATP to form a covalent NgrRnl–AMP intermediate, transfer of AMP to the nick 5′-PO4, and attack of the RNA 3′-OH on the adenylylated nick to form a 3′–5′ phosphodiester. Unlike members of the four known families of ATP-dependent RNA ligases, NgrRnl lacks a carboxy-terminal appendage to its nucleotidyltransferase domain. Instead, it contains a defining amino-terminal domain that we show is important for 3′-OH/5′-PO4 nick-sealing and ligase adenylylation, but dispensable for phosphodiester synthesis at a preadenylylated nick. We propose that NgrRnl, DraRnl, and their homologs from diverse bacteria, viruses, and unicellular eukarya comprise a new “Rnl5 family” of nick-sealing ligases with a signature domain organization. PMID:25740837

  11. Characterization of the structure and melting of DNAs containing backbone nicks and gaps

    SciTech Connect

    Snowden-Ifft, E.A.; Wemmer, D.E. )

    1990-06-26

    A DNA molecule containing a gap (a missing phosphate) has been examined and compared to two other molecules of the same sequence, one containing a nick (a phosphorylated gap) and the other a normal duplex containing no break in the backbone. A second gapped sequence was also compared to a normal duplex of the same sequence. The molecules containing nicks or gaps were generated as dumbbell molecules, short helices closed by a loop at each end. The dumbbells were formed by the association of two hairpins with self-complementary dangling 5'-ends. Nuclear magnetic resonance was used to monitor the melting transition and to probe structural differences between molecules. Under the conditions used here no change in stability was observed upon phosphorylation of the gap. Structural changes upon phosphorylation of a gap or closure of a nick were minimal and were localized to the region immediately around the gap or nick. Two transitions can be observed as a gapped or nicked molecule melts, although the resolution of the two transitions varies with the salt concentration. At moderate to high salt (greater than or equal to 30 mM) the molecule melts essentially all at once. At low salt the two transitions occur at temperatures that differ by as much as 15 degrees C. In addition, comparison with other NMR melting studies indicates that the duplex formed by the overlap of the dangling ends of the hairpins is stabilized relative to a free duplex of the same sequence, probably by stacking onto the hairpin stem.

  12. A pioneer of tropical medicine worldwide: Andrew Balfour, of Khartoum

    PubMed Central

    Adeel, Ahmed A. A.

    2013-01-01

    This is an archival account of the career of Sir Andrew Balfour in Khartoum, Sudan during the period 1902 to 1913. As the first director of the Wellcome Tropical Research Laboratories in Khartoum during the period, Andrew Balfour was tasked with establishing the laboratories and at the same time he was engaged in founding the health services in Khartoum. Balfour worked in close collaboration and support from Henry Wellcome and Reginald Wingate, the Governor General of the Sudan. The energetic and meticulous sanitary work of Balfour had a remarkable impact, with Khartoum declared mosquito-free by 1910. Establishing a research base in the laboratories was met with many challenges but eventually Balfour managed to recruit a team of dedicated researchers and to produce well-circulated publications in tropical medicine. Balfour’s work in Khartoum later lead him to a distinguished career in tropical medicine. In 1923 he was appointed the first Director of London School of Hygiene and Tropical Medicine. He was also elected President of the Royal Society of Tropical Medicine and Hygiene (1925–27). Sir Andrew Balfour, KCMG, CB, LL D (1873 –1931) PMID:27493361

  13. To Nick or Not to Nick: Comparison of I-SceI Single- and Double-Strand Break-Induced Recombination in Yeast and Human Cells

    PubMed Central

    Katz, Samantha S.; Gimble, Frederick S.; Storici, Francesca

    2014-01-01

    Genetic modification of a chromosomal locus to replace an existing dysfunctional allele with a corrected sequence can be accomplished through targeted gene correction using the cell's homologous recombination (HR) machinery. Gene targeting is stimulated by generation of a DNA double-strand break (DSB) at or near the site of correction, but repair of the break via non-homologous end-joining without using the homologous template can lead to deleterious genomic changes such as in/del mutations, or chromosomal rearrangements. By contrast, generation of a DNA single-strand break (SSB), or nick, can stimulate gene correction without the problems of DSB repair because the uncut DNA strand acts as a template to permit healing without alteration of genetic material. Here, we examine the ability of a nicking variant of the I-SceI endonuclease (K223I I-SceI) to stimulate gene targeting in yeast Saccharomyces cerevisiae and in human embryonic kidney (HEK-293) cells. K223I I-SceI is proficient in both yeast and human cells and promotes gene correction up to 12-fold. We show that K223I I-SceI-driven recombination follows a different mechanism than wild-type I-SceI-driven recombination, thus indicating that the initial DNA break that stimulates recombination is not a low-level DSB but a nick. We also demonstrate that K223I I-SceI efficiently elevates gene targeting at loci distant from the break site in yeast cells. These findings establish the capability of the I-SceI nickase to enhance recombination in yeast and human cells, strengthening the notion that nicking enzymes could be effective tools in gene correction strategies for applications in molecular biology, biotechnology, and gene therapy. PMID:24558436

  14. ANDREWS MOUNTAIN, MAZOURKA, AND PAIUTE ROADLESS AREAS, CALIFORNIA.

    USGS Publications Warehouse

    McKee, Edwin H.; Schmauch, Steven W.

    1984-01-01

    On the basis of a mineral survey, local areas near and within the Andrews Mountain, Mazourka, and Paiute Roadless Areas, California have probable and substantiated mineral-resource potential. The principal metallic mineral resources in these roadless areas are gold, copper, and silver with lead, zinc, and tungsten, as lesser resources. A zone of probable resource potential for talc, graphite, and marble is identified in the Mazourka Roadless Area. Metallic mineralization occurs mostly in vein deposits in silicic and carbonate metasedimentary rocks peripheral to Mesozoic plutons and locally in granitic rocks as well. There is little promise for the occurrence of fossil fuel resources in the roadless areas.

  15. Carpet in Andrews High School. A Report by the Carpet Evaluation Team.

    ERIC Educational Resources Information Center

    Wallace, Morris S.; And Others

    In the spring of 1965, the Board of Trustees of Andrews Independent School District entered into a contract with the carpet evaluation team to analyze and evaluate the use of carpeting in the Andrews Public Schools, with emphasis on the senior high school. The two $5,000 grants served as the basis for paying for the expenses and professional…

  16. 33 CFR 334.761 - Naval Support Activity Panama City; St. Andrews Bay; restricted areas.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... City; St. Andrews Bay; restricted areas. 334.761 Section 334.761 Navigation and Navigable Waters CORPS... REGULATIONS § 334.761 Naval Support Activity Panama City; St. Andrews Bay; restricted areas. (a) The areas—(1... in this section shall be enforced by the Commanding Officer, Naval Support Activity, Panama...

  17. A Meta-Analytic Review of the MacAndrew Alcoholism Scale.

    ERIC Educational Resources Information Center

    Cooper-Hakim, Amy; Viswesvaran, Chockalingam

    2002-01-01

    Using meta analysis, examined the predictive validity of scores on the MacAndrew Alcoholism Scale (C. MacAndrew, 1965). Compared results for 161 studies with results for 63 studies using cut scores. Discusses why the use of continuous measures rather than cut scores is recommended. (SLD)

  18. The Pilgrimage of Joel Andrews: Aging in the Autobiography of a Yankee Farmer.

    ERIC Educational Resources Information Center

    Cole, Thomas R.; Premo, Terri

    1987-01-01

    Presents autobiographical writing as an untapped resource for the historical phenomenology of aging. Interprets the autobiography of Joel Andrews, a farmer who lived from the American Revolution through the Civil War. Argues that Andrews' autobiography reflects and helps accomplish his central task in old age, the religiously sanctioned transition…

  19. The beginnings of modern astronomy at the University of St Andrews

    NASA Astrophysics Data System (ADS)

    Batten, Alan H.

    2014-03-01

    Although the University of St Andrews is much older, teaching of and research in modern astronomy began there little more than sixty years ago. Their inception was strongly associated with one man, Erwin Finlay-Freundlich. Some account is given here of his work in St Andrews and the influence he had on younger generations.

  20. Generation of supercoils in nicked and gapped DNA drives DNA unknotting and postreplicative decatenation

    PubMed Central

    Racko, Dusan; Benedetti, Fabrizio; Dorier, Julien; Burnier, Yannis; Stasiak, Andrzej

    2015-01-01

    Due to the helical structure of DNA the process of DNA replication is topologically complex. Freshly replicated DNA molecules are catenated with each other and are frequently knotted. For proper functioning of DNA it is necessary to remove all of these entanglements. This is done by DNA topoisomerases that pass DNA segments through each other. However, it has been a riddle how DNA topoisomerases select the sites of their action. In highly crowded DNA in living cells random passages between contacting segments would only increase the extent of entanglement. Using molecular dynamics simulations we observed that in actively supercoiled DNA molecules the entanglements resulting from DNA knotting or catenation spontaneously approach sites of nicks and gaps in the DNA. Type I topoisomerases, that preferentially act at sites of nick and gaps, are thus naturally provided with DNA–DNA juxtapositions where a passage results in an error-free DNA unknotting or DNA decatenation. PMID:26150424

  1. Purification of a DNA nicking-closing enzyme from mouse L cells.

    PubMed Central

    Tang, D

    1978-01-01

    A DNA nicking-closing enzyme has been purified from the nuclei of mouse L cells to 90% homogeneity. The denatured and reduced form of the enzyme has a molecular weight of 68,000 which is in agreement with the molecular weight of the native enzyme as determined by gel filtration and by sucrose sedimentation velocity assuming the protein is globular. Therefore, the active form of the enzyme is a monopolypeptide. Its isoelectric point is pH 4.2 +/- 0.2. The nicking-closing activity does not require a cofactor and does not involve any sulfhydryl group. The enzyme requires 0.2 M NaCl and pH in the range of 6.5-7.5 for optimal activity. Images PMID:211488

  2. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity

    PubMed Central

    Ran, F. Ann; Hsu, Patrick D.; Lin, Chie-Yu; Gootenberg, Jonathan S.; Konermann, Silvana; Trevino, Alexandro; Scott, David A.; Inoue, Azusa; Matoba, Shogo; Zhang, Yi; Zhang, Feng

    2013-01-01

    Targeted genome editing technologies have enabled a broad range of research and medical applications. The Cas9 nuclease from the microbial CRISPR-Cas system is targeted to specific genomic loci by a 20-nt guide sequence, which can tolerate certain mismatches to the DNA target and thereby promote undesired off-target mutagenesis. Here, we describe an approach that combines a Cas9 nickase mutant with pairs of guide RNAs to introduce targeted double-strand breaks. Given that individual nicks in the genome are repaired with high fidelity, simultaneous nicking via appropriately offset guide RNAs effectively extends the number of specifically recognized bases in the target site. We demonstrate that paired nicking can be used to reduce off-target activity by 50–1,000 fold in cell lines and facilitate gene knockout in mouse zygotes without sacrificing on-target cleavage efficiency. This versatile strategy thus enables a wide variety of genome editing applications with higher levels of specificity. PMID:23992846

  3. Trapping and breaking of in vivo nicked DNA during pulsed field gel electrophoresis.

    PubMed

    Khan, Sharik R; Kuzminov, Andrei

    2013-12-15

    Pulsed field gel electrophoresis (PFGE) offers a high-resolution approach to quantify chromosomal fragmentation in bacteria, measured as percentage of chromosomal DNA entering the gel. The degree of separation in pulsed field gel (PFG) depends on the size of DNA as well as various conditions of electrophoresis such as electric field strength, time of electrophoresis, switch time, and buffer composition. Here we describe a new parameter, the structural integrity of the sample DNA itself, that influences its migration through PFGs. We show that subchromosomal fragments containing both spontaneous and DNA damage-induced nicks are prone to breakage during PFGE. Such breakage at single-strand interruptions results in artifactual decrease in molecular weight of linear DNA making accurate determination of the number of double-strand breaks difficult. Although breakage of nicked subchromosomal fragments is field strength independent, some high-molecular-weight subchromosomal fragments are also trapped within wells under the standard PFGE conditions. This trapping can be minimized by lowering the field strength and increasing the time of electrophoresis. We discuss how breakage of nicked DNA may be mechanistically linked to trapping. Our results suggest how to optimize conditions for PFGE when quantifying chromosomal fragmentation induced by DNA damage. PMID:23770235

  4. Evaluation of nicked human chorionic gonadotropin content in clinical specimens by a specific immunometric assay.

    PubMed

    Kovalevskaya, G; Birken, S; Kakuma, T; Schlatterer, J; O'Connor, J F

    1999-01-01

    We report the development and characterization of an IRMA for the direct measurement of nicked human chorionic gonadotropin (hCGn) in blood and urine. hCGn derived from a reference preparation of hCG used as an immunogen elicits monoclonal antibodies (mAbs) with enhanced recognition of human luteinizing hormone epitopes. The most specific assay for pregnancy hCGn is an IRMA composed of one mAb to choriocarcinoma-derived hCGn (C5) and a second mAb developed from immunization with normal-pregnancy hCGn. This assay was used to evaluate hCGn profiles in normal, in vitro fertilization, Down syndrome, and ectopic pregnancies. In all pregnancies, hCGn was usually present in much lower concentrations than the non-nicked hCG isoform. Our results suggest that some form of physical separation from the overwhelming quantities of non-nicked hCG present in clinical specimens will be required before accurate immunochemical estimations of hCGn can be made. PMID:9895340

  5. PARP3 is a sensor of nicked nucleosomes and monoribosylates histone H2B(Glu2).

    PubMed

    Grundy, Gabrielle J; Polo, Luis M; Zeng, Zhihong; Rulten, Stuart L; Hoch, Nicolas C; Paomephan, Pathompong; Xu, Yingqi; Sweet, Steve M; Thorne, Alan W; Oliver, Antony W; Matthews, Steve J; Pearl, Laurence H; Caldecott, Keith W

    2016-01-01

    PARP3 is a member of the ADP-ribosyl transferase superfamily that we show accelerates the repair of chromosomal DNA single-strand breaks in avian DT40 cells. Two-dimensional nuclear magnetic resonance experiments reveal that PARP3 employs a conserved DNA-binding interface to detect and stably bind DNA breaks and to accumulate at sites of chromosome damage. PARP3 preferentially binds to and is activated by mononucleosomes containing nicked DNA and which target PARP3 trans-ribosylation activity to a single-histone substrate. Although nicks in naked DNA stimulate PARP3 autoribosylation, nicks in mononucleosomes promote the trans-ribosylation of histone H2B specifically at Glu2. These data identify PARP3 as a molecular sensor of nicked nucleosomes and demonstrate, for the first time, the ribosylation of chromatin at a site-specific DNA single-strand break. PMID:27530147

  6. The Structure-Specific Nicking of Small Heteroduplexes by the RAG Complex: Implications for Lymphoid Chromosomal Translocations

    PubMed Central

    Raghavan, Sathees C.; Gu, Jiafeng; Swanson, Patrick C.; Lieber, Michael R.

    2009-01-01

    During V(D)J recombination, the RAG complex binds at recombination signal sequences and creates double-strand breaks. In addition to this sequence-specific recognition of the RSS, the RAG complex has been shown to be a structure-specific nuclease, cleaving 3′ overhangs and 3′ flaps, and, more recently, 10 nucleotides (nt) bubble (heteroduplex) structures. Here, we assess the smallest size heteroduplex that core and full-length RAGs can cleave. We also test whether bubbles adjacent to a partial RSS are nicked any differently or any more efficiently than bubbles that are surrounded by random sequence. These points are important in considering what types and what size of non-B DNA structure that the RAG complex can nick, and this helps assess the role of the RAG complex in mediating lymphoid chromosomal translocations. We find that the smallest bubble nicked by the RAG complex is 3 nt, and proximity to a partial or full RSS sequence does not affect the nicking by RAGs. RAG nicking efficiency increases with the size of the heteroduplex and is only about two-fold less efficient than an RSS when the bubble is 6 nt. We consider these findings in the context of RAG nicking at non-B DNA structures in lymphoid chromosomal translocations. PMID:17307402

  7. The structure-specific nicking of small heteroduplexes by the RAG complex: implications for lymphoid chromosomal translocations.

    PubMed

    Raghavan, Sathees C; Gu, Jiafeng; Swanson, Patrick C; Lieber, Michael R

    2007-06-01

    During V(D)J recombination, the RAG complex binds at recombination signal sequences and creates double-strand breaks. In addition to this sequence-specific recognition of the RSS, the RAG complex has been shown to be a structure-specific nuclease, cleaving 3' overhangs and 3' flaps, and, more recently, 10 nucleotides (nt) bubble (heteroduplex) structures. Here, we assess the smallest size heteroduplex that core and full-length RAGs can cleave. We also test whether bubbles adjacent to a partial RSS are nicked any differently or any more efficiently than bubbles that are surrounded by random sequence. These points are important in considering what types and what size of non-B DNA structure that the RAG complex can nick, and this helps assess the role of the RAG complex in mediating lymphoid chromosomal translocations. We find that the smallest bubble nicked by the RAG complex is 3nt, and proximity to a partial or full RSS sequence does not affect the nicking by RAGs. RAG nicking efficiency increases with the size of the heteroduplex and is only about two-fold less efficient than an RSS when the bubble is 6nt. We consider these findings in the context of RAG nicking at non-B DNA structures in lymphoid chromosomal translocations. PMID:17307402

  8. A transnational conference romance: Elsie Andrews, Hildegarde Kneeland, and the Pan-Pacific Women's Association.

    PubMed

    Laurie, Alison J

    2009-01-01

    Elsie Andrews, a feminist activist from New Zealand, met Dr. Hildegarde Kneeland, a progressive economist from the United States, at the 1934 Pan-Pacific Women's Association conference in Honolulu. Andrews wrote diaries of her attendance at conferences, and in these writes openly of her attraction and romantic feelings for Kneeland, despite her own long-term domestic partnership back in New Plymouth with Muriel Kirton. This article considers the role conference romances may have played for Andrews and others in encouraging their interest in women's organizations, in the context of literature on romantic friendships and lesbianism. PMID:19830617

  9. ISS Update: RATS Principal Investigator Andrew Abercromby -- 08.29.12

    NASA Video Gallery

    NASA Public Affairs Officer Brandi Dean talks to the Research And Technology Studies (RATS) Principal Investigator Andrew Abercromby in the Space Vehicle Mock-Up Facility at Johnson Space Center in...

  10. 33 CFR 334.761 - Naval Support Activity Panama City; St. Andrews Bay; restricted areas.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... City; St. Andrews Bay; restricted areas. 334.761 Section 334.761 Navigation and Navigable Waters CORPS... REGULATIONS § 334.761 Naval Support Activity Panama City; St. Andrews Bay; restricted areas. (a) The areas—(1... waterline to 30°09′57.5″ N, 085°44′37″ W; then northerly to point of origin. (2) Area BA-1. The area...

  11. 33 CFR 334.761 - Naval Support Activity Panama City; St. Andrews Bay; restricted areas.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... City; St. Andrews Bay; restricted areas. 334.761 Section 334.761 Navigation and Navigable Waters CORPS... REGULATIONS § 334.761 Naval Support Activity Panama City; St. Andrews Bay; restricted areas. (a) The areas—(1... waterline to 30°09′57.5″ N, 085°44′37″ W; then northerly to point of origin. (2) Area BA-1. The area...

  12. Trapping of DNA topoisomerase I on nick-containing DNA in cell free extracts of Saccharomyces cerevisiae.

    PubMed

    Lebedeva, Natalia; Auffret Vander Kemp, Patricia; Bjornsti, Mary-Ann; Lavrik, Olga; Boiteux, Serge

    2006-07-13

    The aim of the present study was to identify proteins that bind nicked DNA intermediates formed in the course of base excision repair (BER) in cell free extracts of Saccharomyces cerevisiae. In mammalian cells, nicks in DNA are targets of proteins such as PARP-1 or XRCC1 that have no homologues in yeast. One of the most promising methodologies to trap proteins that interact with damaged DNA lies in using a photocrosslinking technique with photoactivable dNTP analogues such as exo-N-{2-[N-(4-azido-2,5-difluoro-3-chloropyridine-6-yl)-3-aminopropionyl]-aminoethyl}-2'-deoxycytidine-5'-triphosphate (FAP-dCTP) for enzymatic synthesis of DNA probes with a photoreactive dNMP residue at the 3'-margin of a nick. Using this approach, we identified a major covalent DNA-protein adduct between a nick-containing 34-mer DNA duplex and a protein of a molecular mass of around 100-kDa. Unexpectedly, the formation of the 100-kDa adduct did not require the incorporation of the photoreactive dNMP residue at the 3'-margin of the nick nor exposure to near UV-light. However, the formation of the 100-kDa adduct strictly required a nick or a short gap in the DNA probe. Furthermore, the 100-kDa adduct was not detected in yeast extracts lacking DNA topoisomerase I (Top1). To further establish the nature of crosslinked protein, yeast Top1 was tagged with a Myc-epitope. In this case, the mobility of the Top1-DNA adduct increased by 7- kDa. Therefore, our data speak in favor of Top1 trapping by nicked DNA. In support of this hypothesis, purified yeast Top1 was also crosslinked to nicked DNA structures. Undamaged, uracil- and abasic (AP) site-containing DNAs were unable to trap Top1 under the same assay conditions. Since nicked DNA structures are frequently formed in the course of BER, their covalent linkage to Top1 has the potential to interfere with BER in vivo. PMID:16713756

  13. Free energy analysis and mechanism of base pair stacking in nicked DNA.

    PubMed

    Häse, Florian; Zacharias, Martin

    2016-09-01

    The equilibrium of stacked and unstacked base pairs is of central importance for all nucleic acid structure formation processes. The stacking equilibrium is influenced by intramolecular interactions between nucleosides but also by interactions with the solvent. Realistic simulations on nucleic acid structure formation and flexibility require an accurate description of the stacking geometry and stability and its sequence dependence. Free energy simulations have been conducted on a series of double stranded DNA molecules with a central strand break (nick) in one strand. The change in free energy upon unstacking was calculated for all ten possible base pair steps using umbrella sampling along a center-of-mass separation coordinate and including a comparison of different water models. Comparison to experimental studies indicates qualitative agreement of the stability order but a general overestimation of base pair stacking interactions in the simulations. A significant dependence of calculated nucleobase stacking free energies on the employed water model was observed with the tendency of stacking free energies being more accurately reproduced by more complex water models. The simulation studies also suggest a mechanism of stacking/unstacking that involves significant motions perpendicular to the reaction coordinate and indicate that the equilibrium nicked base pair step may slightly differ from regular B-DNA geometry in a sequence-dependent manner. PMID:27407106

  14. Real-time quantitative nicking endonuclease-mediated isothermal amplification with small molecular beacons.

    PubMed

    Xu, Wentao; Wang, Chenguang; Zhu, Pengyu; Guo, Tianxiao; Xu, Yuancong; Huang, Kunlun; Luo, Yunbo

    2016-04-21

    Techniques of isothermal amplification have recently made great strides, and have generated significant interest in the field of point-of-care detection. Nicking endonuclease-mediated isothermal amplification (NEMA) is an example of simple isothermal technology. In this paper, a real-time quantitative nicking endonuclease-mediated isothermal amplification with small molecular beacons (SMB-NEMA) of improved specificity and sensitivity is described. First, we optimized the prohibition of de novo synthesis by choosing Nt·BstNBI endonuclease. Second, the whole genome was successfully amplified with Nt·BstNBI (6 U), betaine (1 M) and trehalose (60 mM) for the first time. Third, we achieved 10 pg sensitivity for the first time after adding a small molecular beacon that spontaneously undergoes a conformational change when hybridizing to target, and the practical test validated the assay's application. The small molecular beacon has a similar melting temperature to the reaction temperature, but is approximately 10 bp shorter than the length of a traditional molecular beacon. A new threshold regulation was also established for isothermal conditions. Finally, we established a thermodynamic model for designing small molecular beacons. This multistate model is more correct than the traditional algorithm. This theoretical and practical basis will help us to monitor SMB-NEMA in a quantitative way. In summary, our SMB-NEMA method allows the simple, specific and sensitive assessment of isothermal DNA quantification. PMID:27027375

  15. Free energy analysis and mechanism of base pair stacking in nicked DNA

    PubMed Central

    Häse, Florian; Zacharias, Martin

    2016-01-01

    The equilibrium of stacked and unstacked base pairs is of central importance for all nucleic acid structure formation processes. The stacking equilibrium is influenced by intramolecular interactions between nucleosides but also by interactions with the solvent. Realistic simulations on nucleic acid structure formation and flexibility require an accurate description of the stacking geometry and stability and its sequence dependence. Free energy simulations have been conducted on a series of double stranded DNA molecules with a central strand break (nick) in one strand. The change in free energy upon unstacking was calculated for all ten possible base pair steps using umbrella sampling along a center-of-mass separation coordinate and including a comparison of different water models. Comparison to experimental studies indicates qualitative agreement of the stability order but a general overestimation of base pair stacking interactions in the simulations. A significant dependence of calculated nucleobase stacking free energies on the employed water model was observed with the tendency of stacking free energies being more accurately reproduced by more complex water models. The simulation studies also suggest a mechanism of stacking/unstacking that involves significant motions perpendicular to the reaction coordinate and indicate that the equilibrium nicked base pair step may slightly differ from regular B-DNA geometry in a sequence-dependent manner. PMID:27407106

  16. Rep-mediated nicking of the adeno-associated virus origin requires two biochemical activities, DNA helicase activity and transesterification.

    PubMed

    Brister, J R; Muzyczka, N

    1999-11-01

    The single-stranded adeno-associated virus (AAV) genome is flanked by terminal hairpinned origins of DNA replication (terminal repeats [TRs]) that are nicked at the terminal resolution site (trs) by the AAV Rep protein in an ATP-dependent, site-specific manner. Here we determine the minimal trs sequence necessary for Rep cleavage, 3'-CCGGT/TG-5', and show that this 7-base core sequence is required only on the nicked strand. We also identify a potential stem-loop structure at the trs. Interestingly, Rep nicking on a TR substrate that fixes this trs stem-loop in the extruded form no longer requires ATP. This suggests that ATP-dependent Rep helicase activity is necessary to unwind the duplex trs and extrude the stem-loop structure, prior to the ATP-independent Rep transesterification reaction. The extrusion of origin stem-loop structures prior to nicking appears to be a general mechanism shared by plant and animal viruses and bacterial plasmids. In the case of AAV, this mechanism of TR nicking would provide a possible regulatory function. PMID:10516041

  17. Kinetic mechanism and fidelity of nick sealing by Escherichia coli NAD+-dependent DNA ligase (LigA).

    PubMed

    Chauleau, Mathieu; Shuman, Stewart

    2016-03-18

    Escherichia coli DNA ligase (EcoLigA) repairs 3'-OH/5'-PO4 nicks in duplex DNA via reaction of LigA with NAD(+) to form a covalent LigA-(lysyl-Nζ)-AMP intermediate (step 1); transfer of AMP to the nick 5'-PO4 to form an AppDNA intermediate (step 2); and attack of the nick 3'-OH on AppDNA to form a 3'-5' phosphodiester (step 3). A distinctive feature of EcoLigA is its stimulation by ammonium ion. Here we used rapid mix-quench methods to analyze the kinetic mechanism of single-turnover nick sealing by EcoLigA-AMP. For substrates with correctly base-paired 3'-OH/5'-PO4 nicks, kstep2 was fast (6.8-27 s(-1)) and similar to kstep3 (8.3-42 s(-1)). Absent ammonium, kstep2 and kstep3 were 48-fold and 16-fold slower, respectively. EcoLigA was exquisitely sensitive to 3'-OH base mispairs and 3' N:abasic lesions, which elicited 1000- to >20000-fold decrements in kstep2. The exception was the non-canonical 3' A:oxoG configuration, which EcoLigA accepted as correctly paired for rapid sealing. These results underscore: (i) how EcoLigA requires proper positioning of the nick 3' nucleoside for catalysis of 5' adenylylation; and (ii) EcoLigA's potential to embed mutations during the repair of oxidative damage. EcoLigA was relatively tolerant of 5'-phosphate base mispairs and 5' N:abasic lesions. PMID:26857547

  18. Kinetic mechanism and fidelity of nick sealing by Escherichia coli NAD+-dependent DNA ligase (LigA)

    PubMed Central

    Chauleau, Mathieu; Shuman, Stewart

    2016-01-01

    Escherichia coli DNA ligase (EcoLigA) repairs 3′-OH/5′-PO4 nicks in duplex DNA via reaction of LigA with NAD+ to form a covalent LigA-(lysyl-Nζ)–AMP intermediate (step 1); transfer of AMP to the nick 5′-PO4 to form an AppDNA intermediate (step 2); and attack of the nick 3′-OH on AppDNA to form a 3′-5′ phosphodiester (step 3). A distinctive feature of EcoLigA is its stimulation by ammonium ion. Here we used rapid mix-quench methods to analyze the kinetic mechanism of single-turnover nick sealing by EcoLigA–AMP. For substrates with correctly base-paired 3′-OH/5′-PO4 nicks, kstep2 was fast (6.8–27 s−1) and similar to kstep3 (8.3–42 s−1). Absent ammonium, kstep2 and kstep3 were 48-fold and 16-fold slower, respectively. EcoLigA was exquisitely sensitive to 3′-OH base mispairs and 3′ N:abasic lesions, which elicited 1000- to >20000-fold decrements in kstep2. The exception was the non-canonical 3′ A:oxoG configuration, which EcoLigA accepted as correctly paired for rapid sealing. These results underscore: (i) how EcoLigA requires proper positioning of the nick 3′ nucleoside for catalysis of 5′ adenylylation; and (ii) EcoLigA's potential to embed mutations during the repair of oxidative damage. EcoLigA was relatively tolerant of 5′-phosphate base mispairs and 5′ N:abasic lesions. PMID:26857547

  19. The McAndrews Leadership Lecture: February 2015, by Dr Scott Haldeman. Challenges of the Past, Challenges of the Present

    PubMed Central

    Haldeman, Scott; McAndrews, George P.; Goertz, Christine; Sportelli, Louis; Hamm, Anthony W.; Johnson, Claire

    2015-01-01

    The McAndrews Leadership Lecture was developed by the American Chiropractic Association to honor the legacy of Jerome F. McAndrews, DC, and George P. McAndrews, JD, and their contributions to the chiropractic profession. This article is a transcription of the presentation made by Dr Scott Haldeman on February 28, 2015, in Washington, DC, at the National Chiropractic Leadership Conference. PMID:26770177

  20. Hurricane Andrew's impact on natural gas and oil facilities on the outer continental shelf (interim report as of November 1993)

    SciTech Connect

    Daniels, G.R.

    1994-01-01

    The interim report reviews Hurricane Andrew's impact on Federal Outer Continental Shelf (OCS) natural gas and oil drilling and production facilities. The report provides background on Hurricane Andrew's progression, discusses how OCS operators responded to the storm, summarizes the types of damage to offshore facilies caused by Hurricane Andrew, and discusses Minerals Management Service's continuing damage assessment and repair efforts. The summaries of damage estimates are presented in tables in Appendix 1. A glossary of report terminology is provided in Appendix 2.

  1. Isothermal amplification detection of nucleic acids by a double-nicked beacon.

    PubMed

    Shi, Chao; Zhou, Meiling; Pan, Mei; Zhong, Guilin; Ma, Cuiping

    2016-03-01

    Isothermal and rapid amplification detection of nucleic acids is an important technology in environmental monitoring, foodborne pathogen detection, and point-of-care clinical diagnostics. Here we have developed a novel method of isothermal signal amplification for single-stranded DNA (ssDNA) detection. The ssDNA target could be used as an initiator, coupled with a double-nicked molecular beacon, to originate amplification cycles, achieving cascade signal amplification. In addition, the method showed good specificity and strong anti-jamming capability. Overall, it is a one-pot and isothermal strand displacement amplification method without the requirement of a stepwise procedure, which greatly simplifies the experimental procedure and decreases the probability of contamination of samples. With its advantages, the method would be very useful to detect nucleic acids in point-of-care or field use. PMID:26706801

  2. Design and analysis of site-specific single-strand nicking endonucleases for gene correction.

    PubMed

    Metzger, Michael J; Certo, Michael T

    2014-01-01

    Single-strand nicking endonucleases ("nickases") have been shown to induce homology-mediated gene correction with reduced toxicity of DNA double-strand break-producing enzymes, and nickases have been engineered from both homing endonuclease and FokI-based scaffolds. We describe the strategies used to engineer these site-specific nickases as well as the in vitro methods used to confirm their activity and specificity. Additionally, we describe the Traffic Light Reporter system, which uses a flow cytometric assay to simultaneously detect both gene repair and mutagenic nonhomologous end-joining outcomes at a single targeted site in mammalian cells. With these methods, novel nickases can be designed and tested for use in gene correction with novel target sites. PMID:24557907

  3. Lessons from isolable nickel(I) precursor complexes for small molecule activation.

    PubMed

    Yao, Shenglai; Driess, Matthias

    2012-02-21

    Small-molecule activation by transition metals is essential to numerous organic transformations, both biological and industrial. Creating useful metal-mediated activation systems often depends on stabilizing the metal with uncommon low oxidation states and low coordination numbers. This provides a redox-active metal center with vacant coordination sites well suited for interacting with small molecules. Monovalent nickel species, with their d(9) electronic configuration, are moderately strong one-electron reducing agents that are synthetically attractive if they can be isolated. They represent suitable reagents for closing the knowledge gap in nickel-mediated activation of small molecules. Recently, the first strikingly stable dinuclear β-diketiminate nickel(I) precursor complexes were synthesized, proving to be suitable promoters for small-molecule binding and activation. They have led to many unprecedented nickel complexes bearing activated small molecules in different reduction stages. In this Account, we describe selected achievements in the activation of nitrous oxide (N(2)O), O(2), the heavier chalcogens (S, Se, and Te), and white phosphorus (P(4)) through this β-diketiminatonickel(I) precursor species. We emphasize the reductive activation of O(2), owing to its promise in oxidation processes. The one-electron-reduced O(2) activation product, that is, the corresponding β-diketiminato-supported Ni-O(2) complex, is a genuine superoxonickel(II) complex, representing an important intermediate in the early stages of O(2) activation. It selectively acts as an oxygen-atom transfer agent, hydrogen-atom scavenger, or both towards exogenous organic substrates to yield oxidation products. The one-electron reduction of the superoxonickel(II) moiety was examined by using elemental potassium, β-diketiminatozinc(II) chloride, and β-diketiminatoiron(I) complexes, affording the first heterobimetallic complexes featuring a [NiO(2)M] subunit (M is K, Zn, or Fe). Through

  4. Development of a nicking endonuclease-assisted method for the purification of minicircles.

    PubMed

    Alves, Cláudia P A; Šimčíková, Michaela; Brito, Liliana; Monteiro, Gabriel A; Prazeres, Duarte Miguel F

    2016-04-22

    Minicircle (MC) DNA vectors are able to generate a high-level transgene expression in vivo, which is superior to the one afforded by conventional plasmids. MC vectors are produced by replicating a parental plasmid (PP) and promoting its recombination in Escherichia coli. This generates a MC with the expression cassette, and a miniplasmid (MP) with the replication segment. Unfortunately, wider use of MC vectors is hampered by difficulties in isolating the target MCs from their MP counterpart. In this proof-of-concept study, a reproducible process is described to improve the purification of supercoiled (sc) MCs that combines an in vitro enzymatic relaxation of sc MP impurities with topoisomer separation and RNA clearance by hydrophobic interaction chromatography (HIC) step. At the early stage of vector design, a site for the nicking endonuclease Nb.BbvCI was strategically placed in the MP part of the PP backbone. A process was then established that involves E. coli culture and recombination of PPs into target MC, cell harvesting and alkaline lysis, precipitation with isopropanol and ammonium sulfate and diafiltration/concentration by microfiltration. Next, an in vitro digestion step was carried out with Nb.BbvCI to nick of one of the strands of the MPs and of non-recombined PPs by Nb.BbvCI. As a result, sc MPs and non-recombined PPs were converted into the corresponding open circular (oc) forms whereas sc MCs remain unaffected. Finally, sc MC was isolated from oc DNA molecules (oc MPs, oc MC) and RNA by performing HIC with a phenyl-Sepharose column using a series of elution steps with decreasing ammonium sulfate concentrations. On the basis of agarose gel electrophoresis analysis, the sc MC-containing fractions were determined to be virtually free from nucleic acid impurities. PMID:27016116

  5. Assistant DNA recycling with nicking endonuclease and molecular beacon for signal amplification using a target-complementary arched structure.

    PubMed

    Gao, Fenglei; Lei, Jianping; Ju, Huangxian

    2013-05-11

    A simple and universal method for ultrasensitive "signal on" detection of DNA was developed with a target-complementary arched structure to release assistant DNA, which was recycled with nicking endonuclease to amplify the detectable fluorescent signal of molecular beacons. PMID:23563493

  6. A quantitative study of the flexibility contributed to RNA structures by nicks and single-stranded gaps.

    PubMed Central

    Cohen, S B; Cech, T R

    1998-01-01

    Disulfide crosslinking via thiol-disulfide interchange was applied to quantitate the relative flexibility contributed by nicks and single-stranded gaps in an RNA structure. An RNA duplex comprised of three strands was constructed containing the disulfide crosslink precursors 1 and 2 at opposite ends of the duplex on opposite strands. The third strand was of varying length to yield a nick or single-stranded gaps of 1, 2, or 3 nt. Crosslinking rates Indicated relative flexibilities of the resulting two-helix junctions. Crosslinking in the nicked duplex occurred two orders of magnitude slower than in a duplex containing a 3-nt gap. Rates of crosslinking in duplexes with 3-and 2-nt gaps showed only modest dependence on the gap sequence. Many natural RNAs, including ribozymes, contain two-helix junctions related to the model system described here. The data suggest that two-helix junctions containing a nick in one strand will retain substantial rigidity, whereas one or more single-stranded nucleotides at a two-helix junction allow significant flexibility. PMID:9769093

  7. Andrew Sexton Gray (1826-1907). A founder of Australian ophthalmology: his life and times.

    PubMed

    Lowe, R F

    1985-11-01

    Andrew Sexton Gray was born in Limerick, Ireland, medically trained in Dublin, and was assistant to William Wilde, the distinguished oculist and aurist. He migrated to Victoria in 1859, was surgeon to a railway's construction company, then in 1862 began practice as a surgeon and oculist in Melbourne. In 1863 he founded a charitable eye and ear hospital, and had a very active, long life devoted mostly to ophthalmology. The hospital progressively expanded and became the centre for training for many ophthalmologists, as well as the nucleus for the cohesion of Victorian ophthalmology. History shows Andrew Sexton Gray to have been a founder of Australian ophthalmology. PMID:3914312

  8. 33 CFR 334.760 - Naval Support Activity Panama City and Alligator Bayou, a tributary of St. Andrew Bay, Fla...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... City and Alligator Bayou, a tributary of St. Andrew Bay, Fla.; naval restricted area. 334.760 Section... Alligator Bayou, a tributary of St. Andrew Bay, Fla.; naval restricted area. (a) The area. The waters within... the south side of the entrance to Alligator Bayou; thence directly across the entrance to a point...

  9. 33 CFR 334.760 - Naval Support Activity Panama City and Alligator Bayou, a tributary of St. Andrew Bay, Fla...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... City and Alligator Bayou, a tributary of St. Andrew Bay, Fla.; naval restricted area. 334.760 Section... Alligator Bayou, a tributary of St. Andrew Bay, Fla.; naval restricted area. (a) The area. The waters within... the south side of the entrance to Alligator Bayou; thence directly across the entrance to a point...

  10. 33 CFR 334.760 - Naval Support Activity Panama City and Alligator Bayou, a tributary of St. Andrew Bay, Fla...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... City and Alligator Bayou, a tributary of St. Andrew Bay, Fla.; naval restricted area. 334.760 Section... Alligator Bayou, a tributary of St. Andrew Bay, Fla.; naval restricted area. (a) The area. The waters within... the south side of the entrance to Alligator Bayou; thence directly across the entrance to a point...

  11. 33 CFR 334.760 - Naval Support Activity Panama City and Alligator Bayou, a tributary of St. Andrew Bay, Fla...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... City and Alligator Bayou, a tributary of St. Andrew Bay, Fla.; naval restricted area. 334.760 Section... Alligator Bayou, a tributary of St. Andrew Bay, Fla.; naval restricted area. (a) The area. The waters within... the south side of the entrance to Alligator Bayou; thence directly across the entrance to a point...

  12. 33 CFR 334.760 - Naval Support Activity Panama City and Alligator Bayou, a tributary of St. Andrew Bay, Fla...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... City and Alligator Bayou, a tributary of St. Andrew Bay, Fla.; naval restricted area. 334.760 Section... Alligator Bayou, a tributary of St. Andrew Bay, Fla.; naval restricted area. (a) The area. The waters within... the south side of the entrance to Alligator Bayou; thence directly across the entrance to a point...

  13. Commentary on Andrew Coulson's "Comparing Public, Private, and Market Schools: The International Evidence"

    ERIC Educational Resources Information Center

    Wolfram, Gary; Coulson, Andrew J.

    2009-01-01

    In this article, the authors comment on Andrew Coulson's "Comparing Public, Private, and Market Schools: The International Evidence." The authors believe that Coulson's paper is a very interesting review of the literature on the ability of market-produced education to outperform government-produced education. Coulson's response on this commentary…

  14. 77 FR 2968 - Pomperaug Hydro Project, Andrew Peklo III; Notice Establishing Deadline for Comments and Reply...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-20

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Pomperaug Hydro Project, Andrew Peklo III; Notice Establishing Deadline for Comments and Reply Comments On December 15, 2011, the Commission issued notice that Office of Energy Projects staff will hold a site visit...

  15. Astronauts Mario Runco, Jr. and Andrew S. W. Thomas, both mission specialists, pose for photo while

    NASA Technical Reports Server (NTRS)

    1996-01-01

    STS-77 ESC VIEW --- Astronauts Mario Runco, Jr. and Andrew S. W. Thomas, both mission specialists, pose for photo while in the mid-deck of the Earth-orbiting Space Shuttle Endeavour. The scene was recorded with an Electronic Still Camera (ESC).

  16. 78 FR 78349 - Andrew Peklo III; Notice of Availability of Draft Environmental Assessment

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-26

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Andrew Peklo III; Notice of Availability of Draft Environmental Assessment... Commission's (Commission) regulations, 18 CFR Part 380 (Order No. 486, 52 FR 47897), the Office of...

  17. Visions and Vanities: John Andrew Rice of Black Mountain College. Southern Biography Series.

    ERIC Educational Resources Information Center

    Reynolds, Katherine Chaddock

    This biography presents the life of John Andrew Rice, who founded Black Mountain College (North Carolina) in 1933 to implement his philosophy of education, including the centrality of artistic experience and emotional development to learning in all disciplines and the need for democratic governance shared between faculty and students. Born in…

  18. 75 FR 41895 - Whirlpool Corporation, Evansville Division, Including On-Site Leased Workers From Andrews...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-19

    ... notice was published in the Federal Register on March 5, 2010 (75 FR 10321). The notice was amended on... published on the Federal Register on June 7, 2010 (75 FR 32221). At the request of the petitioners, the... Workers From Andrews International, Inc., M.H. Equipment, and Kenco Logistics Services, LLC,...

  19. 22. View of Andrew McLean Company Textile Mill looking north; ...

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

    22. View of Andrew McLean Company Textile Mill looking north; Building No. 1 at left, Building No. 4 at right - Dundee Canal Industrial Historic District, Beginning at George Street in Passaic & extending north along Dundee Canal approximately 1.2 miles to Canal headgates opposite East Clifton Avenue in Clifton, Passaic, Passaic County, NJ

  20. 23. View of open firststory passageway of Andrew McLean Company ...

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

    23. View of open first-story passageway of Andrew McLean Company Textile Mill Building No. 1, looking west - Dundee Canal Industrial Historic District, Beginning at George Street in Passaic & extending north along Dundee Canal approximately 1.2 miles to Canal headgates opposite East Clifton Avenue in Clifton, Passaic, Passaic County, NJ

  1. 16. View of Andrew McLean Company Textile Mill looking southeast; ...

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

    16. View of Andrew McLean Company Textile Mill looking southeast; Building No. 6 at center, roof of Building No. 1 at left - Dundee Canal Industrial Historic District, Beginning at George Street in Passaic & extending north along Dundee Canal approximately 1.2 miles to Canal headgates opposite East Clifton Avenue in Clifton, Passaic, Passaic County, NJ

  2. 14. View of Andrew McLean Company Textile Mill looking north; ...

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

    14. View of Andrew McLean Company Textile Mill looking north; Building No. 6 at right, Building No. 1 in background, gateposts in foreground - Dundee Canal Industrial Historic District, Beginning at George Street in Passaic & extending north along Dundee Canal approximately 1.2 miles to Canal headgates opposite East Clifton Avenue in Clifton, Passaic, Passaic County, NJ

  3. 20. View of Andrew McLean Company Textile Mill looking southeast; ...

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

    20. View of Andrew McLean Company Textile Mill looking southeast; Building No. 2 at left, Building No. 3 at right - Dundee Canal Industrial Historic District, Beginning at George Street in Passaic & extending north along Dundee Canal approximately 1.2 miles to Canal headgates opposite East Clifton Avenue in Clifton, Passaic, Passaic County, NJ

  4. 15. View of Andrew McLean Company Textile Mill looking northeast; ...

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

    15. View of Andrew McLean Company Textile Mill looking northeast; Building No. 1 at left, Building No. 6 at center - Dundee Canal Industrial Historic District, Beginning at George Street in Passaic & extending north along Dundee Canal approximately 1.2 miles to Canal headgates opposite East Clifton Avenue in Clifton, Passaic, Passaic County, NJ

  5. 18. View of Andrew McLean Company Textile Mill looking north; ...

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

    18. View of Andrew McLean Company Textile Mill looking north; Building No. 3 at center right, Building No. 2 at center distance, Dundee Canal at left - Dundee Canal Industrial Historic District, Beginning at George Street in Passaic & extending north along Dundee Canal approximately 1.2 miles to Canal headgates opposite East Clifton Avenue in Clifton, Passaic, Passaic County, NJ

  6. Astronaut Andrew M. Allen, mission commander, sets up systems for a television downlink on the

    NASA Technical Reports Server (NTRS)

    1996-01-01

    STS-75 ONBOARD VIEW --- Astronaut Andrew M. Allen, mission commander, sets up systems for a television downlink on the flight deck of the Space Shuttle Columbia. Allen was joined by four other astronauts and an international payload specialist for more than 16 days of research aboard Columbia. The photograph was taken with a 70mm handheld camera.

  7. 33 CFR 334.761 - Naval Support Activity Panama City; St. Andrews Bay; restricted areas.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 3 2011-07-01 2011-07-01 false Naval Support Activity Panama... REGULATIONS § 334.761 Naval Support Activity Panama City; St. Andrews Bay; restricted areas. (a) The areas—(1... in this section shall be enforced by the Commanding Officer, Naval Support Activity, Panama...

  8. 33 CFR 334.761 - Naval Support Activity Panama City; St. Andrews Bay; restricted areas.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Naval Support Activity Panama... REGULATIONS § 334.761 Naval Support Activity Panama City; St. Andrews Bay; restricted areas. (a) The areas—(1... in this section shall be enforced by the Commanding Officer, Naval Support Activity, Panama...

  9. Athena, Andrew and Stanford: A Look at Implementation and Evaluation in Three Large Projects.

    ERIC Educational Resources Information Center

    Isaacs, Geoff

    1989-01-01

    Describes implementation, support, and evaluation of computer assisted learning (CAL) projects at three universities: Project Athena at Massachusetts Institute of Technology; the Andrew network at Carnegie Mellon University; and a project at Stanford University. Topics discussed include work stations, microcomputers, computer networks, graphics,…

  10. Amos Kendall's Role in the Election of Andrew Jackson as President of the United States, 1828.

    ERIC Educational Resources Information Center

    Nowell, Bob

    Amos Kendall's place in journalism history rests largely on his service as a journalist turned government official in the two administrations of President Andrew Jackson. Historians have claimed that Kendall was an influential journalist of the "partisan press" era, but they have provided little documentation. That documentation has been provided…

  11. Spanish Poetry and Anglo-American Modernism: The Legacy of Andrew P. Debicki.

    ERIC Educational Resources Information Center

    Mayhew, Jonathan

    2001-01-01

    Discusses the work of Andrew Debicki, an academician with a commitment to twentieth century poetry. Considers the definition of poetic modernity, one of the central issues in the study of literature in the past century. Examines the extent to which it is possible to assimilate modern Spanish poetry to the ideals of Anglo-American poetry.…

  12. 19. View of Andrew McLean Company Textile Mill looking south; ...

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

    19. View of Andrew McLean Company Textile Mill looking south; Building No. 2 at center, Botany Mills Lanolin Retrieval plant site in foreground - Dundee Canal Industrial Historic District, Beginning at George Street in Passaic & extending north along Dundee Canal approximately 1.2 miles to Canal headgates opposite East Clifton Avenue in Clifton, Passaic, Passaic County, NJ

  13. 31. View looking north from Andrew McLean Company Textile Mill; ...

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

    31. View looking north from Andrew McLean Company Textile Mill; Dundee Canal at center, Botany Worsted Mills in background - Dundee Canal Industrial Historic District, Beginning at George Street in Passaic & extending north along Dundee Canal approximately 1.2 miles to Canal headgates opposite East Clifton Avenue in Clifton, Passaic, Passaic County, NJ

  14. 17. View looking north; Andrew McLean Company Textile Mill, Building ...

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

    17. View looking north; Andrew McLean Company Textile Mill, Building No. 1, at right, Botany Worsted Mills at left distance - Dundee Canal Industrial Historic District, Beginning at George Street in Passaic & extending north along Dundee Canal approximately 1.2 miles to Canal headgates opposite East Clifton Avenue in Clifton, Passaic, Passaic County, NJ

  15. 30. View looking north from Andrew McLean Company Textile Mill; ...

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

    30. View looking north from Andrew McLean Company Textile Mill; Dundee Canal at center, Botany Worsted Mills in background - Dundee Canal Industrial Historic District, Beginning at George Street in Passaic & extending north along Dundee Canal approximately 1.2 miles to Canal headgates opposite East Clifton Avenue in Clifton, Passaic, Passaic County, NJ

  16. 56. Aerial view looking west; Andrew McLean Company Textile Mill ...

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

    56. Aerial view looking west; Andrew McLean Company Textile Mill at bottom, Dundee Canal at center, Botany Worsted Mills at top - Dundee Canal Industrial Historic District, Beginning at George Street in Passaic & extending north along Dundee Canal approximately 1.2 miles to Canal headgates opposite East Clifton Avenue in Clifton, Passaic, Passaic County, NJ

  17. Because Everyone Has a Story to Tell: Interview with Andrew Wright

    ERIC Educational Resources Information Center

    Floris, Flora Debora

    2016-01-01

    This article presents an interview with Andrew Wright, a widely recognized author, illustrator, storyteller, and teacher trainer. Wright has published many ELT books, authored six "Spellbinder" graded readers (1992-1994), and a collection of short stories. As a teacher trainer, Wright worked extensively with both teachers and students in…

  18. Traversing the Gap: Andrew Wright, John Hick and Critical Religious Education

    ERIC Educational Resources Information Center

    Teece, Geoff

    2005-01-01

    This paper discusses aspects of Andrew Wright's version of a liberal, critical religious education and his criticisms of some other views of modern religious education. This is attempted not by examining these "other views" as such but by concentrating on the work of John Hick. The reason for this is that Wright, like Cooling (in his book "A…

  19. Structure and two-metal mechanism of a eukaryal nick-sealing RNA ligase

    PubMed Central

    Unciuleac, Mihaela-Carmen; Goldgur, Yehuda; Shuman, Stewart

    2015-01-01

    ATP-dependent RNA ligases are agents of RNA repair that join 3′-OH and 5′-PO4 RNA ends. Naegleria gruberi RNA ligase (NgrRnl) exemplifies a family of RNA nick-sealing enzymes found in bacteria, viruses, and eukarya. Crystal structures of NgrRnl at three discrete steps along the reaction pathway—covalent ligase-(lysyl-Nζ)–AMP•Mn2+ intermediate; ligase•ATP•(Mn2+)2 Michaelis complex; and ligase•Mn2+ complex—highlight a two-metal mechanism of nucleotidyl transfer, whereby (i) an enzyme-bound “catalytic” metal coordination complex lowers the pKa of the lysine nucleophile and stabilizes the transition state of the ATP α phosphate; and (ii) a second metal coordination complex bridges the β- and γ-phosphates. The NgrRnl N domain is a distinctively embellished oligonucleotide-binding (OB) fold that engages the γ-phosphate and associated metal complex and orients the pyrophosphate leaving group for in-line catalysis with stereochemical inversion at the AMP phosphate. The unique domain architecture of NgrRnl fortifies the theme that RNA ligases have evolved many times, and independently, by fusions of a shared nucleotidyltransferase domain to structurally diverse flanking modules. The mechanistic insights to lysine adenylylation gained from the NgrRnl structures are likely to apply broadly to the covalent nucleotidyltransferase superfamily of RNA ligases, DNA ligases, and RNA capping enzymes. PMID:26512110

  20. Photoinduced Oxidative DNA Damage Revealed by an Agarose Gel Nicking Assay: A Biophysical Chemistry Laboratory Experiment

    NASA Astrophysics Data System (ADS)

    Shafirovich, Vladimir; Singh, Carolyn; Geacintov, Nicholas E.

    2003-11-01

    Oxidative damage of DNA molecules associated with electron-transfer reactions is an important phenomenon in living cells, which can lead to mutations and contribute to carcinogenesis and the aging processes. This article describes the design of several simple experiments to explore DNA damage initiated by photoinduced electron-transfer reactions sensitized by the acridine derivative, proflavine (PF). A supercoiled DNA agarose gel nicking assay is employed as a sensitive probe of DNA strand cleavage. A low-cost experimental and computer-interfaced imaging apparatus is described allowing for the digital recording and analysis of the gel electrophoresis results. The first experiment describes the formation of direct strand breaks in double-stranded DNA induced by photoexcitation of the intercalated PF molecules. The second experiment demonstrates that the addition of the well-known electron acceptor, methylviologen, gives rise to a significant enhancement of the photochemical DNA strand cleavage effect. This occurs by an electron transfer step to methylviologen that renders the inital photoinduced charge separation between photoexcited PF and DNA irreversible. The third experiment demonstrates that the action spectrum of the DNA photocleavage matches the absorption spectrum of DNA-bound, intercalated PF molecules, which differs from that of free PF molecules. This result demonstrates that the photoinduced DNA strand cleavage is initiated by intercalated rather than free PF molecules.

  1. Standard and AEGIS nicking molecular beacons detect amplicons from the Middle East respiratory syndrome coronavirus.

    PubMed

    Yaren, Ozlem; Glushakova, Lyudmyla G; Bradley, Kevin M; Hoshika, Shuichi; Benner, Steven A

    2016-10-01

    This paper combines two advances to detect MERS-CoV, the causative agent of Middle East Respiratory Syndrome, that have emerged over the past few years from the new field of "synthetic biology". Both are based on an older concept, where molecular beacons are used as the downstream detection of viral RNA in biological mixtures followed by reverse transcription PCR amplification. The first advance exploits the artificially expanded genetic information systems (AEGIS). AEGIS adds nucleotides to the four found in standard DNA and RNA (xNA); AEGIS nucleotides pair orthogonally to the A:T and G:C pairs. Placing AEGIS components in the stems of molecular beacons is shown to lower noise by preventing unwanted stem invasion by adventitious natural xNA. This should improve the signal-to-noise ratio of molecular beacons operating in complex biological mixtures. The second advance introduces a nicking enzyme that allows a single target molecule to activate more than one beacon, allowing "signal amplification". Combining these technologies in primers with components of a self-avoiding molecular recognition system (SAMRS), we detect 50 copies of MERS-CoV RNA in a multiplexed respiratory virus panel by generating fluorescence signal visible to human eye and/or camera. PMID:27421627

  2. Discovery of natural nicking endonucleases Nb.BsrDI and Nb.BtsI and engineering of top-strand nicking variants from BsrDI and BtsI.

    PubMed

    Xu, Shuang-Yong; Zhu, Zhenyu; Zhang, Penghua; Chan, Siu-Hong; Samuelson, James C; Xiao, Jianping; Ingalls, Debra; Wilson, Geoffrey G

    2007-01-01

    BsrDI and BtsI restriction endonucleases recognize and cleave double-strand DNA at the sequences GCAATG (2/0) and GCAGTG (2/0), respectively. We have purified and partially characterized these two enzymes, and analyzed the genes that encode them. BsrDI and BtsI are unusual in two respects: each cleaves DNA as a heterodimer of one large subunit (B subunit) and one small subunit (A subunit); and, in the absence of their small subunits, the large subunits behave as sequence-specific DNA nicking enzymes and only nick the bottom strand of the sequences at these respective positions: GCAATG (-/0) and GCAGTG (-/0). We refer to the single subunit, the bottom-strand nicking forms as 'hemidimers'. Amino acid sequence comparisons reveal that BsrDI and BtsI belong to a family of restriction enzymes that possess two catalytic sites: a canonical PD-X(n)-EXK and a second non-canonical PD-X(n)-E-X12-QR. Interestingly, the other family members, which include BsrI (ACTGG 1/-1) and BsmI/Mva1269I (GAATGC 1/-1) are single polypeptide chains, i.e. monomers, rather than heterodimers. In BsrDI and BtsI, the two catalytic sites are found in two separate subunits. Site-directed mutagenesis confirmed that the canonical catalytic site located at the N-terminus of the large subunit is responsible for the bottom-strand cleavage, whereas the non-canonical catalytic site located in the small subunit is responsible for hydrolysis of the top strand. Top-strand specific nicking variants, Nt.BsrDI and Nt.BtsI, were successfully engineered by combining the catalytic-deficient B subunit with wild-type A subunit. PMID:17586812

  3. Nick translation of HeLa cell nuclei as a probe for locating DNase I-sensitive nucleosomes

    SciTech Connect

    Javaherian, K.; Fasman, G.D.

    1984-03-10

    The technique of nick translation of nuclei has been used in HeLa cells to label DNase I-sensitive regions. Micrococcal nuclease digestion of the nick translated nuclei was followed by a low ionic strength gel electrophoresis system which separates different types of mononucleosomes. The major label was observed in the vicinity of high mobility group protein containing mononucleosomes. However, further analysis revealed that the particle does not sediment in the position of mononucleosomes on a sucrose gradient. Two alternative explanations are discussed as the possible source of this particle. It is either a high mobility group protein containing nucleosome in some unfolded conformation or the labeled particle originates from discrete DNA fragments, wrapped around some nonhistone proteins, located in a highly DNase I-sensitive region, which is resistant to micrococcal nuclease digestion. 36 references, 7 figures.

  4. Nicking enzyme and graphene oxide-based dual signal amplification for ultrasensitive aptamer-based fluorescence polarization assays.

    PubMed

    Huang, Yong; Liu, Xiaoqian; Zhang, Liangliang; Hu, Kun; Zhao, Shulin; Fang, Baizong; Chen, Zhen-Feng; Liang, Hong

    2015-01-15

    In this work, two different configurations for novel amplified fluorescence polarization (FP) aptasensors based on nicking enzyme signal amplification (NESA) and graphene oxide (GO) enhancement have been developed for ultrasensitive and selective detection of biomolecules in homogeneous solution. One approach involves the aptamer-target binding induced the stable hybridization between an aptamer probe and a fluorophore-labeled DNA probe linked to GO, and forms a nicking site-containing duplex DNA region due to the enhancement of base stacking. The second analytical method involves the target induced the assembly of two aptamer subunits into an aptamer-target complex, and then hybridizes with a fluorophore-labeled DNA probe linked to GO, forming a nicking site-containing duplex DNA region. The formation of the duplex DNA region in both methods triggers the NESA process, resulting in the release of many short DNA fragments carrying the fluorophore from GO, generating a significant decrease of the FP value that provides the readout signal for the amplified sensing process. By using the NESA coupled GO enhancement path, the sensitivity of the developed aptasensors can be significantly improved by four orders of magnitude over traditional aptamer-based homogeneous assays. Moreover, these aptasensors also exhibit high specificity for target molecules, which are capable of detecting target molecule in biological samples. Considering these qualities, the proposed FP aptasensors based NESA and GO enhancement can be expected to provide an ultrasensitive platform for amplified analysis of target molecules. PMID:25087158

  5. MGME1 processes flaps into ligatable nicks in concert with DNA polymerase γ during mtDNA replication

    PubMed Central

    Uhler, Jay P.; Thörn, Christian; Nicholls, Thomas J.; Matic, Stanka; Milenkovic, Dusanka; Gustafsson, Claes M.; Falkenberg, Maria

    2016-01-01

    Recently, MGME1 was identified as a mitochondrial DNA nuclease with preference for single-stranded DNA (ssDNA) substrates. Loss-of-function mutations in patients lead to mitochondrial disease with DNA depletion, deletions, duplications and rearrangements. Here, we assess the biochemical role of MGME1 in the processing of flap intermediates during mitochondrial DNA replication using reconstituted systems. We show that MGME1 can cleave flaps to enable efficient ligation of newly replicated DNA strands in combination with POLγ. MGME1 generates a pool of imprecisely cut products (short flaps, nicks and gaps) that are converted to ligatable nicks by POLγ through extension or excision of the 3′-end strand. This is dependent on the 3′-5′ exonuclease activity of POLγ which limits strand displacement activity and enables POLγ to back up to the nick by 3′-5′ degradation. We also demonstrate that POLγ-driven strand displacement is sufficient to generate DNA- but not RNA-flap substrates suitable for MGME1 cleavage and ligation during replication. Our findings have implications for RNA primer removal models, the 5′-end processing of nascent DNA at OriH, and DNA repair. PMID:27220468

  6. MGME1 processes flaps into ligatable nicks in concert with DNA polymerase γ during mtDNA replication.

    PubMed

    Uhler, Jay P; Thörn, Christian; Nicholls, Thomas J; Matic, Stanka; Milenkovic, Dusanka; Gustafsson, Claes M; Falkenberg, Maria

    2016-07-01

    Recently, MGME1 was identified as a mitochondrial DNA nuclease with preference for single-stranded DNA (ssDNA) substrates. Loss-of-function mutations in patients lead to mitochondrial disease with DNA depletion, deletions, duplications and rearrangements. Here, we assess the biochemical role of MGME1 in the processing of flap intermediates during mitochondrial DNA replication using reconstituted systems. We show that MGME1 can cleave flaps to enable efficient ligation of newly replicated DNA strands in combination with POLγ. MGME1 generates a pool of imprecisely cut products (short flaps, nicks and gaps) that are converted to ligatable nicks by POLγ through extension or excision of the 3'-end strand. This is dependent on the 3'-5' exonuclease activity of POLγ which limits strand displacement activity and enables POLγ to back up to the nick by 3'-5' degradation. We also demonstrate that POLγ-driven strand displacement is sufficient to generate DNA- but not RNA-flap substrates suitable for MGME1 cleavage and ligation during replication. Our findings have implications for RNA primer removal models, the 5'-end processing of nascent DNA at OriH, and DNA repair. PMID:27220468

  7. Optimization of a DNA Nicking Assay to Evaluate Oenocarpus bataua and Camellia sinensis Antioxidant Capacity

    PubMed Central

    Leba, Louis-Jérôme; Brunschwig, Christel; Saout, Mona; Martial, Karine; Vulcain, Emmanuelle; Bereau, Didier; Robinson, Jean-Charles

    2014-01-01

    This study was aimed at assessing the DNA damage protective activity of different types of extracts (aqueous, methanolic and acetonic) using an in vitro DNA nicking assay. Several parameters were optimized using the pUC18 plasmid, especially FeSO4, EDTA, solvent concentrations and incubation time. Special attention has been paid to removing the protective and damaging effect of the solvent and FeSO4 respectively, as well as to identifying the relevant positive and negative controls. For each solvent, the optimal conditions were determined: (i) for aqueous extracts, 0.33 mM of FeSO4 and 0.62 mM of EDTA were incubated for 20 min at 37 °C; (ii) for acetone extracts, 1.16% solvent were incubated for 15 min at 37 °C with 1.3 mM of FeSO4 and 2.5 mM of EDTA and (iii) for methanol extracts, 0.16% solvent, were incubated for 1.5 h at 37 °C with 0.33 mM of FeSO4 and 0.62 mM of EDTA. Using the optimized conditions, the DNA damage protective activity of aqueous, methanolic and acetonic extracts of an Amazonian palm berry (Oenocarpus bataua) and green tea (Camellia sinensis) was assessed. Aqueous and acetonic Oenocarpus bataua extracts were protective against DNA damage, whereas aqueous, methanolic and acetonic extracts of Camellia sinensis extracts induced DNA damage. PMID:25302614

  8. Impact of an extreme event on the sediment budget: Hurricane Andrew in the Louisiana barrier islands

    USGS Publications Warehouse

    List, Jeffrey H.; Hansen, Mark E.; Sallenger,, Asbury H., Jr.; Jaffe, Bruce E.

    1997-01-01

    This paper examines the influence of Hurricane Andrew on the sediment budget of an 80-kilometer section of the Louisiana barrier islands west of the modern Mississippi delta. Because long-term bathymetric change has been extensively studied in this area, excellent baseline data are available for evaluating the impact of Hurricane Andrew. Results show that despite the high intensity of the storm and a storm track optimally positioned to impact the study area, the storm did not have an overwhelming influence on the sediment budget when compared to the changes occurring over the previous 50 years. For the Louisiana barrier islands, a 50-year record appears to be adequate for averaging the long-term contributions of both major and minor storm events to the sediment budget.

  9. Analyzing after-action reports from Hurricanes Andrew and Katrina: repeated, modified, and newly created recommendations.

    PubMed

    Knox, Claire Connolly

    2013-01-01

    Thirteen years after Hurricane Andrew struck Homestead, FL, Hurricane Katrina devastated the Gulf Coast of Mississippi, Alabama, and southeastern Louisiana. Along with all its destruction, the term "catastrophic" was redefined. This article extends the literature on these hurricanes by providing a macrolevel analysis of The Governor's Disaster Planning and Response Review Committee Final Report from Hurricane Andrew and three federal after-action reports from Hurricane Katrina, as well as a cursory review of relevant literature. Results provide evidence that previous lessons have not been learned or institutionalized with many recommendations being repeated or modified. This article concludes with a discussion of these lessons, as well as new issues arising during Hurricane Katrina. PMID:24180096

  10. Kinetic mechanism of nick sealing by T4 RNA ligase 2 and effects of 3′-OH base mispairs and damaged base lesions

    PubMed Central

    Chauleau, Mathieu; Shuman, Stewart

    2013-01-01

    T4 RNA ligase 2 (Rnl2) repairs 3′-OH/5′-PO4 nicks in duplex nucleic acids in which the broken 3′-OH strand is RNA. Ligation entails three chemical steps: reaction of Rnl2 with ATP to form a covalent Rnl2–(lysyl-Nζ)–AMP intermediate (step 1); transfer of AMP to the 5′-PO4 of the nick to form an activated AppN– intermediate (step 2); and attack by the nick 3′-OH on the AppN– strand to form a 3′–5′ phosphodiester (step 3). Here we used rapid mix-quench methods to analyze the kinetic mechanism and fidelity of single-turnover nick sealing by Rnl2–AMP. For substrates with correctly base-paired 3′-OH nick termini, kstep2 was fast (9.5 to 17.9 sec−1) and similar in magnitude to kstep3 (7.9 to 32 sec−1). Rnl2 fidelity was enforced mainly at the level of step 2 catalysis, whereby 3′-OH base mispairs and oxoguanine, oxoadenine, or abasic lesions opposite the nick 3′-OH elicited severe decrements in the rate of 5′-adenylylation and relatively modest slowing of the rate of phosphodiester synthesis. The exception was the noncanonical A:oxoG base pair, which Rnl2 accepted as a correctly paired end for rapid sealing. These results underscore (1) how Rnl2 requires proper positioning of the 3′-terminal ribonucleoside at the nick for optimal 5′-adenylylation and (2) the potential for nick-sealing ligases to embed mutations during the repair of oxidative damage. PMID:24158792

  11. 21. View of Andrew McLean Company Textile Mill looking west; ...

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

    21. View of Andrew McLean Company Textile Mill looking west; Building No. 4 at left, Building No. 1 at left center, Building No. 3 at center, Building No. 2 at right center, Building No. 5 at right - Dundee Canal Industrial Historic District, Beginning at George Street in Passaic & extending north along Dundee Canal approximately 1.2 miles to Canal headgates opposite East Clifton Avenue in Clifton, Passaic, Passaic County, NJ

  12. Andrew Wyeth and N.C. Wyeth: a psychodynamic perspective on father and son.

    PubMed

    Shaw, Jon A

    2013-01-01

    This paper examines the relationship between two extraordinary artists, father and son--N.C. Wyeth (1882-1945) and Andrew Wyeth (1917-2009)--and their art. N.C. Wyeth, the father, the most famous illustrator of his day, painted scenes full of drama and action, often of men engaged in violent life and death struggles. N.C. was unable to separate from his powerful mother and yearned for his iconic father. He thought himself an artistic failure and dedicated himself to raising his children to be geniuses. The youngest son, Andrew Wyeth, who lived a "secret life," painted scenes often characterized by pathos: bleak and barren landscapes, leaden skies, tire tracks, gray framed houses, desiccated fields, and circling buzzards. In the father-son relationship, we often seen three themes perpetuated developmentally: (1) the son's identification with the innermost conflicts of his father; (2) the yearning for the iconic father of his youth; and (3) a continuation and disavowal of his father's life. These themes are played out in the relationship between Andrew Wyeth and his father. PMID:23965259

  13. 78 FR 6173 - Diana Del Grosso, Ray Smith, Joseph Hatch, Cheryl Hatch, Kathleen Kelley, Andrew Wilklund, and...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-29

    ... From the Federal Register Online via the Government Publishing Office ] DEPARTMENT OF TRANSPORTATION Surface Transportation Board Diana Del Grosso, Ray Smith, Joseph Hatch, Cheryl Hatch, Kathleen... Smith, Joseph Hatch, Cheryl Hatch, Kathleen Kelley, Andrew Wilklund, and Richard Kosiba...

  14. Wireless Andrew.

    ERIC Educational Resources Information Center

    Fickes, Michael

    2000-01-01

    Describes the use of the Internet and laptops help Carnegie Mellon University students carry out sophisticated research anywhere on campus. How the university became a wireless community is discussed. (GR)

  15. Structure-based functional identification of Helicobacter pylori HP0268 as a nuclease with both DNA nicking and RNase activities

    PubMed Central

    Lee, Ki-Young; Lee, Kyu-Yeon; Kim, Ji-Hun; Lee, In-Gyun; Lee, Sung-Hee; Sim, Dae-Won; Won, Hyung-Sik; Lee, Bong-Jin

    2015-01-01

    HP0268 is a conserved, uncharacterized protein from Helicobacter pylori. Here, we determined the solution structure of HP0268 using three-dimensional nuclear magnetic resonance (NMR) spectroscopy, revealing that this protein is structurally most similar to a small MutS-related (SMR) domain that exhibits nicking endonuclease activity. We also demonstrated for the first time that HP0268 is a nicking endonuclease and a purine-specific ribonuclease through gel electrophoresis and fluorescence spectroscopy. The nuclease activities for DNA and RNA were maximally increased by Mn2+ and Mg2+ ions, respectively, and decreased by Cu2+ ions. Using NMR chemical shift perturbations, the metal and nucleotide binding sites of HP0268 were determined to be spatially divided but close to each other. The lysine residues (Lys7, Lys11 and Lys43) are clustered and form the nucleotide binding site. Moreover, site-directed mutagenesis was used to define the catalytic active site of HP0268, revealing that this site contains two acidic residues, Asp50 and Glu54, in the metal binding site. The nucleotide binding and active sites are not conserved in the structural homologues of HP0268. This study will contribute to improving our understanding of the structure and functionality of a wide spectrum of nucleases. PMID:25916841

  16. Activation of Aryl Halides by Nickel(I) Pincer Complexes: Reaction Pathways of Stoichiometric and Catalytic Dehalogenations.

    PubMed

    Rettenmeier, Christoph A; Wenz, Jan; Wadepohl, Hubert; Gade, Lutz H

    2016-08-15

    Homolytic C-X bond cleavage of organohalides by the T-shaped nickel(I) complexes [LigNi(I)] 1 bearing the iso-PyrrMeBox ligand had been found previously to be the crucial activation step in the asymmetric hydrodehalogenation of geminal dihalides. Here, this mechanistic investigation is extended to aryl halides, which allowed a systematic study of the activation process by a combination of experimental data and density functional theory modeling. While the activation of both aryl chlorides and geminal dichlorides appears to proceed via an analogous transition state, the generation of a highly stabile nickel(II)aryl species in the reaction of the aryl chlorides for the former represents a major difference in the reactive behavior. This difference was found to have a crucial impact on the activity of these nickel pincer systems as catalysts in the dehalogenation of aryl chlorides compared to geminal dichlorides and highlights the importance of the regulatory pathways controlling the nickel(I) concentration throughout the catalysis. These results along with the identification and characterization of novel nickel(II)aryl species are presented. PMID:27483018

  17. Management of Oro-Nasal Fistula Using Andrew's Bridge: A Case Report.

    PubMed

    Harish, P V; Bhojaraju, Nandakishore; Sowmya, G R; Gangaiah, Makam

    2014-09-01

    Oro-nasal fistula is the most common complication following the surgical closure of the cleft palate. Retention is the paramount factor in the successful prosthodontic habilitation of cleft palate patients. Various precision attachments have provided us with the opportunity to make the prosthesis fixed removable type; giving a double advantage to the patient i.e. comfort through fixed type and easy maintenance through removal type. This case report describes a case of oro-nasal fistula habilitated with an obturator attached to Andrew's bridge, which had good retention and esthetics. PMID:25183920

  18. Astronaut Andrew S. W. Thomas, mission specialist, interrupts a Spacehab task to pose for an

    NASA Technical Reports Server (NTRS)

    1996-01-01

    STS-77 ESC VIEW --- Astronaut Andrew S. W. Thomas, mission specialist, interrupts a Spacehab task to pose for an Electronic Still Camera (ESC) snapshot inside the Spacehab Module onboard the Earth-orbiting Space Shuttle Endeavour. In upper left is the view port which crew members had used for viewing and photographing operations with the Spartan 207/Inflatable Antenna Experiment (IAE). Thomas has his hand on an aft-bulkhead-mounted locker. The Space Experiment Facility (SEF), designed and managed by the University of Alabama, is just behind his left shoulder.

  19. A comment on Andrew C. Papanicolaou's "Beyond Eddington's argument": pragmatism in scientific knowledge and perception.

    PubMed

    Kono, Tetsuya

    2015-03-01

    I agree with Andrew C. Papanicolaou's claim that human beings' cognitive ability can reach to the real world, but don't agree with his claim that the order of this world is akin to our thought. In this commentary paper, I will first defend a recent pragmatic scientific realism called as "entity realism" or "referential realism" which affirms that we are able to reach the real world not by inference but by technological, engineering settings. In the second half of this paper, I will also affirm that our perceptual ability directly reaches the reality too, in referring to the ecological psychology of James J. Gibson. PMID:24986382

  20. Delayed tree mortality in the Atchafalaya Basin of Southern Louisiana following Hurricane Andrew

    USGS Publications Warehouse

    Keeland, B.D.; Gorham, L.E.

    2009-01-01

    Hurricanes can damage trees in forested wetlands, and the potential for mortality related to these storms exists due to the effects of tree damage over time. In August 1992, Hurricane Andrew passed through the forested wetlands of southern Louisiana with winds in excess of 225 kph. Although more than 78 of the basal area was destroyed in some areas, most trees greater than 2.5 cm dbh were alive and resprouting prolifically the following year (98.8). Survival of most tree species was similarly high two years after the hurricane, but mortality rates of some species increased dramatically. For example, Populus heterophylla (swamp cottonwood) mortality increased from 7.8 to 59.2 (n 76) and Salix interior (sandbar willow) mortality increased from 4.5 to 57.1 (n 21). Stem sprouts on many up-rooted hardwood trees of other species were still alive in 1998, 6 years after the hurricane. Due to the understory tree species composition, regeneration, and high levels of resprouting, there was little change in species composition or perhaps a slight shift toward more shade and flood tolerant species six years following the hurricane event. Triadica sebifera (Chinese tallow) was found on some of the sites heavily disturbed by Hurricane Andrew, and may proliferate at the expense of native tree species. ?? 2009 The Society of Wetland Scientists.

  1. ANDREWES'S CHRISTMAS FAIRY TALE: ATYPICAL THINKING ABOUT CANCER AETIOLOGY IN 1935.

    PubMed

    Sankaran, Neeraja; van Helvoort, Ton

    2016-06-20

    This paper uses a short 'Christmas fairy-story for oncologists' sent by Christopher Andrewes with a 1935 letter to Peyton Rous as the centrepiece of a reflection on the state of knowledge and speculation about the viral aetiology of cancer in the 1930s. Although explicitly not intended for public circulation at the time, the fairy-story merits publication for its significance in the history of ideas about viruses, which are taken for granted today. Andrewes and Rous were prominent members of the international medical research community and yet faced strong resistance to their theory that viruses could cause such tumours as chicken sarcomas and rabbit papillomas. By looking at exchanges between these men among themselves and other proponents of their theories and with their oncologist detractors, we highlight an episode in the behind-the-scenes workings of medical science and show how informal correspondence helped keep alive a vital but then heterodox idea about the role of viruses in causing cancer. PMID:27386716

  2. Ecological evaluation of proposed dredged material from St. Andrew Bay, Florida

    SciTech Connect

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

    1993-10-01

    The US Army Corps of Engineers (USACE), Mobile District, requested that the Battelle/Marine Sciences Laboratory (MSL) conduct field sampling and chemical and biological testing to determine the suitability of potential dredged material for open ocean disposal. Sediment from St. Andrew Bay was chemically characterized and evaluated for biological toxicity and bioaccumulation of contaminants. The Tier III guidance for ocean disposal testing requires tests of water column effects (following dredged material disposal), deposited sediment toxicity, and bioaccumulation of contaminants from deposited sediment (dredged material). To meet these requirements, the MSL conducted suspended-particulate-phase (SPP) toxicity tests, solid-phase toxicity tests, and bioaccumulation testing on sediment representing potential dredged material from Panama City Harbor. Physical and chemical characterization of sediment to support toxicity and bioaccumulation results was also conducted on both the test and reference sediments. The MSL collected sediment samples from five sites in St. Andrew Bay and one reference site near Lands End Peninsula. The five test sediments and the reference sediment were analyzed for physical and chemical sediment characteristics, SPP chemical contaminants, solid-phase toxicity, SPP toxicity, and bioaccumulation of contaminants.

  3. James Gregory, the University observatory and the early acquisition of scientific instruments at the University of St Andrews

    PubMed Central

    Rawson, Helen C.

    2015-01-01

    James Gregory, inventor of the reflecting telescope and Fellow of the Royal Society, was the first Regius Professor of Mathematics of the University of St Andrews, 1668–74. He attempted to establish in St Andrews what would, if completed, have been the first purpose-built observatory in the British Isles. He travelled to London in 1673 to purchase instruments for equipping the observatory and improving the teaching and study of natural philosophy and mathematics in the university, seeking the advice of John Flamsteed, later the first Astronomer Royal. This paper considers the observatory initiative and the early acquisition of instruments at the University of St Andrews, with reference to Gregory's correspondence, inventories made ca. 1699–ca. 1718 and extant instruments themselves, some of which predate Gregory's time. It examines the structure and fate of the university observatory, the legacy of Gregory's teaching and endeavours, and the meridian line laid down in 1748 in the University Library.

  4. Bioassay-guided isolation of novel compound from Paeonia suffruticosa Andrews roots as an IL-1β inhibitor.

    PubMed

    Choi, Yun-Hyeok; Yoo, Hee-Jung; Noh, Ill Chan; Lee, Jeong-Min; Park, Jae Won; Choi, Wahn Soo; Choi, Jung Ho

    2012-05-01

    The inhibition of Interleukin-1beta (IL-1β) is of substantial interest for the treatment of rheumatoid arthritis. Using an in vitro assay with RAW 264.7 cells, oxo-acetic acid 2-ethoxy-4-(3-hydroxy-2-oxopropyl) phenyl ester (1) was isolated from the roots of Paeonia suffruticosa Andrews as an inhibitor of IL-1β with an IC(50) value of 56 μM. Compound 1 is a novel phenylesteric compound from P. suffruticosa Andrews. Compound 1 was shown to inhibit the production of pro-inflammatory cytokines in RAW 264.7 cells. Thus, a possible new action of novel compound is provided explaining the anti-rheumatoid arthritic properties of P. suffruticosa Andrews. PMID:22644848

  5. Genome Editing in Mouse Spermatogonial Stem Cell Lines Using TALEN and Double-Nicking CRISPR/Cas9.

    PubMed

    Sato, Takuya; Sakuma, Tetsushi; Yokonishi, Tetsuhiro; Katagiri, Kumiko; Kamimura, Satoshi; Ogonuki, Narumi; Ogura, Atsuo; Yamamoto, Takashi; Ogawa, Takehiko

    2015-07-14

    Mouse spermatogonial stem cells (SSCs) can be cultured for multiplication and maintained for long periods while preserving their spermatogenic ability. Although the cultured SSCs, named germline stem (GS) cells, are targets of genome modification, this process remains technically difficult. In the present study, we tested TALEN and double-nicking CRISPR/Cas9 on GS cells, targeting Rosa26 and Stra8 loci as representative genes dispensable and indispensable in spermatogenesis, respectively. Harvested GS cell colonies showed a high targeting efficiency with both TALEN and CRISPR/Cas9. The Rosa26-targeted GS cells differentiated into fertility-competent sperm following transplantation. On the other hand, Stra8-targeted GS cells showed defective spermatogenesis following transplantation, confirming its prime role in the initiation of meiosis. TALEN and CRISPR/Cas9, when applied in GS cells, will be valuable tools in the study of spermatogenesis and for revealing the genetic mechanism of spermatogenic failure. PMID:26095606

  6. A flavin-mononucleotide-binding site in Hansenula anomala nicked flavocytochrome b2, requiring the association of two domains.

    PubMed

    Gervais, M; Labeyrie, F; Risler, Y; Vergnes, O

    1980-10-01

    Previous experiments in our laboratory with Saccharomyces cervisiae flavocytochrom b2 indicated that both fragments alpha and beta of the enzyme after cleavage by yeast proteases are required to form the flavin site. More detailed experiments have not been carried out on the nicked Hansenula anomala enzyme obtained by tryptic cleavage. A method has been devised that gives a quantitative separation in 4 M urea of beta, and alpha with its heme still bound. The characteristics of the various species: isolated alpha and beta and mixed alpha + beta were studied in 4 M urea and after elimination of this reagent by dialysis in the presence of FMN and 2-mercaptoethanol. Several methods, including heme spectroscopy, tryptophan fluorescence, sedimentation studies, and titration of bound flavin, were used. The results indicate that isolated alpha and beta have a folded globular structure after renaturation. The flavin binding to the alpha + beta mixture was important (50-100%) with recovery of the flavodehydrogenase activity. In contrast, binding was not detectable (< 0.5%, Kf > 10 mM) for isolated alpha and beta. As far as mononucleotide binding is concerned, such a cooperative requirement for two folding domains has never been reported in other enzymes. The present results are discussed together with others obtained in our laboratory which demonstrate that, as deduced from their sensitivity to trypsin, the structure of S. cerevisiae and H. anomala flavocytochrome b2 protomers is triglobular 'n-x-beta' (n and x combined within alpha). The tetramer assembly, which remains intact as a nicked enzyme (alpha beta)4 after the first trypsin cleavage, is broken down following a second cleavage of the chain into four cytochrome cores (n) and a functional T-flavodehydrogenase entity, a tetramer of the type (x beta)4. PMID:7439181

  7. 33 CFR 334.680 - Gulf of Mexico, southeast of St. Andrew Bay East Entrance, small-arms firing range, Tyndall Air...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 3 2014-07-01 2014-07-01 false Gulf of Mexico, southeast of St... AND RESTRICTED AREA REGULATIONS § 334.680 Gulf of Mexico, southeast of St. Andrew Bay East Entrance... the Gulf of Mexico, southeast of St. Andrew Bay East Entrance within a rectangular area beginning at...

  8. 33 CFR 334.680 - Gulf of Mexico, southeast of St. Andrew Bay East Entrance, small-arms firing range, Tyndall Air...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 3 2013-07-01 2013-07-01 false Gulf of Mexico, southeast of St... AND RESTRICTED AREA REGULATIONS § 334.680 Gulf of Mexico, southeast of St. Andrew Bay East Entrance... the Gulf of Mexico, southeast of St. Andrew Bay East Entrance within a rectangular area beginning at...

  9. 33 CFR 334.680 - Gulf of Mexico, southeast of St. Andrew Bay East Entrance, small-arms firing range, Tyndall Air...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 3 2012-07-01 2012-07-01 false Gulf of Mexico, southeast of St... AND RESTRICTED AREA REGULATIONS § 334.680 Gulf of Mexico, southeast of St. Andrew Bay East Entrance... the Gulf of Mexico, southeast of St. Andrew Bay East Entrance within a rectangular area beginning at...

  10. 33 CFR 334.680 - Gulf of Mexico, southeast of St. Andrew Bay East Entrance, small-arms firing range, Tyndall Air...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 3 2011-07-01 2011-07-01 false Gulf of Mexico, southeast of St... AND RESTRICTED AREA REGULATIONS § 334.680 Gulf of Mexico, southeast of St. Andrew Bay East Entrance... the Gulf of Mexico, southeast of St. Andrew Bay East Entrance within a rectangular area beginning at...

  11. 33 CFR 334.680 - Gulf of Mexico, southeast of St. Andrew Bay East Entrance, small-arms firing range, Tyndall Air...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 3 2010-07-01 2010-07-01 false Gulf of Mexico, southeast of St... AND RESTRICTED AREA REGULATIONS § 334.680 Gulf of Mexico, southeast of St. Andrew Bay East Entrance... the Gulf of Mexico, southeast of St. Andrew Bay East Entrance within a rectangular area beginning at...

  12. Prosthetic rehabilitation of severe Siebert's Class III defect with modified Andrews bridge system.

    PubMed

    Rathee, Manu; Sikka, Neha; Jindal, Sahil; Kaushik, Ashutosh

    2015-03-01

    Prosthetic dentistry involves the replacement of missing and contiguous tissues with artificial substitutes to restore and maintain the oral functions, appearance, and health of the patient. The treatment of edentulous areas with ridge defects poses a challenging task for the dentist. Management of such cases involves a wide range of treatment options comprising mainly of surgical interventions and non surgical techniques such as use of removable, fixed or fixed- removable partial dentures. But each treatment plan undertaken should be customized according to patient needs. A variety of factors such as quality and quantity of existing contiguous hard and soft tissues, systemic condition and economic status of the patient play an important role in treatment planning, clinical outcome and prognosis. This case report presents the restoration of a Seibert's Class III ridge defect by an economical modification of Andrews Bridge in a 32 Year old patient. PMID:25821362

  13. Protocols for Biotechnological Interventions in Improvement of Vanilla (Vanilla planifolia Andrews.).

    PubMed

    Divakaran, Minoo; Babu, K Nirmal; Peter, K V

    2016-01-01

    Vanilla (Vanilla planifolia Andrews (syn. V. fragrans Salisb.), a native of Central America, is the primary source of natural vanillin and plays a major role in the global economy. The gene pool of vanilla is threatened by deforestation and overcollection that has resulted in disappearance of natural habitats and wild species. Continuous vegetative propagation and lack of natural seed set and sufficient variations in the gene pool hamper crop improvement programs. In vitro techniques, one of the key tools of plant biotechnology, can be employed for overcoming specific problems, viz. production of disease-free clones, inducing somaclonal variations, developing hybrids, gene pool conservation, incorporating desired traits by distant hybridization, genetic engineering, etc. However, realization of these objectives necessitates standardization of protocols. This chapter describes the various protocols optimized for crop improvement in Vanilla species. PMID:27108309

  14. The post-disaster negative health legacy: pregnancy outcomes in Louisiana after Hurricane Andrew.

    PubMed

    Antipova, Anzhelika; Curtis, Andrew

    2015-10-01

    Disasters and displacement increasingly affect and challenge urban settings. How do pregnant women fare in the aftermath of a major disaster? This paper investigates the effect of pregnancies in disaster situations. The study tests a hypothesis that pregnant women residing in hurricane-prone areas suffer higher health risks. The setting is Louisiana in the Gulf Coast, United States, a state that continually experiences hurricane impacts. The time period for the analysis is three years following the landfall of Hurricane Andrew in 1992. We analysed low birth weight and preterm deliveries before and after landfall, as a whole and by race. Findings support an association between hazards and health of a community and indicate that pregnant women in the affected area, irrespective of race, are more likely to experience preterm deliveries compared to pre-event births. Results suggest there is a negative health legacy impact in Louisiana as a result of hurricane landfall. PMID:25754615

  15. Comprehensive assessment of health needs 2 months after Hurricane Andrew--Dade County, Florida, 1992.

    PubMed

    1993-06-11

    On August 24, 1992, Hurricane Andrew struck southern Florida. More than 28,000 houses, mobile homes, and apartment buildings were destroyed, and approximately 107,000 additional dwellings sustained major damage. An estimated 180,000 persons were left homeless; insured damages were estimated at $15.5 billion and total damages at more than $30 billion. During the recovery period, many private and public health-care facilities damaged or destroyed in the storm were not functional. During November 3-13, to help prioritize health needs and direct public health resources, the Dade County Public Health Unit of the Florida Department of Health and Rehabilitative Services conducted a survey to assess health needs and the availability of health-care services during the recovery phase with funds provided by the Federal Emergency Management Agency (FEMA). This report summarizes the results of the survey. PMID:8502216

  16. Business closure and relocation: a comparative analysis of the Loma Prieta earthquake and Hurricane Andrew.

    PubMed

    Wasileski, Gabriela; Rodríguez, Havidán; Diaz, Walter

    2011-01-01

    The occurrence of a number of large-scale disasters or catastrophes in recent years, including the Indian Ocean tsunami (2004), the Kashmir earthquake (2005), Hurricane Katrina (2005) and Hurricane Ike (2008), have raised our awareness regarding the devastating effects of disasters on human populations and the importance of developing mitigation and preparedness strategies to limit the consequences of such events. However, there is still a dearth of social science research focusing on the socio-economic impact of disasters on businesses in the United States. This paper contributes to this research literature by focusing on the impact of disasters on business closure and relocation through the use of multivariate logistic regression models, specifically focusing on the Loma Prieta earthquake (1989) and Hurricane Andrew (1992). Using a multivariate model, we examine how physical damage to the infrastructure, lifeline disruption and business characteristics, among others, impact business closure and relocation following major disasters. PMID:20722689

  17. The Relationship of MacAndrew Alcoholism Scale Scores to MMPI Profile Type and Degree of Elevation.

    ERIC Educational Resources Information Center

    Pfost, Karen S.; And Others

    1984-01-01

    Investigated the relationship of the MacAndrew Alcoholism Scale (MAC) to personality type and level of emotional distress using Minnesota Multiphasic Personality Inventory scores of 38 alcoholic males. No relationship was found between the MAC and magnitude of psychological distress, as measured by T scores. (JAC)

  18. 75 FR 81637 - Endangered and Threatened Wildlife and Plants; Notice of Availability of the St. Andrew Beach...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-28

    ... (63 FR 70053). The endangered St. Andrew beach mouse is now found in two populations: East Crooked... recovery plan available for public comment from April 22, 2009 through June 22, 2009 (74 FR 18403). We... feral cats and hogs in beach mouse habitat. 4. In areas with known populations of beach mice...

  19. Should Community College Be Free? Forum. "Education Next" Talks with Sara Goldrick-Rab and Andrew P. Kelly

    ERIC Educational Resources Information Center

    Goldrick-Rab, Sara; Kelly, Andrew P.

    2016-01-01

    In this article, "Education Next" talks with Sara Goldrick-Rab and Andrew Kelly. President Obama's proposal for tuition-free community college, seems to have laid down a marker for the Democratic Party. Vermont senator Bernie Sanders is touting his plan for free four-year public college on the primary trail; Massachusetts senator…

  20. 77 FR 15600 - Special Local Regulation; Emerald Coast Super Boat Grand Prix; Saint Andrew Bay; Panama City, FL

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-16

    ...The Coast Guard is establishing a temporary special local regulation for a portion of Saint Andrew Bay, Panama City, FL. This action is necessary for the safeguard of participants and spectators, including all crews, vessels, and persons on navigable waters during the Emerald Coast Super Boat Grand Prix high speed boat races. Entry into, transiting in or anchoring in this area is prohibited to......

  1. A Comparison of Two Procedures, the Mahalanobis Distance and the Andrews-Pregibon Statistic, for Identifying Multivariate Outliers.

    ERIC Educational Resources Information Center

    Jarrell, Michele Glankler

    This repeated measures factorial design study compared the results of two procedures for identifying multivariate outliers under varying conditions, the Mahalanobis distance and the Andrews-Pregibon statistic. Results were analyzed for the total number of outliers identified and number of false outliers identified. Simulated data were limited to…

  2. A Comparison of Two Procedures, the Mahalanobis Distance and the Andrews-Pregibon Statistic, for Identifying Multivariate Outliers.

    ERIC Educational Resources Information Center

    Jarrell, Michele Glanker

    1994-01-01

    Computer simulations used to compare the Mahalanobis distance procedure with the Andrews-Pregibon statistic for identifying multivariate outliers result in the conclusion that the choice of procedure is not critical, since both identified valid data points as outliers. Results with false outliers as the dependent variable suggest the importance of…

  3. [The Andrew Heiskell Library for the Blind and Physically Handicapped.] A Library with a Difference. Projects and Experiments.

    ERIC Educational Resources Information Center

    Jarkon, Joe; Fitzpatrick, Vicki, Ed.

    This publication describes the Andrew Heiskell Library for the Blind and Physically Handicapped, a regional library for the National Library Service (NLS) example of the creative use of physical space and innovative technology. The publication focuses on the materials-handling system designed for the new facility, including system design…

  4. Highly Selective and Sensitive Electrochemiluminescence Biosensor for p53 DNA Sequence Based on Nicking Endonuclease Assisted Target Recycling and Hyperbranched Rolling Circle Amplification.

    PubMed

    Yang, Linlin; Tao, Yingzhou; Yue, Guiyin; Li, Ruibao; Qiu, Bin; Guo, Longhua; Lin, Zhenyu; Yang, Huang-Hao

    2016-05-17

    An ultrasensitive and specific electrochemiluminescence (ECL) biosensor has been designed for the p53 DNA sequence, which is based on cascade signal amplification of nicking endonuclease assisted target recycling and hyperbranched rolling circle amplification (HRCA). First of all, biotin modified hairpin capture DNA (HP) probe was immobilized on the surface of streptavidin magnespheres paramagnetic particles (PMPs). Target DNA hybridized with the loop portion of the HP probe, therefore unfolding HP to form a double-stranded DNA (dsDNA) containing the specific nicking site of the nicking endonuclease. Then, the nicking endonuclease recognized the specific nicking site and cleaved the HP into two pieces, liberating target DNA and the complementary sequence piece for the padlock probe. The intact target DNA would initiate the next cycle of hybridization and cleavage, thereby releasing multiple complementary sequences for the padlock probes. The liberated complementary sequences hybridized with the padlock probes, subsequently inducing the HRCA reaction and generating numerous dsDNA segments. Herein, Ru(phen)3(2+) was embedded into dsDNA and worked as ECL signal reporter. The reaction products were eventually pretreated by dialysis tube with the cutoff membrane to remove the residual Ru(phen)3(2+) in the solution for the following ECL measurements. Using this cascade amplification strategy, an ultrasensitive p53 DNA sequence detection method was developed with a wide linear range from 0.05 to 100 fM and a low detection limit of 0.02 fM. Moreover, this cascade amplified ECL biosensor had specific recognition capacity for noncomplementary and single- and double-base mismatched DNA. The proposed ECL biosensor might have a great potential in biomedical research and clinic analysis. PMID:27086663

  5. Directional mapping of DNA nicking in ejaculated and cauda epididymidal spermatozoa of the short-beaked echidna (Tachyglossus aculeatus: Monotremata).

    PubMed

    Johnston, S D; López-Fernández, C; Gosálbez, A; Holt, W V; Gosálvez, J

    2009-01-01

    Prototherian spermatozoa are unique amongst the Mammalia in terms of their filiform morphology, tandem arrangement of chromosomes and formation of sperm bundles. In the present study, we provide observations of echidna spermatozoa and note that the superstructure of the bundle is engineered around the shape of the individual sperm head and that this in turn may be a consequence of the unusual circumferential and helicoidal condensation of the DNA during spermiogenesis. Frozen-thawed ejaculated echidna spermatozoa were incubated and examined for the presence of non-typical DNA conformation by means of in situ labelling of DNA breaks using Klenow polymerase and via alkaline single-cell comet assays for detection of fragmented DNA. Both techniques successfully revealed the presence of what appeared to be directional DNA nicking, co-localised with the presence of highly sensitive alkali sites along the length of the sperm nucleus. It was not possible to define whether these alternative DNA configurations were associated with a failure of the sperm nucleus to condense appropriately during spermiogenesis or were evidence of DNA fragmentation following post-thaw incubation or a sequential structural chromatin rearrangement necessary for fertilisation. PMID:19874725

  6. Storm-tide elevations produced by Hurricane Andrew along the southern Florida coasts, August 24, 1992

    USGS Publications Warehouse

    Murray, Mitchell H.

    1994-01-01

    On August 24, 1992, Hurricane Andrew crossed southern peninsular Florida. The combined effects of storm surge from the hurricane and astronomical tide, referred to as storm tide, caused flooding over a large part of southern Florida. Subsequent to the flooding, many high-water marks were identified, described, and surveyed along the south- eastern coast of Florida (Miami to Key Largo) and at selected areas along the southwestern coast of Florida (Flamingo to Goodland). Descriptions of these 336 high-water makrs are presented in tabular form in this report and their locations are plotted on nineteen 7.5-minute topographic quadrangle maps. For the southeastern coast, north-south profiles of the high-water makrs along the outher and inner barrier islands and the western shoreline of Biscayne Bay are presented. Average storm-tide elevations (relative to sea level) ranged from 4 to 6 feet in northern Biscayne Bay, were as much as 17 feet on the western shoreline near the center of the bay and ranged from 3 to 6 feet in southern Biscayne Bay and Barnes Sound. Storm-tide elevations along the southwestern coast ranged from 4 to 5 feet at Flamingo and 5 to 7 feet at Goodland in the Ten Thousand Islands area.

  7. Genomewide scan for adaptive differentiation along altitudinal gradient in the Andrew's toad Bufo andrewsi.

    PubMed

    Guo, Baocheng; Lu, Di; Liao, Wen Bo; Merilä, Juha

    2016-08-01

    Recent studies of humans, dogs and rodents have started to discover the genetic underpinnings of high altitude adaptations, yet amphibians have received little attention in this respect. To identify possible signatures of adaptation to altitude, we performed a genome scan of 15 557 single nucleotide polymorphisms (SNPs) obtained with restriction site-associated DNA sequencing of pooled samples from 11 populations of Andrew's toad (Bufo andrewsi) from the edge of the Tibetan Plateau, spanning an altitudinal gradient from 1690 to 2768 m.a.s.l. We discovered significant geographic differentiation among all sites, with an average FST   = 0.023 across all SNPs. Apart from clear patterns of isolation by distance, we discovered numerous outlier SNPs showing strong associations with variation in altitude (1394 SNPs), average annual temperature (1859 SNPs) or both (1051 SNPs). Levels and patterns of genetic differentiation in these SNPs were consistent with the hypothesis that they have been subject to directional selection and reflect adaptation to altitudinal variation among the study sites. Genes with footprints of selection were significantly enriched in binding and metabolic processes. Several genes potentially related to high altitude adaptation were identified, although the identity and functional significance of most genomic targets of selection remain unknown. In general, the results provide genomic support for results of earlier common garden and low coverage genetic studies that have uncovered substantial adaptive differentiation along altitudinal and latitudinal gradients in amphibians. PMID:27289071

  8. Simulation of Water Balance and Forest Treatment Effects at the H.J. Andrews Experimental Forest

    SciTech Connect

    Waichler, Scott R.; Wemple, Beverley C.; Wigmosta, Mark S.

    2005-10-30

    The watershed model DHSVM was applied to the small watersheds WS1,2,3 in H.J. Andrews Experimental Forest (HJA), Oregon and tested for skill in simulating observed forest treatment effects on streamflow. These watersheds in the rain-snow transition zone underwent road and clearcut treatments during 1959-66 and subsequent natural regeneration. DHSVM was applied with 10 m and 1 hr resolution to 1958-98, most of the period of record. Water balance for old-growth WS2 indicated that evapotranspiration and streamflow were unlikely to be the only loss terms, and groundwater recharge was included to account for about 12% of precipitation; this term was assumed zero in previous studies. After limited calibration, overall efficiency in simulating hourly streamflow exceeded 0.7, and mean annual error was less than 10%. Model skill decreased at the margins, with overprediction of low flows and underprediction of high flows. However, statistical analyses of simulated and observed peakflows yielded similar characterizations of treatment effects. Primary simulation weaknesses were snowpack accumulation, snowmelt under rain-on-snow conditions, and production of quickflow. This challenging test of DHSVM moved the model closer to a practical tool for forest management.

  9. Unsaturated flow modeling for performance assessment of a radioactive waste disposal facility in Andrews County, Texas

    NASA Astrophysics Data System (ADS)

    Martinez Baquero, G. F.; Singh, A.; Holt, R. M.; grisak, G. E.

    2011-12-01

    Quantitifying infiltration rates is a key component of the performance assessment for radioactive waste disposal facilities. In arid regions with scarce infiltration data, this is a challenging problem because of the computational limitations of available numerical implementations to solve water flow and transport equations. This work summarizes methodology and analysis performed to overcome some of these challenges and to generate infiltration scenarios for a low level waste disposal site in Andrews County, Texas. The work presented here includes preparation of a two dimensional finite element model in HYDRUS that includes the cover system and adjacent geologic units, calibration of hydraulic properties and root water uptake parameters based on soft information, preparation of atmospheric forcings based on current and hypothesized future climatic conditions, evaluation of impacts related to temporal and spatial discretization of forcings and model domain, and definition of scenarios for cover degradation and wetter climate conditions. Results of this work include a sensitivity analysis of infiltration rates to changes in boundary conditions under quasi-steady state, evaluation of the impact of temporal discretization of the atmospheric forcings in terms of water balance error and computational efficiency, and the estimation of infiltration rates under different scenarios. Infiltration rates from this work are being incorporated into a transport model to estimate potential radiological doses based on performance assessment modeling analyses. Findings from this work seek to contribute towards robust approaches to estimate infiltration in arid regions.

  10. A single catalytic domain of the junction-resolving enzyme T7 endonuclease I is a non-specific nicking endonuclease

    PubMed Central

    Guan, Chudi; Kumar, Sanjay

    2005-01-01

    A stable heterodimeric protein containing a single correctly folded catalytic domain (SCD) of T7 endonuclease I was produced by means of a trans-splicing intein system. As predicted by a model presented earlier, purified SCD protein acts a non-specific nicking endonuclease on normal linear DNA. The SCD retains some ability to recognize and cleave a deviated DNA double-helix near a nick or a strand-crossing site. Thus, we infer that the non-specific and nicked-site cleavage activities observed for the native T7 endonuclease I (as distinct from the resolution activity) are due to uncoordinated actions of the catalytic domains. The positively charged C-terminus of T7 Endo I is essential for the enzymatic activity of SCD, as it is for the native enzyme. We propose that the preference of the native enzyme for the resolution reaction is achieved by cooperativity in the binding of its two catalytic domains when presented with two of the arms across a four-way junction or cruciform structure. PMID:16264086

  11. The beyond 12/23 restriction is imposed at the nicking and pairing steps of DNA cleavage during V(D)J recombination.

    PubMed

    Drejer-Teel, Anna H; Fugmann, Sebastian D; Schatz, David G

    2007-09-01

    The beyond 12/23 (B12/23) rule ensures inclusion of a Dbeta gene segment in the assembled T-cell receptor (TCR) beta variable region exon and is manifest by a failure of direct Vbeta-to-Jbeta gene segment joining. The restriction is enforced during the DNA cleavage step of V(D)J recombination by the recombination-activating gene 1 and 2 (RAG1/2) proteins and the recombination signal sequences (RSSs) flanking the TCRbeta gene segments. Nothing is known about the step(s) at which DNA cleavage is defective or how TCRbeta locus sequences contribute to these defects. To address this, we examined the steps of DNA cleavage by the RAG proteins using TCRbeta locus V, D, and J RSS oligonucleotide substrates. The results demonstrate that the B12/23 rule is enforced through slow nicking of Jbeta substrates and to some extent through poor synapsis of Vbeta and Jbeta substrates. Nicking is controlled largely by the coding flank and, unexpectedly, the RSS spacer, while synapsis is controlled primarily by the RSS nonamer. The results demonstrate that different Jbeta substrates are crippled at different steps of cleavage by distinct combinations of defects in the various DNA elements and strongly suggest that the DNA nicking step of V(D)J recombination can be rate limiting in vivo. PMID:17636023

  12. The Beyond 12/23 Restriction Is Imposed at the Nicking and Pairing Steps of DNA Cleavage during V(D)J Recombination▿

    PubMed Central

    Drejer-Teel, Anna H.; Fugmann, Sebastian D.; Schatz, David G.

    2007-01-01

    The beyond 12/23 (B12/23) rule ensures inclusion of a Dβ gene segment in the assembled T-cell receptor (TCR) β variable region exon and is manifest by a failure of direct Vβ-to-Jβ gene segment joining. The restriction is enforced during the DNA cleavage step of V(D)J recombination by the recombination-activating gene 1 and 2 (RAG1/2) proteins and the recombination signal sequences (RSSs) flanking the TCRβ gene segments. Nothing is known about the step(s) at which DNA cleavage is defective or how TCRβ locus sequences contribute to these defects. To address this, we examined the steps of DNA cleavage by the RAG proteins using TCRβ locus V, D, and J RSS oligonucleotide substrates. The results demonstrate that the B12/23 rule is enforced through slow nicking of Jβ substrates and to some extent through poor synapsis of Vβ and Jβ substrates. Nicking is controlled largely by the coding flank and, unexpectedly, the RSS spacer, while synapsis is controlled primarily by the RSS nonamer. The results demonstrate that different Jβ substrates are crippled at different steps of cleavage by distinct combinations of defects in the various DNA elements and strongly suggest that the DNA nicking step of V(D)J recombination can be rate limiting in vivo. PMID:17636023

  13. Tests of executive functioning predict scores on the MacAndrew Alcoholism Scale.

    PubMed

    Deckel, A W

    1999-02-01

    1. Previous work reported that tests of executive functioning (EF) predict the risk of alcoholism in subject populations selected for a "high density" of a family history of alcoholism and/or the presence of sociopathic traits. The current experiment examined the ability of EF tests to predict the risk of alcoholism, as measured by the MacAndrew Alcoholism Scale (MAC), in outpatient subjects referred to a general neuropsychological testing service. 2. Sixty-eight male and female subjects referred for neuropsychological testing were assessed for their past drinking histories and administered the Wisconsin Card Sorting Test, the Wechsler Adult Intelligence Scale-Revised, the Trails (Part B) Test, and the MAC. Principal Components analysis (PCA) reduced the number of EF tests to two measures, including one that loaded on the WCST, and one that loaded on the Similarities, Picture Arrangement, and Trails tests. Multiple hierarchical regression first removed the variance from demographic variables, alcohol consumption, and verbal (i.e., Vocabulary) and non-verbal (i.e., Block Design) IQ, and then entered the executive functioning factors into the prediction of the MAC. 3. Seventy-six percent of the subjects were classified as either light, infrequent, or non-drinkers on the Quantity-Frequency-Variability scale. The factor derived from the WCST on PCA significantly added to the prediction of risk on the MAC (p = .0063), as did scores on Block Design (p = .033). Relatively more impaired scores on the WCST factor and Block Design were predictive of higher scores on the MAC. The other factors were not associated with MAC scores. 4. These results support the hypothesis that decrements in EF are associated with risk factors for alcoholism, even in populations where the density of alcoholic behaviors are not unusually high. When taken in conjunction with other findings, these results implicate EF test scores, and prefrontal brain functioning, in the neurobiology of the risk for

  14. Multi-stage impregnation of the lithospheric mantle at the Andrew Bain FZ (SWIR)

    NASA Astrophysics Data System (ADS)

    Paganelli, E.; Brunelli, D.; Bonatti, E.; Cipriani, A.; Ligi, M.

    2008-12-01

    The Southern ridge-transform intersection of Andrew Bain Fracture Zone (ABFZ) is interpreted as a "cold spot" in the mid-ocean ridge system being characterized by a negative thermal anomaly in the oceanic upper mantle. The negative thermal anomaly is associated to the cold-edge effect due to the great age contrast of the active ridge segments. During the oceanic expedition AB06-S23, in 2006, (organized by ISMAR-CNR, Bologna, Italy, and co-financed by PRNA, Italy) with the russian R/V N. Strakhov, several samples of abyssal peridotites have been collected. Textures and modal distribution of the samples have been investigated revealing a multistage impregnation history. Deep spinel-field impregnation assemblages (sp+cpx-ol) are followed by plagioclase-field patches and mineral trails (pl+cpx-ol) and late shallow gabbroic pockets and veins. The major elements mineral chemistry reveals compositional trends of low-P/T subsolidus partial- to-complete re-equilibration undergone by the upper mantle during the upwelling beneath the ridge. These samples have experienced variable degrees of melting and reacted with percolating melts of possible different composition. In particular, samples showing the lowest degrees of melting have interacted with MORB-like melts and pyroxenitic-derived melts in the spinel and plagioclase stability fields. The presence of these two kinds of melts might prove the presence of enriched portions scattered in a normal depleted mantle beneath ocean ridges. MELTS-based runs provide constraints to variable extents of pyroxenitic-derived melt interaction with the mantle source and crystallization at variable depth of the products of such an interaction. Supported by MIUR-PRIN Cofin project 2007

  15. Low-Frequency Response Following the Passage of Hurricane Andrew on the Texas-Louisiana Shelf

    NASA Astrophysics Data System (ADS)

    Pearce, S. M.; Smith, D. C.; Dimarco, S. F.

    2009-12-01

    During August 24th through 27th in 1992, Hurricane Andrew passed through the Gulf Of Mexico almost directly over several moorings on the easternmost Louisiana shelf portion of the Texas-Louisiana Shelf (LATEX) coastal ocean monitoring program. Examination of the current meter time-series showed the existence of fast moving, long shelf waves over the entire Texas-Louisiana shelf west of the storm passage for up to 12 days after direct forcing ceased. The LATEX program featured 31 moorings each with 3 current meters over the 10, 20, 50, and 200 meter isobaths in 5 cross sectional lines with additional coverage on the 200 meter isobath from the Louisiana-Mississippi River delta, to Corpus Christi, Texas. Additionally, several pressure records from LATEX and several NOAA historical coastal tide gauge data from Sabine Pass to Port Isabella, Texas were incorporated. Raw, 3-hour low pass filtered, and 40-hour low pass filtered versions of the current data were analyzed. The pressure data used were detided using a least squares fit, and the tidal records were detided using the NOAA predicted tides for that location. All data were analyzed using a wavelet analysis to determine the spectra over time. The analyzed data shows that the shelf response was largely dominated in the internal Kelvin wave mode. The wave propagated towards the west on the shelf at approximately 400 km/day. These results are contrasted and compared with wave modes predicted for coastal trapped wave solutions. The output of a coastal ocean model simulation using a forced wind field similar to the storm are also contrasted and compared with the observed data.

  16. On remembering and forgetting our autobiographical pasts: retrograde amnesia and Andrew Mayes's contribution to neuropsychological method.

    PubMed

    Kopelman, M D; Bright, P

    2012-11-01

    Andrew Mayes's contribution to the neuropsychology of memory has consisted in steadily teasing out the nature of the memory deficit in the amnesic syndrome. This has been done with careful attention to matters of method at all stages. This particularly applies to his investigations of forgetting rates in amnesia and to his studies of retrograde amnesia. Following a brief outline of his work, the main current theories of retrograde amnesia are considered: consolidation theory, episodic-to-semantic shift theory, and multiple trace theory. Findings across the main studies in Alzheimer dementia are reviewed to illustrate what appears to be consistently found, and what is much more inconsistent. A number of problems and issues in current theories are then highlighted--including the nature of the temporal gradient, correlations with the extent of temporal lobe damage, what we would expect 'normal' remote memory curves to look like, how they would appear in focal retrograde amnesia, and whether we can pinpoint retrograde amnesia to hippocampal/medial temporal damage on the basis of existing studies. A recent study of retrograde amnesia is re-analysed to demonstrate temporal gradients on recollected episodic memories in hippocampal/medial temporal patients. It is concluded that there are two requirements for better understanding of the nature of retrograde amnesia: (i) a tighter, Mayesian attention to method in terms of both the neuropsychology and neuroimaging in investigations of retrograde amnesia; and (ii) acknowledging that there may be multiple factors underlying a temporal gradient, and that episodic and semantic memory show important interdependencies at both encoding and retrieval. Such factors may be critical to understanding what is remembered and what is forgotten from our autobiographical pasts. PMID:22884958

  17. Cylindric partitions, {{\\boldsymbol{ W }}}_{r} characters and the Andrews-Gordon-Bressoud identities

    NASA Astrophysics Data System (ADS)

    Foda, O.; Welsh, T. A.

    2016-04-01

    We study the Andrews-Gordon-Bressoud (AGB) generalisations of the Rogers-Ramanujan q-series identities in the context of cylindric partitions. We recall the definition of r-cylindric partitions, and provide a simple proof of Borodin’s product expression for their generating functions, that can be regarded as a limiting case of an unpublished proof by Krattenthaler. We also recall the relationships between the r-cylindric partition generating functions, the principal characters of {\\hat{{sl}}}r algebras, the {{\\boldsymbol{ M }}}r r,r+d minimal model characters of {{\\boldsymbol{ W }}}r algebras, and the r-string abaci generating functions, providing simple proofs for each. We then set r = 2, and use two-cylindric partitions to re-derive the AGB identities as follows. Firstly, we use Borodin’s product expression for the generating functions of the two-cylindric partitions with infinitely long parts, to obtain the product sides of the AGB identities, times a factor {(q;q)}∞ -1, which is the generating function of ordinary partitions. Next, we obtain a bijection from the two-cylindric partitions, via two-string abaci, into decorated versions of Bressoud’s restricted lattice paths. Extending Bressoud’s method of transforming between restricted paths that obey different restrictions, we obtain sum expressions with manifestly non-negative coefficients for the generating functions of the two-cylindric partitions which contains a factor {(q;q)}∞ -1. Equating the product and sum expressions of the same two-cylindric partitions, and canceling a factor of {(q;q)}∞ -1 on each side, we obtain the AGB identities.

  18. Construction, Startup and Operation of a New LLRW Disposal Facility in Andrews County, Texas - 12151

    SciTech Connect

    Van Vliet, James A.

    2012-07-01

    During this last year, Waste Control Specialists LLC (WCS) completed construction and achieved start of operations of a new low level radioactive waste (LLRW) disposal facility in Andrews County Texas. Disposal operations are underway for commercial LLRW, and start up evolutions are in progress for disposal of Department of Energy (DOE) LLRW. The overall approach to construction and start up are presented as well as some of the more significant challenges and how they were addressed to achieve initial operations of the first new commercial low level radioactive waste disposal facility in more than 30 years. The WCS disposal facility consists of two LLRW disposal cells, one for Texas Compact waste, and a separate disposal cell for DOE waste. Both disposal cells have very robust and unique designs. The cells themselves are constructed entirely in very low permeability red bed clay. The cell liners include a 0.91 meter thick clay liner meeting unprecedented permeability limits, 0.3 meter thick reinforced concrete barriers, as well as the standard geo-synthetic liners. Actions taken to meet performance criteria and install these liners will be discussed. Consistent with this highly protective landfill design, WCS chose to install a zero discharge site water management system. The considerations behind the design and construction of this system will be presented. Other activities essential to successful start of LLRW disposal operations included process and procedure development and refinement, staffing and staff development, and training. Mock ups were built and used for important evolutions and functions. Consistent with the extensive regulation of LLRW operations, engagement with the Texas Commission on Environmental Quality (TCEQ) was continuous and highly interactive. This included daily activity conference calls, weekly coordination calls and numerous topical conference calls and meetings. TCEQ staff and consultants frequently observed specific construction

  19. Evaluation of Hydraulically Significant Discontinuities in Dockum Group Mudrocks in Andrews County, Texas

    NASA Astrophysics Data System (ADS)

    Holt, R. M.; Kuszmaul, J. S.; Cao, S.; Powers, D. W.

    2013-12-01

    Triassic mudrocks of the Dockum Group (Cooper Canyon Formation) host four, below-grade landfills at the Waste Control Specialists (WSC) site in Andrews County, Texas, including: a hazardous waste landfill and three radioactive waste landfills. At the study site, the Dockum consists of mudrocks with sparse siltstone/sandstone interbeds that developed in a semi-arid environment from an ephemeral meandering fluvial system. Sedimentary studies reveal that the mudrocks are ancient floodplain vertisols (soils with swelling clays) and siltstone/sandstone interbeds are fluvial channel deposits that were frequently subaerially exposed. Rock discontinuities, including fractures and syndepositional slickensided surfaces, were mapped during the excavation of the WCS radioactive waste landfills along vertical faces prepared by the construction contractor. Face locations were selected to insure a sampled area with nearly complete vertical coverage for each landfill. Individual discontinuities were mapped and their strike, dip, length, roughness, curvature, staining, and evidence of displacement were described. In the three radioactive waste disposal landfills, over 1750 discontinuities across 35 excavated faces were mapped and described, where each face was nominally 8 to 10 ft tall and 50 to 100 ft long. Genetic units related to paleosol development were identified. On average, the orientation of the discontinuities was horizontal, and no other significant trends were observed. Mapping within the landfill excavations shows that most discontinuities within Dockum rocks are horizontal, concave upward, slickensided surfaces that developed in the depositional environment, as repeated wetting and drying cycles led to shrinking and swelling of floodplain vertisols. Fractures that showed staining (a possible indicator of past or present hydraulic activity) are rare, vertical to near-vertical, and occur mainly in, and adjacent to, mechanically stiff siltstone and sandstone interbeds

  20. The structure of new nickel(I) oxides: LnSr 5Ni 3O 8 (Ln = Y, Dy, Ho, Er and Tm)

    NASA Astrophysics Data System (ADS)

    James, M.; Attfield, J. P.

    1994-12-01

    Stoichiometric oxides of 3d 9 nickel(I), LnSr 5Ni 3O 8 (Ln = Y, Dy, Ho, Er and Tm), have been prepared through the hydrogen reduction of LnSr 5Ni 3O 11, resulting in a change from a tetragonal K 2NiF 4 type structure to an orthorhombic Sr 2CuO 3 arrangement in which {1}/{3} of the bridging oxygen atoms are missing from chains of apex-linked nickel oxide square planes.

  1. Effect of Hurricane Andrew on the Turkey Point Nuclear Generating Station from August 20--30, 1992. [Final report

    SciTech Connect

    Hebdon, F.J.

    1993-03-01

    On August 24, 1992, Hurricane Andrew, a Category 4 hurricane, struck the Turkey Point Electrical Generating Station with sustained winds of 145 mph (233 km/h). This is the report of the team that the US Nuclear Regulatory Commission (NRC) and the Institute of Nuclear Power Operations (INPO) jointly sponsored (1) to review the damage that the hurricane caused the nuclear units and the utility`s actions to prepare for the storm and recover from it, and (2) to compile lessons that might benefit other nuclear reactor facilities.

  2. A tale of two storms: Surges and sediment deposition from Hurricanes Andrew and Wilma in Florida’s southwest coast mangrove forests: Chapter 6G in Science and the storms-the USGS response to the hurricanes of 2005

    USGS Publications Warehouse

    Smith, Thomas J., III; Anderson, Gordon H.; Tiling, Ginger

    2007-01-01

    Hurricanes can be very different from each other. Here we examine the impacts that two hurricanes, Andrew and Wilma, had in terms of storm surge and sediment deposition on the southwest coast of Florida. Although Wilma was the weaker storm, it had the greater impact. Wilma had the higher storm surge over a larger area and deposited more sediment than did Andrew. This effect was most likely due to the size of Wilma's eye, which was four times larger than that of Andrew.

  3. Patterns and drivers of Holocene vegetational change near the prairie-forest ecotone in Minnesota: revisiting McAndrews' transect.

    PubMed

    Nelson, David M; Hu, Feng Sheng

    2008-07-01

    Holocene vegetational dynamics along the prairie-forest border of Minnesota were first documented in McAndrews' classic work. Despite numerous subsequent paleo-studies, a number of questions remain unanswered about the vegetation history of the region. Here, pollen, stable-isotope, mineral, and charcoal data are described from three lakes near McAndrews' sites. These data were compared with other paleoenvironmental records to reconstruct vegetation, aridity, and fire. The climate was relatively wet with increasing summer temperatures before approximately 8000 yr before present (BP). The rates of changes were asymmetric for the onset and termination of middle-Holocene aridity, with an abrupt increase at approximately 8000 yr BP and a gradual, but variable, decline from approximately 7800 to 4000 yr BP. Early-Holocene coniferous forests changed to mixed-grass prairie without an intervening period of tallgrass prairie or deciduous forest, whereas the retreat of prairie was characterized by transitions from mixed-grass to tallgrass prairie to deciduous forest and finally to coniferous forest. Within the middle Holocene, the composition and structures of grass-dominated vegetation varied both temporally and spatially. Fire primarily responded to changes in climate and fuel loads. Vegetation was more strongly influenced by climatic changes than by fire-regime shifts. PMID:19086180

  4. Site- and strand-specific nicking of DNA by fusion proteins derived from MutH and I-SceI or TALE repeats

    PubMed Central

    Gabsalilow, Lilia; Schierling, Benno; Friedhoff, Peter; Pingoud, Alfred; Wende, Wolfgang

    2013-01-01

    Targeted genome engineering requires nucleases that introduce a highly specific double-strand break in the genome that is either processed by homology-directed repair in the presence of a homologous repair template or by non-homologous end-joining (NHEJ) that usually results in insertions or deletions. The error-prone NHEJ can be efficiently suppressed by ‘nickases’ that produce a single-strand break rather than a double-strand break. Highly specific nickases have been produced by engineering of homing endonucleases and more recently by modifying zinc finger nucleases (ZFNs) composed of a zinc finger array and the catalytic domain of the restriction endonuclease FokI. These ZF-nickases work as heterodimers in which one subunit has a catalytically inactive FokI domain. We present two different approaches to engineer highly specific nickases; both rely on the sequence-specific nicking activity of the DNA mismatch repair endonuclease MutH which we fused to a DNA-binding module, either a catalytically inactive variant of the homing endonuclease I-SceI or the DNA-binding domain of the TALE protein AvrBs4. The fusion proteins nick strand specifically a bipartite recognition sequence consisting of the MutH and the I-SceI or TALE recognition sequences, respectively, with a more than 1000-fold preference over a stand-alone MutH site. TALE–MutH is a programmable nickase. PMID:23408850

  5. Label-free and ratiometric detection of nuclei acids based on graphene quantum dots utilizing cascade amplification by nicking endonuclease and catalytic G-quadruplex DNAzyme.

    PubMed

    Wang, Guang-Li; Fang, Xin; Wu, Xiu-Ming; Hu, Xue-Lian; Li, Zai-Jun

    2016-07-15

    Herein, we report a ratiometric fluorescence assay based on graphene quantum dots (GQDs) for the ultrasensitive DNA detection by coupling the nicking endonuclease assisted target recycling and the G-quadruplex/hemin DNAzyme biocatalysis for cascade signal amplifications. With o-phenylenediamine acted as the substrate of G-quadruplex/hemin DNAzyme, whose oxidization product (that is, 2,3-diaminophenazine, DAP) quenched the fluorescence intensity of GQDs (at 460nm) obviously, accompanied with the emergence of a new emission of DAP (at 564nm). The ratiometric signal variations at the emission wavelengths of 564 and 460nm (I564/I460) were utilized for label-free, sensitive, and selective detection of target DNA. Utilizing the nicking endonuclease assisted target recycling and the G-quadruplex/hemin DNAzyme biocatalysis for amplified cascade generation of DAP, the proposed bioassay exhibited high sensitivity toward target DNA with a detection limit of 30fM. The method also had additional advantages such as facile preparation and easy operation. PMID:26950646

  6. Analysis of DNase 1 sensitivity and methylation of active and inactive X chromosomes of kangaroos (Macropus robustus) by in situ nick translation.

    PubMed

    Loebel, D A; Johnston, P G

    1993-01-01

    The overall nuclease sensitivity and methylation of active and inactive X chromosomes of kangaroos were examined by in situ nick translation. Cultured fibroblasts of subspecies wallaroo-euro (Macropus robustus robustus; Macropus robustus erubescens) hybrids were used, enabling the paternally and maternally derived X chromosomes to be distinguished. No difference was found between the active and inactive X chromosomes with DNase I or MspI digestion. When chromosomes were digested with the methylation sensitive restriction enzymes HpaII and HhaI, the inactive X chromosome was labelled to a greater extent. These results indicate no overall difference in chromatin condensation between the active and inactive X chromosomes and greater overall methylation of the active X chromosome. This relative undermethylation of the inactive X chromosome may be important in X chromosome inactivation, but its function, if any, remains to be determined. PMID:8381740

  7. Plant phenology patterns at three sites on the H.J. Andrews Experimental Forest, Oregon, 1987 to 2007.

    NASA Astrophysics Data System (ADS)

    Shaw, D. C.; Creel, C.; Downing, G.; Remillard, S.; O'Connell, K.

    2007-12-01

    Plant phenology data has been collected at three sites on the H.J. Andrews Experimental Forest, Oregon since the late 1970's. The sites were visited once every three weeks year-round. Current efforts to clean and archive this data are on-going. Here we present on a 20 year data set from 1987 to 2007. The three sites are located at Watersheds (WS) 10, 8, and 7/6, at an elevation of 466 m, 993 m, and 905/950 m respectively. Forests were old growth (WS 8) and regenerating clearcuts (WS 6, 10), or shelterwood clearcut with overstory removed in 1984 (WS 7) dominated by Douglas-fir, western hemlock, true firs, and western redcedar. One tree (Douglas-fir), two evergreen shrubs, three deciduous shrubs, and four herbs were followed for vegetative and flowering phenology, including bud swell, bud bread, leaf expansion, leaf color change, leaf fall, flower bud swell, blooming, petal loss, fruit formation, and seed dispersal. Weather stations are located at each site and tied into a network of stations in this LTER site. Physical factors such as snow depth, snow coverage, freeze-thaw activity, as well as lichen condition were also noted. We are asking two key questions regarding plant phenology patterns. 1. Has the growing season lengthened in the mountainous watershed of the HJ Andrews, and is this similar for a low elevation site (WS 10) versus a mid elevation site (WS 8, 7/6)? 2. Do snow-pack dynamics influence plant phenology more so than temperature (degree days)?

  8. The Pedagogy and Problems of Jane Andrews's "The Seven Little Sisters Who Live on the Round Ball that Floats in the Air" (1861)

    ERIC Educational Resources Information Center

    Tedesco, Laureen

    2006-01-01

    This essay examines the interplay between Jane Andrews's purpose and her pedagogy in "The Seven Little Sisters Who Live on the Round Ball that Floats in the Air." The book demonstrates the teaching strategies she learned at the First State Normal in Massachusetts, moving from what the child knows to new material, engaging the child in personal…

  9. 33 CFR 334.770 - Gulf of Mexico and St. Andrew Sound, south of East Bay, Fla., Tyndall Drone Launch Corridor...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... Sound, south of East Bay, Fla., Tyndall Drone Launch Corridor, Tyndall Air Force Base, Fla.; restricted.... Andrew Sound, south of East Bay, Fla., Tyndall Drone Launch Corridor, Tyndall Air Force Base, Fla... referred to as the “Tyndall Drone Launch Corridor.” (b) The regulations. (1) Military usage of areas...

  10. 33 CFR 334.770 - Gulf of Mexico and St. Andrew Sound, south of East Bay, Fla., Tyndall Drone Launch Corridor...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... Sound, south of East Bay, Fla., Tyndall Drone Launch Corridor, Tyndall Air Force Base, Fla.; restricted.... Andrew Sound, south of East Bay, Fla., Tyndall Drone Launch Corridor, Tyndall Air Force Base, Fla... referred to as the “Tyndall Drone Launch Corridor.” (b) The regulations. (1) Military usage of areas...

  11. 33 CFR 334.770 - Gulf of Mexico and St. Andrew Sound, south of East Bay, Fla., Tyndall Drone Launch Corridor...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Sound, south of East Bay, Fla., Tyndall Drone Launch Corridor, Tyndall Air Force Base, Fla.; restricted.... Andrew Sound, south of East Bay, Fla., Tyndall Drone Launch Corridor, Tyndall Air Force Base, Fla... referred to as the “Tyndall Drone Launch Corridor.” (b) The regulations. (1) Military usage of areas...

  12. 33 CFR 334.770 - Gulf of Mexico and St. Andrew Sound, south of East Bay, Fla., Tyndall Drone Launch Corridor...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... Sound, south of East Bay, Fla., Tyndall Drone Launch Corridor, Tyndall Air Force Base, Fla.; restricted.... Andrew Sound, south of East Bay, Fla., Tyndall Drone Launch Corridor, Tyndall Air Force Base, Fla... referred to as the “Tyndall Drone Launch Corridor.” (b) The regulations. (1) Military usage of areas...

  13. 33 CFR 334.770 - Gulf of Mexico and St. Andrew Sound, south of East Bay, Fla., Tyndall Drone Launch Corridor...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Sound, south of East Bay, Fla., Tyndall Drone Launch Corridor, Tyndall Air Force Base, Fla.; restricted.... Andrew Sound, south of East Bay, Fla., Tyndall Drone Launch Corridor, Tyndall Air Force Base, Fla... referred to as the “Tyndall Drone Launch Corridor.” (b) The regulations. (1) Military usage of areas...

  14. Highly sensitive fluorescence assay of DNA methyltransferase activity via methylation-sensitive cleavage coupled with nicking enzyme-assisted signal amplification.

    PubMed

    Zhao, Yongxi; Chen, Feng; Wu, Yayan; Dong, Yanhua; Fan, Chunhai

    2013-04-15

    Herein, using DNA adenine methylation (Dam) methyltransferase (MTase) as a model analyte, a simple, rapid, and highly sensitive fluorescence sensing platform for monitoring the activity and inhibition of DNA MTase was developed on the basis of methylation-sensitive cleavage and nicking enzyme-assisted signal amplification. In the presence of Dam MTase, an elaborately designed hairpin probe was methylated. With the help of methylation-sensitive restriction endonuclease DpnI, the methylated hairpin probe could be cleaved to release a single-stranded DNA (ssDNA). Subsequently, this released ssDNA would hybridize with the molecular beacon (MB) to open its hairpin structure, resulting in the restoration of fluorescence signal as well as formation of the double-stranded recognition site for nicking enzyme Nt.BbvCI. Eventually, an amplified fluorescence signal was observed through the enzymatic recycling cleavage of MBs. Based on this unique strategy, a very low detection limit down to 0.06 U/mL was achieved within a short assay time (60 min) in one step, which is superior to those of most existing approaches. Owing to the specific site recognition of MTase toward its substrate, the proposed sensing system was able to readily discriminate Dam MTase from other MTase such as M.SssI and even detect the target in complex biological matrix. Furthermore, the application of the proposed sensing strategy for screening Dam MTase inhibitors was also demonstrated with satisfactory results. This novel method not only provides a promising platform for monitoring activity and inhibition of DNA MTases, but also shows great potentials in biological process researches, drugs discovery and clinical diagnostics. PMID:23202331

  15. Label-free and ultrasensitive fluorescence detection of cocaine based on a strategy that utilizes DNA-templated silver nanoclusters and the nicking endonuclease-assisted signal amplification method.

    PubMed

    Zhang, Kai; Wang, Ke; Zhu, Xue; Zhang, Jue; Xu, Lan; Huang, Biao; Xie, Minhao

    2014-01-01

    A general and reliable strategy for the detection of cocaine was proposed utilizing DNA-templated silver nanoclusters as signal indicators and the nicking endonuclease-assisted signal amplification method. This strategy can detect cocaine specifically with a detection limit as low as 2 nM by using a small volume of 5 μL. PMID:24217291

  16. Andrew Halliday, Kt FRCPE (1781-1839): service in the Napoleonic Wars and West Indies, and first physician to the Seamen's Hospital Society.

    PubMed

    Cook, G C

    2004-08-01

    Sir Andrew Halliday (1781-1839) was domestic physician to HRH the Duke of Clarence (1765-1837) (who was later to become King William IV). He also served in the Napoleonic Wars-in Portugal, Spain and Waterloo-as well as in the West Indies, and became the first physician to the Seamen's Hospital Society. Unlike many of his contemporaries, Halliday was also a prolific author, many of his publications being on lunatic asylums in Great Britain and Ireland. PMID:15257347

  17. Validation of the sperm chromatin dispersion (SCD) test in the amphibian Xenopus laevis using in situ nick translation and comet assay.

    PubMed

    Pollock, K; Gosálvez, J; Arroyo, F; López-Fernández, C; Guille, M; Noble, A; Johnston, S D

    2015-11-01

    The integrity of sperm DNA is becoming increasingly recognised as an important parameter of semen quality, but there are no published reports of this procedure for any amphibian. The primary aim of this study was to apply a modified sperm chromatin dispersion (SCD) test (Halomax) to an amphibian sperm model (African clawed frog; Xenopus laevis) and to validate the assay against in situ nick translation (ISNT) and the double-comet assay procedure. Inactivated spermatozoa were collected from fresh testes (n=3). Sperm DNA fragmentation (SDF) for each sperm sample was conducted immediately following activation (T0) and again after 1h (T1) and 24h (T24) of incubation at room temperature in order to produce a range of spermatozoa with differing levels of DNA damage. The SCD procedure resulted in the production of three nuclear morphotypes; amphibian sperm morphotype 1 (ASM-1) and ASM-2 showed no evidence of DNA damage, whereas ASM-3 spermatozoa were highly fragmented with large halos of dispersed DNA fragments and a reduced nuclear core. ISNT confirmed that ASM-3 nuclei contained damaged DNA. There was a significant correlation (r=0.9613) between the levels of ASM-3 detected by the SCD test and SDF revealed by the double-comet assay. PMID:25482041

  18. Nicking endonuclease-assisted signal amplification of a split molecular aptamer beacon for biomolecule detection using graphene oxide as a sensing platform.

    PubMed

    Li, Xiang; Ding, Xuelian; Fan, Jing

    2015-12-01

    Sensitive and selective detection of ultralow concentrations of specific biomolecules is important in early clinical diagnoses and biomedical applications. Many types of aptasensors have been developed for the detection of various biomolecules, but usually suffer from false positive signals and high background signals. In this work, we have developed an amplified fluorescence aptasensor platform for ultrasensitive biomolecule detection based on enzyme-assisted target-recycling signal amplification and graphene oxide. By using a split molecular aptamer beacon and a nicking enzyme, the typical problem of false positive signals can be effectively resolved. Only in the presence of a target biomolecule, the sensor system is able to generate a positive signal, which significantly improves the selectivity of the aptasensor. Moreover, using graphene oxide as a super-quencher can effectively reduce the high background signal of a sensing platform. We select vascular endothelial growth factor (VEGF) and adenosine triphosphate (ATP) as model analytes in the current proof-of-concept experiments. It is shown that under optimized conditions, our strategy exhibits high sensitivity and selectivity for the quantification of VEGF and ATP with a low detection limit (1 pM and 4 nM, respectively). In addition, this biosensor has been successfully utilized in the analysis of real biological samples. PMID:26502364

  19. Ab initio DNA synthesis by Bst polymerase in the presence of nicking endonucleases Nt.AlwI, Nb.BbvCI, and Nb.BsmI.

    PubMed

    Antipova, Valeriya N; Zheleznaya, Lyudmila A; Zyrina, Nadezhda V

    2014-08-01

    In the absence of added DNA, thermophilic DNA polymerases synthesize double-stranded DNA from free dNTPs, which consist of numerous repetitive units (ab initio DNA synthesis). The addition of thermophilic restriction endonuclease (REase), or nicking endonuclease (NEase), effectively stimulates ab initio DNA synthesis and determines the nucleotide sequence of reaction products. We have found that NEases Nt.AlwI, Nb.BbvCI, and Nb.BsmI with non-palindromic recognition sites stimulate the synthesis of sequences organized mainly as palindromes. Moreover, the nucleotide sequence of the palindromes appeared to be dependent on NEase recognition/cleavage modes. Thus, the heterodimeric Nb.BbvCI stimulated the synthesis of palindromes composed of two recognition sites of this NEase, which were separated by AT-reach sequences or (A)n (T)m spacers. Palindromic DNA sequences obtained in the ab initio DNA synthesis with the monomeric NEases Nb.BsmI and Nt.AlwI contained, along with the sites of these NEases, randomly synthesized sequences consisted of blocks of short repeats. These findings could help investigation of the potential abilities of highly productive ab initio DNA synthesis for the creation of DNA molecules with desirable sequence. PMID:24965874

  20. Inhibition of the gastric H+,K+ -ATPase by plectrinone A, a diterpenoid isolated from Plectranthus barbatus Andrews.

    PubMed

    Schultz, Carla; Bossolani, Myllene P; Torres, Luce M B; Lima-Landman, Maria Teresa R; Lapa, Antonio J; Souccar, Caden

    2007-04-20

    This work assessed the mechanism underlying the antisecretory gastric acid effect of Plectranthus barbatus Andrews (Lamiaceae) and active constituents. Popularly known as "false-boldo", this plant is used in Brazilian folk medicine to treat gastrointestinal and hepatic ailments. The plant aqueous extract (AE) and isolated compounds were assayed in vivo in pylorus-ligated mice, and in vitro on acid secretion measured as [(14)C]-aminopyrine ([(14)C]-AP) accumulation in rabbit gastric glands and gastric H(+),K(+)-ATPase preparations. Injected into the duodenal lumen, the AE of the plant leaves (0.5 and 1.0 g/kg) decreased the volume (62 and 76%) and total acidity (23 and 50%) of gastric acid secretion in pylorus-ligated mice. Bioguided purification of the AE yielded an active fraction (IC(50)=24 microg/ml) that inhibited acid secretion in rabbit gastric glands with a potency 10 to 18 times greater than that of the originating extract, on both the basal and stimulated acid secretion by histamine (His) (1 microM) or bethanechol (100 microM). At the same concentrations the gastric H(+),K(+)-ATPase activity was also inhibited. The active constituent was chemically identified as the abietanoid dienedione plectrinone A which reduced the H(+),K(+)-ATPase activity with IC(50)=171 microM. The results indicate that inhibition of the gastric proton pump by this diterpenoid may account for the antisecretory acid effect and reputed anti ulcer activity of Plectranthus barbatus. PMID:17166678

  1. Once a physicist: Nick Horvath

    NASA Astrophysics Data System (ADS)

    Horvath, Nick

    2009-05-01

    How did you get into basketball? That's an easy one: I was tall. I had zero interest in sport at a young age and was pushed into basketball against my will when I was about eight. I hated it. The next year, however, I was so much taller than everyone else that in my first game, even though I had no idea what I was doing, I could simply hold the ball above my head and shoot over everyone. I fell in love with basketball after that first game. If I had played badly that day, it is likely that I would not have played again in my entire life.

  2. Hydrological Controls on Nitrogen and DOC Transport at the Plot, Hillslope and Catchment Scale, HJ Andrews Experimental Forest.

    NASA Astrophysics Data System (ADS)

    van Verseveld, W. J.; McDonnell, J. J.; Lajtha, K.

    2005-12-01

    While the flushing of nutrients at the catchment scale has been described in many forested environments during the last decade, the flushing mechanisms, flowpaths and geographic sources of different N species (DON, NO3- and NH4+) and DOC are still poorly resolved, especially during different storm size and antecedent wetness conditions. We characterized flowpaths of N and DOC at the hillslope scale during and between storm events in WS10, H.J. Andrews, Oregon, USA, for five storms over the period Fall 2004 until Spring 2005. This catchment is dominated by hillslopes with negligible riparian water storage due to 1986 and 1996 debris flows that evacuated the valley bottom. This enabled us to study the hydrological and biogeochemical coupling between the hillslope and catchment in a way unimpeded by riparian zone groundwater dynamics.Through a combination of hydrometric and chemistry data from groundwater wells, tension and zero tension lysimeters at different depths, tensiometers, soil moisture probes and hillslope runoff from a 10 meter wide trench at the hillslope, we were able to resolve the dominant flowpaths. Fluorescence (a proxy for DOC) of hillslope and catchment runoff was monitored continuously with a fluorometer during storms. Preliminary data analysis showed a significant relationship between DOC concentrations and fluorescence values suggesting that fluorescence can be used to characterize DOC dynamics at small time scales. Our high frequency DOC characterization showed a clockwise hystersis pattern of DOC and total N against discharge for both hillslope and catchment runoff. This suggests flushing of nutrients in near and/ or in stream zones during the initial part of the storm. Total N and DOC concentrations in groundwater wells and lysimeters at shallow soil depths were high compared to other potential sources during storms. Our interpretation is that vertical preferential flow of high concentration water drives the groundwater contribution to

  3. Nomina nova in Platyhelminthes pro Macrorhynchus von Graff, 1882 (non [Gmelin, 1801]; non Dunker, 1843), and Leptocleidus Mueller, 1936 (non Andrews, 1922).

    PubMed

    Hornung, Jahn J

    2016-01-01

    Two genus-group names of flat-worms-Leptocleidus Mueller, 1936 and Macrorhynchus von Graff, 1882-are junior homonyms that are preoccupied by fossil diapsid reptile genera-Leptocleidus Andrews, 1922, and Macrorhynchus Dunker, 1843-and an extant teleost fish genus-Macrorhynchus [Gmelin, 1801] ex La Cépède, 1800. These are replaced by nomina nova (Pharyngodytes nom. nov.; Graffiellus nom. nov.). Macrorhynchus [Gmelin, 1801] is an objective senior synonym of Macrorhyncus Dumeríl, 1805 ex La Cépède, 1800 (syn. nov.), and a senior homonym of Macrorhynchus Dunker, 1843, and Macrorhynchus von Graff, 1882. PMID:27615836

  4. New monoterpene glycosides from Paeonia suffruticosa Andrews and their inhibition on NO production in LPS-induced RAW 264.7 cells.

    PubMed

    Ding, Liqin; Zhao, Feng; Chen, Lixia; Jiang, Zhihu; Liu, Yue; Li, Zhuomin; Qiu, Feng; Yao, Xinsheng

    2012-12-01

    Nine new monoterpene glycosides (1-9), together with 18 known compounds were obtained from the n-butanol soluble fraction of ethanol extract from Paeonia suffruticosa Andrews. Their structures were determined on the basis of chemical methods and spectroscopic data. The inhibitory effects of these compounds (except compound 6) on nitric oxide (NO) production in lipopolysaccharide-activated macrophages were evaluated. Compounds 1, 21, 23, 25, and 27 showed strong inhibitory activity on NO production with IC(50) values of 31.25, 36.13, 12.41, 6.87, and 41.94 μM, respectively. PMID:23067550

  5. Tavern patrons and the MacAndrew Alcoholism Scale: self-reported drinking behavior in relation to the MMPI L and K scales.

    PubMed

    Ciancio, C; Saltstone, R; Fraboni, M

    1990-09-01

    This study investigated the ability of the MacAndrew Alcoholism (MAC) Scale to distinguish between alcoholics and nonalcoholics using self-ratings from patrons of taverns (N = 128); while only about 14% of the variance in the MAC Scale was accounted for by the self-rating (alcoholic/nonalcoholic) scale, the MAC Scale correctly identified 70% of those who reported alcohol use to levels consistent with alcoholic dependency after variance in the alcohol use scale attributable to the L and K scales of the MMPI was accounted for. PMID:2246380

  6. Enrico Fermi Awards Ceremony for Dr. Allen J. Bard and Dr. Andrew Sessler, February 2014 (Presentations, including remarks by Energy Secretary, Dr. Ernest Moniz)

    SciTech Connect

    Moniz, Ernest

    2014-02-03

    The Fermi Award is a Presidential award and is one of the oldest and most prestigious science and technology honors bestowed by the U.S. Government. On February 3, 2014 it was conferred upon two exceptional scientists. The first to be recognized is Dr. Allen J. Bard, 'for international leadership in electrochemical science and technology, for advances in photoelectrochemistry and photocatalytic materials, processes, and devices, and for discovery and development of electrochemical methods including electrogenerated chemiluminescence and scanning electrochemical microscopy.' The other honoree is Dr. Andrew Sessler, 'for advancing accelerators as powerful tools of scientific discovery, for visionary direction of the research enterprise focused on challenges in energy and the environment, and for championing outreach and freedom of scientific inquiry worldwide.' Dr. Patricia Dehmer opened the ceremony, and Dr. Ernest Moniz presented the awards.

  7. Hurricane Frederic tidal floods of September 12-13, 1979, along the Gulf Coast, Pine Beach, St. Andrews Bay and Fort Morgan quadrangles, Alabama

    USGS Publications Warehouse

    Scott, John C.; Bohman, Larry R.

    1980-01-01

    Shown on a topographic map are floodmark elevations and approximate areas flooded by Hurricane Frederic tides of September 12-13, 1979, along the shores of St. Andrews Bay, Mobile Bay, and Bon Secour Bay from Fort Morgan eastward to about four miles east of Gasque, Ala. The storm tide went completely across the land between the beach and Mobile Bay throughout much of the area. Most homes on the beach side of Alabama State Highway 180 were completely destroyed, and the highway was washed out in several places. Damage to homes and other structures on the bay side was not as great. Storm-tide frequency and records of annual maximum tides at Mobile, Ala., since 1772, are presented. Offshore winds reached about 160 miles per hour. A wind-velocity of about 145 miles per hour was recorded near Dauphin Island, Ala. (USGS)

  8. The work of Andrew Weil and Deepak Chopra--two holistic health/New Age gurus: a critique of the holistic health/New Age movements.

    PubMed

    Baer, Hans A

    2003-06-01

    Despite the popular roots of the holistic health/New Age movements, a growing number of biomedical physicians have become proponents of holistic health as well as New Age healing. Over the past two decades, Andrew Weil and Deepak Chopra, two biomedically trained physicians, have emerged as the visible and financially successful spokespersons of the movement. This article provides brief biographical sketches of Weil and Chopra and compares and contrasts their respective views on health, illness, healing, and health care. It also considers the response of various biomedical parties to these holistic health/New Age gurus who have attempted to integrate biomedicine and various alternative healing and metaphysical systems. Finally, this article argues that Weil and Chopra both epitomize the limitations of the holistic health/New Age movements, albeit in different ways. PMID:12846118

  9. Enrico Fermi Awards Ceremony for Dr. Allen J. Bard and Dr. Andrew Sessler, February 2014 (Presentations, including remarks by Energy Secretary, Dr. Ernest Moniz)

    ScienceCinema

    Moniz, Ernest [U.S. Energy Secretary

    2014-08-22

    The Fermi Award is a Presidential award and is one of the oldest and most prestigious science and technology honors bestowed by the U.S. Government. On February 3, 2014 it was conferred upon two exceptional scientists. The first to be recognized is Dr. Allen J. Bard, 'for international leadership in electrochemical science and technology, for advances in photoelectrochemistry and photocatalytic materials, processes, and devices, and for discovery and development of electrochemical methods including electrogenerated chemiluminescence and scanning electrochemical microscopy.' The other honoree is Dr. Andrew Sessler, 'for advancing accelerators as powerful tools of scientific discovery, for visionary direction of the research enterprise focused on challenges in energy and the environment, and for championing outreach and freedom of scientific inquiry worldwide.' Dr. Patricia Dehmer opened the ceremony, and Dr. Ernest Moniz presented the awards.

  10. Observations on some of the plates used to illustrate the Lymphatics section of Andrew Fyfe's Compendium of the Anatomy of the Human Body, Published in 1800.

    PubMed

    Kaufman, M H

    1999-01-01

    An engraving displaying A General View of the Absorbent System was used as one of many plates illustrating the Lymphatics section of Andrew Fyfe's Compendium of the Anatomy of the Human Body published in 1800. It is a scaled-down version of a life-size engraving displayed in the museum of the Department of Anatomy at the University of Edinburgh, and is based on a cadaver specially dissected and injected with mercury in 1788 by Alexander Monro secundus, probably with the assistance of Fyfe, who was his 'dissector'. Only recently has the relationship between these two engravings been established, and the Figure Legend in Fyfe's Compendium now provides the missing key to the features illustrated in the life-size engraving. The source and very variable quality of some of Fyfe's other plates, both in the Lymphatics section and elsewhere in the book, are discussed. PMID:9890727

  11. An Analysis and Comparison of Two Short Writings: "Inaugural Address at the University of St. Andrew's" by J.S. Mill and "The University of Utopia" by R.M. Hutchins, Based on Five Criteria.

    ERIC Educational Resources Information Center

    Poirier, Jeannine M.

    Focusing on the concept of education for work vs. education for living, the author presents a comparative analysis of two works on liberal education, each of which was originally delivered orally to university students: "The Inaugural Address at the University of St. Andrew" by John Stuart Mill and "The University of Utopia" by Robert Maynard…

  12. DFT analysis of g and 13C hyperfine coupling tensors for model Ni(I)(CO)(n)L(m) (n = 1-4, L = H2O, OH-) complexes epitomizing surface nickel(I) carbonyls.

    PubMed

    Pietrzyk, Piotr; Podolska, Katarzyna; Sojka, Zbigniew

    2008-11-27

    Relativistic calculations within the spin-orbit mean-field (SOMF) approximation, the zero-order regular approximation (ZORA), and the scalar relativistic method based on the Pauli Hamiltonian were performed for the prediction and interpretation of the electronic g tensor and (13)C hyperfine tensor for a set of model polycarbonyl nickel(I) complexes with aqua or hydroxy coligands. They exhibit extensive similarities with heterogeneous [Ni(I)(CO)(n)]-surface complexes produced upon adsorption of carbon monoxide on Ni(I) ions grafted on silica or inside the zeolite channels. Benchmark calculations showing the influence of the exchange-correlation functional on the g tensor were carried out for well-defined nickel(I) complexes of known structure. On this basis, the SOMF-B3LYP scheme was chosen for calculations of the g tensor, and the obtained results were in satisfactory agreement with literature EPR data found for the [Ni(I)(CO)(n)]/SiO(2) system. The calculated g and A((13)C) tensors allowed polycarbonyl complexes of various stereochemistries to be distinguished. The nature of the Deltag(ii) shifts was assessed in terms of the molecular orbital contributions due to the magnetic-field-induced couplings and their structure sensitivity. The noncoincidence of g and (13)C hyperfine principal axes and their orientation with respect to the molecular framework was also examined. The ability of DFT calculations to follow consistently variations of the EPR parameters induced by stereochemical changes around the Ni(I) center provides an invaluable reference for the interpretation of experimental results. PMID:18986126

  13. Comparisons of Aquatic Invertebrate Assemblages in Small, Old Growth and Second Growth Forested Catchments of the H.J. Andrews Experimental Forest, Oregon

    NASA Astrophysics Data System (ADS)

    Frady, C. H.; Johnson, S. L.; Li, J. L.

    2005-05-01

    In small streams, riparian vegetation often composes the food base for many aquatic invertebrates. Forest harvest can result in major changes to riparian vegetation. If abundance, richness, or community structure of invertebrate assemblages is affected by removal of riparian vegetation, are legacies of these practices evident 20-40 years post-harvest? If so, are these differences uniform through time, or are they temporally dependant? We investigated stream invertebrate assemblage dynamics between old growth and second growth forest types and across seasons in six small-basins in the H.J. Andrews Experimental Forest. Individual basins range from 500m to 1000m in elevation and 12.4ha to 98.1ha in area. Six benthic samples and four, 1-week emergence samples were collected in each basin each season (June 2003 through May 2004). Preliminary results from benthic samples suggest strong changes in community structure between seasons as additional taxa not found in summer (i.e. Agathon, Anagapetus, Chernokrilus, and Rhyacophila "angelita group") were collected in autumn and winter samples. However, results from summer comparisons demonstrate no differences in benthic and emergence abundance (p = 0.47, and p = 0.98, respectively) or benthic richness (p = 0.41) between old growth and second growth invertebrate assemblages.

  14. Flood of September 7-9, 1987, in Lexington and Richland counties in the vicinity of Saint Andrews Road and Irmo, South Carolina

    USGS Publications Warehouse

    Guimaraes, W.B.

    1989-01-01

    Localized heavy rainfall on September 7, 1987, in Lexington and Richland Counties, South Carolina, caused severe flooding in the basins of Kinley Creek, Rawls Creek, and Stoop Creek, in the vicinity of Saint Andrews Road and the town of Irmo, South Carolina. The flooding damaged homes, furnishings, and landscaping. Rainfall, peak discharges, high-water elevations, and frequency relations of rainfall and discharge are tabulated and plotted for selected streams. The rain was most intense in the area along Rawls Creek, R-2 (tributary to Rawls Creek), Koon Branch (tributary to Rawls Creek), and the upper part of Kinley Creek. A rainfall of about 5.5 inches in 3 hours, which has a recurrence interval in excess of 100 years, was reported by local residents along these streams. High-water marks are presented in this report for Stoop Creek, Kinley Creek, K-1 (tributary to Kinley Creek), K-2 (tributary to Kinley Creek), unnamed tributary to Kinley Creek, Lowery Creek (tributary to Kinley Creek), Rawls Creek, R-2 (tributary to Rawls Creek), and Koon Branch (tributary to Rawls Creek). Peak discharges at the most downstream sites on Rawls Creek and Koon Branch had recurrence intervals of 75 years and 60 years, respectively. Peak discharges on Kinley Creek varied from 20 to 25 years north of K-1 basin to less than 10 years at K-1. The Stoop Creek basin had a recurrence interval of 10 years. (USGS)

  15. Ethanol extract of paeonia suffruticosa Andrews (PSE) induced AGS human gastric cancer cell apoptosis via fas-dependent apoptosis and MDM2-p53 pathways

    PubMed Central

    2012-01-01

    Background The root bark of Paeonia suffruticosa Andrews (PSE), also known as Moutan Cortex, has been widely used in Asia to treat various diseases. The molecular mechanisms by which PSE exerts its anti-oxidant and anti-inflammatory activities are well known, but its anti-cancer activity is not yet well understood. Here, we present evidence demonstrating that PSE can be used as a potent anti-cancer agent to treat gastric cancer. Methods The effects of the ethanol extract of PSE on cell proliferation were determined using an MTT (1-(4,5-dimethylthiazol-2-yl)-3,5-diphenylformazan) assay. Cell cytotoxicity induced by the PSE extact is measured using an LDH leakage assay. Flow cytometry was used to analyze the cell cycle and to measure the subG0/G1 apoptotic cell fraction. Apoptosis induced by the PSE extact is also examined using a DNA fragmentation assay. Western blot analysis is used to measure the levels of apoptotic proteins such as Fas receptor, caspase-8, caspase-3, PARP, Bax, Bcl-2, MDM2, and p53. Results This study demonstrated that treating AGS cells with the PSE extact significantly inhibited cell proliferation and induced cytotoxicity in a dose- and time-dependent manner. The PSE extract also induced apoptosis in AGS cells, as measured by flow cytometry and a DNA fragmentation assay. We found that the PSE extract induced apoptosis via the extrinsic Fas-mediated apoptosis pathway, which was concurrent with the activation of caspases, including caspase-8 and caspase-3, and cleavage of PARP. The MDM2-p53 pathway also played a role in the apoptosis of AGS cells that was induced by the PSE extract. Conclusions These results clearly demonstrate that the PSE extact displays growth-suppressive activity and induces apoptosis in AGS cells. Our data suggest that the PSE extact might be a potential anti-cancer agent for gastric cancer. PMID:22963678

  16. Spatial distribution and compositional variation of APS minerals related to uranium deposits in the Kiggavik-Andrew Lake structural trend, Nunavut, Canada

    NASA Astrophysics Data System (ADS)

    Riegler, Thomas; Quirt, Dave; Beaufort, Daniel

    2016-02-01

    The Kiggavik-Andrew Lake structural trend consists of four mineralized zones, partially outcropping, lying 2 km south of the erosional contact with the unmetamorphosed sandstone and basal conglomerates of the Paleoproterozoic Thelon Formation. The mineralization is controlled by a major E-W fault system associated with illite and sudoite alteration halos developed in the Archean metagraywackes of the Woodburn Lake Group. Aluminum phosphate sulfate (APS) minerals from the alunite group crystallized in association with the clay minerals in the basement alteration halo as well as in the overlying sandstones, which underwent mostly diagenesis. APS minerals are Sr- and S-rich (svanbergite end-member) in the sedimentary cover overlying the unconformity, whereas they are light rare earth elements (LREE)-rich (florencite end-member) in the altered basement rocks below the unconformity. The geochemical signature of each group of APS minerals together with the petrography indicates three distinct generations of APS minerals related to the following: (1) paleoweathering of continental surfaces prior to the basin occurrence, (2) diagenetic processes during the burial history of the lower unit of the Thelon sandstones, and (3) hydrothermal alteration processes which accompanied the uranium deposition in the basement rocks and partially overlap the sedimentary-diagenetic mineral parageneses. In addition, the association of a first generation of APS minerals with both detrital cerium oxide and aluminum oxy-hydroxide highlights the fact that a part of the detrital material of the basal Thelon Formation originated from eroded paleolaterite (allochthonous regolith). The primary rare earth element (REE)-bearing minerals (e.g., monazite, REE carbonates, and allanite) of the host rocks were characterized to identify the potential sources of REE. The REE chemical composition highlights a local re-incorporation of the REE released from the alteration processes in the APS minerals of

  17. Computer Modeling of Hydrology, Weathering, and Isotopic Fractionation in Andrews Creek, Rocky Mountain National Park, Colorado for Water Years 1992 through 2012

    NASA Astrophysics Data System (ADS)

    Webb, R. M. T.; Parkhurst, D. L.; Mast, A.; Clow, D. W.

    2014-12-01

    The U.S. Geological Survey's (USGS) Water, Energy, and Biogeochemical Model (WEBMOD) was used to simulate hydrology, weathering, and isotopic fractionation in the 1.7 square kilometer Andrews Creek alpine watershed. WEBMOD includes hydrologic modules derived from the USGS Precipitation Runoff Modeling System, the National Weather Service Hydro-17 snow model, and TOPMODEL. PHREEQC, a geochemical reaction model, is coupled with the hydrologic model to simulate the geochemical evolution of waters as they evaporate, mix, and react within the landscape. Major solute concentrations and δ18O were modeled over the period 1992-2012. Variations of chloride and inorganic nitrogen respond almost entirely to variations in atmospheric deposition and preferential elution of snowpack. Both evaporation and melting result in isotopic enrichment of heavy isotopes in the residual snowpack throughout the summer. Magnesium and potassium, derived mostly from weathering with some atmospheric inputs, vary seasonally with uptake during the growing season and release during the fall and winter. The weathering of granitic minerals—oligoclase, biotite, chlorite, pyrite, calcite, and formation of secondary minerals—kaolinite, goethite, gibbsite, and smectite-illite—were selected as primary reactions based on mole-balance modeling of basin outflows. The rates of these reactions were quantified by calibrating WEBMOD to match observed concentrations and loads. Exported annual loads of most weathering products are highly correlated with discharge, whereas silica loads are less correlated with discharge, suggesting a source that is more active during dry years and less active during wet years. Potential sources include net dissolution of kaolinite and smectite-illite or mineralization of colloids with high silica content. WEBMOD is a valuable tool for simulating water quality variations in response to climate change, acid mine drainage, acid rain, biological transformations, and other

  18. Hyporheic Geophysics: D.C. Resistivity Imaging of Valley-bottom Alluvium in a 3rd-order Mountain Stream, HJ Andrews Experimental Forest, Oregon, USA

    NASA Astrophysics Data System (ADS)

    Zarnetske, J. P.; Haggerty, R.; Crook, N.; Robinson, D. A.

    2006-12-01

    The hyporheic zone (HZ) can serve as either a source or a sink for nutrients (e.g., nitrogen) and moderates biogeochemical and temperature signals in stream ecosystems. Understanding of the HZ is hampered by lack of subsurface images, particularly ones that are non-invasive and fast. Geophysical imaging, combined with extant empirical methods and hydrodynamic models provides an opportunity to improve precision in modeling HZ transport and nutrient retention. With the aid of CUAHSI HMF, we completed a d.c. resistivity survey of an existing stream denitrification study site (Mack Creek, H.J. Andrews Experimental Forest, OR, a Long-term Ecological Research site) to quantify the geometry of the valley bottom alluvial aquifer and HZ. The non- invasive d.c. resistivity survey successfully produced a quantitative 3-dimensional image of the variable alluvial aquifer thickness below and adjacent to the stream channel. We extensively imaged one area, 50 m x 28 m with 10 transects, in an old growth Douglas fir (Pseudotsuga menziesii) stand which incorporated a large woody debris log jam, to determine that alluvial thickness averages 4.1 m and varies between 0 m and 8 m. We completed a single 50 m longitudinal section in an adjacent downstream logged block (harvested 1964-65) to determine that alluvial thickness averages 0.3 m and varies between 0 m and 1 m. The presence of valley- bottom bedrock exposures at the study site helped to constrain and verify the d.c. resistivity interpretation of the bedrock-alluvium interface. Some d.c. survey challenges were encountered, including the confinement of electrode lines to the channel or near channel because dry organic layers or fallen trees across much of the forest floor prevented good electrode contact with the ground. Ultimately, this geophysics-enhanced knowledge of the stream-adjacent aquifer will allow for more accurate interpretation of hyporheic observations and parameterization of hyporheic hydraulic and denitrification

  19. H3K4me3 Stimulates the V(D)J RAG Complex for Both Nicking and Hairpinning in Trans in Addition to Tethering in Cis: Implications for Translocations

    PubMed Central

    Shimazaki, Noriko; Tsai, Albert G.; Lieber, Michael R.

    2010-01-01

    SUMMARY The PHD finger of the RAG2 polypeptide of the RAG1/RAG2 complex binds to the histone H3 modification, trimethylated lysine 4 (H3K4me3), and in some manner increases V(D)J recombination. However, in the absence of biochemical studies of H3K4me3 on purified RAG enzyme activity, the precise role of H3K4me3 has not been clear. Here, we find that H3K4me3 stimulates purified RAG enzymatic activity at both the nicking (2 to 5-fold) and hairpinning (3 to 11-fold) steps of V(D)J recombination. Remarkably, this stimulation can be achieved with free H3K4me3 peptide (in trans). This indicates that H3K4me3 functions via two distinct mechanisms. It not only tethers the RAG enzyme complex to a region of DNA, but it also induces a substantial increase in the catalytic turnover number (kcat) of the RAG complex. The H3K4me3 catalytic stimulation applies to suboptimal cryptic RSS sites located at H3K4me3 peaks that are critical in the inception of human T-cell acute lymphoblastic lymphomas. PMID:19524534

  20. Analysis of Apoptosis in Ultraviolet-Induced Sea Cucumber (Stichopus japonicus) Melting Using Terminal Deoxynucleotidyl-Transferase-Mediated dUTP Nick End-Labeling Assay and Cleaved Caspase-3 Immunohistochemistry.

    PubMed

    Yang, Jing-Feng; Gao, Rong-Chun; Wu, Hai-Tao; Li, Peng-Fei; Hu, Xian-Shu; Zhou, Da-Yong; Zhu, Bei-Wei; Su, Yi-Cheng

    2015-11-01

    The sea cucumber body wall melting phenomenon occurs under certain circumstances, and the mechanism of this phenomenon remains unclear. This study investigated the apoptosis in the ultraviolet (UV)-induced sea cucumber melting phenomenon. Fresh sea cucumbers (Stichopus japonicus) were exposed to UV radiation for half an hour at an intensity of 0.056 mW/cm(2) and then held at room temperature for melting development. The samples were histologically processed into formalin-fixed paraffin-embedded tissues. The apoptosis of samples was analyzed with the terminal deoxynucleotidyl-transferase-mediated dUTP nick end-labeling (TUNEL) assay and cleaved caspase-3 immunohistochemistry. The emergence of TUNEL-positive cells speeds up between 0.5 and 2 h after UV irradiation. Cleaved caspase-3 positive cells were obviously detected in sample tissues immediately after the UV irradiation. These results demonstrated that sea cucumber melting induced by UV irradiation was triggered by the activation of caspase-3 followed by DNA fragmentation in sea cucumber tissue, which was attributed to apoptosis but was not a consequence of autolysis activity. PMID:26484758

  1. Spatial and Temporal Trends in the Carbon, Nitrogen, and Sulfur Isotopes of Stream DOM From 10 Watersheds at the HJ Andrews Experimental Forest.

    NASA Astrophysics Data System (ADS)

    Frentress, J.; Kendall, C.; Lajtha, K.; Jones, J.

    2008-12-01

    In order to better understand sources of dissolved organic matter (DOM) in streams from the small to large watershed scales, we initiated a one-year investigation of the chemical and isotopic characteristics of DOM at the HJ Andrews Experimental Forest (HJA) in Blue River, OR. DOM is a biologically significant loss from these watersheds, but its sources (forest floor, mineral soil, riparian zones, stream biota) are debated. Traditional chemical characterizations of DOM like SUVA and FI have been useful in conceptualizing and modeling streamflow sources, however, an improved method for assessing DOM quality is needed to adequately differentiate DOM from sources within the watershed. The isotopic characterization of inorganic molecules like nitrate has provided insight to the role of subsurface and surface processes governing the production and transport of critical nutrients, and yet to date, little work has been done to examine the usefulness of isotopic characterization of organically bound nutrients. We apply the isotopic characterization approach to DOM in order to better understand DOM production, transformation, and transport to streams in a range of watershed sizes. Major questions addressed in this research are: 1) Where in the watershed does stream DOM come from? 2) How do DOM sources vary temporally? 3) How do physical attributes of the watershed mediate DOM quality? A relatively new solid-phase extraction technique using C-18 resin was used to isolate DOM in water samples from 10 watersheds, ranging in size from 10 to 6200 hectares, on 3-week intervals from May 2007 to June 2008. The modified technique allowed for small (1 Liter) sample sizes and short processing times to reduce the costs of analysis. The capacity of carbon, nitrogen and sulfur isotopic characterizations of DOM, as well as traditional methods like SUVA and C:N, to predict physical watershed attributes (i.e. mean residence time, soil depth, elevation, gradient) and land use history (timber

  2. Deep versus shallow melt stagnation in an ultra-slow / ultra-cold ridge segment: the Andrew Bain southern RTI (SWIR)

    NASA Astrophysics Data System (ADS)

    Paganelli, E.; Brunelli, D.; Seyler, M.; Bonatti, E.; Cipriani, A.; Ligi, M.

    2011-12-01

    The Andrew Bain Fracture Zone (ABFZ) represents one of the largest transform faults in the ridge system spanning 750 km in length with a characteristic lens-shape structure. The southern Ridge-Transform Intersection represents the deepest sector of the whole South West Indian Ridge system. During the Italian-Russian expedition S23-AB06, the seafloor in the Southern Ridge Transform Intersection (RTI) has been sampled recovering only ultramafic material in the majority of the dredging sites. The sampled spinel and plagioclase peridotites show hybrid textures, characterized either by deep spinel-field impregnation assemblages (sp+cpx±opx±ol) or by plagioclase-field equilibrated patches and mineral trails (pl+cpx±ol) marked by both crystallization of newly formed plagioclase-field equilibrated trails and formation of plagioclase coronas around spinel. The ones collected from ridge axis show also late gabbroic pockets and veins, variably enriched in clinopyroxene. Overall textures account for important melt percolation/stagnation events occurred in the plagioclase and spinel field. Major and trace element distribution in pyroxenes and spinels from spinel-bearing peridotites overall follow a general melting trend accompanied by a progressive re-equilibration to lower P/T facies at all scales. However, only few samples can be linked to near fractional melting, while the majority of them shows REE pattern and trace element concentrations that cannot be reproduced by fractional melting process. Open-system melting (OSM) better reproduces measured REE patterns. Modeling melting in an open system scenario requires high residual porosity to be accounted for along with generally enriched melts to influx the melting parcel at depth. Melting at high residual porosity suggests a near-batch regime in which enriched melts stagnate in the spinel field. Inhibition of melt segregation during melt/rock interaction asks for a permeability barrier to develop in the region where the

  3. Target-triggered three-way junction structure and polymerase/nicking enzyme synergetic isothermal quadratic DNA machine for highly specific, one-step, and rapid microRNA detection at attomolar level.

    PubMed

    Zhang, Qing; Chen, Feng; Xu, Feng; Zhao, Yongxi; Fan, Chunhai

    2014-08-19

    MicroRNAs (miRNAs) play important roles in many biological processes and are regarded as promising cancer biomarkers. Herein, a highly specific, one-step, and rapid miRNAs detection strategy with attomolar sensitivity has been developed on the basis of a target-triggered three-way junction (3-WJ) structure and polymerase/nicking enzyme synergetic isothermal quadratic DNA machine (ESQM). To this end, 3-WJ probes (primer and template) are designed to selectively recognize target miRNA and form the stable 3-WJ structure to trigger ESQM, resulting in a high quadratic amplified signal. A high specificity is demonstrated by the excellent discrimination of even single-base mismatched homologous sequences with mismatched bases in varied locations (close to the 3'-end, the 5'-end, and the middle). In addition, a low detection limit down to 2 amol was achieved within 30 min. This sensitivity is much higher than those of most linear amplification-based approaches and is even comparable to those of some exponential amplification-based methods. Furthermore, the applicability of this method in complex samples was demonstrated by the analysis of cancer cell small RNA extracts, results of which were in good agreement with those obtained by a commercial miRNA kit and previously published data. The miRNA with a 3' end modification (2'-O-methylation), such as plant miRNA, was also successfully detected, confirming the good universality of the proposed strategy. It is worthwhile to point out that several well-established methods using miRNA as primer for polymerization reaction are of relatively poor performance in the analysis of these modified miRNA. Therefore, these merits endow the developed strategy with powerful implications for biological research and an effective diagnostic assay. PMID:25072308

  4. Magnitude and extent of sediment toxicity in four bays of the Florida Panhandle: Pensacola, Choctawhatchee, St. Andrew and Apalachicola. National status and trends program for marine environmental quality: Technical memo

    SciTech Connect

    Long, E.R.; Sloane, G.M.; Carr, R.S.; Scott, K.J.; Thursby, G.B.

    1997-10-01

    The toxicity of sediments in Pensacola, Choctawhatcheee, St. Andrew and Apalachicola Bays was determined as part of bioeffects assessments performed by NOAA`s National Status and Trends Program. The objectives of the survey were to determine: (1) the spatial patterns in toxicity throughout each bay, (2) the spatial extent of toxicity throughout and among the bays, (3) the severity of degree of toxicity, and (4) the relationships between chemical contamination and toxicity. The survey was conducted over two years: Pensacola Bay and St. Andrew Bay were sampled in 1993; and Choctawhatchee Bay, Apalachicola Bay and Bayou Chico (a sub-basin of Pensacola Bay) were sampled during 1994. Surficial sediment samples were collected from 123 randomly-chosen locations throughout the five areas. Multiple toxicity tests were conducted on all samples, and chemical analyses were performed on 102 of the 123 samples. Toxicological tests were conducted to determine survival, reproductive success, morphological development, metabolic activity, and genotoxicity; all bays showed toxicity in at least some of the samples.

  5. A comparison of mercury burdens between St. Marks National Wildlife Refuge and St. Andrew Bay, Florida: Evaluation of fish body burdens and physiological responses in largemouth bass, spotted seatrout, striped mullet, and sunfish

    USGS Publications Warehouse

    Huge, D.H.; Rauschenberger, R.H.; Wieser, F.M.; Hemming, J.M.

    2011-01-01

    Musculature from the dorsal region of 130 largemouth bass (Micropterus salmoides), 140 sunfish (Lepomis sp.), 41 spotted seatrout (Cynoscion nebulosus) and 67 striped mullet (Mugil cephalus) were collected from five estuarine and five freshwater sites within the St. Marks National Wildlife Refuge and two estuarine and two freshwater sites from St. Andrew Bay, Florida, United States of America. Musculature was analyzed for total mercury content, sagittal otoliths were removed for age determination and physiological responses were measured. Largemouth bass and sunfish from the refuge had higher mercury concentrations in musculature than those from the bay. Male spotted seatrout, male striped mullet, male and female sunfish and female largemouth bass had mercury burdens positively correlated with length. The majority of all four species of fish from both study areas contained mercury levels below 1.5 part per million, the limit for safe consumption recommended the Florida Department of Health. In comparison, a significant percentage of largemouth bass and sunfish from several sampled sites, most notably Otter Lake and Lake Renfroe within St. Marks National Wildlife Refuge, had mercury levels consistent with the health department's guidelines of 'limited consumption' or 'no consumption guidelines.'

  6. The Future of the Andrew File System

    ScienceCinema

    None

    2011-04-25

    The talk will discuss the ten operational capabilities that have made AFS unique in the distributed file system space and how these capabilities are being expanded upon to meet the needs of the 21st century. Derrick Brashear and Jeffrey Altman will present a technical road map of new features and technical innovations that are under development by the OpenAFS community and Your File System, Inc. funded by a U.S. Department of Energy Small Business Innovative Research grant. The talk will end with a comparison of AFS to its modern days competitors.

  7. Wireless Andrew: Everywhere You Want To Be.

    ERIC Educational Resources Information Center

    Futhey, Tracy

    2000-01-01

    Describes the wireless local area network at Carnegie Mellon University. Highlights include classroom applications, particularly in the Business School; the use of laptop computers configured with wireless technology; handheld computers, including use for testing; and assuring appropriate uses of wireless technology. (LRW)

  8. The Future of the Andrew File System

    SciTech Connect

    2011-02-23

    The talk will discuss the ten operational capabilities that have made AFS unique in the distributed file system space and how these capabilities are being expanded upon to meet the needs of the 21st century. Derrick Brashear and Jeffrey Altman will present a technical road map of new features and technical innovations that are under development by the OpenAFS community and Your File System, Inc. funded by a U.S. Department of Energy Small Business Innovative Research grant. The talk will end with a comparison of AFS to its modern days competitors.

  9. Nick Sagan Reflects on Voyager 1 and the Golden Record

    NASA Astrophysics Data System (ADS)

    Showstack, Randy

    2013-10-01

    When scientists confirmed on 12 September that NASA's Voyager 1 spacecraft had entered interstellar space (Eos, 94(39), 339, doi:10.1002/2013EO390003), the probe was acknowledged as the first human-made object to travel into that realm. The probe and its twin, Voyager 2, each carry a 12-inch gold-plated copper disk, known as the Golden Record.

  10. Speaking Unassisted: Comments on a Paper by Andrews et al.

    ERIC Educational Resources Information Center

    Wingate, Marcel E.

    1983-01-01

    In a reply to a review of replicated findings on stuttering, the author adds 14 points concerning symptoms, prevalence, incidence, stutterer-nonstutterer differences, and variability of stuttering. He takes exception to the review's statements on treatment and theories of stuttering. (CL)

  11. A resolution honoring the life of Andrew Wyeth.

    THOMAS, 111th Congress

    Sen. Casey, Robert P., Jr. [D-PA

    2009-01-27

    01/27/2009 Submitted in the Senate, considered, and agreed to without amendment and with a preamble by Unanimous Consent. (consideration: CR S946-947; text as passed Senate: CR S947; text of measure as introduced: CR S899-900) (All Actions) Tracker: This bill has the status Passed SenateHere are the steps for Status of Legislation:

  12. General Christopher C. Andrews: Leading the Minnesota Forestry Revolution

    ERIC Educational Resources Information Center

    Rice, Anna M.

    2002-01-01

    In the nineteenth century, America's burgeoning population certainly did grab all the timber it could. Vast pine forests stretched from Maine to Dakota, and the lumber industry voraciously consumed them from east to west. In 1800, the Minnesota territory was sparsely sprinkled with fur traders and American Indians. By 1850, its bounteous forests…

  13. Investigation by EPR and ENDOR spectroscopy of the nickel(I) form of cofactor F{sub 430} of Methanobacterium thermoautorophicum and of nickel(I) octaethylisobacteriochlorin

    SciTech Connect

    Telser, J.; Fann, Y.C.; Hoffman, B.M.; Renner, M.W.; Fajer, J.; Wang, S.; Zhang, H.; Scott, R.A.

    1997-01-29

    The terminal step in methane generation by the archaeon Methanobacterium thermoautotrophicum is catalyzed by the enzyme S-methyl coenzyme M reductase (methylreductase). This enzyme contains a Ni(II) tetrapyrrole cofactor, F{sub 430}, at the active site in the resting state. A Ni(I) state (Ni{sup I}F{sub 430}) has been proposed as the active form of the cofactor. Nickel isobacteriochlorins have been used to model F{sub 430}. We have investigated both Ni{sup I}F{sub 430} and Ni{sup I}OEiBC using CW and pulsed EPR and ENDOR spectroscopy at X-band and Q-band microwave frequencies. In agreement with a previous X-band EPR and ESEEM study, at Q-band, the g tensor of Ni{sup I}F{sub 430} appears axial and {sup 1,2}H ENDOR of Ni{sup I}F{sub 430} in H{sub 2}O versus D{sub 2}O solvent shows no evidence for strongly coupled, solvent-exchangeable hydrogens, and this indicates that there is no water axially coordinated to Ni(I) in contrast to the Ni(II) resting state. Both Ni{sup I}F{sub 430} and Ni{sup I}OEiBC give {sup 14}N ENDOR signals arising from the four pyrrole nitrogen ligands to Ni(I). Previous EXAFS studies of Ni{sup I}OEiBC and Ni{sup I}F{sub 430}Me{sub 5} showed two sets of Ni(I)-N distances differing by nearly 8%, and in agreement with this, the {sup 14}N ENDOR signals for both Ni{sup I}OEiBC and Ni{sup I}F{sub 430} can be analyzed in terms of superimposed signals from two distinct types of nitrogen ligand. 86 refs., 5 figs., 3 tabs.

  14. Magnetic Contribution to Heat Capacity and Entropy of Nicke Ferrite (NiFe2O4)

    SciTech Connect

    S Ziemniak, L Anovitz, R Castelli

    2005-12-15

    The heat capacity of nickel ferrite was measured as a function of temperature over the range from 50 to 1200 C using a differential scanning calorimeter. A thermal anomaly was observed at 584.9 C, the expected Curie temperature, T{sub c}. The observed behavior was interpreted by recognizing the sum of three contributions: (1) lattice (vibrational), (2) a spin wave (magnetic) component and (3) a {lambda}-transition (antiferromagnetic-paramagnetic transition) at the Curie temperature. The first was modeled using vibrational frequencies derived from an experimentally-based ir absorption spectrum, while the second was modeled using a spin wave analysis that provided a T{sup 3/2} dependency in the low temperature limit, but incorporated an exchange interaction between cation spins in the octahedral and tetrahedral sites at elevated temperatures, as first suggested by Grimes [15]. The {lambda}-transition was fitted to an Inden-type model which consisted of two truncated power law series in dimensionless temperature (T/T{sub c}). Exponential equality was observed below and above T{sub c}, indicating symmetry about the Curie temperature. Application of the methodology to existing heat capacity data for other transition metal ferrites (AFe{sub 2}O{sub 4}, A = Fe, Co) revealed the same exponential equality, i.e., m = n = 5.

  15. Processing of Nonconjugative Resistance Plasmids by Conjugation Nicking Enzyme of Staphylococci

    PubMed Central

    Pollet, Rebecca M.; Ingle, James D.; Hymes, Jeff P.; Eakes, Thomas C.; Eto, Karina Yui; Kwong, Stephen M.; Ramsay, Joshua P.; Firth, Neville

    2016-01-01

    ABSTRACT Antimicrobial resistance in Staphylococcus aureus presents an increasing threat to human health. This resistance is often encoded on mobile plasmids, such as pSK41; however, the mechanism of transfer of these plasmids is not well understood. In this study, we first examine key protein-DNA interactions formed by the relaxase enzyme, NES, which initiates and terminates the transfer of the multidrug resistance plasmid pSK41. Two loops on the NES protein, hairpin loops 1 and 2, form extensive contacts with the DNA hairpin formed at the oriT region of pSK41, and here we establish that these contacts are essential for proper DNA cleavage and religation by the full 665-residue NES protein in vitro. Second, pSK156 and pCA347 are nonconjugative Staphylococcus aureus plasmids that contain sequences similar to the oriT region of pSK41 but differ in the sequence predicted to form a DNA hairpin. We show that pSK41-encoded NES is able to bind, cleave, and religate the oriT sequences of these nonconjugative plasmids in vitro. Although pSK41 could mobilize a coresident plasmid harboring its cognate oriT, it was unable to mobilize plasmids containing the pSK156 and pCA347 variant oriT mimics, suggesting that an accessory protein like that previously shown to confer specificity in the pWBG749 system may also be involved in transmission of plasmids containing a pSK41-like oriT. These data indicate that the conjugative relaxase in trans mechanism recently described for the pWBG749 family of plasmids also applies to the pSK41 family of plasmids, further heightening the potential significance of this mechanism in the horizontal transfer of staphylococcal plasmids. IMPORTANCE Understanding the mechanism of antimicrobial resistance transfer in bacteria such as Staphylococcus aureus is an important step toward potentially slowing the spread of antimicrobial-resistant infections. This work establishes protein-DNA interactions essential for the transfer of the Staphylococcus aureus multiresistance plasmid pSK41 by its relaxase, NES. This enzyme also processed variant oriT-like sequences found on numerous plasmids previously considered nontransmissible, suggesting that in conjunction with an uncharacterized accessory protein, these plasmids may be transferred horizontally via a relaxase in trans mechanism. These findings have important implications for our understanding of staphylococcal resistance plasmid evolution. PMID:26728193

  16. Structures of minute virus of mice replication initiator protein N-terminal domain: Insights into DNA nicking and origin binding

    SciTech Connect

    Tewary, Sunil K.; Liang, Lingfei; Lin, Zihan; Lynn, Annie; Cotmore, Susan F.; Tattersall, Peter; Zhao, Haiyan; Tang, Liang

    2015-02-15

    Members of the Parvoviridae family all encode a non-structural protein 1 (NS1) that directs replication of single-stranded viral DNA, packages viral DNA into capsid, and serves as a potent transcriptional activator. Here we report the X-ray structure of the minute virus of mice (MVM) NS1 N-terminal domain at 1.45 Å resolution, showing that sites for dsDNA binding, ssDNA binding and cleavage, nuclear localization, and other functions are integrated on a canonical fold of the histidine-hydrophobic-histidine superfamily of nucleases, including elements specific for this Protoparvovirus but distinct from its Bocaparvovirus or Dependoparvovirus orthologs. High resolution structural analysis reveals a nickase active site with an architecture that allows highly versatile metal ligand binding. The structures support a unified mechanism of replication origin recognition for homotelomeric and heterotelomeric parvoviruses, mediated by a basic-residue-rich hairpin and an adjacent helix in the initiator proteins and by tandem tetranucleotide motifs in the replication origins. - Highlights: • The structure of a parvovirus replication initiator protein has been determined; • The structure sheds light on mechanisms of ssDNA binding and cleavage; • The nickase active site is preconfigured for versatile metal ligand binding; • The binding site for the double-stranded replication origin DNA is identified; • A single domain integrates multiple functions in virus replication.

  17. Talking about Life

    NASA Astrophysics Data System (ADS)

    Impey, Chris

    2010-08-01

    Preface; Part I. Introduction Timothy Ferris, Iris Fry, Steven Dick, Ann Druyan, Pinky Nelson, Neil Tyson, Steve Benner and William Bains; Part II. Earth Roger Buick, Lynn Rothschild, John Baross, Joe Kirschvink, Andrew Knoll, Simon Conway Morris, Roger Hanlon and Lori Marino; Part III. Solar System Chris McKay, David Grinspoon, Jonathan Lunine, Carolyn Porco, Laurie Leshin, Guy Consolmagno and Peter Smith; Part IV. Exoplanets Alan Boss, Geoff Marcy, Debra Fischer, Sara Seager, David Charbonneau and Vikki Meadows; Part V. Frontiers Jill Tarter, Seth Shostak, Ray Kurzweil, Nick Bostrom, Paul Davies, Martin Rees, Ben Bova and Jennifer Michael Hecht; Reading list; Glossary; Index.

  18. Involvement of Colonizing Bacillus Isolates in Glucovanillin Hydrolysis during the Curing of Vanilla planifolia Andrews.

    PubMed

    Chen, Yonggan; Gu, Fenglin; Li, Jihua; He, Shuzhen; Xu, Fei; Fang, Yiming

    2015-08-01

    Vanilla beans were analyzed using biochemical methods, which revealed that glucovanillin disperses from the inner part to the outer part of the vanilla bean during the curing process and is simultaneously hydrolyzed by β-d-glucosidase. Enzymatic hydrolysis was found to occur on the surface of the vanilla beans. Transcripts of the β-d-glucosidase gene (bgl) of colonizing microorganisms were detected. The results directly indicate that colonizing microorganisms are involved in glucovanillin hydrolysis. Phylogenetic analysis based on 16S rRNA gene sequences showed that the colonizing microorganisms mainly belonged to the Bacillus genus. bgl was detected in all the isolates and presented clustering similar to that of the isolate taxonomy. Furthermore, inoculation of green fluorescent protein-tagged isolates showed that the Bacillus isolates can colonize vanilla beans. Glucovanillin was metabolized as the sole source of carbon in a culture of the isolates within 24 h. These isolates presented unique glucovanillin degradation capabilities. Vanillin was the major volatile compound in the culture. Other compounds, such as α-cubebene, β-pinene, and guaiacol, were detected in some isolate cultures. Colonizing Bacillus isolates were found to hydrolyze glucovanillin in culture, indirectly demonstrating the involvement of colonizing Bacillus isolates in glucovanillin hydrolysis during the vanilla curing process. Based on these results, we conclude that colonizing Bacillus isolates produce β-d-glucosidase, which mediates glucovanillin hydrolysis and influences flavor formation. PMID:25979899

  19. Detectives Nemorin and Andrews Anti-Gun Trafficking Act of 2013

    THOMAS, 113th Congress

    Rep. King, Peter T. [R-NY-2

    2013-02-14

    04/08/2013 Referred to the Subcommittee on Crime, Terrorism, Homeland Security, And Investigations. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  20. Enhancing Pupils' Aspirations to University: The St Andrews Sutton Trust School Experience

    ERIC Educational Resources Information Center

    Lasselle, Laurence; Keir, Fraser; Smith, Ian

    2009-01-01

    The Sutton Trust Summer School offers to S5/Year 12 pupils the opportunity to sample student life for a week at one of five selecting universities in the UK. Most of the participants on the Sutton Trust Summer School will be the first generation in their family to attend university and have come from schools which traditionally send low numbers to…

  1. A resolution honoring former Senator and Rear Admiral Jeremiah Andrew Denton, Jr.

    THOMAS, 113th Congress

    Sen. Sessions, Jeff [R-AL

    2014-03-31

    03/31/2014 Submitted in the Senate, considered, and agreed to without amendment and with a preamble by Unanimous Consent. (consideration: CR S1881; text as passed Senate: CR S1874) (All Actions) Tracker: This bill has the status Passed SenateHere are the steps for Status of Legislation:

  2. Hematopoietic Stem Cell Transplantation for Primary Immunodeficiencies By Elizabeth Kang and Andrew Gennery

    PubMed Central

    Kang, Elizabeth; Gennery, Andrew

    2014-01-01

    Allogeneic Hematopoietic Stem Cell Transplantation has been shown to be curative for well described as well as newly discovered immunodeficiencies. However it is difficulty to define a universal transplant regimen given the rarity of these disorders and the varied pathophysiology these disorders encompass. This review will discuss those primary immunodeficiencies most commonly treated by hematopoietic stem cell transplant and describe the transplant issues specific to these disorders. PMID:25459185

  3. Multiple species of wild tree peonies gave rise to the 'king of flowers', Paeonia suffruticosa Andrews.

    PubMed

    Zhou, Shi-Liang; Zou, Xin-Hui; Zhou, Zhi-Qin; Liu, Jing; Xu, Chao; Yu, Jing; Wang, Qiang; Zhang, Da-Ming; Wang, Xiao-Quan; Ge, Song; Sang, Tao; Pan, Kai-Yu; Hong, De-Yuan

    2014-12-22

    The origin of cultivated tree peonies, known as the 'king of flowers' in China for more than 1000 years, has attracted considerable interest, but remained unsolved. Here, we conducted phylogenetic analyses of explicitly sampled traditional cultivars of tree peonies and all wild species from the shrubby section Moutan of the genus Paeonia based on sequences of 14 fast-evolved chloroplast regions and 25 presumably single-copy nuclear markers identified from RNA-seq data. The phylogeny of the wild species inferred from the nuclear markers was fully resolved and largely congruent with morphology and classification. The incongruence between the nuclear and chloroplast trees suggested that there had been gene flow between the wild species. The comparison of nuclear and chloroplast phylogenies including cultivars showed that the cultivated tree peonies originated from homoploid hybridization among five wild species. Since the origin, thousands of cultivated varieties have spread worldwide, whereas four parental species are currently endangered or on the verge of extinction. The documentation of extensive homoploid hybridization involved in tree peony domestication provides new insights into the mechanisms underlying the origins of garden ornamentals and the way of preserving natural genetic resources through domestication. PMID:25377453

  4. 77 FR 59163 - Andrew Pickens Ranger District; South Carolina; AP Loblolly Pine Removal and Restoration Project

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-26

    ... CONTACT: Victor Wyant, 864-638-9568. Correction 1. In the Federal Register of March 8, 2010, in FR/Vol. 75... expected by December 2012. 2. In the Federal Register of March 8, 2010, in FR/Vol. 75, No. 44, on page..., 2010, in FR/Vol. 75, No. 44, on page 10458, in the first column, correct the ``Purpose and Need...

  5. Involvement of Colonizing Bacillus Isolates in Glucovanillin Hydrolysis during the Curing of Vanilla planifolia Andrews

    PubMed Central

    Chen, Yonggan; Li, Jihua; He, Shuzhen; Xu, Fei; Fang, Yiming

    2015-01-01

    Vanilla beans were analyzed using biochemical methods, which revealed that glucovanillin disperses from the inner part to the outer part of the vanilla bean during the curing process and is simultaneously hydrolyzed by β-d-glucosidase. Enzymatic hydrolysis was found to occur on the surface of the vanilla beans. Transcripts of the β-d-glucosidase gene (bgl) of colonizing microorganisms were detected. The results directly indicate that colonizing microorganisms are involved in glucovanillin hydrolysis. Phylogenetic analysis based on 16S rRNA gene sequences showed that the colonizing microorganisms mainly belonged to the Bacillus genus. bgl was detected in all the isolates and presented clustering similar to that of the isolate taxonomy. Furthermore, inoculation of green fluorescent protein-tagged isolates showed that the Bacillus isolates can colonize vanilla beans. Glucovanillin was metabolized as the sole source of carbon in a culture of the isolates within 24 h. These isolates presented unique glucovanillin degradation capabilities. Vanillin was the major volatile compound in the culture. Other compounds, such as α-cubebene, β-pinene, and guaiacol, were detected in some isolate cultures. Colonizing Bacillus isolates were found to hydrolyze glucovanillin in culture, indirectly demonstrating the involvement of colonizing Bacillus isolates in glucovanillin hydrolysis during the vanilla curing process. Based on these results, we conclude that colonizing Bacillus isolates produce β-d-glucosidase, which mediates glucovanillin hydrolysis and influences flavor formation. PMID:25979899

  6. Detecting Outliers in Marathon Data by Means of the Andrews Plot

    NASA Astrophysics Data System (ADS)

    Stehlík, Milan; Wald, Helmut; Bielik, Viktor; Petrovič, Juraj

    2011-09-01

    For an optimal race performance, it is important, that the runner keeps steady pace during most of the time of the competition. First time runners or athletes without many competitions often experience an "blow out" after a few kilometers of the race. This could happen, because of strong emotional experiences or low control of running intensity. Competition pace of half marathon of the middle level recreational athletes is approximately 10 sec quicker than their training pace. If an athlete runs the first third of race (7 km) at a pace that is 20 sec quicker than is his capacity (trainability), he would experience an "blow out" in the last third of the race. This would be reflected by reducing the running intensity and inability to keep steady pace in the last kilometers of the race and in the final time as well. In sports science, there are many diagnostic methods ([3], [2], [6]) that are used for prediction of optimal race pace tempo and final time. Otherwise there is lacking practical evidence of diagnostics methods and its use in the field (competition, race). One of the conditions that needs to be carried out is that athletes have not only similar final times, but it is important that they keep constant pace as much as possible during whole race. For this reason it is very important to find outliers. Our experimental group consisted of 20 recreational trained athletes (mean age 32,6 years±8,9). Before the race the athletes were instructed to run on the basis of their subjective feeling and previous experience. The data (running pace of each kilometer, average and maximal heart rate of each kilometer) were collected by GPS-enabled personal trainer Forerunner 305.

  7. 76 FR 57043 - Andrew N. Finkel; Analysis of Proposed Consent Order to Aid Public Comment

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-15

    ... service. Visit the Commission Web site at http://www.ftc.gov to read this Notice and the news release... Pwner which respondent developed and sold in Google's Android Marketplace. Respondent claimed that...

  8. 75 FR 32221 - Whirlpool Corporation, Evansville Division, Including On-Site Leased Workers from Andrews...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-07

    ... (75 FR 10321). At the request of the State Agency, the Department reviewed the certification for... under Chapter 2 of Title II of the Trade Act of 1974, as amended. Elliott S. Kushner, Certifying...

  9. Seizing Opportunities: Genie Tyburski--Ballard Spahr Andrews & Ingersoll, LLP, Philadelphia

    ERIC Educational Resources Information Center

    Library Journal, 2004

    2004-01-01

    Genie Tyburski did not set out to be a law librarian. When asked at Drexel's library school what kind of librarian she wanted to be, she was surprised that "a good one" was not one of the options. But six weeks into the semester, she landed a part-time cataloging job at Community Legal Services in Philadelphia; six months later she was the library…

  10. 75 FR 10457 - Andrew Pickens Ranger District; South Carolina; AP Loblolly Pine Removal and Restoration Project

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-08

    ... manual and mechanical treatment. Woodlands are forests with relatively low tree densities of 25-60... density of trees in these stands range from sparse to a dense stocking basal area of 160 square feet per... as add to habitat diversity. Woodlands are forests with relatively low tree densities of...