WorldWideScience

Sample records for boat basic oligonucleotide

  1. BASIC CHARACTERISTICS AND ROWING TECHNIQUES WITH TOURIST CANOE BOATS

    Directory of Open Access Journals (Sweden)

    Zvezdan Savić

    2007-05-01

    Full Text Available By its appearance canoe boats, both competitive and tourist, differ from kayak boats. Main differences are in length, width and the physical appearance of the boats. Canoe rowers use one-leaf paddle, while kayak rowers use two-leaf paddles which are set at the angle of 90 degrees or less. By their main functions, canoe boats can be divided into two groups: 1 competitive and 2 recreational – tourist. Tourist canoe, by its characteristics is a recreational boat for calm waters, though it could be used in the fast – wild waters, in extreme situations. This boat is very stable and a favorite among athletes, campers, adventurers, and all nature lovers. Rowing technique in the tourist boat represents the main way of setting canoe in motion by using the rowers force in specifi c direction. It is, also, the way to keep the canoe stable on the surface. Rowing technique is the same as the rowing mechanics with the competitive canoes. Rower’s strokes should be calm, synchronized and long enough, harmonized with the canoe and water movement. They, also, should be mechanically well performed so that the canoe would move in the desired direction. Rowing technique understands fallowing strokes: stroke for moving canoe straight ahead, turning canoe left, right, reverse and for moving sidewise. This paper describes and explains characteristics and mechanics of rowing in the tourist canoe boat

  2. Boats

    CERN Document Server

    Rivera, Andrea

    2016-01-01

    From paddles to sails, learn about the science and technologies that help boats float across the water. Easy-to-read text and vibrant, full-color photos captivate young readers. Plus, bolded glossary terms and a key stats section make it easy to zoom in and learn more. Aligned to Common Core Standards and correlated to state standards. Abdo Zoom is a division of ABDO.

  3. The big book of wooden boat restoration basic techniques, maintenance, and repair

    CERN Document Server

    Larsson, Thomas

    2016-01-01

    An excellent manual for embarking on a wooden boat restoration project. The Big Book of Wooden Boat Restoration is the perfect introduction or reference guide for both novice and experienced wooden boat enthusiasts. Author Thomas Larsson, one of Sweden's most experienced and premier wooden boat restorers, has compiled his knowledge of the craft for readers and placed it in this book. This ultimate guide to restoration contains useful facts and an extensive glossary, accessible to both new hobbyists and longtime boat lovers. Also within this book are chapters on boat care, including winter maintenance, racing, finishing, and stripping. Additionally, there is updated information on boat building, gluing, and tools. The most extensive part of this book consists of chapters that describe the detailed clean repair of wooden boats—everything from plug accession and bonding to changing socks and bottom engine installation. Larsson includes a history of boat building and provides a nice glimpse of different wooden b...

  4. Boat sampling

    International Nuclear Information System (INIS)

    Citanovic, M.; Bezlaj, H.

    1994-01-01

    This presentation describes essential boat sampling activities: on site boat sampling process optimization and qualification; boat sampling of base material (beltline region); boat sampling of weld material (weld No. 4); problems accompanied with weld crown varieties, RPV shell inner radius tolerance, local corrosion pitting and water clarity. The equipment used for boat sampling is described too. 7 pictures

  5. Guam Boat-based Creel Survey

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Similar to other boat-based survey in basic design, this system is run by the Div. of Aquatic and Wildlife Resources (DAWR) and has been in operation since about...

  6. Boat boarding ladder placement

    Science.gov (United States)

    1998-04-01

    Presented in three volumes; 'Boat Boarding Ladder Placement,' which explores safety considerations including potential for human contact with a rotating propeller; 'Boat Handhold Placement,' which explores essential principles and methods of fall con...

  7. New Russian Combat Small Boats

    Directory of Open Access Journals (Sweden)

    Aleksandr F. Mitrofanov

    2016-12-01

    Full Text Available The article presents an overview of small combat boats. The author provides a description and gives an analysis of the characteristics of the boat "Raptor", boat "BK-16", boat "Strizh-4-1 DSh", and assault boat "BK-10".

  8. Propulsion of the Putt-Putt Boat - I

    Indian Academy of Sciences (India)

    motor that can be termed a pulsating water jet engine. The propulsion mechanism that drives the putt-putt boat uses simple physical principles in an ingenious way. It basically consists of a small shallow chamber, covered by a thin copper diaphragm. This is connected to the water astern of the boat by two pipes of 3mm bore ...

  9. Bible for boats

    NARCIS (Netherlands)

    Keuning, L.; Wassink, J.

    2013-01-01

    After nearly forty years researching yacht hulls in the Delft towing tank, boat expert Dr. Lex Keuning has decided to share his life’s work with yacht builders and researchers. The Delft Systematic Yacht Hull Series is available online.

  10. Antisense oligonucleotides: the state of the art.

    Science.gov (United States)

    Aboul-Fadl, T

    2005-01-01

    The use of antisense oligonucleotides as therapeutic agents has generated considerable enthusiasm in the research and medical community. Antisense oligonucleotides as therapeutic agents were proposed as far back as in the 1970s when the antisense strategy was initially developed. Nonetheless, it has taken almost a quarter of a century for this potential to be realized. The principle of antisense technology is the sequence-specific binding of an antisense oligonucleotide to target mRNA, resulting in the prevention of gene translation. The specificity of hybridization by Watson-Crick base pairing make antisense oligonucleotides attractive as tools for targeted validation and functionalization, and as therapeutics to selectively modulate the expression of genes involved in the pathogenesis of diseases. The last few years have seen a rapid increase in the number of antisense molecules progressing past Phase I, II and III clinical trials. This review outlines the basic concept of the antisense technology, its development and recent potential therapeutic applications.

  11. Hydrography - Boating Special Regulation Streams

    Data.gov (United States)

    NSGIC Education | GIS Inventory — This layer contains those streams/rivers within Pennsylvania that have specifc special regulations related to boating as defined by the Pennsylvania Fish and Boat...

  12. Hybridization with synthetic oligonucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Szostak, J.W.; Stiles, J.I.; Tye, B.K.; Sherman, F.; Wu, R.

    1978-01-01

    Procedures are described for the use of synthetic oligonucleotides for Southern blot experiments and gene bank screening, and the effect of various mismatches on the efficiency of hybridization is demonstrated. The following topics are discussed: sensitivity vs. specificity, hybridization of a 12-mer to the lambda endolysin gene; hybridization of oligonucleotide probes to the E. coli lac operator; hybridization of synthetic probes to the CYC1 gene of yeast; and cloning eucaryotic genes. (HLW)

  13. BASIC

    DEFF Research Database (Denmark)

    Hansen, Pelle Guldborg; Schmidt, Karsten

    2017-01-01

    BPP. Tilgangen består dels af den overordnede proces-model BASIC og dels af et iboende framework, ABCD, der er en model for systematisk adfærdsanalyse, udvikling, test og implementering af adfærdsrettede løsningskoncepter. Den samlede model gør det muligt for forskere såvel som offentligt ansatte...

  14. Cost Benefit Analysis of Boat Lifts

    Science.gov (United States)

    2014-09-01

    transferred to the Boat Inventory Manager ( BIM ). Custodians are responsible for maintaining boats and small craft in good working order at all times...identify funding to return the boat to a serviceable condition. The BIM has boat disposition authority. Boat dispositions, turn-in, transfer and disposal...including cannibalization) are authorized by the BIM . Typical reasons for removing a boat from service are: 1) Operational/mission obsolescence; 2

  15. Sick boat syndrome

    Directory of Open Access Journals (Sweden)

    Dąbrowiecki Zbigniew

    2015-12-01

    Full Text Available Many pathogenic micro-organisms are likely to attack passengers of cruise ships and other vessels or travel between continents as a peculiar type of a “stowaway”. The epidemiological tests conducted since 1987 with regard to watercraft led to the coining of a term known as the Sick Boat Syndrome (SBS. The main illnesses encountered on watercraft include gastrointestinal diseases (foodborne and Legionellosis. Additionally, the ventilation and airconditioning systems of old commercial ships (the so-called Tramps constitute a real technical challenge. Conditioned air (with removed undesired odour and micro-organisms should constitute ca. 25% of circulating air. In practice this situation is not typical for vessels of this class. Unclean air poses a real hazard for the crew.

  16. By boat to CERN

    CERN Multimedia

    2009-01-01

    Hello, my name is Jordan Juras. I will be here at CERN for a 2-month period spanning mid-June through mid-August working as Student Journalist for The Bulletin. This is a conventional position, but the manner with which I arrived at CERN is quite the opposite. Sitting at work one May 12th morning, I came across a Bulletin article (No. 20-21/2009) while perusing the LHC website. It was advertising ‘Fisica in Barca in Europe 2009’. They were looking for physicists living along the Mediterranean coast between Lisbon and Genoa to help out with the programme. Though I do not hold the title of physicist, nor do I live in Europe (in fact I live just outside of Harrow, Ontario, Canada), I felt compelled to write an email, expressing my love for physics and my interest in helping out with the programme. To my surprise, my help on board was welcome, and I managed to find some discount airfare and I set out for the South of Italy to meet the boat in Bari. Between Bari and Tries...

  17. Hydrography - Boating Special Regulation Lakes (Polygons)

    Data.gov (United States)

    NSGIC Education | GIS Inventory — This layer contains those lakes within Pennsylvania that have specifc special regulations related to boating as defined by the Pennsylvania Fish and Boat Commission.

  18. Conductive composites for oligonucleotide detection

    Directory of Open Access Journals (Sweden)

    David C. Ferrier

    2018-02-01

    Full Text Available A new method for oligonucleotide detection is presented based on oligonucleotide cross-linked polymer composites. Conductive carbon nanoparticles are incorporated into a DNA-functionalised polymer, containing partially complementary oligonucleotide cross-linkers, which is polymerised in situ upon interdigitated electrodes. In the presence of an aqueous solution of a specific analyte oligonucleotide sequence, the cross-linkers are cleaved, leading to increased swelling. As the polymer swells the relative density of the conductive particles decreases, leading to an easily measurable decrease in electrical conductivity. We demonstrate that such are capable of discriminating between analyte and control solutions, with single-base specificity, in under 3 min. The lower detection limit of these composites is of the order of 10 nM. The swelling characteristics of these composites is confirmed by optical imaging and the effects of varying temperature upon such composites are also reported.

  19. Fully automated parallel oligonucleotide synthesizer

    Czech Academy of Sciences Publication Activity Database

    Lebl, M.; Burger, Ch.; Ellman, B.; Heiner, D.; Ibrahim, G.; Jones, A.; Nibbe, M.; Thompson, J.; Mudra, Petr; Pokorný, Vít; Poncar, Pavel; Ženíšek, Karel

    2001-01-01

    Roč. 66, č. 8 (2001), s. 1299-1314 ISSN 0010-0765 Institutional research plan: CEZ:AV0Z4055905 Keywords : automated oligonucleotide synthesizer Subject RIV: CC - Organic Chemistry Impact factor: 0.778, year: 2001

  20. Alternative Design of Boat Fenders

    DEFF Research Database (Denmark)

    Banke, Lars

    1996-01-01

    On offshore platforms the purpose of fenders is to protect the oil-risers against minor accidental collisions with supply vessels. Normally, the fender is designed by use of thin-walled tubes. However, the tube itself is not capable of resisting the impact load of the boat. Therefore, alternative...

  1. Waterway Equipment - Boat, Barge, Motor

    Science.gov (United States)

    2012-09-25

    cargo they are designed to carry. These vessels include high speed wave-piercing catamarans and beaching craft. Non-propelled Barges, Conversion...Bulkhead A term applied to the vertical partition walls that divide the interior of a ship into compartments. Catamaran A boat with twin side-by-side

  2. 76 FR 49666 - Safety Zone; East Coast Drag Boat Bucksport Blowout Boat Race, Waccamaw River, Bucksport, SC

    Science.gov (United States)

    2011-08-11

    ... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; East Coast Drag Boat Bucksport Blowout Boat... East Coast Drag Boat Bucksport Blowout in Bucksport, South Carolina. The East Coast Drag Boat Bucksport... September 18, 2011, the East Coast Drag Boat Association will host the East Coast Drag Boat Bucksport...

  3. Electronic Structures of LNA Phosphorothioate Oligonucleotides

    DEFF Research Database (Denmark)

    Bohr, Henrik G.; Shim, Irene; Stein, Cy

    2017-01-01

    Important oligonucleotides in anti-sense research have been investigated in silico and experimentally. This involves quantum mechanical (QM) calculations and chromatography experiments on locked nucleic acid (LNA) phosphorothioate (PS) oligonucleotides. iso-potential electrostatic surfaces are es...

  4. Peptide-LNA oligonucleotide conjugates

    DEFF Research Database (Denmark)

    Astakhova, I Kira; Hansen, Lykke Haastrup; Vester, Birte

    2013-01-01

    properties, peptides were introduced into oligonucleotides via a 2'-alkyne-2'-amino-LNA scaffold. Derivatives of methionine- and leucine-enkephalins were chosen as model peptides of mixed amino acid content, which were singly and doubly incorporated into LNA/DNA strands using highly efficient copper...

  5. Swiss fuel cell passenger and pleasure boats

    Energy Technology Data Exchange (ETDEWEB)

    Affolter, J.-F.

    2000-07-01

    This paper published by the University of Applied Science in Yverdon-les-Bains, Switzerland, looks at the development of electrically driven small boats that are powered by fuel cells. The various implementations of the test boats are described. Starting with a 100-watt PEM fuel cell built by the Paul Scherrer Institute (PSI) and the University of Applied Science in Solothurn, Switzerland, for educational purposes, a small pedal-boat was electrified. The paper describes the development of four further prototypes and introduces a new project for a 6-passenger leisure boat powered by a 2 kW PEFC fuel cell. Apart from the fuel cells, various other components such as propellers and control electronics are discussed as are the remaining problems still to be solved before the cells and boats can be marketed. Since they were carried out at a technical university, these projects are said to have provided an excellent way of teaching new technologies to students.

  6. Characteristics of small boat acoustic signatures

    Science.gov (United States)

    Barlett, Martin L.; Wilson, Gary R.

    2002-11-01

    Small boats are often a dominant noise source in harbors, coastal regions, and lakes. However, detailed information about acoustic characteristics is not generally available. To remedy this deficiency, measurements of underwater acoustic signatures from various small boats have been conducted under controlled conditions. Boats used in the measurements were powered by a variety of gasoline and diesel motors in outboard, inboard-outboard, and inboard drive configurations. Measurements were made using a bottom mounted hydrophone in about 100 feet of water. In many instances, the boats were instrumented with a system that recorded the GPS position and engine RPM permitting accurate determinations of platform operating parameters. Measured small boat signatures contain both narrowband and broadband acoustic components. Narrowband components are generally associated with sources from the engine or drive. Narrowband levels in the observed spectra were found to exhibit significant variations and are believed to originate from fluctuations in the load on the engine and drive. Broadband energy was observed to be a dominant noise source at frequencies above several hundred Hertz and is a characteristic feature in all small boat signatures. Examples of small boat signatures will be presented and representative acoustic characteristics of this type of watercraft will be discussed.

  7. The Medicinal Chemistry of Therapeutic Oligonucleotides.

    Science.gov (United States)

    Wan, W Brad; Seth, Punit P

    2016-11-10

    Oligonucleotide-based therapeutics have made rapid progress in the clinic for treatment of a variety of disease indications. Unmodified oligonucleotides are polyanionic macromolecules with poor drug-like properties. Over the past two decades, medicinal chemists have identified a number of chemical modification and conjugation strategies which can improve the nuclease stability, RNA-binding affinity, and pharmacokinetic properties of oligonucleotides for therapeutic applications. In this perspective, we present a summary of the most commonly used nucleobase, sugar and backbone modification, and conjugation strategies used in oligonucleotide medicinal chemistry.

  8. Propulsion of the Putt-Putt Boat - I

    Indian Academy of Sciences (India)

    putt boat. Introduction. The putt-putt boat is a little toy that has fascinated everyone from children to physicists for over a hundred years now. This boat is powered, not by a conventional heat engine, but by a motor that can be termed a pulsating water jet engine. The propulsion mechanism that drives the putt-putt boat uses.

  9. Marianas Boat Fishing Cost Earnings Study 2011

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data represent a cost-earnings study of the boat based fishing in the Mariana Archipelago fielded in 2011. Data collected include fisher classification, vessel...

  10. Boat And Shore Oracle Data Tables

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Oracle Tables To Provide Boat and Shore Data which contains the object of this system is to provide an inventory of vessels that answer two fundamental questions:...

  11. A study of traditional boats of Goa

    Digital Repository Service at National Institute of Oceanography (India)

    Shaikh, Z.A.; Tripati, S.; Shinde, V.

    Goa, being situated along the Arabian Sea of India, is known for maritime activities and traditional boat building throughout the history. Traditional folk songs of Goa frequently mention ‘Vodem’ which denotes canoe. The recent discovery of stone...

  12. Small-boat Cetacean Surveys Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The database contains multiple spreadsheets that hold data collected during each small-boat survey project conducted by the PIFSC CRP. This includes a summary of the...

  13. American Samoa Boat-based Creel Survey

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Boat-based creel survey data have been collected and processed by the American Samoa Department of Marine and Wildlife Resources (DMWR) staff since about 1982 and...

  14. Controlling lipid micelle stability using oligonucleotide headgroups.

    Science.gov (United States)

    Wilner, Samantha E; Sparks, Samuel E; Cowburn, David; Girvin, Mark E; Levy, Matthew

    2015-02-18

    Lipid-based micelles provide an attractive option for therapeutic and diagnostic applications because of their small size (24 h. Using antisense oligonucleotides we demonstrated that disruption of the quadruplex leads to micelle destabilization and cargo release. The ability to use oligonucleotide interactions to control lipid particle stability represents a new approach in the design of programmed nanoscale devices.

  15. 76 FR 18391 - Safety Zone; Texas International Boat Show Power Boat Races; Corpus Christi Marina, Corpus...

    Science.gov (United States)

    2011-04-04

    ...-AA00 Safety Zone; Texas International Boat Show Power Boat Races; Corpus Christi Marina, Corpus Christi... temporary safety zone in the Corpus Christi, Texas for North American Tri-Hull Championship scheduled to...-mail LT Wes Geyer, Sector Corpus Christi Waterways Management Division, Coast Guard; telephone 361-888...

  16. Oligonucleotide microarrays: immobilization of phosphorylated oligonucleotides on epoxylated surface.

    Science.gov (United States)

    Mahajan, S; Kumar, P; Gupta, K C

    2006-01-01

    A facile and efficient method for direct immobilization of phosphorylated oligonucleotides on an epoxy-activated glass surface is described. The new immobilization strategy has been analyzed for its performance in DNA microarray under both microwave and thermal conditions. It reflects high immobilization efficiency ( approximately 23%), and signal-to-noise ratio ( approximately 98) and resulted in high hybridization efficiency ( approximately 36%) in comparison to those obtained with standard methods, viz., NTMTA ( approximately 9.76%) and epoxide-amine ( approximately 9.82%). The probes immobilized through the new strategy were found to be heat-stable, since the performance of microarray decreased by only approximately 7% after subjecting it to 20 PCR-like heat cycles, suggesting that the chemistry could be used in integrated PCR/microarray devices. The immobilization of probes following the proposed chemistry resulted in spots of superior quality in terms of spot morphology, spot homogeneity, and signal reproducibility. The constructed microarrays have been successfully used for the discrimination of nucleotide mismatches. In conclusion, these features make the new immobilization strategy ideal for facile, efficient, and cost-effective manufacturing of DNA microarrays.

  17. Injection site reactions after subcutaneous oligonucleotide therapy

    NARCIS (Netherlands)

    van Meer, L. (Leonie); M. Moerland (Matthijs); Gallagher, J. (Jolie); M.B.A. van Doorn (Martijn); E.P. Prens (Errol); A.F. Cohen; Rissmann, R. (Robert); J. Burggraaf (Jacobus)

    2016-01-01

    textabstractOligonucleotides (ONs) are short fragments of nucleic acids, currently being investigated as therapeutic agents. When administered subcutaneously (sc), ONs cause a specific local reaction originating around the injection site, such as erythema, itching, discomfort and pain, including

  18. Dragon Boat Festival (Dyun Ngh Jit).

    Science.gov (United States)

    Wu, Julia; Quan, Ella Y.

    This bilingual-bicultural reader in Cantonese and English is intended for elementary school children in a bilingual education setting. Pen-and-ink drawings illustrate the story of the traditional dragon boat festival. Each page of the text is written in Chinese characters, Romanized form, and in English. (NCR)

  19. Design of boat powered photovoltaic systems

    International Nuclear Information System (INIS)

    Syafaruddin; Galla, D; Ajami, W.A.F.A.

    2014-01-01

    The solar energy has high potential applications in Indonesia since the country is located close to the equatorial region that makes the sun is almost bright along the day. In this paper, the boat power photovoltaic system is proposed. Such design may promote new innovations technically and economically in water transportation system since the country demography is almost 75% surrounded by water. The electricity energy is harvested from the sun through the PV panel then stored in the battery by solar charge control mechanism in order to rotate the prime mover of the boat by means the DC motor. The shaft of the DC motor is directly connected to the boat propeller and the speed motor is regulated by the pulse width modulation (PWM) technique generated from the AVR microcontroller ATmega16. The final design is obtained that for the boat with the total weight of 531.1758 kg, it may operate for 1.26 hours with the knot speed of 3.11 when 2 PV panels of 50 W, 2 DC motor of 0.3 kW and battery of 100 Ah capacity are used with the overall efficiency performance not less than 87.4%. (author)

  20. Recreational Boating Accidents and the Contribution of Boating Under the Influence

    Data.gov (United States)

    Department of Homeland Security — This report includes statistical information for the fifty states, five U.S. territories, and the District of Columbia on recreational boating accident data and the...

  1. Analysis of Costs and Returns of Mechanized Fishing Boat ...

    African Journals Online (AJOL)

    Administrator

    Analysis of Costs and Returns of Mechanized Fishing Boat Operations in India. EJBE Vol. 1, No. 2/2010. Page 129 effective management of this economically backward sector in India. Mechanized fishing boat ... economics of operation of the 17.5 m indigenous mechanized fishing boat along the Kerala Coast and ...

  2. 21 CFR 1240.95 - Sanitation of water boats.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Sanitation of water boats. 1240.95 Section 1240.95... DISEASES Source and Use of Potable Water § 1240.95 Sanitation of water boats. No vessel engaged in interstate traffic shall obtain water for drinking and culinary purposes from any water boat unless the tanks...

  3. 78 FR 53156 - Sport Fishing and Boating Partnership Council; Teleconference

    Science.gov (United States)

    2013-08-28

    ... Fish and Wildlife Service Sport Fishing and Boating Partnership Council; Teleconference AGENCY: Fish... Wildlife Service (Service), announce a public teleconference of the Sport Fishing and Boating Partnership.... App., we announce that Sport Fishing and Boating Partnership Council will hold a teleconference...

  4. 77 FR 31147 - National Safe Boating Week, 2012

    Science.gov (United States)

    2012-05-24

    ... ensure America's waterways are safe and secure for all. In recognition of the importance of safe boating... Safe Boating Week, 2012 By the President of the United States of America A Proclamation For generations... the water, boaters can minimize the risk of accident or injury by taking a boating safety course...

  5. 36 CFR 1002.63 - Boating and water use activities.

    Science.gov (United States)

    2010-07-01

    ... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Boating and water use..., PUBLIC USE AND RECREATION § 1002.63 Boating and water use activities. Swimming, boating and the use of any water vessel are prohibited within the area administered by the Presidio Trust. ...

  6. 76 FR 47606 - Sport Fishing and Boating Partnership Council

    Science.gov (United States)

    2011-08-05

    ...] Sport Fishing and Boating Partnership Council AGENCY: Fish and Wildlife Service, Interior. ACTION... Sport Fishing and Boating Partnership Council (Council). DATES: The meeting will be held on Wednesday... Advisory Committee Act, 5 U.S.C. App., we announce that the Sport Fishing and Boating Partnership Council...

  7. 78 FR 33856 - Sport Fishing and Boating Partnership Council

    Science.gov (United States)

    2013-06-05

    ...-FVWF97920900000-XXX] Sport Fishing and Boating Partnership Council AGENCY: Fish and Wildlife Service, Interior... public teleconference of the Sport Fishing and Boating Partnership Council (Council). DATES... announce that Sport Fishing and Boating Partnership Council will hold a teleconference. Background The...

  8. 76 FR 7579 - Sport Fishing and Boating Partnership Council

    Science.gov (United States)

    2011-02-10

    ... Boating Partnership Council AGENCY: Fish and Wildlife Service, Interior. ACTION: Notice of meeting... Boating Partnership Council (Council). DATES: The meeting will be held on Thursday, March 3, 2011, from 1... announce that the Sport Fishing and Boating Partnership Council will hold a meeting on Thursday, March 3...

  9. 77 FR 26784 - Sport Fishing and Boating Partnership Council

    Science.gov (United States)

    2012-05-07

    ...-FVWF979209000005D-XXX] Sport Fishing and Boating Partnership Council AGENCY: Fish and Wildlife Service, Interior... public teleconference of the Sport Fishing and Boating Partnership Council (Council). DATES... Fishing and Boating Partnership Council will hold a teleconference. Background The Council was formed in...

  10. 76 FR 1628 - Sport Fishing and Boating Partnership Council

    Science.gov (United States)

    2011-01-11

    ...] Sport Fishing and Boating Partnership Council AGENCY: Fish and Wildlife Service, Interior. ACTION... teleconference of the Sport Fishing and Boating Partnership Council (Council). DATE(S): We will hold the... sport fishing, boating, and conservation communities and is organized to enhance partnerships among...

  11. 78 FR 4161 - Sport Fishing and Boating Partnership Council

    Science.gov (United States)

    2013-01-18

    ...-FVWF97920900000-XXX] Sport Fishing and Boating Partnership Council AGENCY: Fish and Wildlife Service, Interior... public teleconference of the Sport Fishing and Boating Partnership Council (Council). DATES... Fishing and Boating Partnership Council will hold a teleconference. Background The Council was formed in...

  12. 75 FR 47624 - Sport Fishing and Boating Partnership Council

    Science.gov (United States)

    2010-08-06

    ... Boating Partnership Council AGENCY: Fish and Wildlife Service, Interior. ACTION: Notice of meeting... Boating Partnership Council (Council). DATES: The meeting will be held on Wednesday, September 8, 2010... Sport Fishing and Boating Partnership Council will hold a meeting on Wednesday, September 8, 2010, from...

  13. Oligonucleotides conjugated to short lysine chains.

    Science.gov (United States)

    Winkler, Johannes; Urban, Ernst; Noe, Christian R

    2005-01-01

    A new method for synthesizing oligonucleotide peptide conjugates by an in-line approach is presented. A phosphorothioate oligonucleotide with the sequence of bcl-2 targeted Oblimersen by employing a modified 2'-amino-2'-desoxy-uridine nucleotide bearing a succinyl linker at the 2' position was prepared. The carboxyl group was protected for solid-phase synthesis as the benzyl ester. Ester cleavage was afforded by a phase transfer reaction using palladium nanoparticles as catalyst and cyclohexadiene as hydrogen donor. Short tails of up to three lysyl residues were conjugated to the oligonucleotide by an inverse stepwise peptide synthesis. The conjugates were characterized by HPLC, mass spectrometry, and circular dichroism. Influence of lysyl tails on CD spectra were minimal. Melting profiles revealed only minimal destabilizing effects on duplexes by conjugation of peptides.

  14. Radio-marking and in vivo imagery of oligonucleotides

    International Nuclear Information System (INIS)

    Kuehnast, Bertrand

    2000-01-01

    This research thesis is part of activities aimed at the development of new molecules like oligonucleotides. Its first objective was the development and validation of a marking method with fluorine-18 of oligonucleotides for their in-vivo pharmacological assessment with positron emission tomography (PET). Further investigations addressed the use of iodine-125 for oligonucleotide marking purpose. This radio-marking, and in vivo and ex vivo imagery techniques are described, and their potential is highlighted for the pharmacological assessment of different oligonucleotides

  15. A comparative analysis of existing oligonucleotides selection ...

    African Journals Online (AJOL)

    technology at the front and back ends, respectively, are the selection of optimal DNA oligonucleotides (henceforth oligos) and computational analysis of the genes expression data. A computational comparative analysis of the methods used to select oligos is important since the design and quality of the microarray probes ...

  16. Associating Oligonucleotides with Positively Charged Liposomes

    Czech Academy of Sciences Publication Activity Database

    Jurkiewicz, P.; Okruszek, A.; Hof, Martin; Langner, M.

    2003-01-01

    Roč. 8, č. 1 (2003), s. 77-84 ISSN 1425-8153 R&D Projects: GA MŠk LN00A032 Institutional research plan: CEZ:AV0Z4040901 Keywords : oligonucleotides * fluorescence correlation spectroscopy * DOTAP Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 0.455, year: 2003

  17. Propulsion of the Putt-Putt Boat - 2

    Indian Academy of Sciences (India)

    [1] I Finnie and R L Curl, Phys- ics in a Toy Boat, American. Journal of Physics, Vol. 31,p. 289, 1962. [2] J S Miller, Physics in a Toy. Boat, American Journal of. Physics, Vol. 26, p.199, 1958. [3] R S Mackay,Boat Driven by. Thennal Oscillations, Am- erican Journal of Physics,. Vo1.26, p.583, 1958. Figure 4. P-V plot averaged.

  18. Behavioral responses to encounter of fishing boats in wandering albatrosses.

    Science.gov (United States)

    Collet, Julien; Patrick, Samantha C; Weimerskirch, Henri

    2017-05-01

    Animals are attracted to human food subsidies worldwide. The behavioral response of individuals to these resources is rarely described in detail, beyond chances of encounters. Seabirds for instance scavenge in large numbers at fishing boats, triggering crucial conservation issues, but how the response to boats varies across encounters is poorly known. Here we examine the behavioral response of wandering albatrosses ( Diomedea exulans ), equipped with GPS tags, to longline fishing boats operating near their colony for which we had access to vessel monitoring system data. We distinguish between encounters (flying within 30 km of a boat) and attendance behavior (sitting on the sea within 3 km of a boat), and examine factors affecting each. In particular, we test hypotheses that the response to encountered boats should vary with sex and age in this long-lived dimorphic species. Among the 60% trips that encountered boats at least once, 80% of them contained attendance (but attendance followed only 60% of each single encounter). Birds were more attracted and remained attending longer when boats were hauling lines, despite the measures enforced by this fleet to limit food availability during operations. Sex and age of birds had low influence on the response to boats, except the year when fewer boats came fishing in the area, and younger birds were attending further from boats compared to older birds. Net mass gain of birds was similar across sex and not affected by time spent attending boats. Our results indicate albatrosses extensively attend this fishery, with no clear advantages, questioning impacts on foraging time budgets. Factors responsible for sex foraging segregation at larger scale seem not to operate at this fleet near the colony and are not consistent with predictions of optimal foraging theory on potential individual dominance asymmetries. This approach complements studies of large-scale overlap of animals with human subsidies.

  19. Liver as a target for oligonucleotide therapeutics.

    Science.gov (United States)

    Sehgal, Alfica; Vaishnaw, Akshay; Fitzgerald, Kevin

    2013-12-01

    Oligonucleotide-based therapeutics are an emerging class of drugs that hold the promise for silencing "un-druggable" targets,thus creating unique opportunities for innovative medicines. As opposed to gene therapy, oligonucleotides are considered to be more akin to small molecule therapeutics because they are small,completely synthetic in origin, do not integrate into the host genome,and have a defined duration of therapeutic activity after which effects recover to baseline. They offer a high degree of specificity at the genetic level, thereby reducing off-target effects.At the same time, they provide a strategy for targeting any gene in the genome, including transcripts that produce mutated proteins.Oligonucleotide-based therapeutics include short interfering RNA (siRNA), that degrade target mRNA through RISC mediated RNAi; anti-miRs, that target miRNAs; miRNA mimics, that regulate target mRNA; antisense oligonucleotides, that may be working through RNAseH mediated mRNA decay; mRNA upregulation,by targeting long non-coding RNAs; and oligonucleotides induced alternative splicing [1]. All these approaches require some minimal degree of homology at the nucleic acid sequence level for them to be functional. The different mechanisms of action and their relevant activity are outlined in Fig. 1. Besides homology,RNA secondary structure has also been exploited in the case of ribozymes and aptamers, which act by binding to nucleic acids or proteins, respectively. While there have been many reports of gene knockdown and gene modulation in cell lines and mice with all these methods, very few have advanced to clinical stages.The main obstacle to date has been the safe and effective intracellular delivery of these compounds in higher species, including humans. Indeed, their action requires direct interaction with DNA/RNA within the target cell so even when one solves the issues of tissue and cellular access, intracellular/intranuclear location represents yet another barrier to

  20. Synthesis and hybridization property of a boat-shaped pyranosyl nucleic acid containing an exocyclic methylene group in the sugar moiety.

    Science.gov (United States)

    Mori, Kazuto; Kodama, Tetsuya; Obika, Satoshi

    2015-01-01

    A boat-shaped pyranosyl nucleic acid (BsNA) having an exocyclic methylene group in the sugar moiety was synthesized to investigate the possibility that the axial H3' of original BsNA is the cause of its duplex destabilization. The synthesized BsNA analog was chemically stable against various nucleophiles. From the thermal stability of duplex oligonucleotides including the BsNA analog, it was found that the duplex-forming ability can be sensitive to the size of functional groups at the 3'-position. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. Design Considerations for Array CGH to OligonucleotideArrays

    Energy Technology Data Exchange (ETDEWEB)

    Baldocchi, R.A.; Glynne, R.J.; Chin, K.; Kowbel, D.; Collins, C.; Mack, D.H.; Gray, J.W.

    2005-03-04

    Background: Representational oligonucleotide microarray analysis has been developed for detection of single nucleotide polymorphisms and/or for genome copy number changes. In this process, the intensity of hybridization to oligonucleotides arrays is increased by hybridizing a polymerase chain reaction (PCR)-amplified representation of reduced genomic complexity. However, hybridization to some oligonucleotides is not sufficiently high to allow precise analysis of that portion of the genome. Methods: In an effort to identify aspects of oligonucleotide hybridization affecting signal intensity, we explored the importance of the PCR product strand to which each oligonucleotide is homologous and the sequence of the array oligonucleotides. We accomplished this by hybridizing multiple PCR-amplified products to oligonucleotide arrays carrying two sense and two antisense 50-mer oligonucleotides for each PCR amplicon. Results: In some cases, hybridization intensity depended more strongly on the PCR amplicon strand (i.e., sense vs. antisense) than on the detection oligonucleotide sequence. In other cases, the oligonucleotide sequence seemed to dominate. Conclusion: Oligonucleotide arrays for analysis of DNA copy number or for single nucleotide polymorphism content should be designed to carry probes to sense and antisense strands of each PCR amplicon to ensure sufficient hybridization and signal intensity.

  2. Spatially Defined Oligonucleotide Arrays. Technical Report for Phase II; FINAL

    International Nuclear Information System (INIS)

    None

    2000-01-01

    The goal of the Human Genome Project is to sequence all 3 billion base pairs of the human genome. Progress in this has been rapid; GenBank(reg s ign) finished 1994 with 286 million bases of sequence and grew by 2470 in the first quarter of 1995. The challenge to the scientific community is to understand the biological relevance of this genetic information. In most cases the sequence being generated for any single region of the genome represents the genotype of a single individual. A complete understanding of the function of specific genes and other regions of the genome and their role in human disease and development will only become apparent when the sequence of many more individuals is known. Access to genetic information is ultimately limited by the ability to screen DNA sequence. Although the pioneering sequencing methods of Sanger et al. (15) and Maxam and Gilbert (11) have become standard in virtually all molecular biology laboratories, the basic protocols remain largely unchanged. The throughput of this sequencing technology is now becoming the rate-limiting step in both large-scale sequencing projects such as the Human Genome Project and the subsequent efforts to understand genetic diversity. This has inspired the development of advanced DNA sequencing technologies (9), Incremental improvements to Sanger sequencing have been made in DNA labeling and detection. High-speed electrophoresis methods using ultrathin gels or capillary arrays are now being more widely employed. However, these methods are throughput-limited by their sequential nature and the speed and resolution of separations. This limitation will become more pronounced as the need to rapidly screen newly discovered genes for biologically relevant polymorphisms increases. An alternative to gel-based sequencing is to use high-density oligonucleotide probe arrays. Oligonucleotide probe arrays display specific oligonucleotide probes at precise locations in a high density, information-rich format (5

  3. 77 FR 17084 - National Boating Safety Advisory Council

    Science.gov (United States)

    2012-03-23

    ... DEPARTMENT OF HOMELAND SECURITY Coast Guard [Docket No. USCG-2010-0164] National Boating Safety..., Virginia, to discuss issues relating to recreational boating safety. The meetings will be open to the... Arlington, 4610 N. Fairfax Drive, Arlington, VA 22203. The hotel's Web site is: http://www.hiarlington.com...

  4. 46 CFR 131.855 - Lifeboats and rescue boats.

    Science.gov (United States)

    2010-10-01

    ... must be plainly marked or painted on each side of the bow of each lifeboat and rescue boat in block... port whose marking on the stern is required by § 67.123 of this chapter. (b) The following must be plainly marked or painted on each side of the bow of each lifeboat and rescue boat in block capital...

  5. Maxillofacial skeletal injuries following boat accidents in a Coastal ...

    African Journals Online (AJOL)

    Objectives: The purpose of this article is to highlight the increasing occurrence of maxillofacial skeletal injuries from boat accidents in our environment and also to present our management modalities as experienced in our center. Materials and Methods: The case notes of the 6 maxillofacial skeletal injuries from boat ...

  6. 78 FR 30723 - National Safe Boating Week, 2013

    Science.gov (United States)

    2013-05-22

    ... oceans safe for all to enjoy. In recognition of the importance of safe boating practices, the Congress... Boating Week, 2013 By the President of the United States of America A Proclamation Every year, the United... the water should prepare by filing a float plan with family or a friend, getting a free vessel safety...

  7. 75 FR 29391 - National Safe Boating Week, 2010

    Science.gov (United States)

    2010-05-26

    .... In recognition of the importance of safe boating practices, the Congress, by Joint Resolution... Safe Boating Week, 2010 By the President of the United States of America A Proclamation Our Nation's... reflection. As the weather warms and people prepare to spend time on the water, let us recommit during...

  8. Analysis of costs and returns of mechanized fishing boat operations ...

    African Journals Online (AJOL)

    Analysis of costs and returns of mechanized fishing boat operations in India. KS Bose, PV Sarma. Abstract. This article makes an attempt to analyze the cost and returns of Mechanized Fishing Boat Operators (MFBO's) and the determinants of the selected MFBOs. The study is based on a sample of 180 MFBOs operating ...

  9. A whispering boat on photovoltaic energy; Een fluisterboot op zonnestroom

    Energy Technology Data Exchange (ETDEWEB)

    Vaessen, M.; Robles, M. [eds.

    1998-02-18

    A brief impression is given of the newly developed solar energy-driven catamaran `Blaustirns`. The boat is developed for excursions in the nature reserve `De Alde Feanen` in the Dutch province Friesland. The boat must make no noise and not pollute the nature reserve

  10. 77 FR 29359 - Sport Fishing and Boating Partnership Council

    Science.gov (United States)

    2012-05-17

    ...-FVWF979209000005D-XXX] Sport Fishing and Boating Partnership Council AGENCY: Fish and Wildlife Service, Interior... meeting of the Sport Fishing and Boating Partnership Council (Council). A Federal advisory committee, the Council was created in part to foster partnerships to enhance public awareness of the importance of...

  11. 78 FR 23587 - Sport Fishing and Boating Partnership Council

    Science.gov (United States)

    2013-04-19

    ...-FVWF97920900000-XXX] Sport Fishing and Boating Partnership Council AGENCY: Fish and Wildlife Service, Interior... meeting of the Sport Fishing and Boating Partnership Council (Council). A Federal advisory committee, the Council was created in part to foster partnerships to enhance public awareness of the importance of...

  12. 75 FR 22423 - Sport Fishing and Boating Partnership Council

    Science.gov (United States)

    2010-04-28

    ... Boating Partnership Council AGENCY: Fish and Wildlife Service, Interior. ACTION: Notice of meeting... Boating Partnership Council (Council). DATES: The meeting will be held on Wednesday, May 26, 2010, from 10... Partnership Council will hold a meeting. Background The Council was formed in January 1993 to advise the...

  13. 77 FR 61626 - Sport Fishing and Boating Partnership Council

    Science.gov (United States)

    2012-10-10

    ...-FVWF97920900000-XXX] Sport Fishing and Boating Partnership Council AGENCY: Fish and Wildlife Service, Interior... meeting of the Sport Fishing and Boating Partnership Council (Council). A Federal advisory committee, the Council was created in part to foster partnerships to enhance public awareness of the importance of...

  14. 76 FR 75898 - Sport Fishing and Boating Partnership Council

    Science.gov (United States)

    2011-12-05

    ...-FVWF979209000005D-XXX] Sport Fishing and Boating Partnership Council AGENCY: Fish and Wildlife Service, Interior... public teleconference of the Sport Fishing and Boating Partnership Council (Council). DATES: We will hold... organized to enhance partnerships among industry, constituency groups, and government. The 18-member Council...

  15. Traditional boat-building and navigational techniques of southern Orissa

    Digital Repository Service at National Institute of Oceanography (India)

    Tripati, S.

    coastline extending from Subarnarekha river in the north to Sunapur in the south. The existing small-scale boat-building industry of coastal Orissa has been inherited. The people of the littoral districts have been building boats for coastal transportation...

  16. 78 FR 61866 - Sport Fishing and Boating Partnership Council

    Science.gov (United States)

    2013-10-04

    ... government. The Council represents the interests of the public and private sectors of the recreational... and education, and tourism. Background information on the Council is available at http://www.fws.gov... the Gulf coast, including fishery management, boating, and tourism; Issues regarding the Boating...

  17. Hybridization properties of 4'-branched oligonucleotides

    Czech Academy of Sciences Publication Activity Database

    Liboska, Radek; Buděšínský, Miloš; Kavenová, Ivana; Páv, Ondřej; Rosenberg, Ivan

    2002-01-01

    Roč. 96, č. 11 (2002), s. 933 ISSN 0009-2770. [Konference Pokroky v organické, bioorganické a farmaceutické chemii /37./. 22.11.2002-24.11.2002, Liblice] R&D Projects: GA AV ČR IAA4055101; GA ČR GA203/01/1166 Institutional research plan: CEZ:AV0Z4055905 Keywords : oligonucleotides Subject RIV: CC - Organic Chemistry

  18. Hybridization properties of 4'-branched oligonucleotides

    Czech Academy of Sciences Publication Activity Database

    Liboska, Radek; Buděšínský, Miloš; Kavenová, Ivana; Páv, Ondřej; Rosenberg, Ivan

    2003-01-01

    Roč. 22, 5/8 (2003), s. 1057-1060 ISSN 1525-7770. [International Roundtable Nucleosides, Nucleotides and Nucleic Acids /15./. Leuven, 10.09.2002-14.09.2002] R&D Projects: GA ČR GA203/01/1166; GA AV ČR IAA4055101 Institutional research plan: CEZ:AV0Z4055905 Keywords : 4'-branched oligonucleotides * hybridization * triplexes Subject RIV: CC - Organic Chemistry Impact factor: 0.813, year: 2003

  19. Louisiana Marinas and Boat Launches, Geographic NAD83, LOSCO (2004) [marinas_LOSCO_2004

    Data.gov (United States)

    Louisiana Geographic Information Center — The dataset defines the location and supplemental information for marinas and boat launches in southern Louisiana. The boat launch database includes public and...

  20. Drop drying on surfaces determines chemical reactivity - the specific case of immobilization of oligonucleotides on microarrays

    Science.gov (United States)

    2013-01-01

    Background Drop drying is a key factor in a wide range of technical applications, including spotted microarrays. The applied nL liquid volume provides specific reaction conditions for the immobilization of probe molecules to a chemically modified surface. Results We investigated the influence of nL and μL liquid drop volumes on the process of probe immobilization and compare the results obtained to the situation in liquid solution. In our data, we observe a strong relationship between drop drying effects on immobilization and surface chemistry. In this work, we present results on the immobilization of dye labeled 20mer oligonucleotides with and without an activating 5′-aminoheptyl linker onto a 2D epoxysilane and a 3D NHS activated hydrogel surface. Conclusions Our experiments identified two basic processes determining immobilization. First, the rate of drop drying that depends on the drop volume and the ambient relative humidity. Oligonucleotides in a dried spot react unspecifically with the surface and long reaction times are needed. 3D hydrogel surfaces allow for immobilization in a liquid environment under diffusive conditions. Here, oligonucleotide immobilization is much faster and a specific reaction with the reactive linker group is observed. Second, the effect of increasing probe concentration as a result of drop drying. On a 3D hydrogel, the increasing concentration of probe molecules in nL spotting volumes accelerates immobilization dramatically. In case of μL volumes, immobilization depends on whether the drop is allowed to dry completely. At non-drying conditions, very limited immobilization is observed due to the low oligonucleotide concentration used in microarray spotting solutions. The results of our study provide a general guideline for microarray assay development. They allow for the initial definition and further optimization of reaction conditions for the immobilization of oligonucleotides and other probe molecule classes to different

  1. Flight of the loon : solar-powered boating

    Energy Technology Data Exchange (ETDEWEB)

    Anon.

    2006-04-01

    Details of the first solar-powered, zero-emission boat to venture across the Trent-Severn waterway were presented. Called the 'Loon', the boat is now being manufactured for environmentally-conscious boaters around the world. The seating arrangement, pontoon design, and propulsion system were all designed to minimize impacts on the ecosystem. A prototype boat was built and tested in the summer of 2005 to determine the viability of the solar-powered boat, and a family trip down the waterway was completed in August. Results of the trip encouraged the inventor to raise capital and a suitable production facility. After several months of development, the first production boat was completed with many improvements to the original prototype. An entrepreneur from Belize was the first person to place an order after he discovered that most commercially-available solar-powered boats were higher-priced and less capable than the Loon. High gas prices and the detrimental effects of fuel exhaust in lakes have caused many people to become sensitive to the issues surrounding fuel use and pleasure boats. It was concluded that a storefront has recently been opened north of Orillia in order to sell the solar-powered craft. 3 figs.

  2. Blending Biodiesel in Fishing Boat Fuels for Improved Fuel Characteristics

    International Nuclear Information System (INIS)

    Lin, Cherng-Yuan

    2014-01-01

    Biodiesel is a renewable, clean, alternative energy source with advantages, such as excellent lubricity, superior biodegradability, and high combustion efficiency. Biodiesel is considered for mixing with fishing boat fuels to adjust their fuel characteristics so that toxic pollutants and greenhouse-effect gas emissions from such shipping might be reduced. The effects of blending fishing boat fuels A and B with various weight proportions of biodiesel are experimentally investigated in this study. The results show that biodiesel blending can significantly improve the inferior fuel properties of both fishing boat fuels and particularly fuel B. The flash points of both of these fuels increases significantly with the addition of biodiesel and thus enhances the safety of transporting and storing these blended fuels. The flash point of fishing boat fuel B even increases by 16% if 25 wt.% biodiesel is blended. The blending of biodiesel with no sulfur content is found to be one of the most effective ways to reduce the high sulfur content of fishing boat fuel, resulting in a reduction in the emission of sulfur oxides. The addition of only 25 wt.% biodiesel decreased the sulfur content of the fishing boat fuel by 37%. The high kinematic viscosity of fishing boat fuel B was also observed to be reduced by 63% with the blending of just 25 wt.% biodiesel. However, biodiesel blending caused a slight decrease in heating value around 1–4.5%.

  3. Labeling of phosphorothioate antisense oligonucleotides with yttrium-90

    International Nuclear Information System (INIS)

    Watanabe, Naoyuki; Sawai, Hiroaki; Endo, Keigo; Shinozuka, Kazuo; Ozaki, Hiroaki; Tanada, Shuji; Murata, Hajime; Sasaki, Yasuhito

    1999-01-01

    Novel yttrium-90 ( 90 Y)-labeled phosphorothioate antisense oligonucleotides were designed as a potential targeted radionuclide method for the purification of IQNP for use imer phosphorothioate antisense oligonucleotide, which was complementary to the translation start region of the N-myc oncogene mRNA, was conjugated with isothiocyanobenzyl ethylenediamine tetraacetic acid (SCN-Bn-EDTA), via a C-5-substituted deoxyuridine that had replaced a thymine in the oligonucleotide, and was then labeled with 90 Y-acetate. Following purification, the radiochemical purity of the 90 Y-Bn-EDTA-phosphorothioate antisense oligonucleotides was estimated by 2.0% agarose gel electrophoresis, and the specific hybridization of 90 Y-Bn-EDTA-phosphorothioate antisense oligonucleotide to a phosphorodiester sense oligonucleotide was investigated by 20% polyacrylamide gel electrophoresis in a cell-free system. Radiochemical purity was 98.7±0.4% at 72 h after labeling and 90.3±0.9% after 72-h incubation with human normal serum. The 90 Y-Bn-EDTA-phosphorothioate antisense oligonucleotide hybridized specifically to a complementary phosphorodiester sense oligonucleotide. In conclusion, phosphorothioate antisense oligonucleotides can be labeled stably with 90 Y using SCN-Bn-EDTA without loss of hybridization properties

  4. A comparative analysis of measles virus RNA by oligonucleotide fingerprinting

    International Nuclear Information System (INIS)

    Stephenson, J.R.; Meulen, V. ter

    1982-01-01

    Isolates from two cases of acute measles, one case of acute measles encephalitis and three patients with subacute sclerosing panencephalitis were compared. This comparison was based upon the electrophoretic analysis of T 1 oligonucleotides from single-stranded, full-length RNA isolated from cytoplasmic nucleocapsids. Although all viruses have oligonucleotides in common, each isolate generated a unique pattern of oligonucleotides. However, no group of oligonucleotides was observed which would allow differentiation between viruses isolated from acute infections and those isolated from CNS diseases; indicating that probably all measles viruses differ in their nucleotide sequence, regardless of origin. (Author)

  5. The Vine Trust's Amazon Hope boats--providing a dental service on the Amazon.

    Science.gov (United States)

    Mason, Shona M C

    2013-01-01

    The Vine Trust's Amazon Hope Project is a medical and dental programme providing healthcare to communities along the Amazon River in Peru. Volunteers from the UK and other countries work alongside Peruvian staff employed by their partner organization, Union Biblica del Peru, to provide a health service from a boat which serves communities on several tributaries who otherwise would have no other access to care. The dental programme involves a basic restorative and extraction service, with scope to develop a preventive programme. Dentists'and DCPs' skills are transferable globally: this article illustrates how one volunteer dental project is working to provide relevant and sustainable dental health care in the Amazon jungle.

  6. 78 FR 57063 - Special Local Regulations; Jacksonville Dragon Boat Festival; St. Johns River; Jacksonville, FL

    Science.gov (United States)

    2013-09-17

    ... 1625-AA08 Special Local Regulations; Jacksonville Dragon Boat Festival; St. Johns River; Jacksonville... Jacksonville Dragon Boat Festival, a series of paddle boat races. The event is scheduled to take place on... States during the Jacksonville Dragon Boat Festival. C. Discussion of the Final Rule On Saturday...

  7. 76 FR 34859 - Safety Zone; Augusta Southern Nationals Drag Boat Race, Savannah River, Augusta, GA

    Science.gov (United States)

    2011-06-15

    ... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Augusta Southern Nationals Drag Boat Race... during the Augusta Southern Nationals Drag Boat Race. The Augusta Southern Nationals Drag Boat Race will..., 2011 Augusta Southern Nationals, Inc. is hosting the Augusta Southern Nationals Drag Boat Race, a...

  8. Electric Boat Corporation, CWA-01-2018-0002

    Science.gov (United States)

    Notice of Proposed Assessment of Class II Civil Penalty and Notice of Opportunity for a Hearing under Sections 309(g) of the Clean Water Act (CWA) for Electric Boat Corporation, Groton, CT, CWA-01-2018-0002

  9. Hawaii Small Boat Cost-Earnings Data: 2014

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data represent a cost-earnings study of the Hawaii small boat fishery in 2014. Data collected include fisher classification, vessel characteristics, levels of...

  10. Hawaii Small Boat Cost-Earnings Data: 1995-1996

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data represent a cost-earnings study of the Hawaii small boat fishery in 1995-1996. Data collected include fisher classification, vessel characteristics,...

  11. Nets, Boats and Fishing in the Roman World

    DEFF Research Database (Denmark)

    Bekker-Nielsen, Tønnes

    2002-01-01

    Ithas been claimed that in Roman times, net fishing was a shore-based technology, but a study of literary sources and pictorial evidence, mainly mosaics, show that net fishing from boats was widespread throughout the first four centuries AD....

  12. Boat Waves on Johnson Lake and Kenai River, Alaska

    National Research Council Canada - National Science Library

    Maynord, Stephen

    2001-01-01

    .... The State of Alaska and U.S. Army Corps of Engineers (USACE) are concerned about bank erosion from the combined effects of the high summer flows and the high volume of boat traffic related to the salmon...

  13. Hawaii Small Boat Cost-Earnings Data: 2007-2008

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data represent a cost-earnings study of the Hawaii small boat fishery in 2007-2008. Data collected include fisher classification, vessel characteristics,...

  14. The Patrol Boat Navy: An Emergent Force in the Mediterranean

    Science.gov (United States)

    1976-03-01

    patrol boat navies is offered with particular attention given to the Arab -Israeli Conflict, Foreign Power Interests, and the move for Arab ...development of patrol boat navies is offered with particular attention given to the Arab -Israeli Conflict, Foreign Power Interests, and the move for... Arab Independence. Finally, the study serves to illustrate the threat posed by missile-armed patrol craft in emerging navies world-wide. TABLE OF

  15. Deployment of Lightweight Shock Mitigating Boat Manufacturing Innovation

    Science.gov (United States)

    2012-12-21

    Manufacturing Innovation SP4701-10-C-0028 Tasks 1-4 Kelley, Danna M. Lewit, Scott Wolfe, Art Baker, Patricia SCRA Applied R&D 81 Technology Drive, Suite...Hull and deck, shock mitigation, rigid inflatable boat U U U UU 162 Danna Kelley 864-646-4505 Deployment of Lightweight Shock Mitigating Boat...ambient lab conditions, unless otherwise noted. October 19, 2011 Danna Kelley Senior Program Manager Advanced Technology International

  16. 36 CFR 3.2 - Do other boating laws and regulations apply to me when I operate my boat on park waters?

    Science.gov (United States)

    2010-07-01

    ... regulations apply to me when I operate my boat on park waters? 3.2 Section 3.2 Parks, Forests, and Public... boating laws and regulations apply to me when I operate my boat on park waters? (a) In addition to the.... NPS applies the adopted laws and regulations to vessels and their operation on all waters (navigable...

  17. Design and analysis of mismatch probes for long oligonucleotide microarrays

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Ye; He, Zhili; Van Nostrand, Joy D.; Zhou, Jizhong

    2008-08-15

    Nonspecific hybridization is currently a major concern with microarray technology. One of most effective approaches to estimating nonspecific hybridizations in oligonucleotide microarrays is the utilization of mismatch probes; however, this approach has not been used for longer oligonucleotide probes. Here, an oligonucleotide microarray was constructed to evaluate and optimize parameters for 50-mer mismatch probe design. A perfect match (PM) and 28 mismatch (MM) probes were designed for each of ten target genes selected from three microorganisms. The microarrays were hybridized with synthesized complementary oligonucleotide targets at different temperatures (e.g., 42, 45 and 50 C). In general, the probes with evenly distributed mismatches were more distinguishable than those with randomly distributed mismatches. MM probes with 3, 4 and 5 mismatched nucleotides were differentiated for 50-mer oligonucleotide probes hybridized at 50, 45 and 42 C, respectively. Based on the experimental data generated from this study, a modified positional dependent nearest neighbor (MPDNN) model was constructed to adjust the thermodynamic parameters of matched and mismatched dimer nucleotides in the microarray environment. The MM probes with four flexible positional mismatches were designed using the newly established MPDNN model and the experimental results demonstrated that the redesigned MM probes could yield more consistent hybridizations. Conclusions: This study provides guidance on the design of MM probes for long oligonucleotides (e.g., 50 mers). The novel MPDNN model has improved the consistency for long MM probes, and this modeling method can potentially be used for the prediction of oligonucleotide microarray hybridizations.

  18. Regulation of Gene Expression with Double-Stranded Phosphorothioate Oligonucleotides

    Science.gov (United States)

    Bielinska, Anna; Shivdasani, Ramesh A.; Zhang, Liquan; Nabel, Gary J.

    1990-11-01

    Alteration of gene transcription by inhibition of specific transcriptional regulatory proteins is necessary for determining how these factors participate in cellular differentiation. The functions of these proteins can be antagonized by several methods, each with specific limitations. Inhibition of sequence-specific DNA-binding proteins was achieved with double-stranded (ds) phosphorothioate oligonucleotides that contained octamer or kappaB consensus sequences. The phosphorothioate oligonucleotides specifically bound either octamer transcription factor or nuclear factor (NF)-kappaB. The modified oligonucleotides accumulated in cells more effectively than standard ds oligonucleotides and modulated gene expression in a specific manner. Octamer-dependent activation of a reporter plasmid or NF-kappaB-dependent activation of the human immunodeficiency virus (HIV) enhancer was inhibited when the appropriate phosphorothioate oligonucleotide was added to a transiently transfected B cell line. Addition of phosphorothioate oligonucleotides that contained the octamer consensus to Jurkat T leukemia cells inhibited interleukin-2 (IL-2) secretion to a degree similar to that observed with a mutated octamer site in the IL-2 enhancer. The ds phosphorothioate oligonucleotides probably compete for binding of specific transcription factors and may provide anti-viral, immunosuppressive, or other therapeutic effects.

  19. Antisense Oligonucleotide-Based Therapy for Neuromuscular Disease

    Directory of Open Access Journals (Sweden)

    Valentina Sardone

    2017-04-01

    Full Text Available Neuromuscular disorders such as Duchenne Muscular Dystrophy and Spinal Muscular Atrophy are neurodegenerative genetic diseases characterized primarily by muscle weakness and wasting. Until recently there were no effective therapies for these conditions, but antisense oligonucleotides, a new class of synthetic single stranded molecules of nucleic acids, have demonstrated promising experimental results and are at different stages of regulatory approval. The antisense oligonucleotides can modulate the protein expression via targeting hnRNAs or mRNAs and inducing interference with splicing, mRNA degradation, or arrest of translation, finally, resulting in rescue or reduction of the target protein expression. Different classes of antisense oligonucleotides are being tested in several clinical trials, and limitations of their clinical efficacy and toxicity have been reported for some of these compounds, while more encouraging results have supported the development of others. New generation antisense oligonucleotides are also being tested in preclinical models together with specific delivery systems that could allow some of the limitations of current antisense oligonucleotides to be overcome, to improve the cell penetration, to achieve more robust target engagement, and hopefully also be associated with acceptable toxicity. This review article describes the chemical properties and molecular mechanisms of action of the antisense oligonucleotides and the therapeutic implications these compounds have in neuromuscular diseases. Current strategies and carrier systems available for the oligonucleotides delivery will be also described to provide an overview on the past, present and future of these appealing molecules.

  20. Brain Basics

    Medline Plus

    Full Text Available ... About Us Home > Health & Education > Educational Resources Brain Basics Introduction The Growing Brain The Working Brain Brain ... called the hypothalamic-pituitary-adrenal (HPA) axis. Brain Basics in Real Life Brain Basics in Real Life— ...

  1. Brain Basics

    Medline Plus

    Full Text Available ... Brain Research Glossary Brain Basics (PDF, 10 pages) Introduction Watch the Brain Basics video Welcome. Brain Basics provides information on how the brain works, how mental illnesses ...

  2. Optical Characterization of Oligonucleotide DNA Influenced by Magnetic Fields

    Directory of Open Access Journals (Sweden)

    Seyedeh Maryam Banihashemian

    2013-09-01

    Full Text Available UV-VIS spectroscopic analysis of oligonucleotide DNA exposed to different magnetic fields was performed in order to investigate the relationship between DNA extinction coefficients and optical parameters according to magnetic-field strength. The results with the oligonucleotides adenine-thymine 100 mer (AT-100 DNA and cytosine-guanine 100 mer (CG-100 DNA indicate that the magnetic field influences DNA molar extinction coefficients and refractive indexes. The imaginary parts of the refractive index and molar extinction coefficients of the AT-100 and CG-100 DNA decreased after exposure to a magnetic field of 750 mT due to cleavage of the DNA oligonucleotides into smaller segments.

  3. Identification of mycotoxigenic fungi using an oligonucleotide microarray

    CSIR Research Space (South Africa)

    Barros, E

    2013-01-01

    Full Text Available the development of an oligonucleotide microarray specific for eleven mycotoxigenic fungi isolated from different food commodities in South Africa. This array is suitable for the detection and identification of cultures of potential mycotoxigenic fungi in both...

  4. Sequence-dependent theory of oligonucleotide hybridization kinetics

    International Nuclear Information System (INIS)

    Marimuthu, Karthikeyan; Chakrabarti, Raj

    2014-01-01

    A theoretical approach to the prediction of the sequence and temperature-dependent rate constants for oligonucleotide hybridization reactions has been developed based on the theory of relaxation kinetics. One-sided and two-sided melting reaction mechanisms for oligonucleotide hybridization reactions have been considered, analyzed, modified, and compared to select a physically consistent as well as robust model for prediction of the relaxation times of DNA hybridization reactions that agrees with the experimental evidence. The temperature- and sequence-dependent parameters of the proposed model have been estimated using available experimental data. The relaxation time model that we developed has been combined with the nearest neighbor model of hybridization thermodynamics to estimate the temperature- and sequence-dependent rate constants of an oligonucleotide hybridization reaction. The model-predicted rate constants are compared to experimentally determined rate constants for the same oligonucleotide hybridization reactions. Finally, we consider a few important applications of kinetically controlled DNA hybridization reactions

  5. Oligonucleotide-based theranostic nanoparticles in cancer therapy

    Science.gov (United States)

    Shahbazi, Reza; Ozpolat, Bulent; Ulubayram, Kezban

    2016-01-01

    Theranostic approaches, combining the functionality of both therapy and imaging, have shown potential in cancer nanomedicine. Oligonucleotides such as small interfering RNA and microRNA, which are powerful therapeutic agents, have been effectively employed in theranostic systems against various cancers. Nanoparticles are used to deliver oligonucleotides into tumors by passive or active targeting while protecting the oligonucleotides from nucleases in the extracellular environment. The use of quantum dots, iron oxide nanoparticles and gold nanoparticles and tagging with contrast agents, like fluorescent dyes, optical or magnetic agents and various radioisotopes, has facilitated early detection of tumors and evaluation of therapeutic efficacy. In this article, we review the advantages of theranostic applications in cancer therapy and imaging, with special attention to oligonucleotide-based therapeutics. PMID:27102380

  6. Brain Basics

    Medline Plus

    Full Text Available ... at NIMH News & Events About Us Home > Health & Education > Educational Resources Brain Basics Introduction The Growing Brain The Working Brain Brain Basics in Real Life Brain Research Glossary Brain Basics (PDF, 10 pages) Introduction Watch the Brain Basics video ...

  7. Development of plasmid and oligonucleotide nanometric particles.

    Science.gov (United States)

    Dauty, E; Behr, J-P; Remy, J-S

    2002-06-01

    Nucleic acids delivery vectors have shown promising therapeutic potential in model systems. However, comparable clinical success is delayed essentially because of their poor biodistribution and of their ineffective intracellular trafficking. The size of condensed DNA particles is a key determinant for in vivo diffusion, as well as for gene delivery to the cell nucleus. Towards this goal, we have developed cationic thiol-detergents that individually compact plasmid DNA molecules into anionic particles. These particles are then 'stabilized' by air-induced dimerization of the detergent into a disulfide lipid on the template DNA. The particles all measure approximately 30 nm, which corresponds to the volume of a single molecule of plasmid DNA. The gel electrophoretic mobility of the anionic particles was found to be higher than that of the plasmid DNA itself. Similarly, particles formed with a 31-mer oligonucleotide measured 19 nm. Improved in vivo diffusion, as well as improved intracellular trafficking may be inferred from the faster migration of the complexes. Moreover, the size of the particles remains compatible with nuclear pore crossing. Finally, in an attempt to improve the biodistribution of these particles, we have coated the monomolecular particles with a poly(ethylene glycol) corona.

  8. Hole hopping rates in single strand oligonucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Borrelli, Raffaele [Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università di Torino, Largo Paolo Braccini 2, I-10095 Grugliasco, TO (Italy); Capobianco, Amedeo [Dipartimento di Chimica e Biologia, Università di Salerno, Via Giovanni Paolo II, I-84084 Fisciano, SA (Italy); Peluso, Andrea, E-mail: apeluso@unisa.it [Dipartimento di Chimica e Biologia, Università di Salerno, Via Giovanni Paolo II, I-84084 Fisciano, SA (Italy)

    2014-08-31

    Highlights: • DNA hole transfer rates have been computed. • Delocalized adenine domains significantly affect hole transfer rates in DNA. • Franck–Condon weighted density of state from DFT normal modes. • DNA application in molecular electronics. - Abstract: The rates of hole transfer between guanine and adenine in single strand DNA have been evaluated by using Fermi’s golden rule and Kubo’s generating function approach for the Franck–Condon weighted density of states. The whole sets of the normal modes and vibrational frequencies of the two nucleobases, obtained at DFT/B3LYP level of calculation, have been considered in computations. The results show that in single strand the pyramidalization/planarization mode of the amino groups of both nucleobases plays the major role. At room temperature, the Franck–Condon density of states extends over a wide range of hole site energy difference, 0–1 eV, giving some hints about the design of oligonucleotides of potential technological interest.

  9. Spotted cotton oligonucleotide microarrays for gene expression analysis

    Directory of Open Access Journals (Sweden)

    Nettleton Dan

    2007-03-01

    Full Text Available Abstract Background Microarrays offer a powerful tool for diverse applications plant biology and crop improvement. Recently, two comprehensive assemblies of cotton ESTs were constructed based on three Gossypium species. Using these assemblies as templates, we describe the design and creation and of a publicly available oligonucleotide array for cotton, useful for all four of the cultivated species. Results Synthetic oligonucleotide probes were generated from exemplar sequences of a global assembly of 211,397 cotton ESTs derived from >50 different cDNA libraries representing many different tissue types and tissue treatments. A total of 22,787 oligonucleotide probes are included on the arrays, optimized to target the diversity of the transcriptome and previously studied cotton genes, transcription factors, and genes with homology to Arabidopsis. A small portion of the oligonucleotides target unidentified protein coding sequences, thereby providing an element of gene discovery. Because many oligonucleotides were based on ESTs from fiber-specific cDNA libraries, the microarray has direct application for analysis of the fiber transcriptome. To illustrate the utility of the microarray, we hybridized labeled bud and leaf cDNAs from G. hirsutum and demonstrate technical consistency of results. Conclusion The cotton oligonucleotide microarray provides a reproducible platform for transcription profiling in cotton, and is made publicly available through http://cottonevolution.info.

  10. Synthesis and evaluation of phosphorescent oligonucleotide probes for hybridisation assays

    Science.gov (United States)

    O’Sullivan, Paul J.; Burke, Martina; Soini, Aleksi E.; Papkovsky, Dmitri B.

    2002-01-01

    Monofunctional, p-isothiocyanatophenyl-derivatives of platinum (II)-coproporphyrin-I (PtCP-NCS) were evaluated as phosphorescent labelling reagents for synthetic oligonucleotides containing a 3′- or 5′-amino modification. Synthesis and purification conditions were optimised to generate high yields and purity of PtCP-labelled oligonucleotide probes. Phosphorescent properties of the PtCP label have been shown to be largely unaffected by conjugation to oligonucleotides of various length, GC composition and label attachment site. 5′-PtCP-labelled oligonucleotides were shown to work efficiently as primers in a standard PCR. A dedicated 532 nm laser-based time-resolved fluorescence plate reader enabled highly sensitive detection of PtCP-labelled oligonucleotides and PCR products, both in solution and in agarose gels, with limits of detection in the order of 0.3 pM. A model system employing two complementary oligonucleotides labelled with PtCP and QSY® 7 dye (dark quencher) showed strong (∼20-fold) and specific proximity quenching of PtCP label upon hybridisation in solution. The potential applications of PtCP-labelled probes in hybridisation assays were discussed. PMID:12409473

  11. Silver and Cyanine Staining of Oligonucleotides in Polyacrylamide Gel.

    Science.gov (United States)

    Tang, Weizhong; Zhou, Huafu; Li, Wei

    2015-01-01

    To explore why some oligonucleotides in denaturing polyacrylamide gel could not be silver-stained, 134 different oligonucleotides were analyzed using denaturing polyacrylamide gel electrophoresis stained with silver and asymmetric cyanine. As a result, we found that the sensitivity of oligos (dA), (dC), (dG) and (dT) to silver staining could be ranged as (dA) > (dG) > (dC) > (dT) from high to low. It was unexpected that oligo (dT) was hard to be silver-stained. Moreover, the silver staining of an oligonucleotide containing base T could be partially or completely inhibited by base T. The inhibition of silver staining by base T was a competitive inhibition which could be affected by the amounts of the argyrophil nucleobase and base T, the cis-distance between the argyrophil nucleobase and base T, and the gel concentration. The changes of the intensity of an oligonucleotide band caused by the changes of DNA base composition were diverse and interesting. The intensity of some oligonucleotide bands would significantly change when the changes of DNA base composition accumulated to a certain extent (usually ≥ 4 nt). The sensitivity of cyanine staining of ≤ 11-nt long oligonucleotides could be enhanced about 250-fold by fixing the gels with methanol fixing solution.

  12. 46 CFR 199.175 - Survival craft and rescue boat equipment.

    Science.gov (United States)

    2010-10-01

    ... medication sufficient for one person for 48 hours, and instructions for using the medication. Each... required for boats of self-bailing design. 3 Not required for inflated or rigid-inflated rescue boats. 4 A...

  13. 77 FR 33229 - Sport Fishing and Boating Partnership Council Charter

    Science.gov (United States)

    2012-06-05

    ..., the following national interest groups: (a) State fish and wildlife resource management agencies (2... resource management organizations; (g) Aquatic resource outreach and education organizations; and (h) The tourism industry. Members must be senior-level representatives of recreational fishing, boating, and...

  14. A comparison of the boating and swimming microbial water quality ...

    African Journals Online (AJOL)

    Calabar River Estuary is often used by both locals and tourists for boating and swimming making it necessary to assess the microbial recreational water quality of this water body. Five sampling stations were established – 3 in Calabar River and 2 in the Estuary. Calabar River stations were inshore while the estuarine ...

  15. Effect of boat noise and angling on lake fish behaviour

    DEFF Research Database (Denmark)

    Jacobsen, Lene; Baktoft, Henrik; Jepsen, Niels

    2014-01-01

    The effects of disturbances from recreational activities on the swimming speed and habitat use of roach Rutilus rutilus, perch Perca fluviatilis and pike Esox lucius were explored. Disturbances were applied for 4h as (1) boating in short intervals with a small outboard internal combustion engine...

  16. Physiological consequences of military high-speed boat transits.

    Science.gov (United States)

    Myers, Stephen D; Dobbins, Trevor D; King, Stuart; Hall, Benjamin; Ayling, Ruth M; Holmes, Sharon R; Gunston, Tom; Dyson, Rosemary

    2011-09-01

    The purpose of this study was to investigate the consequences of a high-speed boat transit on physical performance. Twenty-four Royal Marines were randomly assigned to a control (CON) or transit (TRAN) group. The CON group sat onshore for 3 h whilst the TRAN group completed a 3-h transit in open-boats running side-by-side, at 40 knots in moderate-to-rough seas, with boat deck and seat-pan acceleration recorded. Performance tests (exhaustive shuttle-run, handgrip, vertical-jump, push-up) were completed pre- and immediately post-transit/sit, with peak heart rate (HRpeak) and rating of perceived exertion (RPE) recorded. Serial blood samples (pre, 24, 36, 48, 72 h) were analyzed for creatine kinase (CK) activity. The transit was typified by frequent high shock impacts, but moderate mean heart rates (Forces/naval/police/rescue services carrying out demanding, high-risk physical tasks during and immediately after high-speed boat transits.

  17. Water Pressure Distribution on a Flying Boat Hull

    Science.gov (United States)

    Thompson, F L

    1931-01-01

    This is the third in a series of investigations of the water pressures on seaplane floats and hulls, and completes the present program. It consisted of determining the water pressures and accelerations on a Curtiss H-16 flying boat during landing and taxiing maneuvers in smooth and rough water.

  18. The Team Boat Exercise: Enhancing Team Communication Midsemester

    Science.gov (United States)

    Cox, Pamela L.; Friedman, Barry A.

    2009-01-01

    This paper discusses the Team Boat Exercise, which was developed to provide students with a mechanism for addressing team problems and enhancing team communication midsemester. The inspiration for the exercise came from a video by Prentice Hall, Inc. (2001). Part III of the video, entitled "Corporate Coaching," shows senior staff members from the…

  19. Foreign body in scrotum following a boat engine blast accident ...

    African Journals Online (AJOL)

    Male genital injuries, demand prompt management to prevent long-term sexual and psychological damage. Injuries to the scrotum and contents may produce impaired fertility.We report our experience in diagnosing and managing a case of a foreign body in the scrotum following a boat engine blast accident. This case ...

  20. Modified technique of using conventional slider boat for liquid phase ...

    Indian Academy of Sciences (India)

    Unknown

    after baking. After HCl treatment it was repeatedly washed in deionized water and finally dried. To load the boat, the solid mass was placed over freshly cleaned surface of a source silicon wafer placed in first groove of slider unit B with both the units B and C mounted on. A as seen in figure 2a. The process tube was again ...

  1. Modified technique of using conventional slider boat for liquid phase ...

    Indian Academy of Sciences (India)

    Epitaxial layers of silicon are grown on single crystal Si-substrate from a solution of silicon in indium using conventional graphite slider boat technique. The important problems of natural convection due to lower density of silicon compared to indium, poor wetting of substrate due to high angle of contact of indium solution on ...

  2. Experimental Evaluation of the Hydrodynamic Response of Crew Boat Hulls

    DEFF Research Database (Denmark)

    Pecher, Arthur; Kofoed, Jens Peter

    This report presents the results of an experimental study on 3 different hulls of crew boats intended for service to offshore wind turbines. Their hydrodynamic behaviour has been tested in various sea states representing general wave conditions that could be expected at offshore wind farms. Two...

  3. 78 FR 22814 - Special Local Regulations; Miami Super Boat Grand Prix, Atlantic Ocean; Miami Beach, FL

    Science.gov (United States)

    2013-04-17

    ..., Atlantic Ocean; Miami Beach, FL AGENCY: Coast Guard, DHS. ACTION: Notice of proposed rulemaking. SUMMARY... Miami Beach, Florida during the Miami Super Boat Grand Prix. The Miami Super Boat Grand Prix will... Beach, Florida. Approximately 25 high- speed power boats will be participating in the races, and it is...

  4. Kepatuhan Nahkoda Melakukan Pemeriksaan Boat Berdasarkan Check- List Harian untuk Keselamatan Pelayaran di Perusahaan Pelayaran

    OpenAIRE

    B, Rinto; Shaluhiyah, Zahroh; Kurniawan, Bina

    2012-01-01

    Terdapat penyimpangan prosedur dalam pemeriksaan boat berdasarkan checklist inspeksiyang sudah ada dimana rata-rata nahkoda melakukan pencontrengan checklist tanpamelakukan uji coba alat-alat keselamatan dan mesin di dalam boat. Tujuan penelitian iniadalah untuk mengeksplorasi gambaran tentang perilaku kepatuhan nahkoda di Perusahaanpelayaran ini dalam melakukan pemeriksaan boat berdasarkan checklist. Penelitian inimenggunakan metode penelitian kualitatif dengan melakukan wawancara yang menda...

  5. 46 CFR 133.175 - Survival craft and rescue boat equipment.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 4 2010-10-01 2010-10-01 false Survival craft and rescue boat equipment. 133.175... LIFESAVING SYSTEMS Requirements for All OSVs § 133.175 Survival craft and rescue boat equipment. (a) All... survival craft or rescue boat; or (iii) Overload the launching appliance. (b) Each rigid liferaft and...

  6. 46 CFR 108.575 - Survival craft and rescue boat equipment.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 4 2010-10-01 2010-10-01 false Survival craft and rescue boat equipment. 108.575... DRILLING UNITS DESIGN AND EQUIPMENT Lifesaving Equipment § 108.575 Survival craft and rescue boat equipment... seaworthiness of the survival craft or rescue boat; or (iii) Overload the launching appliance. (b) Each lifeboat...

  7. 7 CFR 58.317 - Bulk butter trucks, boats, texturizers, and packers.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Bulk butter trucks, boats, texturizers, and packers... and Grading Service 1 Equipment and Utensils § 58.317 Bulk butter trucks, boats, texturizers, and packers. Bulk butter trucks, boats, texturizers, and packers shall be constructed of aluminum, stainless...

  8. A demand-based management option to address boat congestion at ...

    African Journals Online (AJOL)

    2015-07-04

    speed boating and jet skiing represent. 20%, 65%, 7.5% and 7.5%, respectively. This implies 4.6 angling boats, 48.75 leisure boats, 0.675 water skiers or speed boaters ..... Theory and Application to Travel Demand. MIT Press ...

  9. Brain Basics

    Medline Plus

    Full Text Available ... as depression. The Growing Brain Inside the Brain: Neurons & Neural Circuits Neurons are the basic working unit of the brain ... specialized for the function of conducting messages. A neuron has three basic parts: Cell body which includes ...

  10. Brain Basics

    Medline Plus

    Full Text Available ... in Real Life Brain Research Glossary Brain Basics (PDF, 10 pages) Introduction Watch the Brain Basics video ... and epigenetic changes can be passed on to future generations. Further understanding of genes and epigenetics may ...

  11. Biominetic High Density Lipoproteins for the Delivery of Therapeutic Oligonucleotides

    Science.gov (United States)

    Tripathy, Sushant

    Advances in nanotechnology have brought about novel inorganic and hybrid nanoparticles with unique physico-chemical properties that make them suitable for a broad range of applications---from nano-circuitry to drug delivery. A significant part of those advancements have led to ground-breaking discoveries that have changed the approaches to formulation of therapeutics against diseases, such as cancer. Now-a-days the focus does not lie solely on finding a candidate small-molecule therapeutic with minimal adverse effects, but researchers are looking up to nanoparticles to improve biodistribution and biocompatibility profile of clinically proven therapeutics. The plethora of conjugation chemistries offered by currently extant inorganic nanoparticles have, in recent years, led to great leaps in the field of biomimicry---a modality that promises high biocompatibility. Further, in the pursuit of highly specific therapeutic molecules, researchers have turned to silencing oligonucleotides and some have already brought together the strengths of nanoparticles and silencing oligonucleotides in search of an efficacious therapy for cancer with minimal adverse effects. This dissertation work focuses on such a biomimetic platform---a gold nanoparticle based high density lipoprotein biomimetic (HDL NP), for the delivery of therapeutic oligonucleotides. The first chapter of this body of work introduces the molecular target of the silencing oligonucleotides---VEGFR2, and its role in the progression of solid tumor cancers. The background information also covers important aspects of natural high density lipoproteins (HDL), especially their innate capacity to bind and deliver exogenous and endogenous silencing oligonucleotides to tissues that express their high affinity receptor SRB1. We subsequently describe the synthesis of the biomimetic HDL NP and its oligonucleotide conjugates, and establish their biocompatibility. Further on, experimental data demonstrate the efficacy of silencing

  12. Boats 'n Kids, Part I. Instructor Guide and Children's Workbook. Boating Safety Program for Children and Youth.

    Science.gov (United States)

    Coast Guard Auxiliary, St. Louis, MO. Dept. of Education.

    This packet contains a children's workbook on boating safety and a guide for Coast Guard Auxiliary members making brief safety presentations to elementary school students, aged 5-10. Section I of the guide covers school arrangements (district approval requirements and relationships with teachers and administrators), recordkeeping, equipment to…

  13. Investigations of oligonucleotide usage variance within and between prokaryotes

    DEFF Research Database (Denmark)

    Bohlin, J.; Skjerve, E.; Ussery, David

    2008-01-01

    Oligonucleotide usage in archaeal and bacterial genomes can be linked to a number of properties, including codon usage (trinucleotides), DNA base-stacking energy (dinucleotides), and DNA structural conformation (di-to tetranucleotides). We wanted to assess the statistical information potential...... was that prokaryotic chromosomes can be described by hexanucleotide frequencies, suggesting that prokaryotic DNA is predominantly short range correlated, i. e., information in prokaryotic genomes is encoded in short oligonucleotides. Oligonucleotide usage varied more within AT-rich and host-associated genomes than...... in GC-rich and free-living genomes, and this variation was mainly located in non-coding regions. Bias (selectional pressure) in tetranucleotide usage correlated with GC content, and coding regions were more biased than non-coding regions. Non-coding regions were also found to be approximately 5.5% more...

  14. Delivery of RNAi-Based Oligonucleotides by Electropermeabilization

    Directory of Open Access Journals (Sweden)

    Muriel Golzio

    2013-04-01

    Full Text Available For more than a decade, understanding of RNA interference (RNAi has been a growing field of interest. The potent gene silencing ability that small oligonucleotides have offers new perspectives for cancer therapeutics. One of the present limits is that many biological barriers exist for their efficient delivery into target cells or tissues. Electropermeabilization (EP is one of the physical methods successfully used to transfer small oligonucleotides into cells or tissues. EP consists in the direct application of calibrated electric pulses to cells or tissues that transiently permeabilize the plasma membranes, allowing efficient in vitro and in vivo. cytoplasmic delivery of exogenous molecules. The present review reports on the type of therapeutic RNAi-based oligonucleotides that can be electrotransferred, the mechanism(s of their electrotransfer and the technical settings for pre-clinical purposes.

  15. Challenges to oligonucleotides-based therapeutics for Duchenne muscular dystrophy

    Directory of Open Access Journals (Sweden)

    Goyenvalle Aurélie

    2011-02-01

    Full Text Available Abstract Antisense oligonucleotides are short nucleic acids designed to bind to specific messenger RNAs in order to modulate splicing patterns or inhibit protein translation. As such, they represent promising therapeutic tools for many disorders and have been actively developed for more than 20 years as a form of molecular medicine. Although significant progress has been made in developing these agents as drugs, they are yet not recognized as effective therapeutics and several hurdles remain to be overcome. Within the last few years, however, the prospect of successful oligonucleotides-based therapies has moved a step closer, in particular for Duchenne muscular dystrophy. Clinical trials have recently been conducted for this myopathy, where exon skipping is being used to achieve therapeutic outcomes. In this review, the recent developments and clinical trials using antisense oligonucleotides for Duchenne muscular dystrophy are discussed, with emphasis on the challenges ahead for this type of therapy, especially with regards to delivery and regulatory issues.

  16. 77 FR 15600 - Special Local Regulation; Emerald Coast Super Boat Grand Prix; Saint Andrew Bay; Panama City, FL

    Science.gov (United States)

    2012-03-16

    ...-AA08 Special Local Regulation; Emerald Coast Super Boat Grand Prix; Saint Andrew Bay; Panama City, FL... navigable waters during the Emerald Coast Super Boat Grand Prix high speed boat races. Entry into... needed to safeguard persons and vessels from safety hazards associated with the Emerald Coast Super Boat...

  17. Amino acids attached to 2'-amino-LNA: Synthesis of DNA mixmer oligonucleotides with increased duplex stability

    DEFF Research Database (Denmark)

    Johannsen, Marie Willaing; Wengel, Jesper; Wamberg, Michael Chr.

    2010-01-01

    -LNA nucleosides derivatized with amino acids have been synthesized and incorporated into DNA oligonucleotides. Following oligonucleotide synthesis, peptides have been added using solid phase peptide coupling chem. Modification of oligonucleotides with pos. charged residues greatly improves thermal stability....

  18. Oligonucleotide Therapy for Obstructive and Restrictive Respiratory Diseases

    Directory of Open Access Journals (Sweden)

    Wupeng Liao

    2017-01-01

    Full Text Available Inhaled oligonucleotide is an emerging therapeutic modality for various common respiratory diseases, including obstructive airway diseases like asthma and chronic obstructive pulmonary disease (COPD and restrictive airway diseases like idiopathic pulmonary fibrosis (IPF. The advantage of direct accessibility for oligonucleotide molecules to the lung target sites, bypassing systemic administration, makes this therapeutic approach promising with minimized potential systemic side effects. Asthma, COPD, and IPF are common chronic respiratory diseases, characterized by persistent airway inflammation and dysregulated tissue repair and remodeling, although each individual disease has its unique etiology. Corticosteroids have been widely prescribed for the treatment of asthma, COPD, and IPF. However, the effectiveness of corticosteroids as an anti-inflammatory drug is limited by steroid resistance in severe asthma, the majority of COPD cases, and pulmonary fibrosis. There is an urgent medical need to develop target-specific drugs for the treatment of these respiratory conditions. Oligonucleotide therapies, including antisense oligonucleotide (ASO, small interfering RNA (siRNA, and microRNA (miRNA are now being evaluated both pre-clinically and clinically as potential therapeutics. The mechanisms of action of ASO and siRNA are highly target mRNA specific, ultimately leading to target protein knockdown. miRNA has both biomarker and therapeutic values, and its knockdown by a miRNA antagonist (antagomir has a broader but potentially more non-specific biological outcome. This review will compile the current findings of oligonucleotide therapeutic targets, verified in various respiratory disease models and in clinical trials, and evaluate different chemical modification approaches to improve the stability and potency of oligonucleotides for the treatment of respiratory diseases.

  19. Optimizing the design of oligonucleotides for homology directed gene targeting.

    Science.gov (United States)

    Miné-Hattab, Judith; Fleury, Geneviève; Prevost, Chantal; Dutreix, Marie; Viovy, Jean-Louis

    2011-04-05

    Gene targeting depends on the ability of cells to use homologous recombination to integrate exogenous DNA into their own genome. A robust mechanistic model of homologous recombination is necessary to fully exploit gene targeting for therapeutic benefit. In this work, our recently developed numerical simulation model for homology search is employed to develop rules for the design of oligonucleotides used in gene targeting. A Metropolis Monte-Carlo algorithm is used to predict the pairing dynamics of an oligonucleotide with the target double-stranded DNA. The model calculates the base-alignment between a long, target double-stranded DNA and a probe nucleoprotein filament comprised of homologous recombination proteins (Rad51 or RecA) polymerized on a single strand DNA. In this study, we considered different sizes of oligonucleotides containing 1 or 3 base heterologies with the target; different positions on the probe were tested to investigate the effect of the mismatch position on the pairing dynamics and stability. We show that the optimal design is a compromise between the mean time to reach a perfect alignment between the two molecules and the stability of the complex. A single heterology can be placed anywhere without significantly affecting the stability of the triplex. In the case of three consecutive heterologies, our modeling recommends using long oligonucleotides (at least 35 bases) in which the heterologous sequences are positioned at an intermediate position. Oligonucleotides should not contain more than 10% consecutive heterologies to guarantee a stable pairing with the target dsDNA. Theoretical modeling cannot replace experiments, but we believe that our model can considerably accelerate optimization of oligonucleotides for gene therapy by predicting their pairing dynamics with the target dsDNA.

  20. Optimizing the design of oligonucleotides for homology directed gene targeting.

    Directory of Open Access Journals (Sweden)

    Judith Miné-Hattab

    Full Text Available BACKGROUND: Gene targeting depends on the ability of cells to use homologous recombination to integrate exogenous DNA into their own genome. A robust mechanistic model of homologous recombination is necessary to fully exploit gene targeting for therapeutic benefit. METHODOLOGY/PRINCIPAL FINDINGS: In this work, our recently developed numerical simulation model for homology search is employed to develop rules for the design of oligonucleotides used in gene targeting. A Metropolis Monte-Carlo algorithm is used to predict the pairing dynamics of an oligonucleotide with the target double-stranded DNA. The model calculates the base-alignment between a long, target double-stranded DNA and a probe nucleoprotein filament comprised of homologous recombination proteins (Rad51 or RecA polymerized on a single strand DNA. In this study, we considered different sizes of oligonucleotides containing 1 or 3 base heterologies with the target; different positions on the probe were tested to investigate the effect of the mismatch position on the pairing dynamics and stability. We show that the optimal design is a compromise between the mean time to reach a perfect alignment between the two molecules and the stability of the complex. CONCLUSION AND SIGNIFICANCE: A single heterology can be placed anywhere without significantly affecting the stability of the triplex. In the case of three consecutive heterologies, our modeling recommends using long oligonucleotides (at least 35 bases in which the heterologous sequences are positioned at an intermediate position. Oligonucleotides should not contain more than 10% consecutive heterologies to guarantee a stable pairing with the target dsDNA. Theoretical modeling cannot replace experiments, but we believe that our model can considerably accelerate optimization of oligonucleotides for gene therapy by predicting their pairing dynamics with the target dsDNA.

  1. Basic electrotechnology

    CERN Document Server

    Ashen, R A

    2013-01-01

    BASIC Electrotechnology discusses the applications of Beginner's All-purpose Symbolic Instruction Code (BASIC) in engineering, particularly in solving electrotechnology-related problems. The book is comprised of six chapters that cover several topics relevant to BASIC and electrotechnology. Chapter 1 provides an introduction to BASIC, and Chapter 2 talks about the use of complex numbers in a.c. circuit analysis. Chapter 3 covers linear circuit analysis with d.c. and sinusoidal a.c. supplies. The book also discusses the elementary magnetic circuit theory. The theory and performance of two windi

  2. Impact of boat-generated waves on intertidal estuarine sediments

    Science.gov (United States)

    Blanpain, O.; Deloffre, J.; Lafite, R.; Gomit, G.; Calluaud, D.; David, L.

    2010-12-01

    Hydrodynamics in the macrotidal Seine estuary (France) are controlled by the semi-diurnal tidal regime modulated seasonally by the fluvial discharge. Wind effect on sediment transport (through wind waves and swell) is observed at the mouth of the estuary. Over the last century, authorities have put emphasis on facilitating economic exchanges by means of embankment building and increased dredging activity. These developments led to allow and secure sea vessel traffic in the Seine estuary (from its mouth to the port of Rouen, 125 km upstream) but they also resulted in a change of estuarine hydrodynamics and sediment transport features. A riversides restoration policy has been recently started by port authorities. In this context, the objective of the field-based study presented is to connect vessel characteristics (i.e. speed, draft...), boat-generated waves and their sedimentary impacts. Such information will be used by stakeholders to manage riverside. The natural intertidal site of interest is located in the fluvial freshwater part of the Seine estuary characterized by a 4.5 m maximum tidal range. The foreshore slope is gently decreasing and surface sediments are composed of fine to coarse sand with occasional mud drapes. In order to decipher boat-generated events, the sampling strategy is based on continuous ADV measurements coupled with a turbidimeter and an altimeter to study sediment dynamics. These instruments are settled in the lower part of the foreshore (i) to obtain a significant dataset (i.e. oceanic instruments are not measuring in air) on a zone statically affected by boat waves and (ii) because most of boat traffic occurs during early flood or late ebb period. Spatial variations are assessed along a cross-section through grain-size analysis of surface sediments and topography measurements using pole technique. Results enhance hydrodynamic and sedimentary impacts of boat-generated waves compared respectively to tidal and wind effects. Long

  3. Biodeterioration of wooden boats: a major problem facing marine fisheries

    OpenAIRE

    Santhakumaran, L.N.

    1988-01-01

    In India, the fishing industry alone incurs an annual loss of over 120 million rupees on account of biodeterioration of wooden fishing craft. None of the timber species, currently in demand for boat-building, possesses an natural bioresistance and will be completely destroyed within 6 to 12 months. Preventive measures against biodeterioration range from application of several indigenous formulations to metallic sheathings and pressure impregnation of wood with preservative chemicals. These me...

  4. Investigation of longitudinal control system for a small hydrofoil boat

    Science.gov (United States)

    Phillips, W. H.; Shaughnessy, J. D.

    1976-01-01

    An analysis of a hydromechanical system for longitudinal control of a small hydrofoil boat is presented. The system incorporates height and acceleration sensors operating flaps on the foils through a mechanical linkage. Effects of some of the system parameters on the stability and response to waves are shown. The results indicate that the system is capable of providing adequate stability, but the response to stern waves at low frequencies is larger than desired.

  5. Genoa Boat Show – Good Example of Event Management

    Directory of Open Access Journals (Sweden)

    Dunja Demirović

    2012-07-01

    Full Text Available International Boat Show, a business and tourist event, has been held annually in Italian city of Genoa since 1962. The fair is one of the oldest, largest and best known in the field of boating industry worldwide, primarily due to good management of the event and it can serve as case study for domestic fair organizers to improve the quality of their business and services. Since Belgrade is the city of fairs, but compared to Genoa still underdeveloped in terms of trade shows, the following tasks imposed naturally in this study: to determine the relationship of the organizers of Genoa Boat Show in the sector of preparation and fair offer, in the sector of selection and communication with specific target groups (especially visitors, services during the fair and functioning of the city during the fair. During the research the authors have mostly used historical method, comparison, synthesis and the interview method. The results of theoretical research, in addition, may help not only managers of fair shows and of exhibitions, but also to organizers of other events in our country

  6. Anesthesia Basics

    Science.gov (United States)

    ... Staying Safe Videos for Educators Search English Español Anesthesia Basics KidsHealth / For Teens / Anesthesia Basics What's in ... español Conceptos básicos sobre la anestesia What Is Anesthesia? No doubt about it, getting an operation can ...

  7. Brain Basics

    Medline Plus

    Full Text Available ... pituitary-adrenal (HPA) axis. Brain Basics in Real Life Brain Basics in Real Life—How Depression affects the Brain Meet Sarah Sarah ... having trouble coping with the stresses in her life. She began to think of suicide because she ...

  8. Folding Topology of a Short Coiled-Coil Peptide Structure Templated by an Oligonucleotide Triplex

    DEFF Research Database (Denmark)

    Lou, Chenguang; Christensen, Niels Johan; Martos Maldonado, Manuel Cristo

    2017-01-01

    by oligonucleotide duplex and triplex formation. POC synthesis was achieved by copper-free alkyne-azide cycloaddition between three oligonucleotides and a 23-mer peptide, which by itself exhibited multiple oligomeric states in solution. The oligonucleotide domain was designed to furnish a stable parallel triplex...

  9. Paramagnetic labelling of proteins and oligonucleotides for NMR

    International Nuclear Information System (INIS)

    Su Xuncheng; Otting, Gottfried

    2010-01-01

    Paramagnetic effects offer a rich source of long-range structural restraints. Here we review current methods for site-specific tagging of proteins and oligonucleotides with paramagnetic molecules. The paramagnetic tags include nitroxide radicals and metal chelators. Particular emphasis is placed on tags suitable for site-specific and rigid attachment of lanthanide ions to macromolecules.

  10. Tandem Oligonucleotide Probe Annealing and Elongation To Discriminate Viral Sequence

    DEFF Research Database (Denmark)

    Taskova, Maria; Uhd, Jesper; Miotke, Laura

    2017-01-01

    opportunities in transcriptome analysis, virology, and other fields. Herein, we report for the first time a "click" chemistry approach to oligonucleotide probe elongation as a novel approach to specifically detect a viral sequence. We hybridized a library of short, terminally labeled probes to Ebola virus RNA...

  11. Oligonucleotide-directed mutagenesis for precision gene editing.

    Science.gov (United States)

    Sauer, Noel J; Mozoruk, Jerry; Miller, Ryan B; Warburg, Zachary J; Walker, Keith A; Beetham, Peter R; Schöpke, Christian R; Gocal, Greg F W

    2016-02-01

    Differences in gene sequences, many of which are single nucleotide polymorphisms, underlie some of the most important traits in plants. With humanity facing significant challenges to increase global agricultural productivity, there is an urgent need to accelerate the development of these traits in plants. oligonucleotide-directed mutagenesis (ODM), one of the many tools of Cibus' Rapid Trait Development System (RTDS(™) ) technology, offers a rapid, precise and non-transgenic breeding alternative for trait improvement in agriculture to address this urgent need. This review explores the application of ODM as a precision genome editing technology, with emphasis on using oligonucleotides to make targeted edits in plasmid, episomal and chromosomal DNA of bacterial, fungal, mammalian and plant systems. The process of employing ODM by way of RTDS technology has been improved in many ways by utilizing a fluorescence conversion system wherein a blue fluorescent protein (BFP) can be changed to a green fluorescent protein (GFP) by editing a single nucleotide of the BFP gene (CAC→TAC; H66 to Y66). For example, dependent on oligonucleotide length, applying oligonucleotide-mediated technology to target the BFP transgene in Arabidopsis thaliana protoplasts resulted in up to 0.05% precisely edited GFP loci. Here, the development of traits in commercially relevant plant varieties to improve crop performance by genome editing technologies such as ODM, and by extension RTDS, is reviewed. © 2015 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  12. Lipid-modified G4-decoy oligonucleotide anchored to nanoparticles

    DEFF Research Database (Denmark)

    Cogoi, S; Jakobsen, U; Pedersen, E B

    2016-01-01

    KRAS is mutated in >90% of pancreatic ductal adenocarcinomas. As its inactivation leads to tumour regression, mutant KRAS is considered an attractive target for anticancer drugs. In this study we report a new delivery strategy for a G4-decoy oligonucleotide that sequesters MAZ, a transcription fa...

  13. Basic hydraulics

    CERN Document Server

    Smith, P D

    1982-01-01

    BASIC Hydraulics aims to help students both to become proficient in the BASIC programming language by actually using the language in an important field of engineering and to use computing as a means of mastering the subject of hydraulics. The book begins with a summary of the technique of computing in BASIC together with comments and listing of the main commands and statements. Subsequent chapters introduce the fundamental concepts and appropriate governing equations. Topics covered include principles of fluid mechanics; flow in pipes, pipe networks and open channels; hydraulic machinery;

  14. Brain Basics

    Medline Plus

    Full Text Available ... normal brain development and function can go awry, leading to mental illnesses. Brain Basics will introduce you ... of DNA. Sometimes this copying process is imperfect, leading to a gene mutation that causes the gene ...

  15. Brain Basics

    Medline Plus

    Full Text Available ... Real Life Brain Basics in Real Life—How Depression affects the Brain Meet Sarah Sarah is a ... in controlling movement, managing the release of various hormones, and aiding the flow of information to the ...

  16. Brain Basics

    Medline Plus

    Full Text Available ... Events About Us Home > Health & Education > Educational Resources Brain Basics Introduction The Growing Brain The Working Brain ... to mental disorders, such as depression. The Growing Brain Inside the Brain: Neurons & Neural Circuits Neurons are ...

  17. Basic Finance

    Science.gov (United States)

    Vittek, J. F.

    1972-01-01

    A discussion of the basic measures of corporate financial strength, and the sources of the information is reported. Considered are: balance sheet, income statement, funds and cash flow, and financial ratios.

  18. Brain Basics

    Medline Plus

    Full Text Available ... effectively coordinate the billions of cells in the body, the results can affect many aspects of life. ... messages. A neuron has three basic parts: Cell body which includes the nucleus, cytoplasm, and cell organelles. ...

  19. Brain Basics

    Medline Plus

    Full Text Available ... Real Life Brain Basics in Real Life—How Depression affects the Brain Meet Sarah Sarah is a ... brain. DNA —The "recipe of life," containing inherited genetic information that helps to define physical and some ...

  20. Brain Basics

    Medline Plus

    Full Text Available ... Brain Basics provides information on how the brain works, how mental illnesses are disorders of the brain, ... learning more about how the brain grows and works in healthy people, and how normal brain development ...

  1. Brain Basics

    Medline Plus

    Full Text Available ... science, such as: How the brain develops How genes and the environment affect the brain The basic ... that with brain development in people mental disorders. Genes and environmental cues both help to direct this ...

  2. Brain Basics

    Medline Plus

    Full Text Available ... Real Life Brain Basics in Real Life—How Depression affects the Brain Meet Sarah Sarah is a ... blues" from time to time. In contrast, major depression is a serious disorder that lasts for weeks. ...

  3. Brain Basics

    Medline Plus

    Full Text Available ... How the brain develops How genes and the environment affect the brain The basic structure of the ... inside contents of the cell from its surrounding environment and controls what enters and leaves the cell, ...

  4. Brain Basics

    Medline Plus

    Full Text Available ... depression. The Growing Brain Inside the Brain: Neurons & Neural Circuits Neurons are the basic working unit of ... but sometimes give rise to disabilities or diseases. neural circuit —A network of neurons and their interconnections. ...

  5. Brain Basics

    Medline Plus

    Full Text Available ... in the anatomy, physiology, and chemistry of the nervous system. When the brain cannot effectively coordinate the billions ... the basic working unit of the brain and nervous system. These cells are highly specialized for the function ...

  6. Brain Basics

    Medline Plus

    Full Text Available ... the anatomy, physiology, and chemistry of the nervous system. When the brain cannot effectively coordinate the billions ... basic working unit of the brain and nervous system. These cells are highly specialized for the function ...

  7. Behavioural and biochemical stress responses of Palinurus elephas after exposure to boat noise pollution in tank.

    Science.gov (United States)

    Filiciotto, Francesco; Vazzana, Mirella; Celi, Monica; Maccarrone, Vincenzo; Ceraulo, Maria; Buffa, Gaspare; Di Stefano, Vincenzo; Mazzola, Salvatore; Buscaino, Giuseppa

    2014-07-15

    This study examined the effects of boat noise on the behavioural and biochemical parameters of the Mediterranean spiny lobster (Palinurus elephas). The experiment was conducted in a tank equipped with a video and audio recording system. 18 experimental trials, assigned to boat noise and control conditions, were performed using lobsters in single and group of 4 specimens. After a 1h habituation period, we audio- and video-recorded the lobsters for 1h. During the experimental phase, the animals assigned to the boat groups were exposed to boat noise pollution (a random sequence of boat noises). Exposure to the noise produced significant variations in locomotor behaviours and haemolymphatic parameters. Our results indicate that the lobsters exposed to boat noises increased significantly their locomotor activities and haemolymphatic bioindicator of stressful conditions such as glucose, total proteins, Hsp70 expression and THC when tested both singly and in groups. Copyright © 2014 Elsevier Ltd. All rights reserved.

  8. The behavioural response of Australian fur seals to motor boat noise.

    Directory of Open Access Journals (Sweden)

    Joy S Tripovich

    Full Text Available Australian fur seals breed on thirteen islands located in the Bass Strait, Australia. Land access to these islands is restricted, minimising human presence but boat access is still permissible with limitations on approach distances. Thirty-two controlled noise exposure experiments were conducted on breeding Australian fur seals to determine their behavioural response to controlled in-air motor boat noise on Kanowna Island (39°10'S, 146°18'E. Our results show there were significant differences in the seals' behaviour at low (64-70 dB versus high (75-85 dB sound levels, with seals orientating themselves towards or physically moving away from the louder boat noise at three different sound levels. Furthermore, seals responded more aggressively with one another and were more alert when they heard louder boat noise. Australian fur seals demonstrated plasticity in their vocal responses to boat noise with calls being significantly different between the various sound intensities and barks tending to get faster as the boat noise got louder. These results suggest that Australian fur seals on Kanowna Island show behavioural disturbance to high level boat noise. Consequently, it is recommended that an appropriate level of received boat sound emissions at breeding fur seal colonies be below 74 dB and that these findings be taken into account when evaluating appropriate approach distances and speed limits for boats.

  9. Dating the Bibong-ri Neolithic site in Korea: Excavating the oldest ancient boat

    Energy Technology Data Exchange (ETDEWEB)

    Park, Gyujun, E-mail: danielp@kigam.re.k [Geochemical Analysis Center, Geologic Environment Division, Korea Institute of Geoscience and Mineral Resources 305-350 (Korea, Republic of); Kim, Jong-Chan [Department of Physics and Astronomy, Seoul National University, Seoul 151-742 (Korea, Republic of); Youn, Minyoung; Yun, Chongcheol; Kang, Jin; Song, Yong-Mi; Song, Su-Jin; Noh, Hye-Jin [Electrostatic Accelerator Research Center, NCIRF, Seoul National University, Seoul 151-742 (Korea, Republic of); Kim, Do-Kyun [Department of Physics and Astronomy, Seoul National University, Seoul 151-742 (Korea, Republic of); Im, Hack-Jong [Gimhae National Museum, Gimhae, Gyeongsangnam-do 621-060 (Korea, Republic of)

    2010-04-15

    The remains of an ancient wooden boat were unearthed at the Bibong-ri shell mound site. The site was located at Bibong-ri, Bugog-myeon, Changnyeong-gun, Gyeongsangnam-do in South Korea. A substantial fragment of the vessel was discovered in the lowest layer of the site. We collected 17 samples of charcoal and wood from pebble, sand, and shell layers. Sample preparation extracted the carbon from each sample material and converted it into graphite for AMS radiocarbon dating. Radiocarbon dates of the samples indicate that they belong to the Neolithic period and that the boat dates from ca. 5700 BC. To this point, the oldest known boat in the world has been a wooden boat dating from ca. 5500 BC in China. Other ancient boats from around the world include a logboat dating from ca. 3600 BC in Japan and a fleet of wooden boats dating from ca. 3000 BC in Egypt. The Bibong-ri boat is the first boat from the Neolithic period ever found in South Korea and must represent one of the world's oldest known boats.

  10. Dating the Bibong-ri Neolithic site in Korea: Excavating the oldest ancient boat

    International Nuclear Information System (INIS)

    Park, Gyujun; Kim, Jong-Chan; Youn, Minyoung; Yun, Chongcheol; Kang, Jin; Song, Yong-Mi; Song, Su-Jin; Noh, Hye-Jin; Kim, Do-Kyun; Im, Hack-Jong

    2010-01-01

    The remains of an ancient wooden boat were unearthed at the Bibong-ri shell mound site. The site was located at Bibong-ri, Bugog-myeon, Changnyeong-gun, Gyeongsangnam-do in South Korea. A substantial fragment of the vessel was discovered in the lowest layer of the site. We collected 17 samples of charcoal and wood from pebble, sand, and shell layers. Sample preparation extracted the carbon from each sample material and converted it into graphite for AMS radiocarbon dating. Radiocarbon dates of the samples indicate that they belong to the Neolithic period and that the boat dates from ca. 5700 BC. To this point, the oldest known boat in the world has been a wooden boat dating from ca. 5500 BC in China. Other ancient boats from around the world include a logboat dating from ca. 3600 BC in Japan and a fleet of wooden boats dating from ca. 3000 BC in Egypt. The Bibong-ri boat is the first boat from the Neolithic period ever found in South Korea and must represent one of the world's oldest known boats.

  11. Business opportunities of new energy systems for boats; Veneiden uusien energiajearjestelmien liiketoimintamahdollisuudet

    Energy Technology Data Exchange (ETDEWEB)

    Koskinen, O.; Hyyppae, P.; Enkvist, D.

    2010-07-01

    During the last years the principal theme for many international boat events has been new energy solutions and Green Boating. Within this topic there are several open questions, like how rapidly will the industry follow the trend of the car industry towards electrical and hybrid engine solutions. One of the key questions in the boat branch is how customers will embrace these new energy solutions and how strong the demand will be. This project, mainly financed by Tekes, has as an objective to study what business opportunities these new energy solutions can offer to boat manufactures and to other actors within the business. The research began on Helsinki Boatshow 2010 where 135 visitors answered the survey. After this 18 boat industry actors in Ostrobothnia region were interviewed about how they see the possibilities of new energy systems. Both boaters and boat industry considered that green values will boost the sales, albeit there were some surprising differences e.g. between age groups of consumers (the biggest gap between group under 30 years and the age group 30-45 years). The overall results of this study claim that Finnish boat industry is quite customer oriented and there was no big difference between the boat owners' thoughts and the thinking of boat branch representatives. Instead there was a clear difference between tho motor and sail boat sectors according to both boaters and companies within boat field. Sail boat owners and sail boat manufactures had a clearly more positive attitude toward propulsion by electricity and hybrid engines or the usage of solar panels than the motor boat owners or manufacturer had. Finnish boat owners consider that electrical engines suit well in small boats (under 4 meters), but this is offering very limited new business opportunities because it is hard to compete with the existing Asian manufacturing and the supply chain of these products is in Finland already comprehensive. According to this research Finnish boat

  12. Small Boat Displays: Towards Generality and Ease of Use

    Science.gov (United States)

    Bushell, Peter

    Electronic navigation systems are now well established on commercial vessels throughout the world. In a big ship it is entirely feasible (and probably necessary) to design the system to suit the ship. Budgets are large and there are few space constraints, so that many separate displays may be used on a bridge which would not look out of place on the USS Enterprise. This is definitely not so for a small sailing cruiser or powered leisure craft. Neither is it true for many fishing vessels. It is to those with an interest in these small boats that I address this paper.

  13. Compression fractures of the vertebrae during a "bumpy" boat ride.

    LENUS (Irish Health Repository)

    Chukwunyerenwa, C K

    2012-01-31

    INTRODUCTION: Compression fracture of the vertebrae is common, often the result of falls from height and motor vehicle accidents in the younger age groups. It can occur following minor trauma in the elderly and in those with osteoporosis. MATERIALS AND METHODS: We present an interesting case of compression fracture of the vertebral bodies occurring simultaneously in a couple during a boat ride while on holiday. One individual had fracture of the T8, while the other fractured the L1 vertebrae. Both injuries were treated conservatively with Taylor braces. CONCLUSION: We highlight one of the potential hazards of this recreational activity, and the almost identical fracture pattern in this couple.

  14. Boats in fields. Uwe Janson's Peer Gynt (2006

    Directory of Open Access Journals (Sweden)

    Tanya Thresher

    2015-02-01

    Full Text Available This article analyses Uwe Janson’s 2006 TV-film adaptation of Peer Gynt. This 81-minute-long film was shot on the island of Usedom in the Baltic Sea and makes extensive use of the landscape in its investigation of identity. The article examines the effects of limiting the geographical space of Peer’s journey of self-discovery and pays particular attention to the symbolic use of boats. It also explores how Janson mirrors the self-reflexivity of Ibsen’s work and maintains the romantic/anti-romantic dichotomy evident in the poetic text.

  15. Basic electronics

    CERN Document Server

    Holbrook, Harold D

    1971-01-01

    Basic Electronics is an elementary text designed for basic instruction in electricity and electronics. It gives emphasis on electronic emission and the vacuum tube and shows transistor circuits in parallel with electron tube circuits. This book also demonstrates how the transistor merely replaces the tube, with proper change of circuit constants as required. Many problems are presented at the end of each chapter. This book is comprised of 17 chapters and opens with an overview of electron theory, followed by a discussion on resistance, inductance, and capacitance, along with their effects on t

  16. Basic conceptions

    International Nuclear Information System (INIS)

    Khasanov, A.Kh.

    1988-01-01

    In this part of book author presents the basic conceptions of minerals studying. The course of minerals deposits is the most important branch of geology science and studying the geology, material constitution, formation conditions and regularity of distribution in earth crust different types of mineral raw materials

  17. Brain Basics

    Medline Plus

    Full Text Available ... mental illnesses. Search the NIMH Website: Home Health & Education Mental Health Information Statistics Consumer Health Publications Help for Mental Illnesses Clinical Trials Outreach Research Priorities Funding Labs at ... Health & Education > Educational Resources Brain Basics Introduction The Growing Brain ...

  18. Brain Basics

    Medline Plus

    Full Text Available ... Real Life Brain Basics in Real Life—How Depression affects the Brain Meet Sarah Sarah is a ... MSC 9663 Bethesda, MD 20892-9663 Follow Us Facebook Twitter YouTube Google Plus NIMH Newsletter NIMH RSS ...

  19. Brain Basics

    Medline Plus

    Full Text Available ... by which the cell sends information to receiving neurons. cell body —Contains the nucleus and cytoplasm of a ... circuit —A network of neurons and their interconnections. neuron —A nerve cell that is the basic, working unit of the ...

  20. Brain Basics

    Medline Plus

    Full Text Available ... Join A Study News & Events News & Events Home Science News Events Multimedia Social Media Press Resources Newsletters NIMH News Feeds About Us About Us Home About the Director Advisory Boards and ... Basics will introduce you to some of this science, such as: How the brain develops How genes ...

  1. Ethanol Basics

    Energy Technology Data Exchange (ETDEWEB)

    None

    2015-01-30

    Ethanol is a widely-used, domestically-produced renewable fuel made from corn and other plant materials. More than 96% of gasoline sold in the United States contains ethanol. Learn more about this alternative fuel in the Ethanol Basics Fact Sheet, produced by the U.S. Department of Energy's Clean Cities program.

  2. WAGO IPCs manage energy on unique solar-powered boat

    Energy Technology Data Exchange (ETDEWEB)

    Anon.

    2010-07-15

    This article described WAGO's contribution to the world's largest solar-powered boat, the Turanor PlanetSolar, a catamaran research vessel that was developed for solar power research. The boat has over 500 square metres of photovoltaic (PV) panels and 11 tons of batteries, including the 388 V lithium ion (NCA) battery. WAGO provided three 758 Series IPCs with control functionality and electrical components. The IPCs control charging for 3 batteries and 10 Drivetek Maximum Power Pick Trackers by way of 13 CAN buscouplers. The high-end DC/DC converters improve the solar absorption of the PV panels, which are fixed and mounted on the deck. For dependability in severe marine environments, WAGO's electrical components feature gas-tight connections that are vibration and thermal-cycling resistant. The Turanor accommodates a crew of four and has no gasoline back-ups for steering or propulsion. In 2011, the Turanor will embark on the first solar-powered circumnavigation of the globe by any means of transport. 1 fig.

  3. Persistence of TBT and copper in excess on leisure boat hulls around the Baltic Sea.

    Science.gov (United States)

    Eklund, Britta; Watermann, Burkard

    2018-03-12

    A handheld XRF-analyzer specially calibrated for measurements of metals on plastic boat hulls has been used on leisure boats in Denmark (DK), Finland (FI), and Germany (DE). The results on tin and copper are presented as μg metal/cm 2 . Tin is a proxy for the occurrence of organotin compounds on the boat. Two or three sites were visited in each country and between 25 and 90 boats were measured at each site. Every boat was measured at six to eight places, and the results are presented both as mean and median values. Linear regression of mean to median values of the 377 data pairs shows high relationship with R 2  = 0.9566 for tin and R 2 of 0.9724 for copper and thus both ways of calculation may be used. However, for regulative use, it is suggested that all individual measurements on each boat should be presented and used for decisions of removal or sealing of boat hulls. The results are compared with published data from different parts of Sweden, i.e., boats in fresh water, brackish water, and salt water. The results show that tin with mean values > 50 μg Sn/cm 2 is still found on 42, 24, and 23% of the boats in DK, FI, and DE, respectively. The corresponding percentages based on median values are 38, 22, and 18% for DK, FI, and DE, respectively. The variation among boats is high with a maximum mean value of 2000 μg Sn/cm 2 . As comparison, one layer of an old TBT antifouling paint Hempels Hard racing superior, corresponds to 300 μg Sn/cm 2 . The percentage of boats with tin > 400 μg Sn/cm 2 content based on mean values was 10% in DK, 5% in FI, and 1% in DE. The corresponding median values were 9, 6, and 1% for DK, FI, and DE. Copper, > 100 μg Cu/cm 2 , was detected on all measured boats in DK and in DE and on all but 3% of the FI boats. One layer of Hempels MilleXtra corresponds to ̴ 4000 μg Cu/cm 2 . The recommendation on the can is to apply two layers. The proportion of boats with higher mean copper values than 8000 μg Cu/cm 2

  4. Thermoplastic polymers surfaces for Dip-Pen Nanolithography of oligonucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Suriano, Raffaella [Dipartimento di Chimica, Materiali e Ingegneria Chimica “Giulio Natta”, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Biella, Serena, E-mail: serena.biella@polimi.it [Dipartimento di Chimica, Materiali e Ingegneria Chimica “Giulio Natta”, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Cesura, Federico; Levi, Marinella; Turri, Stefano [Dipartimento di Chimica, Materiali e Ingegneria Chimica “Giulio Natta”, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano (Italy)

    2013-05-15

    Different thermoplastic polymers were spin-coated to prepare smooth surfaces for the direct deposition of end-group modified oligonucleotides by Dip-Pen Nanolithography. A study of the diffusion process was done in order to investigate the dependence of calibration coefficient and quality of deposited features on environmental parameters (temperature, relative humidity) and ink's molecular weight and functionality. The optimization of the process parameters led to the realization of high quality and density nanoarrays on plastics.

  5. Oligonucleotide N3'-->P5' phosphoramidates as antisense agents.

    Science.gov (United States)

    Gryaznov, S; Skorski, T; Cucco, C; Nieborowska-Skorska, M; Chiu, C Y; Lloyd, D; Chen, J K; Koziolkiewicz, M; Calabretta, B

    1996-01-01

    Uniformly modified oligonucleotide N3'-->P5' phosphoramidates, where every 3'-oxygen is replaced by a 3'-amino group, were synthesized. These compounds have very high affinity to single-stranded RNAs and thus have potential utility as antisense agents. As was shown in this study, the oligonucleotide phosphoramidates are resistant to digestion with snake venom phosphodiesterase, to nuclease activity in a HeLa cell nuclear extract, or to nuclease activity in 50% human plasma, where no significant hydrolysis was observed after 8 h. These compounds were used in various in vitro cellular systems as antisense compounds addressed to different targeted regions of c-myb, c-myc and bcr-abl mRNAs. C-myb antisense phosphoramidates at 5 microM caused sequence and dose-dependent inhibition of HL-60 cell proliferation and a 75% reduction in c-myb protein and RNA levels, as determined by Western blot and RT-PCR analysis. Analogous results were observed for anti-c-myc phosphoramidates, where a complete cytostatic effect for HL-60 cells was observed at 1 microM concentration for fully complementary, but not for mismatched compounds, which were indistinguishable from untreated controls. This was correlated with a 93% reduction in c-myc protein level. Moreover, colony formation by the primary CML cells was also inhibited 75-95% and up to 99% by anti-c-myc and anti-bcr-abl phosphoramidate oligonucleotides, respectively, in a sequence- and dose-dependent manner within a 0.5 nM-5 microM dose range. At these concentrations the colony-forming ability of normal bone marrow cells was not affected. The presented in vitro data indicate that oligonucleotide N3'-->P5' phosphoramidates could be used as specific and efficient antisense agents. PMID:8628685

  6. ŕ-Hydroxyphosphonate oligonucleotides: A promising DNA type?

    Czech Academy of Sciences Publication Activity Database

    Králíková, Šárka; Buděšínský, Miloš; Rosenberg, Ivan

    2003-01-01

    Roč. 22, 5/8 (2003), s. 1061-1064 ISSN 1525-7770. [International Roundtable Nucleosides, Nucleotides and Nucleic Acids /15./. Leuven, 10.09.2002-14.09.2002] R&D Projects: GA ČR GA203/01/1166; GA AV ČR IAA4055101 Institutional research plan: CEZ:AV0Z4055905 Keywords : isopolar phosphonate oligonucleotides * nucleoside 5'-phosphonic acids * phosphotriester method Subject RIV: CC - Organic Chemistry Impact factor: 0.813, year: 2003

  7. Novel isosteric, isopolar phosphonate analogs of oligonucleotides: Preparation and properties

    Czech Academy of Sciences Publication Activity Database

    Točík, Zdeněk; Barvík Jr., I.; Buděšínský, Miloš; Rosenberg, Ivan

    2006-01-01

    Roč. 83, č. 4 (2006), s. 400-413 ISSN 0006-3525 R&D Projects: GA ČR(CZ) GA203/05/0827; GA ČR(CZ) GA202/05/0628; GA MŠk(CZ) LC512 Institutional research plan: CEZ:AV0Z40550506 Keywords : oligonucleotide * phosphonate * isosteric * hybridization Subject RIV: CC - Organic Chemistry Impact factor: 2.480, year: 2006

  8. Direct oligonucleotide synthesis onto super-paramagnetic beads

    Science.gov (United States)

    Jensen, Michael A; Akhras, Michael S.; Fukushima, Marilyn; Pourmand, Nader; Davis, Ron W.

    2013-01-01

    Super-paramagnetic beads (SPMB)s used for a variety of molecular diagnostic assays are prepared by attaching pre-synthesized oligonucleotides to the surface via a cumbersome and low efficient method of carbodiimide-mediated amide bond formation. To mainstream the process, we describe a novel procedure of direct oligonucleotide synthesis onto the surface of SPMBs (e.g. MyOne Dynabeads). With the many challenges surrounding containment of paramagnetic beads (≤ 1 μm) during automated oligonucleotide synthesis, we show that by applying a magnetic force directly to the SPMBs we prevent their loss caused by high-pressure drain steps during synthesis. To date we have synthesized 40mers using a Spacer 9 phosphoramidite (triethylene glycol) coupled to the surface of hydroxylated SPMBs. HPLC analysis shows successful product generation with an average yield of 200 pmoles per sample. Furthermore, because of the versatility of this powerful research tool, we envision its use in any laboratory working with conventional synthesis automation, as employed for single columns and for multi-well titer plates. In addition to direct synthesis of oligodeoxynucleotides (DNA) onto SPMBs, this platform also has the potential for RNA and peptide nucleic acid synthesis. PMID:23942380

  9. Computational modeling of oligonucleotide positional densities for human promoter prediction.

    Science.gov (United States)

    Narang, Vipin; Sung, Wing-Kin; Mittal, Ankush

    2005-01-01

    The gene promoter region controls transcriptional initiation of a gene, which is the most important step in gene regulation. In-silico detection of promoter region in genomic sequences has a number of applications in gene discovery and understanding gene expression regulation. However, computational prediction of eukaryotic poly-II promoters has remained a difficult task. This paper introduces a novel statistical technique for detecting promoter regions in long genomic sequences. A number of existing techniques analyze the occurrence frequencies of oligonucleotides in promoter sequences as compared to other genomic regions. In contrast, the present work studies the positional densities of oligonucleotides in promoter sequences. The analysis does not require any non-promoter sequence dataset or any model of the background oligonucleotide content of the genome. The statistical model learnt from a dataset of promoter sequences automatically recognizes a number of transcription factor binding sites simultaneously with their occurrence positions relative to the transcription start site. Based on this model, a continuous naïve Bayes classifier is developed for the detection of human promoters and transcription start sites in genomic sequences. The present study extends the scope of statistical models in general promoter modeling and prediction. Promoter sequence features learnt by the model correlate well with known biological facts. Results of human transcription start site prediction compare favorably with existing 2nd generation promoter prediction tools.

  10. G-Quadruplex Forming Oligonucleotides as Anti-HIV Agents.

    Science.gov (United States)

    Musumeci, Domenica; Riccardi, Claudia; Montesarchio, Daniela

    2015-09-22

    Though a variety of different non-canonical nucleic acids conformations have been recognized, G-quadruplex structures are probably the structural motifs most commonly found within known oligonucleotide-based aptamers. This could be ascribed to several factors, as their large conformational diversity, marked responsiveness of their folding/unfolding processes to external stimuli, high structural compactness and chemo-enzymatic and thermodynamic stability. A number of G-quadruplex-forming oligonucleotides having relevant in vitro anti-HIV activity have been discovered in the last two decades through either SELEX or rational design approaches. Improved aptamers have been obtained by chemical modifications of natural oligonucleotides, as terminal conjugations with large hydrophobic groups, replacement of phosphodiester linkages with phosphorothioate bonds or other surrogates, insertion of base-modified monomers, etc. In turn, detailed structural studies have elucidated the peculiar architectures adopted by many G-quadruplex-based aptamers and provided insight into their mechanism of action. An overview of the state-of-the-art knowledge of the relevance of putative G-quadruplex forming sequences within the viral genome and of the most studied G-quadruplex-forming aptamers, selectively targeting HIV proteins, is here presented.

  11. 33 CFR 100.740 - Annual Offshore Super Series Boat Race; Fort Myers Beach, FL.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Annual Offshore Super Series Boat Race; Fort Myers Beach, FL. 100.740 Section 100.740 Navigation and Navigable Waters COAST GUARD... Annual Offshore Super Series Boat Race; Fort Myers Beach, FL. (a) Regulated area. (1) The regulated area...

  12. 33 CFR 100.909 - Chinatown Chamber of Commerce Dragon Boat Race; Chicago, IL.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Chinatown Chamber of Commerce Dragon Boat Race; Chicago, IL. 100.909 Section 100.909 Navigation and Navigable Waters COAST GUARD... Chinatown Chamber of Commerce Dragon Boat Race; Chicago, IL. (a) Regulated Area. All waters of the South...

  13. 78 FR 59819 - Special Local Regulation; Clearwater Super Boat National Championship Race, Gulf of Mexico...

    Science.gov (United States)

    2013-09-30

    ... Championship Race, Gulf of Mexico; Clearwater, FL AGENCY: Coast Guard, DHS. ACTION: Temporary final rule... the vicinity of Clearwater, Florida during the Clearwater Super Boat National Championship Race. The race is scheduled to take place from 9:30 a.m. to 4 p.m. on September 29, 2013. Approximately 35 boats...

  14. 78 FR 35593 - Special Local Regulation; Christmas Boat Parade, San Juan Harbor; San Juan, PR

    Science.gov (United States)

    2013-06-13

    ... DEPARTMENT OF HOMELAND SECURITY Coast Guard 33 CFR Part 100 [Docket Number USCG-2013-0295] RIN 1625-AA08 Special Local Regulation; Christmas Boat Parade, San Juan Harbor; San Juan, PR AGENCY: Coast... Regulation; Christmas Boat Parade, San Juan Harbor; San Juan, PR (a) Regulated Area. The following regulated...

  15. 46 CFR 199.220 - Survival craft and rescue boat embarkation arrangements.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 7 2010-10-01 2010-10-01 false Survival craft and rescue boat embarkation arrangements. 199.220 Section 199.220 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) LIFESAVING... Passenger Vessels § 199.220 Survival craft and rescue boat embarkation arrangements. (a) Survival craft...

  16. 46 CFR 111.75-16 - Lighting of survival craft and rescue boats.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 4 2010-10-01 2010-10-01 false Lighting of survival craft and rescue boats. 111.75-16... craft and rescue boats. (a) During preparation, launching, and recovery, each survival craft and rescue... of circuits must be such that the lighting for adjacent launching stations for survival craft or...

  17. 75 FR 49869 - Changes to Standard Numbering System, Vessel Identification System, and Boating Accident Report...

    Science.gov (United States)

    2010-08-16

    ... SECURITY Coast Guard 33 CFR Parts 173, 174, 181, and 187 RIN 1625-AB45 Changes to Standard Numbering System, Vessel Identification System, and Boating Accident Report Database AGENCY: Coast Guard, DHS. ACTION..., Vessel Identification System, and Boating Accident Report Database. DATES: Comments and related material...

  18. 78 FR 6732 - Changes to Standard Numbering System, Vessel Identification System, and Boating Accident Report...

    Science.gov (United States)

    2013-01-31

    ... SECURITY Coast Guard 33 CFR Parts 173, 174, 181, and 187 RIN 1625-AB45 Changes to Standard Numbering System, Vessel Identification System, and Boating Accident Report Database AGENCY: Coast Guard, DHS. ACTION: Rule... Numbering System, Vessel Identification System, and Boating Accident Report Database rule became effective...

  19. Dynamics of a camphoric acid boat at the air-water interface

    Science.gov (United States)

    Akella, V. S.; Singh, Dhiraj K.; Mandre, Shreyas; Bandi, M. M.

    2018-05-01

    We report experiments on an agarose gel tablet loaded with camphoric acid (c-boat) spontaneously set into motion by surface tension gradients on the water surface. We observe three distinct modes of c-boat motion: harmonic mode where the c-boat speed oscillates sinusoidally in time, a steady mode where the c-boat maintains constant speed, and an intermittent mode where the c-boat maintains near-zero speed between sudden jumps in speed. Whereas all three modes have been separately reported before in different systems, controlled release of Camphoric Acid (CA) from the agarose gel matrix allowed the observation of all the three modes in the same system. These three modes are a result of a competition between the driving (surface tension gradients) and drag forces acting on the c-boat. Moreover we suggest that there exist two time scales corresponding to spreading of CA and boat motion and the mismatch of these two time scales give rise to the three modes in boat motion. We reproduced all the modes of motion by varying the air-water interfacial tension using Sodium Dodecyl Sulfate (SDS).

  20. Static magnetic field reduced exogenous oligonucleotide uptake by spermatozoa using magnetic nanoparticle gene delivery system

    Energy Technology Data Exchange (ETDEWEB)

    Katebi, Samira; Esmaeili, Abolghasem, E-mail: aesmaeili@sci.ui.ac.ir; Ghaedi, Kamran

    2016-03-15

    Spermatozoa could introduce exogenous oligonucleotides of interest to the oocyte. The most important reason of low efficiency of sperm mediated gene transfer (SMGT) is low uptake of exogenous DNA by spermatozoa. The aim of this study was to evaluate the effects of static magnetic field on exogenous oligonucleotide uptake of spermatozoa using magnetofection method. Magnetic nanoparticles (MNPs) associated with the labeled oligonucleotides were used to increase the efficiency of exogenous oligonucleotide uptake by rooster spermatozoa. We used high-field/high-gradient magnet (NdFeB) to enhance and accelerate exogenous DNA sedimentation at the spermatozoa surface. Flow cytometry analysis was performed to measure viability and percentage of exogenous oligonucleotide uptake by sperm. Flow cytometry analysis showed a significant increase in exogenous oligonucleotide uptake by rooster spermatozoa (P<0.001) when spermatozoa were incubated in exogenous oligonucleotide solution and MNPs. However, by applying static magnetic field during magnetofection method, a significant decrease in exogenous oligonucleotide uptake was observed (P<0.05). Findings of this study showed that MNPs were effective to increase exogenous oligonucleotide uptake by rooster spermatozoa; however unlike others studies, static magnetic field, was not only ineffective to enhance exogenous oligonucleotide uptake by rooster spermatozoa but also led to reduction in efficiency of magnetic nanoparticles in gene transfer. - Highlights: • Core/shell type Iron oxide nanoparticles were used as a novel and efficient method. • This method increases exogenous DNA uptake by rooster spermatozoa. • Static magnetic field decreased DNA uptake by rooster spermatozoa.

  1. Wavelet basics

    CERN Document Server

    Chan, Y T

    1995-01-01

    Since the study of wavelets is a relatively new area, much of the research coming from mathematicians, most of the literature uses terminology, concepts and proofs that may, at times, be difficult and intimidating for the engineer. Wavelet Basics has therefore been written as an introductory book for scientists and engineers. The mathematical presentation has been kept simple, the concepts being presented in elaborate detail in a terminology that engineers will find familiar. Difficult ideas are illustrated with examples which will also aid in the development of an intuitive insight. Chapter 1 reviews the basics of signal transformation and discusses the concepts of duals and frames. Chapter 2 introduces the wavelet transform, contrasts it with the short-time Fourier transform and clarifies the names of the different types of wavelet transforms. Chapter 3 links multiresolution analysis, orthonormal wavelets and the design of digital filters. Chapter 4 gives a tour d'horizon of topics of current interest: wave...

  2. "We're All in the Same Boat": A Review of the Benefits of Dragon Boat Racing for Women Living with Breast Cancer.

    Science.gov (United States)

    Harris, Susan R

    2012-01-01

    This narrative review summarizes findings from quantitative and qualitative research literature that has been published over the past 15 years since an initial, community-based pilot study first challenged the long-held medical belief that vigorous, upper-body exercise would lead to lymphedema in women who were at risk due to treatments for breast cancer. Dragon boat racing originated in China more than 2000 years ago and has become a popular recreational and competitive support around the world. From the advent of the world's first breast cancer survivor dragon boat team, Abreast in a Boat launched in Vancouver, British Columbia, in 1996, there are now more than 140 breast cancer survivor dragon boat teams paddling and competing in 12 different countries. The wealth of quantitative and qualitative research that has ensued since that pilot study further supports the initial hypothesis that resistance exercise, for example, dragon boat paddling, is not only safe for women recovering from conventional breast cancer therapies but also shows that dragon boating has been embraced as a complementary exercise therapy by the cancer survivors participating in this magical sport.

  3. Analysis of calibrated sea clutter and boat reflectivity data at C- and X-band in South African coastal waters

    CSIR Research Space (South Africa)

    Herselman, PLR

    2007-10-01

    Full Text Available The temporal characteristics of low grazing angle sea clutter and boat reflectivity are considered for both fixed and stepped frequency waveforms under a range of environmental conditions and geometrical configurations. Detectability of boats using...

  4. Analysis decorating design on Perahu Buatan Barat, the Malay traditional boat by using frieze pattern

    Science.gov (United States)

    Wahab, Mohd Rohaizat Abdul; Ramli, Zuliskandar; Zakaria, Ros Mahwati Ahmad; Samad, Mohammad Anis Abdul

    2017-01-01

    Boat building tradition is one of the skills mastered by Malay craftsmen. Decoration on the Perahu Buatan Barat, the Malay traditional boat is one of the uniqueness of the production of traditional boats in East Coast of Malaysia. The tradition of Malay boat building, each plank was given specific names based on the line of planks. There is one line called `papan tarik' or `papan cantik' was usually decorated with paintings by a variety of motifs and patterns from the bow to the stern of the boat. The motifs usually taken from the surrounding environment as well as flora and fauna will be painted with motifs repeated but with differing formations. The aim of this study is to identify the motifs and analyze the formation of motifs by using mathematical methods of frieze pattern.

  5. Sediment Contaminants and Infauna Associated with Recreational Boating Structures in a Multi-Use Marine Park

    Science.gov (United States)

    Sim, Vivian X. Y.; Dafforn, Katherine A.; Simpson, Stuart L.; Kelaher, Brendan P.; Johnston, Emma L.

    2015-01-01

    Multi-use marine parks achieve conservation through spatial management of activities. Zoning of marine parks in New South Wales, Australia, includes high conservation areas and special purpose zones (SPZ) where maritime activities are concentrated. Although such measures geographically constrain anthropogenic impacts, we have limited understanding of potential ecological effects. We assessed sediment communities and contaminants adjacent to boating infrastructure (boat ramps, jetties and a marina) in a SPZ from the Clyde Estuary in Batemans Marine Park. Metal concentrations and fines content were elevated at boating structures compared to reference sites. Species richness was higher at sites with boating structures, where capitellid polychaetes and nematodes dominated the communities. Changes associated with boating structures were localised and did not extend beyond breakwalls or to reference sites outside the SPZ. The study highlights the benefits of appropriate zoning in a multi-use marine park and the potential to minimise stress on pristine areas through the application of spatial management. PMID:26086427

  6. Quagga and zebra mussel risk via veliger transfer by overland hauled boats

    Directory of Open Access Journals (Sweden)

    Larry B. Dalton

    2013-04-01

    Full Text Available Invasive quagga and zebra mussels (Dreissena rostriformis bugensis and Dreissena polymorpha, respectively pose a great threat to USwaters. Recreational boats constitute a significant risk for spreading the organisms. Recreational boats circulate large amounts of raw waterwhen in use, and if not drained and dried correctly can transport many mussel larvae, called veligers. Veligers experience very high mortality rates; however, the number of potentially transported veligers can be a serious risk to non-infested bodies of water, especially if multiple boats are involved. The risk of veliger transport was calculated for Lake Mead and Lake Michigan using boat capacities for water circulation and specific veliger density data. Results illustrate the importance of draining, drying, and/or decontaminating recreational boats after use.

  7. A new oligonucleotide microarray for detection of pathogenic and non-pathogenic Legionella spp.

    Directory of Open Access Journals (Sweden)

    Boyang Cao

    Full Text Available Legionella pneumophila has been recognized as the major cause of legionellosis since the discovery of the deadly disease. Legionella spp. other than L. pneumophila were later found to be responsible to many non-pneumophila infections. The non-L. pneumophila infections are likely under-detected because of a lack of effective diagnosis. In this report, we have sequenced the 16S-23S rRNA gene internal transcribed spacer (ITS of 10 Legionella species and subspecies, including L. anisa, L. bozemanii, L. dumoffii, L. fairfieldensis, L. gormanii, L. jordanis, L. maceachernii, L. micdadei, L. pneumophila subspp. fraseri and L. pneumophila subspp. pasculleii, and developed a rapid oligonucleotide microarray detection technique accordingly to identify 12 most common Legionella spp., which consist of 11 pathogenic species of L. anisa, L. bozemanii, L. dumoffii, L. gormanii, L. jordanis, L. longbeachae, L. maceachernii, L. micdadei, and L. pneumophila (including subspp. pneumophila, subspp. fraseri, and subspp. pasculleii and one non-pathogenic species, L. fairfieldensis. Twenty-nine probes that reproducibly detected multiple Legionella species with high specificity were included in the array. A total of 52 strains, including 30 target pathogens and 22 non-target bacteria, were used to verify the oligonucleotide microarray assay. The sensitivity of the detection was at 1.0 ng with genomic DNA or 13 CFU/100 mL with Legionella cultures. The microarray detected seven samples of air conditioner-condensed water with 100% accuracy, validating the technique as a promising method for applications in basic microbiology, clinical diagnosis, food safety, and epidemiological surveillance. The phylogenetic study based on the ITS has also revealed that the non-pathogenic L. fairfieldensis is the closest to L. pneumophila than the nine other pathogenic Legionella spp.

  8. 40 CFR 63.5743 - What standards must I meet for aluminum recreational boat surface coating operations?

    Science.gov (United States)

    2010-07-01

    ... recreational boat surface coating operations? 63.5743 Section 63.5743 Protection of Environment ENVIRONMENTAL... Manufacturing Standards for Aluminum Recreational Boat Surface Coating Operations § 63.5743 What standards must I meet for aluminum recreational boat surface coating operations? (a) For aluminum wipedown solvent...

  9. 78 FR 42733 - Safety Zone; Cleveland Dragon Boat Festival and Head of the Cuyahoga, Cuyahoga River, Cleveland, OH

    Science.gov (United States)

    2013-07-17

    ...-AA00 Safety Zone; Cleveland Dragon Boat Festival and Head of the Cuyahoga, Cuyahoga River, Cleveland... intended to restrict vessels from a portion of the Cuyahoga River during the Dragon Boat Festival and Head... over a decade and the Dragon Boat Festival for the last 7 years. In response to past years' events, the...

  10. Breast cancer survivors' decisions to join a dragon boating team.

    Science.gov (United States)

    Weisenbach, Beth B; McDonough, Meghan H

    2014-12-01

    Physical activity is associated with psychosocial and physical health benefits for breast cancer survivors. Little is known, however, about survivors' decision-making processes when considering joining group physical activity programs designed for survivors. Guided by interpretive description methodology (Thorne, 2008), N = 15 breast cancer survivors who were considering or had made the decision to join a dragon boating team were interviewed about their decisions to participate. Four patterns of decision making were identified: searching for a way to care for physical and social needs, taking advantage of opportunities created by breast cancer, dove in with little contemplation, and hesitant to connect with other survivors. Results have implications for understanding decisions to participate in physical activity groups in this population and overcoming challenges to participation.

  11. Basic electronics

    CERN Document Server

    Tayal, DC

    2010-01-01

    The second edition of this book incorporates the comments and suggestions of my friends and students who have critically studied the first edition. In this edition the changes and additions have been made and subject matter has been rearranged at some places. The purpose of this text is to provide a comprehensive and up-to-date study of the principles of operation of solid state devices, their basic circuits and application of these circuits to various electronic systems, so that it can serve as a standard text not only for universities and colleges but also for technical institutes. This book

  12. Basic principles

    International Nuclear Information System (INIS)

    Wilson, P.D.

    1996-01-01

    Some basic explanations are given of the principles underlying the nuclear fuel cycle, starting with the physics of atomic and nuclear structure and continuing with nuclear energy and reactors, fuel and waste management and finally a discussion of economics and the future. An important aspect of the fuel cycle concerns the possibility of ''closing the back end'' i.e. reprocessing the waste or unused fuel in order to re-use it in reactors of various kinds. The alternative, the ''oncethrough'' cycle, discards the discharged fuel completely. An interim measure involves the prolonged storage of highly radioactive waste fuel. (UK)

  13. In vivo recombineering of bacteriophage λ by PCR fragments and single-strand oligonucleotides

    International Nuclear Information System (INIS)

    Oppenheim, Amos B.; Rattray, Alison J.; Bubunenko, Mikhail; Thomason, Lynn C.; Court, Donald L.

    2004-01-01

    We demonstrate that the bacteriophage λ Red functions efficiently recombine linear DNA or single-strand oligonucleotides (ss-oligos) into bacteriophage λ to create specific changes in the viral genome. Point mutations, deletions, and gene replacements have been created. While recombineering with oligonucleotides, we encountered other mutations accompanying the desired point mutational change. DNA sequence analysis suggests that these unwanted mutations are mainly frameshift deletions introduced during oligonucleotide synthesis

  14. Terahertz response of DNA oligonucleotides on the surface of silicon nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Bagraev, N. T., E-mail: bagraev@mail.ioffe.ru [Peter the Great Saint-Petersburg Polytechnic University (Russian Federation); Chernev, A. L. [Russian Academy of Sciences, Saint Petersburg Academic University—Nanotechnology Research and Education Center (Russian Federation); Klyachkin, L. E.; Malyarenko, A. M. [Russian Academy of Sciences, Ioffe Physical–Technical Institute (Russian Federation); Emel’yanov, A. K.; Dubina, M. V. [Russian Academy of Sciences, Saint Petersburg Academic University—Nanotechnology Research and Education Center (Russian Federation)

    2016-09-15

    The possibility of identifying DNA oligonucleotides deposited onto the region of the edge channels of silicon nanostructures is considered. The role of various THz (terahertz) radiation harmonics of silicon nanostructures in the resonance response of oligonucleotides is analyzed. In particular, this makes it possible to compare single-stranded 100- and 50-mer DNA oligonucleotides. A technique for the rapid identification of different oligonucleotides by measuring changes in the conductance and transverse potential difference of silicon nanostructures with microcavities, embedded in the edge channels for selecting THz radiation characteristics, is proposed.

  15. Static magnetic field reduced exogenous oligonucleotide uptake by spermatozoa using magnetic nanoparticle gene delivery system

    Science.gov (United States)

    Katebi, Samira; Esmaeili, Abolghasem; Ghaedi, Kamran

    2016-03-01

    Spermatozoa could introduce exogenous oligonucleotides of interest to the oocyte. The most important reason of low efficiency of sperm mediated gene transfer (SMGT) is low uptake of exogenous DNA by spermatozoa. The aim of this study was to evaluate the effects of static magnetic field on exogenous oligonucleotide uptake of spermatozoa using magnetofection method. Magnetic nanoparticles (MNPs) associated with the labeled oligonucleotides were used to increase the efficiency of exogenous oligonucleotide uptake by rooster spermatozoa. We used high-field/high-gradient magnet (NdFeB) to enhance and accelerate exogenous DNA sedimentation at the spermatozoa surface. Flow cytometry analysis was performed to measure viability and percentage of exogenous oligonucleotide uptake by sperm. Flow cytometry analysis showed a significant increase in exogenous oligonucleotide uptake by rooster spermatozoa (Pspermatozoa were incubated in exogenous oligonucleotide solution and MNPs. However, by applying static magnetic field during magnetofection method, a significant decrease in exogenous oligonucleotide uptake was observed (Pspermatozoa; however unlike others studies, static magnetic field, was not only ineffective to enhance exogenous oligonucleotide uptake by rooster spermatozoa but also led to reduction in efficiency of magnetic nanoparticles in gene transfer.

  16. New oligonucleotide microarray for rapid diagnosis of avian viral diseases.

    Science.gov (United States)

    Sultankulova, Kulyaisan T; Kozhabergenov, Nurlan S; Strochkov, Vitaliy M; Burashev, Yerbol D; Shorayeva, Kamshat A; Chervyakova, Olga V; Rametov, Nurkuisa M; Sandybayev, Nurlan T; Sansyzbay, Abylay R; Orynbayev, Mukhit B

    2017-04-05

    We developed a new oligonucleotide microarray comprising 16 identical subarrays for simultaneous rapid detection of avian viruses: avian influenza virus (AIV), Newcastle disease virus (NDV), infection bronchitis virus (IBV), and infectious bursal disease virus (IBDV) in single- and mixed-virus infections. The objective of the study was to develop an oligonucleotide microarray for rapid diagnosis of avian diseases that would be used in the course of mass analysis for routine epidemiological surveillance owing to its ability to test one specimen for several infections. The paper describes the technique for rapid and simultaneous diagnosis of avian diseases such as avian influenza, Newcastle disease, infectious bronchitis and infectious bursal disease with use of oligonucleotide microarray, conditions for hybridization of fluorescent-labelled viral cDNA on the microarray and its specificity tested with use of AIV, NDV, IBV, IBDV strains as well as biomaterials from poultry. Sensitivity and specificity of the developed microarray was evaluated with use of 122 specimens of biological material: 44 cloacal swabs from sick birds and 78 tissue specimens from dead wild and domestic birds, as well as with use of 15 AIV, NDV, IBV and IBDV strains, different in their origin, epidemiological and biological characteristics (RIBSP Microbial Collection). This microarray demonstrates high diagnostic sensitivity (99.16% within 95% CI limits 97.36-100%) and specificity (100%). Specificity of the developed technique was confirmed by direct sequencing of NP and M (AIV), VP2 (IBDV), S1 (IBV), NP (NDV) gene fragments. Diagnostic effectiveness of the developed DNA microarray is 99.18% and therefore it can be used in mass survey for specific detection of AIV, NDV, IBV and IBDV circulating in the region in the course of epidemiological surveillance. Rather simple method for rapid diagnosis of avian viral diseases that several times shortens duration of assay versus classical diagnostic

  17. Effect of normalization on significance testing for oligonucleotide microarrays.

    Science.gov (United States)

    Parrish, Rudolph S; Spencer, Horace J

    2004-08-01

    Normalization techniques are used to reduce variation among gene expression measurements in oligonucleotide microarrays in an effort to improve the quality of the data and the power of significance tests for detecting differential expression. Of several such proposed methods, two that have commonly been employed include median-interquartile range normalization and quantile normalization. The median-IQR method applied directly to fold-changes for paired data also was considered. Two methods for calculating gene expression values include the MAS 5.0 algorithm [Affymetrix. (2002). Statistical Algorithms Description Document. Santa Clara, CA: Affymetrix, Inc. http://www.affymetrix.com/support/technical/whitepapers/sadd-whitepaper.pdf] and the RMA method [Irizarry, R. A., Bolstad, B. M., Collin, F., Cope, L. M., Hobbs, B., Speed, T. P. (2003a). Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31(4,e15); Irizarry, R. A., Hobbs, B., Collin, F., Beazer-Barclay, Y. D., Antonellis, K. J., Scherf, U., Speed, T. P. (2003b). Exploration, normalization, and summaries of high density oligonucleotide array probe-level data. Biostatistics 4(2):249-264; Irizarry, R. A., Gautier, L., Cope, L. (2003c). An R package for analysis of Affymetrix oligonucleotide arrays. In: Parmigiani, R. I. G., Garrett, E. S., Ziegler, S., eds. The Analysis of Gene Expression Data: Methods and Software. Berlin: Springer, pp. 102-119]. In considering these methods applied to a prostate cancer data set derived from paired samples on normal and tumor tissue, it is shown that normalization methods may lead to substantial inflation of the number of genes identified by paired-t significance tests even after adjustment for multiple testing. This is shown to be due primarily to an unintended effect that normalization has on the experimental error variance. The impact appears to be greater in the RMA method compared to the MAS 5.0 algorithm and for quantile normalization compared to median

  18. Technical Suitability and Static Stability of Sungkur Fishing Boats for Fish and Shrimp Catching

    Science.gov (United States)

    Rusmilyansari; Rosadi, E.; Iriansyah

    2017-10-01

    Sungkur fishing gear is operated actively on one the side of fishing boat, which requires technical suitability and fishing gear stability to ensure success in fish catching. This is a case study which aimed to analyze some technical issues related to the boat, boat’s hydrostatic parameters, and the boat’s stability. The data were collected though observation, measuring the boat to obtain the offset table. The data were analyzed numerically and descriptively. The data were processed with technical formula, Microsoft Office’s Excel software, graphic display, minitab, statistical data processing, and maxsurf program. The research results showed that: (1) the sungkur fishing boat dimensional ratio L/B (6.47 - 7.00); L/D (10.90 - 11.20) and B/D (1.60 - 1.668) is within the range value of Indonesian fishing boats suitable to operate the fishing gear by towing or dragging. However, during fish catching operation, there have been problems in a hydrodynamic force due to the fishing gear movement, which affect the fish catching efficiency. (2) The boat’s coefficient of fineness is in the fine type shape; the displacement on each waterline has increased; the loads of the boat are getting larger following the increase of waterline from one to five; this is also shown from the increasing midship area value. Ton per centimeter immersion to change wl 1 by 1 cm needs 0.04 tons of weight. (3) Sungkur fishing boat have a good static stability, which is proven by the positive value of angle of maximum GZ by 79.1 - 83.6. In other words, the boat has the ability to return to its original position after tilting; however, stability dynamics happens because fishing gear operation are located on just one side of boat.

  19. PCR amplification on microarrays of gel immobilized oligonucleotides

    Science.gov (United States)

    Strizhkov, Boris; Tillib, Sergei; Mikhailovich, Vladimir; Mirzabekov, Andrei

    2003-11-04

    The invention relates two general methods for performing PCR amplification, combined with the detection and analysis of the PCR products on a microchip. In the first method, the amplification occurs both outside and within a plurality of gel pads on a microchip, with at least one oligonucleotide primer immobilized in a gel pad. In the second method, PCR amplification also takes place within gel pads on a microchip, but the pads are surrounded by a hydrophobic liquid such as that which separates the individual gel pads into environments which resemble micro-miniaturized test tubes.

  20. Chemically modified oligonucleotides with efficient RNase H response

    DEFF Research Database (Denmark)

    Vester, Birte; Boel, Anne Marie; Lobedanz, Sune

    2008-01-01

    Ten different chemically modified nucleosides were incorporated into short DNA strands (chimeric oligonucleotides ON3-ON12 and ON15-ON24) and then tested for their capacity to mediate RNAse H cleavage of the complementary RNA strand. The modifications were placed at two central positions directly...... in the RNase H cleaving region. The RNA strand of duplexes with ON3, ON5 and ON12 were cleaved more efficiently than the RNA strand of the DNA:RNA control duplex. There seems to be no correlation between the thermal stability between the duplexes and RNase H cleavage....

  1. The use of oligonucleotide probes for meningococcal serotype characterization

    Directory of Open Access Journals (Sweden)

    SACCHI Claudio Tavares

    1998-01-01

    Full Text Available In the present study we examine the potential use of oligonucleotide probes to characterize Neisseria meningitidis serotypes without the use of monoclonal antibodies (MAbs. Antigenic diversity on PorB protein forms the bases of serotyping method. However, the current panel of MAbs underestimated, by at least 50% the PorB variability, presumably because reagents for several PorB variable regions (VRs are lacking, or because a number of VR variants are not recognized by serotype-defining MAbs12. We analyzed the use of oligonucleotide probes to characterize serotype 10 and serotype 19 of N. meningitidis. The porB gene sequence for the prototype strain of serotype 10 was determined, aligned with 7 other porB sequences from different serotypes, and analysis of individual VRs were performed. The results of DNA probes 21U (VR1-A and 615U (VR3-B used against 72 N. meningitidis strains confirm that VR1 type A and VR3 type B encode epitopes for serotype-defined MAbs 19 and 10, respectively. The use of probes for characterizing serotypes possible can type 100% of the PorB VR diversity. It is a simple and rapid method specially useful for analysis of large number of samples.

  2. Fluorescence Quenching of Carboxyfluoresceins Conjugated Convalently to Oligonucleotides

    Science.gov (United States)

    Povedailo, V. A.; Stupak, A. P.; Tsybulsky, D. A.; Shmanai, V. V.; Yakovlev, D. L.

    2017-07-01

    Dynamic and static quenching of 6-(2',7'-dimethoxy-4',5'-dichloro)carboxyfluorescein (JOE) by nucleosides (deoxyadenosine, deoxycytidine, deoxyguanosine, thymidine, and deoxyuridine) in Tris-acetate buffer solution was analyzed using the Stern-Volmer equation. Only one of the five nucleosides, deoxyguanosine, exhibited predominantly static quenching. The fluorescence quantum yields in buffer solution of 5- and 6-carboxyfluorescein (FAM) and 5-and 6-JOE bound covalently to the oligonucleotide by a rigid linker (4-trans-aminocyclohexanol) were greater than those of their analogs with a flexible linker (6-aminohexanol). It was shown that fluorescence quenching in systems with a flexible linker occurred mainly through van-der-Waals contact of the fluorophore with guanine. An increase in the number of consecutively located guanines in the oligonucleotides and their duplexes bound to the dye by a linker decreased the fluorescence quantum yield. Quantum-chemical calculations using the Gaussian 09 program provided an interpretation for the low-frequency shifts of 5-FAM and 5-JOE absorption and fluorescence spectra relative to those of the 6-isomers.

  3. Topical delivery of anti-sense oligonucleotides using low-frequency sonophoresis.

    Science.gov (United States)

    Tezel, Ahmet; Dokka, Sujatha; Kelly, Susan; Hardee, Gregory E; Mitragotri, Samir

    2004-12-01

    Topical delivery of oligonucleotides, though attractive for the treatment of skin disorders, is limited by the low permeability of the stratum corneum. Herein, we assessed the potential of low-frequency ultrasound (20 kHz, 2.4 W/cm2) in delivering therapeutically significant quantities of anti-sense oligonucleotides into skin. Dermal penetration of oligonucleotides penetration was quantified in vitro using radiolabeled oligonucleotides. Estimated concentrations of oligonucleotides (ODNs) in the superficial layers of the skin ranged from approximately 0.5% to 5% of the donor concentration after a 10-min application of ultrasound and ODN. Microscopic evaluations using fluorescently labeled oligonucleotides and sulforhodamine B revealed heterogeneous penetration into the skin. Heterogenous penetration led to the formation of localized transport pathways (LTPs), which occupied about 5% of the total exposed skin area. Immuno-histochemical studies using an oligonucleotide that reacts specifically with an antibody also confirmed penetration of ODNs into LTPs. Histologic studies revealed that no gross structural changes were induced in the skin due to ultrasound application. These results show successful delivery of anti-sense oligonucleotides using low-frequency ultrasound.

  4. Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays

    DEFF Research Database (Denmark)

    Nielsen, Henrik Bjørn; Wernersson, Rasmus; Knudsen, Steen

    2003-01-01

    Optimal design of oligonucleotides for microarrays involves tedious and laborious work evaluating potential oligonucleotides relative to a series of parameters. The currently available tools for this purpose are limited in their flexibility and do not present the oligonucleotide designer with an ......Optimal design of oligonucleotides for microarrays involves tedious and laborious work evaluating potential oligonucleotides relative to a series of parameters. The currently available tools for this purpose are limited in their flexibility and do not present the oligonucleotide designer...... with an overview of these parameters. We present here a flexible tool named OligoWiz for designing oligonucleotides for multiple purposes. OligoWiz presents a set of parameter scores in a graphical interface to facilitate an overview for the user. Additional custom parameter scores can easily be added...... to the program to extend the default parameters: homology, DeltaTm, low-complexity, position and GATC-only. Furthermore we present an analysis of the limitations in designing oligonucleotide sets that can detect transcripts from multiple organisms. OligoWiz is available at www.cbs.dtu.dk/services/OligoWiz/....

  5. Long-range order of organized oligonucleotide monolayers on Au(111) electrodes

    DEFF Research Database (Denmark)

    Wackerbarth, Hainer; Grubb, Mikala; Zhang, Jingdong

    2004-01-01

    , substantiating that domain formation rests on adsorption of thiol-modified oligonucleotide adsorption in an upright or tilted orientation. The comprehensive, high-resolution information reported may hold prospects for single-molecule electronic conduction and molecular-scale mapping of oligonucleotide...

  6. CNMI, American Samoa, and Guam Small Boat Fishery Trip Expenditure (2009 to present)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This is a time-series dataset of trip expenditure data including actual fishing trip expenses, input usage, and input prices, for boat-based reef fish, bottomfish,...

  7. Analysis and Mitigation of Mechanical Shock Effects on High Speed Planing Boats

    National Research Council Canada - National Science Library

    Keams, Sean

    2001-01-01

    .... Operation of these boats, particularly in rough seas, exposes the occupants to severe mechanical shock exposure that has been linked to significant increase in the rates of acute and chronic injury...

  8. Release of PAHs and heavy metals in coastal environments linked to leisure boats.

    Science.gov (United States)

    Egardt, Jenny; Mørk Larsen, Martin; Lassen, Pia; Dahllöf, Ingela

    2018-02-01

    Leisure boats are responsible for elevated levels of heavy metals and PAHs in sediments in- and near marinas and natural harbours. As these compounds are released directly into the water column they also pose a threat to organisms in the pelagic environment. Passive samplers were deployed during peak and post tourist season in the water column of natural harbours, leisure boat waterways and small marinas to measure the dissolved fraction of PAHs and metal ions. Differences between seasons indicative of leisure boat activities were found as PAH composition differed between peak and post season for natural harbours and waterways, where heavier PAHs increased during peak season. During peak season, metal samplers were covered by biofouling, which likely affected the uptake. Post season metal concentrations differ between locations, with concentrations exceeding quality standards at near mainland locations where boats are maintained, compared to the sites in the archipelago. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Chasing U-Boats and Hunting Insurgents: Lessons from an Underhand Way of War

    National Research Council Canada - National Science Library

    Breemer, Jan S

    2006-01-01

    .... Winston Churchill, then the Royal Navy's political head, was not willing to go quite that far, yet at one point during World War I, he ordered that captured U-boat crews be treated as criminals, not prisoners of war...

  10. American Samoa Small Boat and Spear Cost-Earnings Data: 2015

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data represent a cost-earnings study of the American Samoa small boat and spear fishery in 2015. Data collected include fisher classification, vessel...

  11. A simple method to prepare miniature quartz fiber boats with superhydrophobicity

    Science.gov (United States)

    Jiang, Z. X.; Cheng, X. Q.; Li, J.; Qiu, W. J.; Guan, S. A.; Dong, W.; Ma, Z. Y.; Huang, Y. D.

    2012-01-01

    According to the reformed Cassie-Baxter equation, a superhydrophobic quartz fiber bundle boat was fabricated from mimicking the lotus leaf venation using chemical surface modifications and roughness introductions. Water contact angles as high as 165.8° were achieved for quartz fiber cloths. The loading capacities of the miniature boats made from the superhydrophobic quartz fiber bundles were measured. The highest loading weight, 10.19 g, was obtained by the boats with 2.0 mm spacing distance between fiber bundles. The striking loading capacities were believed to stem from the air film surrounding the superhydrophobic surfaces of the boats. The results of this study presented new applications of artificial hydrophobic surfaces in areas of aquatic devices.

  12. Oligonucleotide-Based Therapy for FTD/ALS Caused by the C9orf72 Repeat Expansion: A Perspective

    Directory of Open Access Journals (Sweden)

    Stephanie A. Fernandes

    2013-01-01

    Full Text Available Amyotrophic lateral sclerosis (ALS is a progressive and lethal disease of motor neuron degeneration, leading to paralysis of voluntary muscles and death by respiratory failure within five years of onset. Frontotemporal dementia (FTD is characterised by degeneration of frontal and temporal lobes, leading to changes in personality, behaviour, and language, culminating in death within 5–10 years. Both of these diseases form a clinical, pathological, and genetic continuum of diseases, and this link has become clearer recently with the discovery of a hexanucleotide repeat expansion in the C9orf72 gene that causes the FTD/ALS spectrum, that is, c9FTD/ALS. Two basic mechanisms have been proposed as being potentially responsible for c9FTD/ALS: loss-of-function of the protein encoded by this gene (associated with aberrant DNA methylation and gain of function through the formation of RNA foci or protein aggregates. These diseases currently lack any cure or effective treatment. Antisense oligonucleotides (ASOs are modified nucleic acids that are able to silence targeted mRNAs or perform splice modulation, and the fact that they have proved efficient in repeat expansion diseases including myotonic dystrophy type 1 makes them ideal candidates for c9FTD/ALS therapy. Here, we discuss potential mechanisms and challenges for developing oligonucleotide-based therapy for c9FTD/ALS.

  13. Nucleobase-modified antisense oligonucleotides containing 5-(phenyltriazol)-2′-deoxyuridine nucleotides induce exon-skipping

    DEFF Research Database (Denmark)

    Le, Bao T.; Hornum, Mick; Sharma, Pawan K.

    2017-01-01

    Chemically-modified antisense oligonucleotide-mediated exon-skipping has been validated as a therapeutic strategy for tackling several disease pathologies, particularly duchenne muscular dystrophy. To date, only sugar-modified and internucleotide linkage-modified oligonucleotide chemistries have...

  14. Regulating antifouling paints for leisure boats - a patchwork of rules across three Baltic Sea countries

    DEFF Research Database (Denmark)

    Kymenvaara, Sara; Anker, Helle Tegner; Baaner, Lasse

    2017-01-01

    This article analyses how the use of antifouling paints for leisure boats is regulated in Denmark, Finland and Sweden. All three countries appear to apply a somewhat fragmented approach to the different matters related to antifouling paints, including environmental quality (e.g. water quality......’ to sufficient environmental protection. Another option could be to encourage private law arrangements and “self- enforcement” by e.g. the marinas or boat owner associations....

  15. XRF measurements of tin, copper and zinc in antifouling paints coated on leisure boats.

    Science.gov (United States)

    Ytreberg, Erik; Bighiu, Maria Alexandra; Lundgren, Lennart; Eklund, Britta

    2016-06-01

    Tributyltin (TBT) and other organotin compounds have been restricted for use on leisure boats since 1989 in the EU. Nonetheless, release of TBT is observed from leisure boats during hull maintenance work, such as pressure hosing. In this work, we used a handheld X-ray Fluorescence analyser (XRF) calibrated for antifouling paint matrixes to measure tin, copper and zinc in antifouling paints coated on leisure boats in Sweden. Our results show that over 10% of the leisure boats (n = 686) contain >400 μg/cm(2) of tin in their antifouling coatings. For comparison, one layer (40 μm dry film) of a TBT-paint equals ≈ 800 μg Sn/cm(2). To our knowledge, tin has never been used in other forms than organotin (OT) in antifouling paints. Thus, even though the XRF analysis does not provide any information on the speciation of tin, the high concentrations indicate that these leisure boats still have OT coatings present on their hull. On several leisure boats we performed additional XRF measurements by progressively scraping off the top coatings and analysing each underlying layer. The XRF data show that when tin is detected, it is most likely present in coatings close to the hull with several layers of other coatings on top. Thus, leaching of OT compounds from the hull into the water is presumed to be negligible. The risk for environmental impacts arises during maintenance work such as scraping, blasting and high pressure hosing activities. The data also show that many boat owners apply excessive paint layers when following paint manufacturers recommendations. Moreover, high loads of copper were detected even on boats sailing in freshwater, despite the more than 20 year old ban, which poses an environmental risk that has not been addressed until now. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  16. THE IMPACTS OF BIRD FAECES ON BOAT TEXTILES AND FINISHING COMPOSITION

    OpenAIRE

    Wandah, Lewis

    2010-01-01

    This thesis deals with the damage caused by bird faeces to boat textiles and finishing compositions. A survey was conducted to find out from boaters perspective if the bird faeces cause any damage on the boat textiles and the environment or not? Samples of bird faeces were collected from three strategic sites in Kokkola. They were classified using a gas and ion chromatographic techniques, and an atomic absorption spectrophotometer to determine the contaminants content. The detrimental aspects...

  17. Kinetic model studies on the chemical ligation of oligonucleotides via hydrazone formation.

    Science.gov (United States)

    Achilles, K; Kiedrowski, G V

    2005-02-15

    We report on the suitability of hydrazone formation for activator-free ligation of oligonucleotides. 5'-Acyl hydrazides were synthesized using a previously described phosphoramidite modifier, whereas 3'-hydrazides resulted from a hydrazinolysis of an ester group serving as a linker to the solid support. Aromatic aldehydes could be directly introduced on the 5'-terminus via the respective phosphoramidates. Aliphatic aldehydes were generated by periodate cleavage of the corresponding 3'- and 5'-modified diol precursors. Ligation of a 3'-hydrazide-modified oligonucleotide with oligonucleotides bearing an aromatic aldehyde in 5'-position showed a fast reaction kinetics (k(1) about 10(-1) M(-1)s(-1)) [corrected] and irreversible hydrazone formation. The ligation of a 5'-hydrazide-modified oligonucleotide and a 3'-ribobisaldehyde appeared to proceed reversibly at the beginning, but became irreversible with increasing reaction time. Hydrazide-modified oligonucleotides were found to be somewhat unstable in aqueous solutions.

  18. Versatile procedure of multiple introduction of 8-aminomethylene blue into oligonucleotides.

    Science.gov (United States)

    Möller, U; Schubert, F; Cech, D

    1995-01-01

    The coupling of 8-aminomethylene blue to oligonucleotides via poly-L-glutamic acid linker using carboxy-anchor groups will be described. The introduction of carboxy-anchor groups into oligonucleotides proceeds both during automated synthesis using 6-(ethoxycarbonyl)hexyl 1-O-phosphoramidite and by reaction of 5'-amino-functionalized oligonucleotides with succinic anhydride. O-(N-Succinimidyl)-1,1,3,3-tetramethyluronium tetrafluoroborate was used as activating reagent for binding of poly-L-glutamic acid to the carboxylated oligonucleotides. The successful 5'-carboxylation and poly-L-glutamic acid coupling were proven both by polyacrylamide gel electrophoreses and HPLC. 8-Aminomethylene blue in its leucoform was covalently coupled to the oligonucleotides in the presence of water soluble carbodiimide.

  19. CONTROLLING RISK DUE TO NOISE ON FERRY BOAT

    Directory of Open Access Journals (Sweden)

    Aleksandar Nikolic

    2013-07-01

    Full Text Available Environmental and occupational noise is common nuisance that affects the health of employees. Performed health checks of employees engaged by Company “Pomorski Saobraćaj” showed that 5% of examined sailors had hearing loss. The results were a trigger for starting experiment on noise risk assessment with objective to discover possibilities of noise pollution presence, precise significant noise sources and describe solutions for eliminating negative effects. Several measurements on five positions were performed on ferry boat “KAMENARI”, according to EC Physical Agents Directive and Merchant Shipping and Fishing Vessels Regulations 2007. Noise on selected positions exceeded the limit for about 1-5dB. Noise exposure level was 84.5dB. Diesel engine, exhaust system and structural noise were main sources of excessive noise. Experiment shows noise presence as nuisance that affects sailors. Noise presents a serious threat for sailor’s health. It interferes with crew communication and jeopardizes navigation safety. Technical measures, crew health checks and noise monitoring could prevent all negative effects.

  20. Assembly of Space CFRP Structures with Racing Sailing Boats Technology

    Science.gov (United States)

    Nieto, Jose; Yuste, Laura; Pipo, Alvaro; Santarsiero, Pablo; Bureo, Rafael

    2014-06-01

    Carbon Fiber Reinforced Plastic (CFRP) is commonly used in space applications to get structures with good mechanical performances and a reduced mass. Most of larger parts of spatial structures are already made of CFRP but the achieved weight saving may be jeopardized by the use of metallic brackets as joining elements. This paper describes the work carried out to study and evaluate ways of reducing weight and costs of the joints between structural elements commonly used in space applications.The main objective of this project is to adapt design solutions coming from the racing sailing boats technology to space applications: the use of out-of autoclave (OoA) cured CFRP joints. In addition to that other CFRP solution common in space business, 3D- RTM Bracket, has been evaluated.This development studies the manufacturing and assembly feasibility making use of these CFRP technologies.This study also compares traditional metallic solutions with innovative CFRP ones in terms of mechanical performances at elementary level. Weight and cost of presented solutions are also compared.

  1. [Oligonucleotide derivatives in the nucleic acid hybridization analysis. I. Covalent immobilization of oligonucleotide probes onto the nylon].

    Science.gov (United States)

    Dmitrienko, E V; Pyshnaia, I A; Pyshnyĭ, D V

    2010-01-01

    The features of UV-induced immobilization of oligonucleotides on a nylon membranes and the effectiveness of enzymatic labeling of immobilized probes at heterophase detection of nucleic acids are studied. Short terminal oligothymidilate (up to 10 nt) sequences are suggested to attach to the probe via a flexible ethylene glycol based linker. The presence of such fragment enhances the intensity of immobilization and reduces UV-dependent degradation of the targeted (sequence-specific) part of the probe by reducing the dose needed for the immobilization of DNA. The optimum dose of UV-irradiation is determined to be ~0.4 J/cm(2) at the wavelength 254 nm. This dose provides high level of hybridization signal for immobilized probes with various nucleotide composition of the sequence specific moiety. The amide groups of the polyamide are shown to play the key role in the photoinduced immobilization of nucleic acids, whereas the primary amino groups in the structure of PA is not the center responsible for the covalent binding of DNA by UV-irradiation, as previously believed. Various additives in the soaking solution during the membrane of UV-dependent immobilization of probes are shown to influence its effectiveness. The use of alternative to UV-irradiation system of radical generation are shown to provide the immobilization of oligonucleotides onto the nylon membrane.

  2. The Spectral Properties and Photostability of DNA, RNA and Oligonucleotides

    International Nuclear Information System (INIS)

    Kudrya, V.Yu.; Yashchuk, V.M.

    2012-01-01

    The present work discusses the results of comparative investigations of the optical absorption, luminescence, and photostability of the biomacromolecules (DNA, RNA), as well as synthetic poly- and oligonucleotides. The separate nucleotides in DNA and RNA are examined as almost independent absorbing centers. It is confirmed that the main triplet excitons traps responsible for the DNA phosphorescence emission are AT-complexes in DNA. In contrast to DNA, the main triplet excitons traps in RNA are adenosine bases. These bases are the most photostable against UV-irradiation as compared with all other nucleotides in both DNA and RNA. The fact of the photostability of adenosine bases and the AT-complex provides the existence of the DNA/RNA self-protection mechanisms against a damage caused by UV-irradiation. It is found the deoxyribonucleotides are more photostable than the corresponding ribonucleotides. So, the results presented here show that DNA is more photostable than RNA.

  3. Intracerebral Infusion of Antisense Oligonucleotides Into Prion-infected Mice

    Directory of Open Access Journals (Sweden)

    Karah Nazor Friberg

    2012-01-01

    Full Text Available Mice deficient for the cellular prion protein (PrPC do not develop prion disease; accordingly, gene-based strategies to diminish PrPC expression are of interest. We synthesized a series of chemically modified antisense oligonucleotides (ASOs targeted against mouse Prnp messenger RNA (mRNA and identified those that were most effective in decreasing PrPC expression. Those ASOs were also evaluated in scrapie-infected cultured cells (ScN2a for their efficacy in diminishing the levels of the disease-causing prion protein (PrPSc. When the optimal ASO was infused intracerebrally into FVB mice over a 14-day period beginning 1 day after infection with the Rocky Mountain Laboratory (RML strain of mouse prions, a prolongation of the incubation period of almost 2 months was observed. Whether ASOs can be used to develop an effective therapy for patients dying of Creutzfeldt–Jakob disease remains to be established.

  4. Chemical Ligation Reactions of Oligonucleotides for Biological and Medicinal Applications.

    Science.gov (United States)

    Abe, Hiroshi; Kimura, Yasuaki

    2018-01-01

    Chemical ligation of oligonucleotides (ONs) is the key reaction for various ON-based technologies. We have tried to solve the problems of RNA interference (RNAi) technology by applying ON chemical ligation to RNAi. We designed a new RNAi system, called intracellular buildup RNAi (IBR-RNAi), where the RNA fragments are built up into active small-interference RNA (siRNA) in cells through a chemical ligation reaction. Using the phosphorothioate and iodoacetyl groups as reactive functional groups for the ligation, we achieved RNAi effects without inducing immune responses. Additionally, we developed a new chemical ligation for IBR-RNAi, which affords a more native-like structure in the ligated product. The new ligation method should be useful not only for IBR-RNAi but also for the chemical synthesis of biofunctional ONs.

  5. Oligonucleotides with 1,4-dioxane-based nucleotide monomers

    DEFF Research Database (Denmark)

    Madsen, Andreas S; Wengel, Jesper

    2012-01-01

    An epimeric mixture of H-phosphonates 5R and 5S has been synthesized in three steps from known secouridine 1. Separation of the epimers has been accomplished by RP-HPLC, allowing full characterization and incorporation of monomers X and Y into 9-mer oligonucleotides using H-phosphonates building...... blocks 5R and 5S, respectively. A single incorporation of either monomer X or monomer Y in the central position of a DNA 9-mer results in decreased thermal affinity toward both DNA and RNA complements (ΔT(m) = -3.5 °C/-3.5 °C for monomer X and ΔT(m) = -11.0 °C/-6.5 °C for monomer Y). CD measurements do...

  6. Dissecting the hybridization of oligonucleotides to structured complementary sequences.

    Science.gov (United States)

    Peracchi, Alessio

    2016-06-01

    When oligonucleotides hybridize to long target molecules, the process is slowed by the secondary structure in the targets. The phenomenon has been analyzed in several previous studies, but many details remain poorly understood. I used a spectrofluorometric strategy, focusing on the formation/breaking of individual base pairs, to study the kinetics of association between a DNA hairpin and >20 complementary oligonucleotides ('antisenses'). Hybridization rates differed by over three orders of magnitude. Association was toehold-mediated, both for antisenses binding to the target's ends and for those designed to interact with the loop. Binding of these latter, besides being consistently slower, was affected to variable, non-uniform extents by the asymmetric loop structure. Divalent metal ions accelerated hybridization, more pronouncedly when nucleation occurred at the loop. Incorporation of locked nucleic acid (LNA) residues in the antisenses substantially improved the kinetics only when LNAs participated to the earliest hybridization steps. The effects of individual LNAs placed along the antisense indicated that the reaction transition state occurred after invading at least the first base pair of the stem. The experimental approach helps dissect hybridization reactions involving structured nucleic acids. Toehold-dependent, nucleation-invasion models appear fully appropriate for describing such reactions. Estimating the stability of nucleation complexes formed at internal toeholds is the major hurdle for the quantitative prediction of hybridization rates. While analyzing the mechanisms of a fundamental biochemical process (hybridization), this work also provides suggestions for the improvement of technologies that rely on such process. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Combining gene expression data from different generations of oligonucleotide arrays

    Directory of Open Access Journals (Sweden)

    Kong Sek

    2004-10-01

    Full Text Available Abstract Background One of the important challenges in microarray analysis is to take full advantage of previously accumulated data, both from one's own laboratory and from public repositories. Through a comparative analysis on a variety of datasets, a more comprehensive view of the underlying mechanism or structure can be obtained. However, as we discover in this work, continual changes in genomic sequence annotations and probe design criteria make it difficult to compare gene expression data even from different generations of the same microarray platform. Results We first describe the extent of discordance between the results derived from two generations of Affymetrix oligonucleotide arrays, as revealed in cluster analysis and in identification of differentially expressed genes. We then propose a method for increasing comparability. The dataset we use consists of a set of 14 human muscle biopsy samples from patients with inflammatory myopathies that were hybridized on both HG-U95Av2 and HG-U133A human arrays. We find that the use of the probe set matching table for comparative analysis provided by Affymetrix produces better results than matching by UniGene or LocusLink identifiers but still remains inadequate. Rescaling of expression values for each gene across samples and data filtering by expression values enhance comparability but only for few specific analyses. As a generic method for improving comparability, we select a subset of probes with overlapping sequence segments in the two array types and recalculate expression values based only on the selected probes. We show that this filtering of probes significantly improves the comparability while retaining a sufficient number of probe sets for further analysis. Conclusions Compatibility between high-density oligonucleotide arrays is significantly affected by probe-level sequence information. With a careful filtering of the probes based on their sequence overlaps, data from different

  8. Direct microcontact printing of oligonucleotides for biochip applications

    Directory of Open Access Journals (Sweden)

    Trévisiol E

    2005-07-01

    Full Text Available Abstract Background A critical step in the fabrication of biochips is the controlled placement of probes molecules on solid surfaces. This is currently performed by sequential deposition of probes on a target surface with split or solid pins. In this article, we present a cost-effective procedure namely microcontact printing using stamps, for a parallel deposition of probes applicable for manufacturing biochips. Results Contrary to a previous work, we showed that the stamps tailored with an elastomeric poly(dimethylsiloxane material did not require any surface modification to be able to adsorb oligonucleotides or PCR products. The adsorbed DNA molecules are subsequently printed efficiently on a target surface with high sub-micron resolution. Secondly, we showed that successive stamping is characterized by an exponential decay of the amount of transferred DNA molecules to the surface up the 4th print, then followed by a second regime of transfer that was dependent on the contact time and which resulted in reduced quality of the features. Thus, while consecutive stamping was possible, this procedure turned out to be less reproducible and more time consuming than simply re-inking the stamps between each print. Thirdly, we showed that the hybridization signals on arrays made by microcontact printing were 5 to 10-times higher than those made by conventional spotting methods. Finally, we demonstrated the validity of this microcontact printing method in manufacturing oligonucleotides arrays for mutations recognition in a yeast gene. Conclusion The microcontact printing can be considered as a new potential technology platform to pattern DNA microarrays that may have significant advantages over the conventional spotting technologies as it is easy to implement, it uses low cost material to make the stamp, and the arrays made by this technology are 10-times more sensitive in term of hybridization signals than those manufactured by conventional spotting

  9. Pharmacokinetic Profiling of Conjugated Therapeutic Oligonucleotides: A High-Throughput Method Based Upon Serial Blood Microsampling Coupled to Peptide Nucleic Acid Hybridization Assay.

    Science.gov (United States)

    Godinho, Bruno M D C; Gilbert, James W; Haraszti, Reka A; Coles, Andrew H; Biscans, Annabelle; Roux, Loic; Nikan, Mehran; Echeverria, Dimas; Hassler, Matthew; Khvorova, Anastasia

    2017-12-01

    Therapeutic oligonucleotides, such as small interfering RNAs (siRNAs), hold great promise for the treatment of incurable genetically defined disorders by targeting cognate toxic gene products for degradation. To achieve meaningful tissue distribution and efficacy in vivo, siRNAs must be conjugated or formulated. Clear understanding of the pharmacokinetic (PK)/pharmacodynamic behavior of these compounds is necessary to optimize and characterize the performance of therapeutic oligonucleotides in vivo. In this study, we describe a simple and reproducible methodology for the evaluation of in vivo blood/plasma PK profiles and tissue distribution of oligonucleotides. The method is based on serial blood microsampling from the saphenous vein, coupled to peptide nucleic acid hybridization assay for quantification of guide strands. Performed with minimal number of animals, this method allowed unequivocal detection and sensitive quantification without the need for amplification, or further modification of the oligonucleotides. Using this methodology, we compared plasma clearances and tissue distribution profiles of two different hydrophobically modified siRNAs (hsiRNAs). Notably, cholesterol-hsiRNA presented slow plasma clearances and mainly accumulated in the liver, whereas, phosphocholine-docosahexaenoic acid-hsiRNA was rapidly cleared from the plasma and preferably accumulated in the kidney. These data suggest that the PK/biodistribution profiles of modified hsiRNAs are determined by the chemical nature of the conjugate. Importantly, the method described in this study constitutes a simple platform to conduct pilot assessments of the basic clearance and tissue distribution profiles, which can be broadly applied for evaluation of new chemical variants of siRNAs and micro-RNAs.

  10. The May 2015 boat crisis: the Rohingya in Aceh

    Directory of Open Access Journals (Sweden)

    Graham Thom

    2016-07-01

    Full Text Available Abstract In May 2015, Indonesia permitted the disembarkation of approximately 1,800 people who had been stranded at sea. The discovery of mass graves in Thailand’s Sadao district, on the border with Malaysia, led to a crack down on people smugglers by the Thai and Malaysian authorities. This saw thousands of Rohingya left stranded at sea as smugglers abandoned their human cargo. While initially pushed back by the Indonesian navy, after being rescued by Indonesian fishermen the Rohingya, on the three boats rescued, were permitted to stay in Indonesia’s Aceh province and seek protection. As part of an Amnesty International research team, conducting research in Aceh in August 2015, our aim was to document the reasons driving the Rohingya to leave Myanmar and Bangladesh, the human rights abuses they experienced at sea and the conditions they are experiencing in Aceh. The subsequent Amnesty International report primarily documented the abuses suffered by those on board the smuggling/trafficking vessels. It also highlighted a number of issues now facing those allowed to remain in Aceh (Amnesty International, 2015. This article will further examine the human rights situation facing the Rohingya in Aceh, why they have been treated differently from previous Rohingya groups who have arrived in Aceh and the ongoing sustainability of the current model. Significantly, the majority of those that arrived have subsequently escaped from the “sites”[1], having again engaged smugglers to reach Malaysia. Given that a process already exists for refugees arriving in Indonesia, the differing treatment received by the Rohingya arriving in May 2015 raises a number of questions. This paper will conclude that the current situation is not sustainable and the treatment of refugees in Aceh should be included in a broader national approach commensurate to the treatment of refugees and asylum seekers throughout Indonesia. [1] Rather than detention centres or camps, the

  11. Polymerase-endonuclease amplification reaction (PEAR for large-scale enzymatic production of antisense oligonucleotides.

    Directory of Open Access Journals (Sweden)

    Xiaolong Wang

    Full Text Available Antisense oligonucleotides targeting microRNAs or their mRNA targets prove to be powerful tools for molecular biology research and may eventually emerge as new therapeutic agents. Synthetic oligonucleotides are often contaminated with highly homologous failure sequences. Synthesis of a certain oligonucleotide is difficult to scale up because it requires expensive equipment, hazardous chemicals and a tedious purification process. Here we report a novel thermocyclic reaction, polymerase-endonuclease amplification reaction (PEAR, for the amplification of oligonucleotides. A target oligonucleotide and a tandem repeated antisense probe are subjected to repeated cycles of denaturing, annealing, elongation and cleaving, in which thermostable DNA polymerase elongation and strand slipping generate duplex tandem repeats, and thermostable endonuclease (PspGI cleavage releases monomeric duplex oligonucleotides. Each round of PEAR achieves over 100-fold amplification. The product can be used in one more round of PEAR directly, and the process can be further repeated. In addition to avoiding dangerous materials and improved product purity, this reaction is easy to scale up and amenable to full automation. PEAR has the potential to be a useful tool for large-scale production of antisense oligonucleotide drugs.

  12. Ultramild protein-mediated click chemistry creates efficient oligonucleotide probes for targeting and detecting nucleic acids

    DEFF Research Database (Denmark)

    Nåbo, Lina J.; Madsen, Charlotte S.; Jensen, Knud J.

    2015-01-01

    Functionalized synthetic oligonucleotides are finding growing applications in research, clinical studies, and therapy. However, it is not easy to prepare them in a biocompatible and highly efficient manner. We report a new strategy to synthesize oligonucleotides with promising nucleic acid...... targeting and detection properties. We focus in particular on the pH sensitivity of these new probes and their high target specificity. For the first time, human copper(I)-binding chaperon Cox17 was applied to effectively catalyze click labeling of oligonucleotides. This was performed under ultramild...

  13. Solid-phase synthesis of 2{sup '}-O-methoxyethyl oligonucleotides using dimeric phosphoramidate blocks

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Gi Weon; Kang, Yong Han [Dept. of Applied Chemistry, Hanyang University, Ansan (Korea, Republic of)

    2016-11-15

    This research focused on the method of using dimeric phosphoramidite blocks to synthesize oligonucleotides for development as oligonucleotide drugs. A 16-mer oligonucleotide with the randomly selected sequence of C*C*T*C*G*C *T*C*T*C*G*C*C* C*G*C was synthesized using CC, GC, and TC dimers, a combination of monomers and dimers, or only monomers as building blocks. Using dimer blocks in this synthetic method provided a significant decrease in critical impurities that had similar properties to the main product, which was confirmed by LC-MS and HPLC analysis.

  14. Synthetic Method for Oligonucleotide Block by Using Alkyl-Chain-Soluble Support.

    Science.gov (United States)

    Matsuno, Yuki; Shoji, Takao; Kim, Shokaku; Chiba, Kazuhiro

    2016-02-19

    A straightforward method for the synthesis of oligonucleotide blocks using a Cbz-type alkyl-chain-soluble support (Z-ACSS) attached to the 3'-OH group of 3'-terminal nucleosides was developed. The Z-ACSS allowed for the preparation of fully protected deoxyribo- and ribo-oligonucleotides without chromatographic purification and released dimer- to tetramer-size oligonucleotide blocks via hydrogenation using a Pd/C catalyst without significant loss or migration of protective groups such as 5'-end 4,4'-dimethoxtrityl, 2-cyanoethyl on internucleotide bonds, or 2'-TBS.

  15. The Use of Gel Electrophoresis to Study the Reactions of Activated Amino Acids with Oligonucleotides

    Science.gov (United States)

    Zieboll, Gerhard; Orgel, Leslie E.

    1994-01-01

    We have used gel electrophoresis to study the primary covalent addition of amino acids to oligonu-cleotides or their analogs and the subsequent addition of further molecules of the amino acids to generate peptides covalently linked to the oligonucleotides. We have surveyed the reactions of a variety of amino acids with the phosphoramidates derived from oligonucleotide 5 inches phosphates and ethylenediamine. We find that arginine and amino acids can interact with oligonucleotidesl through stacking interactions react most efficiently. D- and L-amino acids give indistinguishable families of products.

  16. Small Rov Marine Boat for Bathymetry Surveys of Shallow Waters - Potential Implementation in Malaysia

    Science.gov (United States)

    Suhari, K. T.; Karim, H.; Gunawan, P. H.; Purwanto, H.

    2017-10-01

    Current practices in bathymetry survey (available method) are indeed having some limitations. New technologies for bathymetry survey such as using unmanned boat has becoming popular in developed countries - filled in and served those limitations of existing survey methods. Malaysia as one of tropical country has it own river/water body characteristics and suitable approaches in conducting bathymetry survey. Thus, a study on this emerging technology should be conducted using enhanced version of small ROV boat with Malaysian rivers and best approaches so that the surveyors get benefits from the innovative surveying product. Among the available ROV boat for bathymetry surveying in the market, an Indonesian product called SHUMOO is among the promising products - economically and practically proven using a few sample areas in Indonesia. The boat was equipped and integrated with systems of remote sensing technology, GNSS, echo sounder and navigational engine. It was designed for riverbed surveys on shallow area such as small /medium river, lakes, reservoirs, oxidation/detention pond and other water bodies. This paper tries to highlight the needs and enhancement offered to Malaysian' bathymetry surveyors/practitioners on the new ROV boat which make their task easier, faster, safer, economically effective and better riverbed modelling results. The discussion continues with a sample of Indonesia river (data collection and modelling) since it is mostly similar to Malaysia's river characteristics and suggests some improvement for Malaysia best practice.

  17. SMALL ROV MARINE BOAT FOR BATHYMETRY SURVEYS OF SHALLOW WATERS – POTENTIAL IMPLEMENTATION IN MALAYSIA

    Directory of Open Access Journals (Sweden)

    K. T. Suhari

    2017-10-01

    Full Text Available Current practices in bathymetry survey (available method are indeed having some limitations. New technologies for bathymetry survey such as using unmanned boat has becoming popular in developed countries - filled in and served those limitations of existing survey methods. Malaysia as one of tropical country has it own river/water body characteristics and suitable approaches in conducting bathymetry survey. Thus, a study on this emerging technology should be conducted using enhanced version of small ROV boat with Malaysian rivers and best approaches so that the surveyors get benefits from the innovative surveying product. Among the available ROV boat for bathymetry surveying in the market, an Indonesian product called SHUMOO is among the promising products – economically and practically proven using a few sample areas in Indonesia. The boat was equipped and integrated with systems of remote sensing technology, GNSS, echo sounder and navigational engine. It was designed for riverbed surveys on shallow area such as small /medium river, lakes, reservoirs, oxidation/detention pond and other water bodies. This paper tries to highlight the needs and enhancement offered to Malaysian’ bathymetry surveyors/practitioners on the new ROV boat which make their task easier, faster, safer, economically effective and better riverbed modelling results. The discussion continues with a sample of Indonesia river (data collection and modelling since it is mostly similar to Malaysia’s river characteristics and suggests some improvement for Malaysia best practice.

  18. Design of a semi-autonomous boat for measurements of coastal sedimentation and erosion

    Directory of Open Access Journals (Sweden)

    D. Smith

    2015-03-01

    Full Text Available Measurement of sediment deposition and erosion in coastal areas is a challenge due to soft shifting sediments, but is critical to assessing loss or restoration of coastal sediments and wetlands. The aim of this project was to design and construct a semi-autonomous boat with water depth measuring capabilities. It was intended to map the depth of coastal wetlands to determine erosion rates and assess coastal restoration effects. Depth-measuring equipment was incorporated into an autonomous pontoon boat powered by solar panels. The propulsion system consisted of two paddlewheels and two-way motors to allow movement and positioning for measurements. Modifications included a lightweight, hard coating on the pontoons and powder-coating the frame to extend their usable life. A microcontroller controlled the boat and captured depth data from sensors and location data with a GPS system. The depth measuring system consisted of a pulley and counter system that completed each measurement in less than 45 seconds. This allowed the boat to take approximately 400 measurements per day. Net accuracy was approximately 3 cm in the tested configuration. The boat can continually measure the depth of specified areas in the wetlands; with this data, the change in depth can be monitored to see the effects of restoration projects.

  19. Design of a semi-autonomous boat for measurements of coastal sedimentation and erosion

    Science.gov (United States)

    Smith, D.; Cross, L.; Rivet, J.; Hall, S.

    2015-03-01

    Measurement of sediment deposition and erosion in coastal areas is a challenge due to soft shifting sediments, but is critical to assessing loss or restoration of coastal sediments and wetlands. The aim of this project was to design and construct a semi-autonomous boat with water depth measuring capabilities. It was intended to map the depth of coastal wetlands to determine erosion rates and assess coastal restoration effects. Depth-measuring equipment was incorporated into an autonomous pontoon boat powered by solar panels. The propulsion system consisted of two paddlewheels and two-way motors to allow movement and positioning for measurements. Modifications included a lightweight, hard coating on the pontoons and powder-coating the frame to extend their usable life. A microcontroller controlled the boat and captured depth data from sensors and location data with a GPS system. The depth measuring system consisted of a pulley and counter system that completed each measurement in less than 45 seconds. This allowed the boat to take approximately 400 measurements per day. Net accuracy was approximately 3 cm in the tested configuration. The boat can continually measure the depth of specified areas in the wetlands; with this data, the change in depth can be monitored to see the effects of restoration projects.

  20. EvOligo: A Novel Software to Design and Group Libraries of Oligonucleotides Applicable for Nucleic Acid-Based Experiments.

    Science.gov (United States)

    Milewski, Marek C; Kamel, Karol; Kurzynska-Kokorniak, Anna; Chmielewski, Marcin K; Figlerowicz, Marek

    2017-10-01

    Experimental methods based on DNA and RNA hybridization, such as multiplex polymerase chain reaction, multiplex ligation-dependent probe amplification, or microarray analysis, require the use of mixtures of multiple oligonucleotides (primers or probes) in a single test tube. To provide an optimal reaction environment, minimal self- and cross-hybridization must be achieved among these oligonucleotides. To address this problem, we developed EvOligo, which is a software package that provides the means to design and group DNA and RNA molecules with defined lengths. EvOligo combines two modules. The first module performs oligonucleotide design, and the second module performs oligonucleotide grouping. The software applies a nearest-neighbor model of nucleic acid interactions coupled with a parallel evolutionary algorithm to construct individual oligonucleotides, and to group the molecules that are characterized by the weakest possible cross-interactions. To provide optimal solutions, the evolutionary algorithm sorts oligonucleotides into sets, preserves preselected parts of the oligonucleotides, and shapes their remaining parts. In addition, the oligonucleotide sets can be designed and grouped based on their melting temperatures. For the user's convenience, EvOligo is provided with a user-friendly graphical interface. EvOligo was used to design individual oligonucleotides, oligonucleotide pairs, and groups of oligonucleotide pairs that are characterized by the following parameters: (1) weaker cross-interactions between the non-complementary oligonucleotides and (2) more uniform ranges of the oligonucleotide pair melting temperatures than other available software products. In addition, in contrast to other grouping algorithms, EvOligo offers time-efficient sorting of paired and unpaired oligonucleotides based on various parameters defined by the user.

  1. Take One Boat: from offshore science to onshore art

    Science.gov (United States)

    Cotterill, C.

    2017-12-01

    The International Ocean Discovery Program (IODP) is a collaborative programme that works to explore the oceans and the rocks beneath them. Working from shallow to deep waters, and in ice covered to more tropical areas, scientists work together to sample ocean sediments and rocks, and install subsea observatories, in order to investigate our planets dynamic history. The European Consortium for Ocean Research Drilling (ECORD) are one arm of IODP, and the Education and Outreach Task Force are investigating ways of taking education and outreach further - how can we convey the excitement of this program to others and inspire careers in STEM subjects?Cape Farewell are a think / do tank who gather artists, designers, filmmakers and writers to interact with scientists and find ways to address climate change. From creation of internationally touring artworks to films and novels, Cape Farewell continues to educate engage and inspire. For 3 years the author was involved in Cape Farewell not only as a research scientist, but also as a mentor within the educational programme. Over the course of two expeditions, students were invited to design both a science research project and an accompanying arts project that investigated climate change in this fragile environment, replicating the model used for professional scientists and artists. The long term aim of the project was to support peer to peer learning, with students working as youth ambassadors within their schools and communities. With outputs from this style of engagement now including digital artwork exhibitions, a multi-disciplinary arts school, online resources and the initiation of the youth climate change summit, this talk investigates what lessons can be learnt from this dynamic combination of arts and science, to develop a programme that takes just one boat, and makes a big change in how we communicate science. "The art the students have been producing has been inspired by the science they have learnt, what they

  2. Carboranyl Oligonucleotides for Neutron Capture Therapy Final Report

    International Nuclear Information System (INIS)

    Schinazi, Raymond F.

    2004-01-01

    This proposal enabled us to synthesize and develop boron-rich nucleosides and oligonucleotide analogues for boron neutron capture therapy (BNCT) and the treatment of various malignancies. First, we determined the relationship between structure, cellular accumulation and tissue distribution of 5-o-carboranyl-2'-deoxyuridine (D-CDU) and its derivatives D-ribo-CU and 5-o-carboranyluracil (CU), to potentially target brain and other solid tumors for neutron capture therapy. Synthesized carborane containing nucleoside derivatives of CDU, D- and L-enantiomers of CDU, D-ribo-CU and CU were used. We measured tissue disposition in xenografted mice bearing 9479 human prostate tumors xenografts and in rats bearing 9L gliosarcoma isografts in their flanks and intracranially. The accumulation of D-CDU, 1-(β-L-arabinosyl)-5-o-carboranyluracil, D-ribo-CU, and CU were also studied in LnCap human prostate tumor cells and their retention was measured in male nude mice bearing LnCap and 9479 human prostate tumor xenografts. D-CDU, D-ribo-CU and CU levels were measured after administration in mice bearing 9479 human prostate tumors in their flanks. D-CDU achieved high cellular concentrations in LnCap cells and up to 2.5% of the total cellular compound was recovered in the 5'-monophosphorylated form. D-CDU cellular concentrations were similar in LnCap and 9479 tumor xenografts. Studies in tumor bearing animals indicated that increasing the number of hydroxyl moieties in the sugar constituent of the carboranyl nucleosides lead to increased rate and extent of renal elimination, a decrease in serum half-lives and an increased tissue specificity. Tumor/brain ratios were greatest for CDU and D-ribo-CU, while tumor/prostate ratios were greatest with CU. CDU and D-ribo-CU have potential for BNCT of brain malignancies, while CU may be further developed for prostate cancer. A method was developed for the solid phase synthesis of oligonucleotides containing (ocarboran-1-yl

  3. Thermal Stability of Modified i-Motif Oligonucleotides with Naphthalimide Intercalating Nucleic Acids

    DEFF Research Database (Denmark)

    El-Sayed, Ahmed Ali; Pedersen, Erik B.; Khaireldin, Nahid Y.

    2016-01-01

    In continuation of our investigation of characteristics and thermodynamic properties of the i-motif 5′-d[(CCCTAA)3CCCT)] upon insertion of intercalating nucleotides into the cytosine-rich oligonucleotide, this article evaluates the stabilities of i-motif oligonucleotides upon insertion of naphtha......In continuation of our investigation of characteristics and thermodynamic properties of the i-motif 5′-d[(CCCTAA)3CCCT)] upon insertion of intercalating nucleotides into the cytosine-rich oligonucleotide, this article evaluates the stabilities of i-motif oligonucleotides upon insertion...... of naphthalimide (1H-benzo[de]isoquinoline-1,3(2H)-dione) as the intercalating nucleic acid. The stabilities of i-motif structures with inserted naphthalimide intercalating nucleotides were studied using UV melting temperatures (Tm) and circular dichroism spectra at different pH values and conditions (crowding...

  4. Functionalization of PVC membrane with ss oligonucleotides for a potentiometric biosensor.

    Science.gov (United States)

    Shishkanova, T V; Volf, R; Krondak, M; Král, V

    2007-05-15

    A novel application of a single stranded (ss) oligonucleotide as an active component of polymeric membrane in an ion-selective electrode (ISE) is described. The original oligonucleotides, oligo(dA)(15), modified by cholesterol, triphenylmethyl and hexadecyl derivatives, were immobilized into poly(vinyl chloride) (PVC) membrane using extraction protocol. In parallel, the adsorption protocol was used to immobilize unmodified oligo(dA)(15) on the PVC membrane based on tridodecylmethyammonium chloride (TDDMA(+)Cl(-)). Immobilization of ss oligonucleotide probe through spacer was more effective for the potentiometric detection of the hybridization between complementary oligonucleotides. It was found that cholesterol-oligo(dA)(15) modified membranes were sensitive toward complementary oligo(dT)(15) in the concentration range 2-80 nM at pH 7. An explanation for the detection mechanism is proposed.

  5. Oligonucleotide-based biosensors for in vitro diagnostics and environmental hazard detection.

    Science.gov (United States)

    Jung, Il Young; Lee, Eun Hee; Suh, Ah Young; Lee, Seung Jin; Lee, Hyukjin

    2016-04-01

    Oligonucleotide-based biosensors have drawn much attention because of their broad applications in in vitro diagnostics and environmental hazard detection. They are particularly of interest to many researchers because of their high specificity as well as excellent sensitivity. Recently, oligonucleotide-based biosensors have been used to achieve not only genetic detection of targets but also the detection of small molecules, peptides, and proteins. This has further broadened the applications of these sensors in the medical and health care industry. In this review, we highlight various examples of oligonucleotide-based biosensors for the detection of diseases, drugs, and environmentally hazardous chemicals. Each example is provided with detailed schematics of the detection mechanism in addition to the supporting experimental results. Furthermore, future perspectives and new challenges in oligonucleotide-based biosensors are discussed.

  6. Novel approaches to study low-energy electron-induced damage to DNA oligonucleotides

    International Nuclear Information System (INIS)

    Rackwitz, Jenny; Bald, Ilko; Ranković, Miloš Lj; Milosavljević, Aleksandar R

    2015-01-01

    The novel approach of DNA origami structures as templates for precise quantification of various well- defined oligonucleotides provides the opportunity to determine the sensitivity of complex DNA sequences towards low-energy electrons. (paper)

  7. Research and development of Ro-boat: an autonomous river cleaning robot

    Science.gov (United States)

    Sinha, Aakash; Bhardwaj, Prashant; Vaibhav, Bipul; Mohommad, Noor

    2013-12-01

    Ro-Boat is an autonomous river cleaning intelligent robot incorporating mechanical design and computer vision algorithm to achieve autonomous river cleaning and provide a sustainable environment. Ro-boat is designed in a modular fashion with design details such as mechanical structural design, hydrodynamic design and vibrational analysis. It is incorporated with a stable mechanical system with air and water propulsion, robotic arms and solar energy source and it is proceed to become autonomous by using computer vision. Both "HSV Color Space" and "SURF" are proposed to use for measurements in Kalman Filter resulting in extremely robust pollutant tracking. The system has been tested with successful results in the Yamuna River in New Delhi. We foresee that a system of Ro-boats working autonomously 24x7 can clean a major river in a city on about six months time, which is unmatched by alternative methods of river cleaning.

  8. ASSESSMENT OF THE ELECTRIC POWER QUALITY ON THE POLISH FISHING BOATS

    Directory of Open Access Journals (Sweden)

    Dariusz TARNAPOWICZ

    2015-07-01

    Full Text Available Power quality is an important problem for electrical systems. Electricity receivers should operate at nominal conditions. Each deviation from nominal values may cause the malfunction of electrical devices, decreasing their durability and per-manently damage the appliance. The importance of electric power quality for technical systems and individual electrical devices on fishing boats is fundamental. Utilization of equipment powered by electrical energy with a reduced quality resulting in economical losses and the treat to the screw's safety. Researches of the electrical energy's quality were carried out almost any type of fishing boats. This article presents the results of researches concerning the quality of electrical energy performed on a representative type of fishing boats. It shortly evaluates the results of tests and suggests solutions to improve the power quality parameters.

  9. Rental solar boat on the lake of Zurich; Miet-Solarboot auf dem Zuerichsee

    Energy Technology Data Exchange (ETDEWEB)

    Schmid, R.

    2002-07-01

    This final report for the Swiss Federal Office of Energy (SFOE) describes a solar-powered motor boat that can be rented on the Lake of Zurich in Switzerland. The development and construction of the boat, which was built under the auspices of the Zurich regional group of the Swiss Solar Energy Society is described. The ideas behind the project are explained. Its financing and the many tests and acceptance trials that had to be made by the various authorities concerned are discussed. Experience gained during the first year of operation is presented. The report is completed with an appendix containing a comprehensive description of the boat, including technical drawings and a documentation of its construction.

  10. Synthesis and Excellent Duplex Stability of Oligonucleotides Containing 2'-Amino-LNA Functionalized with Galactose Units.

    Science.gov (United States)

    Kumar, Rajesh; Ries, Annika; Wengel, Jesper

    2017-05-21

    A convenient method for the preparation of oligonucleotides containing internally-attached galactose and triantennary galactose units has been developed based on click chemistry between 2'- N -alkyne 2'-amino-LNA nucleosides and azido-functionalized galactosyl building blocks. The synthesized oligonucleotides show excellent binding affinity and selectivity towards complementary DNA/RNA strands with an increase in the melting temperature of up to +23.5 °C for triply-modified variants.

  11. Development of oligonucleotide microarrays onto si-based surfaces via thioether linkage mediated by UV irradiation

    OpenAIRE

    Escorihuela Fuentes, Jorge; Bañuls Polo, Mª José; Puchades Pla, Rosa; Maquieira Catala, Ángel

    2012-01-01

    Selective covalent immobilization of thiolated oligonucleotides onto an epoxy-functionalized silicon-substrate can be achieved via light radiation (365 nm). Following this approach, thiol-modified oligonucleotide probes were covalently attached as microarrays, reaching an immobilization density of 2.5 pmol·cm -2, with a yield of 53%. The developed method presents the advantages of spatially controlled probe anchoring (by means of using a photomask), direct attachment without using cross-linke...

  12. Scalable Amplification of Strand Subsets from Chip-Synthesized Oligonucleotide Libraries (Open Access)

    Science.gov (United States)

    2015-11-16

    Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA. 2Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240...quantities (each) would receive a boost from a largely reduced oligonucleotide cost and an automatable production pipeline . Methods Materials. Enzymes...genome-wide codon replacement . Science 333, 348–353 (2011). 13. Yamada, N. A. et al. Visualization of fine-scale genomic structure by oligonucleotide-based

  13. [Oligonucleotide derivatives in the nucleic acid hybridization analysis. III. Synthesis and investigation of properties of oligonucleotides, bearing bifunctional non-nucleotide insert].

    Science.gov (United States)

    Kupriushkin, M S; Pyshnyĭ, D V

    2012-01-01

    Non-nucleotide phosporamidites were synthetized, having branched backbone with different position of functional groups. Obtained phosphoramidite monomers contain intercalator moiety--6-chloro-2-methoxyacridine, and additional hydroxyl residue protected with dimethoxytrityl group or with tert-butyldimethylsilyl group for post-synthetic modification. Synthesized oligothymidilates contain one or more modified units in different positions of sequence. Melting temperature and thermodynamic parameters of formation of complementary duplexes formed by modified oligonucleotides was defined (change in enthalpy and entropy). The introduction of intercalating residue causes a significant stabilization of DNA duplexes. It is shown that the efficiency of the fluorescence of acridine residue in the oligonucleotide conjugate significantly changes upon hybridization with DNA.

  14. [HLA-DQA1 genotyping by using oligonucleotide microarrays].

    Science.gov (United States)

    Wang, Tong; Wang, Tian-Jiao; He, Qun; Zhang, Yu-Kui; Ma, Jia-Ming; Hou, Wei-Jian; Wang, Shao-Cheng; Pan, Zhong-Cheng; Zhao, Yu-Jie

    2006-02-01

    In order to fabricate the HLA-DQA1 genotyping chip and develop an integrated, parallel technical platform to type HLA system, a pair of primers and a set of probes were designed according to the sequences of HLA-DQA1 exon 2, where the polymorphism is concentrated. The oligonucleotide chip was made with the methods developed in our laboratory. The target DNA was asymmetrically amplified with the labeled sense primer. The signals were scanned and analyzed after the hybridization between microarray and PCR product. The allele types of the samples were identified. The result was verified by the standard DNA and DNA sequencing. The results showed that the genotyping was successfully carried out in 50 standard DNA samples and 50 clinical samples. Among them, results of the 50 standard DNA samples matched their templates. In the other 50 samples, results of the randomly selected 10 matched their sequencing results except that two of them got the incompletely result. In reproducible tests, the signal reappear rate was 95%. It is concluded that HLA-DQA1 genotyping by using our array system is simple and convenient with satisfied accuracy and reproducibility.

  15. Oligonucleotide length dependent formation of virus-like particles.

    Science.gov (United States)

    Maassen, Stan J; de Ruiter, Mark Vincent; Lindhoud, Saskia; Cornelissen, Jeroen J L M

    2018-03-08

    Understanding the assembly pathway of viruses can contribute to creating monodisperse virus-based materials. In this study the Cowpea Chlorotic Mottle Virus is used to determine the interactions between the capsid proteins of viruses and their cargo. The assembly of the capsid proteins in the presence of different lengths of short single-stranded DNA is studied at neutral pH, where the protein-protein interactions are weak. Chromatography, electrophoresis, microscopy, and light scattering shows that the assembly efficiency and speed of the particles increases with increasing length of oligonucleotides. The minimal length required for assembly at the conditions used here is shown to be 14 nucleotides. Assembly of particles containing such short strands of ssDNA can take almost a month. This slow assembly process enabled the study of intermediate states, confirming a low cooperative assembly for CCMV and allows for further expansion of current assembly theories. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Antineoplastic Effect of Decoy Oligonucleotide Derived from MGMT Enhancer

    Science.gov (United States)

    Refael, Miri; Zrihan, Daniel; Siegal, Tali; Lavon, Iris

    2014-01-01

    Silencing of O(6)-methylguanine-DNA-methyltransferase (MGMT) in tumors, mainly through promoter methylation, correlates with a better therapeutic response and with increased survival. Therefore, it is conceivable to consider MGMT as a potential therapeutic target for the treatment of cancers. Our previous results demonstrated the pivotal role of NF-kappaB in MGMT expression, mediated mainly through p65/NF-kappaB homodimers. Here we show that the non-canonical NF-KappaB motif (MGMT-kappaB1) within MGMT enhancer is probably the major inducer of MGMT expression following NF-kappaB activation. Thus, in an attempt to attenuate the transcription activity of MGMT in tumors we designed locked nucleic acids (LNA) modified decoy oligonucleotides corresponding to the specific sequence of MGMT-kappaB1 (MGMT-kB1-LODN). Following confirmation of the ability of MGMT-kB1-LODN to interfere with the binding of p65/NF-kappaB to the NF-KappaB motif within MGMT enhancer, the efficacy of the decoy was studied in-vitro and in-vivo. The results of these experiments show that the decoy MGMT-kB1-LODN have a substantial antineoplastic effect when used either in combination with temozolomide or as monotherapy. Our results suggest that MGMT-kB1-LODN may provide a novel strategy for cancer therapy. PMID:25460932

  17. Antineoplastic effect of decoy oligonucleotide derived from MGMT enhancer.

    Directory of Open Access Journals (Sweden)

    Tamar Canello

    Full Text Available Silencing of O(6-methylguanine-DNA-methyltransferase (MGMT in tumors, mainly through promoter methylation, correlates with a better therapeutic response and with increased survival. Therefore, it is conceivable to consider MGMT as a potential therapeutic target for the treatment of cancers. Our previous results demonstrated the pivotal role of NF-kappaB in MGMT expression, mediated mainly through p65/NF-kappaB homodimers. Here we show that the non-canonical NF-KappaB motif (MGMT-kappaB1 within MGMT enhancer is probably the major inducer of MGMT expression following NF-kappaB activation. Thus, in an attempt to attenuate the transcription activity of MGMT in tumors we designed locked nucleic acids (LNA modified decoy oligonucleotides corresponding to the specific sequence of MGMT-kappaB1 (MGMT-kB1-LODN. Following confirmation of the ability of MGMT-kB1-LODN to interfere with the binding of p65/NF-kappaB to the NF-KappaB motif within MGMT enhancer, the efficacy of the decoy was studied in-vitro and in-vivo. The results of these experiments show that the decoy MGMT-kB1-LODN have a substantial antineoplastic effect when used either in combination with temozolomide or as monotherapy. Our results suggest that MGMT-kB1-LODN may provide a novel strategy for cancer therapy.

  18. Effect of oligonucleotide primers in determining viral variability within hosts

    Directory of Open Access Journals (Sweden)

    Moya Andrés

    2004-12-01

    Full Text Available Abstract Background Genetic variability in viral populations is usually estimated by means of polymerase chain reaction (PCR based methods in which the relative abundance of each amplicon is assumed to be proportional to the frequency of the corresponding template in the initial sample. Although bias in template-to-product ratios has been described before, its relevance in describing viral genetic variability at the intrapatient level has not been fully assessed yet. Results To investigate the role of oligonucleotide design in estimating viral variability within hosts, genetic diversity in hepatitis C virus (HCV populations from eight infected patients was characterised by two parallel PCR amplifications performed with two slightly different sets of primers, followed by cloning and sequencing (mean = 89 cloned sequences per patient. Population genetics analyses of viral populations recovered by pairs of amplifications revealed that in seven patients statistically significant differences were detected between populations sampled with different set of primers. Conclusions Genetic variability analyses demonstrates that PCR selection due to the choice of primers, differing in their degeneracy degree at some nucleotide positions, can eclipse totally or partially viral variants, hence yielding significant different estimates of viral variability within a single patient and therefore eventually producing quite different qualitative and quantitative descriptions of viral populations within each host.

  19. Effect of oligonucleotide primers in determining viral variability within hosts.

    Science.gov (United States)

    Bracho, Maria Alma; García-Robles, Inmaculada; Jiménez, Nuria; Torres-Puente, Manuela; Moya, Andrés; González-Candelas, Fernando

    2004-12-09

    Genetic variability in viral populations is usually estimated by means of polymerase chain reaction (PCR) based methods in which the relative abundance of each amplicon is assumed to be proportional to the frequency of the corresponding template in the initial sample. Although bias in template-to-product ratios has been described before, its relevance in describing viral genetic variability at the intrapatient level has not been fully assessed yet. To investigate the role of oligonucleotide design in estimating viral variability within hosts, genetic diversity in hepatitis C virus (HCV) populations from eight infected patients was characterised by two parallel PCR amplifications performed with two slightly different sets of primers, followed by cloning and sequencing (mean = 89 cloned sequences per patient). Population genetics analyses of viral populations recovered by pairs of amplifications revealed that in seven patients statistically significant differences were detected between populations sampled with different set of primers. Genetic variability analyses demonstrates that PCR selection due to the choice of primers, differing in their degeneracy degree at some nucleotide positions, can eclipse totally or partially viral variants, hence yielding significant different estimates of viral variability within a single patient and therefore eventually producing quite different qualitative and quantitative descriptions of viral populations within each host.

  20. DNA unwinding assay using streptavidin-bound oligonucleotides

    Directory of Open Access Journals (Sweden)

    Kelman Zvi

    2006-11-01

    Full Text Available Abstract Background Helicases play essential roles in many cellular processes including replication, transcription and translation. Most helicases translocate along one strand of the duplex while displacing the complementary strand (of either DNA or RNA. Thus, helicases have directionality. They move along nucleic acids in either the 3'→ 5' or 5'→ 3' direction. The directionality of helicases with low activity or of those that cannot initiate duplex unwinding from a substrate that contains only one single-stranded overhang region is difficult to determine. Results An improved assay to determine helicase directionality was developed that uses a substrate containing biotinylated oligonucleotides. As a proof of concept, it was shown that the substrates substantially improve helicase activity and directionality determination for several DNA helicases in comparison to more traditional substrates. In addition, a universal substrate that can be used to determine the directionality of both 3'→ 5' and 5'→ 3' helicases was developed. Conclusion It is shown here that the use of a biotin-streptavidin complex as a helicase substrate improves helicase activity and the determination of helicase directionality. The method described is simpler that the currently available techniques.

  1. EvoOligo: oligonucleotide probe design with multiobjective evolutionary algorithms.

    Science.gov (United States)

    Shin, Soo-Yong; Lee, In-Hee; Cho, Young-Min; Yang, Kyung-Ae; Zhang, Byoung-Tak

    2009-12-01

    Probe design is one of the most important tasks in successful deoxyribonucleic acid microarray experiments. We propose a multiobjective evolutionary optimization method for oligonucleotide probe design based on the multiobjective nature of the probe design problem. The proposed multiobjective evolutionary approach has several distinguished features, compared with previous methods. First, the evolutionary approach can find better probe sets than existing simple filtering methods with fixed threshold values. Second, the multiobjective approach can easily incorporate the user's custom criteria or change the existing criteria. Third, our approach tries to optimize the combination of probes for the given set of genes, in contrast to other tools that independently search each gene for qualifying probes. Lastly, the multiobjective optimization method provides various sets of probe combinations, among which the user can choose, depending on the target application. The proposed method is implemented as a platform called EvoOligo and is available for service on the web. We test the performance of EvoOligo by designing probe sets for 19 types of Human Papillomavirus and 52 genes in the Arabidopsis Calmodulin multigene family. The design results from EvoOligo are proven to be superior to those from well-known existing probe design tools, such as OligoArray and OligoWiz.

  2. Characterization of adjacent breast tumors using oligonucleotide microarrays

    International Nuclear Information System (INIS)

    Unger, Meredith A; Rishi, Mazhar; Clemmer, Virginia B; Hartman, Jennifer L; Keiper, Elizabeth A; Greshock, Joel D; Chodosh, Lewis A; Liebman, Michael N; Weber, Barbara L

    2001-01-01

    Current methodology often cannot distinguish second primary breast cancers from multifocal disease, a potentially important distinction for clinical management. In the present study we evaluated the use of oligonucleotide-based microarray analysis in determining the clonality of tumors by comparing gene expression profiles. Total RNA was extracted from two tumors with no apparent physical connection that were located in the right breast of an 87-year-old woman diagnosed with invasive ductal carcinoma (IDC). The RNA was hybridized to the Affymetrix Human Genome U95A Gene Chip ® (12,500 known human genes) and analyzed using the Gene Chip Analysis Suite ® 3.3 (Affymetrix, Inc, Santa Clara, CA, USA) and JMPIN ® 3.2.6 (SAS Institute, Inc, Cary, NC, USA). Gene expression profiles of tumors from five additional patients were compared in order to evaluate the heterogeneity in gene expression between tumors with similar clinical characteristics. The adjacent breast tumors had a pairwise correlation coefficient of 0.987, and were essentially indistinguishable by microarray analysis. Analysis of gene expression profiles from different individuals, however, generated a pairwise correlation coefficient of 0.710. Transcriptional profiling may be a useful diagnostic tool for determining tumor clonality and heterogeneity, and may ultimately impact on therapeutic decision making

  3. Clinical approaches in the treatment of Duchenne muscular dystrophy (DMD) using oligonucleotides.

    Science.gov (United States)

    Bertoni, Carmen

    2008-01-01

    Duchenne Muscular dystrophy (DMD) is one of the most severe forms of hereditary diseases in muscles. The identification and characterization of dystrophin, the gene responsible for the disease has lead to the development of potential gene therapy treatments for this disorder. The complex structure and size of the dystrophin gene represent a challenge for some gene therapy approaches such as gene replacement mediated by viral vectors. Others, including oligonucleotide-mediated gene therapies have allowed forms of manipulation in the dystrophin gene not possible with other disorders. The use of oligonucleotides to modulate gene expression has shown to be a feasible alternative treatment to DMD. Antisense-mediated technologies have made outstanding progress in the last decade and two phase I clinical trials for exon skipping in DMD are already in progress. Gene correction mediated by oligonucleotides faces much greater obstacles, but the outcome of the approach, permanent correction of the gene defect, represents an ideal treatment to the disease. Gene therapy mediated by antisense oligonucleotides or oligonucleotide mediated gene editing have the potential to have a primary role in gene therapy applications to muscles, but they are still far from representing an effective cure. Factors like safety and sustained beneficial effects in patients will have to be considered in detail before this technology can become applicable to the treatment of muscles disorders. Ultimately the need for production of oligonucleotides in large scale and the cost of treatment for each individual patient will play a big role in the feasibility of these approaches in DMD.

  4. Application of oligonucleotide array technology for the rapid detection of pathogenic bacteria of foodborne infections.

    Science.gov (United States)

    Hong, Bang-Xing; Jiang, Li-Fang; Hu, Yu-Shan; Fang, Dan-Yun; Guo, Hui-Yu

    2004-09-01

    A rapid and accurate method for detection for common pathogenic bacteria in foodborne infections was established by using oligonucleotide array technology. Nylon membrane was used as the array support. A mutation region of the 23S rRNA gene was selected as the discrimination target from 14 species (genera) of bacteria causing foodborne infections and two unrelated bacterial species. A pair of universal primers was designed for PCR amplification of the 23S rRNA gene. Twenty-one species (genera)-specific oligonucleotide detection probes were synthesized and spotted onto the nylon membranes. The 23S rRNA gene amplification products of 14 species of pathogenic bacteria were hybridized to the oligonucleotide array. Hybridization results were analyzed with digoxigenin-linked enzyme reaction. Results indicated that nine species of pathogenic bacteria (Escherichia coli, Campylobacter jejuni, Shigella dysenteriae, Vibrio cholerae, Vibrio parahaemolyticus, Proteus vulgaris, Bacillus cereus, Listeria monocytogenes and Clostridium botulinum) showed high sensitivity and specificity for the oligonucleotide array. Two other species (Salmonella enterica and Yersinia enterocolitica) gave weak cross-reaction with E. coli, but the reaction did not affect their detection. After redesigning the probes, positive hybridization results were obtained with Staphylococcus aureus, but not with Clostridium perfringens and Streptococcus pyogenes. The oligonucleotide array can also be applied to samples collected in clinical settings of foodborne infections. The superiority of oligonucleotide array over other tests lies on its rapidity, accuracy and efficiency in the diagnosis, treatment and control of foodborne infections.

  5. Small-Boat Noise Impacts Natural Settlement Behavior of Coral Reef Fish Larvae.

    Science.gov (United States)

    Simpson, Stephen D; Radford, Andrew N; Holles, Sophie; Ferarri, Maud C O; Chivers, Douglas P; McCormick, Mark I; Meekan, Mark G

    2016-01-01

    After a pelagic larval phase, settlement-stage coral reef fish must locate a suitable reef habitat for juvenile life. Reef noise, produced by resident fish and invertebrates, provides an important cue for orientation and habitat selection during this process, which must often occur in environments impacted by anthropogenic noise. We adapted an established field-based protocol to test whether recorded boat noise influenced the settlement behavior of reef fish. Fewer fish settled to patch reefs broadcasting boat + reef noise compared with reef noise alone. This study suggests that boat noise, now a common feature of many reefs, can compromise critical settlement behavior of reef fishes.

  6. Discriminating small extended targets at sea from clutter and other classes of boats in infrared and visual light imagery

    NARCIS (Netherlands)

    Broek, S.P. van den; Bouma, H.; Degache, M.A.C.

    2008-01-01

    Operating in a coastal environment, with a multitude of boats of different sizes, detection of small extended targets is only one problem. A further difficulty is in discriminating detections of possible threats from alarms due to sea and coastal clutter, and from boats that are neutral for a

  7. 77 FR 73432 - Proposed Information Collection; Comment Request; Survey of Shore-Based and Boat-Based Non...

    Science.gov (United States)

    2012-12-10

    ..., 14th and Constitution Avenue NW., Washington, DC 20230 (or via the Internet at [email protected] ). FOR... them to balance the need for more effective fishery management with social, economic and cultural... collection activities: (1) A survey of fishers at boat ramps and, (2) a count of boat trailers or vehicles at...

  8. Real-World Emission Factors of Gaseous and Particulate Pollutants from Marine Fishing Boats and Their Total Emissions in China.

    Science.gov (United States)

    Zhang, Fan; Chen, Yingjun; Chen, Qi; Feng, Yanli; Shang, Yu; Yang, Xin; Gao, Huiwang; Tian, Chongguo; Li, Jun; Zhang, Gan; Matthias, Volker; Xie, Zhiyong

    2018-04-17

    Pollutants from fishing boats have generally been neglected worldwide, and there is an acute shortage of measured emission data, especially in China. Therefore, on-board measurements of pollutants emitted from 12 different fishing boats in China (including gill net, angling, and trawler boats) were carried out in this study to investigate emission factors (EFs), characteristics and total emissions. The average EFs for CO 2 , CO, NO x , PM, and SO 2 were 3074 ± 55.9, 50.6 ± 31.7, 54.2 ± 30.7, 9.54 ± 2.24, and 5.94 ± 6.38 g (kg fuel) -1 , respectively, which were higher than those from previous studies of fishing boats. When compared to medium-speed and slow-speed engine vessels, high-speed engines on fishing boats had higher CO EFs but lower NO x EFs. Notably, when fishing boats were in low-load conditions, they always had higher EFs of CO, PM, and NO 2 compared to other operating modes. The estimated results showed that emissions from motor-powered fishing boats in China in 2012 (232, 379, and 61.8 kt CO, NO x and PM) accounted for 10.7%, 10.9%, and 19.3% of the total CO, NO x and PM emitted from nonroad mobile sources, which means significant contribution of fishing boats to air pollution, especially in southern China areas.

  9. 33 CFR 149.303 - What survival craft and rescue boats may be used on a manned deepwater port?

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false What survival craft and rescue boats may be used on a manned deepwater port? 149.303 Section 149.303 Navigation and Navigable Waters... craft and rescue boats may be used on a manned deepwater port? (a) Each survival craft on a manned...

  10. 77 FR 15006 - Special Local Regulations; Third Annual Space Coast Super Boat Grand Prix, Atlantic Ocean, Cocoa...

    Science.gov (United States)

    2012-03-14

    ...-AA08 Special Local Regulations; Third Annual Space Coast Super Boat Grand Prix, Atlantic Ocean, Cocoa... proposes to establish special local regulations on the waters of the Atlantic Ocean east of Cocoa Beach... waters of the Atlantic Ocean east of Cocoa Beach, Florida. Approximately 30 high- speed power boats are...

  11. 76 FR 26931 - Safety Zone; Second Annual Space Coast Super Boat Grand Prix, Atlantic Ocean, Cocoa Beach, FL

    Science.gov (United States)

    2011-05-10

    ...-AA00 Safety Zone; Second Annual Space Coast Super Boat Grand Prix, Atlantic Ocean, Cocoa Beach, FL... temporary safety zone on the waters of the Atlantic Ocean east of Cocoa Beach, Florida during the Second... Atlantic Ocean east of Cocoa Beach, Florida. Approximately 30 high-speed power boats will be participating...

  12. 76 FR 77125 - Safety Zone; Sausalito Yacht Club's Annual Lighted Boat Parade and Fireworks Display, Sausalito, CA

    Science.gov (United States)

    2011-12-12

    ... procedures; and related management systems practices) that are developed or adopted by voluntary consensus...-AA00 Safety Zone; Sausalito Yacht Club's Annual Lighted Boat Parade and Fireworks Display, Sausalito... of the Sausalito Yacht Club's Annual Lighted Boat Parade and Fireworks Display. This temporary safety...

  13. 19 CFR 10.36a - Vehicles, pleasure boats and aircraft brought in for repair or alteration.

    Science.gov (United States)

    2010-04-01

    ... aircraft brought in for repair or alteration. (a) A vehicle (such as an automobile, truck, bus, motorcycle... vehicle, pleasure boat, or aircraft for repair or alteration (as defined in §§ 10.8, 10.490, 10.570, and... 19 Customs Duties 1 2010-04-01 2010-04-01 false Vehicles, pleasure boats and aircraft brought in...

  14. Integrated synoptic surveys of the hydrodynamics and water-quality distributions in two Lake Michigan rivermouth mixing zones using an autonomous underwater vehicle and a manned boat

    Science.gov (United States)

    Jackson, P. Ryan; Reneau, Paul C.

    2014-01-01

    The U.S. Geological Survey (USGS), in cooperation with the National Monitoring Network for U.S. Coastal Waters and Tributaries, launched a pilot project in 2010 to determine the value of integrated synoptic surveys of rivermouths using autonomous underwater vehicle technology in response to a call for rivermouth research, which includes study domains that envelop both the fluvial and lacustrine boundaries of the rivermouth mixing zone. The pilot project was implemented at two Lake Michigan rivermouths with largely different scales, hydrodynamics, and settings, but employing primarily the same survey techniques and methods. The Milwaukee River Estuary Area of Concern (AOC) survey included measurements in the lower 2 to 3 miles of the Milwaukee, Menomonee, and Kinnickinnic Rivers and inner and outer Milwaukee Harbor. This estuary is situated in downtown Milwaukee, Wisconsin, and is the most populated basin that flows directly into Lake Michigan. In contrast, the Manitowoc rivermouth has a relatively small harbor separating the rivermouth from Lake Michigan, and the Manitowoc River Watershed is primarily agricultural. Both the Milwaukee and Manitowoc rivermouths are unregulated and allow free exchange of water with Lake Michigan. This pilot study of the Milwaukee River Estuary and Manitowoc rivermouth using an autonomous underwater vehicle (AUV) paired with a manned survey boat resulted in high spatial and temporal resolution datasets of basic water-quality parameter distributions and hydrodynamics. The AUV performed well in these environments and was found primarily well-suited for harbor and nearshore surveys of three-dimensional water-quality distributions. Both case studies revealed that the use of a manned boat equipped with an acoustic Doppler current profiler (ADCP) and multiparameter sonde (and an optional flow-through water-quality sampling system) was the best option for riverine surveys. To ensure that the most accurate and highest resolution velocity data

  15. Mongersen, an oral SMAD7 antisense oligonucleotide, and Crohn's disease.

    Science.gov (United States)

    Monteleone, Giovanni; Neurath, Markus F; Ardizzone, Sandro; Di Sabatino, Antonio; Fantini, Massimo C; Castiglione, Fabiana; Scribano, Maria L; Armuzzi, Alessandro; Caprioli, Flavio; Sturniolo, Giacomo C; Rogai, Francesca; Vecchi, Maurizio; Atreya, Raja; Bossa, Fabrizio; Onali, Sara; Fichera, Maria; Corazza, Gino R; Biancone, Livia; Savarino, Vincenzo; Pica, Roberta; Orlando, Ambrogio; Pallone, Francesco

    2015-03-19

    Crohn's disease-related inflammation is characterized by reduced activity of the immunosuppressive cytokine transforming growth factor β1 (TGF-β1) due to high levels of SMAD7, an inhibitor of TGF-β1 signaling. Preclinical studies and a phase 1 study have shown that an oral SMAD7 antisense oligonucleotide, mongersen, targets ileal and colonic SMAD7. In a double-blind, placebo-controlled, phase 2 trial, we evaluated the efficacy of mongersen for the treatment of persons with active Crohn's disease. Patients were randomly assigned to receive 10, 40, or 160 mg of mongersen or placebo per day for 2 weeks. The primary outcomes were clinical remission at day 15, defined as a Crohn's Disease Activity Index (CDAI) score of less than 150, with maintenance of remission for at least 2 weeks, and the safety of mongersen treatment. A secondary outcome was clinical response (defined as a reduction of 100 points or more in the CDAI score) at day 28. The proportions of patients who reached the primary end point were 55% and 65% for the 40-mg and 160-mg mongersen groups, respectively, as compared with 10% for the placebo group (P<0.001). There was no significant difference in the percentage of participants reaching clinical remission between the 10-mg group (12%) and the placebo group. The rate of clinical response was significantly greater among patients receiving 10 mg (37%), 40 mg (58%), or 160 mg (72%) of mongersen than among those receiving placebo (17%) (P=0.04, P<0.001, and P<0.001, respectively). Most adverse events were related to complications and symptoms of Crohn's disease. We found that study participants with Crohn's disease who received mongersen had significantly higher rates of remission and clinical response than those who received placebo. (Funded by Giuliani; EudraCT number, 2011-002640-27.).

  16. A dystrophic Duchenne mouse model for testing human antisense oligonucleotides.

    Directory of Open Access Journals (Sweden)

    Marcel Veltrop

    Full Text Available Duchenne muscular dystrophy (DMD is a severe muscle-wasting disease generally caused by reading frame disrupting mutations in the DMD gene resulting in loss of functional dystrophin protein. The reading frame can be restored by antisense oligonucleotide (AON-mediated exon skipping, allowing production of internally deleted, but partially functional dystrophin proteins as found in the less severe Becker muscular dystrophy. Due to genetic variation between species, mouse models with mutations in the murine genes are of limited use to test and further optimize human specific AONs in vivo. To address this we have generated the del52hDMD/mdx mouse. This model carries both murine and human DMD genes. However, mouse dystrophin expression is abolished due to a stop mutation in exon 23, while the expression of human dystrophin is abolished due to a deletion of exon 52. The del52hDMD/mdx model, like mdx, shows signs of muscle dystrophy on a histological level and phenotypically mild functional impairment. Local administration of human specific vivo morpholinos induces exon skipping and dystrophin restoration in these mice. Depending on the number of mismatches, occasional skipping of the murine Dmd gene, albeit at low levels, could be observed. Unlike previous models, the del52hDMD/mdx model enables the in vivo analysis of human specific AONs targeting exon 51 or exon 53 on RNA and protein level and muscle quality and function. Therefore, it will be a valuable tool for optimizing human specific AONs and genome editing approaches for DMD.

  17. Profiled support vector machines for antisense oligonucleotide efficacy prediction

    Directory of Open Access Journals (Sweden)

    Martín-Guerrero José D

    2004-09-01

    Full Text Available Abstract Background This paper presents the use of Support Vector Machines (SVMs for prediction and analysis of antisense oligonucleotide (AO efficacy. The collected database comprises 315 AO molecules including 68 features each, inducing a problem well-suited to SVMs. The task of feature selection is crucial given the presence of noisy or redundant features, and the well-known problem of the curse of dimensionality. We propose a two-stage strategy to develop an optimal model: (1 feature selection using correlation analysis, mutual information, and SVM-based recursive feature elimination (SVM-RFE, and (2 AO prediction using standard and profiled SVM formulations. A profiled SVM gives different weights to different parts of the training data to focus the training on the most important regions. Results In the first stage, the SVM-RFE technique was most efficient and robust in the presence of low number of samples and high input space dimension. This method yielded an optimal subset of 14 representative features, which were all related to energy and sequence motifs. The second stage evaluated the performance of the predictors (overall correlation coefficient between observed and predicted efficacy, r; mean error, ME; and root-mean-square-error, RMSE using 8-fold and minus-one-RNA cross-validation methods. The profiled SVM produced the best results (r = 0.44, ME = 0.022, and RMSE= 0.278 and predicted high (>75% inhibition of gene expression and low efficacy (http://aosvm.cgb.ki.se/. Conclusions The SVM approach is well suited to the AO prediction problem, and yields a prediction accuracy superior to previous methods. The profiled SVM was found to perform better than the standard SVM, suggesting that it could lead to improvements in other prediction problems as well.

  18. National Park Service Primer on the construction of Ferry Boats and Ferry Terminal Facilities Program (FBP)

    Science.gov (United States)

    2014-12-01

    Many National Park Service units are located in areas which are served by vehicle or passenger ferry. These National Park : Service units and their partners may be eligible to use funding from the FHWA Construction of Ferry Boats and Ferry : Terminal...

  19. A ship/boat is travelling parallel to a river bank and a patrol vehicle ...

    Indian Academy of Sciences (India)

    A ship/boat is travelling parallel to a river bank and a patrol vehicle is approaching the river along a road perpendicular to the river bank, i.e., the ship and the vehicle are moving at right angles to each other with uniform speeds. The patrol vehicle focuses a search light on the ship at all time instants, implying continuous ...

  20. 33 CFR 100.109 - Winter Harbor Lobster Boat Race, Winter Harbor, ME.

    Science.gov (United States)

    2010-07-01

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

  1. An assessment of participation, catch and effort in the offshore boat ...

    African Journals Online (AJOL)

    It is recommended that stock assessments of the priority species should be conducted in the near future and steps should be taken to encourage rebuilding of overexploited species. This must include urgent regulation of the burgeoning charter boat-fishery as well as increased attempts to establish more marine protected ...

  2. 75 FR 43823 - Safety Zone; He'eia Kea Small Boat Harbor, Kaneohe Bay, Oahu, HI

    Science.gov (United States)

    2010-07-27

    ... DEPARTMENT OF HOMELAND SECURITY Coast Guard 33 CFR Part 165 [Docket No. USCG-2010-0458] RIN 1625-AA00 Safety Zone; He'eia Kea Small Boat Harbor, Kaneohe Bay, Oahu, HI AGENCY: Coast Guard, DHS. ACTION: Temporary Final Rule. SUMMARY: The Coast Guard is establishing a temporary safety zone in He'eia Kea Small...

  3. 78 FR 35092 - Requested Administrative Waiver of the Coastwise Trade Laws: Vessel BEAR BOAT; Invitation for...

    Science.gov (United States)

    2013-06-11

    ... DEPARTMENT OF TRANSPORTATION Maritime Administration [Docket No. MARAD-2013-0069] Requested Administrative Waiver of the Coastwise Trade Laws: Vessel BEAR BOAT; Invitation for Public Comments AGENCY....gov . SUPPLEMENTARY INFORMATION: As described by the applicant the intended service of the vessel BEAR...

  4. The Feasibility of Boat Lift Net in the Archipelagic Fishing Port of Karangantu Banten Province

    Directory of Open Access Journals (Sweden)

    Epry Rahmawati

    2017-11-01

    Full Text Available This research was conducted in the Archipelagic Fishing Port of Karangantu Banten Province. It aimed to analyze the feasibility of a boat lift net based on Archipelagic Fishing Port of Karangantu. The research was conducted in November 2015 to January 2016. The method used in this study is a survey method. Operation boat lift net in Archipelagic Fishing Port of Karangantu have done by two days fishing (two nights three days. Based on the results of analysis feasibility (BCR, BEP, and PP business boat lift net worth the effort throughout the year (peak season, regular season, and off season. However, from the profits analysis, the revenue during the bad season is lower than the cost incurred. The results of a financial analysis on the operation of the boat lift net in two seasons are BCR 1.38 (before fuel down and 1.41 (after fuel down, BEP Rp. 198,846,000 (before fuel down and Rp. 188,090,000 (after fuel down, and PP 1.48 years or 18 months (before fuel down and 1.38 years or 16 months (before fuel down, payback included in the category of fast because the value of PP < 3 years.

  5. 77 FR 18689 - Changes to Standard Numbering System, Vessel Identification System, and Boating Accident Report...

    Science.gov (United States)

    2012-03-28

    .... Indian Tribal Governments K. Energy Effects L. Technical Standards M. Environment I. Abbreviations BARD... function. State government officials with recreational boating responsibilities submitted most of the...' ability to analyze historical data or that risk data corruption during database updates. One of these...

  6. 46 CFR 116.1120 - Drainage of cockpit vessels, well deck vessels, and open boats.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 4 2010-10-01 2010-10-01 false Drainage of cockpit vessels, well deck vessels, and open... PASSENGERS CONSTRUCTION AND ARRANGEMENT Drainage and Watertight Integrity of Weather Decks § 116.1120 Drainage of cockpit vessels, well deck vessels, and open boats. Drainage of cockpit vessels, well deck...

  7. 78 FR 24065 - Special Local Regulation; Tuscaloosa Dragon Boat Races; Black Warrior River; Tuscaloosa, AL

    Science.gov (United States)

    2013-04-24

    ... by the Captain of the Port (COTP) Mobile or a designated representative. DATES: This rule is... rule, call or email LT Lenell J. Carson, Sector Mobile, Waterways Division, U.S. Coast Guard; telephone... Boat Races. This event is advertised as scheduled and participants, sponsors and spectators have...

  8. 3 CFR 8381 - Proclamation 8381 of May 15, 2009. National Safe Boating Week, 2009

    Science.gov (United States)

    2010-01-01

    ..., enjoy quiet solitude, or relax with family and friends. Unfortunately, accidents can occur as Americans... should also wear a Coast Guard-approved life jacket and never boat under the influence of drugs or alcohol. These critical precautions can save lives and help ensure a fulfilling experience. Each year...

  9. 'We get nothing from fishing' : Fishing for boat opportunities amongst Senegalese fisher migrants

    NARCIS (Netherlands)

    Nyamnjoh, Henrietta Mambo

    2010-01-01

    The world is regularly confronted in the media with dramatic images of African boat migrants. Seemingly desperate, these Africans, most of them males, are willing to risk a perilous journey at sea, hoping for a better life in Europe. And, even worse, hundreds more are believed to die each year,

  10. 75 FR 17754 - Certificate of Alternative Compliance for the Lift Boat GARY CHIASSON ELEVATOR

    Science.gov (United States)

    2010-04-07

    ... masthead light to be offset from the centerline 6' to port. Placing the masthead light on the centerline as... light obstructed by the forward leg of the lift boat. In addition the sidelights may be located on the outermost edges of the top of the pilothouse. Due to the pilothouse being offset to port, the sidelights...

  11. 78 FR 18617 - Recreational Boating Safety Projects, Programs and Activities Funded Under Provisions of the...

    Science.gov (United States)

    2013-03-27

    .... Specific Accounting of Funds Factory Visit Program/Boat Testing Program: Funding was provided to continue... Safety Projects, Programs and Activities Funded Under Provisions of the Transportation Equity Act for the 21st Century; Accounting of ACTION: Notice. SUMMARY: In 1999, the Transportation Equity Act for the...

  12. 77 FR 43513 - Olympia Harbor Days Tug Boat Races, Budd Inlet, WA

    Science.gov (United States)

    2012-07-25

    ... Harbor Days Tug Boat Races, Budd Inlet, WA AGENCY: Coast Guard, DHS. ACTION: Notice of enforcement of... Races, Budd Inlet, WA from 12 p.m. through 8 p.m. on September 2, 2012. This action is necessary to restrict vessel movement within the specified race area immediately prior to, during, and immediately after...

  13. 78 FR 75899 - Safety Zone; 2013 Holiday Boat Parades, Captain of the Port Miami Zone; FL

    Science.gov (United States)

    2013-12-13

    .... The moving zone will include a buffer zone extending 50 yards ahead of the lead parade vessel, 50... include a buffer zone extending to 50 yards ahead of the lead vessel, 50 yards astern of the last... 1625-AA00 Safety Zone; 2013 Holiday Boat Parades, Captain of the Port Miami Zone; FL AGENCY: Coast...

  14. 75 FR 22150 - Certificate of Alternative Compliance for the Ferry Boat CHARLEVOIX

    Science.gov (United States)

    2010-04-27

    ... permanent hearing loss. The Commandant, U.S. Coast Guard, certifies that full compliance with the Inland... Occupational Safety and Health states that exposure to sounds over 85 decibels for periods greater than eight hours will cause permanent hearing damage. The crew on the ferry boat CHARLEVOIX works eight hour shifts...

  15. Stone sculptures of goddesses on the boats from Goa, west coast of India

    Digital Repository Service at National Institute of Oceanography (India)

    Gaur, A; Kerkar, R.

    goddess panels. A few sculptures reflect influence of folk art traditions in Goa. On the basis of lion figures in a few sculptured panels indicate that these boat motifs must have been engraved during the Kadamba period (10 th - 13 th) when Goa witnessed...

  16. Environmental Assessment for Construction of a 20-Slip Boat Dock Structure MacDill AFB, Florida

    Science.gov (United States)

    2008-01-01

    polychaete worms, pink shrimp, blue crab (Callinectes sapidus), seahorses ( Hippocampus spp.), snapper, mullet (Mugilidae spp.), and bonefish (FNAI and... sinking ordamage from high winds, this plan fails to predict how the dock would handle this many l~ge boats in high winds or surge. This is an open

  17. 33 CFR 149.304 - What type and how many survival craft and rescue boats must a manned deepwater port have?

    Science.gov (United States)

    2010-07-01

    ... craft and rescue boats must a manned deepwater port have? 149.304 Section 149.304 Navigation and... What type and how many survival craft and rescue boats must a manned deepwater port have? (a) Except as... of survival craft and the number of rescue boats indicated for the deepwater port in paragraphs (a)(1...

  18. Combined in vitro transcription and reverse transcription to amplify and label complex synthetic oligonucleotide probe libraries

    Science.gov (United States)

    Murgha, Yusuf; Beliveau, Brian; Semrau, Kassandra; Schwartz, Donald; Wu, Chao-ting; Gulari, Erdogan; Rouillard, Jean-Marie

    2016-01-01

    Oligonucleotide microarrays allow the production of complex custom oligonucleotide libraries for nucleic acid detection–based applications such as fluorescence in situ hybridization (FISH). We have developed a PCR-free method to make single-stranded DNA (ssDNA) fluorescent probes through an intermediate RNA library. A double-stranded oligonucleotide library is amplified by transcription to create an RNA library. Next, dye- or hapten-conjugate primers are used to reverse transcribe the RNA to produce a dye-labeled cDNA library. Finally the RNA is hydrolyzed under alkaline conditions to obtain the single-stranded fluorescent probes library. Starting from unique oligonucleotide library constructs, we present two methods to produce single-stranded probe libraries. The two methods differ in the type of reverse transcription (RT) primer, the incorporation of fluorescent dye, and the purification of fluorescent probes. The first method employs dye-labeled reverse transcription primers to produce multiple differentially single-labeled probe subsets from one microarray library. The fluorescent probes are purified from excess primers by oligonucleotide-bead capture. The second method uses an RNA:DNA chimeric primer and amino-modified nucleotides to produce amino-allyl probes. The excess primers and RNA are hydrolyzed under alkaline conditions, followed by probe purification and labeling with amino-reactive dyes. The fluorescent probes created by the combination of transcription and reverse transcription can be used for FISH and to detect any RNA and DNA targets via hybridization. PMID:26054766

  19. Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L.) gene expression oligonucleotide microarray.

    Science.gov (United States)

    Fernandez, Paula; Soria, Marcelo; Blesa, David; DiRienzo, Julio; Moschen, Sebastian; Rivarola, Maximo; Clavijo, Bernardo Jose; Gonzalez, Sergio; Peluffo, Lucila; Príncipi, Dario; Dosio, Guillermo; Aguirrezabal, Luis; García-García, Francisco; Conesa, Ana; Hopp, Esteban; Dopazo, Joaquín; Heinz, Ruth Amelia; Paniego, Norma

    2012-01-01

    Oligonucleotide-based microarrays with accurate gene coverage represent a key strategy for transcriptional studies in orphan species such as sunflower, H. annuus L., which lacks full genome sequences. The goal of this study was the development and functional annotation of a comprehensive sunflower unigene collection and the design and validation of a custom sunflower oligonucleotide-based microarray. A large scale EST (>130,000 ESTs) curation, assembly and sequence annotation was performed using Blast2GO (www.blast2go.de). The EST assembly comprises 41,013 putative transcripts (12,924 contigs and 28,089 singletons). The resulting Sunflower Unigen Resource (SUR version 1.0) was used to design an oligonucleotide-based Agilent microarray for cultivated sunflower. This microarray includes a total of 42,326 features: 1,417 Agilent controls, 74 control probes for sunflower replicated 10 times (740 controls) and 40,169 different non-control probes. Microarray performance was validated using a model experiment examining the induction of senescence by water deficit. Pre-processing and differential expression analysis of Agilent microarrays was performed using the Bioconductor limma package. The analyses based on p-values calculated by eBayes (psunflower unigene collection, and a custom, validated sunflower oligonucleotide-based microarray using Agilent technology. Both the curated unigene collection and the validated oligonucleotide microarray provide key resources for sunflower genome analysis, transcriptional studies, and molecular breeding for crop improvement.

  20. Combined in vitro transcription and reverse transcription to amplify and label complex synthetic oligonucleotide probe libraries.

    Science.gov (United States)

    Murgha, Yusuf; Beliveau, Brian; Semrau, Kassandra; Schwartz, Donald; Wu, Chao-Ting; Gulari, Erdogan; Rouillard, Jean-Marie

    2015-06-01

    Oligonucleotide microarrays allow the production of complex custom oligonucleotide libraries for nucleic acid detection-based applications such as fluorescence in situ hybridization (FISH). We have developed a PCR-free method to make single-stranded DNA (ssDNA) fluorescent probes through an intermediate RNA library. A double-stranded oligonucleotide library is amplified by transcription to create an RNA library. Next, dye- or hapten-conjugate primers are used to reverse transcribe the RNA to produce a dye-labeled cDNA library. Finally the RNA is hydrolyzed under alkaline conditions to obtain the single-stranded fluorescent probes library. Starting from unique oligonucleotide library constructs, we present two methods to produce single-stranded probe libraries. The two methods differ in the type of reverse transcription (RT) primer, the incorporation of fluorescent dye, and the purification of fluorescent probes. The first method employs dye-labeled reverse transcription primers to produce multiple differentially single-labeled probe subsets from one microarray library. The fluorescent probes are purified from excess primers by oligonucleotide-bead capture. The second method uses an RNA:DNA chimeric primer and amino-modified nucleotides to produce amino-allyl probes. The excess primers and RNA are hydrolyzed under alkaline conditions, followed by probe purification and labeling with amino-reactive dyes. The fluorescent probes created by the combination of transcription and reverse transcription can be used for FISH and to detect any RNA and DNA targets via hybridization.

  1. Simultaneous Detection of Escherichia coli, Salmonella enterica, Listeria monocytegenes and Bacillus cereus by Oligonucleotide Microarray

    Directory of Open Access Journals (Sweden)

    Meysam Sarshar

    2015-11-01

    Full Text Available Background: Traditional laboratory methods to detect pathogenic bacteria are time consuming and laborious. Therefore, it is essential to use powerful and reliable molecular methods for quick and simultaneous detection of microbial pathogens. Objectives: The current study aimed to evaluate the capability and efficiency of 23S rDNA sequence for rapid and simultaneous detection of four important food-borne pathogens by an oligonucleotide microarray technique. Materials and Methods: The 23S rDNA sequences of Escherichia coli, Salmonella enterica, Listeria monocytogenes and Bacillus cereus were obtained from GenBank databases and used to design the oligonucleotide probes and primers by Vector NTI software. Oligonucleotide probes were placed on a nylon membrane and hybridization was performed between probes and 23S rDNA digoxigenin-labeled polymerase chain reaction (PCR products. Hybridization signals were visualized by NBT/BCIP color development. Results: Positive hybridization color was produced for Escherichia coli, Salmonella enterica, Listeria monocytogenes and Bacillus cereus. The oligonucleotide microarray detected all bacterial strains in a single reaction in less than five hours. The sensitivity of the performed microarray assay was 103 cfu/mL for each species of pathogen. No cross reaction was found between the tested bacterial species. Conclusions: The obtained results indicated that amplification of 23S rDNA gene followed by oligonucleotide microarray hybridization is a rapid and reliable method to identify and discriminate foodborne pathogens tested under the study.

  2. Design of Fishing Boat for Pelabuhanratu Fishermen as One of Effort to Increase Production of Capture Fisheries

    Science.gov (United States)

    Nur, Iswadi; Joko Suranto, Purwo

    2018-02-01

    Design of fishing boat for Pelabuhanratu fisherman as one of effort to increase production of capture fisheries. The fishing boat should be proper for the characteristic of its service area, as; capacity of fishing boat up to 60 GT, the fishing boat has minimum 6 fish holds and location of fish hold in the middle body, the fishing boat hull has the bilge keel plate, and the material of hull fishing boat to be made of wooden, steel, aluminium, or fiberglass. Main dimesion of fishing boat is Length Over All = 25.436 m, Breadth = 4.55 m, Draft = 1.6 m, Speed = 12.5 knots. The research had been known every thing that will be supporting the production of capture fisheries like ; amount of fish production = 25.030 ton per day, the fishing port capacity approximately 268.957GT per day, the area of fishing port data research result less than standard of Oceanic Fising Port. So Pelabuhanratu National Fishing Port can not be changed to Oceanic Fishing Port.

  3. Evaluation of ADCP apparent bed load velocity in a large sand-bed river: Moving versus stationary boat conditions

    Science.gov (United States)

    Jamieson, E.C.; Rennie, C.D.; Jacobson, R.B.; Townsend, R.D.

    2011-01-01

    Detailed mapping of bathymetry and apparent bed load velocity using a boat-mounted acoustic Doppler current profiler (ADCP) was carried out along a 388-m section of the lower Missouri River near Columbia, Missouri. Sampling transects (moving boat) were completed at 5- and 20-m spacing along the study section. Stationary (fixed-boat) measurements were made by maintaining constant boat position over a target point where the position of the boat did not deviate more than 3 m in any direction. For each transect and stationary measurement, apparent bed load velocity (vb) was estimated using ADCP bottom tracking data and high precision real-time kinematic (RTK) global positioning system (GPS). The principal objectives of this research are to (1) determine whether boat motion introduces a bias in apparent bed load velocity measurements; and (2) evaluate the reliability of ADCP bed velocity measurements for a range of sediment transport environments. Results indicate that both high transport (vb>0.6 m/s) and moving-boat conditions (for both high and low transport environments) increase the relative variability in estimates of mean bed velocity. Despite this, the spatially dense single-transect measurements were capable of producing detailed bed velocity maps that correspond closely with the expected pattern of sediment transport over large dunes. ?? 2011 American Society of Civil Engineers.

  4. Efficient oligonucleotide probe selection for pan-genomic tiling arrays

    Directory of Open Access Journals (Sweden)

    Zhang Wei

    2009-09-01

    Full Text Available Abstract Background Array comparative genomic hybridization is a fast and cost-effective method for detecting, genotyping, and comparing the genomic sequence of unknown bacterial isolates. This method, as with all microarray applications, requires adequate coverage of probes targeting the regions of interest. An unbiased tiling of probes across the entire length of the genome is the most flexible design approach. However, such a whole-genome tiling requires that the genome sequence is known in advance. For the accurate analysis of uncharacterized bacteria, an array must query a fully representative set of sequences from the species' pan-genome. Prior microarrays have included only a single strain per array or the conserved sequences of gene families. These arrays omit potentially important genes and sequence variants from the pan-genome. Results This paper presents a new probe selection algorithm (PanArray that can tile multiple whole genomes using a minimal number of probes. Unlike arrays built on clustered gene families, PanArray uses an unbiased, probe-centric approach that does not rely on annotations, gene clustering, or multi-alignments. Instead, probes are evenly tiled across all sequences of the pan-genome at a consistent level of coverage. To minimize the required number of probes, probes conserved across multiple strains in the pan-genome are selected first, and additional probes are used only where necessary to span polymorphic regions of the genome. The viability of the algorithm is demonstrated by array designs for seven different bacterial pan-genomes and, in particular, the design of a 385,000 probe array that fully tiles the genomes of 20 different Listeria monocytogenes strains with overlapping probes at greater than twofold coverage. Conclusion PanArray is an oligonucleotide probe selection algorithm for tiling multiple genome sequences using a minimal number of probes. It is capable of fully tiling all genomes of a species on

  5. A novel multifunctional oligonucleotide microarray for Toxoplasma gondii

    Directory of Open Access Journals (Sweden)

    Chen Feng

    2010-10-01

    Full Text Available Abstract Background Microarrays are invaluable tools for genome interrogation, SNP detection, and expression analysis, among other applications. Such broad capabilities would be of value to many pathogen research communities, although the development and use of genome-scale microarrays is often a costly undertaking. Therefore, effective methods for reducing unnecessary probes while maintaining or expanding functionality would be relevant to many investigators. Results Taking advantage of available genome sequences and annotation for Toxoplasma gondii (a pathogenic parasite responsible for illness in immunocompromised individuals and Plasmodium falciparum (a related parasite responsible for severe human malaria, we designed a single oligonucleotide microarray capable of supporting a wide range of applications at relatively low cost, including genome-wide expression profiling for Toxoplasma, and single-nucleotide polymorphism (SNP-based genotyping of both T. gondii and P. falciparum. Expression profiling of the three clonotypic lineages dominating T. gondii populations in North America and Europe provides a first comprehensive view of the parasite transcriptome, revealing that ~49% of all annotated genes are expressed in parasite tachyzoites (the acutely lytic stage responsible for pathogenesis and 26% of genes are differentially expressed among strains. A novel design utilizing few probes provided high confidence genotyping, used here to resolve recombination points in the clonal progeny of sexual crosses. Recent sequencing of additional T. gondii isolates identifies >620 K new SNPs, including ~11 K that intersect with expression profiling probes, yielding additional markers for genotyping studies, and further validating the utility of a combined expression profiling/genotyping array design. Additional applications facilitating SNP and transcript discovery, alternative statistical methods for quantifying gene expression, etc. are also pursued at

  6. Hydration-dependent dynamics of human telomeric oligonucleotides in the picosecond timescale: A neutron scattering study

    Energy Technology Data Exchange (ETDEWEB)

    Sebastiani, F.; Comez, L.; Sacchetti, F. [Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia (Italy); CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia (Italy); Longo, M. [Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia (Italy); Elettra—Sincrotrone Trieste, 34149 Basovizza, Trieste (Italy); Orecchini, A.; Petrillo, C.; Paciaroni, A., E-mail: alessandro.paciaroni@fisica.unipg.it [Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia (Italy); De Francesco, A. [CNR-IOM OGG c/o Institut Laue-Langevin, 71 Avenue des Martyrs, CS20156, 38042 Grenoble Cedex 9 (France); Muthmann, M. [Jülich Centre for Neutron Science, Forschungszentrum Jülich GmbH, Outstation at Heinz Maier-Leibnitz Zentrum, Lichtenbergstrasse 1, 85747 Garching (Germany); Teixeira, S. C. M. [EPSAM, Keele University, Staffordshire ST5 5BG (United Kingdom); Institut Laue–Langevin, 71 Avenue des Martyrs, CS20156, 38042 Grenoble Cedex 9 (France)

    2015-07-07

    The dynamics of the human oligonucleotide AG{sub 3}(T{sub 2}AG{sub 3}){sub 3} has been investigated by incoherent neutron scattering in the sub-nanosecond timescale. A hydration-dependent dynamical activation of thermal fluctuations in weakly hydrated samples was found, similar to that of protein powders. The amplitudes of such thermal fluctuations were evaluated in two different exchanged wave-vector ranges, so as to single out the different contributions from intra- and inter-nucleotide dynamics. The activation energy was calculated from the temperature-dependent characteristic times of the corresponding dynamical processes. The trends of both amplitudes and activation energies support a picture where oligonucleotides possess a larger conformational flexibility than long DNA sequences. This additional flexibility, which likely results from a significant relative chain-end contribution to the average chain dynamics, could be related to the strong structural polymorphism of the investigated oligonucleotides.

  7. Streptavidin-coated gold nanoparticles: critical role of oligonucleotides on stability and fractal aggregation

    Directory of Open Access Journals (Sweden)

    Roberta D'Agata

    2017-01-01

    Full Text Available Gold nanoparticles (AuNPs exhibit unique properties that can be modulated through a tailored surface functionalization, enabling their targeted use in biochemical sensing and medical diagnostics. In particular, streptavidin-modified AuNPs are increasingly used for biosensing purposes. We report here a study of AuNPs surface-functionalized with streptavidin-biotinylated oligonucleotide, focussing on the role played by the oligonucleotide probes in the stabilization/destabilization of the functionalized nanoparticle dispersion. The behaviour of the modified AuNP dispersion as a consequence of the competitive displacement of the biotinylated oligonucleotide has been investigated and the critical role of displaced oligonucletides in triggering the quasi one-dimensional aggregation of nanoparticles is demonstrated for the first time. The thorough understanding of the fundamental properties of bioconjugated AuNPs is of great importance for the design of highly sensitive and reliable functionalized AuNP-based assays.

  8. Perceptions of recreational fishing boat captains: knowledge and effects of fish consumption advisories.

    Science.gov (United States)

    Burger, J; Johnson, B B; Shukla, S; Gochfeld, M

    2003-04-01

    The impacts of fish consumption advisories on recreational and subsistence fishing, particularly in fresh waters, have been examined extensively. By contrast, little attention has focused on organized recreational fishing, such as from party and charter boats, and particularly for salt water fish. We interviewed 93 New Jersey boat captains to determine their knowledge about fish consumption advisories, and whether, in their opinion, clients knew of fish consumption advisories, and whether they thought advisories had an effect on recreational fishing and their businesses. Advisories were ranked by captains as a moderate influence on the success of their business, less so than number of fish caught, strength of the economy, overfishing by commercial boats, and management regulations. Only one boat captain had not heard warnings about eating fish, but what captains said they had heard was mixed in its accuracy and completeness. Clients expect captains to know about fish, and about half of boat captains said clients had asked about the safety of eating fish. Captains who felt advisories were affecting their businesses tended to fish for species without high levels of mercury (except for bluefish) or PCBs, the primary contaminants of concern for state advisories and federal advice. However, these captains worked closer to areas (e.g., Raritan Bay complex and New York Harbor) subject to advisories than did other captains, and were more prone to say that management regulations (e.g., fish size, creel limits, seasons) and marketing and advertising by the industry or state were strong influences on the success of their seasons. Comparing captains who thought advisories had some or great effect (60%) versus those reporting "no effect" (40%), there was no difference in the mean percentage of trips targeting high mercury species such as swordfish and shark. Many captains said they would or might post advisories, but 42% of the boat captains said they would not post consumption

  9. Ultrasensitive Hybridization-Based ELISA Method for the Determination of Phosphorodiamidate Morpholino Oligonucleotides in Biological samples.

    Science.gov (United States)

    Burki, Umar; Straub, Volker

    2017-01-01

    Determining the concentration of oligonucleotide in biological samples such as tissue lysate and serum is essential for determining the biodistribution and pharmacokinetic profile, respectively. ELISA-based assays have shown far greater sensitivities compared to other methods such as HPLC and LC/MS. Here, we describe a novel ultrasensitive hybridization-based ELISA method for quantitating morpholino oligonucleotides in mouse tissue lysate and serum samples. The assay has a linear detection range of 5-250 pM (R2 > 0.99).

  10. Preparation of rabbit antibodies to 4,4'-dimethoxytriphenylmethyl, the protective group in oligonucleotide synthesis.

    Science.gov (United States)

    Chersi, A; Romano, T F; Evangelista, M; Mileo, A M; Falasca, G

    1991-09-01

    Antibodies were raised in 2 rabbits by immunization with carrier proteins covalently bound to deoxyguanosine bearing a 4,4'-dimethoxytriphenylmethyl group protecting the 5'-hydroxy terminus of deoxyribose. After several injections with such complexes, immune sera were tested with an immuno-enzymatic method using as antigens several compounds containing the hapten, as well as synthetic oligonucleotides bearing, or not, this protective group at the 5' terminus. One of the two antisera appeared to recognize the dimethoxytrityl group bound to carrier molecules, and thus might find a useful application for the detection, quantitation, and control of oligonucleotides obtained by automatic synthesis.

  11. Enhanced anti-tumor effects with microencapsulated c-myc antisense oligonucleotide.

    Science.gov (United States)

    Putney, S D; Brown, J; Cucco, C; Lee, R; Skorski, T; Leonetti, C; Geiser, T; Calabretta, B; Zupi, G; Zon, G

    1999-10-01

    A phosphorothioate c-myc antisense oligonucleotide was complexed with zinc and encapsulated into injectable biodegradable microspheres. The efficacy of this novel formulation was compared with intravenous administration of the unencapsulated drug in human melanoma and leukemia xenografts in immunocompromised mice. The microencapsulated formulation was more effective as shown by reduced tumor growth, a decreased number of metastases, reduced c-myc expression, and increased survival in the melanoma model, and decreased metastatic potential and increased survival in the leukemia model. These results show that, as has been demonstrated previously with protein and peptide drugs, greater therapeutic efficacy can be obtained when antisense oligonucleotides are delivered from sustained-release formulations.

  12. Direct Mutagenesis of Thousands of Genomic Targets using Microarray-derived Oligonucleotides

    DEFF Research Database (Denmark)

    Bonde, Mads; Kosuri, Sriram; Genee, Hans Jasper

    2015-01-01

    Multiplex Automated Genome Engineering (MAGE) allows simultaneous mutagenesis of multiple target sites in bacterial genomes using short oligonucleotides. However, large-scale mutagenesis requires hundreds to thousands of unique oligos, which are costly to synthesize and impossible to scale...... operons in E. coli using this method, which we call Microarray-Oligonucleotide (MO)-MAGE. The resulting mutant library was characterized by high-throughput sequencing to show that all attempted insertions were estimated to have occurred at an average frequency of 0.02 % per loci with 0.4 average...

  13. Health Insurance Basics

    Science.gov (United States)

    ... Safe Videos for Educators Search English Español Health Insurance Basics KidsHealth / For Teens / Health Insurance Basics What's ... advanced calculus was confusing. What Exactly Is Health Insurance? Health insurance is a plan that people buy ...

  14. PASCAL vs BASIC

    Science.gov (United States)

    Mundie, David A.

    1978-01-01

    A comparison between PASCAL and BASIC as general purpose microprocessor languages rates PASCAL above BASIC in such points as program structure, data types, structuring methods, control structures, procedures and functions, and ease in learning. (CMV)

  15. Basic Research Firing Facility

    Data.gov (United States)

    Federal Laboratory Consortium — The Basic Research Firing Facility is an indoor ballistic test facility that has recently transitioned from a customer-based facility to a dedicated basic research...

  16. Basics of SCI Rehabilitation

    Medline Plus

    Full Text Available ... Injury Medical Expert Videos Topics menu Topics The Basics of Spinal Cord Injury Rehabilitation Adult Injuries Spinal ... Spinal Cord Injury 101 Lawrence Vogel, MD The Basics of Pediatric SCI Rehabilitation Sara Klaas, MSW Transitions ...

  17. Synthesis and Biophysical Investigations of Oligonucleotides Containing Galactose-Modified DNA, LNA and 2'-Amino-LNA Monomers

    DEFF Research Database (Denmark)

    Ries, Annika; Kumar, Rajesh; Lou, Chenguang

    2016-01-01

    Galactose-modified thymidine, LNA-T and 2'-amino-LNA-T nucleosides were synthesized, converted into the corresponding phosphoramidite derivatives and introduced into short oligonucleotides. Compared to the unmodified control strands, the galactose-modified oligonucleotides in general, and the N2...

  18. Antisense oligonucleotide inhibition of Heat Shock Protein (HSP 47 improves bleomycin-induced pulmonary fibrosis in rats

    Directory of Open Access Journals (Sweden)

    Noguchi Takayuki

    2007-05-01

    Full Text Available Abstract Background The most common pathologic form of pulmonary fibrosis arises from excessive deposition of extracellular matrix proteins such as collagen. The 47 kDa heat shock protein 47 (HSP47 is a collagen-specific molecular chaperone that has been shown to play a major role during the processing and/or secretion of procollagen. Objectives To determine whether inhibition of HSP47 could have beneficial effects in mitigating bleomycin-induced pulmonary fibrosis in rats. Methods All experiments were performed with 250–300 g male Wistar rats. Animals were randomly divided into five experimental groups that were administered: 1 saline alone, 2 bleomycin alone, 3 antisense HSP47 oligonucleotides alone, 4 bleomycin + antisense HSP47 oligonucleotides, and 5 bleomycin + sense control oligonucleotides. We investigated lung histopathology and performed immunoblot and immunohistochemistry analyses. Results In rats treated with HSP47 antisense oligonucleotides, pulmonary fibrosis was significantly reduced. In addition, treatment with HSP47 antisense oligonucleotides significantly improved bleomycin-induced morphological changes. Treatment with HSP47 antisense oligonucleotides alone did not produce any significant changes to lung morphology. Immunoblot analyses of lung homogenates confirmed the inhibition of HSP47 protein by antisense oligonucleotides. The bleo + sense group, however, did not exhibit any improvement in lung pathology compared to bleomycin alone groups, and also had no effect on HSP47 expression. Conclusion These findings suggest that HSP47 antisense oligonucleotide inhibition of HSP47 improves bleomycin-induced pulmonary fibrosis pathology in rats.

  19. Basic Cake Decorating Workbook.

    Science.gov (United States)

    Bogdany, Mel

    Included in this student workbook for basic cake decorating are the following: (1) Drawings of steps in a basic way to ice a layer cake, how to make a paper cone, various sizes of flower nails, various sizes and types of tin pastry tubes, and special rose tubes; (2) recipes for basic decorating icings (buttercream, rose paste, and royal icing);…

  20. Programming Visual Basic 2005

    CERN Document Server

    Liberty, Jesse

    2005-01-01

    This information-packed guide helps you understand Visual Basic 2005, the next-generation release of the popular Visual Basic programming language. This book aims to make you immediately productive in creating Windows and web applications using Visual Basic 2005 and all of its tools. Perfect for experienced VB6 and novice programmers

  1. Effect of bow spray strips and Ω-type freeboard on high-speed boats

    Directory of Open Access Journals (Sweden)

    WEI Chengzhu

    2017-01-01

    Full Text Available A high-speed boat may encounter severe wave-making at the bow and become wetter at high speed. Some measures can be taken to overcome these disadvantages. In order to compare the effect of bow spray strips and Ω-type freeboards on a high-speed boat, hull wetness, resistance, hull motion, stability and the restoring moment of the heel at high speed of models with these two kinds of auxiliaries were calculated and measured. CFD methods and model tests were adopted. Both of these two auxiliaries can reduce hull wetness, and the model with a Ω-type freeboard has a better initial stability and larger restoring moment of the heel at high speed. A free running model test also indicates that the Ω-type freeboard has a fine performance.

  2. Variance of discharge estimates sampled using acoustic Doppler current profilers from moving boats

    Science.gov (United States)

    Garcia, Carlos M.; Tarrab, Leticia; Oberg, Kevin; Szupiany, Ricardo; Cantero, Mariano I.

    2012-01-01

    This paper presents a model for quantifying the random errors (i.e., variance) of acoustic Doppler current profiler (ADCP) discharge measurements from moving boats for different sampling times. The model focuses on the random processes in the sampled flow field and has been developed using statistical methods currently available for uncertainty analysis of velocity time series. Analysis of field data collected using ADCP from moving boats from three natural rivers of varying sizes and flow conditions shows that, even though the estimate of the integral time scale of the actual turbulent flow field is larger than the sampling interval, the integral time scale of the sampled flow field is on the order of the sampling interval. Thus, an equation for computing the variance error in discharge measurements associated with different sampling times, assuming uncorrelated flow fields is appropriate. The approach is used to help define optimal sampling strategies by choosing the exposure time required for ADCPs to accurately measure flow discharge.

  3. The Battle Against the U-Boat in the American Theater: December 7, 1941-September 2, 1945

    National Research Council Canada - National Science Library

    Warnock, A. T

    1994-01-01

    ...: the menace of the U-boat. Fast, well-armed, and long-ranged, Hitler's submarines attacked shipping zones throughout the North Atlantic, often within sight of America's coastal towns and cities...

  4. 77 FR 38077 - Notice of Intent To Prepare an Environmental Impact Statement on a Proposed Boat-House Facility...

    Science.gov (United States)

    2012-06-26

    ... assess the impacts of constructing a boathouse facility and floating docks for non-motorized boats at... Bridge, one proposed site is near Gravelly Point and the 14th Street Bridge, and one proposed site is on...

  5. METHODOLOGY OF THE HYBRID PROPULSION SYSTEM (DMP & DEP FOR TRIMARAN TYPE FAST PATROL BOAT

    Directory of Open Access Journals (Sweden)

    Aulia Widyandari

    2012-04-01

    Full Text Available There are lot of research done to develop a patrol boat, from the modification of hull model until propulsion system equipment. For example the model ship type AMV (Advanced Marine Vehicle was developed starting from the Catamaran, Trimaran and  Pentamaran model. Everything is aimed at obtaining the ship design that has the speed and stability. In addition to achieving high-speed vessel must be equipped with propulsion (Main Power is great, that means the main engine dimensions, auxiliary equipments and fuel tanks is too large. Many Limitations of space on the ship's engine room trimaran vessel is the main obstacle in designing propulsion system. Beside that Patrol boat should have many missions speed, so propulsion system should be designed at that conditions.   Hybrid propulsion is a combination of Diesel Mechanical Propulsion (DMP with Diesel Electric Propulsion (DEP. DMP system is connected directly to the propeller shaft (or through a reduction-gear. DMP has provide more efficiency rate of 95%. While DEP is only able to provide efficiency by 85% - 89% is slightly lower than DMP, but the DEP offers many advantages such as simplicity and suitability in the rotational speed settings, control systems, engine power production Redundancy, Flexibility in the design of equipments layout in engine rooms, noise, vibration and fuel consumption efficiency which affects the lower pollution.   Design of Hybrid Propulsion system can be satisfied and achieved the Power requirements and optimally at all speed condition of patrol boat. Therefore the author made using modeling Maxsurf-11.12 software and carried out various optimization of the choice of main engine, propeller and system conditions for fast patrol boat cruise. 

  6. Development of Fluorescence Imaging Lidar for Boat-Based Coral Observation

    Directory of Open Access Journals (Sweden)

    Sasano Masahiko

    2016-01-01

    Full Text Available A fluorescence imaging lidar system installed in a boat-towable buoy has been developed for the observation of reef-building corals. Long-range fluorescent images of the sea bed can be recorded in the daytime with this system. The viability of corals is clear in these fluorescent images because of the innate fluorescent proteins. In this study, the specifications and performance of the system are shown.

  7. Analysis of X-band calibrated sea clutter and small boat reflectivity at medium-to-low grazing angles

    CSIR Research Space (South Africa)

    Herselman, PL

    2008-11-01

    Full Text Available of less than 2 seconds. 5. DETECTABILITY OF SMALL BOATS This section presents the detectability of small boats under- going diff erent manoeuvres using the ALQ detector as an example of the asymptotically optimal class of detectors. 5.1. Overview... in the datasets and subsequent analysis. Copyright © 2008 P. L. Herselman et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided...

  8. Differential loggerhead by-catch and direct mortality due to surface longlines according to boat strata and gear type

    Directory of Open Access Journals (Sweden)

    Juan A. Camiñas

    2006-12-01

    Full Text Available Surface longline gears are used to fish different species, mainly albacore Thunnus alalunga (Bonnaterre, 1788, bluefin tuna Thunnus thynnus (Linnaeus, 1758, and swordfish Xiphias gladius Linnaeus, 1758, and are considered highly dangerous for threatened marine turtles. Loggerheads Caretta caretta (Linnaeus, 1758 can be incidentally captured by surface longlines. A number of captured individuals die during the fishing operation, which we consider direct mortality due to fishing. We analysed the relative loggerhead by-catch and direct mortality associated with each type of boat and gear from April to December during the period 1999-2004 in the Spanish surface longline fleet that fishes in the western Mediterranean Sea, an important fishing area for this fleet. We used different indices to compute the catch per unit effort (CPUE according to the number of hooks and to the number of fishing operations for each type of boat and gear. Both by-catch and direct mortality differed significantly according to the type of boat and gear. With respect to the number of hooks, boats longer than 12 m not using a roller and targeting bluefin tuna captured the highest number of loggerheads, whereas boats longer than 12 m with a roller that targeted swordfish caused the highest direct mortality. With respect to the number of fishing operations, boats longer than 12 m without a roller that targeted albacore captured the highest number of loggerheads; the highest direct mortality was caused by this type of boat and by boats longer than 12 m using a roller and targeting swordfish.

  9. Dragon boat racing and health-related quality of life of breast cancer survivors: a mixed methods evaluation

    Science.gov (United States)

    2013-01-01

    Background Breast cancer survivors who participate in physical activity (PA) are reported to experience improved health-related quality of life (HRQOL). However, the quantitative research exploring the relationship between the team-based activity of dragon boat racing and the HRQOL of breast cancer survivors is limited. Given the rising number of breast cancer survivors, and their growing attraction to dragon boating, further exploration of the influence of this activity on HRQOL is warranted. Methods This study is designed to: 1) quantitatively assess whether and how breast cancer survivors’ participation in a season of dragon boat racing is related to HRQOL and 2) qualitatively explore the survivors’ lived experience of dragon boating and how and why this experience is perceived to influence HRQOL. A mixed methods sequential explanatory design was used with the purpose of complementing quantitative findings with qualitative data. Quantitative data measuring HRQOL were collected at baseline and post-season (N = 100); semi-structured qualitative interviews were used to elicit a personal account of the dragon boat experience (N = 15). Results Statistically significant improvements were shown for HRQOL, physical, functional, emotional and spiritual well-being, breast cancer-specific concerns and cancer-related fatigue. A trend towards significance was shown for social/family well-being. Qualitative data elaborated on the quantitative findings, greatly enhancing the understanding of how and why dragon boat racing influences HRQOL. Conclusions The use of a mixed methods design effectively captured the complex yet positive influence of dragon boating on survivor HRQOL. These findings contribute to a growing body of literature supporting the value of dragon boat racing as a viable PA intervention for enhancing survivor HRQOL. PMID:23915045

  10. HORIZONTAL AXIS MARINE CURRENT TURBINE DESIGN FOR WIND-ELECTRIC HYBRID SAILING BOAT

    Directory of Open Access Journals (Sweden)

    Serkan Ekinci

    2017-01-01

    Full Text Available In recent decades, the number of theoretical studies and applications on electric power production from renewable sources such as wind, solar, sea and tidal flows, has been increasing rapidly. Marine Current Turbines (MCTs, among the power turbines, produce power from alternating flows and are a means of power production even at lower flow rates in oceans and seas. In this study, while maintaining functional requirements, an initial and detailed design (mechanic and hydrodynamic, of an MCT fixed on a sailing boat and at sail which extracts power from the flow around the boat, is undertaken. In the design stages, for analysis and optimization of the marine turbine blade design, the Momentum Blade Element Method is utilized. The Horizontal Axis Marine Turbine (HAMT, determined by the initial and mechanical design, is illustrated with its components included. Computational fluid dynamics (CFD analyses, covering turbine pod geometry at required flow rates and turbine speeds are performed. These analyses are performed very close to real conditions, considering sailing with and without the turbine running (on and off states. The alternator is determined from the results, and the final design which meets the design requirements, is obtained. As a result, a user friendly and innovative turbine design for sail boats, offering more power and efficiency, which is longer lasting compared to solar and wind technologies, that also makes use of renewable sources, such as wind and/or solar, and in addition stores and uses accumulated energy when needed, is proposed.

  11. The Study on Stability and Seakeeping Characteristics of the Glass Bottom Boat Trimaran in Karimunjawa Island

    Science.gov (United States)

    Arswendo Adietya, Berlian; Windyandari, Aulia; Fauzan Zakki, Ahmad

    2018-03-01

    Recently the diversity of fish populations in the waters Karimunjawa Island is only appreciated by those who have the ability to play diving and snorkeling. It is due to the unavailability of a vehicle that is specially made to delight in the fascination of the underwater panorama. One of the alternative solutions is using the glass bottom boat technology which is using transparent bottom that might look out the underwater scenery instead of swimming and snorkeling. The paper has focused on the study of intact stability and seakeeping characteristics of glass bottom boat trimaran in Karimunjawa Island. The intact stability characteristics will be investigated at the various load cases and weight distribution configurations which are influenced by the passenger positions and fuel tank condition. Regarding the seakeeping performance analysis, the ITTC-Bretschneider will be adopted as the wave spectrum at the wave parameters defined from the operational environment. The influence of the parameters on the stability and seakeeping of the glass bottom boat trimaran are presented and discussed.

  12. Drug evaluation: ISIS-301012, an antisense oligonucleotide for the treatment of hypercholesterolemia.

    Science.gov (United States)

    Burnett, John R

    2006-10-01

    ISIS-301012 is an antisense oligonucleotide inhibitor of apolipoprotein B-100, which is being developed by Isis Pharmaceuticals Inc for the potential treatment of hypercholesterolemia. A subcutaneous injectable formulation is currently undergoing phase 11 clinical trials, while phase I trials are underway with an oral formulation of the drug.

  13. Cellular Internalization of Therapeutic Oligonucleotides by Peptide Amphiphile Nanofibers and Nanospheres.

    Science.gov (United States)

    Mumcuoglu, Didem; Sardan Ekiz, Melis; Gunay, Gokhan; Tekinay, Turgay; Tekinay, Ayse B; Guler, Mustafa O

    2016-05-11

    Oligonucleotides are promising drug candidates due to the exceptionally high specificity they exhibit toward their target DNA and RNA sequences. However, their poor pharmacokinetic and pharmacodynamic properties, in conjunction with problems associated with their internalization by cells, necessitates their delivery through specialized carrier systems for efficient therapy. Here, we investigate the effects of carrier morphology on the cellular internalization mechanisms of oligonucleotides by using self-assembled fibrous or spherical peptide nanostructures. Size and geometry were both found to be important parameters for the oligonucleotide internalization process; direct penetration was determined to be the major mechanism for the internalization of nanosphere carriers, whereas nanofibers were internalized by clathrin- and dynamin-dependent endocytosis pathways. We further showed that glucose conjugation to carrier nanosystems improved cellular internalization in cancer cells due to the enhanced glucose metabolism associated with oncogenesis, and the internalization of the glucose-conjugated peptide/oligonucleotide complexes was found to be dependent on glucose transporters present on the surface of the cell membrane.

  14. Design and analysis of effects of triplet repeat oligonucleotides in cell models for myotonic dystrophy

    NARCIS (Netherlands)

    Gonzalez-Barriga, A.; Mulders, S.A.M.; Giessen, J. van der; Hooijer, J.D.; Bijl, S.; Kessel, I.D.G. van; Beers, J. van; Deutekom, J.C. van; Fransen, J.A.M.; Wieringa, B.; Wansink, D.G.

    2013-01-01

    Myotonic dystrophy type 1 (DM1) is caused by DM protein kinase (DMPK) transcripts containing an expanded (CUG)n repeat. Antisense oligonucleotide (AON)-mediated suppression of these mutant RNAs is considered a promising therapeutic strategy for this severe disorder. Earlier, we identified a

  15. Photodynamic antisense regulation of mRNA having a point mutation with psoralen-conjugated oligonucleotide.

    Science.gov (United States)

    Higuchi, Maiko; Yamayoshi, Asako; Kobori, Akio; Murakami, Akira

    2008-01-01

    Nucleic acid-based drugs, such as antisense oligonucleotide, ribozyme, and small interfering RNA, are specific compounds that inhibit gene expression at the post-transcriptional level. To develop more effective nucleic acid-based drugs, we focused on photo-reactive antisense oligonucleotides. We have optimized the structure of psoralen-conjugated oligonucleotide to improve their sequence selectivity and photo-crosslinking efficiency. Previously, we reported that photo reactive oligonucleotides containing 2'-O-psoralenyl-methoxyethyl adenosine (2'-Ps-eom) showed drastic photo-reactivity with a strictly sequence specific manner in vitro. In this report, we evaluated the binding ability toward intracellular target mRNA. The 2'-Ps-eom selectively photo-cross-linked to the target mRNA extracted from cells. The 2'-Ps-eom also cross-linked to target mRNA in cells. Furthermore, 2'-Ps-eom did not cross-link to mRNA having a mismatch base. These results suggest that 2'-Ps-eom is a powerful antisense molecule to inhibit the expression of mRNA having a point mutation.

  16. Synthesis and Excellent Duplex Stability of Oligonucleotides Containing 2'-Amino-LNA Functionalized with Galactose Units

    DEFF Research Database (Denmark)

    Kumar, Rajesh; Ries, Annika; Wengel, Jesper

    2017-01-01

    A convenient method for the preparation of oligonucleotides containing internally-attached galactose and triantennary galactose units has been developed based on click chemistry between 2'-N-alkyne 2'-amino-LNA nucleosides and azido-functionalized galactosyl building blocks. The synthesized...

  17. A triple-helix forming oligonucleotide targeting genomic DNA fails to induce mutation.

    Science.gov (United States)

    Reshat, Reshat; Priestley, Catherine C; Gooderham, Nigel J

    2012-11-01

    Purine tracts in duplex DNA can bind oligonucleotide strands in a sequence specific manner to form triple-helix structures. Triple-helix forming oligonucleotides (TFOs) targeting supFG1 constructs have previously been shown to be mutagenic raising safety concerns for oligonucleotide-based pharmaceuticals. We have engineered a TFO, TFO27, to target the genomic Hypoxanthine-guanine phosphoribosyltransferase (HPRT) locus to define the mutagenic potential of such structures at genomic DNA. We report that TFO27 was resistant to nuclease degradation and readily binds to its target motif in a cell free system. Contrary to previous studies using the supFG1 reporter construct, TFO27 failed to induce mutation within the genomic HPRT locus. We suggest that it is possible that previous reports of triplex-mediated mutation using the supFG1 reporter construct could be confounded by DNA quadruplex formation. Although the present study indicates that a TFO targeting a genomic locus lacks mutagenic activity, it is unclear if this finding can be generalised to all TFOs and their targets. For the present, we suggest that it is prudent to avoid large purine stretches in oligonucleotide pharmaceutical design to minimise concern regarding off-target genotoxicity.

  18. The illusion of specific capture: surface and solution studies of suboptimal oligonucleotide hybridization

    Science.gov (United States)

    2013-01-01

    Background Hybridization based assays and capture systems depend on the specificity of hybridization between a probe and its intended target. A common guideline in the construction of DNA microarrays, for instance, is that avoiding complementary stretches of more than 15 nucleic acids in a 50 or 60-mer probe will eliminate sequence specific cross-hybridization reactions. Here we present a study of the behavior of partially matched oligonucleotide pairs with complementary stretches starting well below this threshold complementarity length – in silico, in solution, and at the microarray surface. The modeled behavior of pairs of oligonucleotide probes and their targets suggests that even a complementary stretch of sequence 12 nt in length would give rise to specific cross-hybridization. We designed a set of binding partners to a 50-mer oligonucleotide containing complementary stretches from 6 nt to 21 nt in length. Results Solution melting experiments demonstrate that stable partial duplexes can form when only 12 bp of complementary sequence are present; surface hybridization experiments confirm that a signal close in magnitude to full-strength signal can be obtained from hybridization of a 12 bp duplex within a 50mer oligonucleotide. Conclusions Microarray and other molecular capture strategies that rely on a 15 nt lower complementarity bound for eliminating specific cross-hybridization may not be sufficiently conservative. PMID:23445545

  19. Mapping of HIV-1 integrase preferences for target site selection with various oligonucleotides

    Czech Academy of Sciences Publication Activity Database

    Snášel, Jan; Rosenberg, Ivan; Pačes, Ondřej; Pichová, Iva

    2009-01-01

    Roč. 488, č. 2 (2009), s. 153-162 ISSN 0003-9861 R&D Projects: GA MŠk 1M0508; GA MŠk(CZ) LC06077 Institutional research plan: CEZ:AV0Z40550506 Keywords : HIV integrase * strand transfer reaction * oligonucleotide substrates Subject RIV: CE - Biochemistry Impact factor: 3.046, year: 2009

  20. Synthetic Nucleic Acid Analogues in Gene Therapy: An Update for Peptide–Oligonucleotide Conjugates

    DEFF Research Database (Denmark)

    Taskova, Maria; Mantsiou, Anna; Astakhova, Kira

    2017-01-01

    The main objective of this work is to provide an update on synthetic nucleic acid analogues and nanoassemblies as tools in gene therapy. In particular, the synthesis and properties of peptide–oligonucleotide conjugates (POCs), which have high potential in research and as therapeutics, are described...

  1. nuID: a universal naming scheme of oligonucleotides for Illumina, Affymetrix, and other microarrays

    Directory of Open Access Journals (Sweden)

    Kibbe Warren A

    2007-05-01

    Full Text Available Abstract Background Oligonucleotide probes that are sequence identical may have different identifiers between manufacturers and even between different versions of the same company's microarray; and sometimes the same identifier is reused and represents a completely different oligonucleotide, resulting in ambiguity and potentially mis-identification of the genes hybridizing to that probe. Results We have devised a unique, non-degenerate encoding scheme that can be used as a universal representation to identify an oligonucleotide across manufacturers. We have named the encoded representation 'nuID', for nucleotide universal identifier. Inspired by the fact that the raw sequence of the oligonucleotide is the true definition of identity for a probe, the encoding algorithm uniquely and non-degenerately transforms the sequence itself into a compact identifier (a lossless compression. In addition, we added a redundancy check (checksum to validate the integrity of the identifier. These two steps, encoding plus checksum, result in an nuID, which is a unique, non-degenerate, permanent, robust and efficient representation of the probe sequence. For commercial applications that require the sequence identity to be confidential, we have an encryption schema for nuID. We demonstrate the utility of nuIDs for the annotation of Illumina microarrays, and we believe it has universal applicability as a source-independent naming convention for oligomers. Reviewers This article was reviewed by Itai Yanai, Rong Chen (nominated by Mark Gerstein, and Gregory Schuler (nominated by David Lipman.

  2. Methods for the preparation of large quantities of complex single-stranded oligonucleotide libraries.

    Science.gov (United States)

    Murgha, Yusuf E; Rouillard, Jean-Marie; Gulari, Erdogan

    2014-01-01

    Custom-defined oligonucleotide collections have a broad range of applications in fields of synthetic biology, targeted sequencing, and cytogenetics. Also, they are used to encode information for technologies like RNA interference, protein engineering and DNA-encoded libraries. High-throughput parallel DNA synthesis technologies developed for the manufacture of DNA microarrays can produce libraries of large numbers of different oligonucleotides, but in very limited amounts. Here, we compare three approaches to prepare large quantities of single-stranded oligonucleotide libraries derived from microarray synthesized collections. The first approach, alkaline melting of double-stranded PCR amplified libraries with a biotinylated strand captured on streptavidin coated magnetic beads results in little or no non-biotinylated ssDNA. The second method wherein the phosphorylated strand of PCR amplified libraries is nucleolyticaly hydrolyzed is recommended when small amounts of libraries are needed. The third method combining in vitro transcription of PCR amplified libraries to reverse transcription of the RNA product into single-stranded cDNA is our recommended method to produce large amounts of oligonucleotide libraries. Finally, we propose a method to remove any primer binding sequences introduced during library amplification.

  3. A New Achiral Linker Reagent for the Incorporation of Multiple Amino Groups Into Oligonucleotides

    DEFF Research Database (Denmark)

    1997-01-01

    with the linker in conventional phosphoamidite or H-phosphonate DNA syntheses. Directly, or via a post modification step, an oligonucleotide is labelled with one or more reporter moieties, e.g. dansyl (5-dimethylamino)-1-naphthalenesulfonyl), biotin, digoxigenin, DOXYL (N-oxyl-4,4-dimethyloxazolidine), PROXYL (N...

  4. Effect of LNA-and OMeN-modified oligonucleotide probes on the ...

    Indian Academy of Sciences (India)

    Previous studies have focused attention on their properties of duplex stabilities, hybridization kinetics and resistance against nuclease digestion; however, their ability to discriminate mismatched hybridizations has been explored much less. In this study, LNA- and OMeN-modified oligonucleotide probes have been prepared ...

  5. Quantitation of ultraviolet-induced single-strand breaks using oligonucleotide chip

    International Nuclear Information System (INIS)

    Pal, Sukdeb; Kim, Min Jung; Choo, Jaebum; Kang, Seong Ho; Lee, Kyeong-Hee; Song, Joon Myong

    2008-01-01

    A simple, accurate and robust methodology was established for the direct quantification of ultraviolet (UV)-induced single-strand break (SSB) using oligonucleotide chip. Oligonucleotide chips were fabricated by covalently anchoring the fluorescent-labeled ssDNAs onto silicon dioxide chip surfaces. Assuming that the possibility of more than one UV-induced SSB to be generated in a small oligonucleotide is extremely low, SSB formation was investigated quantifying the endpoint probe density by fluorescence measurement upon UV irradiation. The SSB yields obtained based on the highly sensitive laser-induced fluorometric determination of fluorophore-labeled oligonucleotides were found to coincide well with that predicted from a theoretical extrapolation of the results obtained for plasmid DNAs using conventional agarose gel electrophoresis. The developed method has the potential to serve as a high throughput, sample-thrifty, and time saving tool to realize more realistic, and direct quantification of radiation and chemical-induced strand breaks. It will be especially useful for determining the frequency of SSBs or lesions convertible to SSBs by specific cleaving reagents or enzymes

  6. N-Branched acyclic nucleoside phosphonates as monomers for the synthesis of modified oligonucleotides

    Czech Academy of Sciences Publication Activity Database

    Hocková, Dana; Rosenbergová, Šárka; Ménová, Petra; Páv, Ondřej; Pohl, Radek; Novák, Pavel; Rosenberg, Ivan

    2015-01-01

    Roč. 13, č. 15 (2015), s. 4449-4458 ISSN 1477-0520 R&D Projects: GA ČR GAP207/11/0108; GA ČR GA13-26526S Institutional support: RVO:61388963 Keywords : acyclic nucleoside phosphonates * oligonucleotides * solid phase synthesis Subject RIV: CC - Organic Chemistry Impact factor: 3.559, year: 2015

  7. Precise construction of oligonucleotide-Fab fragment conjugate for homogeneous immunoassay using HaloTag technology.

    Science.gov (United States)

    Päkkilä, Henna; Peltomaa, Riikka; Lamminmäki, Urpo; Soukka, Tero

    2015-03-01

    The use of oligonucleotide-protein conjugates enables the development of novel types of bioanalytical assays. However, convenient methods for producing covalent and stoichiometric oligonucleotide-protein conjugates are still rare. Here we demonstrate, for the first time, covalent conjugation of DNA oligonucleotide to Fab fragments with a 1:1 ratio using HaloTag self-labeling technology. The oligonucleotide coupling was carried out while the Fab was attached to protein G matrix, thereby enabling straightforward production of covalent conjugates. Furthermore, it allowed convenient purification of the product because the unreacted components were easily removed before the elution of the high-purity conjugate. The prepared conjugate was employed in a homogeneous immunoassay where prostate-specific antigen was used as a model analyte. Switchable lanthanide luminescence was used for detection, and the obtained limit of detection was 0.27 ng/ml. In the future, the developed method for covalent conjugation and successive purification in protein G column could also be applied for introducing other kinds of modifications to Fab fragments in a simple and site-specific manner. Copyright © 2014 Elsevier Inc. All rights reserved.

  8. Labelling of nucleosides and oligonucleotides by solvatochromic 4-aminophthalimide fluorophore for studying DNA–protein interactions

    Czech Academy of Sciences Publication Activity Database

    Riedl, Jan; Pohl, Radek; Ernsting, N. P.; Orság, Petr; Fojta, Miroslav; Hocek, Michal

    2012-01-01

    Roč. 3, č. 9 (2012), s. 2797-2806 ISSN 2041-6520 R&D Projects: GA ČR GA203/09/0317; GA ČR GBP206/12/G151 Institutional support: RVO:61388963 ; RVO:68081707 Keywords : DNA * oligonucleotides * polymerase * phthalimide * nucleotides * fluorescent labeling Subject RIV: CC - Organic Chemistry Impact factor: 8.314, year: 2012

  9. A new achiral reagent for the incorporation of multiple amino groups into oligonucleotides

    DEFF Research Database (Denmark)

    Behrens, Carsten; Petersen, Kenneth H.; Egholm, Michael

    1995-01-01

    The synthesis of a new functionalized achiral linker reagent (10) for the incorporation of multiple primary amino groups into oligonucleotides is described. The linker reagent is compatible with conventional DNA-synthesis following the phosphoramidite methodology, and the linker can be incorporated...

  10. Short G-rich oligonucleotides as a potential therapeutic for Huntington's Disease

    Directory of Open Access Journals (Sweden)

    Parekh-Olmedo Hetal

    2006-10-01

    Full Text Available Abstract Background Huntington's Disease (HD is an inherited autosomal dominant genetic disorder in which neuronal tissue degenerates. The pathogenesis of the disease appears to center on the development of protein aggregates that arise initially from the misfolding of the mutant HD protein. Mutant huntingtin (Htt is produced by HD genes that contain an increased number of glutamine codons within the first exon and this expansion leads to the production of a protein that misfolds. Recent studies suggest that mutant Htt can nucleate protein aggregation and interfere with a multitude of normal cellular functions. Results As such, efforts to find a therapy for HD have focused on agents that disrupt or block the mutant Htt aggregation pathway. Here, we report that short guanosine monotonic oligonucleotides capable of adopting a G-quartet structure, are effective inhibitors of aggregation. By utilizing a biochemical/immunoblotting assay as an initial screen, we identified a 20-mer, all G-oligonucleotide (HDG as an active molecule. Subsequent testing in a cell-based assay revealed that HDG was an effective inhibitor of aggregation of a fusion protein, comprised of a mutant Htt fragment and green fluorescent protein (eGFP. Taken together, our results suggest that a monotonic G-oligonucleotide, capable of adopting a G-quartet conformation is an effective inhibitor of aggregation. This oligonucleotide can also enable cell survival in PC12 cells overexpressing a mutant Htt fragment fusion gene. Conclusion Single-stranded DNA oligonucleotides capable of forming stable G-quartets can inhibit aggregation of the mutant Htt fragment protein. This activity maybe an important part of the pathogenecity of Huntington's Disease. Our results reveal a new class of agents that could be developed as a therapeutic approach for Huntington's Disease.

  11. Development, characterization and experimental validation of a cultivated sunflower (Helianthus annuus L. gene expression oligonucleotide microarray.

    Directory of Open Access Journals (Sweden)

    Paula Fernandez

    Full Text Available Oligonucleotide-based microarrays with accurate gene coverage represent a key strategy for transcriptional studies in orphan species such as sunflower, H. annuus L., which lacks full genome sequences. The goal of this study was the development and functional annotation of a comprehensive sunflower unigene collection and the design and validation of a custom sunflower oligonucleotide-based microarray. A large scale EST (>130,000 ESTs curation, assembly and sequence annotation was performed using Blast2GO (www.blast2go.de. The EST assembly comprises 41,013 putative transcripts (12,924 contigs and 28,089 singletons. The resulting Sunflower Unigen Resource (SUR version 1.0 was used to design an oligonucleotide-based Agilent microarray for cultivated sunflower. This microarray includes a total of 42,326 features: 1,417 Agilent controls, 74 control probes for sunflower replicated 10 times (740 controls and 40,169 different non-control probes. Microarray performance was validated using a model experiment examining the induction of senescence by water deficit. Pre-processing and differential expression analysis of Agilent microarrays was performed using the Bioconductor limma package. The analyses based on p-values calculated by eBayes (p<0.01 allowed the detection of 558 differentially expressed genes between water stress and control conditions; from these, ten genes were further validated by qPCR. Over-represented ontologies were identified using FatiScan in the Babelomics suite. This work generated a curated and trustable sunflower unigene collection, and a custom, validated sunflower oligonucleotide-based microarray using Agilent technology. Both the curated unigene collection and the validated oligonucleotide microarray provide key resources for sunflower genome analysis, transcriptional studies, and molecular breeding for crop improvement.

  12. Modulation of 5' splice site selection using tailed oligonucleotides carrying splicing signals

    Directory of Open Access Journals (Sweden)

    Elela Sherif

    2006-01-01

    Full Text Available Abstract Background We previously described the use of tailed oligonucleotides as a means of reprogramming alternative pre-mRNA splicing in vitro and in vivo. The tailed oligonucleotides that were used interfere with splicing because they contain a portion complementary to sequences immediately upstream of the target 5' splice site combined with a non-hybridizing 5' tail carrying binding sites for the hnRNP A1/A2 proteins. In the present study, we have tested the inhibitory activity of RNA oligonucleotides carrying different tail structures. Results We show that an oligonucleotide with a 5' tail containing the human β-globin branch site sequence inhibits the use of the 5' splice site of Bcl-xL, albeit less efficiently than a tail containing binding sites for the hnRNP A1/A2 proteins. A branch site-containing tail positioned at the 3' end of the oligonucleotide also elicited splicing inhibition but not as efficiently as a 5' tail. The interfering activity of a 3' tail was improved by adding a 5' splice site sequence next to the branch site sequence. A 3' tail carrying a Y-shaped branch structure promoted similar splicing interference. The inclusion of branch site or 5' splice site sequences in the Y-shaped 3' tail further improved splicing inhibition. Conclusion Our in vitro results indicate that a variety of tail architectures can be used to elicit splicing interference at low nanomolar concentrations, thereby broadening the scope and the potential impact of this antisense technology.

  13. Phage annealing proteins promote oligonucleotide-directed mutagenesis in Escherichia coli and mouse ES cells

    Directory of Open Access Journals (Sweden)

    Muyrers Joep PP

    2003-01-01

    Full Text Available Abstract Background The phage protein pairs, RecE/RecT from Rac or Redα/Redβ from λ, initiate efficient double strand break repair (DSBR in Escherichia coli that has proven very useful for DNA engineering. These phage pairs initiate DSBR either by annealing or by another mechanism that is not defined. Results Here we report that these proteins also mediate single strand oligonucleotide repair (ssOR at high efficiencies. The ssOR activity, unlike DSBR, does not require a phage exonuclease (RecE or Redα but only requires a phage annealing protein (RecT or Redβ. Notably, the P22 phage annealing protein Erf, which does not mediate the same DSBR reactions, also delivers ssOR activity. By altering aspects of the oligonucleotides, we document length and design parameters that affect ssOR efficiency to show a simple relationship to homologies either side of the repair site. Notably, ssOR shows strand bias. Oligonucleotides that can prime lagging strand replication deliver more ssOR than their leading complements. This suggests a model in which the annealing proteins hybridize the oligonucleotides to single stranded regions near the replication fork. We also show that ssOR is a highly efficient way to engineer BACs and can be detected in a eukaryotic cell upon expression of a phage annealing protein. Conclusion Phage annealing proteins can initiate the recombination of single stranded oligonucleotides into endogenous targets in Escherichia coli at very high efficiencies. This expands the repertoire of useful DNA engineering strategies, shows promise for applications in eukaryotic cells, and has implications for the unanswered questions regarding DSBR mediated by RecE/RecT and Redα/Redβ.

  14. Basic digital signal processing

    CERN Document Server

    Lockhart, Gordon B

    1985-01-01

    Basic Digital Signal Processing describes the principles of digital signal processing and experiments with BASIC programs involving the fast Fourier theorem (FFT). The book reviews the fundamentals of the BASIC program, continuous and discrete time signals including analog signals, Fourier analysis, discrete Fourier transform, signal energy, power. The text also explains digital signal processing involving digital filters, linear time-variant systems, discrete time unit impulse, discrete-time convolution, and the alternative structure for second order infinite impulse response (IIR) sections.

  15. Basic algebraic topology

    CERN Document Server

    Shastri, Anant R

    2013-01-01

    Introduction The Basic Problem Fundamental Group Function Spaces and Quotient Spaces Relative Homotopy Some Typical Constructions Cofibrations Fibrations Categories and Functors Cell Complexes and Simplicial Complexes Basics of Convex Polytopes Cell Complexes Product of Cell Complexes Homotopical Aspects Cellular Maps Abstract Simplicial Complexes Geometric Realization of Simplicial Complexes Barycentric Subdivision Simplicial Approximation Links and Stars Covering Spaces and Fundamental Group Basic Definitions Lifting Properties Relation with the Fundamental Group Classification of Covering P

  16. Hydromechanics - basic properties

    International Nuclear Information System (INIS)

    Lee, Sung Tak; Lee, Je Geun

    1987-03-01

    This book tells of hydromechanics, which is about basic properties of hydromechanics such as conception, definition, mass, power and weight, and perfect fluid and perfect gas, hydrostatics with summary, basic equation of hydrostatics, relative balance of hydrostatics, and kinematics of hydromechanics, description method of floating, hydromechanics about basic knowledge, equation of moment, energy equation and application of Bernoulli equation, application of momentum theory, inviscid flow and fluid measuring.

  17. Basic molecular spectroscopy

    CERN Document Server

    Gorry, PA

    1985-01-01

    BASIC Molecular Spectroscopy discusses the utilization of the Beginner's All-purpose Symbolic Instruction Code (BASIC) programming language in molecular spectroscopy. The book is comprised of five chapters that provide an introduction to molecular spectroscopy through programs written in BASIC. The coverage of the text includes rotational spectra, vibrational spectra, and Raman and electronic spectra. The book will be of great use to students who are currently taking a course in molecular spectroscopy.

  18. Physical Activity Basics

    Science.gov (United States)

    ... Weight Breastfeeding Micronutrient Malnutrition State and Local Programs Physical Activity Basics Recommend on Facebook Tweet Share Compartir How much physical activity do you need? Regular physical activity helps ...

  19. Binding of Dumbbell Oligonucleotides to MoMuLV Reverse Transcriptase: Inhibitory Properties of RNase H Activity

    Directory of Open Access Journals (Sweden)

    Ajay Kumar

    2010-01-01

    Full Text Available Dumbbell oligonucleotides with loops of various chemistry were synthesized. Incubation of dumbbell oligonucleotides containing phosphorothioate bonds or trimethylene phosphate linkages in loops with S1 nuclease did not result in significant cleavage under conditions which led to the degradation of dumbbell oligonucleotide containing phophodiester bonds in the loops. The binding of reverse transcriptase of Moloney Murine Leukemia Virus (MoMuLV was evaluated with all the five oligonucleotides. The protein binds to all the dumbbell oligonucleotides with similar affinity. The dissociation constants evaluated using PAGE band mobility shift assays were of the order of 10-7. The inhibitory properties of the retroviral RNase H activity was evaluated using 3H –UTP-labeled RNA:RNA-DNA hybrid. It was found that the best dumbbell oligonucleotide, inhibitor contained phosphorothioate residues in both the loops. Our value studies demonstrated that this particularly designed oligonucleotide displays an IC50 of 18 nM in its inhibition on the reverse transcriptase RNase H activity, a magnitude lower than that of first nucleotide reverse transcriptase of HIV-1, tenofovir, introduced by Gilead Science in the market.

  20. The Dynamics of Compound, Transcript, and Protein Effects After Treatment With 2OMePS Antisense Oligonucleotides in mdx Mice

    Directory of Open Access Journals (Sweden)

    Ingrid E C Verhaart

    2014-01-01

    Full Text Available Antisense-mediated exon skipping is currently in clinical development for Duchenne muscular dystrophy (DMD to amend the consequences of the underlying genetic defect and restore dystrophin expression. Due to turnover of compound, transcript, and protein, chronic treatment with effector molecules (antisense oligonucleotides will be required. To investigate the dynamics and persistence of antisense 2′-O-methyl phosphorothioate oligonucleotides, exon skipping, and dystrophin expression after dosing was concluded, mdx mice were treated subcutaneously for 8 weeks with 100 mg/kg oligonucleotides twice weekly. Thereafter, mice were sacrificed at different time points after the final injection (36 hours–24 weeks. Oligonucleotide half-life was longer in heart (~65 days compared with that in skeletal muscle, liver, and kidney (~35 days. Exon skipping half-lives varied between 33 and 53 days, whereas dystrophin protein showed a long half-life (>100 days. Oligonucleotide and exon-skipping levels peaked in the first week and declined thereafter. By contrast, dystrophin expression peaked after 3–8 weeks and then slowly declined, remaining detectable after 24 weeks. Concordance between levels of oligonucleotides, exon skipping, and proteins was observed, except in heart, wherein high oligonucleotide levels but low exon skipping and dystrophin expression were seen. Overall, these results enhance our understanding of the pharmacokinetics and pharmacodynamics of 2′-O-methyl phosphorothioate oligos used for the treatment of DMD.

  1. Characterization of the nanostructure of complexes formed by single- or double-stranded oligonucleotides with a cationic surfactant.

    Science.gov (United States)

    Liu, Xiaoyang; Abbott, Nicholas L

    2010-12-02

    We report the use of dynamic light scattering (DLS), small-angle neutron scattering (SANS), and small-angle X-ray scattering (SAXS) to characterize the nanostructure of complexes formed by either single- or double-stranded oligonucleotides with a cationic surfactant (cetyltrimethylammonium bromide, CTAB) in aqueous solution (1 mM Li(2)SO(4)). For single-stranded oligonucleotides 5'-A(20)-3' and 5'-CCCCATTCTAGCAGCCCGGG-3', both the appearance of two Bragg peaks (at 0.14 and 0.28 Å(-1)) in SAXS spectra with a spacing of 1:2 and form factor fits to SANS spectra are consistent with the presence of multilamellar vesicles (with, on average, 6-9 layers with a periodicity of 45-48 Å). Some samples showed evidence of an additional Bragg peak (at 0.20 Å(-1)) associated with periodic packing (with a periodicity of 31 Å) of the oligonucleotides within the lamellae of the nanostructure. The nucleotide composition of the single-stranded oligonucleotides was also found to impact the number and size of the complexes formed with CTAB. In contrast to 5'-A(20)-3' and 5'-CCCCATTCTAGCAGCCCGGG-3', 5'-T(20)-3' did not change the state of aggregation of CTAB (globular micelles) over a wide range of oligonucleotide:CTAB charge ratios. These results support the proposition that hydrophobic interactions, as well as electrostatics, play a central role in the formation of complexes between cationic amphiphiles and single-stranded oligonucleotides and thus give rise to nanostructures that depend on nucleotide composition. In contrast to the single-stranded oligonucleotides, for double-stranded oligonucleotides mixed with CTAB, three Bragg peaks (0.13, 0.23, and 0.25 Å(-1)) in SAXS spectra with a spacing ratio of 1:√3:√4 and characteristic changes in SANS spectra indicate formation of a hexagonal nanostructure. Also, the composition of the double-stranded oligonucleotides did not measurably impact the nanostructure of complexes formed with CTAB, suggesting that electrostatic

  2. BASIC Beats PASCAL.

    Science.gov (United States)

    Ever, Jacob

    1981-01-01

    Features of two versions of the BASIC programing language are compared with the features of the PASCAL programing language. The application chosen for comparison was a word processor. The conclusion was that PASCAL had the best language features, but BASIC had better systems capabilities. (MP)

  3. Basic Electronics I.

    Science.gov (United States)

    Robertson, L. Paul

    Designed for use in basic electronics programs, this curriculum guide is comprised of twenty-nine units of instruction in five major content areas: Orientation, Basic Principles of Electricity/Electronics, Fundamentals of Direct Current, Fundamentals of Alternating Current, and Applying for a Job. Each instructional unit includes some or all of…

  4. Finding Basic Writing's Place.

    Science.gov (United States)

    Sheridan-Rabideau, Mary P.; Brossell, Gordon

    1995-01-01

    Posits that basic writing serves a vital function by providing writing support for at-risk students and serves the needs of a growing student population that universities accept yet feel needs additional writing instruction. Concludes that the basic writing classroom is the most effective educational support for at-risk students and their writing.…

  5. Basic Cancer Terms

    Science.gov (United States)

    ... basics of cancer . Carcinoma Cancer that starts in skin or tissues that line the inside or cover the outside of internal organs. Cells The basic units that make up the human body. Chemoprevention The use of natural, synthetic (made in a laboratory), or biologic (from a ...

  6. Nuclear multifragmentation: Basic concepts

    Indian Academy of Sciences (India)

    2014-05-02

    May 2, 2014 ... Abstract. We present a brief overview of nuclear multifragmentation reaction. Basic formalism of canonical thermodynamical model based on equilibrium statistical mechanics is described. This model is used to calculate basic observables of nuclear multifragmentation like mass distribution, fragment ...

  7. Blood alcohol concentrations in apprehended drivers of cars and boats suspected to be impaired by the police.

    Science.gov (United States)

    Khiabani, Hassan Z; Opdal, Mimi Stokke; Mørland, Jørg

    2008-03-01

    According to the Norwegian Road Traffic Act, car drivers are not allowed to operate a vehicle with a blood alcohol concentration (BAC) above 0.2 g/kg. Depending on the size of the boat or ship, boat drivers/captains/first mates are not allowed to conduct the boat with a BAC above 0.8 g/kg when driving small boats (length less than 15 m) and above 1.5 g/kg when running larger vessels/ships. The new Sea Act of June 2005 states that captains/first mates cannot conduct a ship if he/she has a BAC above 0.2 g/kg. Our aim was to determine the current median BAC in a large population of car and boat drivers in Norway. Our other aim was to study if median BAC was higher in boat drivers than in car drivers who were suspected by the police to be impaired. Furthermore, we wanted to investigate if the BAC levels were differently distributed by gender or age within and between these two groups. The Norwegian Institute of Public Health analyzes blood samples from all car/boat drivers suspected of driving under the influence of alcohol and non-alcoholic drugs. In the present study, samples submitted between 01.05 and 01.09 in 2002-2004 were included. Drivers, who in addition tested positive for drugs or abuse substances other than ethanol were excluded. There were 321 boat drivers and 3,061 car drivers who were suspected to be under the influence of ethanol only. The median BAC in boat drivers (1.76 g/kg [range 0.02-3.54]) was significantly higher compared to that in car drivers (1.54 g/kg [range 0.00-4.27]). In the car driver group, the mean BAC did not differ significantly between men and women. The median level of BAC was significantly higher in men than in women in the boat driver group (1.77 g/kg with CI 1.69-1.85 vs. 1.27 g/kg with CI 0.78-1.76). Alcohol impairment of car drivers is known to be considered the most important contributing cause of car crash injuries. Driving a boat may demand the same degree of performance skills as driving a car. The median BAC in apprehended

  8. Modeling the Impacts of Cetacean-Focused Tourism in Taiwan: Observations from Cetacean Watching Boats: 2002-2005

    Science.gov (United States)

    Tseng, Yung-Ping; Huang, Yu-Chin; Kyle, Gerard T.; Yang, Ming-Ching

    2011-01-01

    Cetacean-focused tourism in Taiwan has grown rapidly since 1997. This development, measured in terms of both number of tour boats and visitors, has resulted in many resource management challenges stemming from the absence of regulation and scientific data. To fill this void in empirical evidence, we used 464 sighting records from 2002 to 2005 to model the impact of cetacean-focused tourism. Cox proportional hazard analysis indicated cetacean avoidance responses to cetacean watching boats were strongly associated with pod size, mother-calf pairs, and cetacean-vessel distances. Mother-calf pairs abandoned their avoidance tactic by 55% compared to noncalf groups when tour boats approached. Second, the hazard ratio of abundance was 0.996, suggesting that the odds of encountering avoidance responses by the cetaceans decreased by 42% for every 100-member increase in the cetacean pod size. Last, distances maintained by boats from the cetaceans was positively related to avoidance responses (i.e., less avoidance behavior with closer interaction). Based on our findings, we have the following recommendations: (a) limit vessels from approaching mothers with calves, (b) limit vessels from approaching small groups of cetaceans, (c) reduced avoidance behavior to boat traffic may be a red flag for potential long-term disturbance, and (d) apply the "precautionary principle" based on the best scientific information available in cetacean-based tourism in Taiwan. These recommendations will help contribute to the sustainable development of cetacean-focused tourism in Taiwan.

  9. Modeling the impacts of cetacean-focused tourism in Taiwan: observations from cetacean watching boats: 2002-2005.

    Science.gov (United States)

    Tseng, Yung-Ping; Huang, Yu-Chin; Kyle, Gerard T; Yang, Ming-Ching

    2011-01-01

    Cetacean-focused tourism in Taiwan has grown rapidly since 1997. This development, measured in terms of both number of tour boats and visitors, has resulted in many resource management challenges stemming from the absence of regulation and scientific data. To fill this void in empirical evidence, we used 464 sighting records from 2002 to 2005 to model the impact of cetacean-focused tourism. Cox proportional hazard analysis indicated cetacean avoidance responses to cetacean watching boats were strongly associated with pod size, mother-calf pairs, and cetacean-vessel distances. Mother-calf pairs abandoned their avoidance tactic by 55% compared to noncalf groups when tour boats approached. Second, the hazard ratio of abundance was 0.996, suggesting that the odds of encountering avoidance responses by the cetaceans decreased by 42% for every 100-member increase in the cetacean pod size. Last, distances maintained by boats from the cetaceans was positively related to avoidance responses (i.e., less avoidance behavior with closer interaction). Based on our findings, we have the following recommendations: (a) limit vessels from approaching mothers with calves, (b) limit vessels from approaching small groups of cetaceans, (c) reduced avoidance behavior to boat traffic may be a red flag for potential long-term disturbance, and (d) apply the "precautionary principle" based on the best scientific information available in cetacean-based tourism in Taiwan. These recommendations will help contribute to the sustainable development of cetacean-focused tourism in Taiwan.

  10. Commuter exposure to black carbon, carbon monoxide, and noise in the mass transport khlong boats of Bangkok, Thailand

    Science.gov (United States)

    Ziegler, A. D.; Velasco, E.; Ho, K. J.

    2013-12-01

    Khlong (canal) boats are a unique mass transport alternative in the congested city of Bangkok. Canals and rivers provide exclusive transit-ways for reducing the commuting time of thousands of city residents daily. However, as a consequence of the service characteristics and boats design and state of repair, they can represent a potential public health risk and an important source of black carbon and greenhouse gases. This work quantifies commuter exposure to black carbon, CO and noise when waiting for and travelling in these diesel fueled boats. Exposure to toxic pollutants and acute noise is similar or worse than for other transportation modes. Mean black carbon concentrations observed at one busy pier and along the main canal were much higher than ambient concentrations at sites impacted by vehicular traffic. Concentrations of CO were similar to those reported for roadside areas of Bangkok. The equivalent continuous sound levels registered at the landing pier were similar to those reported for roadsides, but values recorded inside the boats were significantly higher. We believe that the boat service is a viable alternative mode of mass transport, but public safety could be improved to provide a high quality service, comparable to modern rail systems or emerging bus rapid transit systems. These investments would also contribute to reduce the emission of black carbon and other greenhouse and toxic pollutants.

  11. Bathymetry mapping using a GPS-sonar equipped remote control boat: Application in waste stabilisation ponds

    Science.gov (United States)

    Coggins, Liah; Ghadouani, Anas; Ghisalberti, Marco

    2014-05-01

    Traditionally, bathymetry mapping of ponds, lakes and rivers have used techniques which are low in spatial resolution, sometimes subjective in terms of precision and accuracy, labour intensive, and that require a high level of safety precautions. In waste stabilisation ponds (WSP) in particular, sludge heights, and thus sludge volume, are commonly measured using a sludge judge (a clear plastic pipe with length markings). A remote control boat fitted with a GPS-equipped sonar unit can improve the resolution of depth measurements, and reduce safety and labour requirements. Sonar devices equipped with GPS technology, also known as fish finders, are readily available and widely used by people in boating. Through the use of GPS technology in conjunction with sonar, the location and depth can be recorded electronically onto a memory card. However, despite its high applicability to the field, this technology has so far been underutilised. In the case of WSP, the sonar can measure the water depth to the top of the sludge layer, which can then be used to develop contour maps of sludge distribution and to determine sludge volume. The coupling of sonar technology with a remotely operative vehicle has several advantages of traditional measurement techniques, particularly in removing human subjectivity of readings, and the sonar being able to collect more data points in a shorter period of time, and continuously, with a much higher spatial resolution. The GPS-sonar equipped remote control boat has been tested on in excess of 50 WSP within Western Australia, and has shown a very strong correlation (R2 = 0.98) between spot readings taken with the sonar compared to a sludge judge. This has shown that the remote control boat with GPS-sonar device is capable of providing sludge bathymetry with greatly increased spatial resolution, while greatly reducing profiling time. Remotely operated vehicles, such as the one built in this study, are useful for not only determining sludge

  12. Long-tail shaft drive for energy-efficient boats. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Hastrup, H.

    1981-02-01

    A long-tail shaft drive utilized in a propulsion system for small boats is described. The objectives of the grant are discussed. The performance of the long-tail shaft indicates a savings of approximately 50% of the fuel used by the conventional outboard motor with comparable horsepower. A summary of actions taken in regard to the reversible pitch propeller, propeller shrouds, and the tail shaft are presented. Eight test procedures are briefly outlined. Information on materials and manufacturing was sought and applied to the experimental work. Patent, manufacturing, and marketing considerations are noted. Conclusions and recommendations are summarized. (MCW)

  13. Operational Energy Capability Portfolio Analysis for Protection of Maritime Forces Against Small Boat Swarms

    Science.gov (United States)

    2016-09-01

    development RAM rolling airframe missile RPG rocket-propelled grenade SAM surface-to-air missile SE systems engineering SM standard missile...propelled grenades ( RPG ) to ASCMs. They find that against the small boat attackers with ASCMs, it is useful to employ helicopters or unmanned combat...type 1 RPG /suicide bombs (3-500 m),” “type 2 multiple launch rocket system (MLRS) rocket (8 km),” and “type 3–missile/torpedo.” This research focuses

  14. Recreational Boat Safety Collision Research - Phase 2. Volume 2. Collision Accident Investigations - 1975

    Science.gov (United States)

    1976-07-01

    weight corresponds closely to the standard aluminum alloy gage of 0.072". This is a gage that could well be used for a quality aluminum boat. The next...determine. Normally, we would feel that alloy 5052 would be used due to its ready availcbility, weldability, and excellent corrosion resistance to marine...2i a alloy such as clad 6061-T6. If this latter alloy w~re used, the minimum yield strength of the material would be 35,000 psi. If ally 5052 were

  15. A traditional boats and navigational history of Odisha, East coast of India

    Digital Repository Service at National Institute of Oceanography (India)

    Tripati, S.

    and commerce. 6    Pota (dugout) Pota was directly scooped out from the log. As it was scooped out from the log, its durability is much greater than other traditional crafts. Its shape is like a long tub and its lower portion looks like a half circle..., purgoa, malangi and holah. These were used for loading and unloading cargo from mother boats anchored in the sea. Sometimes these were also used for inland waters. With the increase of trade and commerce in the 16th century, shipbuilding industry...

  16. Basic rocks in Finland

    International Nuclear Information System (INIS)

    Piirainen, T.; Gehoer, S.; Iljina, M.; Kaerki, A.; Paakkola, J.; Vuollo, J.

    1992-10-01

    Basic igneous rocks, containing less than 52% SiO 2 , constitute an important part of the Finnish Archaean and Proterozoic crust. In the Archaean crust exist two units which contain the majority of the basic rocks. The Arcaean basic rocks are metavolcanics and situated in the Greenstone Belts of Eastern Finland. They are divided into two units. The greenstones of the lower one are tholeiites, komatiites and basaltic komatiites. The upper consists of bimodal series of volcanics and the basic rocks of which are Fe-tholeiites, basaltic komatiites and komatiites. Proterozoic basic rocks are divided into seven groups according to their ages. The Proterozoic igneous activity started by the volominous basic magmatism 2.44 Ga ago. During this stage formed the layered intrusions and related dykes in the Northern Finland. 2.2 Ga old basic rocks are situated at the margins of Karelian formations. 2.1 Ga aged Fe-tholeiitic magmatic activity is widespread in Eastern and Northern Finland. The basic rocks of 1.97 Ga age group are met within the Karelian Schist Belts as obducted ophiolite complexes but they occur also as tholeiitic diabase dykes cutting the Karelian schists and Archean basement. The intrusions and the volcanics of the 1.9 Ga old basic igneous activity are mostly encountered around the Granitoid Complex of Central Finland. Subjotnian, 1.6 Ga aged tholeiitic diabases are situated around the Rapakivi massifs of Southern Finland, and postjotnian, 1.2 Ga diabases in Western Finland where they form dykes cutting Svecofennian rocks

  17. From basic needs to basic rights.

    Science.gov (United States)

    Facio, A

    1995-06-01

    After arriving at an understanding that basic rights refer to all human needs, it is clear that a recognition of the basic needs of female humans must precede the realization of their rights. The old Women in Development (WID) framework only understood women's needs from an androcentric perspective which was limited to practical interests. Instead, women's primary need is to be free from their subordination to men. Such an understanding places all of women's immediate needs in a new light. A human rights approach to development would see women not as beneficiaries but as people entitled to enjoy the benefits of development. Discussion of what equality before the law should mean to women began at the Third World Conference on Women in Nairobi where the issue of violence against women was first linked to development. While debate continues about the distinction between civil and political rights and economic, social, and cultural rights, the realities of women's lives do not permit such a distinction. The concept of the universality of human rights did not become codified until the UN proclaimed the Universal Declaration of Human Rights in 1948. The declaration has been criticized by feminists because the view of human rights it embodies has been too strongly influenced by a liberal Western philosophy which stresses individual rights and because it is ambiguous on the distinction between human rights and the rights of a citizen. The protection of rights afforded by the Declaration, however, should not be viewed as a final achievement but as an ongoing struggle. International conferences have led to an analysis of the human-rights approach to sustainable development which concludes that women continue to face the routine denial of their rights. Each human right must be redefined from the perspective of women's needs, which must also be redefined. Women must forego challenging the concept of the universality of human rights in order to overcome the argument of cultural

  18. Basic stress analysis

    CERN Document Server

    Iremonger, M J

    1982-01-01

    BASIC Stress Analysis aims to help students to become proficient at BASIC programming by actually using it in an important engineering subject. It also enables the student to use computing as a means of learning stress analysis because writing a program is analogous to teaching-it is necessary to understand the subject matter. The book begins by introducing the BASIC approach and the concept of stress analysis at first- and second-year undergraduate level. Subsequent chapters contain a summary of relevant theory, worked examples containing computer programs, and a set of problems. Topics c

  19. Quantum electronics basic theory

    CERN Document Server

    Fain, V M; Sanders, J H

    1969-01-01

    Quantum Electronics, Volume 1: Basic Theory is a condensed and generalized description of the many research and rapid progress done on the subject. It is translated from the Russian language. The volume describes the basic theory of quantum electronics, and shows how the concepts and equations followed in quantum electronics arise from the basic principles of theoretical physics. The book then briefly discusses the interaction of an electromagnetic field with matter. The text also covers the quantum theory of relaxation process when a quantum system approaches an equilibrium state, and explai

  20. Synthesis of 5'-oligonucleotide hydrazide derivatives and their use in preparation of enzyme-nucleic acid hybridization probes.

    Science.gov (United States)

    Ghosh, S S; Kao, P M; Kwoh, D Y

    1989-04-01

    A hydrazone-based method for conjugating synthetic nucleic acids and reporter molecules for use as nonradioactive hybridization probes is presented. Oligonucleotides complementary to the hepatitis B virus were derivatized at their 5' ends with hydrazine or homobifunctional acyl hydrazides. These derivatives reacted facilely with aldehydes to give hydrazones, which were characterized by uv spectroscopy and HPLC. Coupling of aldehyde-modified alkaline phosphatase with carbohydrazide-oligonucleotide derivatives provided a mixture of two enzyme-nucleic acid conjugates in 80-85% yield. The conjugates had a 1:1 and a 2:1 oligonucleotide/enzyme ratio, respectively, and were separated by ion-exchange chromatography. Both conjugates were able to detect 7 amol of target DNA in 1 h, using a colorimetric assay. In contrast, oligonucleotide-horseradish peroxidase conjugates were 40-fold lower in sensitivity of detection.

  1. Crystallization of a member of the recFOR DNA repair pathway, RecO, with and without bound oligonucleotide

    Energy Technology Data Exchange (ETDEWEB)

    Aono, Shelly; Hartsch, Thomas; Schulze-Gahmen, Ursula

    2003-01-22

    RecFOR proteins are important for DNA repair by homologous recombination in bacteria. The RecO protein from Thermus thermophilus was cloned, purified and characterized for its binding to oligonucleotides. The protein was crystallized alone and in complex with a 14-mer oligonucleotide. Both crystal forms grow under different crystallization conditions in the same space group, P3121 or P3221, with almost identical unit cell parameters. Complete data sets were collected to 2.8 Angstrom and 2.5 Angstrom for RecO alone and the RecO-oligonucleotide complex, respectively. Visual comparison of the diffraction patterns between the two crystal forms and calculation of an Rmerge of 33.9 percent on F indicate that one of the crystal forms is indeed a complex of RecO with bound oligonucleotide.

  2. Covalent immobilization of oligonucleotides on p-aminophenyl-modified carbon screen-printed electrodes for viral DNA sensing.

    Science.gov (United States)

    Ruffien, Audrey; Dequaire, Murielle; Brossier, Pierre

    2003-04-07

    DNA-sensing platforms were prepared by covalently attaching oligonucleotide capture probes onto p-aminophenyl-functionalized carbon surfaces and applied to the determination of an amplified herpes virus DNA sequence in an electrochemical hybridization assay.

  3. Heated oligonucleotide ligation assay (HOLA): an affordable single nucleotide polymorphism assay.

    Science.gov (United States)

    Black, W C; Gorrochotegui-Escalante, N; Duteau, N M

    2006-03-01

    Most single nucleotide polymorphism (SNP) detection requires expensive equipment and reagents. The oligonucleotide ligation assay (OLA) is an inexpensive SNP assay that detects ligation between a biotinylated "allele-specific detector" and a 3' fluorescein-labeled "reporter" oligonucleotide. No ligation occurs unless the 3' detector nucleotide is complementary to the SNP nucleotide. The original OLA used chemical denaturation and neutralization. Heated OLA (HOLA) instead uses a thermal stable ligase and cycles of denaturing and hybridization for ligation and SNP detection. The cost per genotype is approximately US$1.25 with two-allele SNPs or approximately US$1.75 with three-allele SNPs. We illustrate the development of HOLA for SNP detection in the Early Trypsin and Abundant Trypsin loci in the mosquito Aedes aegypti (L.) and at the a-glycerophosphate dehydrogenase locus in the mosquito Anopheles gambiae s.s.

  4. Single-Labeled Oligonucleotides Showing Fluorescence Changes upon Hybridization with Target Nucleic Acids

    Directory of Open Access Journals (Sweden)

    Gil Tae Hwang

    2018-01-01

    Full Text Available Sequence-specific detection of nucleic acids has been intensively studied in the field of molecular diagnostics. In particular, the detection and analysis of single-nucleotide polymorphisms (SNPs is crucial for the identification of disease-causing genes and diagnosis of diseases. Sequence-specific hybridization probes, such as molecular beacons bearing the fluorophore and quencher at both ends of the stem, have been developed to enable DNA mutation detection. Interestingly, DNA mutations can be detected using fluorescently labeled oligonucleotide probes with only one fluorophore. This review summarizes recent research on single-labeled oligonucleotide probes that exhibit fluorescence changes after encountering target nucleic acids, such as guanine-quenching probes, cyanine-containing probes, probes containing a fluorophore-labeled base, and microenvironment-sensitive probes.

  5. Synthesis and hybridization of oligonucleotides modified at AMP sites with adenine pyrrolidine phosphonate nucleotides

    Czech Academy of Sciences Publication Activity Database

    Rejman, Dominik; Kočalka, Petr; Pohl, Radek; Točík, Zdeněk; Rosenberg, Ivan

    2009-01-01

    Roč. 74, č. 6 (2009), s. 935-955 ISSN 0010-0765 R&D Projects: GA MŠk 2B06065; GA MŠk(CZ) LC06077; GA MŠk(CZ) LC06061; GA AV ČR KAN200520801 Institutional research plan: CEZ:AV0Z40550506 Keywords : oligonucleotide * pyrrolidine * phosphonate Subject RIV: CC - Organic Chemistry Impact factor: 0.856, year: 2009

  6. Intrinsically Labeled Fluorescent Oligonucleotide Probes on Quantum Dots for Transduction of Nucleic Acid Hybridization.

    Science.gov (United States)

    Shahmuradyan, Anna; Krull, Ulrich J

    2016-03-15

    Quantum dots (QDs) have been widely used in chemical and biosensing due to their unique photoelectrical properties and are well suited as donors in fluorescence resonance energy transfer (FRET). Selective hybridization interactions of oligonucleotides on QDs have been determined by FRET. Typically, the QD-FRET constructs have made use of labeled targets or have implemented labeled sandwich format assays to introduce dyes in proximity to the QDs for the FRET process. The intention of this new work is to explore a method to incorporate the acceptor dye into the probe molecule. Thiazole orange (TO) derivatives are fluorescent intercalating dyes that have been used for detection of double-stranded nucleic acids. One such dye system has been reported in which single-stranded oligonucleotide probes were doubly labeled with adjacent thiazole orange derivatives. In the absence of the fully complementary (FC) oligonucleotide target, the dyes form an H-aggregate, which results in quenching of fluorescence emission due to excitonic interactions between the dyes. The hybridization of the FC target to the probe provides for dissociation of the aggregate as the dyes intercalate into the double stranded duplex, resulting in increased fluorescence. This work reports investigation of the dependence of the ratiometric signal on the type of linkage used to conjugate the dyes to the probe, the location of the dye along the length of the probe, and the distance between adjacent dye molecules. The limit of detection for 34mer and 90mer targets was found to be identical and was 10 nM (2 pmol), similar to analogous QD-FRET using labeled oligonucleotide target. The detection system could discriminate a one base pair mismatch (1BPM) target and was functional without substantial compromise of the signal in 75% serum. The 1BPM was found to reduce background signal, indicating that the structure of the mismatch affected the environment of the intercalating dyes.

  7. Oligonucleotide fishing for STAT6: cross-talk between IL-4 and chemokines

    DEFF Research Database (Denmark)

    Eriksen, K W; Nielsen, M; Kaltoft, K

    2001-01-01

    Signal transducer and activator of transcription 6 (STAT6) is essential for the biological activities of interleukin-4 (IL-4) and the development of allergic responses in mice. Here we report on a sensitive and specific assay for STAT6 activation in response to IL-4. We took advantage of double-s...... activation, whereas other chemokines and cytokines do not. In conclusion, our data show that oligonucleotide fishing is a supplementary tool for studying cytokine cross-talk at a genomic level....

  8. High-frequency genome editing using ssDNA oligonucleotides with zinc-finger nucleases

    DEFF Research Database (Denmark)

    Chen, Fuqiang; Pruett-Miller, Shondra M; Huang, Yuping

    2011-01-01

    Zinc-finger nucleases (ZFNs) have enabled highly efficient gene targeting in multiple cell types and organisms. Here we describe methods for using simple ssDNA oligonucleotides in tandem with ZFNs to efficiently produce human cell lines with three distinct genetic outcomes: (i) targeted point...... mutation, (ii) targeted genomic deletion of up to 100 kb and (iii) targeted insertion of small genetic elements concomitant with large genomic deletions....

  9. Genome dynamics of short oligonucleotides: the example of bacterial DNA uptake enhancing sequences.

    Directory of Open Access Journals (Sweden)

    Mohammed Bakkali

    Full Text Available Among the many bacteria naturally competent for transformation by DNA uptake-a phenomenon with significant clinical and financial implications- Pasteurellaceae and Neisseriaceae species preferentially take up DNA containing specific short sequences. The genomic overrepresentation of these DNA uptake enhancing sequences (DUES causes preferential uptake of conspecific DNA, but the function(s behind this overrepresentation and its evolution are still a matter for discovery. Here I analyze DUES genome dynamics and evolution and test the validity of the results to other selectively constrained oligonucleotides. I use statistical methods and computer simulations to examine DUESs accumulation in Haemophilus influenzae and Neisseria gonorrhoeae genomes. I analyze DUESs sequence and nucleotide frequencies, as well as those of all their mismatched forms, and prove the dependence of DUESs genomic overrepresentation on their preferential uptake by quantifying and correlating both characteristics. I then argue that mutation, uptake bias, and weak selection against DUESs in less constrained parts of the genome combined are sufficient enough to cause DUESs accumulation in susceptible parts of the genome with no need for other DUES function. The distribution of overrepresentation values across sequences with different mismatch loads compared to the DUES suggests a gradual yet not linear molecular drive of DNA sequences depending on their similarity to the DUES. Other genomically overrepresented sequences, both pro- and eukaryotic, show similar distribution of frequencies suggesting that the molecular drive reported above applies to other frequent oligonucleotides. Rare oligonucleotides, however, seem to be gradually drawn to genomic underrepresentation, thus, suggesting a molecular drag. To my knowledge this work provides the first clear evidence of the gradual evolution of selectively constrained oligonucleotides, including repeated, palindromic and protein

  10. Proposal for new European pharmaceutical legislation to permit access to custom-made anti-sense oligonucleotide medicinal products.

    Science.gov (United States)

    Johnston, John D; Feldschreiber, Peter

    2014-06-01

    Current European pharmaceutical legislation is not adequate to meet advances in science and technologies that will lead to rapid development of custom-made medicines. Using existing legislation for custom-made medical devices as a template and anti-sense oligonucleotides as model medicinal products, we propose new European pharmaceutical legislation to permit timely access to custom-made anti-sense oligonucleotide medicinal products. The proposals may be more widely applicable to other medicinal products. © 2013 The British Pharmacological Society.

  11. Hetero-oligonucleotide nanoscale tiles capable of two-dimensional lattice formation as testbeds for a rapid, affordable purification methodology.

    Science.gov (United States)

    Lukeman, Philip S

    2013-06-21

    New nanoscale hetero-oligonucleotide tiles are assembled from DNA, RNA and morpholino oligos and purified using size exclusion filtration. Homo-oligonucleotide tiles assembled from RP-cartridge processed DNA oligos are purified by nondenaturing gel electrophoresis. These tiles' purity and homogeneity are demonstrated by gel electrophoresis and their incorporation into two-dimensional arrays visualized by AFM. This purification methodology increases throughput and decreases costs for researchers who wish to screen multiple tiles for utilization in structural or analytical studies.

  12. HIV Treatment: The Basics

    Science.gov (United States)

    ... AIDS Drugs Clinical Trials Apps skip to content HIV Treatment Home Understanding HIV/AIDS Fact Sheets HIV ... 4 p.m. ET) Send us an email HIV Treatment: The Basics Last Reviewed: March 22, 2018 ...

  13. Basics of SCI Rehabilitation

    Medline Plus

    Full Text Available ... Peer Counseling Blog About Media Donate Spinal Cord Injury Medical Expert Videos Topics menu Topics The Basics of Spinal Cord Injury Rehabilitation Adult Injuries Spinal Cord Injury 101 David ...

  14. Basics of SCI Rehabilitation

    Medline Plus

    Full Text Available ... Topic Resources Peer Counseling Blog About Media Donate Spinal Cord Injury Medical Expert Videos Topics menu Topics The Basics of Spinal Cord Injury Rehabilitation Adult Injuries Spinal Cord Injury 101 David ...

  15. Basics of SCI Rehabilitation

    Medline Plus

    Full Text Available ... About Media Donate Spinal Cord Injury Medical Expert Videos Topics menu Topics The Basics of Spinal Cord ... LLC Understanding Spinal Cord Injury About Us Expert Videos Contact Us Personal Experience Videos Blog Videos By ...

  16. Noise Radar Technology Basics

    National Research Council Canada - National Science Library

    Thayaparan, T; Wernik, C

    2006-01-01

    .... In this report, the basic theory of noise radar design is treated. The theory supports the use of noise waveforms for radar detection and imaging in such applications as covert military surveillance and reconnaissance...

  17. Basics of SCI Rehabilitation

    Medline Plus

    Full Text Available ... Counseling Blog About Media Donate Spinal Cord Injury Medical Expert Videos Topics menu Topics The Basics of ... injury? What is a Spinal Cord Injury? SCI Medical Experts People Living With SCI Personal Experiences By ...

  18. Basics of SCI Rehabilitation

    Medline Plus

    Full Text Available ... Topic Resources Peer Counseling Blog About Media Donate Spinal Cord Injury Medical Expert Videos Topics menu Topics The Basics of Spinal Cord Injury Rehabilitation Adult Injuries Spinal Cord Injury 101 ...

  19. Video Screen Capture Basics

    Science.gov (United States)

    Dunbar, Laura

    2014-01-01

    This article is an introduction to video screen capture. Basic information of two software programs, QuickTime for Mac and BlueBerry Flashback Express for PC, are also discussed. Practical applications for video screen capture are given.

  20. Basics of SCI Rehabilitation

    Medline Plus

    Full Text Available ... RN Pediatric Injuries Pediatric Spinal Cord Injury 101 Lawrence Vogel, MD The Basics of Pediatric SCI Rehabilitation ... Rogers, PT Recreational Therapy after Spinal Cord Injury Jennifer Piatt, PhD Kristine Cichowski, MS Read Bio Founding ...

  1. Basic Information about Mercury

    Science.gov (United States)

    ... Your Environment Contact Us Share Basic Information about Mercury On this page: What is mercury? Emissions of ... Consumer products that traditionally contain mercury What is Mercury? Mercury is a naturally-occurring chemical element found ...

  2. Basics of SCI Rehabilitation

    Medline Plus

    Full Text Available ... How Peer Counseling Works Julie Gassaway, MS, RN Pediatric Injuries Pediatric Spinal Cord Injury 101 Lawrence Vogel, MD The Basics of Pediatric SCI Rehabilitation Sara Klaas, MSW Transitions for Children ...

  3. Basics of SCI Rehabilitation

    Medline Plus

    Full Text Available ... Spinal Cord Injury 101 Lawrence Vogel, MD The Basics of Pediatric SCI Rehabilitation Sara Klaas, MSW Transitions for Children with Spinal Cord Injury Patricia Mucia, RN Family Life After Pediatric Spinal Injury Dawn Sheaffer, MSW Rehabilitation ...

  4. Basics of SCI Rehabilitation

    Medline Plus

    Full Text Available ... Cord Injury Medical Expert Videos Topics menu Topics The Basics of Spinal Cord Injury Rehabilitation Adult Injuries ... Therapy-Lokomat T. George Hornby, PhD, PT Empowering the Patient After Spinal Cord Injury Guy W. Fried, ...

  5. Radionuclide Basics: Iodine

    Science.gov (United States)

    ... Search Radiation Protection Contact Us Share Radionuclide Basics: Iodine Iodine (chemical symbol I) is a chemical element. ... in the environment Iodine sources Iodine and health Iodine in the Environment All 37 isotopes of iodine ...

  6. Basic Concurrency Theory

    DEFF Research Database (Denmark)

    Løvengreen, Hans Henrik

    2002-01-01

    In this set of notes, we present some of the basic theory underlying the discipline of programming with concurrent processes/threads. The notes are intended to supplement a standard textbook on concurrent programming.......In this set of notes, we present some of the basic theory underlying the discipline of programming with concurrent processes/threads. The notes are intended to supplement a standard textbook on concurrent programming....

  7. Transportation Emissions: some basics

    DEFF Research Database (Denmark)

    Kontovas, Christos A.; Psaraftis, Harilaos N.

    2016-01-01

    . The main purpose of this chapter is to introduce some basic concepts that are relevant in the quest of green transportation logistics. First, we present the basics of estimating emissions from transportation activities, the current statistics and future trends, as well as the total impact of air emissions...... of the energy efficiency gap and examines why governments and companies may forego cost-effective investments in energy efficiency, even though they could significantly reduce energy consumption at a lower cost....

  8. Basic Finite Element Method

    International Nuclear Information System (INIS)

    Lee, Byeong Hae

    1992-02-01

    This book gives descriptions of basic finite element method, which includes basic finite element method and data, black box, writing of data, definition of VECTOR, definition of matrix, matrix and multiplication of matrix, addition of matrix, and unit matrix, conception of hardness matrix like spring power and displacement, governed equation of an elastic body, finite element method, Fortran method and programming such as composition of computer, order of programming and data card and Fortran card, finite element program and application of nonelastic problem.

  9. Basic Monetary Economics

    OpenAIRE

    Farm, Ante

    2017-01-01

    This is an introduction to money and the workings of the financial system. The creation of money is discussed in detail in Chapter 1. Chapter 2 explains how international payments can add to money creation but also generate a new type of money, usually called Eurodollars. Basic securities are defined and characterized in Chapter 3, namely bills, bonds and shares, but basic derivatives, like futures, swaps, and options, are also discussed. Chapter 4 deals with pricing by banks when extending l...

  10. Catalyst in Basic Oleochemicals

    OpenAIRE

    Eva Suyenty; Herlina Sentosa; Mariani Agustine; Sandy Anwar; Abun Lie; Erwin Sutanto

    2007-01-01

    Currently Indonesia is the world largest palm oil producer with production volume reaching 16 million tones per annum. The high crude oil and ethylene prices in the last 3 – 4 years contribute to the healthy demand growth for basic oleochemicals: fatty acids and fatty alcohols. Oleochemicals are starting to replace crude oil derived products in various applications. As widely practiced in petrochemical industry, catalyst plays a very important role in the production of basic oleochemic...

  11. Molecular phylogenetics before sequences: oligonucleotide catalogs as k-mer spectra.

    Science.gov (United States)

    Ragan, Mark A; Bernard, Guillaume; Chan, Cheong Xin

    2014-01-01

    From 1971 to 1985, Carl Woese and colleagues generated oligonucleotide catalogs of 16S/18S rRNAs from more than 400 organisms. Using these incomplete and imperfect data, Carl and his colleagues developed unprecedented insights into the structure, function, and evolution of the large RNA components of the translational apparatus. They recognized a third domain of life, revealed the phylogenetic backbone of bacteria (and its limitations), delineated taxa, and explored the tempo and mode of microbial evolution. For these discoveries to have stood the test of time, oligonucleotide catalogs must carry significant phylogenetic signal; they thus bear re-examination in view of the current interest in alignment-free phylogenetics based on k-mers. Here we consider the aims, successes, and limitations of this early phase of molecular phylogenetics. We computationally generate oligonucleotide sets (e-catalogs) from 16S/18S rRNA sequences, calculate pairwise distances between them based on D 2 statistics, compute distance trees, and compare their performance against alignment-based and k-mer trees. Although the catalogs themselves were superseded by full-length sequences, this stage in the development of computational molecular biology remains instructive for us today.

  12. Sequence-Dependent Mechanism of DNA Oligonucleotide Dehybridization Resolved through Infrared Spectroscopy.

    Science.gov (United States)

    Sanstead, Paul J; Stevenson, Paul; Tokmakoff, Andrei

    2016-09-14

    Despite its important role in biology and nanotechnology, many questions remain regarding the molecular mechanism and dynamics by which oligonucleotides recognize and hybridize to their complementary sequence. The thermodynamics and kinetics of DNA oligonucleotide hybridization and dehybridization are often assumed to involve an all-or-nothing two-state dissociation pathway, but deviations from this behavior can be considerable even for short sequences. We introduce a new strategy to characterize the base-pair-specific thermal dissociation mechanism of DNA oligonucleotides through steady-state and time-resolved infrared spectroscopy. Experiments are interpreted with a lattice model to provide a structure-specific interpretation. This method is applied to a model set of self-complementary 10-base-pair sequences in which the placement of GC base pairs is varied in an otherwise AT strand. Through a combination of Fourier transform infrared and two-dimensional infrared spectroscopy, experiments reveal varying degrees of deviation from simple two-state behavior. As the temperature is increased, duplexes dissociate through a path in which the terminal bases fray, without any significant contribution from loop configurations. Transient temperature jump experiments reveal time scales of 70-100 ns for fraying and 10-30 μs for complete dissociation near the melting temperature. Whether or not frayed states are metastable intermediates or short-lived configurations during the full dissociation of the duplex is dictated by the nucleobase sequence.

  13. Intercalation of single-strand oligonucleotides between nucleolipid anionic membranes: a neutron diffraction study.

    Science.gov (United States)

    Milani, Silvia; Berti, Debora; Dante, Silvia; Hauss, Thomas; Baglioni, Piero

    2009-04-07

    This contribution presents a neutron diffraction investigation of anionic lamellar phases composed of mixtures of 1-palmitoyl, 2-oleoyl phosphatidyl-nucleosides (POPN, where N is either adenosine or uridine), and POPC (1-palmitoyl,2-oleoyl-phosphatidyl-choline). Their behavior is studied for two different mole ratios and in the presence of nucleic acids. The samples are formed by the evaporation of liposomal dispersions prepared in water or in solutions containing single-strand oligonucleotides. Previous small angle X-ray scattering (SAXS) experiments on the system POPA/polyU (polyuridylic acid, high degree of polymerization, synthetic ribonucleic acid) proved that the insertion and ordering of the biopolymer in the phospholipid lamellae were driven by molecular recognition. In the present study, we extend the previous investigation to single-strand monodisperse oligonucleotides (50-mers). Structural details of the membranes were obtained from the analysis of the neutron diffraction scattering length density profiles. The evidence of direct and specific interactions, driven by molecular recognition between the nucleic polar heads of the nucleolipid and the single-strand nucleic acid, is strengthened by the comparison with identically charged bilayers formed by POPG/POPC. These results contribute to the understanding of the parameters governing the interactions between nucleolipid membranes and oligonucleotides, providing a novel strategy for the design of lipid-based vehicles for nucleic acids.

  14. Development of Multiexon Skipping Antisense Oligonucleotide Therapy for Duchenne Muscular Dystrophy

    Directory of Open Access Journals (Sweden)

    Yoshitsugu Aoki

    2013-01-01

    Full Text Available Duchenne muscular dystrophy (DMD is an incurable, X-linked progressive muscle degenerative disorder that results from the absence of dystrophin protein and leads to premature death in affected individuals due to respiratory and/or cardiac failure typically by age of 30. Very recently the exciting prospect of an effective oligonucleotide therapy has emerged which restores dystrophin protein expression to affected tissues in DMD patients with highly promising data from a series of clinical trials. This therapeutic approach is highly mutation specific and thus is personalised. Therefore DMD has emerged as a model genetic disorder for understanding and overcoming of the challenges of developing personalised genetic medicines. One of the greatest weaknesses of the current oligonucleotide approach is that it is a mutation-specific therapy. To address this limitation, we have recently demonstrated that exons 45–55 skipping therapy has the potential to treat clusters of mutations that cause DMD, which could significantly reduce the number of compounds that would need to be developed in order to successfully treat all DMD patients. Here we discuss and review the latest preclinical work in this area as well as a variety of accompanying issues, including efficacy and potential toxicity of antisense oligonucleotides, prior to human clinical trials.

  15. 18F-labelling of oligonucleotides using succinimido 4-[18F]fluorobenzoat

    International Nuclear Information System (INIS)

    Hedberg, Elisabeth; Laangstroem, Bengt

    1998-01-01

    A general method for the labelling of oligodeoxynucleotide and oligonucleoside phosphorothioates in the 5'-position with the positron-emitting radionuclide 18 F (t 1/2 = 110 min) is described. The label was incorporated by the reaction of succinimido 4 -[ 18 F]fluorobenzoate 4 with oligonucleotides (18- and 20-mers) modified in the 5'-position with a hexylamine linker. Oligodeoxynucleotides 5'-GCT,AAG,CGA,TGC,CTC,CGT-3' (MTCa) and 5'-GAA,CCT,CTG,AGA,GTT,CAT,CT-3' (CROa) were labelled in 20±3 % (MTCa) and 13±3 % (CROa) radiochemical yields (non-isolated, decay-corrected and based on 4). Oligonucleoside phosphorotioates MTCa (S-MTCa) and CROa (S-CROa) were labelled in 9 and 7% isolated radiochemical yield, respectively (decay-corrected and based on 4). Labelled oligonucleotides and phosphorothioate analogues were separated from their unlabelled counterparts using reversed-phase perfusion chromatography. The molecular mass of a labelled oligonucleotide CROa was determined by ESI-MS after a mixed 18 F/ 19 F fluorobenzoate labelling experiment and corresponded with the expected structure. (au)

  16. Specificity tests of an oligonucleotide probe against food-outbreak salmonella for biosensor detection

    Science.gov (United States)

    Chen, I.-H.; Horikawa, S.; Xi, J.; Wikle, H. C.; Barbaree, J. M.; Chin, B. A.

    2017-05-01

    Phage based magneto-elastic (ME) biosensors have been shown to be able to rapidly detect Salmonella in various food systems to serve food pathogen monitoring purposes. In this ME biosensor platform, the free-standing strip-shaped magneto-elastic sensor is the transducer and the phage probe that recognizes Salmonella in food serves as the bio-recognition element. According to Sorokulova et al. at 2005, a developed oligonucleotide probe E2 was reported to have high specificity to Salmonella enterica Typhimurium. In the report, the specificity tests were focused in most of Enterobacterace groups outside of Salmonella family. Here, to understand the specificity of phage E2 to different Salmonella enterica serotypes within Salmonella Family, we further tested the specificity of the phage probe to thirty-two Salmonella serotypes that were present in the major foodborne outbreaks during the past ten years (according to Centers for Disease Control and Prevention). The tests were conducted through an Enzyme linked Immunosorbent Assay (ELISA) format. This assay can mimic probe immobilized conditions on the magnetoelastic biosensor platform and also enable to study the binding specificity of oligonucleotide probes toward different Salmonella while avoiding phage/ sensor lot variations. Test results confirmed that this oligonucleotide probe E2 was high specific to Salmonella Typhimurium cells but showed cross reactivity to Salmonella Tennessee and four other serotypes among the thirty-two tested Salmonella serotypes.

  17. Development of Multiexon Skipping Antisense Oligonucleotide Therapy for Duchenne Muscular Dystrophy

    Science.gov (United States)

    Yokota, Toshifumi; Wood, Matthew J. A.

    2013-01-01

    Duchenne muscular dystrophy (DMD) is an incurable, X-linked progressive muscle degenerative disorder that results from the absence of dystrophin protein and leads to premature death in affected individuals due to respiratory and/or cardiac failure typically by age of 30. Very recently the exciting prospect of an effective oligonucleotide therapy has emerged which restores dystrophin protein expression to affected tissues in DMD patients with highly promising data from a series of clinical trials. This therapeutic approach is highly mutation specific and thus is personalised. Therefore DMD has emerged as a model genetic disorder for understanding and overcoming of the challenges of developing personalised genetic medicines. One of the greatest weaknesses of the current oligonucleotide approach is that it is a mutation-specific therapy. To address this limitation, we have recently demonstrated that exons 45–55 skipping therapy has the potential to treat clusters of mutations that cause DMD, which could significantly reduce the number of compounds that would need to be developed in order to successfully treat all DMD patients. Here we discuss and review the latest preclinical work in this area as well as a variety of accompanying issues, including efficacy and potential toxicity of antisense oligonucleotides, prior to human clinical trials. PMID:23984357

  18. An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes.

    Science.gov (United States)

    Le Brigand, Kévin; Russell, Roslin; Moreilhon, Chimène; Rouillard, Jean-Marie; Jost, Bernard; Amiot, Franck; Magnone, Virginie; Bole-Feysot, Christine; Rostagno, Philippe; Virolle, Virginie; Defamie, Virginie; Dessen, Philippe; Williams, Gary; Lyons, Paul; Rios, Géraldine; Mari, Bernard; Gulari, Erdogan; Kastner, Philippe; Gidrol, Xavier; Freeman, Tom C; Barbry, Pascal

    2006-07-19

    Two collections of oligonucleotides have been designed for preparing pangenomic human and mouse microarrays. A total of 148,993 and 121,703 oligonucleotides were designed against human and mouse transcripts. Quality scores were created in order to select 25,342 human and 24,109 mouse oligonucleotides. They correspond to: (i) a BLAST-specificity score; (ii) the number of expressed sequence tags matching each probe; (iii) the distance to the 3' end of the target mRNA. Scores were also used to compare in silico the two microarrays with commercial microarrays. The sets described here, called RNG/MRC collections, appear at least as specific and sensitive as those from the commercial platforms. The RNG/MRC collections have now been used by an Anglo-French consortium to distribute more than 3500 microarrays to the academic community. Ad hoc identification of tissue-specific transcripts and a approximately 80% correlation with hybridizations performed on Affymetrix GeneChiptrade mark suggest that the RNG/MRC microarrays perform well. This work provides a comprehensive open resource for investigators working on human and mouse transcriptomes, as well as a generic method to generate new microarray collections in other organisms. All information related to these probes, as well as additional information about commercial microarrays have been stored in a freely-accessible database called MEDIANTE.

  19. Methicillin-Resistant Bacteria Inhabiting Surface Waters Monitored by mecA-Targeted Oligonucleotide Probes.

    Science.gov (United States)

    Seyedmonir, Elnaz; Yilmaz, Fadime; Icgen, Bulent

    2016-08-01

    Part of a 20-60 kb staphylococcal chromosome cassette called mecA encodes low-affinity penicillin-binding protein PBP2a and causes methicillin resistance. Among all methicillin-resistant bacteria, methicillin-resistant Staphylococcus aureus is a major pathogen and main concern worldwide. Although the origin of the mecA is not very well-defined, mecA homologues are also ubiquitous in methicillin-resistant non-staphylococcal bacteria. Due to the dissemination of methicillin resistance through the transmission of mecA gene among staphylococcal and non-staphylococcal bacteria inhabiting surface waters, there is a need to monitor mecA gene in these waters for public health safety. Therefore, this study aimed at monitoring mecA harboring bacteria inhabiting surface waters by using fluorescently labelled mecA-targeted oligonucleotide probes. Under the hybridization conditions of 55 % formamide and 0.020 M NaCl at 46°C, the oligonucleotide probe used in the study showed high hybridization stringency to the mecA gene targeted. The strong linear relationships observed between the signal intensity and the target gene were used to assess the population dynamics of mecA harboring isolates over a 2-year-period. The results indicated that mecA-targeted oligonucleotide probes can be effectively used for in situ monitoring of methicillin resistant isolates inhabiting surface waters.

  20. Controlling with light the interaction between trans-tetrapyridyl ruthenium complexes and an oligonucleotide.

    Science.gov (United States)

    van Rixel, Vincent H S; Moolenaar, Geri F; Siegler, Maxime A; Messori, Luigi; Bonnet, Sylvestre

    2018-01-02

    Three new trans-ruthenium(ii) complexes coordinated to tetrapyridyl ligands, namely [Ru(bapbpy)(dmso)Cl]Cl ([2]Cl), [Ru(bapbpy)(Hmte) 2 ](PF 6 ) 2 ([3](PF 6 ) 2 ), and [Ru(biqbpy)(Hmte) 2 ](PF 6 ) 2 ([4](PF 6 ) 2 ), were prepared as analogues of [Ru(biqbpy)(dmso)Cl]Cl ([1]Cl), a recently described photoactivated chemotherapy agent. The new complexes were characterized, and their crystal structures showed the distorted coordination octahedron typical of this family of complexes. Their photoreactivity in solution was analyzed by spectrophotometry and mass spectrometry, which showed that the sulfur ligand was substituted upon blue light irradiation. The binding of the ruthenium complexes to a reference single-stranded oligonucleotide (s( 5' CTACGGTTTCAC 3' )) was explored both in the dark and under light irradiation by gel electrophoresis and high-resolution mass spectrometry. While adduct formation in the dark was negligible for the four complexes, light irradiation led to the formation of adducts with one or two ruthenium centers per oligonucleotide. The absence of interactions in the dark and the presence of complex-oligonucleotide adducts demonstrate that visible light controls the interaction of these ruthenium complexes with nucleic acids.

  1. Membrane-based oligonucleotide array developed from multiple markers for the detection of many Phytophthora species.

    Science.gov (United States)

    Chen, Wen; Djama, Zeinab Robleh; Coffey, Michael D; Martin, Frank N; Bilodeau, Guillaume J; Radmer, Lorien; Denton, Geoff; Lévesque, C André

    2013-01-01

    Most Phytophthora spp. are destructive plant pathogens; therefore, effective monitoring and accurate early detection are important means of preventing potential epidemics and outbreaks of diseases. In the current study, a membrane-based oligonucleotide array was developed that can detect Phytophthora spp. reliably using three DNA regions; namely, the internal transcribed spacer (ITS), the 5' end of cytochrome c oxidase 1 gene (cox1), and the intergenic region between cytochrome c oxidase 2 gene (cox2) and cox1 (cox2-1 spacer). Each sequence data set contained ≈250 sequences representing 98 described and 15 undescribed species of Phytophthora. The array was validated with 143 pure cultures and 35 field samples. Together, nonrejected oligonucleotides from all three markers have the ability to reliably detect 82 described and 8 undescribed Phytophthora spp., including several quarantine or regulated pathogens such as Phytophthora ramorum. Our results showed that a DNA array containing signature oligonucleotides designed from multiple genomic regions provided robustness and redundancy for the detection and differentiation of closely related taxon groups. This array has the potential to be used as a routine diagnostic tool for Phytophthora spp. from complex environmental samples without the need for extensive growth of cultures.

  2. Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides

    Directory of Open Access Journals (Sweden)

    Olga A. Krasheninina

    2017-11-01

    Full Text Available In this review, we summarize the recent advances in the use of pyrene-modified oligonucleotides as a platform for functional nucleic acid-based constructs. Pyrene is of special interest for the development of nucleic acid-based tools due to its unique fluorescent properties (sensitivity of fluorescence to the microenvironment, ability to form excimers and exciplexes, long fluorescence lifetime, high quantum yield, ability to intercalate into the nucleic acid duplex, to act as a π-π-stacking (including anchoring moiety, and others. These properties of pyrene have been used to construct novel sensitive fluorescent probes for the sequence-specific detection of nucleic acids and the discrimination of single nucleotide polymorphisms (SNPs, aptamer-based biosensors, agents for binding of double-stranded DNAs, and building blocks for supramolecular complexes. Special attention is paid to the influence of the design of pyrene-modified oligonucleotides on their properties, i.e., the structure-function relationships. The perspectives for the applications of pyrene-modified oligonucleotides in biomolecular studies, diagnostics, and nanotechnology are discussed.

  3. Surface patterns of Sotalia guianensis (Cetacea: Delphinidae in the presence of boats in Port of Malhado, Ilhéus, Bahia, Brazil

    Directory of Open Access Journals (Sweden)

    Mariana S Santos

    2013-03-01

    Full Text Available Interactions with boats can cause several behavioural changes in cetaceans. The purpose of this research is to analyse if Guiana dolphins, Sotalia guianensis, change their surfacing patterns in the presence of different boat categories, and their contact distances to boats at Port of Malhado, Ilheus, Bahia, Brazil. Data were collected from a fixed point from September 2008 to August 2009 and totalled 362.6 h of sampling effort and 213.22 h of effective effort. The number of dolphin breathing events was recorded during one minute periods, every time a boat passed nearby, and the same measurements were performed during periods of boat absence (control. Dolphin group composition was classified into groups with calves and groups without calves. Boat types were classified as inboard motor (IM, outboard motor (OM, ships (S and without a motor (WM. Distances between the dolphins and passing boats were classified as near, intermediate and far. In total, 365 samples of one minute observations in absence of boats, and 379 observations in their presence were collected. Inboard motorboats had the highest occurrence in the study area (n = 478 and in interactions with Guiana dolphins (n = 260. However, outboard motorboats were mainly responsible for the reduction in surface patterns with an average of 1.82 and median of 2.2. In groups with calves, the number of breaths decreased significantly with an average of 2.13 per minute. There were no significant variations concerning the distances in the breathing pattern for any of the boat categories. The variation in the S. guianensis breathing pattern in the presence of boats may be a strategy of boat avoidance or a response to the difficulty of communication between animals.

  4. Development of boats propelled by fuel cells; Developpement d'embarcations mues par piles a combustible

    Energy Technology Data Exchange (ETDEWEB)

    Affolter, J.F.; Mariotti, P. [Ecole d' Ingenieurs du Canton de Vaud, HES-SO, Yverdon les Bains (Switzerland)

    2000-07-01

    An important European demand for propulsion systems lead us to think that the number of electric ships is growing rapidly. A lot of lakes in Europe are not allowed to the thermal navigation. The aim is to offer a maximum of comfort, reliability, silence, lack of pollution and respect to environment. One of the answers to this expectation is the use of the electric propulsion and a generation of power with fuel cells. After having fabricated the 'Hydroxy100', a single-seater boat propelled by a 100 W fuel cell, and a two-seater boat designed for a 300 W fuel cell, a new plan for a six-seater pleasure boat is being studied. These pilot plans are carried out with the aim to favour the development of this technology. (O.M.)

  5. Oligonucleotide and Parylene Surface Coating of Polystyrene and ePTFE for Improved Endothelial Cell Attachment and Hemocompatibility

    Directory of Open Access Journals (Sweden)

    Martina Schleicher

    2012-01-01

    Full Text Available In vivo self-endothelialization by endothelial cell adhesion on cardiovascular implants is highly desirable. DNA-oligonucleotides are an intriguing coating material with nonimmunogenic characteristics and the feasibility of easy and rapid chemical fabrication. The objective of this study was the creation of cell adhesive DNA-oligonucleotide coatings on vascular implant surfaces. DNA-oligonucleotides immobilized by adsorption on parylene (poly(monoaminomethyl-para-xylene coated polystyrene and ePTFE were resistant to high shear stress (9.5 N/m2 and human blood serum for up to 96 h. Adhesion of murine endothelial progenitor cells, HUVECs and endothelial cells from human adult saphenous veins as well as viability over a period of 14 days of HUVECs on oligonucleotide coated samples under dynamic culture conditions was significantly enhanced (P<0.05. Oligonucleotide-coated surfaces revealed low thrombogenicity and excellent hemocompatibility after incubation with human blood. These properties suggest the suitability of immobilization of DNA-oligonucleotides for biofunctionalization of blood vessel substitutes for improved in vivo endothelialization.

  6. An Energy Management System of a Fuel Cell/Battery Hybrid Boat

    Directory of Open Access Journals (Sweden)

    Jingang Han

    2014-04-01

    Full Text Available All-electric ships are now a standard offering for energy/propulsion systems in boats. In this context, integrating fuel cells (FCs as power sources in hybrid energy systems can be an interesting solution because of their high efficiency and low emission. The energy management strategy for different power sources has a great influence on the fuel consumption, dynamic performance and service life of these power sources. This paper presents a hybrid FC/battery power system for a low power boat. The hybrid system consists of the association of a proton exchange membrane fuel cell (PEMFC and battery bank. The mathematical models for the components of the hybrid system are presented. These models are implemented in Matlab/Simulink environment. Simulations allow analyzing the dynamic performance and power allocation according to a typical driving cycle. In this system, an efficient energy management system (EMS based on operation states is proposed. This EMS strategy determines the operating point of each component of the system in order to maximize the system efficiency. Simulation results validate the adequacy of the hybrid power system and the proposed EMS for real ship driving cycles.

  7. Worlds Apart: Nam Le’s The Boat and Ali Alizadeh’s Transactions

    Directory of Open Access Journals (Sweden)

    Lachlan Brown

    2015-05-01

    Full Text Available This paper reads Ali Alizadeh’s transnational book of short stories (Transactions, 2013 as a curious and pointed response to the kind of literary internationalism seen in Nam Le’s The Boat (2008. Le’s work was first published in the same year as Alizadeh’s The New Angel (which was set during the Iranian revolution. There is a sense in which the spectacular success of Le’s book ‘overshadowed’ the publicity for Alizadeh’s novel in the year of its arrival. But Le’s also work contains a story about an American woman visiting Tehran, and his mimicry perhaps signifies a more problematic representational point of comparison. With this in mind, this paper examines Alizadeh’s Transactions exploring the ways in which Alizadeh’s brutally connected global vision is coded through certain aesthetic choices (including structural, tonal and descriptive that offer something very different to the artisanal and paratactic sensibility of The Boat.

  8. A Path Model of Whitewater Boating Satisfaction on the Cheat River of West Virginia

    Science.gov (United States)

    Whisman; Hollenhorst

    1998-01-01

    / Recreation satisfaction is a complex psychological construct that is difficult to define and measure. Recent approaches suggest that overall satisfaction may be a function of multiple satisfactions derived from specific elements of a recreation experience such as the situational characteristics of a recreation setting or activity and the recreationist's subjective evaluations of the experience. In this paper, a path model of whitewater boating satisfaction was tested using data from a survey of 1210 commercial and 111 private boaters on the Cheat River of West Virginia. The pathmodel included the direct and mediating effects of situational variables and the subjective evaluations of boaters and explained 52% and 54% of the variation in satisfaction of commercial and private boaters, respectively. Factors related to the satisfaction of both groups included a composite variable representing opportunities for challenge, excitement, and skill testing on the river trip; water flow levels; and crowding perceptions. In combination, water flow level and boater's perceptions of opportunities to experience challenge, excitement, and test boating skills were the most important variables for explaining satisfaction of both groups. Additional factors affecting commercial, but not private, boater satisfaction included the motive of escaping the usual demands of life and a social interaction variable. Among private boaters, perceptions of the environmental conditions also contributed to overall satisfaction. The results support the multiple satisfaction approach of previous research. River management implications are discussed.KEY WORDS: Whitewater; River recreation; Satisfaction

  9. Development of Autonomous Boat-Type Robot for Automated Velocity Measurement in Straight Natural River

    Science.gov (United States)

    Sanjou, Michio; Nagasaka, Tsuyoshi

    2017-11-01

    The present study describes an automated system to measure the river flow velocity. A combination of the camera-tracking system and the Proportional/Integral/Derivative (PID) control could enable the boat-type robot to remain in position against the mainstream; this results in reasonable evaluation of the mean velocity by a duty ratio which corresponds to rotation speed of the screw propeller. A laser range finder module was installed to measure the local water depth. Reliable laboratory experiments with the prototype boat robot and electromagnetic velocimetry were conducted to obtain a calibration curve that connects the duty ratio and mean current velocity. The remaining accuracy in the target point was also examined quantitatively. The fluctuation in the spanwise direction is within half of the robot length. It was therefore found that the robot remains well within the target region. We used two-dimensional navigation tests to guarantee that the prototype moved smoothly to the target points and successfully measured the streamwise velocity profiles across the mainstream. Moreover, the present robot was found to move successfully not only in the laboratory flume but also in a small natural river. The robot could move smoothly from the starting point near the operator's site toward the target point where the velocity is measured, and it could evaluate the cross-sectional discharge.

  10. Development and evaluation of a boat-mounted RFID antenna for monitoring freshwater mussels

    Science.gov (United States)

    Fischer, Jesse R.; Neebling, Travis E.; Quist, Michael C.

    2012-01-01

    Development of radio frequency identification (RFID) technology and passive integrated transponder (PIT) tags has substantially increased the ability of researchers and managers to monitor populations of aquatic organisms. However, use of transportable RFID antenna systems (i.e., backpack-mounted) is currently limited to wadeable aquatic environments (RFID antenna to detect individually PIT-tagged benthic aquatic organisms (mussels). We evaluated the effects of tag orientation on detection distances in water with a 32-mm half-duplex PIT tag. Detection distances up to 50 cm from the antenna coils were obtained, but detection distance was dependent on tag orientation. We also evaluated detection distance of PIT tags beneath the sediment to simulate detection of burrowing mussels with 23- and 32-mm tags. In sand substrate, the maximum detection distance varied from 3.5 cm and 4.5 cm (vertical tag orientation) to 24.7 cm and 39.4 cm (45° tag orientation) for the 23- and 32-mm PIT tags, respectively. Our results suggest a 1.4-m total detection width for tagged mussels on the substrate surface by the boat-mounted antenna system regardless of tag orientation. However, burrowed mussels may require multiple passes to increase detection that would be influenced by depth, tag orientation, and tag size. Construction of the boat-mounted antenna was relatively low in cost (<500 USD) and had several advantages (less labor and time intensive, increased safety) over traditional mussel sampling techniques (diving, snorkeling) in nonwadeable habitats.

  11. Metal contamination of sediment by paint peeling from abandoned boats, with particular reference to lead.

    Science.gov (United States)

    Rees, Aldous B; Turner, Andrew; Comber, Sean

    2014-10-01

    Fragments of flaking paint have been sampled from eighteen boats (including sailing barges, houseboats, a trawler and a ferry) abandoned on the intertidal mudflats of two estuaries in eastern England and analysed for Cu, Pb and Zn by X-ray fluorescence (XRF) spectrometry. Median concentrations of Pb on each boat ranged from about 350 to 35,000 μg g(-1), with individual concentrations exceeding 200,000 μg g(-1) in several cases. Median concentrations of Cu and Zn ranged from about 50 to 1900 μg g(-1) and 50 to 10,000 μg g(-1), respectively, with respective maxima of 172,000 μg g(-1) and 239,000 μg g(-1). Because of peeling paint, local sediment (analysed by ICP following acid digestion) was often measurably contaminated by the metals and, based on median, Al-normalised enrichment factors, in the order Pb>Zn>Cu. Due to its abundance and persistence in old paints, Pb is of greatest concern from both environmental and human health perspectives. Copyright © 2014 Elsevier B.V. All rights reserved.

  12. Toxicological assessment and management options for boat pressure-washing wastewater.

    Science.gov (United States)

    Gerić, Marko; Gajski, Goran; Oreščanin, Višnja; Kollar, Robert; Franekić, Jasna; Garaj-Vrhovac, Vera

    2015-04-01

    Boats are washed periodically for maintenance in order to remove biofoulants from hulls, which results in the generation of wastewater. This study aimed at evaluating the cyto/genotoxic and mutagenic properties of wastewater produced by pressure washing of boats. The chemical characterisation of this wastewater showed that Cu, Zn, V, Cr, Fe, Pb, and select organic contaminants exceeded the maximum allowable values from 1.7 up to 96 times. The wastewater produced negative effects on human lymphocytes resulting in decreased cell viability after 4 and 24h of exposure. Chromosome aberration, micronucleus, and comet assay parameters were significantly higher after 24h of exposure. At the same time, the Salmonella typhimurium test showed negative for both TA98 and TA100 strains at all of the concentrations tested. After the treatment of wastewater using electrochemical methods/ozonation during real scale treatment plant, removal rates of colour, turbidity and heavy metals ranged from 99.4% to 99.9%, while the removal of total organic carbon (TOC) and chemical oxygen demand (COD) was above 85%. This was reflected in the removal of the wastewater's cyto/genotoxicity, which was comparable to negative controls in all of the conducted tests, suggesting that such plants could be implemented in marinas to minimise human impact on marine systems. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. Feasibility of using Big Area Additive Manufacturing to Directly Manufacture Boat Molds

    Energy Technology Data Exchange (ETDEWEB)

    Post, Brian K. [ORNL; Chesser, Phillip C. [ORNL; Lind, Randall F. [ORNL; Sallas, Matthew R. [ORNL; Love, Lonnie J. [ORNL

    2018-01-01

    The goal of this project was to explore the feasibility of using Big Area Additive Manufacturing (BAAM) to directly manufacture a boat mold without the need for coatings. All prior tooling projects with BAAM required the use to thick coatings to overcome the surface finish limitations of the BAAM process. While the BAAM process significantly lowers the cost of building the mold, the high cost element rapidly became the coatings (cost of the material, labor on coating, and finishing). As an example, the time and cost to manufacture the molds for the Wind Turbine project with TPI Composites Inc. and the molds for the submarine project with Carderock Naval Warfare Systems was a fraction of the time and cost of the coatings. For this project, a catamaran boat hull mold was designed, manufactured, and assembled with an additional 0.15” thickness of material on all mold surfaces. After printing, the mold was immediately machined and assembled. Alliance MG, LLC (AMG), the industry partner of this project, experimented with mold release agents on the carbon-fiber reinforced acrylonitrile butadiene styrene (CF ABS) to verify that the material can be directly used as a mold (rather than needing a coating). In addition, for large molds (such as the wind turbine mold with TPI Composites Inc.), the mold only provided the target surface. A steel subframe had to be manufactured to provide structural integrity. If successful, this will significantly reduce the time and cost necessary for manufacturing large resin infusion molds using the BAAM process.

  14. Pellet-press-to-sintering-boat nuclear fuel pellet loading system

    International Nuclear Information System (INIS)

    Bucher, G.D.

    1988-01-01

    This patent describes a system for loading nuclear fuel pellets into a sintering boat from a pellet press which ejects newly made the pellets from a pellet press die table surface. The system consists of: (a) a bowl having an inner surface, a longitudinal axis, an open and generally circular top of larger diameter, and an open and generally circular bottom of smaller diameter; (b) means for supporting the bowl in a generally upright position such that the bowl is rotatable about its longitudinal axis; (c) means for receiving the ejected pellets proximate the die table surface of the pellet press and for discharging the received pellets into the bowl at a location proximate the inner surface towards the top of the bowl with a pellet velocity having a horizontal component which is generally tangent to the inner surface of the bowl proximate the location; (d) means for rotating the bowl about the longitudinal axis such that the bowl proximate the location has a velocity generally equal, in magnitude and direction, to the horizontal component of the pellet velocity at the location; and (e) means for moving the sintering boat generally horizontally beneath and proximate the bottom of the bowl

  15. The Effect of STEM Learning through the Project of Designing Boat Model toward Student STEM Literacy

    Science.gov (United States)

    Tati, T.; Firman, H.; Riandi, R.

    2017-09-01

    STEM Learning focusses on development of STEM-literate society, the research about implementation of STEM learning to develope students’ STEM literacy is still limited. This study is aimed to examine the effect of implementation STEM learning through the project of designing boat model on students STEM literacy in energy topic. The method of this study was a quasi-experiment with non-randomized pretest-posttest control group design. There were two classes involved, the experiment class used Project Based Learning with STEM approach and control class used Project-Based Learning without STEM approach. A STEM Literacy test instrument was developed to measure students STEM literacy which consists of science literacy, mathematics literacy, and technology-engineering literacy. The analysis showed that there were significant differences on improvement science literacy, mathematics technology-engineering between experiment class and control class with effect size more than 0.8 (large effect). The difference of improvement of STEM literacy between experiment class and control class is caused by the existence of design engineering activity which required students to apply the knowledge from every field of STEM. The challenge that was faced in STEM learning through design engineering activity was how to give the students practice to integrate STEM field in solving the problems. In additional, most of the students gave positive response toward implementation of STEM learning through design boat model project.

  16. Measuring discharge with acoustic Doppler current profilers from a moving boat

    Science.gov (United States)

    Mueller, David S.; Wagner, Chad R.; Rehmel, Michael S.; Oberg, Kevin A.; Rainville, Francois

    2013-01-01

    The use of acoustic Doppler current profilers (ADCPs) from a moving boat is now a commonly used method for measuring streamflow. The technology and methods for making ADCP-based discharge measurements are different from the technology and methods used to make traditional discharge measurements with mechanical meters. Although the ADCP is a valuable tool for measuring streamflow, it is only accurate when used with appropriate techniques. This report presents guidance on the use of ADCPs for measuring streamflow; this guidance is based on the experience of U.S. Geological Survey employees and published reports, papers, and memorandums of the U.S. Geological Survey. The guidance is presented in a logical progression, from predeployment planning, to field data collection, and finally to post processing of the collected data. Acoustic Doppler technology and the instruments currently (2013) available also are discussed to highlight the advantages and limitations of the technology. More in-depth, technical explanations of how an ADCP measures streamflow and what to do when measuring in moving-bed conditions are presented in the appendixes. ADCP users need to know the proper procedures for measuring discharge from a moving boat and why those procedures are required, so that when the user encounters unusual field conditions, the procedures can be adapted without sacrificing the accuracy of the streamflow-measurement data.

  17. Basic Electromagnetism and Materials

    CERN Document Server

    Moliton, André

    2007-01-01

    Basic Electromagnetism and Materials is the product of many years of teaching basic and applied electromagnetism. This textbook can be used to teach electromagnetism to a wide range of undergraduate science majors in physics, electrical engineering or materials science. However, by making lesser demands on mathematical knowledge than competing texts, and by emphasizing electromagnetic properties of materials and their applications, this textbook is uniquely suited to students of materials science. Many competing texts focus on the study of propagation waves either in the microwave or optical domain, whereas Basic Electromagnetism and Materials covers the entire electromagnetic domain and the physical response of materials to these waves. Professor André Moliton is Director of the Unité de Microélectronique, Optoélectronique et Polymères (Université de Limoges, France), which brings together three groups studying the optoelectronics of molecular and polymer layers, micro-optoelectronic systems for teleco...

  18. Comprehensive basic mathematics

    CERN Document Server

    Veena, GR

    2005-01-01

    Salient Features As per II PUC Basic Mathematics syllabus of Karnataka. Provides an introduction to various basic mathematical techniques and the situations where these could be usefully employed. The language is simple and the material is self-explanatory with a large number of illustrations. Assists the reader in gaining proficiency to solve diverse variety of problems. A special capsule containing a gist and list of formulae titled ''REMEMBER! Additional chapterwise arranged question bank and 3 model papers in a separate section---''EXAMINATION CORNER''.

  19. Basic Financial Accounting

    DEFF Research Database (Denmark)

    Wiborg, Karsten

    This textbook on Basic Financial Accounting is targeted students in the economics studies at universities and business colleges having an introductory subject in the external dimension of the company's economic reporting, including bookkeeping, etc. The book includes the following subjects: busin......: business entities, the transformation process, types of businesses, stakeholders, legislation, the annual report, the VAT system, double-entry bookkeeping, inventories, and year-end cast flow analysis.......This textbook on Basic Financial Accounting is targeted students in the economics studies at universities and business colleges having an introductory subject in the external dimension of the company's economic reporting, including bookkeeping, etc. The book includes the following subjects...

  20. Ecology and basic laws

    International Nuclear Information System (INIS)

    Mayer-Tasch, P.C.

    1980-01-01

    The author sketches the critical relation between ecology and basic law - critical in more than one sense. He points out the incompatibility of constitutional states and atomic states which is due to constitutional order being jeopardised by nuclear policy. He traces back the continuously rising awareness of pollution and the modern youth movement to their common root i.e. the awakening, the youth movement of the turn of the century. Eventually, he considers an economical, political, and social decentralization as a feasible alternative which would considerably relieve our basic living conditions from the threatening forms of civilization prevailing. (HSCH) [de

  1. Basic set theory

    CERN Document Server

    Levy, Azriel

    2002-01-01

    An advanced-level treatment of the basics of set theory, this text offers students a firm foundation, stopping just short of the areas employing model-theoretic methods. Geared toward upper-level undergraduate and graduate students, it consists of two parts: the first covers pure set theory, including the basic motions, order and well-foundedness, cardinal numbers, the ordinals, and the axiom of choice and some of it consequences; the second deals with applications and advanced topics such as point set topology, real spaces, Boolean algebras, and infinite combinatorics and large cardinals. An

  2. Basic properties of semiconductors

    CERN Document Server

    Landsberg, PT

    2013-01-01

    Since Volume 1 was published in 1982, the centres of interest in the basic physics of semiconductors have shifted. Volume 1 was called Band Theory and Transport Properties in the first edition, but the subject has broadened to such an extent that Basic Properties is now a more suitable title. Seven chapters have been rewritten by the original authors. However, twelve chapters are essentially new, with the bulk of this work being devoted to important current topics which give this volume an almost encyclopaedic form. The first three chapters discuss various aspects of modern band theory and the

  3. DETECTING LOW-LEVEL SYNTHESIS IMPURITIES IN MODIFIED PHOSPHOROTHIOATE OLIGONUCLEOTIDES USING LIQUID CHROMATOGRAPHY – HIGH RESOLUTION MASS SPECTROMETRY

    Science.gov (United States)

    Nikcevic, Irena; Wyrzykiewicz, Tadeusz K.; Limbach, Patrick A.

    2010-01-01

    Summary An LC-MS method based on the use of high resolution Fourier transform ion cyclotron resonance mass spectrometry (FTIRCMS) for profiling oligonucleotides synthesis impurities is described. Oligonucleotide phosphorothioatediesters (phosphorothioate oligonucleotides), in which one of the non-bridging oxygen atoms at each phosphorus center is replaced by a sulfur atom, are now one of the most popular oligonucleotide modifications due to their ease of chemical synthesis and advantageous pharmacokinetic properties. Despite significant progress in the solid-phase oligomerization chemistry used in the manufacturing of these oligonucleotides, multiple classes of low-level impurities always accompany synthetic oligonucleotides. Liquid chromatography-mass spectrometry has emerged as a powerful technique for the identification of these synthesis impurities. However, impurity profiling, where the entire complement of low-level synthetic impurities is identified in a single analysis, is more challenging. Here we present an LC-MS method based the use of high resolution-mass spectrometry, specifically Fourier transform ion cyclotron resonance mass spectrometry (FTIRCMS or FTMS). The optimal LC-FTMS conditions, including the stationary phase and mobile phases for the separation and identification of phosphorothioate oligonucleotides, were found. The characteristics of FTMS enable charge state determination from single m/z values of low-level impurities. Charge state information then enables more accurate modeling of the detected isotopic distribution for identification of the chemical composition of the detected impurity. Using this approach, a number of phosphorothioate impurities can be detected by LC-FTMS including failure sequences carrying 3′-terminal phosphate monoester and 3′-terminal phosphorothioate monoester, incomplete backbone sulfurization and desulfurization products, high molecular weight impurities, and chloral, isobutyryl, and N3 (2-cyanoethyl) adducts

  4. Foundation of Basic Arithmetic

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 2. Foundation of Basic Arithmetic. Jasbir S Chahal. General Article Volume 11 Issue 2 February 2006 pp 6-16. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/011/02/0006-0016. Keywords. Different ...

  5. Basic Tuberculosis Facts

    Centers for Disease Control (CDC) Podcasts

    2012-03-12

    In this podcast, Dr. Kenneth Castro, Director of the Division of Tuberculosis Elimination, discusses basic TB prevention, testing, and treatment information.  Created: 3/12/2012 by National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention (NCHHSTP).   Date Released: 3/12/2012.

  6. Basics of SCI Rehabilitation

    Medline Plus

    Full Text Available ... Heather Taylor, PhD Michelle Meade, PhD Jonathon Rose, PhD The Basics of Spinal Cord Injury Rehabilitation Kristine Cichowski, ... Cord Injury Katie Powell, OT Mary Jane Mulcahey, PhD, OTR/L Sarah Harrison, OT Anne Bryden, OT The Role of the Social Worker after Spinal Cord ...

  7. Basic radiation oncology

    International Nuclear Information System (INIS)

    Beyzadeoglu, M. M.; Ebruli, C.

    2008-01-01

    Basic Radiation Oncology is an all-in-one book. It is an up-to-date bedside oriented book integrating the radiation physics, radiobiology and clinical radiation oncology. It includes the essentials of all aspects of radiation oncology with more than 300 practical illustrations, black and white and color figures. The layout and presentation is very practical and enriched with many pearl boxes. Key studies particularly randomized ones are also included at the end of each clinical chapter. Basic knowledge of all high-tech radiation teletherapy units such as tomotherapy, cyberknife, and proton therapy are also given. The first 2 sections review concepts that are crucial in radiation physics and radiobiology. The remaining 11 chapters describe treatment regimens for main cancer sites and tumor types. Basic Radiation Oncology will greatly help meeting the needs for a practical and bedside oriented oncology book for residents, fellows, and clinicians of Radiation, Medical and Surgical Oncology as well as medical students, physicians and medical physicists interested in Clinical Oncology. English Edition of the book Temel Radyasyon Onkolojisi is being published by Springer Heidelberg this year with updated 2009 AJCC Staging as Basic Radiation Oncology

  8. Basic physics for all

    CERN Document Server

    Kumar, B N

    2012-01-01

    This is a simple, concise book for both student and non-physics students, presenting basic facts in straightforward form and conveying fundamental principles and theories of physics. This book will be helpful as a supplement to class teaching and to aid those who have difficulty in mastering concepts and principles.

  9. Basic Electronics II.

    Science.gov (United States)

    Willison, Neal A.; Shelton, James K.

    Designed for use in basic electronics programs, this curriculum guide is comprised of 15 units of instruction. Unit titles are Review of the Nature of Matter and the P-N Junction, Rectifiers, Filters, Special Semiconductor Diodes, Bipolar-Junction Diodes, Bipolar Transistor Circuits, Transistor Amplifiers, Operational Amplifiers, Logic Devices,…

  10. Greek Basic Course.

    Science.gov (United States)

    Defense Language Inst., Washington, DC.

    This course in Modern Greek, consisting of 100 lesson units in 13 volumes, is one of the Defense Language Institute's Basic Course Series. The course is designed to train native English language speakers to Level 3 proficiency in comprehension, speaking, reading, and writing Modern Greek. (Level 5 is native-speaker proficiency.) Lesson units…

  11. Basic Self-Esteem.

    Science.gov (United States)

    Kaeter, Margaret

    1993-01-01

    Training employees in basic skills necessitates sensitivity to their self-esteem. This can be achieved if the organizational culture supports training, the program is voluntary, it uses the group's strengths, it challenges them on an adult level, it does not resemble traditional schooling, and it builds in quick success. (SK)

  12. Basic Exchange Rate Theories

    NARCIS (Netherlands)

    J.G.M. van Marrewijk (Charles)

    2005-01-01

    textabstractThis four-chapter overview of basic exchange rate theories discusses (i) the elasticity and absorption approach, (ii) the (long-run) implications of the monetary approach, (iii) the short-run effects of monetary and fiscal policy under various economic conditions, and (iv) the transition

  13. Ethanol Basics (Fact Sheet)

    Energy Technology Data Exchange (ETDEWEB)

    2015-01-01

    Ethanol is a widely-used, domestically-produced renewable fuel made from corn and other plant materials. More than 96% of gasoline sold in the United States contains ethanol. Learn more about this alternative fuel in the Ethanol Basics Fact Sheet, produced by the U.S. Department of Energy's Clean Cities program.

  14. Basic Soils. Revision.

    Science.gov (United States)

    Montana State Univ., Bozeman. Dept. of Agricultural and Industrial Education.

    This curriculum guide is designed for use in teaching a course in basic soils that is intended for college freshmen. Addressed in the individual lessons of the unit are the following topics: the way in which soil is formed, the physical properties of soil, the chemical properties of soil, the biotic properties of soil, plant-soil-water…

  15. 40 CFR 63.5755 - How do I demonstrate compliance with the aluminum recreational boat surface coating spray gun...

    Science.gov (United States)

    2010-07-01

    ... the aluminum recreational boat surface coating spray gun cleaning work practice standards? 63.5755... surface coating spray gun cleaning work practice standards? You must demonstrate compliance with the aluminum coating spray gun cleaning work practice standards by meeting the requirements of paragraph (a) or...

  16. Polymorphic transformation of dense ZnO nanoparticles: Implications for chair/boat-type Peierls distortions of AB semiconductor

    DEFF Research Database (Denmark)

    Chen, Shuei-Yuan; Shen, Pouyan; Jiang, Jianzhong

    2004-01-01

    ) and then transformation strain induced (11 (1) over bar)(R) //((1) over bar 011)(W); [011](R) //[01 (1) over bar1](W). The two relationships can be rationalized by specified extent of chair- and boat-type Peierls distortions accompanied with band gap opening and intermediate {111}(R) slip for energetically favorable {111...

  17. Landowner perceptions of three types of boating in the Saranac Lakes area of New York State׳s Adirondack Park

    Science.gov (United States)

    Kuehn, Diane; Schuster, Rudy; Nordman, Erik

    2015-01-01

    In order for natural resource managers to better understand conflicting landowner perspectives related to non-motorized, motorized, and personal watercraft use, this study examines the demographic and experiential characteristics, values, attitudes, and beliefs of landowners in the Saranac Lakes area of the Adirondack Park in New York State. A mixed-methods approach, composed of 20 in-depth interviews with land managers and a mail survey of 1000 landowners, was used. Three path analyses were completed, one for each type of boat use. Results indicate that resource-related values influence beliefs and attitudes related to boat use, supporting the cognitive hierarchy model of human behavior (Fulton, D. C., Manfredo, M. J., & Lipscomb, J. (1996). Wildlife value orientations: a conceptual and measurement approach. Human Dimensions of Wildlife, 1, 24–47). In addition, length of residence in the area, past participation in non-motorized and motorized boating, age, and education were found to influence attitudes towards certain types of boating. The results of this study can be used by natural resource managers to identify management strategies that better address the values and recreational interests of landowners.

  18. 78 FR 25574 - Special Local Regulations; Third Annual Space Coast Super Boat Grand Prix, Atlantic Ocean; Cocoa...

    Science.gov (United States)

    2013-05-02

    ...-AA08 Special Local Regulations; Third Annual Space Coast Super Boat Grand Prix, Atlantic Ocean; Cocoa... establishing a special local regulation on the waters of the Atlantic Ocean east of Cocoa Beach, Florida during... event will be held on the waters of the Atlantic Ocean east of Cocoa Beach, Florida. Approximately 30...

  19. extrap: Software to assist the selection of extrapolation methods for moving-boat ADCP streamflow measurements

    Science.gov (United States)

    Mueller, David S.

    2013-01-01

    Selection of the appropriate extrapolation methods for computing the discharge in the unmeasured top and bottom parts of a moving-boat acoustic Doppler current profiler (ADCP) streamflow measurement is critical to the total discharge computation. The software tool, extrap, combines normalized velocity

  20. Mid- to high-frequency noise from high-speed boats and its potential impacts on humpback dolphins.

    Science.gov (United States)

    Li, Songhai; Wu, Haiping; Xu, Youhou; Peng, Chongwei; Fang, Liang; Lin, Mingli; Xing, Luru; Zhang, Peijun

    2015-08-01

    The impact of noise made by vessels on marine animals has come under increased concern. However, most measurements on noise from vessels have only taken into account the low-frequency components. For cetaceans operating in the mid- and high-frequencies, such as the Indo-Pacific humpback dolphin (Sousa chinensis), mid- to high-frequency noise components may be of more concern, in terms of their potential impacts. In this study, noise made by a small high-speed boat was recorded using a broadband recording system in a dolphin watching area focusing on the effects on humpback dolphins in Sanniang Bay, China. The high-speed boat produced substantial mid- to high-frequency noise components with frequencies to >100 kHz, measured at three speeds: ∼40, 30, and 15 km/h. The noise from the boat raised the ambient noise levels from ∼5 to 47 decibels (dB) root-mean-square (rms) across frequency bands ranging from 1 to 125 kHz at a distance of 20 to 85 m, with louder levels recorded at higher speeds and at closer distances. To conclude, the noise produced by the small high-speed boat could be heard by Sousa chinensis and therefore potentially had adverse effects on the dolphins.

  1. Synthesis and properties of triplex-forming oligonucleotides containing 2'-O-(2-methoxyethyl)-5-(3-aminoprop-1-ynyl)-uridine

    DEFF Research Database (Denmark)

    Lou, Chenguang; Xiao, Qiang; Brennan, Lavinia

    2010-01-01

    2'-O-(2-Methoxyethyl)-5-(3-aminoprop-1-ynyl)-uridine phosphoramidite (MEPU) has been synthesized from d-ribose and 5-iodouracil and incorporated into triplex-forming oligonucleotides (TFOs) by automated solid-phase oligonucleotide synthesis. The TFOs gave very high triplex stability with their ta......2'-O-(2-Methoxyethyl)-5-(3-aminoprop-1-ynyl)-uridine phosphoramidite (MEPU) has been synthesized from d-ribose and 5-iodouracil and incorporated into triplex-forming oligonucleotides (TFOs) by automated solid-phase oligonucleotide synthesis. The TFOs gave very high triplex stability...

  2. The detrimental consequences for seagrass of ineffective marine park management related to boat anchoring.

    Science.gov (United States)

    La Manna, G; Donno, Y; Sarà, G; Ceccherelli, G

    2015-01-15

    Posidonia oceanica (L.) Delile meadows are recognized as priority habitat for conservation by the EU Habitats Directive. The La Maddalena Archipelago National Park (Mediterranean Sea) P. oceanica meadow, the dominant coastal habitat of the area, is mostly threatened by boat anchoring. 12 years after the establishment of mooring fields and anchoring restrictions, a study was conducted to measure their effectiveness on the conservation of seagrass and the mitigation of anchoring damage. We found that: (i) the condition of P. oceanica was disturbed, both in the mooring fields and in control locations; (ii) mooring fields and anchoring restrictions did not show to be an efficient system for the protection of seagrass, in fact anchor scars increased after the tourist season; (iii) the mooring systems had an impact on the surrounding area of the meadow, probably due to their misuse. On the basis of these results, management recommendations for marine parks are proposed. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Vietnam and Britain agree to forced return of Vietnamese boat people in Hong Kong.

    Science.gov (United States)

    1991-10-31

    On 29 October 1991, the Governments of the United Kingdom and Viet Nam reached an Agreement on the return of certain categories of Vietnamese "boat people," i.e., persons who fled from Viet Nam to Hong Kong. Under the Agreement, Vietnamese who arrive in Hong Kong after the date of the Agreement and who do not qualify for refugee status will be returned first. The determination of such status is to occur within six weeks of their arrival. Later, Vietnamese in Hong Kong who have already failed to qualify for refugee status will be returned. The Agreement follows an Agreement earlier in October to return Vietnamese arriving in Hong Kong who are known as "double backers," i.e., persons who had previously voluntarily been repatriated to Viet Nam only to return to Hong Kong.

  4. Effects of tour boats on dolphin activity examined with sensitivity analysis of Markov chains.

    Science.gov (United States)

    Dans, Silvana Laura; Degrati, Mariana; Pedraza, Susana Noemí; Crespo, Enrique Alberto

    2012-08-01

    In Patagonia, Argentina, watching dolphins, especially dusky dolphins (Lagenorhynchus obscurus), is a new tourist activity. Feeding time decreases and time to return to feeding after feeding is abandoned and time it takes a group of dolphins to feed increase in the presence of boats. Such effects on feeding behavior may exert energetic costs on dolphins and thus reduce an individual's survival and reproductive capacity or maybe associated with shifts in distribution. We sought to predict which behavioral changes modify the activity pattern of dolphins the most. We modeled behavioral sequences of dusky dolphins with Markov chains. We calculated transition probabilities from one activity to another and arranged them in a stochastic matrix model. The proportion of time dolphins dedicated to a given activity (activity budget) and the time it took a dolphin to resume that activity after it had been abandoned (recurrence time) were calculated. We used a sensitivity analysis of Markov chains to calculate the sensitivity of the time budget and the activity-resumption time to changes in behavioral transition probabilities. Feeding-time budget was most sensitive to changes in the probability of dolphins switching from traveling to feeding behavior and of maintaining feeding behavior. Thus, an increase in these probabilities would be associated with the largest reduction in the time dedicated to feeding. A reduction in the probability of changing from traveling to feeding would also be associated with the largest increases in the time it takes dolphins to resume feeding. To approach dolphins when they are traveling would not affect behavior less because presence of the boat may keep dolphins from returning to feeding. Our results may help operators of dolphin-watching vessels minimize negative effects on dolphins. ©2012 Society for Conservation Biology.

  5. Analysis of oligonucleotide array experiments with repeated measures using mixed models

    Directory of Open Access Journals (Sweden)

    Getchell Thomas V

    2004-12-01

    Full Text Available Abstract Background Two or more factor mixed factorial experiments are becoming increasingly common in microarray data analysis. In this case study, the two factors are presence (Patients with Alzheimer's disease or absence (Control of the disease, and brain regions including olfactory bulb (OB or cerebellum (CER. In the design considered in this manuscript, OB and CER are repeated measurements from the same subject and, hence, are correlated. It is critical to identify sources of variability in the analysis of oligonucleotide array experiments with repeated measures and correlations among data points have to be considered. In addition, multiple testing problems are more complicated in experiments with multi-level treatments or treatment combinations. Results In this study we adopted a linear mixed model to analyze oligonucleotide array experiments with repeated measures. We first construct a generalized F test to select differentially expressed genes. The Benjamini and Hochberg (BH procedure of controlling false discovery rate (FDR at 5% was applied to the P values of the generalized F test. For those genes with significant generalized F test, we then categorize them based on whether the interaction terms were significant or not at the α-level (αnew = 0.0033 determined by the FDR procedure. Since simple effects may be examined for the genes with significant interaction effect, we adopt the protected Fisher's least significant difference test (LSD procedure at the level of αnew to control the family-wise error rate (FWER for each gene examined. Conclusions A linear mixed model is appropriate for analysis of oligonucleotide array experiments with repeated measures. We constructed a generalized F test to select differentially expressed genes, and then applied a specific sequence of tests to identify factorial effects. This sequence of tests applied was designed to control for gene based FWER.

  6. Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays

    Directory of Open Access Journals (Sweden)

    Jee Justin

    2008-12-01

    Full Text Available Abstract Background Mismatched oligonucleotides are widely used on microarrays to differentiate specific from nonspecific hybridization. While many experiments rely on such oligos, the hybridization behavior of various degrees of mismatch (MM structure has not been extensively studied. Here, we present the results of two large-scale microarray experiments on S. cerevisiae and H. sapiens genomic DNA, to explore MM oligonucleotide behavior with real sample mixtures under tiling-array conditions. Results We examined all possible nucleotide substitutions at the central position of 36-nucleotide probes, and found that nonspecific binding by MM oligos depends upon the individual nucleotide substitutions they incorporate: C→A, C→G and T→A (yielding purine-purine mispairs are most disruptive, whereas A→X were least disruptive. We also quantify a marked GC skew effect: substitutions raising probe GC content exhibit higher intensity (and vice versa. This skew is small in highly-expressed regions (± 0.5% of total intensity range and large (± 2% or more elsewhere. Multiple mismatches per oligo are largely additive in effect: each MM added in a distributed fashion causes an additional 21% intensity drop relative to PM, three-fold more disruptive than adding adjacent mispairs (7% drop per MM. Conclusion We investigate several parameters for oligonucleotide design, including the effects of each central nucleotide substitution on array signal intensity and of multiple MM per oligo. To avoid GC skew, individual substitutions should not alter probe GC content. RNA sample mixture complexity may increase the amount of nonspecific hybridization, magnify GC skew and boost the intensity of MM oligos at all levels.

  7. Ultrasensitive electrochemical biosensor based on the oligonucleotide self-assembled monolayer-mediated immunosensing interface

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Dengyou; Luo, Qimei [Science College of Hunan Agricultural University, Changsha 410128 (China); Deng, Fawen [The Fourth Hospital of Chansha, Changsha 410006 (China); Li, Zhen [Science College of Hunan Agricultural University, Changsha 410128 (China); Li, Benxiang, E-mail: 172170960@qq.com [Science College of Hunan Agricultural University, Changsha 410128 (China); Shen, Zhifa, E-mail: shenzhifa@wmu.edu.cn [Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035 (China)

    2017-06-08

    Highly sensitive and selective quantitation of a variety of proteins over a wide concentration range is highly desirable for increased accuracy of biomarker detection or for multidisease diagnostics. In the present contribution, using human immunoglobulin G (HIgG) as the model target protein, an electrochemical ultrasensitive immunosensing platform was developed based on the oligonucleotide self-assembled monolayer-mediated (OSAM) sensing interface. For this immunosensor, the “signal-on” signaling mechanism and enzymatic signal amplification effect were integrated into one sensing architecture. Moreover, the thiolated flexible single-stranded DNAs immobilized onto gold electrode surface not only performs the wobbling motion to facilitate the electron transfer between the electrode surface and biosensing layer but also fundamentally prohibiting the direct interaction of proteins with gold substrate. Thus, the electrochemical signal could be efficiently enhanced and the unspecific adsorption or cross-reaction might be eliminated. As a result, utilizing the newly-proposed immunosensor, the HIgG can be detected down to 0.5 ng/mL, and the high detection specificity is offered. The successful design of OSAM and the highly desirable detection capability of new immunosensor are expected to provide a perspective for fabricating new robust immunosensing platform and for promising potential of oligonucleotide probe in biological research and biomedical diagnosis. - Highlights: • An electrochemical ultrasensitive immunosensing platform was developed based on the oligonucleotide self-assembled monolayer (OASM). • OASM severs as a flexible monolayer to promote electron transfer and prohibits the direct interaction of proteins with gold substrate. • The electrochemical signal is efficiently enhanced and the unspecific adsorption or cross-reaction is eliminated. • Target protein can be detected down to 0.5 ng/mL, and the high detection specificity can be obtained.

  8. Simplified Paper Format for Detecting HIV Drug Resistance in Clinical Specimens by Oligonucleotide Ligation

    Science.gov (United States)

    Panpradist, Nuttada; Beck, Ingrid A.; Chung, Michael H.; Kiarie, James N.; Frenkel, Lisa M.; Lutz, Barry R.

    2016-01-01

    Human immunodeficiency virus (HIV) is a chronic infection that can be managed by antiretroviral treatment (ART). However, periods of suboptimal viral suppression during lifelong ART can select for HIV drug resistant (DR) variants. Transmission of drug resistant virus can lessen or abrogate ART efficacy. Therefore, testing of individuals for drug resistance prior to initiation of treatment is recommended to ensure effective ART. Sensitive and inexpensive HIV genotyping methods are needed in low-resource settings where most HIV infections occur. The oligonucleotide ligation assay (OLA) is a sensitive point mutation assay for detection of drug resistance mutations in HIV pol. The current OLA involves four main steps from sample to analysis: (1) lysis and/or nucleic acid extraction, (2) amplification of HIV RNA or DNA, (3) ligation of oligonucleotide probes designed to detect single nucleotide mutations that confer HIV drug resistance, and (4) analysis via oligonucleotide surface capture, denaturation, and detection (CDD). The relative complexity of these steps has limited its adoption in resource-limited laboratories. Here we describe a simplification of the 2.5-hour plate-format CDD to a 45-minute paper-format CDD that eliminates the need for a plate reader. Analysis of mutations at four HIV-1 DR codons (K103N, Y181C, M184V, and G190A) in 26 blood specimens showed a strong correlation of the ratios of mutant signal to total signal between the paper CDD and the plate CDD. The assay described makes the OLA easier to perform in low resource laboratories. PMID:26751207

  9. Development and production of an oligonucleotide MuscleChip: use for validation of ambiguous ESTs

    Directory of Open Access Journals (Sweden)

    Lanfranchi Gerolamo

    2002-10-01

    Full Text Available Abstract Background We describe the development, validation, and use of a highly redundant 120,000 oligonucleotide microarray (MuscleChip containing 4,601 probe sets representing 1,150 known genes expressed in muscle and 2,075 EST clusters from a non-normalized subtracted muscle EST sequencing project (28,074 EST sequences. This set included 369 novel EST clusters showing no match to previously characterized proteins in any database. Each probe set was designed to contain 20–32 25 mer oligonucleotides (10–16 paired perfect match and mismatch probe pairs per gene, with each probe evaluated for hybridization kinetics (Tm and similarity to other sequences. The 120,000 oligonucleotides were synthesized by photolithography and light-activated chemistry on each microarray. Results Hybridization of human muscle cRNAs to this MuscleChip (33 samples showed a correlation of 0.6 between the number of ESTs sequenced in each cluster and hybridization intensity. Out of 369 novel EST clusters not showing any similarity to previously characterized proteins, we focused on 250 EST clusters that were represented by robust probe sets on the MuscleChip fulfilling all stringent rules. 102 (41% were found to be consistently "present" by analysis of hybridization to human muscle RNA, of which 40 ESTs (39% could be genome anchored to potential transcription units in the human genome sequence. 19 ESTs of the 40 ESTs were furthermore computer-predicted as exons by one or more than three gene identification algorithms. Conclusion Our analysis found 40 transcriptionally validated, genome-anchored novel EST clusters to be expressed in human muscle. As most of these ESTs were low copy clusters (duplex and triplex in the original 28,000 EST project, the identification of these as significantly expressed is a robust validation of the transcript units that permits subsequent focus on the novel proteins encoded by these genes.

  10. Simplified Paper Format for Detecting HIV Drug Resistance in Clinical Specimens by Oligonucleotide Ligation.

    Directory of Open Access Journals (Sweden)

    Nuttada Panpradist

    Full Text Available Human immunodeficiency virus (HIV is a chronic infection that can be managed by antiretroviral treatment (ART. However, periods of suboptimal viral suppression during lifelong ART can select for HIV drug resistant (DR variants. Transmission of drug resistant virus can lessen or abrogate ART efficacy. Therefore, testing of individuals for drug resistance prior to initiation of treatment is recommended to ensure effective ART. Sensitive and inexpensive HIV genotyping methods are needed in low-resource settings where most HIV infections occur. The oligonucleotide ligation assay (OLA is a sensitive point mutation assay for detection of drug resistance mutations in HIV pol. The current OLA involves four main steps from sample to analysis: (1 lysis and/or nucleic acid extraction, (2 amplification of HIV RNA or DNA, (3 ligation of oligonucleotide probes designed to detect single nucleotide mutations that confer HIV drug resistance, and (4 analysis via oligonucleotide surface capture, denaturation, and detection (CDD. The relative complexity of these steps has limited its adoption in resource-limited laboratories. Here we describe a simplification of the 2.5-hour plate-format CDD to a 45-minute paper-format CDD that eliminates the need for a plate reader. Analysis of mutations at four HIV-1 DR codons (K103N, Y181C, M184V, and G190A in 26 blood specimens showed a strong correlation of the ratios of mutant signal to total signal between the paper CDD and the plate CDD. The assay described makes the OLA easier to perform in low resource laboratories.

  11. Characterization of the overall and internal dynamics of short oligonucleotides by depolarized dynamic light scattering and NMR relaxation measurements

    International Nuclear Information System (INIS)

    Eimer, W.; Williamson, J.R.; Boxer, S.G.; Pecora, R.

    1990-01-01

    The dynamics of three synthetic oligonucleotides d(CG) 4 , d(CG) 6 , and d(CGCGTTGTTCGCG) of different length and shape were studied in solution by depolarized dynamic light scattering (DDLS) and time-resolved nuclear Overhauser effect cross-relaxation measurements. For cylindrically symmetric molecules the DDLS spectrum is dominated by the rotation of the main symmetry axis of the cylinder. The experimental correlation times describe the rotation of the oligonucleotides under hydrodynamic stick boundary conditions. It is shown that the hydrodynamic theory of Tirado and Garcia de la Torre gives good predictions of the rotational diffusion coefficients of cylindrically symmetric molecules of the small axial ratios studied here. These relations are used to calculate the solution dimensions of the DNA fragments from measured correlation times. The DDLS relaxations measurements provide a power method for distinguishing between different conformations of the oligonucleotides. Furthermore, the rotational correlation times are a very sensitive probe of the length of different fragments. The NMR results reflect the anisotropic motion of the molecules as well as the amount of local internal motion present. The experimental correlation time from NMR is determined by the rotation of both the short and long axes of the oligonucleotide. The authors results are compared with those from NMR relaxation measurements on other short oligonucleotides with lengths of up to 20 base pairs. Various dynamic models for the reorientation of the internuclear vector are applied to their interpretation

  12. Resolving prokaryotic taxonomy without rRNA: longer oligonucleotide word lengths improve genome and metagenome taxonomic classification.

    Directory of Open Access Journals (Sweden)

    Eric B Alsop

    Full Text Available Oligonucleotide signatures, especially tetranucleotide signatures, have been used as method for homology binning by exploiting an organism's inherent biases towards the use of specific oligonucleotide words. Tetranucleotide signatures have been especially useful in environmental metagenomics samples as many of these samples contain organisms from poorly classified phyla which cannot be easily identified using traditional homology methods, including NCBI BLAST. This study examines oligonucleotide signatures across 1,424 completed genomes from across the tree of life, substantially expanding upon previous work. A comprehensive analysis of mononucleotide through nonanucleotide word lengths suggests that longer word lengths substantially improve the classification of DNA fragments across a range of sizes of relevance to high throughput sequencing. We find that, at present, heptanucleotide signatures represent an optimal balance between prediction accuracy and computational time for resolving taxonomy using both genomic and metagenomic fragments. We directly compare the ability of tetranucleotide and heptanucleotide world lengths (tetranucleotide signatures are the current standard for oligonucleotide word usage analyses for taxonomic binning of metagenome reads. We present evidence that heptanucleotide word lengths consistently provide more taxonomic resolving power, particularly in distinguishing between closely related organisms that are often present in metagenomic samples. This implies that longer oligonucleotide word lengths should replace tetranucleotide signatures for most analyses. Finally, we show that the application of longer word lengths to metagenomic datasets leads to more accurate taxonomic binning of DNA scaffolds and have the potential to substantially improve taxonomic assignment and assembly of metagenomic data.

  13. Chemosensitization of Human Renal Cell Cancer Using Antisense Oligonucleotides Targeting the Antiapoptotic Gene Clusterin

    Directory of Open Access Journals (Sweden)

    Tobias Zellweger

    2001-01-01

    Full Text Available BACKGROUND: Renal cell cancer (RCC is a chemoresistant disease with no active chemotherapeutic agent achieving objective response rates higher than 15%. Clusterin is a cell survival gene that increases in human renal tubular epithelial cells after various states of injury and disease. Downregulation of clusterin, using antisense oligonucleotides (ASO, has recently been shown to increase chemosensitivity in several prostate cancer models. The objectives in this study were to evaluate clusterin expression levels in human RCC and normal kidney tissue, and to test whether clusterin ASO could also enhance chemosensitivity in human RCC Caki-2 cells both in vitro and in vivo. METHODS: Immunohistochemical staining was used to characterize clusterin expression in 67 RCC and normal kidney tissues obtained from radical nephrectomy specimens. Northern blot analysis was used to assess changes in clusterin mRNA expression after ASO and paclitaxel treatment. The effects of combined clusterin ASO and paclitaxel treatment on Caki-2 cell growth was examined using an MTT assay. Athymic mice bearing Caki-2 tumors were treated with clusterin ASO alone, clusterin ASO plus paclitaxel, and mismatch control oligonucleotides plus paclitaxel, over a period of 28 days with measurement of tumor volumes once weekly over 8 weeks. RESULTS: Immunohistochemistry of normal and malignant kidney tissue sections of 67 patients demonstrated positive clusterin staining for almost all RCC (98% and an overexpression, compared to normal tissue, in a majority of RCC (69%. Clusterin ASO, but not mismatch control oligonucleotides, decreased clusterin mRNA expression in Caki-2 cells in a dosedependent and sequence-specific manner. Pretreatment of Caki-2 cells with clusterin ASO significantly enhanced chemosensitivity to paclitaxel in vitro. Characteristic apoptotic DNA laddering was observed after combined treatment with ASO plus paclitaxel, but not with either agent alone. In vivo

  14. Synthesis of modified oligonucleotides that contain purine and pyrimidine radio-induced base lesions

    International Nuclear Information System (INIS)

    Romieu, Anthony

    1999-01-01

    Different factors as oxidizing or carcinogenesis agents, UV and ionizing radiations,.... can generate a wide, spectrum of DNA base damages. In order to study the biochemical and structural features of these DNA damages, it is important to prepare short DNA fragments (20 to 50 bases long) bearing a single or several modifications at specific sites in their sequences. The chemical synthesis is a powerful tool to prepare such modified DNA fragments. This work focusses on the chemical incorporation of several modified nucleosides formed in DNA by ionizing radiations or by photo-sensitization. The first part of this study describes the preparation of a phosphoramidite synthon of 5-hydroxy-2'-deoxyuridine and its subsequent incorporation into synthetic oligonucleotides ranging from 14 to 33 bases long. In a second part (chapters Ill and IV), the synthesis and incorporation of original radiation-induced tandem lesions: the carbon-bridged cyclo-nucleosides are presented. Both (5'R)- and (5'S) diastereomers of 5',8-cyclo-2'-deoxyadenosine and 5',8-cyclo-2'-deoxyguanosine have been individually inserted into various different oligonucleotides (3 to 22 bases long) by using the standard phosphoramidite chemistry. The chemical incorporation of a pyrimidine analogue: (5'S, 6S)-5',6-cyclo-5,6-dihydro-thymidine has been also achieved. The loss of aromaticity of this modified nucleoside and its poor reactivity required the development of a synthetic strategy entirely different from that used for the preparation and subsequent incorporation of the phosphoramidite synthons of 5',8-cyclo-purine-2'-deoxyribo-nucleosides. The third part of this study deals with the synthesis of a phosphoramidite synthon of 4-hydroxy-8-oxo-4,8-dihydro-2'-deoxyguanosine. The two (4R)- and (4S)- diastereomers of this oxidized purine have been separated and individually inserted in several synthetic DNA fragments. No epimerization of C-4 position

  15. A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray

    DEFF Research Database (Denmark)

    Stolc, Viktor; Li, Lei; Wang, Xiangfeng

    2005-01-01

    As the international efforts to sequence the rice genome are completed, an immediate challenge and opportunity is to comprehensively and accurately define all transcription units in the rice genome. Here we describe a strategy of using high-density oligonucleotide tiling-path microarrays to map...... gene models in a mixture of four RNA populations. Moreover, significant transcriptional activities were found in many of the previously annotated intergenic regions. These preliminary results demonstrate the utility of genome tiling microarrays in evaluating annotated rice gene models...

  16. Fatty Acid-Modified Gapmer Antisense Oligonucleotide and Serum Albumin Constructs for Pharmacokinetic Modulation

    DEFF Research Database (Denmark)

    Hvam, Michael Lykke; Cai, Yunpeng; Dagnæs-Hansen, Frederik

    2017-01-01

    oligonucleotides (ASOs)/albumin constructs. We show by an electrophoretic mobility assay that fatty acid-modified gapmer and human serum albumin (HSA) can self-assemble into constructs that offer favorable pharmacokinetics. The interaction was dependent on fatty acid type (either palmitic or myristic acid), number......, and position within the gapmer ASO sequence, as well as phosphorothioate (PS) backbone modifications. Binding correlated with increased blood circulation in mice (t1/2 increased from 23 to 49 min for phosphodiester [PO] gapmer ASOs and from 28 to 66 min for PS gapmer ASOs with 2× palmitic acid modification...

  17. CTG repeat-targeting oligonucleotides for down-regulating Huntingtin expression

    DEFF Research Database (Denmark)

    Zaghloul, Eman M; Gissberg, Olof; Moreno, Pedro M D

    2017-01-01

    Huntington's disease (HD) is a fatal, neurodegenerative disorder in which patients suffer from mobility, psychological and cognitive impairments. Existing therapeutics are only symptomatic and do not significantly alter the disease progression or increase life expectancy. HD is caused by expansion....... Thus, reduction of both muHTT mRNA and protein levels would ideally be the most useful therapeutic option. We herein present a novel strategy for HD treatment using oligonucleotides (ONs) directly targeting the HTT trinucleotide repeat DNA. A partial, but significant and potentially long-term, HTT...

  18. An oligonucleotide-tagged microarray for routine diagnostics of colon cancer by genotyping KRAS mutations

    DEFF Research Database (Denmark)

    Liu, Yuliang; Guðnason, Haukur; Li, Yiping

    2014-01-01

    mutations at codon 12 of KRAS derived from cancer cells and clinical samples could be unambiguously detected. KRAS mutations were accurately detected when the mutant DNA was present only in 10% of the starting mixed materials including wild-type genomic DNA, which was isolated from either cancer cells...... or spiked fecal samples. The immobilized tag-probes were stable under multiple thermal cycling treatments, allowing re-use of the tag-microarray and further optimization to solid PCR. Our results demonstrated that a novel oligonucleotide-tagged microarray system has been developed which would be suitable...

  19. Information Limited Oligonucleotide Amplification Assay for Affinity-Based, Parallel Detection Studies.

    Directory of Open Access Journals (Sweden)

    Harish Bokkasam

    Full Text Available Molecular communication systems encounter similar constraints as telecommunications. In either case, channel crosstalk at the receiver end will result in information loss that statistical analysis cannot compensate. This is because in any communication channel there is a physical limit to the amount of information that can be transmitted. We present a novel and simple modified end amplification (MEA technique to generate reduced and defined amounts of specific information in form of short fragments from an oligonucleotide source that also contains unrelated and redundant information. Our method can be a valuable tool to investigate information overflow and channel capacity in biomolecular recognition systems.

  20. Basics of statistical physics

    CERN Document Server

    Müller-Kirsten, Harald J W

    2013-01-01

    Statistics links microscopic and macroscopic phenomena, and requires for this reason a large number of microscopic elements like atoms. The results are values of maximum probability or of averaging. This introduction to statistical physics concentrates on the basic principles, and attempts to explain these in simple terms supplemented by numerous examples. These basic principles include the difference between classical and quantum statistics, a priori probabilities as related to degeneracies, the vital aspect of indistinguishability as compared with distinguishability in classical physics, the differences between conserved and non-conserved elements, the different ways of counting arrangements in the three statistics (Maxwell-Boltzmann, Fermi-Dirac, Bose-Einstein), the difference between maximization of the number of arrangements of elements, and averaging in the Darwin-Fowler method. Significant applications to solids, radiation and electrons in metals are treated in separate chapters, as well as Bose-Eins...