WorldWideScience

Sample records for boat basic oligonucleotide

  1. Boat sampling

    International Nuclear Information System (INIS)

    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

  2. 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...

  3. Clay catalysis of oligonucleotide formation: kinetics of the reaction of the 5'-phosphorimidazolides of nucleotides with the non-basic heterocycles uracil and hypoxanthine

    Science.gov (United States)

    Kawamura, K.; Ferris, J. P.

    1999-01-01

    The montmorillonite clay catalyzed condensation of activated monocleotides to oligomers of RNA is a possible first step in the formation of the proposed RNA world. The rate constants for the condensation of the phosphorimidazolide of adenosine were measured previously and these studies have been extended to the phosphorimidazolides of inosine and uridine in the present work to determine of substitution of neutral heterocycles for the basic adenine ring changes the reaction rate or regioselectivity. The oligomerization reactions of the 5'-phosphoromidazolides of uridine (ImpU) and inosine (ImpI) on montmorillonite yield oligo(U)s and oligo(I)s as long as heptamers. The rate constants for oligonucleotide formation were determined by measuring the rates of formation of the oligomers by HPLC. Both the apparent rate constants in the reaction mixture and the rate constants on the clay surface were calculated using the partition coefficients of the oligomers between the aqueous and clay phases. The rate constants for trimer formation are much greater than those dimer synthesis but there was little difference in the rate constants for the formation of trimers and higher oligomers. The overall rates of oligomerization of the phosphorimidazolides of purine and pyrimidine nucleosides in the presence of montmorillonite clay are the same suggesting that RNA formed on the primitive Earth could have contained a variety of heterocyclic bases. The rate constants for oligomerization of pyrimidine nucleotides on the clay surface are significantly higher than those of purine nucleotides since the pyrimidine nucleotides bind less strongly to the clay than do the purine nucleotides. The differences in the binding is probably due to Van der Waals interactions between the purine bases and the clay surface. Differences in the basicity of the heterocyclic ring in the nucleotide have little effect on the oligomerization process.

  4. Cytokines and therapeutic oligonucleotides.

    Science.gov (United States)

    Hartmann, G; Bidlingmaier, M; Eigler, A; Hacker, U; Endres, S

    1997-12-01

    Therapeutic oligonucleotides - short strands of synthetic nucleic acids - encompass antisense and aptamer oligonucleotides. Antisense oligonucleotides are designed to bind to target RNA by complementary base pairing and to inhibit translation of the target protein. Antisense oligonucleotides enable specific inhibition of cytokine synthesis. In contrast, aptamer oligonucleotides are able to bind directly to specific proteins. This binding depends on the sequence of the oligonucleotide. Aptamer oligonucleotides with CpG motifs can exert strong immunostimulatory effects. Both kinds of therapeutic oligonucleotides - antisense and aptamer oligonucleotides - provide promising tools to modulate immunological functions. Recently, therapeutic oligonucleotides have moved towards clinical application. An antisense oligonucleotide directed against the proinflammatory intercellular adhesion molecule 1 (ICAM-1) is currently being tested in clinical trials for therapy of inflammatory disease. Immunostimulatory aptamer oligonucleotides are in preclinical development for immunotherapy. In the present review we summarize the application of therapeutic oligonucleotides to modulate immunological functions. We include technological aspects as well as current therapeutic concepts and clinical studies. PMID:9740353

  5. 77 FR 31147 - National Safe Boating Week, 2012

    Science.gov (United States)

    2012-05-24

    ... waterways. By planning ahead and taking basic safety precautions, boat operators and passengers can help... organizations and governments across our country to prevent loss of life, personal harm, and property damage... recognition of the importance of safe boating practices, the Congress, by joint resolution approved June...

  6. Powering light boats

    Energy Technology Data Exchange (ETDEWEB)

    Affolter, J.-F.

    1999-07-01

    This short paper reports on a workshop held in Horw, Switzerland, on the application potential of low-temperature fuel cells. It looks at the increasing interest in small, electrically-driven boats in Europe and, in particular, at the option of powering them with fuel cells. A prototype implementation of a test boat is described. Powered by a 300-watt portable PEFC fuel cell constructed by the Paul Scherrer Institute (PSI) and the University of Applied Science in Solothurn, Switzerland, the boat is part of a project to study the technical feasibility of such drive systems for leisure craft and small boats. The paper addresses hydrogen security questions, energy-efficient drives and controllers, maintenance questions and discusses if a combination of fuel cells and photovoltaics would be viable. Also, the design of the boat's hull and the propellers that are used are looked at critically. The economic viability of fuel-cell powered boats is examined. The authors state that they are convinced that such fuel cell drives could be commercially interesting for larger passenger boats, too.

  7. Recreational Boating Statistics 2012

    Data.gov (United States)

    Department of Homeland Security — Every year, the USCG compiles statistics on reported recreational boating accidents. These statistics are derived from accident reports that are filed by the owners...

  8. Recreational Boating Statistics 2013

    Data.gov (United States)

    Department of Homeland Security — Every year, the USCG compiles statistics on reported recreational boating accidents. These statistics are derived from accident reports that are filed by the owners...

  9. Recreational Boating Statistics 2011

    Data.gov (United States)

    Department of Homeland Security — Every year, the USCG compiles statistics on reported recreational boating accidents. These statistics are derived from accident reports that are filed by the owners...

  10. The cocktail boat.

    Science.gov (United States)

    Burton, Lisa J; Cheng, Nadia; Bush, John W M

    2014-12-01

    We describe the inspiration, development, and deployment of a novel cocktail device modeled after a class of water-walking insects. Semi-aquatic insects like Microvelia and Velia evade predators by releasing a surfactant that quickly propels them across the water. We exploit an analogous propulsion mechanism in the design of an edible cocktail boat. We discuss how gradients in surface tension lead to motion across the water's surface, and detail the design considerations associated with the insect-inspired cocktail boat. PMID:24853727

  11. In the Same Boat

    Institute of Scientific and Technical Information of China (English)

    VALERIE; SARTOR

    2008-01-01

    Unlike the National Day or Spring Festival holidays that create massive logistical travel and traffic problems,the Dragon Boat Festival,falling on the fifth day of the fifth month of the Chinese lunar calendar or June 8 this year

  12. Dragon Boat Festival.

    Science.gov (United States)

    Lew, Gordon

    This is one of a series of elementary readers written in Cantonese and English and designed to familiarize children with the traditional major Chinese festivals celebrated by the Chinese in America. This booklet describes the celebration of the Dragon Boat Festival, which marks the beginning of summer. A brief background to the festival is…

  13. Eleven cities Solar boat challenge

    OpenAIRE

    Verdult, E.

    2012-01-01

    TU Delft students are participating for the fourth time in the world championship solar boat race in Friesland, which begins on 8 July. Expectations are high because the TU Delft students were world champions in 2006 and 2008. In 2010, the solar boat was equipped with hydrofoils for the first time. Unfortunately, the hydrofoils caused the boat to rise so far out of the water at top speed that it tilted and only achieved a third place. The big question is whether this year's new boat is fast e...

  14. Eleven cities Solar boat challenge

    NARCIS (Netherlands)

    Verdult, E.

    2012-01-01

    TU Delft students are participating for the fourth time in the world championship solar boat race in Friesland, which begins on 8 July. Expectations are high because the TU Delft students were world champions in 2006 and 2008. In 2010, the solar boat was equipped with hydrofoils for the first time.

  15. Row, Row, Row Your Boat...

    Institute of Scientific and Technical Information of China (English)

    PHILIP JONES

    2010-01-01

    @@ My afternoon plans to go dragon boat racing on Houhai Lake in downtown Beijing could have started better. Cycling across town, a pedal snapped off my bicycle as I was aggressively building up speed across a Second Ring Road junction.

  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. The market introduction of solar boats

    International Nuclear Information System (INIS)

    There is a large potential (50 MWp) for photovoltaic electrically-driven boats in the Netherlands. A brief overview is given of the results of solar boat demonstration projects in the Netherlands so far

  18. 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...

  19. Working with Oligonucleotide Arrays.

    Science.gov (United States)

    Carvalho, Benilton S

    2016-01-01

    Preprocessing microarray data consists of a number of statistical procedures that convert the observed intensities into quantities that represent biological events of interest, like gene expression and allele-specific abundances. Here, we present a summary of the theory behind microarray data preprocessing for expression, whole transcriptome and SNP designs and focus on the computational protocol used to obtain processed data that will be used on downstream analyses. We describe the main features of the oligo Bioconductor package, an application designed to support oligonucleotide microarrays using the R statistical environment and the infrastructure provided by Bioconductor, allowing the researcher to handle probe-level data and interface with advanced statistical tools under a simplified framework. We demonstrate the use of the package by preprocessing data originated from three different designs. PMID:27008013

  20. A study of traditional boats of Goa

    Digital Repository Service at National Institute of Oceanography (India)

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

    prominent role in distribution of traditional watercraft (Fig. 1). Skin boats are found in rivers because of calm water (Fig. 2) but dugouts and dugouts with outrigger are found mostly in rivers, tributaries, estuaries and all along the coastline. Extended... fishing (short distance) III Sewn Plank Boat with keel Revechem hode Tiracol, Chapora, Amona 10 to 12 Removal of sand from river bed IV Skin boat Karnataka Inland fishing 4 outrigger. Instead of using different types of timber builders...

  1. 'Boat People' and the battle for labels

    OpenAIRE

    Thulin, Sabina

    2013-01-01

    This paper seeks to examine the relationship between the public perception of asylum seekers arriving by boat in Australia and the exclusion of certain rights. The asylum seekers arriving by boat have been central in the political debate for over a decade and are an issue that divides the public. The asylum seekers arriving by boat are generally referred to as ‘boat people’ but also labelled in more hostile terms as ‘illegal asylum seekers’, ‘queue jumpers’, and ‘illegal maritime arrivals’. F...

  2. 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...

  3. Cardboard Boat Building in Math Class

    Science.gov (United States)

    Omundsen, John

    2014-01-01

    If you want to get the attention of a group of eighth grade math students, tell them they are going to build a life-size cardboard boat. To increase interest, follow up this statement by telling them that two to four of them will actually be rowing this boat across a small pond. Eighth grade math students at Oasis Charter Middle School in…

  4. 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.

  5. Thermodynamics of Oligonucleotide Duplex Melting

    Science.gov (United States)

    Schreiber-Gosche, Sherrie; Edwards, Robert A.

    2009-01-01

    Melting temperatures of oligonucleotides are useful for a number of molecular biology applications, such as the polymerase chain reaction (PCR). Although melting temperatures are often calculated with simplistic empirical equations, application of thermodynamics provides more accurate melting temperatures and an opportunity for students to apply…

  6. Antisense Oligonucleotides: Treating Neurodegeneration at the Level of RNA

    OpenAIRE

    DeVos, Sarah L.; Miller, Timothy M.

    2013-01-01

    Adequate therapies are lacking for Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, amyotrophic lateral sclerosis, and other neurodegenerative diseases. The ability to use antisense oligonucleotides (ASOs) to target disease-associated genes by means of RNA may offer a potent approach for the treatment of these, and other, neurodegenerative disorders. In modifying the basic backbone chemistry, chemical groups, and target sequence, ASOs can act through numerous mechanisms to decr...

  7. [Study toward practical use of oligonucleotide therapeutics].

    Science.gov (United States)

    Inoue, Takao; Yoshida, Tokuyuki

    2014-01-01

    Over the past decade, oligonucleotide-based therapeutics such as antisense oligonucleotides and small interfering RNAs (siRNAs) have been developed extensively. For example, mipomersen (Kynamro; ISIS Pharmaceuticals), which is a second-generation antisense oligonucleotide administered by subcutaneous injection, has recently been approved by the FDA for the treatment of homozygous familial hypercholesterolemia. On the other hands, methods for the evaluation of quality, efficacy and safety of oligonucleotide therapeutics have not been fully discussed. Furthermore, the regulatory guidance specific for oligonucleotide therapeutics has not been established yet. Under these circumstances, we started to collaborate with Osaka University and PMDA to discuss regulatory science focused on oligonucleotide therapeutics. Through the collaboration, we would like to propose the possible design of quality evaluation and preclinical safety-evaluation of oligonucleotide therapeutics. PMID:25707197

  8. 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...

  9. Measuring water properties from a moving boat

    Science.gov (United States)

    Lawson, A. G.

    1980-01-01

    Modification of commercial water analyzer permits measurement of pH, temperature, dissolved oxygen, conductivity, and turbidity for continuous water flow. Ram pressure on inlet tube mounted below power boat drives water through modified sample chamber where it is analyzed.

  10. 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,...

  11. Food Safety While Hiking, Camping and Boating

    Science.gov (United States)

    ... Standard Forms FSIS United States Department of Agriculture Food Safety and Inspection Service About FSIS District Offices ... Web Content Viewer (JSR 286) Actions ${title} Loading... Food Safety While Hiking, Camping & Boating Outdoor activities are ...

  12. Improvement and Validation of the BOAT Algorithm

    Directory of Open Access Journals (Sweden)

    Yingchun Liu

    2014-04-01

    Full Text Available The main objective of this paper is improving the BOAT classification algorithm and applying it in credit card big data analysis. Decision tree algorithm is a data analysis method for the classification which can be used to describe the extract important data class models or predict future data trends. The BOAT algorithm can reduce the data during reading and writing the operations, the improved algorithms in large data sets under the operating efficiency, and in line with the popular big data analysis. Through this paper, BOAT algorithm can further improve the performance of the algorithm and the distributed data sources under the performance. In this paper, large banking sectors of credit card data as the being tested data sets. The improved algorithm, the original BOAT algorithms, and the performance of other classical classification algorithms will be compared and analyzed.

  13. An autonomous boat based Synthetic Aperture Sonar

    OpenAIRE

    Sergio Rui Silva; Sergio Cunha; Anibal Matos; Nuno Cruz

    2007-01-01

    This paper describes a Synthetic Aperture Sonar (SAS) system being developed at the University of Porto to be used in a small autonomous boat for the survey of shallow water environments, such as rivers, deltas, estuaries and dams. Its purpose is to obtain high resolution echo reflectivity maps through synthetic aperture techniques, taking advantage of the high precision navigation system of the boat. In the future the production of bottom tomography maps is also considered through the use of...

  14. 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......(i)-catalyzed azide-alkyne cycloaddition (CuAAC) "click" chemistry. DNA/RNA target binding affinity and selectivity of the resulting POCs were improved in comparison to LNA/DNA mixmers and unmodified DNA controls. This clearly demonstrates that internal attachment of peptides to oligonucleotides can significantly...... improve biomolecular recognition by synthetic nucleic acid analogues. Circular dichroism (CD) measurements showed no distortion of the duplex structure by the incorporated peptide chains while studies in human serum indicated superior stability of the POCs compared to LNA/DNA mixmers and unmodified DNA...

  15. Autoand heterosuggestion in boat rowing

    Directory of Open Access Journals (Sweden)

    Omelyanenko V.I.

    2013-12-01

    Full Text Available Purpose. Creation of a complex integrated person-centered psychological model of sportsmen preparation for competitions in rowing and canoeing on base of geterosuggestion which includes psychological methods and their modifications as well as Rajah yoga system mindset trainings. Material, methods. In research took part 20 sportsmen in boat rowing of 1st juinor category aged 15 and 16 years old with parental consent. Different variants of combinations of psychological techniques developed psychotherapist with the participation of the team's coach, taking into account specific situations arising for each athlete individually. Results. Found that the experimental group was superior to the competition in scoring control group. Correction rowing technique was observed within 1-3 sessions. An efficiency of use of the developed model in the psychological preparation of rowers. Successfully carried out programming, simulation , correction of motor skills and psycho-emotional state of athletes in training and competitive periods. Conclusions. Stability of high sports results observed on the background of the post-hypnotic suggestion and formed a positive psycho-emotional and motivational attitude. The advantage over geterosuggestion under autosuggestion.

  16. 40 CFR 63.5787 - What if I also manufacture fiberglass boats or boat parts?

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 12 2010-07-01 2010-07-01 true What if I also manufacture fiberglass boats or boat parts? 63.5787 Section 63.5787 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... CATEGORIES National Emissions Standards for Hazardous Air Pollutants: Reinforced Plastic...

  17. Swarming of self-propelled camphor boats

    Science.gov (United States)

    Heisler, Eric; Suematsu, Nobuhiko J.; Awazu, Akinori; Nishimori, Hiraku

    2012-05-01

    When an ensemble of self-propelled camphor boats move in a one-dimensional channel, they exhibit a variety of collective behaviors. Under certain conditions, the boats tend to cluster together and move in a relatively tight formation. This type of behavior, referred to as clustering or swarming here, is one of three types recently observed in experiment. Similar clustering behavior is also reproduced in simulations based on a simple theoretical model. Here we examine this model to determine the clustering mechanism and the conditions under which clustering occurs. We also propose a method of quantifying the behavior that may be used in future experimental work.

  18. 78 FR 33856 - Sport Fishing and Boating Partnership Council

    Science.gov (United States)

    2013-06-05

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

  19. 77 FR 26784 - Sport Fishing and Boating Partnership Council

    Science.gov (United States)

    2012-05-07

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

  20. 76 FR 7579 - Sport Fishing and Boating Partnership Council

    Science.gov (United States)

    2011-02-10

    ... Fish and Wildlife Service Sport Fishing and Boating Partnership Council AGENCY: Fish and Wildlife... public meeting of the Sport Fishing and Boating Partnership Council (Council). DATES: The meeting will be... Federal Advisory Committee Act, 5 U.S.C. App., we announce that the Sport Fishing and Boating...

  1. 76 FR 1628 - Sport Fishing and Boating Partnership Council

    Science.gov (United States)

    2011-01-11

    ... Fish and Wildlife Service Sport Fishing and Boating Partnership Council AGENCY: Fish and Wildlife...), announce a public teleconference of the Sport Fishing and Boating Partnership Council (Council). DATE(S... private sectors of the sport fishing, boating, and conservation communities and is organized to...

  2. 78 FR 4161 - Sport Fishing and Boating Partnership Council

    Science.gov (United States)

    2013-01-18

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

  3. 75 FR 22423 - Sport Fishing and Boating Partnership Council

    Science.gov (United States)

    2010-04-28

    ... Fish and Wildlife Service Sport Fishing and Boating Partnership Council AGENCY: Fish and Wildlife... public meeting of the Sport Fishing and Boating Partnership Council (Council). DATES: The meeting will be... announce that the Sport Fishing and Boating Partnership Council will hold a meeting. Background The...

  4. 77 FR 61626 - Sport Fishing and Boating Partnership Council

    Science.gov (United States)

    2012-10-10

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

  5. 75 FR 47624 - Sport Fishing and Boating Partnership Council

    Science.gov (United States)

    2010-08-06

    ... Fish and Wildlife Service Sport Fishing and Boating Partnership Council AGENCY: Fish and Wildlife... public meeting of the Sport Fishing and Boating Partnership Council (Council). DATES: The meeting will be.... App., we announce that the Sport Fishing and Boating Partnership Council will hold a meeting...

  6. 7 CFR 503.6 - Camping, boating, and fishing.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 6 2010-01-01 2010-01-01 false Camping, boating, and fishing. 503.6 Section 503.6... OF AGRICULTURE CONDUCT ON PLUM ISLAND ANIMAL DISEASE CENTER § 503.6 Camping, boating, and fishing. The use of PIADC as a recreational area for camping, boating, fishing, and picnicking is...

  7. Oligonucleotide therapeutics: chemistry, delivery and clinical progress.

    Science.gov (United States)

    Sharma, Vivek K; Watts, Jonathan K

    2015-01-01

    Oligonucleotide therapeutics have the potential to become a third pillar of drug development after small molecules and protein therapeutics. However, the three approved oligonucleotide drugs over the past 17 years have not proven to be highly successful in a commercial sense. These trailblazer drugs have nonetheless laid the foundations for entire classes of drug candidates to follow. This review will examine further advances in chemistry that are earlier in the pipeline of oligonucleotide drug candidates. Finally, we consider the possible effect of delivery systems that may provide extra footholds to improve the potency and specificity of oligonucleotide drugs. Our overview focuses on strategies to imbue antisense oligonucleotides with more drug-like properties and their applicability to other nucleic acid therapeutics.

  8. 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...

  9. 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)

  10. Delta Lloyd solar boat team; sailing 30km/h with a solar-powered boat, using hydrofoils

    NARCIS (Netherlands)

    Tra, M.

    2013-01-01

    Every two years since 2006, the Delta Lloyd Solar Boat Team builds a boat to participate in the World Cup for solar-powered boats, across the ‘Elfsteden-route’, the famous tour of the eleven cities in the Dutch province of Friesland. The upcoming year the team, consisting of a new group of students,

  11. Synthesis of 5'-Aldehyde Oligonucleotide.

    Science.gov (United States)

    Lartia, Rémy

    2016-01-01

    Synthesis of oligonucleotide ending with an aldehyde functional group at their 5'-end (5'-AON) is possible for both DNA (5'-AODN) and RNA (5'-AORN) series irrespectively of the nature of the last nucleobase. The 5'-alcohol of on-support ODN is mildly oxidized under Moffat conditions. Transient protection of the resulting aldehyde by N,N'-diphenylethylenediamine derivatives allows cleavage, deprotection, and RP-HPLC purification of the protected 5'-AON. Finally, 5'-AON is deprotected by usual acetic acid treatment. In the aggregates, 5'-AON can be now synthesized and purified as routinely as non-modified ODNs, following procedures similar to the well-known "DMT-On" strategy. PMID:26967469

  12. Archetypal Analysis of The Open Boat

    Institute of Scientific and Technical Information of China (English)

    朱娟

    2013-01-01

      The Open Boat is written by Stephen Crane according to his own experience of encountering a shipwreck. This short nov⁃el is not only a legend, but also a complex of the author’s thinking of life and human and a fable of men’s lives. It is full of symbols and metaphors. To interpret the meaning of this novel, this paper is engaged to have an archetypal analysis of this short story.

  13. Guam's Small-Boat-based Fisheries

    OpenAIRE

    Myers, Robert F.

    1993-01-01

    Recent trends in Guam's small-boat fisheries and current knowledge of their biology, management, and economics are summarized. Annual estimates of participation, effort, and harvest are given for the pelagic and bottomfish fisheries for 1980-91 and for the spearfishing and atulai fisheries for 1985. The pelagic fishery is the largest, with annual landings ranging from 168 to 364 metric tons (t), followed by the bottomfish fishery (14-43 t), spearfishingf ishery (517 t), and bigeye scad fisher...

  14. 78 FR 57063 - Special Local Regulations; Jacksonville Dragon Boat Festival; St. Johns River; Jacksonville, FL

    Science.gov (United States)

    2013-09-17

    ... Jacksonville, Florida during the Jacksonville Dragon Boat Festival, a series of paddle boat races. The event is..., Inc. will host the Jacksonville Dragon Boat Festival, a series of boat races. The Race Area will be...: Sec. 100.35T07-0652 Special Local Regulations; Jacksonville Dragon Boat Festival; St. Johns......

  15. Kinetic effects on signal normalization in oligonucleotide microchips with labeled immobilized probes.

    Science.gov (United States)

    Pan'kov, S V; Chechetkin, V R; Somova, O G; Antonova, O V; Moiseeva, O V; Prokopenko, D V; Yurasov, R A; Gryadunov, D A; Chudinov, A V

    2009-10-01

    Among various factors affecting operation of oligonucleotide microchips, the variations in concentration and in homogeneous distribution of immobilized probes over the cells are one of the most important. The labeling of immobilized probes ensures the complete current monitoring on the probe distribution and is reliable and convenient. Using hydrogel-based oligonucleotide microchips, the applicability of Cy3-labeled immobilized probes for quality control and signal normalization after hybridization with Cy5-labeled target DNA was investigated. This study showed that proper signal normalization should be different in thermodynamic conditions and in transient regime with hybridization far from saturation. This kinetic effect holds for both hydrogel-based and surface oligonucleotide microchips. Besides proving basic features, the technique was assessed on a sampling batch of 50 microchips developed for identifying mutations responsible for rifampicin and isoniazid resistance of Mycobacterium tuberculosis.

  16. 78 FR 6732 - Changes to Standard Numbering System, Vessel Identification System, and Boating Accident Report...

    Science.gov (United States)

    2013-01-31

    ..., Vessel Identification System, and Boating Accident Report Database AGENCY: Coast Guard, DHS. ACTION: Rule... to numbering undocumented vessels and reporting boating accidents. The amendment affects three... agencies involved in issuing vessel registration and reporting boating accidents. This notice...

  17. 76 FR 18391 - Safety Zone; Texas International Boat Show Power Boat Races; Corpus Christi Marina, Corpus...

    Science.gov (United States)

    2011-04-04

    ... Races; Corpus Christi Marina, Corpus Christi, TX AGENCY: Coast Guard, DHS. ACTION: Temporary final rule... public and boating traffic in the Corpus Christi Marina area during this event. This safety zone is intended to restrict vessel traffic from a portion of the Corpus Christi Marina for short durations of...

  18. Radio-controlled boat for measuring water velocities and bathymetry

    Science.gov (United States)

    Vidmar, Andrej; Bezak, Nejc; Sečnik, Matej

    2016-04-01

    Radio-controlled boat named "Hi3" was designed and developed in order to facilitate water velocity and bathymetry measurements. The boat is equipped with the SonTek RiverSurveyor M9 instrument that is designed for measuring open channel hydraulics (discharge and bathymetry). Usually channel cross sections measurements are performed either from a bridge or from a vessel. However, these approaches have some limitations such as performing bathymetry measurements close to the hydropower plant turbine or downstream from a hydropower plant gate where bathymetry changes are often the most extreme. Therefore, the radio-controlled boat was designed, built and tested in order overcome these limitations. The boat is made from a surf board and two additional small balance support floats. Additional floats are used to improve stability in fast flowing and turbulent parts of rivers. The boat is powered by two electric motors, steering is achieved with changing the power applied to left and right motor. Furthermore, remotely controlled boat "Hi3" can be powered in two ways, either by a gasoline electric generator or by lithium batteries. Lithium batteries are lighter, quieter, but they operation time is shorter compared to an electrical generator. With the radio-controlled boat "Hi3" we can perform measurements in potentially dangerous areas such as under the lock gates at hydroelectric power plant or near the turbine outflow. Until today, the boat "Hi3" has driven more than 200 km in lakes and rivers, performing various water speed and bathymetry measurements. Moreover, in future development the boat "Hi3" will be upgraded in order to be able to perform measurements automatically. The future plans are to develop and implement the autopilot. With this approach the user will define the route that has to be driven by the boat and the boat will drive the pre-defined route automatically. This will be possible because of the very accurate differential GPS from the Sontek River

  19. Mercury exposure aboard an ore boat.

    OpenAIRE

    Roach, Richard R; Busch, Stephanie

    2004-01-01

    Two maritime academy interns (X and Y) were exposed to mercury vapor after spilling a bottle of mercury on the floor in an enclosed storeroom while doing inventory aboard an ore boat. During a 3-day period, intern Y suffered transient clinical intoxication that resolved after he was removed from the environment and he showered and discarded all clothing. His initial serum mercury level dropped from 4 ng/mL to < 0.05 ng/mL. Intern X had an initial level of 11 ng/mL, which continued to rise to ...

  20. 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...

  1. Oligonucleotide-based therapy for neurodegenerative diseases.

    Science.gov (United States)

    Magen, Iddo; Hornstein, Eran

    2014-10-10

    Molecular genetics insight into the pathogenesis of several neurodegenerative diseases, such as Alzheimer׳s disease, Parkinson׳s disease, Huntington׳s disease and amyotrophic lateral sclerosis, encourages direct interference with the activity of neurotoxic genes or the molecular activation of neuroprotective pathways. Oligonucleotide-based therapies are recently emerging as an efficient strategy for drug development and these can be employed as new treatments of neurodegenerative states. Here we review advances in this field in recent years which suggest an encouraging assessment that oligonucleotide technologies for targeting of RNAs will enable the development of new therapies and will contribute to preservation of brain integrity. PMID:24727531

  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 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED... DISEASES Source and Use of Potable Water § 1240.95 Sanitation of water boats. No vessel engaged...

  3. 76 FR 81959 - Sport Fishing and Boating Partnership Council

    Science.gov (United States)

    2011-12-29

    ... Fish and Wildlife Service Sport Fishing and Boating Partnership Council AGENCY: Fish and Wildlife... public meeting of the Sport Fishing and Boating Partnership Council (Council). DATES: The meeting will be... with the requirements of the Federal Advisory Committee Act, 5 U.S.C. App., we announce that the...

  4. 76 FR 47606 - Sport Fishing and Boating Partnership Council

    Science.gov (United States)

    2011-08-05

    ... Fish and Wildlife Service Sport Fishing and Boating Partnership Council AGENCY: Fish and Wildlife... public meeting of the Sport Fishing and Boating Partnership Council (Council). DATES: The meeting will be... of the Federal Advisory Committee Act, 5 U.S.C. App., we announce that the Sport Fishing and...

  5. 77 FR 29359 - Sport Fishing and Boating Partnership Council

    Science.gov (United States)

    2012-05-17

    ... Fish and Wildlife Service Sport Fishing and Boating Partnership Council AGENCY: Fish and Wildlife...), announce a public meeting of the Sport Fishing and Boating Partnership Council (Council). A Federal... the requirements of the Federal Advisory Committee Act, 5 U.S.C. App., we announce that the...

  6. 76 FR 75898 - Sport Fishing and Boating Partnership Council

    Science.gov (United States)

    2011-12-05

    ... Fish and Wildlife Service Sport Fishing and Boating Partnership Council AGENCY: Fish and Wildlife... (Service), announce a public teleconference of the Sport Fishing and Boating Partnership Council (Council.... The Council represents the interests of the public and private sectors of the sport fishing,...

  7. 78 FR 61866 - Sport Fishing and Boating Partnership Council

    Science.gov (United States)

    2013-10-04

    ... Fish and Wildlife Service Sport Fishing and Boating Partnership Council AGENCY: Fish and Wildlife...), announce a public meeting of the Sport Fishing and Boating Partnership Council (Council). A Federal... requirements of the Federal Advisory Committee Act, 5 U.S.C. App., we announce that the Sport Fishing...

  8. 78 FR 23587 - Sport Fishing and Boating Partnership Council

    Science.gov (United States)

    2013-04-19

    ... Fish and Wildlife Service Sport Fishing and Boating Partnership Council AGENCY: Fish and Wildlife...), announce a public meeting of the Sport Fishing and Boating Partnership Council (Council). A Federal... requirements of the Federal Advisory Committee Act, 5 U.S.C. App., we announce that the Sport Fishing...

  9. Bald Eagle response to boating activity in northcentral Florida

    Science.gov (United States)

    Wood, P.B.

    1999-01-01

    I examined the effects of weekend and weekday boating activity on Bald Eagle (Haliaeetus leucocephalus) use of three lakes in northcentral Florida during 1988-89. On Lake Lochloosa, which had the highest number of boats of the three lakes, boating activity significantly reduced the numbers of all age classes of eagles using the lake (P < 0.025). Increased boating activity on Lake Wauberg was not related to use by eagles (P = 0.06) likely because boating activity was concentrated during midday while eagles typically foraged early and late in the day. On Newnan's Lake, the number of eagles observed also was not different between weekends and weekdays (P = 0.20). Weekend boating activity did not relate to perch use, habitat use, interactions or age distribution indicating no alteration of eagle behavior patterns. Flush distance did not vary between weekends and weekdays (P = 0.96), but did vary by month (P = 0.0001), with a greater flush distance during months with highest boating activity. Minimal flush distances (x?? = 53m) and lack of measurable effects on behavior suggested that eagles in my study area were tolerant of boat disturbance.

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

    Digital Repository Service at National Institute of Oceanography (India)

    Tripati, S.

    . The construction pattern, size and material differed from those of other regions in India. The navigational proficiency of the sailors and boat-building is also referred to. The current boat-building techniques studied by the authors is dealt with in this paper...

  11. Automatic Boat Identification System for VIIRS Low Light Imaging Data

    Directory of Open Access Journals (Sweden)

    Christopher D. Elvidge

    2015-03-01

    Full Text Available The ability for satellite sensors to detect lit fishing boats has been known since the 1970s. However, the use of the observations has been limited by the lack of an automatic algorithm for reporting the location and brightness of offshore lighting features arising from boats. An examination of lit fishing boat features in Visible Infrared Imaging Radiometer Suite (VIIRS day/night band (DNB data indicates that the features are essentially spikes. We have developed a set of algorithms for automatic detection of spikes and characterization of the sharpness of spike features. A spike detection algorithm generates a list of candidate boat detections. A second algorithm measures the height of the spikes for the discard of ionospheric energetic particle detections and to rate boat detections as either strong or weak. A sharpness index is used to label boat detections that appear blurry due to the scattering of light by clouds. The candidate spikes are then filtered to remove features on land and gas flares. A validation study conducted using analyst selected boat detections found the automatic algorithm detected 99.3% of the reference pixel set. VIIRS boat detection data can provide fishery agencies with up-to-date information of fishing boat activity and changes in this activity in response to new regulations and enforcement regimes. The data can provide indications of illegal fishing activity in restricted areas and incursions across Exclusive Economic Zone (EEZ boundaries. VIIRS boat detections occur widely offshore from East and Southeast Asia, South America and several other regions.

  12. Radio-marking and in vivo imagery of oligonucleotides

    International Nuclear Information System (INIS)

    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

  13. In vivo imaging of oligonucleotidic aptamers

    Energy Technology Data Exchange (ETDEWEB)

    Tavitian, B.; Boisgard, R. [Inserm U803, Laboratoire d' Imagerie Moleculaire Experimentale, Service hospitalier Frederic joliot, Intitut d' Imagerie Biomedicale, CEA, Orsay (France); Duconge, F.; Dolle, F. [Groupe de Radiochimie, Laboratoire d' Imagerie Moleculaire Experimentale, Service hospitalier Frederic joliot, Intitut d' Imagerie Biomedicale, CEA, Orsay (France)

    2009-07-01

    In this chapter we present the methods developed in our laboratory for in vivo imaging of oligonucleotidic aptamers. These methods relate to (i) the labelling of aptamers with fluorine-18, a positron emitter (ii) Positron Emission Tomography imaging of laboratory animals with [({sup 18})F]aptamers and (iii) labelling with fluorescent dyes and optical imaging of aptamers in mice. (authors)

  14. Triplex-forming ability of modified oligonucleotides

    DEFF Research Database (Denmark)

    Højland, Torben; Babu, Bolle Ravindra; Bryld, Torsten;

    2007-01-01

    We present our studies on the ability of several different nucleotide analogs as triplex-forming oligonucleotides. The modifications tested include 4'-C-hydroxymethyl, LNA, 2'-amino-LNA and N2'-functionalized 2'-amino-LNA. Triplexes containing monomers of N2'-glycyl-functionalized 2'-amino-LNA are...

  15. Chemosensitization by antisense oligonucleotides targeting MDM2.

    Science.gov (United States)

    Bianco, Roberto; Ciardiello, Fortunato; Tortora, Giampaolo

    2005-02-01

    The MDM2 oncogene is overexpressed in many human cancers, including sarcomas, certain hematologic malignancies, and breast, colon and prostate cancers. The p53-MDM2 interaction pathway has been suggested as a novel target for cancer therapy. To that end, several strategies have been explored, including the use of small polypeptides targeted to the MDM2-p53 binding domain, anti-MDM2 antisense oligonucleotides, and natural agents. Different generations of anti-human-MDM2 oligonucleotides have been tested in in vitro and in vivo human cancer models, revealing specific inhibition of MDM2 expression and significant antitumor activity. Use of antisense oligos potentiated the effects of growth inhibition, p53 activation and p21 induction by several chemotherapeutic agents. Increased therapeutic effectiveness of chemotherapeutic drugs in human cancer cell lines carrying p53 mutations or deletions have shown the ability of MDM2 inhibitors to act as chemosensitizers in various types of tumors through both p53-dependent and p53-independent mechanisms. Inhibiting MDM2 appears to also have a role in radiation therapy for human cancer, regardless of p53 status, providing a rationale for the development of a new class of radiosensitizers. Moreover, MDM2 antisense oligonucleotides potentiate the effect of epidermal growth factor receptor (EGFR) inhibitors by affecting in vitro and in vivo proliferation, apoptosis and protein expression in hormone-refractory and hormone-dependent human prostate cancer cells. These data support the development, among other MDM2 inhibitors, of anti-MDM2 antisense oligonucleotides as a novel class of anticancer agents, and suggest a potentially relevant role for the oligonucleotides when integrated with conventional treatments and/or other signaling inhibitors in novel therapeutic strategies.

  16. The Boat Girl in the Photo

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    The Little Boat Girl THIS picture was taken at dusk, onestormy day, half a century ago. On April 21, 1949, one million soldiersof the Chinese People’s Liberation Army, alongmore than 500-kilometers of riverbank, quicklybroke through the "thousand-Li line of defence,"which had been painstakingly built up by theKuomintang, and forced the Changjiang River. At dusk on April 22, boatmen from Yangzhong,an island in the Changjiang River, hurried to thebank to row the follow-up units across. Despitearduous weather, the boatmen’s skill in fightingagainst wind and waves was considerable and, inthe soft lights of sunset, the rows of old woodenboats appeared to be flying on the ChangjiangRiver. A most impressive scene. Among the officers waiting on the riverbank tobe ferried across was one tall soldier, deeplyabsorbed in the sight of a young girl, not far away,

  17. Mercury exposure aboard an ore boat.

    Science.gov (United States)

    Roach, Richard R; Busch, Stephanie

    2004-06-01

    Two maritime academy interns (X and Y) were exposed to mercury vapor after spilling a bottle of mercury on the floor in an enclosed storeroom while doing inventory aboard an ore boat. During a 3-day period, intern Y suffered transient clinical intoxication that resolved after he was removed from the environment and he showered and discarded all clothing. His initial serum mercury level dropped from 4 ng/mL to footwear earlier than intern Y. Intern X's continued exposure due to mercury in the contaminated boots during the 2 weeks before hospitalization was presumed to be the cause. Removing his footwear led to resolution of his toxic symptoms and correlated with subsequent lowered serum mercury levels. Chelation was initiated as recommended, despite its uncertain benefit for neurologic intoxication. Mercury is used in the merchant marine industry in ballast monitors called king gauges. New engineering is recommended for ballast monitoring to eliminate this hazard. PMID:15175181

  18. Blending biodiesel in fishing boat fuels for improved fuel characteristics

    Directory of Open Access Journals (Sweden)

    Cherng-Yuan eLin

    2014-02-01

    Full Text Available 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% with 25 wt% biodiesel blending. 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% to 4.5%.

  19. U.S. Coast Guard, Office of Boating Safety

    Science.gov (United States)

    ... Report Recalls Product Assurance Branch Boating Safety Circulars Beacon Alerts Marine Safety Alerts Multimedia PSA's Image Library ... Grants Nonprofit Organization Grants Grant Archives Grant Links Beacon Alerts FY17 National Nonprofit Organization Funding Opportunity Application ...

  20. 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,...

  1. 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,...

  2. 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...

  3. Electrochemical study of hepta–oligonucleotides

    Directory of Open Access Journals (Sweden)

    Zdenka Balcarova

    2010-12-01

    Full Text Available The study deals with the description and characterization of twohepta–oligonucleotides (DNA and RNA forming special structures.We studied their electrochemical behaviour by means of cyclicvoltammetry (CV and elimination voltammetry with linear scan(EVLS in combination with adsorptive stripping (AdS technique.Differences in electrochemical behaviour of hepta–deoxyribonucleotide and its RNA analog were discussed with regardto their different structures in solutions and their melting points.

  4. 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.......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....

  5. Optically Triggered Immune Response through Photocaged Oligonucleotides

    Science.gov (United States)

    Govan, Jeane M.; Young, Douglas D.; Lively, Mark O.

    2015-01-01

    Bacterial and viral CpG oligonculeotides are unmethylated cytosine-phosphate-guanosine dinucleotide sequences and trigger an innate immune response through activation of the toll-like receptor 9 (TLR9). We have developed synthetic photocaged CpGs via site-specific incorporation of nitropiperonyloxymethyl (NPOM)-caged thymidine residues. These oligonucleotides enable the optical control of TLR9 function and thereby provide light-activation of an immune response. We provide a proof-of-concept model by applying a reporter assay in live cells and by quantification of endogenous production of interleukin 6. PMID:26034339

  6. On Naturalism in Stephen Crane’s The Open Boat

    Institute of Scientific and Technical Information of China (English)

    WANG Xiu-hong; CHEN Bei-bei

    2014-01-01

    Stephen Crane is one of the greatest figures in the history of American literature and his novella The Open Boat is wide-ly known by people all over the world as a representative work of Naturalism. This paper aims at exploring Naturalism in Stephen Crane’s The Open Boat, which will guide the readers to understand American Naturalism accurately and thoroughly. It firstly in-troduces the author and his novel The Open Boat. Secondly, it progressively dissects Naturalism. It not only analyses the general characteristics of Naturalism with details in The Open Boat, but also interprets the distinguishing features of American Naturalism so that readers can better understand the features of American Naturalism. Through textual perusal, it further studies the unique characteristics of Stephen Crane’s Naturalism and lays particular emphasis on Crane’s special concern on the awakening of hu-manity. It is hoped that this thesis can help readers get an in-depth comprehension of Naturalism and gain some inspiration from The Open Boat.

  7. Bioconjugation of oligonucleotides for treating liver fibrosis.

    Science.gov (United States)

    Ye, Zhaoyang; Houssein, Houssam S Hajj; Mahato, Ram I

    2007-01-01

    Liver fibrosis results from chronic liver injury due to hepatitis B and C, excessive alcohol ingestion, and metal ion overload. Fibrosis culminates in cirrhosis and results in liver failure. Therefore, a potent antifibrotic therapy is urgently needed to reverse scarring and eliminate progression to cirrhosis. Although activated hepatic stellate cells (HSCs) remain the principle cell type responsible for liver fibrosis, perivascular fibroblasts of portal and central veins as well as periductular fibroblasts are other sources of fibrogenic cells. This review will critically discuss various treatment strategies for liver fibrosis, including prevention of liver injury, reduction of inflammation, inhibition of HSC activation, degradation of scar matrix, and inhibition of aberrant collagen synthesis. Oligonucleotides (ODNs) are short, single-stranded nucleic acids, which disrupt expression of target protein by binding to complementary mRNA or forming triplex with genomic DNA. Triplex forming oligonucleotides (TFOs) provide an attractive strategy for treating liver fibrosis. A series of TFOs have been developed for inhibiting the transcription of alpha1(I) collagen gene, which opens a new area for antifibrotic drugs. There will be in-depth discussion on the use of TFOs and how different bioconjugation strategies can be utilized for their site-specific delivery to HSCs or hepatocytes for enhanced antifibrotic activities. Various insights developed in individual strategy and the need for multipronged approaches will also be discussed. PMID:18154454

  8. Gene cloning based on long oligonucleotide probes

    International Nuclear Information System (INIS)

    The most commonly used technique for gene cloning has been to utilize oligonucleotide probe based on protein sequence data. Of course this approach requires characterized and purified protein so that at least a portion of amino acid sequence can be determined and used to infer the corresponding DNA sequence. Based on the amino acid sequence information, either short or long oligonucleotide probes can be synthesized chemically. Long probes are typically 30-100 nucleotides long and are a single sequence based on a best guess for each codon. The long probe approach was first used to screen for three different genes: bovine trypsin inhibitor, human insulin-like growth factor I, and human factor IX. There are three advantages of long probes. (1) Any stretch of amino acid sequence 10 or longer can be used. (2) The amino acid sequence need not be absolutely correct. (3) These probes can be used to screen high-complexity libraries with fewer false positives. In spite of the uncertainties over codon selection, the long probe approach is currently the method of choice in screening for genes based on protein sequence data

  9. Self-propulsion of a metallic superoleophobic micro-boat.

    Science.gov (United States)

    Musin, Albina; Grynyov, Roman; Frenkel, Mark; Bormashenko, Edward

    2016-10-01

    The self-propulsion of a heavy, superoleophobic, metallic micro-boat carrying a droplet of various aqueous alcohol solutions as a fuel tank is reported. The micro-boat is driven by the solutocapillary Marangoni flow. The jump in the surface tension owing to the condensation of alcohols on the water surface was established experimentally. Maximal velocities of the self-propulsion were registered as high as 0.05m/s. The maximal velocity of the center mass of the boat correlates with the maximal change in the surface tension, due to the condensation of alcohols. The mechanism of the self-locomotion is discussed. The phenomenological dynamic model describing the self-propulsion is reported. PMID:27388132

  10. RESEARCH ON WAKE ENERGY RECOVERY TECHNOLOGIES FOR A FISHING BOAT

    Institute of Scientific and Technical Information of China (English)

    MA Cheng; QIAN Zheng-fang; DU Du; ZHANG Xu

    2005-01-01

    Wake energy recovery of a ship's propeller is an important research subject in ship propulsion field. Based on the study on the mechanism analysis and computation method of the hydrodynamic performance of the propeller-rudder-rudder bubble combination, computer simulation system was built and then used to design and simulate four kinds of rudder bubbles, then the model comparison tests with the original rudder was carried out and the sensible factors influencing the energy-saving effects of rudder bubble was also analyzed. On this basis, a further optimized design of the rudder bubble for a fishing boat was put forward, and comparison test on a real boat was then carried out. It is shown that the optimized rudder bubble design can effectively recover wake energy of ships and the rudder bubble installation features a simple operation and high cost-effectiveness, and the energy-saving effect of real boat test achieves 5.1%.

  11. Adaptive, real-time hypoxia measurements using an autonomous boat

    Science.gov (United States)

    Kerkez, B.; Wong, B. P.; Balzano, L.; Lipor, J.; Scavia, D.

    2015-12-01

    We present an autonomous system to measure hypoxia at high spatial resolutions. The approach combines a robotic boat, cloud hosted data services, and a suite of adaptive sampling algorithms to minimize the number of samples required to delineate hypoxic extents. The boat lowers sensors into the water column to provide depth profiles of temperature and oxygen concentrations. An adaptive path-planning algorithm continuously analyzes the in-situ observations and directs the boat to its next measurement location. This significantly reduces number of samples compared to a gridded sampling approach, while simultaneously improving the certainty with which the hypoxic regions are delineated. The method has been evaluated on small lakes throughout Michigan and shows significant promise to scale to the Great Lakes, where hypoxia is common occurrence that adversely affects various stakeholder and ecosystems.

  12. Investigations of oligonucleotide usage variance within and between prokaryotes

    DEFF Research Database (Denmark)

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

    2008-01-01

    of different DNA 'word-sizes' and explore how oligonucleotide frequencies differ in coding and non-coding regions. In addition, we used oligonucleotide frequencies to investigate DNA composition and how DNA sequence patterns change within and between prokaryotic organisms. Among the results found...

  13. Voltage-gated calcium channel and antisense oligonucleotides thereto

    Science.gov (United States)

    Hruska, Keith A. (Inventor); Friedman, Peter A. (Inventor); Barry, Elizabeth L. R. (Inventor); Duncan, Randall L. (Inventor)

    1998-01-01

    An antisense oligonucleotide of 10 to 35 nucleotides in length that can hybridize with a region of the .alpha..sub.1 subunit of the SA-Cat channel gene DNA or mRNA is provided, together with pharmaceutical compositions containing and methods utilizing such antisense oligonucleotide.

  14. Predicting oligonucleotide-directed mutagenesis failures in protein engineering.

    Science.gov (United States)

    Wassman, Christopher D; Tam, Phillip Y; Lathrop, Richard H; Weiss, Gregory A

    2004-01-01

    Protein engineering uses oligonucleotide-directed mutagenesis to modify DNA sequences through a two-step process of hybridization and enzymatic synthesis. Inefficient reactions confound attempts to introduce mutations, especially for the construction of vast combinatorial protein libraries. This paper applied computational approaches to the problem of inefficient mutagenesis. Several results implicated oligonucleotide annealing to non-target sites, termed 'cross-hybridization', as a significant contributor to mutagenesis reaction failures. Test oligonucleotides demonstrated control over reaction outcomes. A novel cross-hybridization score, quickly computable for any plasmid and oligonucleotide mixture, directly correlated with yields of deleterious mutagenesis side products. Cross-hybridization was confirmed conclusively by partial incorporation of an oligonucleotide at a predicted cross-hybridization site, and by modification of putative template secondary structure to control cross-hybridization. Even in low concentrations, cross-hybridizing species in mixtures poisoned reactions. These results provide a basis for improved mutagenesis efficiencies and increased diversities of cognate protein libraries.

  15. Summary on China boat import and export in 2005

    Institute of Scientific and Technical Information of China (English)

    Zhu Huaixin

    2006-01-01

    @@ According to the latest statistics by the Customs, China exported inflatable recreation/ sports boats in 4 types (as the Customs codes 89039900, 89031000, 89039200& 89039100) increased in large numbers up to 137634 and totaled 63.4096 million US dollars, which increased 40.8% than 2004 and took 1.344% of the total ship export sum of 2005.Besides, it also imported 1162 various boats mounting to 18.108 million US dollars,this increased 80.5% than 2004 and took 3.69%of the total ship import value.

  16. 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...... different directions. • The connection forces between the hulls and the wind turbine pile. • The natural frequency of oscillation. For the study, realistic scale models of the hulls of the crew boats were supplied by the client, Hauschildt Marine. The laboratory tests were performed by Arthur Pecher under...

  17. FLUID DYNAMIC PERFORMANCE OF GROOVED PLANING BOAT AND ITS EFFECT ON RESISTANCE

    Institute of Scientific and Technical Information of China (English)

    SHI Zhong-kun; WU Fang-liang; ZHOU Feng

    2005-01-01

    In this paper, the fluid dynamic performance for a new boat form-grooved planing boats is analyzed, and the results of resistance tests for seven grooved planing boat models of different types are presented in the form of curves of attack angle and resistance-weight ratio versus Froude number. According to these curves, the effect of some parameters of the boat type on the resistance is analyzed.

  18. 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 ...

  19. Asthma Basics

    Science.gov (United States)

    ... Tropical Delight: Melon Smoothie Pregnant? Your Baby's Growth Asthma Basics KidsHealth > For Parents > Asthma Basics Print A ... Asthma Categories en español Asma: aspectos fundamentales About Asthma Asthma is a common lung condition in kids ...

  20. Brain Basics

    Medline Plus

    Full Text Available ... Basics will introduce you to some of this science, such as: How the brain develops How genes and the environment affect the brain The basic structure of the brain How different parts of ...

  1. Backpack Basics

    Science.gov (United States)

    ... How Can I Help a Friend Who Cuts? Backpack Basics KidsHealth > For Teens > Backpack Basics Print A ... it can cause back problems or even injury. Backpacks Are Best Backpacks can't be beat for ...

  2. 77 FR 43513 - Olympia Harbor Days Tug Boat Races, Budd Inlet, WA

    Science.gov (United States)

    2012-07-25

    ... SECURITY Coast Guard 33 CFR Part 100 Olympia Harbor Days Tug Boat Races, Budd Inlet, WA AGENCY: Coast Guard... Local Regulation, Olympia Harbor Days Tug Boat Races, Budd Inlet, WA from 12 p.m. through 8 p.m. on... notice of enforcement of the Special Local Regulation for Olympia Harbor Days Tug Boat Races, Budd...

  3. 77 FR 23125 - Special Local Regulation; Tuscaloosa Dragon Boat Race; Black Warrior River; Tuscaloosa, AL

    Science.gov (United States)

    2012-04-18

    ... SECURITY Coast Guard 33 CFR Part 100 RIN 1625-AA08 Special Local Regulation; Tuscaloosa Dragon Boat Race.... League of Tuscaloosa Dragon Boat Races. Entry into, transiting or anchoring in this area is prohibited to... associated with the Jr. League of Tuscaloosa Dragon Boat Races. This event is advertised as scheduled...

  4. 75 FR 17754 - Certificate of Alternative Compliance for the Lift Boat GARY CHIASSON ELEVATOR

    Science.gov (United States)

    2010-04-07

    ... SECURITY Coast Guard Certificate of Alternative Compliance for the Lift Boat GARY CHIASSON ELEVATOR AGENCY... Compliance was issued for the lift boat GARY CHIASSON ELEVATOR as required by 33 U.S.C. 1605(c) and 33 CFR 81... Regulations, Parts 81 and 89, has been issued for the lift boat GARY CHIASSON ELEVATOR. The Certificate...

  5. 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,...

  6. 19 CFR 148.32 - Vehicles, aircraft, boats, teams and saddle horses taken abroad.

    Science.gov (United States)

    2010-04-01

    ... 19 Customs Duties 2 2010-04-01 2010-04-01 false Vehicles, aircraft, boats, teams and saddle horses... for Returning Residents § 148.32 Vehicles, aircraft, boats, teams and saddle horses taken abroad. (a) Admission free of duty. Automobiles and other vehicles, aircraft, boats, teams and saddle horses,...

  7. 77 FR 55436 - Special Local Regulation; Partnership in Education, Dragon Boat Race; Maumee River, Toledo, OH

    Science.gov (United States)

    2012-09-10

    ... Special Local Regulations, Partnership in Education, Dragon Boat Festival, Toledo, OH. (a) Regulated Area..., Dragon Boat Race; Maumee River, Toledo, OH AGENCY: Coast Guard, DHS. ACTION: Notice of proposed... River during the annual Dragon Boat Races. This special local regulated area is necessary to...

  8. Hole hopping rates in single strand oligonucleotides

    Science.gov (United States)

    Borrelli, Raffaele; Capobianco, Amedeo; Peluso, Andrea

    2014-08-01

    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. Preparation and application of triple helix forming oligonucleotides and single strand oligonucleotide donors for gene correction.

    Science.gov (United States)

    Alam, Rowshon; Thazhathveetil, Arun Kalliat; Li, Hong; Seidman, Michael M

    2014-01-01

    Strategies for site-specific modulation of genomic sequences in mammalian cells require two components. One must be capable of recognizing and activating a specific target sequence in vivo, driving that site into an exploitable repair pathway. Information is transferred to the site via participation in the pathway by the second component, a donor nucleic acid, resulting in a permanent change in the target sequence. We have developed biologically active triple helix forming oligonucleotides (TFOs) as site-specific gene targeting reagents. These TFOs, linked to DNA reactive compounds (such as a cross-linking agent), activate pathways that can engage informational donors. We have used the combination of a psoralen-TFO and single strand oligonucleotide donors to generate novel cell lines with directed sequence changes at the target site. Here we describe the synthesis and purification of bioactive psoralen-linked TFOs, their co-introduction into mammalian cells with donor nucleic acids, and the identification of cells with sequence conversion of the target site. We have emphasized details in the synthesis and purification of the oligonucleotides that are essential for preparation of reagents with optimal activity. PMID:24557899

  10. 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…

  11. 77 FR 33229 - Sport Fishing and Boating Partnership Council Charter

    Science.gov (United States)

    2012-06-05

    ... Coordination Act (16 U.S.C. 661-667e), and Executive Order 12962 of June 7, 1995-Recreational Fisheries (60 FR 30769, June 7, 1995), as amended by Executive Order 13474 of September 26, 2008 (73 FR 57229, October 1... Office of the Secretary Sport Fishing and Boating Partnership Council Charter AGENCY: Office of...

  12. 73m in ocean-going squid angling boat

    Institute of Scientific and Technical Information of China (English)

    Jin Yue

    2004-01-01

    @@ Dalian Fishing Vessel Co., Dalian, China Liaoning Province Sea Fishery Group entrusted Dalian Fishing Vessel Company with working design and technical design of squid angling boat whose model is 8356, and Dalian Fishing Vessel Company is in charge of construction. The summary of this paper is about the characteristics of overall system design of this ship.

  13. 33 CFR 177.08 - Regulated boating areas.

    Science.gov (United States)

    2010-07-01

    ... purpose of this part, the following are regulated boating areas. Note: Geographic coordinates expressed in... referenced horizontal datum is the North American Datum of 1983 (NAD 83), unless such geographic coordinates are expressly labeled NAD 83. Geographic coordinates without the NAD 83 reference may be plotted...

  14. Boat sampling technique for assessment of ageing of components

    International Nuclear Information System (INIS)

    Boat sampling technique (BST) is a surface sampling technique, which has been developed for obtaining, in-situ, metal samples from the surface of an operating component without affecting its operating service life. The BST is non-destructive in nature and the sample is obtained without plastic deformation or without thermal degradation of the parent material. The shape and size of the sample depends upon the shape of the cutter and the surface geometry of the parent material. Miniature test specimens are generated from the sample and the specimens are subjected to various tests, viz. Metallurgical Evaluation, Metallographic Evaluation, Micro-hardness Evaluation, sensitisation test, small punch test etc. to confirm the integrity and assessment of safe operating life of the component. This paper highlights design objective of boat sampling technique, description of sampling module, sampling cutter and its performance evaluation, cutting process, boat samples, operational sequence of sampling module, qualification of sampling module, qualification of sampling technique, qualification of scooped region of the parent material, sample retrieval system, inspection, testing and examination to be carried out on the boat samples and scooped region. (author)

  15. Ca2+ enrichment in culture medium potentiates effect of oligonucleotides.

    Science.gov (United States)

    Hori, Shin-Ichiro; Yamamoto, Tsuyoshi; Waki, Reiko; Wada, Shunsuke; Wada, Fumito; Noda, Mio; Obika, Satoshi

    2015-10-30

    Antisense and RNAi-related oligonucleotides have gained attention as laboratory tools and therapeutic agents based on their ability to manipulate biological events in vitro and in vivo. We show that Ca(2+) enrichment of medium (CEM) potentiates the in vitro activity of multiple types of oligonucleotides, independent of their net charge and modifications, in various cells. In addition, CEM reflects in vivo silencing activity more consistently than conventional transfection methods. Microscopic analysis reveals that CEM provides a subcellular localization pattern of oligonucleotides resembling that obtained by unassisted transfection, but with quantitative improvement. Highly monodispersed nanoparticles ~100 nm in size are found in Ca(2+)-enriched serum-containing medium regardless of the presence or absence of oligonucleotides. Transmission electron microscopy analysis reveals that the 100-nm particles are in fact an ensemble of much smaller nanoparticles (ϕ ∼ 15 nm). The presence of these nanoparticles is critical for the efficient uptake of various oligonucleotides. In contrast, CEM is ineffective for plasmids, which are readily transfected via the conventional calcium phosphate method. Collectively, CEM enables a more accurate prediction of the systemic activity of therapeutic oligonucleotides, while enhancing the broad usability of oligonucleotides in the laboratory. PMID:26101258

  16. Nucleic acid sequence detection using multiplexed oligonucleotide PCR

    Science.gov (United States)

    Nolan, John P.; White, P. Scott

    2006-12-26

    Methods for rapidly detecting single or multiple sequence alleles in a sample nucleic acid are described. Provided are all of the oligonucleotide pairs capable of annealing specifically to a target allele and discriminating among possible sequences thereof, and ligating to each other to form an oligonucleotide complex when a particular sequence feature is present (or, alternatively, absent) in the sample nucleic acid. The design of each oligonucleotide pair permits the subsequent high-level PCR amplification of a specific amplicon when the oligonucleotide complex is formed, but not when the oligonucleotide complex is not formed. The presence or absence of the specific amplicon is used to detect the allele. Detection of the specific amplicon may be achieved using a variety of methods well known in the art, including without limitation, oligonucleotide capture onto DNA chips or microarrays, oligonucleotide capture onto beads or microspheres, electrophoresis, and mass spectrometry. Various labels and address-capture tags may be employed in the amplicon detection step of multiplexed assays, as further described herein.

  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. Ca2+ enrichment in culture medium potentiates effect of oligonucleotides.

    Science.gov (United States)

    Hori, Shin-Ichiro; Yamamoto, Tsuyoshi; Waki, Reiko; Wada, Shunsuke; Wada, Fumito; Noda, Mio; Obika, Satoshi

    2015-10-30

    Antisense and RNAi-related oligonucleotides have gained attention as laboratory tools and therapeutic agents based on their ability to manipulate biological events in vitro and in vivo. We show that Ca(2+) enrichment of medium (CEM) potentiates the in vitro activity of multiple types of oligonucleotides, independent of their net charge and modifications, in various cells. In addition, CEM reflects in vivo silencing activity more consistently than conventional transfection methods. Microscopic analysis reveals that CEM provides a subcellular localization pattern of oligonucleotides resembling that obtained by unassisted transfection, but with quantitative improvement. Highly monodispersed nanoparticles ~100 nm in size are found in Ca(2+)-enriched serum-containing medium regardless of the presence or absence of oligonucleotides. Transmission electron microscopy analysis reveals that the 100-nm particles are in fact an ensemble of much smaller nanoparticles (ϕ ∼ 15 nm). The presence of these nanoparticles is critical for the efficient uptake of various oligonucleotides. In contrast, CEM is ineffective for plasmids, which are readily transfected via the conventional calcium phosphate method. Collectively, CEM enables a more accurate prediction of the systemic activity of therapeutic oligonucleotides, while enhancing the broad usability of oligonucleotides in the laboratory.

  19. Antisense oligonucleotide induction of progerin in human myogenic cells.

    Directory of Open Access Journals (Sweden)

    Yue-Bei Luo

    Full Text Available We sought to use splice-switching antisense oligonucleotides to produce a model of accelerated ageing by enhancing expression of progerin, translated from a mis-spliced lamin A gene (LMNA transcript in human myogenic cells. The progerin transcript (LMNA Δ150 lacks the last 150 bases of exon 11, and is translated into a truncated protein associated with the severe premature ageing disease, Hutchinson-Gilford progeria syndrome (HGPS. HGPS arises from de novo mutations that activate a cryptic splice site in exon 11 of LMNA and result in progerin accumulation in tissues of mesodermal origin. Progerin has also been proposed to play a role in the 'natural' ageing process in tissues. We sought to test this hypothesis by producing a model of accelerated muscle ageing in human myogenic cells. A panel of splice-switching antisense oligonucleotides were designed to anneal across exon 11 of the LMNA pre-mRNA, and these compounds were transfected into primary human myogenic cells. RT-PCR showed that the majority of oligonucleotides were able to modify LMNA transcript processing. Oligonucleotides that annealed within the 150 base region of exon 11 that is missing in the progerin transcript, as well as those that targeted the normal exon 11 donor site induced the LMNA Δ150 transcript, but most oligonucleotides also generated variable levels of LMNA transcript missing the entire exon 11. Upon evaluation of different oligomer chemistries, the morpholino phosphorodiamidate oligonucleotides were found to be more efficient than the equivalent sequences prepared as oligonucleotides with 2'-O-methyl modified bases on a phosphorothioate backbone. The morpholino oligonucleotides induced nuclear localised progerin, demonstrated by immunostaining, and morphological nuclear changes typical of HGPS cells. We show that it is possible to induce progerin expression in myogenic cells using splice-switching oligonucleotides to redirect splicing of LMNA. This may offer a model

  20. 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.

  1. 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

    ... SECURITY Coast Guard 33 CFR Part 100 RIN 1625-AA08 Special Local Regulation; Emerald Coast Super Boat Grand... crews, vessels, and persons on navigable waters during the Emerald Coast Super Boat Grand Prix high... the Emerald Coast Super Boat Grand Prix high speed boat races. Basis and Purpose On January 31,...

  2. 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

    ... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Cleveland Dragon Boat Festival and Head of... during the Dragon Boat Festival and Head of the Cuyahoga boating events. The safety zone established by... (HOTC) rowing regatta has occurred annually for over a decade and the Dragon Boat Festival for the...

  3. 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

  4. The nonenzymatic template-directed ligation of oligonucleotides

    Directory of Open Access Journals (Sweden)

    A.V. Lutay

    2006-01-01

    Full Text Available The nonenzymatic template-directed ligation of oligonucleotides containing 2',3'-cyclic phosphate was investigated in the presence of divalent cations. Ligation of the oligonucleotides readily occurred in the presence of Mg2+, Mn2+, Co2+, Zn2+, Pb2+. Efficacy of the metal ion catalysts inversely correlated with pKa values of the metal-bound water molecules. The intermolecular transesterification reaction yielded at least 95% of 2',5'-phosphodiester bonds independently on the nature of the metal ion. Relatively high reaction yields (up to 15% suggest, that RNA fragmentation to oligonucleotides with 2',3'-cyclic phosphates, followed by reactions of those oligonucleotides could provide a source of new RNA molecules under prebiotic conditions.

  5. Portable System for Microbial Sample Preparation and Oligonucleotide Microarray Analysis

    OpenAIRE

    Bavykin, Sergei G.; Akowski, James P.; Zakhariev, Vladimir M.; Barsky, Viktor E.; Perov, Alexander N.; Mirzabekov, Andrei D.

    2001-01-01

    We have developed a three-component system for microbial identification that consists of (i) a universal syringe-operated silica minicolumn for successive DNA and RNA isolation, fractionation, fragmentation, fluorescent labeling, and removal of excess free label and short oligonucleotides; (ii) microarrays of immobilized oligonucleotide probes for 16S rRNA identification; and (iii) a portable battery-powered device for imaging the hybridization of fluorescently labeled RNA fragments with the ...

  6. Synthesis and applications of oligonucleotides containing 2'-modified nucleosides

    OpenAIRE

    Shelbourne, Montserrat

    2012-01-01

    This thesis describes the synthesis and applications of chemically modified oligonucleotides, principally those containing modifications at the 2?-position of ribose. One application is their use in triplex-forming oligonucleotides (TFOs). DNA triplexes are formed by the binding of a TFO to a DNA duplex. TFOs are potential therapeutic agents against cancer and viral infections. TFOs containing 2?-aminoethoxy-T and 5-MeC were shown by UV melting studies to strongly stabilise parallel triple...

  7. Electron migration in oligonucleotides upon γ-irradiation in solution

    International Nuclear Information System (INIS)

    Electron migration in irradiated solutions of DNA was investigated using 5-bromouracil synthetically incorporated into oligonucleotides of defined base composition as a molecular indicator of electron interactions. Solvated electrons interact quantitatively with 5-bromouracil, leading to a highly reactive 5-yl radical which can abstract an adjacent hydrogen atom to yield uracil. Yields of uracil, or loss of 5-bromouracil, from irradiated oligonucleotide samples were measured using gas chromatography-mass spectrometric analysis of their trimethylsilylated acid hydrolysates. (author)

  8. 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 ...

  9. Brain Basics

    Medline Plus

    Full Text Available ... Basics in Real Life Brain Basics in Real Life—How Depression affects the Brain Meet Sarah Sarah is a middle-aged woman who seemed to have it all. She was happily married and successful in business. Then, after a serious setback at work, she lost interest ...

  10. Potent Antiscrapie Activities of Degenerate Phosphorothioate Oligonucleotides

    Science.gov (United States)

    Kocisko, David A.; Vaillant, Andrew; Lee, Kil Sun; Arnold, Kevin M.; Bertholet, Nadine; Race, Richard E.; Olsen, Emily A.; Juteau, Jean-Marc; Caughey, Byron

    2006-01-01

    Although transmissible spongiform encephalopathies (TSEs) are incurable, a key therapeutic approach is prevention of conversion of the normal, protease-sensitive form of prion protein (PrP-sen) to the disease-specific protease-resistant form of prion protein (PrP-res). Here degenerate phosphorothioate oligonucleotides (PS-ONs) are introduced as low-nM PrP-res conversion inhibitors with strong antiscrapie activities in vivo. Comparisons of various PS-ON analogs indicated that hydrophobicity and size were important, while base composition was only minimally influential. PS-ONs bound avidly to PrP-sen but could be displaced by sulfated glycan PrP-res inhibitors, indicating the presence of overlapping binding sites. Labeled PS-ONs also bound to PrP-sen on live cells and were internalized. This binding likely accounts for the antiscrapie activity. Prophylactic PS-ON treatments more than tripled scrapie survival periods in mice. Survival times also increased when PS-ONs were mixed with scrapie brain inoculum. With these antiscrapie activities and their much lower anticoagulant activities than that of pentosan polysulfate, degenerate PS-ONs are attractive new compounds for the treatment of TSEs. PMID:16495266

  11. 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.

  12. Antisense Oligonucleotide Therapy for Inherited Retinal Dystrophies.

    Science.gov (United States)

    Gerard, Xavier; Garanto, Alejandro; Rozet, Jean-Michel; Collin, Rob W J

    2016-01-01

    Inherited retinal dystrophies (IRDs) are an extremely heterogeneous group of genetic diseases for which currently no effective treatment strategies exist. Over the last decade, significant progress has been made utilizing gene augmentation therapy for a few genetic subtypes of IRD, although several technical challenges so far prevent a broad clinical application of this approach for other forms of IRD. Many of the mutations leading to these retinal diseases affect pre-mRNA splicing of the mutated genes . Antisense oligonucleotide (AON)-mediated splice modulation appears to be a powerful approach to correct the consequences of such mutations at the pre-mRNA level , as demonstrated by promising results in clinical trials for several inherited disorders like Duchenne muscular dystrophy, hypercholesterolemia and various types of cancer. In this mini-review, we summarize ongoing pre-clinical research on AON-based therapy for a few genetic subtypes of IRD , speculate on other potential therapeutic targets, and discuss the opportunities and challenges that lie ahead to translate splice modulation therapy for retinal disorders to the clinic. PMID:26427454

  13. Optimizing antisense oligonucleotides using phosphorodiamidate morpholino oligomers.

    Science.gov (United States)

    Popplewell, Linda J; Malerba, Alberto; Dickson, George

    2012-01-01

    Duchenne muscular dystrophy (DMD) is caused by mutations that disrupt the reading frame of the human DMD gene. Selective removal of exons flanking an out-of-frame DMD mutation can result in an in-frame mRNA transcript that may be translated into an internally deleted Becker muscular dystrophy-like functionally active dystrophin protein with therapeutic activity. Antisense oligonucleotides (AOs) can be designed to bind to complementary sequences in the targeted mRNA and modify pre-mRNA splicing to correct the reading frame of a mutated transcript. AO-induced exon skipping resulting in functional truncated dystrophin has been demonstrated in animal models of DMD both in vitro and in vivo, in DMD patient cells in vitro in culture, and in DMD muscle explants. The recent advances made in this field suggest that it is likely that AO-induced exon skipping will be the first gene therapy for DMD to reach the clinic. However, it should be noted that personalized molecular medicine may be necessary, since the various reading frame-disrupting mutations are spread across the DMD gene. The different deletions that cause DMD would require skipping of different exons, which would require the optimization and clinical trial workup of many specific AOs. This chapter describes the methodologies available for the optimization of AOs, in particular phosphorodiamidate morpholino oligomers, for the targeted skipping of specific exons on the DMD gene. PMID:22454060

  14. Oligonucleotide conjugates - Candidates for gene silencing therapeutics.

    Science.gov (United States)

    Gooding, Matt; Malhotra, Meenakshi; Evans, James C; Darcy, Raphael; O'Driscoll, Caitriona M

    2016-10-01

    The potential therapeutic and diagnostic applications of oligonucleotides (ONs) have attracted great attention in recent years. The capability of ONs to selectively inhibit target genes through antisense and RNA interference mechanisms, without causing un-intended sideeffects has led them to be investigated for various biomedical applications, especially for the treatment of viral diseases and cancer. In recent years, many researchers have focused on enhancing the stability and target specificity of ONs by encapsulating/complexing them with polymers or lipid chains to formulate nanoparticles/nanocomplexes/micelles. Also, chemical modification of nucleic acids has emerged as an alternative to impart stability to ONs against nucleases and other degrading enzymes and proteins found in blood. In addition to chemically modifying the nucleic acids directly, another strategy that has emerged, involves conjugating polymers/peptide/aptamers/antibodies/proteins, preferably to the sense strand (3'end) of siRNAs. Conjugation to the siRNA not only enhances the stability and targeting specificity of the siRNA, but also allows for the development of self-administering siRNA formulations, with a much smaller size than what is usually observed for nanoparticle (∼200nm). This review concentrates mainly on approaches and studies involving ON-conjugates for biomedical applications. PMID:27521696

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

    Directory of Open Access Journals (Sweden)

    Weizhong Tang

    Full Text Available 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.

  16. Carboranyl oligonucleotides. 3. Biochemical properties of oligonucleotides containing 5-(o-carboranyl-l-yl)-2{prime}-deoxyuridine

    Energy Technology Data Exchange (ETDEWEB)

    Lesnikowski, Z.J.; Fulcrand, G.; Lloyd, R.M. Jr. [Veterans Affairs Medical Center and Georgia Research Center for AIDS and HIV Infections, Decatur, GA (United States)]|[Emory Univ. School of Medicine, Atlanta, GA (United States)

    1996-05-07

    Boronated oligonucleotides are potential candidates for boron neutron capture therapy, antisense technology, and as tools in molecular biology. The biological properties of dodecathymidylic acids containing one or more 5-(o-carboran-l-yl)-2{prime}-deoxyuridine residues at different locations within the oligonucleotide chain were studied. 5-(o-carboran-l-yl)-2{prime}-deoxyuridine containing oligonucleotides manifested marked increased lipophilicity and resistance to 3{prime}- or 5{prime}-phosphodiesterases compared to the corresponding unmodified oligomer. They were substrates for T4 polynucleotide kinase and primers for Escherichia coli polymerase I and human immunodeficiency virus type 1 reverse transcriptase but not for human DNA polymerase {alpha} and {beta}. They also formed heteroduplexes that were substrates for E. coli RNase H, an essential property for antisense technology. These studies indicate that the carboranyl-containing oligonucleotides have desirable properties that need to be exploited further in the design of novel biopharmaceuticals. 33 refs., 2 figs., 1 tab.

  17. China's export of boats valued at over200million USD in2010%China's export of boats valued at over 200 million USD in 2010

    Institute of Scientific and Technical Information of China (English)

    Zhang Shouchun

    2011-01-01

    @@ In 2010, China's economy saw a relatively good recovery.The economic operation of the shipbuilding industry was better than expected and the import and export trade of ships developed at high speeds.According to the statistics of China's custom house, thetotal value of the import and export of boats was 295 million USD, up 40.75% from a year ago; the total quantity in import and export trade was 2057200 boats, up 15.26% in quantity from a year ago. Last year, the value of China's export of boats was 204 million USD, up 19.64%;2028700 boats were exported, up 14.79% in the quantity of boats from a year ago.The ratio of the export of boats to the export of ships in 2010 was 1%; the increase rate of boat export was much lower than that of ship export, which was 42.7%.In the first half of 2010, the export trade of boats showed a highspeed increase with monthly average export value of 14.655 million USD while in August and September, export decreased at a significant rate with the lowest value of 9.7324 million USD in September.

  18. 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

  19. Solar Photovoltaic Powered Sailing Boat Using Buck Converter

    Directory of Open Access Journals (Sweden)

    Soumya Das

    2015-03-01

    Full Text Available The main objective of this paper is to establish technical and economical aspects of the application of stand-alone photovoltaic (PV system in sailing boat using a buck converter in order to enhance the power generation and also to minimize the cost. Performance and control of dc-dc converter, suitable for photovoltaic (PV applications, is presented here. A buck converter is employed here which extracts complete power from the PV source and feeds into the dc load. The power, which is fed into the load, is sufficient to drive a boat . With the help of matlab simulink software PV module and buck model has been designed and simulated and also compared with theoretical predictions.

  20. [Recreational boating accidents--Part 1: Catamnestic study].

    Science.gov (United States)

    Lignitz, Eberhard; Lustig, Martina; Scheibe, Ernst

    2014-01-01

    Deaths on the water are common in the autopsy material of medicolegal institutes situated on the coast or big rivers and lakes (illustrated by the example of the Institute of Legal Medicine of Greifswald University). They mostly occur during recreational boating activities. Apart from hydro-meteorological influences, human error is the main cause of accidents. Often it is not sufficiently kept in mind whether the boat crew is fit for sailing and proper seamanship is ensured. Drowning (following initial hypothermia) is the most frequent cause of death. Medicolegal aspects are not decisive for ordering a forensic autopsy. As statistics are not compiled in a uniform way, a comparison of the data of different institutions engaged in investigating deaths at sea and during water sports activities is hardly possible, neither on a national nor an international basis--and the reconstruction of aquatic accidents is generally difficult. Fatal accidents can only be prevented by completely clarifying their causes.

  1. Recreational Boating in Ligurian Marine Protected Areas (Italy): A Quantitative Evaluation for a Sustainable Management.

    Science.gov (United States)

    Venturini, S; Massa, F; Castellano, M; Costa, S; Lavarello, I; Olivari, E; Povero, P

    2016-01-01

    Recreational boating is an important economic activity that can also represent a powerful source of interference for biological communities. The monitoring of the recreational boating in all Marine Protected Areas (MPAs) within the Liguria region was conducted in the 2010 summer season and it allowed to obtain information not provided by any official institution. The collaboration of geographically different MPAs in Liguria has led to the implementation of a monitoring framework of recreational boating, and this has made it possible to develop uniform management strategies for all the Ligurian marine parks. This study identifies the optimal number of boats for each MPAs, the number of boats that can anchor in the various parks without creating any impact on the biocenosis of merit, providing a first characterization of recreational boating in Liguria during the high touristic season and providing management recommendation to each MPAs. Generally, the Ligurian MPAs do not present critical situations, the number of boats in each MPA being below the optimal number, with the exception of Portofino MPA, where in the 12.5 % of monitored days more than 220 boats were counted and the mean density for weekend is 1.19 no boats/ha (4 times higher than weekday). The results confirm the dependence of the boats peaking from the holidays and the months of the summer, but also it highlights other factors that can contribute in the choice of the boaters. PMID:26289349

  2. The solar boat 'Midnight sun'; Solelbaaten 'Midnight sun'

    Energy Technology Data Exchange (ETDEWEB)

    Kohlstroem, Richard; Fiedler, Frank

    2010-12-15

    The solar boat 'Midnight sun' has during the project period been presented and demonstrated at many different events in Sweden. The focus has been on exhibitions for boats, energy and education. There was a great response from visitors but also from various media such as newspapers, radio and television which reported about the solar boat. Solar driven vehicles are a great way to create interest for solar technology. Due to the increased demand for technical improvements and financial efforts we refrained from participating at the solar boat race 'Frisian Solar Challenge' in 2010 in Holland. Instead a solar boat for tourist trade at Fraemby Udde in Falun has been designed and built. The boat will be rented to visitors during the summer period. The electrical components are designed for short trips with a travel time between 3-4 hours. The solar boat at Fraemby Udde shows that it is relatively simple to convert an existing boat to a solar driven boat. Fraemby Udde receives many visitors, so the solar boat will be shown and used by a large number of tourists from Sweden and abroad

  3. 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;

  4. U-Boat Worx出租私人用潜艇

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    荷兰潜艇制造商U—Boat Worx(UBW)现推出两款潜艇对外出租,使个人和科学家们能够深入探索神秘的海底世界。客户可自行探索或专门欣赏海底世界的美景与水生物。

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

    OpenAIRE

    Thom, Graham

    2016-01-01

    The 2015 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. Thousands of Rohingya (as well as Bangladeshi migrants) were left stranded in the Andaman Sea as smugglers abandoned their human cargo. Initially pushed back by the Thai, Malaysian and Indonesian navies, it was only after Indonesian fishermen rescued three boats that approximately 1,800 people were permitted to disembark in...

  6. Collective Motion and Phase Transitions of Symmetric Camphor Boats

    Science.gov (United States)

    Heisler, Eric; Suematsu, Nobuhiko J.; Awazu, Akinori; Nishimori, Hiraku

    2012-07-01

    The motion of several self-propelled boats in a narrow channel displays spontaneous pattern formation and kinetic phase transitions. In contrast with previous studies on self-propelled particles, this model does not require stochastic fluctuations and it is experimentally accessible. By varying the viscosity in the system, it is possible to form either a stationary state, correlated or uncorrelated oscillations, or unidirectional flow. Here, we describe and analyze these self organized patterns and their transitions.

  7. Row Row Row Your Boat%划船歌

    Institute of Scientific and Technical Information of China (English)

    Twins

    2011-01-01

    划,划,划起船,顺流而下。乐哈哈,乐哈哈,乐哈哈,乐哈哈,生活只是一个梦。(重复五次)%Row, row, row your boat,Gently down the stream.Merrily, merrily, merrily, merrily,Life is but a dream.(Repeat 5 times)

  8. 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.

  9. 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

  10. 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 ...

  11. Brain Basics

    Medline Plus

    Full Text Available ... News 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 ...

  12. Brain Basics

    Medline Plus

    Full Text Available ... Trials — Participants Statistics Help for Mental Illnesses Outreach Research Priorities Funding Labs at NIMH News About Us Home > Health & Education > Educational Resources Brain Basics Introduction The Growing Brain The ...

  13. Brain Basics

    Medline Plus

    Full Text Available ... Brain Basics will introduce you to some of this science, such as: How the brain develops How ... cell, and responds to signals from the environment; this all helps the cell maintain its balance with ...

  14. 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, ...

  15. Brain Basics

    Science.gov (United States)

    ... News 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 ...

  16. Cancer Basics

    Science.gov (United States)

    ... Cancer? Breast Cancer Colon/Rectum Cancer Lung Cancer Prostate Cancer Skin Cancer Show All Cancer Types News and Features Cancer Glossary ACS Bookstore Cancer Information Cancer Basics Cancer Prevention & Detection Signs & Symptoms of Cancer Treatments & Side Effects ...

  17. 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 ...

  18. 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.

  19. Brain Basics

    Medline Plus

    Full Text Available ... Brain Basics provides information on how the brain works, how mental illnesses are disorders of the brain, ... others live with symptoms of mental illness every day. They can be moderate, or serious and cause ...

  20. Brain Basics

    Medline Plus

    Full Text Available ... the function of conducting messages. A neuron has three basic parts: Cell body which includes the nucleus, ... Plan in 2016 August 31, 2016, 2:00-3:00 PM ET Recovery Month September 2016 National ...

  1. Blood Basics

    Science.gov (United States)

    ... Patient Group Links Advocacy Toolkit Home For Patients Blood Basics Blood is a specialized body fluid. It ... about 9 pints. Jump To: The Components of Blood and Their Importance Many people have undergone blood ...

  2. Brain Basics

    Medline Plus

    Full Text Available ... for the function of conducting messages. A neuron has three basic parts: Cell body which includes the ... disorder (ADHD) . Glutamate —the most common neurotransmitter, glutamate has many roles throughout the brain and nervous system. ...

  3. Brain Basics

    Medline Plus

    Full Text Available ... interconnections. neuron —A nerve cell that is the basic, working unit of the brain and nervous system, which processes and transmits information. neurotransmitter —A chemical produced by ...

  4. Brain Basics

    Medline Plus

    Full Text Available ... The Growing Brain Inside the Brain: Neurons & Neural Circuits Neurons are the basic working unit of the ... distant nerve cells (via axons) to form brain circuits. These circuits control specific body functions such as ...

  5. 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 ...

  6. Body Basics

    Science.gov (United States)

    ... about how the body works, what basic human anatomy is, and what happens when parts of the body don't function properly. Blood Bones, Muscles, and Joints Brain and Nervous System Digestive System Endocrine System Eyes Female Reproductive System ...

  7. 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. ...

  8. Oligonucleotide recombination in corynebacteria without the expression of exogenous recombinases.

    Science.gov (United States)

    Krylov, Alexander A; Kolontaevsky, Egor E; Mashko, Sergey V

    2014-10-01

    Brevibacterium lactofermentum and Corynebacterium glutamicum are important biotechnology species of the genus Corynebacterium. The single-strand DNA annealing protein (SSAP)-independent oligonucleotide-mediated recombination procedure was successfully applied to the commonly used wild-type strains B. lactofermentum AJ1511 and C. glutamicum ATCC13032. When the rpsL gene was used as a target, the optimized protocol yielded up to (1.4±0.3)×10(3) and (6.7±1.3)×10(3) streptomycin-resistant colonies per 10(8) viable cells for the corresponding strains. We tested the influence of several parameters that are known to enhance the efficiency of oligonucleotide-mediated recombination in other bacterial species. Among them, increasing the concentration of oligonucleotides and targeting the lagging strand of the chromosome have proven to have positive effects on both of the tested species. No difference in the efficiency of recombination was observed between the oligonucleotides phosphorothiorated at the 5' ends and the unmodified oligonucleotides or between the oligonucleotides with four mutated nucleotides and those with one mutated nucleotide. The described approach demonstrates that during the adaptation of the recombineering technique, testing SSAP-independent oligonucleotide-mediated recombination could be a good starting point. Such testing could decrease the probability of an incorrect interpretation of the effect of exogenous protein factors (such as SSAP and/or corresponding exonucleases) due to non-optimal experimental conditions. In addition, SSAP-independent recombination itself could be useful in combination with suitable selection/enrichment methods. PMID:25087479

  9. 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

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

    Digital Repository Service at National Institute of Oceanography (India)

    Tripati, S.

    was most suitable for the surf zone off the Coromandel Coast. “The boats they [of the Coromandel Coast] doe lade and unlade ships or vessels with are built very sleight, haveing no timber in them, save the thafts [thwarts] to hold their sides together... are different from each other (Behera 1993). Out of eight boats four boats were sailed by women, which is highly significant. Similarly, boats depicted on sculptures of Odisha indicate the existence of reverse and clinker construction. One specimen was found...

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

    International Nuclear Information System (INIS)

    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.

  12. 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.

  13. The Behavioural Response of Australian Fur Seals to Motor Boat Noise

    Science.gov (United States)

    Tripovich, Joy S.; Hall-Aspland, Sophie; Charrier, Isabelle; Arnould, John P. Y.

    2012-01-01

    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. PMID:22623998

  14. 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.

  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 Backwardness.

    Science.gov (United States)

    Weingartner, Charles

    This paper argues that the "back to basics" movement is regressive and that regression is the characteristic mode of fear-ridden personalities. It is argued that many people in American society today have lost their ability to laugh and do not have the sense of humor which is crucial to a healthy mental state. Such topics as necrophilia, mental…

  17. Brain Basics

    Medline Plus

    Full Text Available ... Life Brain Basics in Real Life—How Depression affects the Brain Meet Sarah Sarah is a middle-aged woman ... new memories. hypothalmic-pituitary-adrenal (HPA) axis —A brain-body ... stress. impulse —An electrical communication signal sent between neurons ...

  18. Brain Basics

    Medline Plus

    Full Text Available ... Welcome. Brain Basics provides information on how the brain works, how mental illnesses are disorders of the brain, ... highly developed area at the front of the brain that, in humans, plays a role in executive functions such as ...

  19. 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.

  20. Basic Skills.

    Science.gov (United States)

    Luparelli, Augustus N.; And Others

    1981-01-01

    These four articles focus on developing basic reading, science, and job search skills: "Reading Program for Vocational Classes" by Augustus Luparelli; "Why Teach Employability Skills?" by Larry Siefferman; "Improving Vocabulary and Reading Skills" by Edythe Conway; and "Science in Everyday Life" by Virginia Eleazer and George Carney. (SK)

  1. Oligonucleotide Tagging for Copper-Free Click Conjugation

    Directory of Open Access Journals (Sweden)

    Alan Rowan

    2013-06-01

    Full Text Available Copper-free click chemistry between cyclooctynes and azide is a mild, fast and selective technology for conjugation of oligonucleotides. However, technology for site-specific introduction of the requisite probes by automated protocols is scarce, while the reported cyclooctynes are large and hydrophobic. In this work, it is demonstrated that the introduction of bicyclo[6.1.0]nonyne (BCN into synthetic oligonucleotides is feasible by standard solid-phase phosphoramidite chemistry. A range of phosphoramidite building blocks is presented for incoporation of BCN or azide, either on-support or in solution. The usefulness of the approach is demonstrated by the straightforward and high-yielding conjugation of the resulting oligonucleotides, including biotinylation, fluorescent labeling, dimerization and attachment to polymer.

  2. 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.

  3. Rapid and accurate synthesis of TALE genes from synthetic oligonucleotides.

    Science.gov (United States)

    Wang, Fenghua; Zhang, Hefei; Gao, Jingxia; Chen, Fengjiao; Chen, Sijie; Zhang, Cuizhen; Peng, Gang

    2016-01-01

    Custom synthesis of transcription activator-like effector (TALE) genes has relied upon plasmid libraries of pre-fabricated TALE-repeat monomers or oligomers. Here we describe a novel synthesis method that directly incorporates annealed synthetic oligonucleotides into the TALE-repeat units. Our approach utilizes iterative sets of oligonucleotides and a translational frame check strategy to ensure the high efficiency and accuracy of TALE-gene synthesis. TALE arrays of more than 20 repeats can be constructed, and the majority of the synthesized constructs have perfect sequences. In addition, this novel oligonucleotide-based method can readily accommodate design changes to the TALE repeats. We demonstrated an increased gene targeting efficiency against a genomic site containing a potentially methylated cytosine by incorporating non-conventional repeat variable di-residue (RVD) sequences.

  4. 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.

  5. A novel catechol-based universal support for oligonucleotide synthesis.

    Science.gov (United States)

    Anderson, Keith M; Jaquinod, Laurent; Jensen, Michael A; Ngo, Nam; Davis, Ronald W

    2007-12-21

    A novel universal support for deoxyribo- and ribonucleic acid synthesis has been developed. The support, constructed from 1,4-dimethoxycatechol, represents an improvement over existing universal supports because of its ability to cleave and deprotect under mild conditions in standard reagents. Because no nonvolatile additives are required for cleavage and deprotection, the synthesized oligonucleotides do not require purification prior to use in biochemical assays. Using reverse phase HPLC and electrospray mass spectroscopy, it was determined that oligonucleotides synthesized on the universal support (UL1) 3'-dephosphorylate quickly (9 h in 28-30% ammonium hydroxide (NH4OH) at 55 degrees C, 2 h in 28-30% NH4OH at 80 degrees C, or <1 h in ammonium hydroxide/methylamine (1:1) (AMA) at 80 degrees C). Oligonucleotides used as primers for the polymerase chain reaction (PCR) assay were found to perform identically to control primers, demonstrating full biological compatibility. In addition, a method was developed for sintering the universal support directly into a filter plug which can be pressure fit into the synthesis column of a commercial synthesizer. The universal support plugs allow the synthesis of high-quality oligonucleotides at least 120 nucleotides in length, with purity comparable to non-universal commercial supports and approximately 50% lower reagent consumption. The universal support plugs are routinely used to synthesize deoxyribo-, ribo-, 3'-modified, 5'-modified, and thioated oligonucleotides. The flexibility of the universal support and the efficiency of 3'-dephosphorylation are expected to increase the use of universal supports in oligonucleotide synthesis.

  6. Physiological and physical characteristics of elite dragon boat paddlers.

    Science.gov (United States)

    Ho, Sarah R; Smith, Richard M; Chapman, Philip G; Sinclair, Peter J; Funato, Kazuo

    2013-01-01

    The objectives of this study were to profile the physiological and physical characteristics of elite dragon boat paddlers, to identify characteristics that predict race performance and to quantify the metabolic energy contributions to simulated 200-m and 500-m dragon boat racing. Eleven, national level, male, Japanese dragon boat paddlers completed a battery of tests on a paddling ergometer including an incremental maximal aerobic capacity test, a 2-minute maximal accumulated oxygen deficit (MAOD) test, and simulated 200-m and 500-m races. A physiological and physical profile of subjects was compiled. Results showed that 200-m race performance correlated with flexed arm girth and excess postexercise oxygen consumption (EPOC) measured in the 30 minutes after the MAOD test, whereas 500-m race performance correlated with body fat percentage, relaxed and flexed arm girth, MAOD, EPOC, and peak power during the MAOD test. Stepwise multiple regression revealed that flexed arm girth was the most powerful predictor of 200-m and 500-m race performance, followed by EPOC with the combination of these 2 factors able to explain 74% and 68% of the variance in 200-m and 500-m race performance, respectively. Aerobic energy contributions for 200-m (50 seconds) and 500-m (1 minute 50 seconds) races were (mean (95% confidence intervals)) 52.1% (range, 47.4-56.8%) and 67.5% (range, 60.1-77.8%), respectively. In conclusion, coaches should develop training programs targeted at developing upper-body musculature and increasing anaerobic capacity because these factors are the strongest predictors of 200-m and 500-m race performance. Given the substantial aerobic energy contributions even for a 200-m race event, coaches should aim to increase the maximal aerobic capacity of the paddler in preparation for both 200-m and 500-m events.

  7. Introduction of radiolabeled therapeutic oligonucleotides as nanonuclear explosive gene therapy

    International Nuclear Information System (INIS)

    The synthetic oligonucleotide technology is also at early trial points in human testing against HIV, leukemia, Herpes virus, and other diseases, whose outcome will remain for the future. The current status of these varied approaches is presented in later parts in this article: What are therapeutic oligonucleotides?, Why Auger-emitters are useful in gene therapy?, What is the synergistic effect on combining Auger emitter and Triplex-forming ODN?, How have TFO researches evolved from the starting point?, In which areas of clinical research will this research illuminating?

  8. VirOligo: a database of virus-specific oligonucleotides

    OpenAIRE

    Onodera, Kenji; Melcher, Ulrich

    2002-01-01

    VirOligo is a database of virus-specific oligonucleotides. The VirOligo database consists of two tables, Common data and Oligo data. The Oligo data table contains PCR primers and hybridization probes used for detection of viral nucleic acids and the Common data table contains the experimental conditions used in their detection. Each oligonucleotide entry contains links to PubMed, GenBank, NCBI Taxonomy databases and BLAST. As of July 2001, the VirOligo database contains a complete listing of ...

  9. 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.

  10. 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...

  11. Enzymatic Synthesis of Modified Oligonucleotides by PEAR Using Phusion and KOD DNA Polymerases

    OpenAIRE

    Wang, Xuxiang; Zhang, Jianye; Li, Yingjia; Chen, Gang; Wang, Xiaolong

    2015-01-01

    Antisense synthetic oligonucleotides have been developed as potential gene-targeted therapeutics. We previously reported polymerase–endonuclease amplification reaction (PEAR) for amplification of natural and 5′-O-(1-thiotriphosphate) (S)-modified oligonucleotides. Here, we extended the PEAR technique for enzymatic preparation of 2′-deoxy-2′-fluoro-(2′-F) and 2′-F/S double-modified oligonucleotides. The result showed that KOD and Phusion DNA polymerase could synthesize oligonucleotides with on...

  12. 46 CFR 108.575 - Survival craft and rescue boat equipment.

    Science.gov (United States)

    2010-10-01

    ... DRILLING UNITS DESIGN AND EQUIPMENT Lifesaving Equipment § 108.575 Survival craft and rescue boat equipment... Fishing kit 1 1 12 Flashlight 1 1 1 1 1 1 13 Hatchet 2 2 14 Heaving line 2 1 2 2 1 2 15 Instruction card 1.... 2 Bilge pumps are not required for boats of self-bailing design. 3 Not required for inflated...

  13. 76 FR 1384 - Special Local Regulation; Olympia Harbor Days Tug Boat Races, Budd Inlet, WA

    Science.gov (United States)

    2011-01-10

    ... Federal Register (73 FR 3316). Public Meeting We do not now plan to hold a public meeting. But you may... SECURITY Coast Guard 33 CFR Part 100 RIN 1625-AA08 Special Local Regulation; Olympia Harbor Days Tug Boat... annual Olympia Harbor Days tug boat races. This action is necessary to restrict vessel movement...

  14. 75 FR 25137 - Changes to Standard Numbering System, Vessel Identification System, and Boating Accident Report...

    Science.gov (United States)

    2010-05-07

    ... Boating Accident Report Database CFR Code of Federal Regulations DHS Department of Homeland Security FR... notice regarding our public dockets in the January 17, 2008 issue of the Federal Register (73 FR 3316). D..., Vessel Identification System, and Boating Accident Report Database AGENCY: Coast Guard, DHS....

  15. 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...

  16. 78 FR 24065 - Special Local Regulation; Tuscaloosa Dragon Boat Races; Black Warrior River; Tuscaloosa, AL

    Science.gov (United States)

    2013-04-24

    ... Security FR Federal Register NPRM Notice of Proposed Rulemaking COTP Captain of the Port A. Regulatory... SECURITY Coast Guard 33 CFR Part 100 RIN 1625-AA08 Special Local Regulation; Tuscaloosa Dragon Boat Races... the Junior League of Tuscaloosa Dragon Boat Races. Entry into, transiting or anchoring in this area...

  17. 33 CFR 100.1302 - Special Local Regulation, Annual Dragon Boat Races, Portland, Oregon.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Special Local Regulation, Annual Dragon Boat Races, Portland, Oregon. 100.1302 Section 100.1302 Navigation and Navigable Waters COAST... § 100.1302 Special Local Regulation, Annual Dragon Boat Races, Portland, Oregon. (a) Regulated area....

  18. 33 CFR 100.903 - Harborfest Dragon Boat Race; South Haven, MI.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Harborfest Dragon Boat Race; South Haven, MI. 100.903 Section 100.903 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF... Dragon Boat Race; South Haven, MI. (a) Regulated Area. A regulated area is established to include...

  19. 76 FR 27284 - Special Local Regulation; Partnership in Education, Dragon Boat Race; Maumee River, Toledo, OH

    Science.gov (United States)

    2011-05-11

    ..., 2008, issue of the Federal Register (73 FR 3316). Public Meeting We do not now plan to hold a public..., Dragon Boat Race; Maumee River, Toledo, OH AGENCY: Coast Guard, DHS. ACTION: Notice of proposed... during the Dragon Boat Races which take place during the third or fourth weekend in July each year....

  20. 36 CFR 1192.177 - Ferries, excursion boats and other vessels. [Reserved

    Science.gov (United States)

    2010-07-01

    ... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Ferries, excursion boats and other vessels. 1192.177 Section 1192.177 Parks, Forests, and Public Property ARCHITECTURAL AND... TRANSPORTATION VEHICLES Other Vehicles and Systems § 1192.177 Ferries, excursion boats and other vessels....

  1. 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 boats. 116.1120 Section 116.1120 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) SMALL... Drainage of cockpit vessels, well deck vessels, and open boats. Drainage of cockpit vessels, well...

  2. 76 FR 78151 - Special Local Regulations; Boca Raton Holiday Boat Parade, Intracoastal Waterway, Boca Raton, FL

    Science.gov (United States)

    2011-12-16

    ... SECURITY Coast Guard 33 CFR Part 100 RIN 1625-AA08 Special Local Regulations; Boca Raton Holiday Boat Parade, Intracoastal Waterway, Boca Raton, FL AGENCY: Coast Guard, DHS. ACTION: Temporary final rule... Waterway in Boca Raton, Florida during the Boca Raton Holiday Boat Parade on Saturday, December 17,...

  3. 33 CFR 165.162 - Safety Zone: New York Super Boat Race, Hudson River, New York.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Safety Zone: New York Super Boat Race, Hudson River, New York. 165.162 Section 165.162 Navigation and Navigable Waters COAST GUARD... § 165.162 Safety Zone: New York Super Boat Race, Hudson River, New York. (a) Regulated area....

  4. 46 CFR 160.056-4 - Approval tests of prototype rescue boat.

    Science.gov (United States)

    2010-10-01

    ... test. With one man in the rowing position, a second kneeling on the stern thwart facing aft, and a... boat crew. (d) Rowing test. Three men, averaging 165 pounds each, shall be seated on the centerline of the boat, one on each thwart. One man, in the rowing position, using ordinary rowing technique,...

  5. 33 CFR 100.110 - World's Fastest Lobster Boat Race, Jonesport, ME.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false World's Fastest Lobster Boat Race, Jonesport, ME. 100.110 Section 100.110 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY REGATTAS AND MARINE PARADES SAFETY OF LIFE ON NAVIGABLE WATERS § 100.110 World's Fastest Lobster Boat Race, Jonesport, ME....

  6. Comparison of Ferry Boat and Highway Bridge Energy Use

    Directory of Open Access Journals (Sweden)

    Wayne D. Cottrell

    2011-01-01

    Full Text Available Passenger ferries serve a variety of transport needs in the U.S., such as providing vital links across bodies of water, and supplementing highway bridges. In some cases in which there is a ferry connection but no bridge, a bridge would be impractical; in other cases, a bridge might be feasible. The paper compares the energy consumption of ferries and motor vehicles on bridges, to determine which link is more fuel efficient. One finding is that limited data are available on ferry boat fuel consumption: despite there being 208 ferry boat operators in the U.S. as of 2008, only eight were providing energy use data to the National Transit Database. Examinations of three of the systems found that the passenger-MPG of the ferries ranged from 2.61 to 14.00 (1.11 to 5.95 km/L, while that of the motor vehicles on adjacent highway bridge connections ranged from 25.34 to 32.45 (10.77 to 13.79 km/L. Data from the eight systems are used to develop a ferry MPG model. The model is used to show that the Ryer Island and Charles Hall Ferries are less fuel efficient than hypothetical bridges in those locations. The fuel efficiencies and consumptions of the ferries would equal those of motor vehicles on the bridges, however, if smaller vessels were used, and if the frequency of service was reduced.

  7. Fabrication of oligonucleotide microarray for the detection of Japanese encephalitis virus

    Institute of Scientific and Technical Information of China (English)

    HAI YAN ZHANG; WEN LI MA; XIAO MING ZHANG; WEN LING ZHENG

    2006-01-01

    A low-density oligonucleotide microarray was used for the detection of Japanese encephalitis virus (JEV), combining with restriction display PCR labeling method. The hybridization targets were amplified from 6 plasmids containing several JEV gene fragments. Corresponding oligonucleotide probe spots were detected unambiguously. We claim that the oligonucleotide microarray technology is feasible and may have potential for clinical laboratory application.

  8. Systematic design of mouse Vh gene family-specific oligonucleotides

    NARCIS (Netherlands)

    Seijen, AM; Seijen, HG; Bos, NA

    2001-01-01

    Kabat's database has often been used to design mouse Vh gene-specific 5 ' primers. The emphasis was mostly on constructing a universal (degenerate) 5 ' primer or 5 ' primer set, which would be able to match every mouse Vh gene. We were interested in finding oligonucleotides that could be used as pri

  9. 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 ...

  10. LNA 5'-phosphoramidites for 5'→3'-oligonucleotide synthesis

    DEFF Research Database (Denmark)

    Madsen, Andreas Stahl; Kumar, Santhosh T.; Wengel, Jesper

    2010-01-01

    Hereby we report an efficient synthesis of LNA thymine and LNA 5-methylcytosine 5′-phosphoramidites, allowing incorporation of LNA thymine and LNA 5-methylcytosine into oligonucleotides synthesized in the 5′→3′ direction. Key steps include regioselective enzymatic benzoylation of the 5′-hydroxy...

  11. Solid-phase-supported synthesis of morpholinoglycine oligonucleotide mimics

    Directory of Open Access Journals (Sweden)

    Tatyana V. Abramova

    2014-05-01

    Full Text Available An efficient solid-phase-supported peptide synthesis (SPPS of morpholinoglycine oligonucleotide (MorGly mimics has been developed. The proposed strategy includes a novel specially designed labile linker group containing the oxalyl residue and the 2-aminomethylmorpholino nucleoside analogues as first subunits.

  12. 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. PMID:26503400

  13. 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.

  14. Design and realization a skiff racing boat hull made of natural fibers reinforced composite

    Science.gov (United States)

    Collotta, M.; Solazzi, L.; Pandini, S.; Tomasoni, G.; Alberti, M.; Donzella, G.

    2016-05-01

    This paper discusses the development of a racing boat with an hull made of a composite material reinforced by natural fibers. In particular, we report here the design and realization of the boat hull, the assessment of its mechanical performance by means of a computer assisted simulation, and the cost analysis to assess the economic sustainability of the new composite developed. The results have shown that the new composite has a performance comparable with conventional glass fiber reinforced composites employed for the realization of this type of boat, accordingly to the technology employed and the lamination sequence adopted. Moreover, the FEM analysis performed over the skiff of the designed and constructed boat has demonstrated a successful choice of the material for real application, as it was later confirmed by the good performance of the boat in water. Finally, the cost analysis highlighted the economic sustainability of the new composite, allowing a cost saving of over 28% with respect to carbon fiber composites.

  15. Regression Basics

    CERN Document Server

    Kahane, Leo H

    2007-01-01

    Using a friendly, nontechnical approach, the Second Edition of Regression Basics introduces readers to the fundamentals of regression. Accessible to anyone with an introductory statistics background, this book builds from a simple two-variable model to a model of greater complexity. Author Leo H. Kahane weaves four engaging examples throughout the text to illustrate not only the techniques of regression but also how this empirical tool can be applied in creative ways to consider a broad array of topics. New to the Second Edition Offers greater coverage of simple panel-data estimation:

  16. 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

  17. Summarization on the synthesis and radionuclide-labeling of peptide nucleic acid for an oligonucleotide analogue

    International Nuclear Information System (INIS)

    Peptide nucleic acid (PNA), which is one kind of antisense nucleic acid compounds and an oligonucleotide analogue that binds strongly to DNA and RNA in a sequence specific manner, has its unique advantages in the field of molecular diagnostics and treatment of diseases. Now, people gradually attach more importance to PNA. To optimize the application of PNA in genetic re- search and therapy, a great number of backbone modifications on the newly- type structures of PNA were synthesized to improve its physicochemical proper- ties, such as hybridization speciality, solubility in biofluid, or cell permeability. The modified PNA labeled with radionuclides, which can obtain the aim at specific target and minimal non-target trauma, has important role in research and application of tumorous genitherapy. Here a review on the basic synthesis idea and several primary synthetic methods of PNA analogs was given, and also correlative studies and expectation on the compounds belonging to PNA series labeled with radionuclides were included. (authors)

  18. 40 CFR 1045.660 - How do I certify outboard or personal watercraft engines for use in jet boats?

    Science.gov (United States)

    2010-07-01

    ...) The jet boat engines must be in an engine family separate from the corresponding outboard or personal watercraft engines. (d) Jet boat engine families may use emission credits from outboard or personal watercraft engine families, as described in § 1045.701(d). (e) Jet-boat engines certified under...

  19. 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...

  20. 龙舟赛事无形资产的开发与保护%The Development And Protection Of The Intangible Assets Of Dragon Boat Sports

    Institute of Scientific and Technical Information of China (English)

    王震宇; 王跃

    2011-01-01

    As a traditional sport game with a long history,the development of Dragon Boat Sport's intangible assets are still in its starting stage.Since there is great uncertainty of realizing the intangible assets of Dragon Boat Sports,the development of intangible assets need to be started from the basic.Feature of sports, emphasizing on the operation detail of the Dragon Boat Sports,in order to fully dig out the potential of its intangible assets so as to optimize the benefits. At the same time,it is necessary to complete the protection system of the Dragon Boat Sports and optimize the allocation of the resources to realize the balance of all benefits for building a fair and orderly market to promote its rapid and healthy development.%龙舟运动的起源存在多种说法,其中以纪念爱国诗人屈原的流传最为广泛。作为一项历史悠久的传统体育项目,龙舟运动的影响已经覆盖了我国大部分地区,有着良好的群众基础。龙舟运动不仅是健身强体的竞技项目,而且是弘扬中华民族传统文化的有效载体,并蕴涵着潜在的巨大经济效益。在开发利用龙舟赛事无形资产的同时要健全保护机制,优化资源的配置,实现各方利益的平衡,构建公平有序的龙舟赛事市场格局,促进龙舟运动快速、健康的发展。

  1. Biophysical and RNA Interference Inhibitory Properties of Oligonucleotides Carrying Tetrathiafulvalene Groups at Terminal Positions

    Directory of Open Access Journals (Sweden)

    Sónia Pérez-Rentero

    2013-01-01

    Full Text Available Oligonucleotide conjugates carrying a single functionalized tetrathiafulvalene (TTF unit linked through a threoninol molecule to the 3′ or 5′ ends were synthesized together with their complementary oligonucleotides carrying a TTF, pyrene, or pentafluorophenyl group. TTF-oligonucleotide conjugates formed duplexes with higher thermal stability than the corresponding unmodified oligonucleotides and pyrene- and pentafluorophenyl-modified oligonucleotides. TTF-modified oligonucleotides are able to bind to citrate-stabilized gold nanoparticles (AuNPs and produce stable gold AuNPs functionalized with oligonucleotides. Finally, TTF-oligoribonucleotides have been synthesized to produce siRNA duplexes carrying TTF units. The presence of the TTF molecule is compatible with the RNA interference mechanism for gene inhibition.

  2. Failure study of a cracked speed boat steering wheel

    Directory of Open Access Journals (Sweden)

    Goran Vukelic

    2015-10-01

    Full Text Available Failure of a cracked steering wheel is studied in this paper. Steering wheel, mounted on a speed boat, had cracks emanating from one of the fastener holes until final fracture occurred. Failure analysis, combining experimental and numerical techniques, was performed. Experimentally, fasteners torque moments were measured, visual inspection performed and material type determined (aluminum alloy AA 6061. Additionally, scanning electron microscopy examination was employed to characterize the microstructure of the fractured surface. Using finite element analysis, stress analysis of a cracked steering wheel was conducted. Stress intensities of uncracked and cracked steering wheel were compared to find out about stress concentration points. Possible causes of crack occurrence include excessive fastener torque moment, fretting between fastener and hole combined with poor machining that left marks that serve as potential crack initiation points. Obtained results are valuable for predicting fracture behavior of the cracked steering wheel and can be taken as a reference for design and exploitation process of such component.

  3. 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...... was significantly higher during disturbances [both (1) and (2)] with an immediate reaction shortly after the engine started. Perca fluviatilis displayed increased swimming activity during the first hour of disturbance but not during the following hours. Swimming activity of E. lucius was not significantly different...... between disturbance periods and the same periods on days without disturbance (control). Rutilus rutilus increased their use of the central part of the lake during disturbances, whereas no habitat change was observed in P. fluviatilis and E. lucius. No difference in fish response was detected between...

  4. Course Keeping Control of an Autonomous Boat using Low Cost Sensors

    Science.gov (United States)

    Yu, Zhenyu; Bao, Xinping; Nonami, Kenzo

    This paper discusses the course keeping control problem for a small autonomous boat using low cost sensors. Comparing with full scale ships, a small boat is more sensitive to the environmental disturbances because of its small size and low inertia. The sensors available in the boat are a low cost GPS and a rate gyro while the commonly used compass in ship control is absent. The combined effect from disturbance, poor accuracy and significant delay in GPS measurement makes it a challenging task to achieve good performance. In this paper, we propose a simple dynamic model for the boat's horizontal motion. The model is based on the Nomoto's model and can be seen as an extension to it. The model describes the dynamics between rudder deflection and the boat's velocity vector angle while Nomoto's model reveals that between rudder deflection and the boat's yaw angle. With the proposed model there is no need for a yaw sensor for control if the boat's moving direction can be measured. GPS is a convenient device for that job. Based on the derived model, we apply mixed H2/H∞ control method to design the controller. It can guarantee the robust stability, and as the same time it can optimize the performance in the sense of H2 norm. The experimental data show that the proposed approach is proved to be effective and useful.

  5. Inflation Basics

    Energy Technology Data Exchange (ETDEWEB)

    Green, Dan [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States)

    2014-03-01

    inflation since metrical fluctuations, both scalar and tensor, are also produced in inflationary models. Thus, the time appears to be appropriate for a very basic and simple exposition of the inflationary model written from a particle physics perspective. Only the simplest scalar model will be explored because it is easy to understand and contains all the basic elements of the inflationary model.

  6. Discussions on the possible origin of Europe's first boats - 11,500 BP

    Directory of Open Access Journals (Sweden)

    Peter Fletcher

    2015-08-01

    Full Text Available Three decades ago Detlev Ellmers suggested that hide (skin boats were being used to hunt swimming reindeer in glacial lakes of northern Germany's Upper Palaeolithic. This paper presents new material in support of Ellmers' contention. A paleo-osteological study from Stellmoor suggests that arrows were directed at the neck and upper shoulders from above and behind, at close range which can be considered evidence of them being shot by hunters in boats as the animals were swimming. Lyngby axes are linked to this hunting technique which provides possible distribution and dating for this proposed early boat technology.

  7. Palladium-Catalyzed Modification of Unprotected Nucleosides, Nucleotides, and Oligonucleotides

    Directory of Open Access Journals (Sweden)

    Kevin H. Shaughnessy

    2015-05-01

    Full Text Available Synthetic modification of nucleoside structures provides access to molecules of interest as pharmaceuticals, biochemical probes, and models to study diseases. Covalent modification of the purine and pyrimidine bases is an important strategy for the synthesis of these adducts. Palladium-catalyzed cross-coupling is a powerful method to attach groups to the base heterocycles through the formation of new carbon-carbon and carbon-heteroatom bonds. In this review, approaches to palladium-catalyzed modification of unprotected nucleosides, nucleotides, and oligonucleotides are reviewed. Polar reaction media, such as water or polar aprotic solvents, allow reactions to be performed directly on the hydrophilic nucleosides and nucleotides without the need to use protecting groups. Homogeneous aqueous-phase coupling reactions catalyzed by palladium complexes of water-soluble ligands provide a general approach to the synthesis of modified nucleosides, nucleotides, and oligonucleotides.

  8. Typing of enteroviruses by use of microwell oligonucleotide arrays.

    Science.gov (United States)

    Susi, P; Hattara, L; Waris, M; Luoma-Aho, T; Siitari, H; Hyypiä, T; Saviranta, P

    2009-06-01

    We have developed a straightforward assay for the rapid typing of enteroviruses using oligonucleotide arrays in microtiter wells. The viral nucleic acids are concomitantly amplified and labeled during reverse transcription-PCR, and unpurified PCR products are used for hybridization. DNA strands are separated by alkaline denaturation, and hybridization is started by neutralization. The microarray hybridization reactions and the subsequent washes are performed in standard 96-well microtiter plates, which makes the method easily adaptable to high-throughput analysis. We describe here the assay principle and its potential in clinical laboratory use by correctly identifying 10 different enterovirus reference strains. Furthermore, we explore the detection of unknown sequence variants using serotype consensus oligonucleotide probes. With just two consensus probes for the coxsackievirus A9 (CVA9) serotype, we detected 23 out of 25 highly diverse CVA9 isolates. Overall, the assay involves several features aiming at ease of performance, robustness, and applicability to large-scale studies.

  9. One-oligonucleotide method for constructing vectors for RNA interference

    Institute of Scientific and Technical Information of China (English)

    Carlos Fabian FLORES-JASSO; Ines VELAZQUEZ-QUESADA; Carlos LANDA-SOLIS; Andres A GUTIERREZ; Luis VACA

    2005-01-01

    Aim: To develop an easy, fast, automated, and inexpensive method for constructing short-hairpin-RNA cassettes for RNAi studies. Methods: Using single oligonucleotides, a variety of DNA cassettes for RNAi vectors were constructed in only few minutes in an automated manner. The cassettes, targeting the eGFP,were cloned into plasmids driven by RNA polymerase Ⅲ promoter H 1. Then, the plasmids were transfected into HeLa cells that were later infected with a recombinant adenovirus encoding the eGFP gene. The level of eGFP fluorescence was evaluated by confocal imaging and flow cytometry. Results: The plasmids constructed with the DNA cassettes made by the one-oligonucleotide method inhibited eGFP with different potencies, ranging from 55% to 75%. Conclusion: By using the method reported here, it is possible to simultaneously construct hundreds of different DNA cassettes for RNAi experiments in an inexpensive, automated way. This method will facilitate functional genomics studies on mammalian cells.

  10. Fluorescence quenching of TMR by guanosine in oligonucleotides

    Institute of Scientific and Technical Information of China (English)

    QU Peng; CHEN XuDong; ZHOU XiaoXue; LI Xun; ZHAO XinSheng

    2009-01-01

    Nucleotide-specific fluorescence quenching in fluorescently labeled DNA has many applications in biotechnology. We have studied the inter- and intra-molecular quenching of tetramethylrhodamine (TMR) by nucleotides to better understand their quenching mechanism and influencing factors. In agreement with previous work, dGMP can effectively quench TMR, while the quenching of TMR by other nucleotides is negligible. The Stern-Volmer plot between TMR and dGMP delivers a bimolecular quenching constant of Ks= 52.3 M~(-1). The fluorescence of TMR in labeled oligonucleotides decreases efficiently through photoinduced electron transfer by guanosine. The quenching rate constant between TMR and guanosine was measured using fluorescence correlation spectroscopy (FCS). In addition, our data show that the steric hindrance by bases around guanosine has significant effect on the G-quenching. The availability of these data should be useful in designing fluorescent oligonucleotides and understanding the G-quenching process.

  11. Fluorescence quenching of TMR by guanosine in oligonucleotides

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Nucleotide-specific fluorescence quenching in fluorescently labeled DNA has many applications in biotechnology. We have studied the inter-and intra-molecular quenching of tetramethylrhodamine (TMR) by nucleotides to better understand their quenching mechanism and influencing factors. In agreement with previous work, dGMP can effectively quench TMR, while the quenching of TMR by other nucleotides is negligible. The Stern-Volmer plot between TMR and dGMP delivers a bimolecular quenching constant of Ks=52.3 M-1. The fluorescence of TMR in labeled oligonucleotides decreases efficiently through photoinduced electron transfer by guanosine. The quenching rate constant between TMR and guanosine was measured using fluorescence correlation spectroscopy (FCS). In addition, our data show that the steric hindrance by bases around guanosine has significant effect on the G-quenching. The availability of these data should be useful in designing fluorescent oligonucleotides and understanding the G-quenching process.

  12. On the rapid deprotection of synthetic oligonucleotides and analogs.

    OpenAIRE

    Polushin, N N; Morocho, A M; Chen, B. C.; Cohen, J. S.

    1994-01-01

    The efficiency of oligodeoxynucleotide deprotection is greatly enhanced using a combination of: (a) ethanolamine, and especially a mixture of hydrazine, ethanolamine and methanol, in place of the usual aqueous ammonia; (b) tert-butylphenoxyacetyl amino protecting groups, and (c) oxalyl link between the first nucleotide and the polymeric support. The extent of base modification, particularly of C, is shown to be extremely low, and the quality of deprotected oligonucleotides is as high as in th...

  13. Integrated Microfluidic Isolation of Aptamers Using Electrophoretic Oligonucleotide Manipulation

    OpenAIRE

    Jinho Kim; Olsen, Timothy R.; Jing Zhu; Hilton, John P.; Kyung-Ae Yang; Renjun Pei; Stojanovic, Milan N.; Qiao Lin

    2016-01-01

    We present a microfluidic approach to integrated isolation of DNA aptamers via systematic evolution of ligands by exponential enrichment (SELEX). The approach employs a microbead-based protocol for the processes of affinity selection and amplification of target-binding oligonucleotides, and an electrophoretic DNA manipulation scheme for the coupling of these processes, which are required to occur in different buffers. This achieves the full microfluidic integration of SELEX, thereby enabling ...

  14. Molecular Selection, Modification and Development of Therapeutic Oligonucleotide Aptamers

    OpenAIRE

    Yuanyuan Yu; Chao Liang; Quanxia Lv; Defang Li; Xuegong Xu; Baoqin Liu; Aiping Lu; Ge Zhang

    2016-01-01

    Monoclonal antibodies are the dominant agents used in inhibition of biological target molecules for disease therapeutics, but there are concerns of immunogenicity, production, cost and stability. Oligonucleotide aptamers have comparable affinity and specificity to targets with monoclonal antibodies whilst they have minimal immunogenicity, high production, low cost and high stability, thus are promising inhibitors to rival antibodies for disease therapy. In this review, we will compare the det...

  15. Oligonucleotide-mediated gene editing of Apolipoprotein A-I.

    OpenAIRE

    Disterer, P

    2008-01-01

    Apolipoprotein A-I (ApoA-I) is the major protein constituent of high density lipoprotein (HDL) and controls reverse cholesterol transport, an important process in preventing atherosclerosis. A natural point mutation, ApoA-lMiiano (ApoA-Im) enhances the atheroprotective potential of HDL. Here, I attempt to introduce this specific modification into the genome of mammalian cells using the gene therapy strategy of oligonucleotide-mediated gene editing. I showed successful APOA-I gene editing in r...

  16. Repair of DNA lesions associated with triplex-forming oligonucleotides

    OpenAIRE

    Chin, Joanna Y; Glazer, Peter M.

    2009-01-01

    Triplex-forming oligonucleotides (TFOs) are gene targeting tools that can bind in the major groove of duplex DNA in a sequence-specific manner. When bound to DNA, TFOs can inhibit gene expression, can position DNA-reactive agents to specific locations in the genome, or can induce targeted mutagenesis and recombination. There is evidence that third strand binding, alone or with an associated cross-link, is recognized and metabolized by DNA repair factors, particularly the nucleotide excision r...

  17. Oligonucleotide-based strategies to combat polyglutamine diseases

    OpenAIRE

    Fiszer, Agnieszka; Krzyzosiak, Wlodzimierz J.

    2014-01-01

    Considerable advances have been recently made in understanding the molecular aspects of pathogenesis and in developing therapeutic approaches for polyglutamine (polyQ) diseases. Studies on pathogenic mechanisms have extended our knowledge of mutant protein toxicity, confirmed the toxicity of mutant transcript and identified other toxic RNA and protein entities. One very promising therapeutic strategy is targeting the causative gene expression with oligonucleotide (ON) based tools. This straig...

  18. 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.

  19. Long range clustering of oligonucleotides containing the CG signal

    OpenAIRE

    Katsaloulis, P.; T. Theoharis; A. Provata

    2009-01-01

    Abstract The distance distributions between successive occurrences of the same oligonucleotides in chromosomal DNA are studied, in different classes of higher eucaryotic organisms. A two-parameter modeling is undertaken and applied on the distance distribution of quintuplets (sequences of size five bps) and hexaplets (sequences of size six bps); the first parameter k refers to the short range exponential decay of the distributions, whereas the second parameter m refers to the power...

  20. Gene expression profiling in peanut using high density oligonucleotide microarrays

    Directory of Open Access Journals (Sweden)

    Burow Mark

    2009-06-01

    Full Text Available Abstract Background Transcriptome expression analysis in peanut to date has been limited to a relatively small set of genes and only recently has a significant number of ESTs been released into the public domain. Utilization of these ESTs for oligonucleotide microarrays provides a means to investigate large-scale transcript responses to a variety of developmental and environmental signals, ultimately improving our understanding of plant biology. Results We have developed a high-density oligonucleotide microarray for peanut using 49,205 publicly available ESTs and tested the utility of this array for expression profiling in a variety of peanut tissues. To identify putatively tissue-specific genes and demonstrate the utility of this array for expression profiling in a variety of peanut tissues, we compared transcript levels in pod, peg, leaf, stem, and root tissues. Results from this experiment showed 108 putatively pod-specific/abundant genes, as well as transcripts whose expression was low or undetected in pod compared to peg, leaf, stem, or root. The transcripts significantly over-represented in pod include genes responsible for seed storage proteins and desiccation (e.g., late-embryogenesis abundant proteins, aquaporins, legumin B, oil production, and cellular defense. Additionally, almost half of the pod-abundant genes represent unknown genes allowing for the possibility of associating putative function to these previously uncharacterized genes. Conclusion The peanut oligonucleotide array represents the majority of publicly available peanut ESTs and can be used as a tool for expression profiling studies in diverse tissues.

  1. Characterization of self-assembled DNA concatemers from synthetic oligonucleotides

    Directory of Open Access Journals (Sweden)

    Lu Sun

    2014-08-01

    Full Text Available Studies of DNA–ligand interaction on a single molecule level provide opportunities to understand individual behavior of molecules. Construction of DNA molecules with repetitive copies of the same segments of sequences linked in series could be helpful for enhancing the interaction possibility for sequence-specific binding ligand to DNA. Here we report on the use of synthetic oligonucleotides to self-assembly into duplex DNA concatemeric molecules. Two strands of synthetic oligonucleotides used here were designed with 50-mer in length and the sequences are semi-complimentary so to hybridize spontaneously into concatemers of double stranded DNA. In order to optimize the length of the concatemers the oligonucleotides were incubated at different oligomer concentrations, ionic strengths and temperatures for different durations. Increasing the salt concentration to 200 mM NaCl was found to be the major optimizing factor because at this enhanced ionic strength the concatemers formed most quickly and the other parameters had no detectable effect. The size and shape of formed DNA concatemers were studied by gel electrophoresis in agarose, polyacrylamide gels and by AFM. Our results show that linear DNA constructs up to several hundred base pairs were formed and could be separated from a substantial fraction of non-linear constructs.

  2. Therapeutic Antisense Oligonucleotides against Cancer: Hurdling to the Clinic

    Science.gov (United States)

    Moreno, Pedro; Pêgo, Ana

    2014-10-01

    Under clinical development since the early 90’s and with two successfully approved drugs (Fomivirsen and Mipomersen), oligonucleotide-based therapeutics have not yet delivered a clinical drug to the market in the cancer field. Whilst many pre-clinical data has been generated, a lack of understanding still exists on how to efficiently tackle all the different challenges presented for cancer targeting in a clinical setting. Namely, effective drug vectorization, careful choice of target gene or synergistic multi-gene targeting are surely decisive, while caution must be exerted to avoid potential toxic, often misleading off-target-effects. Here a brief overview will be given on the nucleic acid chemistry advances that established oligonucleotide technologies as a promising therapeutic alternative and ongoing cancer related clinical trials. Special attention will be given towards a perspective on the hurdles encountered specifically in the cancer field by this class of therapeutic oligonucleotides and a view on possible avenues for success is presented, with particular focus on the contribution from nanotechnology to the field.

  3. Properties of hybrid TiO2 -oligonucleotide nanocomposites

    International Nuclear Information System (INIS)

    Recent advancements in hybrid nanotechnology involving nucleic acids and inorganic molecules/structures are predominantly oriented towards cellular imaging or DNA microarray development or for nanoconstruction (such as assembly of ordered patterns of nanocrystals). Nevertheless, in this evolving field there is little work reported yet about the development of nanoparticles that can be used to manipulate biological materials in a novel way. We have synthesized TiO2 -DNA nanocomposites as new vehicles for biotechnology that express new biochemical properties, in an attempt to develop them into nanodevices that would be able to enter cells and conduct their functions in vivo and in situ. Absorption of light and ionizing radiation leads to charge separation in TiO2 , and nanocrystallites modified by the presence of oligonucleotides exhibit semiconducting through both constituents. In such a system charge pairs are instantaneously separated and electropositive holes accumulate on the oligonucleotide DNA, leading to a photo-/radio- catalytic DNA endonuclease reaction. In addition, hybrid nanocomposites of 4.5 nm TiO2 nanoparticles covalently attached to DNA oligonucleotides can be transferred across cellular and nuclear membranes using standard transfection techniques and retained inside mammalian cells. Therefore, TiO2 nanoparticles-biopolymer nanocomposites integrate intrinsic biological/ electrochemical (DNA) and photoelectrical (TiO2 ) properties of the biomolecule and inorganic components, which makes them suitable for development of new tools for biology and medicine

  4. Rapid bacterial identification using evanescent-waveguide oligonucleotide microarray classification.

    Science.gov (United States)

    Francois, Patrice; Charbonnier, Yvan; Jacquet, Jean; Utinger, Dominic; Bento, Manuela; Lew, Daniel; Kresbach, Gerhard M; Ehrat, Markus; Schlegel, Werner; Schrenzel, Jacques

    2006-06-01

    Bacterial identification relies primarily on culture-based methodologies and requires 48-72 h to deliver results. We developed and used i) a bioinformatics strategy to select oligonucleotide signature probes, ii) a rapid procedure for RNA labelling and hybridization, iii) an evanescent-waveguide oligoarray with exquisite signal/noise performance, and iv) informatics methods for microarray data analysis. Unique 19-mer signature oligonucleotides were selected in the 5'-end of 16s rDNA genes of human pathogenic bacteria. Oligonucleotides spotted onto a Ta(2)O(5)-coated microarray surface were incubated with chemically labelled total bacterial RNA. Rapid hybridization and stringent washings were performed before scanning and analyzing the slide. In the present paper, the eight most abundant bacterial pathogens representing >54% of positive blood cultures were selected. Hierarchical clustering analysis of hybridization data revealed characteristic patterns, even for closely related species. We then evaluated artificial intelligence-based approaches that outperformed conventional threshold-based identification schemes on cognate probes. At this stage, the complete procedure applied to spiked blood cultures was completed in less than 6 h. In conclusion, when coupled to optimal signal detection strategy, microarrays provide bacterial identification within a few hours post-sampling, allowing targeted antimicrobial prescription. PMID:16216356

  5. Differentiation of regions with atypical oligonucleotide composition in bacterial genomes

    Directory of Open Access Journals (Sweden)

    Reva Oleg N

    2005-10-01

    Full Text Available Abstract Background Complete sequencing of bacterial genomes has become a common technique of present day microbiology. Thereafter, data mining in the complete sequence is an essential step. New in silico methods are needed that rapidly identify the major features of genome organization and facilitate the prediction of the functional class of ORFs. We tested the usefulness of local oligonucleotide usage (OU patterns to recognize and differentiate types of atypical oligonucleotide composition in DNA sequences of bacterial genomes. Results A total of 163 bacterial genomes of eubacteria and archaea published in the NCBI database were analyzed. Local OU patterns exhibit substantial intrachromosomal variation in bacteria. Loci with alternative OU patterns were parts of horizontally acquired gene islands or ancient regions such as genes for ribosomal proteins and RNAs. OU statistical parameters, such as local pattern deviation (D, pattern skew (PS and OU variance (OUV enabled the detection and visualization of gene islands of different functional classes. Conclusion A set of approaches has been designed for the statistical analysis of nucleotide sequences of bacterial genomes. These methods are useful for the visualization and differentiation of regions with atypical oligonucleotide composition prior to or accompanying gene annotation.

  6. Particle-Based Microarrays of Oligonucleotides and Oligopeptides

    Directory of Open Access Journals (Sweden)

    Alexander Nesterov-Mueller

    2014-10-01

    Full Text Available In this review, we describe different methods of microarray fabrication based on the use of micro-particles/-beads and point out future tendencies in the development of particle-based arrays. First, we consider oligonucleotide bead arrays, where each bead is a carrier of one specific sequence of oligonucleotides. This bead-based array approach, appearing in the late 1990s, enabled high-throughput oligonucleotide analysis and had a large impact on genome research. Furthermore, we consider particle-based peptide array fabrication using combinatorial chemistry. In this approach, particles can directly participate in both the synthesis and the transfer of synthesized combinatorial molecules to a substrate. Subsequently, we describe in more detail the synthesis of peptide arrays with amino acid polymer particles, which imbed the amino acids inside their polymer matrix. By heating these particles, the polymer matrix is transformed into a highly viscous gel, and thereby, imbedded monomers are allowed to participate in the coupling reaction. Finally, we focus on combinatorial laser fusing of particles for the synthesis of high-density peptide arrays. This method combines the advantages of particles and combinatorial lithographic approaches.

  7. A quantitative framework for estimating risk of collision between marine mammals and boats

    Science.gov (United States)

    Martin, Julien; Sabatier, Quentin; Gowan, Timothy A.; Giraud, Christophe; Gurarie, Eliezer; Calleson, Scott; Ortega-Ortiz, Joel G.; Deutsch, Charles J.; Rycyk, Athena; Koslovsky, Stacie M.

    2016-01-01

    Speed regulations of watercraft in protected areas are designed to reduce lethal collisions with wildlife but can have economic consequences. We present a quantitative framework for investigating the risk of deadly collisions between boats and wildlife.

  8. 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,...

  9. 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.

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

    Science.gov (United States)

    Cao, Boyang; Liu, Xiangqian; Yu, Xiang; Chen, Min; Feng, Lu; Wang, Lei

    2014-01-01

    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. PMID:25469776

  11. Fuel derived pollutants and boating activity patterns in the Sea of Galilee.

    Science.gov (United States)

    Dinerman, Efrat; Dubowski, Yael; Friedler, Eran

    2011-11-01

    MTBE (Methyl tert-Butyl Ether) is a fuel additive that replaced lead as an antiknock compound in internal combustion motors. Few years after its introduction, detectable levels of MTBE were found in various water bodies. MTBE has a very low taste and odor threshold and is a potential carcinogen. Another group of fuel derived toxic compounds that has been detected in water bodies is BTEX (Benzene, Toluene, Ethylbenzene and Xylene). Boating activity and allochthonous contributions from watersheds are the major sources of fuel derived pollutants in lakes. Their concentrations in lakes thus vary as a function of boating activity intensity, lake surface area and depth, weather and wind regime, land-use in the watershed, etc. The Sea of Galilee (Lake Kinneret) is the only recreational lake in Israel and an important freshwater source. In the current study, a sampling campaign was conducted in order to quantify MTBE and BTEX concentrations in Lake Kinneret, its marinas and its main contributing streams. In addition, a boating-use survey was performed in order to estimate MTBE and BTEX contribution of recreational boating. The sampling campaign revealed that, as expected, MTBE concentrations were higher than BTEX, and that near shore (i.e., marina) concentrations were higher than in-lake concentrations. Despite the clear contribution from boating, high MTBE concentrations were found following a major inflow event in winter, indicating the importance of the allochthonous contribution. The contribution from boating during summer, as measured indirectly by in-lake concentrations, is likely underestimated due to enhanced MTBE volatilization due to strong winds and high temperatures. May-September was found to be the main recreational boating season, with continued boating year round. On average, a single boat is active 23 d/y, with 84% of the watercrafts being active only during weekends and holidays. The survey further indicated that boats stay in the lake for 4.5 h on

  12. The use of vascular plants as traditional boat raw material by Yachai tribe in Mappi Regency

    OpenAIRE

    YOHANES YOSEPH RAHAWARIN; ELISA MARKUS KESAULIJA; SERLLY LANOEROE

    2005-01-01

    This research is executed aim to know the plant species and the way of exploiting permanent wood upon which traditional boat making by Yachai tribe in Mappi regency. The Method that used in this research is descriptive method with the structural semi interview technique and direct perception in field. Result of research indicate that the tribe Yachai exploit the plant species have permanent wood upon which traditional boat as much 26 species from 14 family. There are 8 wood species which is ...

  13. 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. PMID:27016611

  14. Deployable command and control system for over the horizon small boat operations

    OpenAIRE

    Seegar, William D.

    2006-01-01

    The Deployable Navigation System (DeNS) is a prototype system designed to facilitate Command and Control during over the horizon small boat operations. It is designed to allow small boats to deploy from their host ships with a Bluetooth GPS (Global Positioning System) receiver and PDA (Personal Digital Assistant) running the appropriate software which provides a real time navigational picture in terms of position and relation to a predetermined track. This same data is shipped immediately bac...

  15. Robotic-Boat Equipped with Definite Fishing Techniques To Undertake Commercial Fishing

    Directory of Open Access Journals (Sweden)

    Winston Rohan D’Souza

    2013-08-01

    Full Text Available This review paper titled “Robotic-Boat Equipped With Definite Fishing Techniques To Undertake Commercial Fishing” presents a way to develop and fabricate an automated system for commercial fishing. The overall system consists of a robotic boat embedded with desired fishing techniques. The exact location comprising the school of fish is tracked using the remote sensing satellite technology. The remote sensing technology is already existing and is being used for fish tracking. This gives the probable GPS range where the school of fish may be present.Also several fishes present at the bed of the sea which remain immobile for a very long duration of time. These fishes can be tracked using Thermal Imaging Camerasince the temperature of water and the fish will have a considerable difference. Once the GPS location is known the information can be fed into the robotic boat via control station. The updatedGPS location is continuously fed to the Robotic-Boat via Control-Centre and the Robotic-Boat is lead through a definite path to the prescribed GPS location. Once the Robotic-Boat reaches the defined location definite fishing techniques are adopted to undertake the fishing operation. Camera interface can be used to catalyse the fishing operation.

  16. Discrimination of oligonucleotides of different lengths with a wild-type aerolysin nanopore

    Science.gov (United States)

    Cao, Chan; Ying, Yi-Lun; Hu, Zheng-Li; Liao, Dong-Fang; Tian, He; Long, Yi-Tao

    2016-08-01

    Protein nanopores offer an inexpensive, label-free method of analysing single oligonucleotides. The sensitivity of the approach is largely determined by the characteristics of the pore-forming protein employed, and typically relies on nanopores that have been chemically modified or incorporate molecular motors. Effective, high-resolution discrimination of oligonucleotides using wild-type biological nanopores remains difficult to achieve. Here, we show that a wild-type aerolysin nanopore can resolve individual short oligonucleotides that are 2 to 10 bases long. The sensing capabilities are attributed to the geometry of aerolysin and the electrostatic interactions between the nanopore and the oligonucleotides. We also show that the wild-type aerolysin nanopores can distinguish individual oligonucleotides from mixtures and can monitor the stepwise cleavage of oligonucleotides by exonuclease I.

  17. Discrimination of oligonucleotides of different lengths with a wild-type aerolysin nanopore.

    Science.gov (United States)

    Cao, Chan; Ying, Yi-Lun; Hu, Zheng-Li; Liao, Dong-Fang; Tian, He; Long, Yi-Tao

    2016-08-01

    Protein nanopores offer an inexpensive, label-free method of analysing single oligonucleotides. The sensitivity of the approach is largely determined by the characteristics of the pore-forming protein employed, and typically relies on nanopores that have been chemically modified or incorporate molecular motors. Effective, high-resolution discrimination of oligonucleotides using wild-type biological nanopores remains difficult to achieve. Here, we show that a wild-type aerolysin nanopore can resolve individual short oligonucleotides that are 2 to 10 bases long. The sensing capabilities are attributed to the geometry of aerolysin and the electrostatic interactions between the nanopore and the oligonucleotides. We also show that the wild-type aerolysin nanopores can distinguish individual oligonucleotides from mixtures and can monitor the stepwise cleavage of oligonucleotides by exonuclease I. PMID:27111839

  18. Statistical Algorithms for Long DNA Sequences: Oligonucleotide Distributions and Homogeneity Maps

    Directory of Open Access Journals (Sweden)

    P. Katsaloulis

    2005-01-01

    Full Text Available The statistical properties of oligonucleotide appearances within long DNA sequences often reveal useful characteristics of the corresponding DNA areas. Two algorithms to statistically analyze oligonucleotide appearances within long DNA sequences in genome banks are presented. The first algorithm determines statistical indices for arbitrary length oligonucleotides within arbitrary length DNA sequences. The critical exponent μ of the distance distribution between consecutive occurrences of the same oligonucleotide is calculated and its value is shown to characterize the functionality of the oligonucleotide. The second algorithm searches for areas with variable homogeneity, based on the density of oligonucleotides. The two algorithms have been applied to representative eucaryotes (the animal Mus musculusand the plant Arabidopsis thaliana and interesting results were obtained, confirmed by biological observations. All programs are open source and publicly available on our web site.

  19. Hemopoiesis-stimulating activity of immobilized oligonucleotides and hyaluronidase during cytostatic-induced myelosuppression.

    Science.gov (United States)

    Dygai, A M; Skurikhin, E G; Pershina, O V; Zhdanov, V V; Khmelevskaya, A M; Andreeva, T V; Poponina, A M; Zjuzkov, G N; Udut, E V; Khrichkova, T Ju; Simanina, E V; Miroshnichenko, L A; Stavrova, L A; Tchaikovsky, A S; Markova, T S; Gurto, R V; Brjushinina, O S; Slepichev, V A

    2011-03-01

    The hemopoiesis-stimulating effect of combined treatment with immobilized oligonucleotides and hyaluronidase preparations was studied during cytostatic-induced myelosuppression caused by cyclophosphamide administration. Immobilized hyaluronidase was shown to increase the efficiency of correction of changes in the erythroid and granulocytic hemopoietic stems with immobilized oligonucleotides. This potentiation of the effect of immobilized oligonucleotides by immobilized hyaluronidase was related to an increase in functional activity of committed hemopoietic precursors.

  20. Coupling Strategies for the Synthesis of Peptide-Oligonucleotide Conjugates for Patterned Synthetic Biomineralization

    OpenAIRE

    Joshua D. Carter; LaBean, Thomas H.

    2011-01-01

    This work describes preparation strategies for peptide-oligonucleotide conjugates that combine the self-assembling behavior of DNA oligonucleotides with the molecular recognition capabilities of peptides. The syntheses include a solution-phase fragment coupling reaction and a solid-phase fragment coupling strategy where the oligonucleotide has been immobilized on DEAE Sepharose. The yield of four coupling reagents is evaluated, two reagents in water, EDC (1-ethyl-3-(3-dimethylaminopropyl) car...

  1. Oligonucleotide-directed mutagenesis by microscale 'shot-gun' gene synthesis.

    OpenAIRE

    Grundström, T; Zenke, W M; Wintzerith, M; Matthes, H W; Staub, A; Chambon, P

    1985-01-01

    We describe a rapid and efficient microscale method for in vitro site-directed mutagenesis by gene synthesis. Mutants are constructed by "shot-gun ligation" of overlapping synthetic oligonucleotides yielding double stranded synthetic DNA of more than 120 nucleotides in length. The terminal oligonucleotides of the DNA segment to be synthesized are designed to create sticky ends complementary to unique restriction sites of a polylinker present in an M13 vector. The oligonucleotides are hybridiz...

  2. Recruitment of transcription factors to the target site by triplex-forming oligonucleotides.

    OpenAIRE

    Svinarchuk, F; Nagibneva, I; Cherny, D; Ait-Si-Ali, S; Pritchard, L.L.; Robin, P.; Malvy, C; Harel-Bellan, A; Chern, D

    1997-01-01

    Triplex-forming oligonucleotides (TFOs) are generally designed to inhibit transcription or DNA replication but can be used for more diverse purposes. Here we have designed a hairpin-TFO able to recruit transcription factors to a target DNA. The designed oligonucleotide contains a triplex-forming sequence, linked through a nucleotide loop to a double-stranded hairpin including the SRE enhancer of the c-fos gene promoter. We show here that this oligonucleotide can specifically recognise its DNA...

  3. Cationic oligonucleotides can mediate specific inhibition of gene expression in Xenopus oocytes.

    OpenAIRE

    Bailey, C P; Dagle, J M; Weeks, D L

    1998-01-01

    Base-specific hydrogen bonding between an oligonucleotide and the purines in the major groove of a DNA duplex provide an approach to selective inhibition of gene expression. Oligonucleotide-mediated triplex formation in vivo may be enhanced by a number of different chemical modifications. We have previously described an in vitro analysis of triplex formation using oligonucleotides containing internucleoside phosphate linkages modified with the cation N , N -diethyl-ethylenediamine (DEED). Whe...

  4. TmPrime: fast, flexible oligonucleotide design software for gene synthesis

    OpenAIRE

    Bode, Marcus; Khor, Samuel; Ye, Hongye; Li, Mo-Huang; Ying, Jackie Y.

    2009-01-01

    Herein we present TmPrime, a computer program to design oligonucleotide sets for gene assembly by both ligase chain reaction (LCR) and polymerase chain reaction (PCR). TmPrime offers much flexibility with no constraints on the gene and oligonucleotide lengths. The program divides the long input DNA sequence based on the input desired melting temperature, and dynamically optimizes the length of oligonucleotides to achieve homologous melting temperatures. The output reports the melting temperat...

  5. The big crossing: illegal boat migrants in the Mediterranean.

    Science.gov (United States)

    Kassar, Hassène; Dourgnon, Paul

    2014-08-01

    This article explores illegal migration routes and groups across North Africa to Europe. We describe sub-Saharan and cross-Mediterranean routes, and how they changed during the years. We propose an analytical framework for the main factors for these migrations, from local to international and regulatory context. We then describe sea-migrants' nationalities and socio-economic and demographic characteristics, from studies undertook in Tunisia and Morocco. While boat migration represents only a fraction of illegal migration to Europe, it raises humanitarian as well as ethical issues for European and North African (NA) countries, as a non-negligible amount of them end up in death tolls of shipwrecks in the Mediterranean Sea. Moreover, existing statistics show that illegal trans-Mediterranean migration is growing exponentially. Ongoing crises in Africa and the Middle East are likely to prompt even larger outflows of refugees in the near future. This should induce NA countries to share closer public policy concerns with European countries.

  6. Efficient assessment of modified nucleoside stability under conditions of automated oligonucleotide synthesis: characterization of the oxidation and oxidative desulfurization of 2-thiouridine.

    Science.gov (United States)

    Sochacka, E

    2001-01-01

    In order to efficiently assess the chemical stability of modified nucleosides to the reagents and conditions of automated oligonucleotide synthesis, we designed, developed and tested a scheme in which the modified nucleoside, directly attached to a solid support, is exposed to the cyclic chemistry of the instrument. Stability of 2-thiouridine against different oxidizers was investigated. Tertbutyl hydroperoxide (1 M) in anhydrous acetonitrile was a more effective oxidizer for the incorporation of 2-thiouridine into oligonucleotide chains than the same oxidizer in methylene chloride. Carbon tetrachloride/water in the presence of a basic catalyst was superior in maintaining the thiocarbonyl function, but its utility for RNA synthesis has yet to be fully tested, whereas 2-phenylsulfonyloxaziridine was a very efficient reagent for oxidative desulfurization of 2-thiouridine. PMID:11720000

  7. Oligonucleotide microarray for subtyping of influenza A viruses

    Science.gov (United States)

    Klotchenko, S. A.; Vasin, A. V.; Sandybaev, N. T.; Plotnikova, M. A.; Chervyakova, O. V.; Smirnova, E. A.; Kushnareva, E. V.; Strochkov, V. M.; Taylakova, E. T.; Egorov, V. V.; Koshemetov, J. K.; Kiselev, O. I.; Sansyzbay, A. R.

    2012-02-01

    Influenza is one of the most widespread respiratory viral diseases, infecting humans, horses, pigs, poultry and some other animal populations. Influenza A viruses (IAV) are classified into subtypes on the basis of the surface hemagglutinin (H1 to H16) and neuraminidase (N1 to N9) glycoproteins. The correct determination of IAV subtype is necessary for clinical and epidemiological studies. In this article we propose an oligonucleotide microarray for subtyping of IAV using universal one-step multisegment RT-PCR fluorescent labeling of viral gene segments. It showed to be an advanced approach for fast detection and identification of IAV.

  8. 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....

  9. Repair of DNA lesions associated with triplex-forming oligonucleotides.

    Science.gov (United States)

    Chin, Joanna Y; Glazer, Peter M

    2009-04-01

    Triplex-forming oligonucleotides (TFOs) are gene targeting tools that can bind in the major groove of duplex DNA in a sequence-specific manner. When bound to DNA, TFOs can inhibit gene expression, can position DNA-reactive agents to specific locations in the genome, or can induce targeted mutagenesis and recombination. There is evidence that third strand binding, alone or with an associated cross-link, is recognized and metabolized by DNA repair factors, particularly the nucleotide excision repair pathway. This review examines the evidence for DNA repair of triplex-associated lesions. PMID:19072762

  10. Oligonucleotide microarray for subtyping of influenza A viruses

    International Nuclear Information System (INIS)

    Influenza is one of the most widespread respiratory viral diseases, infecting humans, horses, pigs, poultry and some other animal populations. Influenza A viruses (IAV) are classified into subtypes on the basis of the surface hemagglutinin (H1 to H16) and neuraminidase (N1 to N9) glycoproteins. The correct determination of IAV subtype is necessary for clinical and epidemiological studies. In this article we propose an oligonucleotide microarray for subtyping of IAV using universal one-step multisegment RT-PCR fluorescent labeling of viral gene segments. It showed to be an advanced approach for fast detection and identification of IAV.

  11. 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.

  12. Characterization of peptide-oligonucleotide heteroconjugates by mass spectrometry.

    OpenAIRE

    Jensen, O N; Kulkarni, S; Aldrich, J V; Barofsky, D F

    1996-01-01

    Two peptide-oligothymidylic acids, prepared by joining an 11 residue synthetic peptide containing one internal carboxyl group (Asp side chain) to amino-linker-5'pdT6 and amino-linker-5'pdT10 oligonucleotides, were analyzed by matrix-assisted laser desorption/ionization (MALDI) on a linear time-of-flight mass spectrometer and by electrospray ionization (ESI) on a triple-quadrupole system. These synthetic compounds model peptide-nucleic acid heteroconjugates encountered in antisense research an...

  13. New Intelligent Method of Forecasting Control for Fishing Boat Security in the Coastal Area of Fujian

    Directory of Open Access Journals (Sweden)

    Wei He

    2012-12-01

    Full Text Available To ensure the fishing boat security in the coastal area of Fujian, it is imperative to develop efficient forecasting control system to manage the boats operation in a safe and orderly process. The core issue of establishing the forecasting control system is to predict the relationship of the real time traffic flow and the boat security condition. However, literature review shows that limited reports have addressed on this problem. Hence, a new intelligent forecasting control method base on the Chaos-Particle Swarm Optimization (PSO and Fuzzy Neural Network (FNN is proposed for the short time traffic flow prediction in this paper. The Empirical Mode Decomposition (EMD was first used to denoise the original ship traffic flow observation and then the Chaos-PSO-FNN was applied to the forecasting of the ship traffic flow and hence established the relationship of the real time traffic flow and the boat security condition. The advantage of the proposed approach is that the Chaos-PSO is employed to optimize the FNN parameters to overcome the premature problem of the FNN. As a result, the forecasting control performance is enhanced greatly. In the experiment analysis, the fishing boat traffic information provided by the Fujian marine bureau has been used to evaluate the newly proposed method. The analysis results demonstrate that the proposed Chaos-PSO-FNN method can extract distinct features of the traffic data and the prediction rate is beyond 93.7%. In addition, it found that the fishing boats is supposed to be safe when their travel time avoids the rush time of the traffic flow. This result agrees well with the real data. Thus, the new intelligent forecasting control method for fishing boat security can be used in practice.

  14. SOMA: a single oligonucleotide mutagenesis and cloning approach.

    Directory of Open Access Journals (Sweden)

    Thorsten Pfirrmann

    Full Text Available Modern biology research requires simple techniques for efficient and restriction site-independent modification of genetic material. Classical cloning and mutagenesis strategies are limited by their dependency on restriction sites and the use of complementary primer pairs. Here, we describe the Single Oligonucleotide Mutagenesis and Cloning Approach (SOMA that is independent of restriction sites and only requires a single mutagenic oligonucleotide to modify a plasmid. We demonstrate the broad application spectrum of SOMA with three examples. First, we present a novel plasmid that in a standardized and rapid fashion can be used as a template for SOMA to generate GFP-reporters. We successfully use such a reporter to assess the in vivo knock-down quality of morpholinos in Xenopus laevis embryos. In a second example, we show how to use a SOMA-based protocol for restriction-site independent cloning to generate chimeric proteins by domain swapping between the two human hRMD5a and hRMD5b isoforms. Last, we show that SOMA simplifies the generation of randomized single-site mutagenized gene libraries. As an example we random-mutagenize a single codon affecting the catalytic activity of the yeast Ssy5 endoprotease and identify a spectrum of tolerated and non-tolerated substitutions. Thus, SOMA represents a highly efficient alternative to classical cloning and mutagenesis strategies.

  15. Fast comparison of DNA sequences by oligonucleotide profiling

    Directory of Open Access Journals (Sweden)

    Marín Ignacio

    2008-02-01

    Full Text Available Abstract Background The comparison of DNA sequences is a traditional problem in genomics and bioinformatics. Many new opportunities emerge due to the improvement of personal computers, allowing the implementation of novel strategies of analysis. Findings We describe a new program, called UVWORD, which determines the number of times that each DNA word present in a sequence (target is found in a second sequence (source, a procedure that we have called oligonucleotide profiling. On a standard computer, the user may search for words of a size ranging from k = 1 to k = 14 nucleotides. Average counts for groups of contiguous words may also be established. The rate of analysis on standard computers is from 3.4 (k = 14 to 16 millions of words per second (1 ≤ k ≤ 8. This makes feasible the fast screening of even the longest known DNA molecules. Discussion We show that the combination of the ability of analyzing words of relatively long size, which occur very rarely by chance, and the fast speed of the program allows to perform novel types of screenings, complementary to those provided by standard programs such as BLAST. This method can be used to determine oligonucleotide content, to characterize the distribution of repetitive sequences in chromosomes, to determine the evolutionary conservation of sequences in different species, to establish regions of similar DNA among chromosomes or genomes, etc.

  16. In vivo delivery of transcription factors with multifunctional oligonucleotides

    Science.gov (United States)

    Lee, Kunwoo; Rafi, Mohammad; Wang, Xiaojian; Aran, Kiana; Feng, Xuli; Lo Sterzo, Carlo; Tang, Richard; Lingampalli, Nithya; Kim, Hyun Jin; Murthy, Niren

    2015-07-01

    Therapeutics based on transcription factors have the potential to revolutionize medicine but have had limited clinical success as a consequence of delivery problems. The delivery of transcription factors is challenging because it requires the development of a delivery vehicle that can complex transcription factors, target cells and stimulate endosomal disruption, with minimal toxicity. Here, we present a multifunctional oligonucleotide, termed DARTs (DNA assembled recombinant transcription factors), which can deliver transcription factors with high efficiency in vivo. DARTs are composed of an oligonucleotide that contains a transcription-factor-binding sequence and hydrophobic membrane-disruptive chains that are masked by acid-cleavable galactose residues. DARTs have a unique molecular architecture, which allows them to bind transcription factors, trigger endocytosis in hepatocytes, and stimulate endosomal disruption. The DARTs have enhanced uptake in hepatocytes as a result of their galactose residues and can disrupt endosomes efficiently with minimal toxicity, because unmasking of their hydrophobic domains selectively occurs in the acidic environment of the endosome. We show that DARTs can deliver the transcription factor nuclear erythroid 2-related factor 2 (Nrf2) to the liver, catalyse the transcription of Nrf2 downstream genes, and rescue mice from acetaminophen-induced liver injury.

  17. 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

  18. Boats, Borders and the Geo-Imaginaries of the South

    Directory of Open Access Journals (Sweden)

    Francis Maravillas

    2013-02-01

    Full Text Available This paper activates a mode of spatial inquiry into Australia’s identity through an analysis of a number of frames through which the passage and interdiction of boats off the coast of the nation may be viewed. In particular, I explore the way in which Australia’s paradoxical geographical location as South of both the West and Asia play a key role in affixing the horizon within which a conception of the nation and its relationship with the world was – and continues to be – defined and shaped. Moreover, I not only critically probe the constitutive fears and anxieties that underlie bounded conceptions of the trope of the South, but also to examine how such a trope can articulate itself as a site of exchange and negotiation, a distinctive borderland that engenders new cartographies of difference and belonging in an increasingly globalised and interconnected world. I show how these frames overlap and converge on the wider questions of space, place and identity at the very moment when the process of globalisation and migration has done so much to shake any certainties about Australia’s identity as a geographically distinct and spatially bounded nation-state. In so doing, they represent crucial sites for articulating and enacting a transcultural politics of mobility and spatiality that attends to the ways in which the trope of the South may been imagined not as a sphere of containment or an enclaved territory, but as an evolving cartography, the shifting outlines of which opens up new horizons of possibility for rethinking the spatial and temporal coordinates of Australia in a globalizing world.

  19. Wave Motion Compensation Scheme and Its Model Tests for the Salvage of An Ancient Sunken Boat

    Institute of Scientific and Technical Information of China (English)

    YE Jia-wei; CHEN Yuan-ming; WANG Dong-jiao; LIU Yue-qin; SONG Xin; HUANG Yuan-tian

    2006-01-01

    The application of the vertical hoisting jack and wave motion compensation techniques to the salvage of an ancient sunken boat is introduced. The boat is wooden, loaded with cultural relics. It has been immersed at the bottom of the South China Sea for more than 800 years. In order to protect the structure of the boat and the cultural relics inside to the largest extent, an open caisson is used to hold the sunken boat and the silts around before they are raised from the seabed all together as a whole. In the paper, first, the seakeeping model test of the system of the salvage barge and the open caisson is done to determine some important wave response parameters. And then a further experimental study of the application of the vertical hoisting jack and wave motion compensation scheme to the salvage of the sunken boat is carried out. In the model tests, the techniques of the integrative mechanic-electronic-hydraulic control, wave motion forecast and wave motion compensation are used to minimize the heave motion of the open caisson. The results of the model tests show that the heave motion of the open caisson can be reduced effectively by the use of the present method.

  20. 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.

  1. Studies on the Syntheses and Properties of 5'-Branched-sugar Isonucleosides and the Related Oligonucleotides

    Institute of Scientific and Technical Information of China (English)

    Tian Xiaobing; Zhang Lihe; Min Jimei

    2001-01-01

    @@ The chemistry of nucleosides and oligonucleotides is an actively investigated field in the search for new drugs. Thesyntheses and the properties of isonucleosides and oligonucleotides have been investigated to improve their stability,antitumor and antiviral activities, and to reduce their toxicity.

  2. Affinity hydrogels for controlled protein release using nucleic acid aptamers and complementary oligonucleotides.

    Science.gov (United States)

    Soontornworajit, Boonchoy; Zhou, Jing; Snipes, Matthew P; Battig, Mark R; Wang, Yong

    2011-10-01

    Biomaterials for the precise control of protein release are important to the development of new strategies for treating human diseases. This study aimed to fundamentally understand aptamer--protein dissociation triggered by complementary oligonucleotides, and to apply this understanding to develop affinity hydrogels for controlled protein release. The results showed that the oligonucleotide tails of the aptamers played a critical role in inducing intermolecular hybridization and triggering aptamer--protein dissociation. In addition, the attachment of the oligonucleotide tails to the aptamers and the increase of hybridizing length could produce a synergistic effect on the dissociation of bound proteins from their aptamers. More importantly, pegylated complementary oligonucleotides could successfully trigger protein release from the aptamer-functionalized hydrogels at multiple time points. Based on these results, it is believed that aptamer-functionalized hydrogels and complementary oligonucleotides hold great potential of controlling the release of protein drugs to treat human diseases.

  3. 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

    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......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...... 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/....

  4. 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.

  5. Characteristic oscillatory motion of a camphor boat sensitive to physicochemical environment

    Science.gov (United States)

    Nakata, S.; Yoshii, M.; Matsuda, Y.; Suematsu, N. J.

    2015-06-01

    A self-propelled camphor boat on water was investigated from the viewpoint of characteristic features of motion and mode-bifurcation depending on the diffusion length of camphor molecules. When a camphor disk was connected to the bottom of a larger plastic plate and then was placed on water, either oscillatory motion (repetition between rest and motion) or continuous motion was observed. In this paper, we report the novel features of this motion and mode-bifurcation as a function of the diffusion length of camphor molecules, e.g., multiple accelerations during oscillation, period-2 or irregular oscillatory motion, and reciprocating oscillation. These characteristic motion and mode-bifurcation are discussed in relation to the diffusion length of camphor molecules under the camphor boat and the development of camphor molecules from the camphor boat on water.

  6. Basics of SCI Rehabilitation

    Medline Plus

    Full Text Available Experts \\ The Basics of Spinal Cord Injury Rehabilitation Topics Adult Injuries Spinal Cord Injury 101 Spinal Cord Injury 101 The Basics of Spinal Cord Injury Rehabilitation The Basics ...

  7. Basics of SCI Rehabilitation

    Medline Plus

    Full Text Available Experts \\ The Basics of Spinal Cord Injury Rehabilitation Topics Adult Injuries Spinal Cord Injury 101 Spinal Cord Injury 101 The Basics of Spinal Cord Injury Rehabilitation The Basics of Spinal Cord ...

  8. Basics of SCI Rehabilitation

    Medline Plus

    Full Text Available Experts \\ The Basics of Spinal Cord Injury Rehabilitation Topics Adult Injuries Spinal Cord Injury 101 Spinal Cord Injury 101 The Basics of Spinal Cord Injury Rehabilitation The Basics of ...

  9. Stem Cell Basics

    Science.gov (United States)

    ... Information Stem Cell Basics Stem Cell Basics: Introduction Stem Cell Information General Information Clinical Trials Funding Information Current Research Policy Glossary Site Map Stem Cell Basics Introduction: What are stem cells, and why ...

  10. Enhanced gene repair mediated by methyl-CpG-modified single-stranded oligonucleotides

    Science.gov (United States)

    Bertoni, Carmen; Rustagi, Arjun; Rando, Thomas A.

    2009-01-01

    Gene editing mediated by oligonucleotides has been shown to induce stable single base alterations in genomic DNA in both prokaryotic and eukaryotic organisms. However, the low frequencies of gene repair have limited its applicability for both basic manipulation of genomic sequences and for the development of therapeutic approaches for genetic disorders. Here, we show that single-stranded oligodeoxynucleotides (ssODNs) containing a methyl-CpG modification and capable of binding to the methyl-CpG binding domain protein 4 (MBD4) are able to induce >10-fold higher levels of gene correction than ssODNs lacking the specific modification. Correction was stably inherited through cell division and was confirmed at the protein, transcript and genomic levels. Downregulation of MBD4 expression using RNAi prevented the enhancement of gene correction efficacy obtained using the methyl-CpG-modified ssODN, demonstrating the specificity of the repair mechanism being recruited. Our data demonstrate that efficient manipulation of genomic targets can be achieved and controlled by the type of ssODN used and by modulation of the repair mechanism involved in the correction process. This new generation of ssODNs represents an important technological advance that is likely to have an impact on multiple applications, especially for gene therapy where permanent correction of the genetic defect has clear advantages over viral and other nonviral approaches currently being tested. PMID:19854937

  11. 78 FR 25574 - Special Local Regulations; Third Annual Space Coast Super Boat Grand Prix, Atlantic Ocean; Cocoa...

    Science.gov (United States)

    2013-05-02

    ...) 366-9826. SUPPLEMENTARY INFORMATION: Table of Acronyms DHS Department of Homeland Security FR Federal... Super Boat Grand Prix, Atlantic Ocean; Cocoa Beach, FL AGENCY: Coast Guard, DHS. ACTION: Temporary final... Ocean east of Cocoa Beach, Florida during the Space Coast Super Boat Grand Prix, a series of...

  12. 26 CFR 31.3401(a)(17)-1 - Remuneration for services performed on a boat engaged in catching fish.

    Science.gov (United States)

    2010-04-01

    ... 26 Internal Revenue 15 2010-04-01 2010-04-01 false Remuneration for services performed on a boat... Remuneration for services performed on a boat engaged in catching fish. (a) Remuneration for services performed... receive, any cash remuneration, other than remuneration that is described in subparagraph (1) of...

  13. 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

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF THE INTERIOR National Park Service Notice of Intent To Prepare an Environmental Impact Statement on a Proposed Boat-House Facility for Non-Motorized Boats, George Washington Memorial Parkway AGENCY: National Park...

  14. 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...

  15. 40 CFR Table 1 to Subpart Vvvv of... - Compliance Dates for New and Existing Boat Manufacturing Facilities

    Science.gov (United States)

    2010-07-01

    ... Boat Manufacturing Facilities 1 Table 1 to Subpart VVVV of Part 63 Protection of Environment... Manufacturing Pt. 63, Subpt. VVVV, Table 1 Table 1 to Subpart VVVV of Part 63—Compliance Dates for New and Existing Boat Manufacturing Facilities As specified in § 63.5695, you must comply by the dates in...

  16. A review of statistical methods for preprocessing oligonucleotide microarrays.

    Science.gov (United States)

    Wu, Zhijin

    2009-12-01

    Microarrays have become an indispensable tool in biomedical research. This powerful technology not only makes it possible to quantify a large number of nucleic acid molecules simultaneously, but also produces data with many sources of noise. A number of preprocessing steps are therefore necessary to convert the raw data, usually in the form of hybridisation images, to measures of biological meaning that can be used in further statistical analysis. Preprocessing of oligonucleotide arrays includes image processing, background adjustment, data normalisation/transformation and sometimes summarisation when multiple probes are used to target one genomic unit. In this article, we review the issues encountered in each preprocessing step and introduce the statistical models and methods in preprocessing.

  17. 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

  18. 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

  19. Enzymatic synthesis of modified oligonucleotides by PEAR using Phusion and KOD DNA polymerases.

    Science.gov (United States)

    Wang, Xuxiang; Zhang, Jianye; Li, Yingjia; Chen, Gang; Wang, Xiaolong

    2015-02-01

    Antisense synthetic oligonucleotides have been developed as potential gene-targeted therapeutics. We previously reported polymerase-endonuclease amplification reaction (PEAR) for amplification of natural and 5'-O-(1-thiotriphosphate) (S)-modified oligonucleotides. Here, we extended the PEAR technique for enzymatic preparation of 2'-deoxy-2'-fluoro-(2'-F) and 2'-F/S double-modified oligonucleotides. The result showed that KOD and Phusion DNA polymerase could synthesize oligonucleotides with one or two modified nucleotides, and KOD DNA polymerase is more suitable than Phusion DNA polymerase for PEAR amplification of 2'-F and 2'-F/S double modified oligonucleotides. The composition of PEAR products were analyzed by electrospray ionization liquid chromatography mass spectrometry (ESI/LC/MS) detection and showed that the sequence of the PEAR products are maintained at an extremely high accuracy (>99.9%), and after digestion the area percent of full-length modified oligonucleotides reaches 89.24%. PEAR is suitable for synthesis of modified oligonucleotides efficiently and with high purity. PMID:25517220

  20. 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.

  1. 某型艇舱室次声场环境模拟装置的研究%A simulation device of infrasound field in the cabin of a certain naval boat

    Institute of Scientific and Technical Information of China (English)

    罗志辉; 俞悟周; 刘李娜

    2014-01-01

    Objective To develop a simulation device of infrasound field in the cabin of a certain naval boat .Methods Through detection of the infrasound pressure levels and noise spectrum on the deck and in the cabins and analysis of the infrasound field radiation, the principle of secondary infrasound induction was thus obtained .Results The simulation device that complied with real boat infrasound environment was developed successfully .Conclusion The infrasound field generated by the simulation device coinci-ded with the real boat infrasound environment , which could provide basic support for the development of control measures and assess -ment of control effects .%目的:建立某型艇舱室次声场环境模拟装置。方法通过对甲板及各舱室的次声声压级、频谱进行测量及对次声场辐射状况进行分析,得出该型艇二次次声产生的原理。结果研制了符合实艇次声环境的模拟装置。结论该模拟装置产生的次声场与实艇环境工况相吻合,可为治理措施的制订和治理效果的评估提供基础性支撑。

  2. Modulating anti-MicroRNA-21 activity and specificity using oligonucleotide derivatives and length optimization

    DEFF Research Database (Denmark)

    Munoz-Alarcon, Andres; Guterstam, Peter; Romero, Cristian;

    2012-01-01

    MicroRNAs are short, endogenous RNAs that direct posttranscriptional regulation of gene expression vital for many developmental and cellular functions. Implicated in the pathogenesis of several human diseases, this group of RNAs provides interesting targets for therapeutic intervention. Anti......-microRNA oligonucleotides constitute a class of synthetic antisense oligonucleotides used to interfere with microRNAs. In this study, we investigate the effects of chemical modifications and truncations on activity and specificity of anti-microRNA oligonucleotides targeting microRNA-21. We observed an increased activity...

  3. VIP grafted long-circulation liposome for targeted delivery of oligonucleotide to breast cancer cells

    International Nuclear Information System (INIS)

    Purpose: To investigate the use of long-circulation liposome (LCL) for the delivery of encapsulated oligonucleotide with or without radioiodine-125 (125I) to MCF-7 breast cancer cells in vitro. Methods: (1) Oligonucleotide was labeled with 125I using thallium chloride tetrahydrate (TICL3) as an oxidant. 125I-oligonucleotide was separated from free oligonucleotide or 125I by column chromatography (Sephadex G-25). The efficiency of labeling and the radiochemistry purity were obtained using chromatography of paper. (2) Oligonucleotide with or without 125I encapsulating LCL were prepared in the means of reverse-phase evaporation. The crude LCL were then repeatedly extruded through 400 nm, 200 nm, 100 nm polycarbonate membranes consecutively. Uncapsulated oligonucleotide with or without 125I was separated from LCL formulations by passing down a sephadex G-50 column in 0.01 M HEPES buffer. Pooled LCL encapsulated oligonucleotide with or without 125I fractions were sterile through 0.22 μm filters prior to use. The method of protamine sulfate precipitation was utilized to gain the efficiency of encapsulation. (3) MCF-7 cells were grown in RPMI1640 media containing 10% heat-inactivated fetal calf serum. (4)Time-dependent uptake of 125I-oligonucleotide was studied by measuring the radioactivity of MCF-7 cells. Results: The efficiency of labeling and radiochemistry purity of bcl-2 antisense-, sense- and nonsense-oligonucleotide were 84.52% and 97.49%, 58.05% and 95.40%, 74.6% and 98.7%, respectively. The efficiency of encapsulation of bcl-2 antisense-, sense- and nonsense-oligonucleotide is 77.58%, 45.98%, 38.2%, respectively. (3) The par cle size of LCL formulations(∼120 nm) was determined by laser scattering techniques. During the period of observation from 20 min to 300 min, the radioactivity of tumor cells was almost as same as the background. Conclusions: LCL can not effectively deliver oligonucleotide with 125I into MCF-7 cells in vitro. To achieve the active

  4. Transfection Efficiency Comparison of Oligonucleotide and Plasmid to the HL-60 Cell Line with Liposomes

    Institute of Scientific and Technical Information of China (English)

    TANG Yi; LIU Wenli; ZHOU Jianfeng; XU Huizhen; LU Wu

    2005-01-01

    The transfection efficiency of oligonucleotide and plasmid to the HL-60 cell line with lipofectaminePLUS was compared through observing the transfection rate and the expression duration of exogenous gene in the target cells. The results showed that the transfection rate of oligonucleotide to the HL-60 was about 90 %-95 % and it had no obvious attenuation within 84 h. However,the plasmid transfection rate was only 5 %-25 % and it was decreased significantly within 60 h. It was suggested that the transfection of oligonucleotide with liposomes was better than that of plasmid.

  5. 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......, to a method for preparing a labelled oligonucleotide, and to the use of the labelled oligonucleotide as hybridisation probe, in polymerase chain reactions (PCR), in nucleic acid sequencing, in cloning recombinant DNA and $i(in vitro) mutagenesis....

  6. '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, swal

  7. 75 FR 53572 - Safety Zone; Olympia Harbor Days Tug Boat Races, Budd Inlet, WA

    Science.gov (United States)

    2010-09-01

    ... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Olympia Harbor Days Tug Boat Races, Budd... establishing a temporary safety zone within the navigation channel in Budd Inlet, WA during Olympia Harbor Days... to restrict vessel traffic movement on specified waters of the Budd Inlet, WA during Olympia...

  8. 76 FR 30825 - Special Local Regulation; Olympia Harbor Days Tug Boat Races, Budd Inlet, WA

    Science.gov (United States)

    2011-05-27

    ... the Federal Register (76 FR 006). We did not receive any comments on the proposed rule. We did not... SECURITY Coast Guard 33 CFR Part 100 RIN 1625-AA08 Special Local Regulation; Olympia Harbor Days Tug Boat... and an area extending north of the channel in Budd Inlet, WA during the annual Olympia Harbor Days...

  9. 78 FR 35593 - Special Local Regulation; Christmas Boat Parade, San Juan Harbor; San Juan, PR

    Science.gov (United States)

    2013-06-13

    .... SUPPLEMENTARY INFORMATION: Table of Acronyms DHS Department of Homeland Security FR Federal Register NPRM Notice... public dockets in the January 17, 2008, issue of the Federal Register (73, FR 3316). 4. Public Meeting We... SECURITY Coast Guard 33 CFR Part 100 RIN 1625-AA08 Special Local Regulation; Christmas Boat Parade,...

  10. Aliens in Paradise. Boat density and exotic coastal mollusks in Moorea Island (French Polynesia).

    Science.gov (United States)

    Ardura, Alba; Planes, Serge; Garcia-Vazquez, Eva

    2015-12-01

    Pacific islands are particularly vulnerable to the effects of invasive species. After habitat destruction or modification, invasive species are responsible for more biological extinctions than any other cause. Further, the rate of extinction of native species has been higher on islands than anywhere else in the world. Invasive species have also degraded native ecosystems. In order to detect exotic intertidal mollusk species, an extensive sampling around Moorea Island, a more or less unspoiled island surrounded by a rich coral reef habitat, has been developed considering that sampled points have different characteristics in wave exposure, algae coverage, type of substrate, distance to ports, distance to freshwater, distance sewage and boat traffic. Samples were DNA barcoded for unequivocal species assignation. The presence of five NIS among 26 species seems an important signal of introduction of alien biota in Moorea Island coast. However they were represented by a total of 38 individuals among 1487 mollusks (2.55%). While the distance to relatively big ports influenced directly species richness, the intensity of maritime traffic measured as boat density near sampling points was significantly associated with the frequency of exotic species. Other environmental factors did not show significant correlation with the frequency of exotics, suggesting that in an environment without big discontinuities, with little habitat modification, local boat traffic is the most influential factor in the spread of exotic species. This could be mitigated relatively easily by reducing boat density in local zones of ecological interest. PMID:26364683

  11. 77 FR 18689 - Changes to Standard Numbering System, Vessel Identification System, and Boating Accident Report...

    Science.gov (United States)

    2012-03-28

    .... Abbreviations BARD Boating Accident Report Database DHS Department of Homeland Security FR Federal Register HIN... rulemaking (NPRM) bearing the same title as this final rule in the Federal Register (75 FR 25137). We... reopened the comment period to accept comments until October 15, 2010 (75 FR 49869, Aug. 16, 2010)....

  12. 75 FR 49869 - Changes to Standard Numbering System, Vessel Identification System, and Boating Accident Report...

    Science.gov (United States)

    2010-08-16

    ... in the January 17, 2008, issue of the Federal Register (73 FR 3316). Reopening of Comment Period On May 7, 2010, we published a notice of proposed rulemaking (NPRM) in the Federal Register (75 FR 25137..., Vessel Identification System, and Boating Accident Report Database AGENCY: Coast Guard, DHS....

  13. 75 FR 43823 - Safety Zone; He'eia Kea Small Boat Harbor, Kaneohe Bay, Oahu, HI

    Science.gov (United States)

    2010-07-27

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HOMELAND SECURITY Coast Guard 33 CFR Part 165 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...

  14. Simple Verification of the Parabolic Shape of a Rotating Liquid and a Boat on Its Surface

    Science.gov (United States)

    Sabatka, Z.; Dvorak, L.

    2010-01-01

    This article describes a simple and inexpensive way to create and to verify the parabolic surface of a rotating liquid. The liquid is water. The second part of the article deals with the problem of a boat on the surface of a rotating liquid. (Contains 1 table, 10 figures and 5 footnotes.)

  15. Motion induced passenger dislocations in life raft and life boat configurations

    NARCIS (Netherlands)

    Bos, J.E.; Andersen ,O.; Reinke, P.

    2010-01-01

    Within the European project SafeCrafts, dealing with the safe abandoning of ships, the dislocation of passengers aboard life boats and rafts has been considered to be a risk regarding passenger survival at sea. To get an idea about the risks and the affecting factors involved, we studied the effects

  16. 77 FR 3784 - Recreational Boating Safety Projects, Programs and Activities Funded Under Provisions of the...

    Science.gov (United States)

    2012-01-25

    ... of the Transportation Equity Act for the 21st Century; Accounting of ACTION: Notice. SUMMARY: In 1999... notice to satisfy a requirement of the Act that a detailed accounting of the projects, programs, and activities funded under the national recreational boating safety program provision of the Act be...

  17. 78 FR 18617 - Recreational Boating Safety Projects, Programs and Activities Funded Under Provisions of the...

    Science.gov (United States)

    2013-03-27

    ... of the Transportation Equity Act for the 21st Century; Accounting of ACTION: Notice. SUMMARY: In 1999... that a detailed accounting of the projects, programs, and activities funded under the national recreational boating safety program provision of the Act be published annually in the Federal Register. In...

  18. The use of vascular plants as traditional boat raw material by Yachai tribe in Mappi Regency

    Directory of Open Access Journals (Sweden)

    YOHANES YOSEPH RAHAWARIN

    2005-07-01

    Full Text Available This research is executed aim to know the plant species and the way of exploiting permanent wood upon which traditional boat making by Yachai tribe in Mappi regency. The Method that used in this research is descriptive method with the structural semi interview technique and direct perception in field. Result of research indicate that the tribe Yachai exploit the plant species have permanent wood upon which traditional boat as much 26 species from 14 family. There are 8 wood species which is often used for the body of boat and also own the good quality according to Yachai tribe, that is Atam (Scihizomeria serrata Hochr, Batki (Adinandra forbesii Baker. F, Chomach (Gordonia papuana Kobuski, Rupke (Tristania sp., Bao (Dillenia papuana artelli, Top (Buchanania macrocarpa Laut, Mitbo (Cordia Dichtoma Forst., and Yunun (Camnosperma brevipetiolata Volkens. While to part of oar exploit 2 wood species that is Bach (Buchanania Arborescens.Bi and Tup (Litsea ampala Merr. Yachai Tribe recognized 3 boat model owning different size measure and function, that is Junun Ramchai, Junun Pochoi and Junun Toch.

  19. The boat people of Vietnam. Rescue on the South China Sea.

    Science.gov (United States)

    Hayes, T J; Thomas, D; Dewar, E P

    1990-01-01

    Poor economic conditions in Vietnam have encouraged large numbers of people seeking a better life in the West to join the flow of political refugees leaving the country as "boat people". We report the events surrounding one such group of people who were rescued from the South China Sea by the Outback 88 Task Group.

  20. A study of the sewn-plank boats of Goa, India

    Digital Repository Service at National Institute of Oceanography (India)

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

    used in naval warfare. In this paper an attempt has been made to study the sewn-plank boats of Goa, their building techniques and other features in order to understand their quality and how they were used in the past for an inland river-transport system....

  1. 75 FR 78725 - Recreational Boating Safety Projects, Programs and Activities Funded Under Provisions of the...

    Science.gov (United States)

    2010-12-16

    ... From the Federal Register Online via the Government Publishing Office ] DEPARTMENT OF HOMELAND... lag time between available funds and spending. The total amount of funding transferred to the Coast... Responsibly!'', Life Jacket Wear, Vessel Safety Check Program (VSC), Boating Safety Education...

  2. 78 FR 22814 - Special Local Regulations; Miami Super Boat Grand Prix, Atlantic Ocean; Miami Beach, FL

    Science.gov (United States)

    2013-04-17

    ... Department of Homeland Security FR Federal Register NPRM Notice of Proposed Rulemaking A. Public... Federal Register (73 FR 3316). 4. Public Meeting We do not plan to hold a public meeting. But you may... SECURITY Coast Guard 33 CFR Part 100 RIN 1625-AA08 Special Local Regulations; Miami Super Boat Grand...

  3. 76 FR 29642 - Special Local Regulations; Miami Super Boat Grand Prix, Miami Beach, FL

    Science.gov (United States)

    2011-05-23

    ... SECURITY Coast Guard 33 CFR Part 100 RIN 1625-AA08 Special Local Regulations; Miami Super Boat Grand Prix, Miami Beach, FL AGENCY: Coast Guard, DHS. ACTION: Temporary final rule. SUMMARY: The Coast Guard is establishing special local regulations on the waters of the Atlantic Ocean east of ] Miami Beach,...

  4. Carboranyl Nucleosides & Oligonucleotides for Neutron Capture Therapy Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Schinazi, Raymond F.

    2004-12-01

    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-({beta}-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

  5. Carboranyl Oligonucleotides for Neutron Capture Therapy Final Report

    International Nuclear Information System (INIS)

    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

  6. Cleavage of Oligonucleotides Containing a P3’→N5’ Phosphoramidate Linkage Mediated by Single-Stranded Oligonucleotide Templates

    Directory of Open Access Journals (Sweden)

    Takeshi Imanishi

    2011-12-01

    Full Text Available Double-stranded DNA (dsDNA templates can hybridize to and accelerate cleavage of oligonucleotides containing a P3’→N5’ phosphoramidate (P-N linkage. This dsDNA-templated cleavage of P-N linkages could be due to conformational strain placed on the linkage upon triplex formation. To determine whether duplex formation also induced conformational strain, we examined the reactivity of the oligonucleotides with a P-N linkage in the presence of single-stranded templates, and compared these reactions to those with dsDNA templates. P-N oligonucleotides that are cleaved upon duplex formation could be used as probes to detect single-stranded nucleic acids.

  7. 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.

  8. Use of synthetic oligonucleotides for genomic DNA dot hybridization to split the DQw3 haplotype.

    Science.gov (United States)

    Martell, M; Le Gall, I; Millasseau, P; Dausset, J; Cohen, D

    1988-01-01

    Comparison of two different HLA-DQ beta gene sequences from two DR4 individuals, probably corresponding to DQw3.2 (DQR4) and DQw3.1 (DQR5) specificities, has shown several nucleotide variations. Eight oligonucleotides (24 bases long), derived from these polymorphic areas, have been synthesized. Each oligonucleotide was hybridized to BamHI-digested DNA samples from eight families with HLA-DR4 individuals. Four polymorphic BamHI fragments were detected. Two of eight oligonucleotides gave a single signal (8.9 kilobases) on DQw3.2-positive haplotypes. We used one of these oligonucleotides in a genomic DNA dot hybridization and detected a hybridization signal only in DQw3.2-positive individuals. A very simple test like this allows the screening of a large population sample within a very short period. Images PMID:2895927

  9. Nucleoside, nucleotide and oligonucleotide based amphiphiles: a successful marriage of nucleic acids with lipids.

    Science.gov (United States)

    Gissot, Arnaud; Camplo, Michel; Grinstaff, Mark W; Barthélémy, Philippe

    2008-04-21

    Amphiphilic molecules based on nucleosides, nucleotides and oligonucleotides are finding more and more biotechnological applications. This Perspective highlights their synthesis, supramolecular organization as well as their applications in the field of biotechnology.

  10. Sheath liquid effects in capillary high-performance liquid chromatography-electrospray mass spectrometry of oligonucleotides.

    Science.gov (United States)

    Huber, C G; Krajete, A

    2000-02-18

    Fused-silica capillary columns of 200 microm inner diameter were packed with micropellicular, octadecylated, 2.3 microm poly(styrene-divinylbenzene) particles and applied to the separation of oligonucleotides by ion-pair reversed-phase high-performance liquid chromatography. Oligonucleotides were eluted at 50 degrees C with gradients of 3-13% acetonitrile in 50 mM triethylammonium bicarbonate. Addition of sheath liquid to the column effluent allowed the detection of oligonucleotides by electrospray ionization mass spectrometry using full-scan data acquisition with a detectability comparable to that obtained with UV detection. The signal-to-noise ratios with different sheath liquids increased in the order isopropanololigonucleotides longer than 20 nucleotide units whereas no significant effect was observed with shorter oligonucleotides. Organic acids and bases in the sheath liquid generally deteriorated the signal-to-noise ratios in the chromatograms and mass spectra mainly because of increased background noise. Only a few charge states were observed in the mass spectra of oligonucleotides because of charge state reduction due to the presence of carbonic acid in the eluent. With triethylammonium hydrogencarbonate as chromatographic eluent and acetonitrile as sheath liquid, very few cation adducts of oligonucleotides were observed in the mass spectra. However, the presence of small amounts of monopotassium adducts enabled the calculation of the charge state of multiply charged ions. With acetonitrile as sheath liquid, 710 amol of a 16-mer oligonucleotide were detected using selected ion monitoring data acquisition with a signal-to-noise ratio of 3:1. Finally, capillary ion-pair reversed-phase high-performance liquid chromatography-electrospray ionization mass spectrometry was

  11. Synthesis and Properties of Oligonucleotides Carrying Isoquinoline Imidazo[1,2-a]azine Fluorescent Units

    OpenAIRE

    Pérez-Rentero, Sonia; Kielland, Nicola; Terrazas, Montserrat; Lavilla, Rodolfo; Eritja Casadellà, Ramón

    2010-01-01

    Oligonucleotides carrying novel fluorescent compounds with a dipolar isoquinoline imidazo[1,2-a]azine core were prepared. Analysis of the melting curves demonstrates that DNA duplexes carrying these fluorescent labels at their ends have a slight increase in DNA duplex stability. The UV absorption and fluorescent properties of the oligonucleotide conjugates were analyzed. The fluorescent label is sensitive to duplex formation, as cooperative melting curves are also observed at 366 nm and fluor...

  12. Improved bioactivity of G-rich triplex-forming oligonucleotides containing modified guanine bases

    OpenAIRE

    Rogers, Faye A.; Lloyd, Janice A; Tiwari, Meetu Kaushik

    2014-01-01

    Triplex structures generated by sequence-specific triplex-forming oligonucleotides (TFOs) have proven to be promising tools for gene targeting strategies. In addition, triplex technology has been highly utilized to study the molecular mechanisms of DNA repair, recombination and mutagenesis. However, triplex formation utilizing guanine-rich oligonucleotides as third strands can be inhibited by potassium-induced self-association resulting in G-quadruplex formation. We report here that guanine-r...

  13. Understanding oligonucleotide-mediated inhibition of gene expression in Xenopus laevis oocytes

    OpenAIRE

    Bailey, Cheryl; Weeks, Daniel L.

    2000-01-01

    Triplex-forming oligonucleotides (TFOs) modified with N,N-diethylethylenediamine can inhibit the expression of a reporter plasmid in Xenopus oocytes if the triplex is preformed prior to injection while unmodified oligonucleotides cannot. Here we show that merely forming a triplex in a reporter plasmid does not disrupt transcription, but when TFOs are targeted to sites within the transcribed region of a reporter gene then gene activity is inhibited. TFO-based inhibition did not lead to large s...

  14. Positively charged oligonucleotides overcome potassium-mediated inhibition of triplex DNA formation.

    OpenAIRE

    Dagle, J M; Weeks, D L

    1996-01-01

    The formation of triplex DNA using unmodified, purine-rich oligonucleotides (ODNs) is inhibited by physiologic levels of potassium. Changing negative phosphodiester bonds in a triplex forming oligonucleotide (TFO) to neutral linkages causes a small increase in triplex formation. When phosphodiester bonds in a TFO are converted to positively-charged linkages the formation of triplex DNA increases dramatically. In the absence of KCl, a 17mer TFO containing 11 positively-charged linkages at a co...

  15. Synthesis and properties of triplex-forming oligonucleotides containing 2'-modified nucleoside analogues

    OpenAIRE

    Lou, Chenguang

    2011-01-01

    Triplex-forming oligonucleotides (TFOs) bind to the major groove of the DNA duplex via the Hoogsteen interactions to generate triple helices. Potential applications of triplex technology are in regulation of gene expression, site-directed gene-knockout, mutation correction and as tools in molecular biotechnology. The presence of 2’-modified nucleosides in therapeutic oligonucleotides inhibits enzymatic degradation in vivo. Therefore such sugar modifications have the potential to improve the b...

  16. Targeted inhibition of transcription elongation in cells mediated by triplex-forming oligonucleotides

    OpenAIRE

    Faria, M.; Wood, C. D.; Perrouault, L; Nelson, J. S.; Winter, A.; White, M. R. H.; Hélène, C; Giovannangeli, C.

    2000-01-01

    Triple-helix-forming oligonucleotides (TFOs) bind in the major groove of double-stranded DNA at oligopyrimidine⋅oligopurine sequences and therefore are candidate molecules for artificial gene regulation, in vitro and in vivo. We recently have described oligonucleotide analogues containing N3′-P5′ phosphoramidate (np) linkages that exhibited efficient inhibition of transcription elongation in vitro. In the present work we provide conclusive evidence that np-modified TFOs targeted to the HIV-1 ...

  17. In vivo stability and kinetics of absorption and disposition of 3' phosphopropyl amine oligonucleotides.

    OpenAIRE

    Zendegui, J G; Vasquez, K M; Tinsley, J H; Kessler, D J; Hogan, M E

    1992-01-01

    Development of oligonucleotide derivatives as therapeutic agents requires an understanding of their pharmacokinetic behavior. The in vivo disposition and stability of a prototype of such compounds are reported here. The compound studied, a relatively G-rich 38 base 3' phosphopropyl amine oligonucleotide (TFO-1), was cleared from the circulation with a half-life of approximately 10 minutes, displaying distribution kinetics consistent with a two compartment model. TFO-1 was also readily absorbe...

  18. Spatial organization of topoisomerase I-mediated DNA cleavage induced by camptothecin–oligonucleotide conjugates

    OpenAIRE

    Arimondo, Paola B.; Angenault, Stéphane; Halby, Ludovic; Boutorine, Alexandre; Schmidt, Frédéric; Monneret, Claude; Garestier, Thérèse; Sun, Jian-Sheng; Bailly, Christian; Hélène, Claude

    2003-01-01

    Triple helix-forming oligonucleotides covalently linked to topoisomerase I inhibitors, in particular the antitumor agent camptothecin, trigger topoisomerase I-mediated DNA cleavage selectively in the proximity of the binding site of the oligonucleotide vector. In the present study, we have performed a systematic analysis of the DNA cleavage efficiency as a function of the positioning of the camptothecin derivative, either on the 3′ or the 5′ side of the triplex, and the location of the cleava...

  19. Microinjection of antisense c-mos oligonucleotides prevents meiosis II in the maturing mouse egg.

    OpenAIRE

    O'Keefe, S J; Wolfes, H; Kiessling, A A; Cooper, G M

    1989-01-01

    Injection of antisense oligonucleotides was used to investigate the function of c-mos in murine oocytes. Oocytes injected with antisense c-mos oligonucleotides completed the first meiotic division but failed to initiate meiosis II. Instead, loss of c-mos function led to chromosome decondensation, reformation of a nucleus after meiosis I, and cleavage to two cells. Therefore, c-mos is required for meiosis II during murine oocyte maturation.

  20. Complexes of carbon nanotubes with oligonucleotides in thin Langmuir-Blodgett films to detect electrochemically hybridization

    Science.gov (United States)

    Egorov, A. S.; Egorova, V. P.; Krylova, H. V.; Lipnevich, I. V.; Orekhovskaya, T. I.; Veligura, A. A.; Govorov, M. I.; Shulitsky, B. G.

    2014-10-01

    Self-assembled complexes consisting of thin multi-walled carbon nanotubes (MWCNTs) and DNA-oligonucleotides which are able to a cooperative binding to complementary oligonucleotides have been investigated. It was establised a high-performance charge transport in nanostructured Langmuir-Blodgett complexes thin MWCNTs/DNA. A method to electrochemically detect DNA hybridization on the self-organized structures has been proposed.

  1. Respirable antisense oligonucleotides: a new drug class for respiratory disease

    Directory of Open Access Journals (Sweden)

    Tanaka Makoto

    2000-12-01

    Full Text Available Abstract Respirable antisense oligonucleotides (RASONs, which attenuate specific disease-associated mRNAs, represent a new class of respiratory therapeutics with considerable potential. RASONs overcome previous obstacles that have impeded the development of antisense therapeutics targeting diseases in other organ systems. RASONs are delivered directly to the target tissue via inhalation; their uptake seems to be enhanced by cationic properties inherent in pulmonary surfactant, and, because of the markedly different target properties of mRNA and proteins, they can have very long durations of effect compared with traditional drugs targeting the protein of the same gene. RASONs contain chemical modifications that decrease their degradation by cellular nucleases. However, total insensitivity to nucleases is probably not an optimal design criterion for RASONs, because moderate nuclease sensitivity can prevent their systemic delivery, decreasing the potential for systemic toxicity. EPI-2010 is a 21-mer phosphorothioate RASON that attenuates bronchoconstriction, inflammation and surfactant depletion in preclinical models of human asthma, has a duration of effect of seven days, and seems to undergo minimal systemic delivery.

  2. Advancements of antisense oligonucleotides in treatment of breast cancer

    Institute of Scientific and Technical Information of China (English)

    YANGShuan-Ping; SONGSan-Tai; 等

    2003-01-01

    Breast cancer is one kind of multi-gene related malignancy.Overexpression of some oncogenes such as HER-2(c-erbB-2,Neu),bcl-2/bcl-xL,protein kinase A(PKA),and transferrin receptor gene(TfR gene),etc significantly affect the prognosis of breast cancer.It was shown that specific suppression of the overexpressed genes above resulted in the improvement of the therapy of breast cancer.Antisense interference.one of useful tools for inhibiting the overexpression of specific oncogenes,was involved in the therapy of breast cancer in recent years. Data indicated that antisense oligonucleotides(ON)could inhibit specially the expression of the target genes on mRNA or protein levels in most of cases;some ON candidates showed encouraging therapeutic effects in vitro and in vivo on breast cancer cell lines or xenografts.Furthermore,the combination use of the antisense ON and normal chemotherapeutic agents indicated synergistic antitumor effects,which was probably the best utilization of antisense ON in the treatment of breast cancer.

  3. 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

  4. Nanoexplosive gene therapy using triplex-forming oligonucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Oh, Eun Jung; Min, Hye Jung; Choe, Jae Gol; Park, Gil Hong; Kim, Meyoung Kon [College of Medicine, Korea Univ., Seoul (Korea, Republic of)

    2001-07-01

    Triplex forming oligonucleotides (TFO) labeled with Auger emitter could be ideal vehicles for delivering radiation energy to specific DNA sequences, and followed by double-stranded DNA breaks and subsequent inactivation of targeted genes. We designed TFOs targeting the selected DNA fragments (i.e., estrogen receptors and N-myc promoter) and labeled with {sup 125}I and {sup 111}In. Various Cancer cells, e.g., MCF-7 (breast adenocarcinoma), MCF-10A (immortalized breast cells), Jurkat (T-cell leukemia), ARO (thyroid cancer), SNU-449 (Colon Caner), and HL-60 (polymyelocytic leukemia), were prepared and treated with radiolabeled TFO for 24 h. After the incubation, subcellular fractions (i.e., cell nucleus, cytoplasm and cultured medium) were collected and measured radioactivity by a gamma scintillation counter, respectively. The mean value of % injected dose for each fraction was ranged as follows: nucleus, 4.4-20%; cytoplasm, 8.2-29%; and medium, 64-87%. Therefore, we speculated that TFO labeled with Auger emitter could be a next-generation therapeutic tool in nanoexplosive gene therapy.

  5. Dicationic Surfactants with Glycine Counter Ions for Oligonucleotide Transportation.

    Science.gov (United States)

    Pietralik, Zuzanna; Skrzypczak, Andrzej; Kozak, Maciej

    2016-08-01

    Gemini surfactants are good candidates to bind, protect, and deliver nucleic acids. Herein, the concept of amino acids (namely glycine) as counter ions of gemini surfactants for gene therapy application was explored. This study was conducted on DNA and RNA oligomers and two quaternary bis-imidazolium salts, having 2,5-dioxahexane and 2,8-dioxanonane spacer groups. The toxicity level of surfactants was assessed by an MTT assay, and their ability to bind nucleic acids was tested through electrophoresis. The nucleic acid conformation was established based on circular dichroism and infrared spectroscopic analyses. The structures of the formed complexes were characterized by small-angle scattering of synchrotron radiation. Both studied surfactants appear to be suitable for gene therapy; however, although they vary by only three methylene groups in the spacer, they differ in binding ability and toxicity. The tested oligonucleotides maintained their native conformations upon surfactant addition and the studied lipoplexes formed a variety of structures. In systems based on a 2,5-dioxahexane spacer, a hexagonal phase was observed for DNA-surfactant complexes and a micellar phase was dominant with RNA. For the surfactant with a 2,8-dioxanonane spacer group, the primitive cubic phase prevailed. PMID:27214208

  6. Triplex formation on DNA targets: how to choose the oligonucleotide.

    Science.gov (United States)

    Vekhoff, Pierre; Ceccaldi, Alexandre; Polverari, David; Pylouster, Jean; Pisano, Claudio; Arimondo, Paola B

    2008-11-25

    Triplex-forming oligonucleotides (TFOs) are sequence-specific DNA binders. TFOs provide a tool for controlling gene expression or, when attached to an appropriate chemical reagent, for directing DNA damage. Here, we report a set of rules for predicting the best out of five different triple-helical binding motifs (TM, UM, GA, GT, and GU, where M is 5-methyldeoxycytidine and U is deoxyuridine) by taking into consideration the sequence composition of the underlying duplex target. We tested 11 different triplex targets present in genes having an oncogenic role. The rules have predictive power and are very useful in the design of TFOs for antigene applications. Briefly, we retained motifs GU and TM, and when they do form a triplex, TFOs containing G and U are preferred over those containing T and M. In the case of the G-rich TFOs, triplex formation is principally dependent on the percentage of G and the length of the TFO. In the case of the pyrimidine motif, replacement of T with U is destabilizing; triplex formation is dependent on the percentage of T and destabilized by the presence of several contiguous M residues. An equation to choose between a GU and TM motif is given. PMID:18954091

  7. Nanoexplosive gene therapy using triplex-forming oligonucleotides

    International Nuclear Information System (INIS)

    Triplex forming oligonucleotides (TFO) labeled with Auger emitter could be ideal vehicles for delivering radiation energy to specific DNA sequences, and followed by double-stranded DNA breaks and subsequent inactivation of targeted genes. We designed TFOs targeting the selected DNA fragments (i.e., estrogen receptors and N-myc promoter) and labeled with 125I and 111In. Various Cancer cells, e.g., MCF-7 (breast adenocarcinoma), MCF-10A (immortalized breast cells), Jurkat (T-cell leukemia), ARO (thyroid cancer), SNU-449 (Colon Caner), and HL-60 (polymyelocytic leukemia), were prepared and treated with radiolabeled TFO for 24 h. After the incubation, subcellular fractions (i.e., cell nucleus, cytoplasm and cultured medium) were collected and measured radioactivity by a gamma scintillation counter, respectively. The mean value of % injected dose for each fraction was ranged as follows: nucleus, 4.4-20%; cytoplasm, 8.2-29%; and medium, 64-87%. Therefore, we speculated that TFO labeled with Auger emitter could be a next-generation therapeutic tool in nanoexplosive gene therapy

  8. Characterization of adjacent breast tumors using oligonucleotide microarrays

    International Nuclear Information System (INIS)

    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

  9. Integrated Microfluidic Isolation of Aptamers Using Electrophoretic Oligonucleotide Manipulation

    Science.gov (United States)

    Kim, Jinho; Olsen, Timothy R.; Zhu, Jing; Hilton, John P.; Yang, Kyung-Ae; Pei, Renjun; Stojanovic, Milan N.; Lin, Qiao

    2016-05-01

    We present a microfluidic approach to integrated isolation of DNA aptamers via systematic evolution of ligands by exponential enrichment (SELEX). The approach employs a microbead-based protocol for the processes of affinity selection and amplification of target-binding oligonucleotides, and an electrophoretic DNA manipulation scheme for the coupling of these processes, which are required to occur in different buffers. This achieves the full microfluidic integration of SELEX, thereby enabling highly efficient isolation of aptamers in drastically reduced times and with minimized consumption of biological material. The approach as such also offers broad target applicability by allowing selection of aptamers with respect to targets that are either surface-immobilized or solution-borne, potentially allowing aptamers to be developed as readily available affinity reagents for a wide range of targets. We demonstrate the utility of this approach on two different procedures, respectively for isolating aptamers against a surface-immobilized protein (immunoglobulin E) and a solution-phase small molecule (bisboronic acid in the presence of glucose). In both cases aptamer candidates were isolated in three rounds of SELEX within a total process time of approximately 10 hours.

  10. 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.

  11. 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.

  12. 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...

  13. Health Insurance Basics

    Science.gov (United States)

    ... Can I Help a Friend Who Cuts? Health Insurance Basics KidsHealth > For Teens > Health Insurance Basics Print ... advanced calculus was confusing. What Exactly Is Health Insurance? Health insurance is a plan that people buy ...

  14. Climate Change: Basic Information

    Science.gov (United States)

    ... are here: EPA Home Climate Change Basic Information Climate Change: Basic Information On This Page Climate change ... We can make a difference How is the climate changing in the U.S.? Observations across the United ...

  15. Porous silicon-cell penetrating peptide hybrid nanocarrier for intracellular delivery of oligonucleotides.

    Science.gov (United States)

    Rytkönen, Jussi; Arukuusk, Piret; Xu, Wujun; Kurrikoff, Kaido; Langel, Ulo; Lehto, Vesa-Pekka; Närvänen, Ale

    2014-02-01

    The largest obstacle to the use of oligonucleotides as therapeutic agents is the delivery of these large and negatively charged biomolecules through cell membranes into intracellular space. Mesoporous silicon (PSi) is widely recognized as a potential material for drug delivery purposes due to its several beneficial features like large surface area and pore volume, high loading capacity, biocompatibility, and biodegradability. In the present study, PSi nanoparticles stabilized by thermal oxidation or thermal carbonization and subsequently modified by grafting aminosilanes on the surface are utilized as an oligonucleotide carrier. Splice correcting oligonucleotides (SCOs), a model oligonucleotide drug, were loaded into the positively charged PSi nanoparticles with a loading degree as high as 14.3% (w/w). Rapid loading was achieved by electrostatic interactions, with the loading efficiencies reaching 100% within 5 min. The nanoparticles were shown to deliver and release SCOs, in its biologically active form, inside cells when formulated together with cell penetrating peptides (CPP). The biological effect was monitored with splice correction assay and confocal microscopy utilizing HeLa pLuc 705 cells. Furthermore, the use of PSi carrier platform in oligonucleotide delivery did not reduce the cell viability. Additionally, the SCO-CPP complexes formed in the pores of the carrier were stabilized against proteolytic digestion. The advantageous properties of protecting and releasing the cargo and the possibility to further functionalize the carrier surface make the hybrid nanoparticles a potential system for oligonucleotide delivery.

  16. Oligonucleotide chip, real-time PCR and sequencing for genotyping of hepatitis B virus

    Institute of Scientific and Technical Information of China (English)

    Yong-Zhong Wang; Guo-Xiang Wu; Li-Bo Luo; Min Chen; Li-Hua Ruan

    2007-01-01

    AIM: To compare the oligonucleotide chip, real-time PCR and sequencing for genotyping of hepatitis B virus in Chinese patients with chronic hepatitis B.METHODS: Mixture of samples with different genotypes and clinical serum samples from 126 chronic hepatitis B patients was tested for hepatitis B virus genotypes by oligonucleotide chip, real-time PCR and sequencing of PCR products, respectively. Clinical performances, time required and costs of the three assays were evaluated.RESULTS: Oligonucleotide chips and real-time PCR detected 1% and 0.1% genotypes, respectively, in mixed samples. Of the 126 clinical samples from patients with chronic hepatitis B, genotype B was detected in 41(33%), 41 (33%) and 45 (36%) samples, and genotype C in 76 (60%), 76 (60%) and 81 (64%) samples, by oligonucleotide chip, real-time PCR and sequencing,respectively. Oligonucleotide chip and real-time PCR detected mixed genotypes B and C in 9 samples. Realtime PCR was the rapidest and cheapest among the three assays.CONCLUSION: Oligonucleotide chip and real-time PCR are able to detect mixed genotypes, while sequencing only detects the dominant genotype in clinical samples.

  17. Improving signal intensities for genes with low-expression on oligonucleotide microarrays

    Directory of Open Access Journals (Sweden)

    Hu Limei

    2004-06-01

    Full Text Available Abstract Background DNA microarrays using long oligonucleotide probes are widely used to evaluate gene expression in biological samples. These oligonucleotides are pre-synthesized and sequence-optimized to represent specific genes with minimal cross-hybridization to homologous genes. Probe length and concentration are critical factors for signal sensitivity, particularly when genes with various expression levels are being tested. We evaluated the effects of oligonucleotide probe length and concentration on signal intensity measurements of the expression levels of genes in a target sample. Results Selected genes of various expression levels in a single cell line were hybridized to oligonucleotide arrays of four lengths and four concentrations of probes to determine how these critical parameters affected the intensity of the signal representing their expression. We found that oligonucleotides of longer length significantly increased the signals of genes with low-expression in the target. High-expressing gene signals were also boosted but to a lesser degree. Increasing the probe concentration, however, did not linearly increase the signal intensity for either low- or high-expressing genes. Conclusions We conclude that the longer the oligonuclotide probe the better the signal intensities of low expressing genes on oligonucleotide arrays.

  18. Fragment-based solid-phase assembly of oligonucleotide conjugates with peptide and polyethylene glycol ligands.

    Science.gov (United States)

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

    2016-10-01

    Ligand conjugation to oligonucleotides is an attractive strategy for enhancing the therapeutic potential of antisense and siRNA agents by inferring properties such as improved cellular uptake or better pharmacokinetic properties. Disulfide linkages enable dissociation of ligands and oligonucleotides in reducing environments found in endosomal compartments after cellular uptake. Solution-phase fragment coupling procedures for producing oligonucleotide conjugates are often tedious, produce moderate yields and reaction byproducts are frequently difficult to remove. We have developed an improved method for solid-phase coupling of ligands to oligonucleotides via disulfides directly after solid-phase synthesis. A 2'-thiol introduced using a modified nucleotide building block was orthogonally deprotected on the controlled pore glass solid support with N-butylphosphine. Oligolysine peptides and a short monodisperse ethylene glycol chain were successfully coupled to the deprotected thiol. Cleavage from the resin and full removal of oligonucleotide protection groups were achieved using methanolic ammonia. After standard desalting, and without further purification, homogenous conjugates were obtained as demonstrated by HPLC, gel electrophoresis, and mass spectrometry. The attachment of both amphiphilic and cationic ligands proves the versatility of the conjugation procedure. An antisense oligonucleotide conjugate with hexalysine showed pronounced gene silencing in a cell culture tumor model in the absence of a transfection reagent and the corresponding ethylene glycol conjugate resulted in down regulation of the target gene to nearly 50% after naked application. PMID:27236069

  19. Intracerebroventricular Administration of Mineralocorticoid Receptor Antisense Oligonucleotides Attenuates Salt Appetite in the Rat.

    Science.gov (United States)

    Ma; Itharat; Fluharty; Sakai

    1997-10-01

    The anterior ventral third ventricle (AV3V) region of the brain contains high concentrations of mineralocorticoid receptors (MR) and glucocorticoid receptors (GR) that are important in the maintenance of body fluid and electrolyte balance as well as other physiological processes. Daily intracerebroventricular pulse injections of MR antisense oligonucleotides significantly suppressed deoxycorticosterone acetate (DOCA) induced salt appetite in a dose-related manner. Similar administration of GR antisense or scrambled/sense oligonucleotide into the third ventricle failed to inhibit salt appetite. Salt appetite aroused after adrenalectomy was not suppressed by MR antisense oligonucleotide treatments but was suppressed by an antisense oligonucleotide directed against the angiotensin II AT1 receptor subtype. Receptor binding analysis demonstrated that MR and GR oligonucleotide treatments each reduced their respective receptor subtypes. Finally, although GR antisense oligonucleotide treatment was ineffective in suppressing DOCA-induced salt appetite, this treatment did increase stress induced corticosterone release as well as delayed the recovery of corticosterone to basal levels after stress. PMID:9787254

  20. Body Basics Library

    Science.gov (United States)

    ... a Friend Who Cuts? About the Body Basics Library KidsHealth > For Teens > About the Body Basics Library Print A A A Text Size Did you ... system, part, and process works. Use this medical library to find out about basic human anatomy, how ...

  1. 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);…

  2. A Study of the Response of Eastern Spiny Softshell Turtle to Boat Traffic in the Missisquoi River of Northern Vermont

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The purpose of this study was to gauge the degree to which boat traffic in the Missisquoi River affects the basking behavior of the eastern spiny softshell turtle...

  3. Environmental assessment of proposed dredging and disposal activities at the St. George small boat harbor, reconnaissance stage: Planning aid report

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Types of environmental impacts possibly resulting from dredging and disposal activities at the St. George Island small boat harbor include: 1) bottom topographic...

  4. Application of heteronuclear couplings to conformational analysis of oligonucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, G. [Univ. of Maryland, College Park, MD (United States); Live, D. [Memorial Sloan-Kettering Cancer Center, New York, NY (United States); Bax, A. [NIDDK National Institutes of Health, Bethesda, MD (United States)

    1994-12-01

    The value of vicinal coupling constants extracted from NMR spectra in deducing torsion angles for conformational analysis is well recognized. Due to the abundance of protons, their couplings have been mostly widely used. In many instances, couplings between protons and other nuclei may be a valuable complement to proton-proton couplings or, in some instances, may be the only coupling available to characterize the torsion angle about a bond. Recently, heteronuclear couplings have been used to great benefit in studies of isotopically enriched proteins, and this general approach has been extended to peptides at natural abundance. The possibility of using this approach to study oligonucleotides is also attractive but has not as yet been widely exploited. With the development of strategies for labeling such molecules, particularly RNAs, this may become an important component in conformational analysis. For DNA, labeling is less accessible, but sufficient quantities of unlabeled material are readily available for measuring these couplings at natural abundance. We chose several DNA systems to explore the usefulness of heteronuclear couplings in addressing the sugar conformation and the glycosidic torsion angle. Intensities of cross peaks in long-range HMQC experiments can be related to the couplings. Crosspeaks involving H1{prime} and C1{prime} atoms have been emphasized because of the superior shift dispersion at these positions between sugar protons and carbon atoms. Results will be shown for the self-complementary Dickerson duplex dodecamer sequence d(CGCGAATTCGCG) and for d(GGTCGG), which dimerizes to form a G-tetrad structure incorporating both syn and anti base orientations. The couplings provide a clear discrimination between presence of C3{prime}-endo and C2{prime}-endo conformations of the sugars and syn and anti bases arrangements.

  5. Correction of a Cystic Fibrosis Splicing Mutation by Antisense Oligonucleotides.

    Science.gov (United States)

    Igreja, Susana; Clarke, Luka A; Botelho, Hugo M; Marques, Luís; Amaral, Margarida D

    2016-02-01

    Cystic fibrosis (CF), the most common life-threatening genetic disease in Caucasians, is caused by ∼2,000 different mutations in the CF transmembrane conductance regulator (CFTR) gene. A significant fraction of these (∼13%) affect pre-mRNA splicing for which novel therapies have been somewhat neglected. We have previously described the effect of the CFTR splicing mutation c.2657+5G>A in IVS16, showing that it originates transcripts lacking exon 16 as well as wild-type transcripts. Here, we tested an RNA-based antisense oligonucleotide (AON) strategy to correct the aberrant splicing caused by this mutation. Two AONs (AON1/2) complementary to the pre-mRNA IVS16 mutant region were designed and their effect on splicing was assessed at the RNA and protein levels, on intracellular protein localization and function. To this end, we used the 2657+5G>A mutant CFTR minigene stably expressed in HEK293 Flp-In cells that express a single copy of the transgene. RNA data from AON1-treated mutant cells show that exon 16 inclusion was almost completely restored (to 95%), also resulting in increased levels of correctly localized CFTR protein at the plasma membrane (PM) and with increased function. A novel two-color CFTR splicing reporter minigene developed here allowed the quantitative monitoring of splicing by automated microscopy localization of CFTR at the PM. The AON strategy is thus a promising therapeutic approach for the specific correction of alternative splicing.

  6. Inhibition of transcription by platinated triplex-forming oligonucleotides.

    Science.gov (United States)

    Graham, Mindy K; Miller, Paul S

    2012-12-01

    Platinated triplex-forming oligonucleotides (TFOs) consisting of 2'-methoxythymidine and 2'-methoxy-5-methylcytidine and an N-7 platinated deoxyguanosine ((Pt)G) at the 5'-((Pt)G-TFO), 3'-(TFO-G(Pt)), or 3'- and 5'-((Pt)G-TFO-G(Pt)) ends of the TFO form mono-((Pt)G-TFO and TFO-G(Pt)) and interstrand ((Pt)G-TFO-G(Pt)) cross-links with target DNA as a result of reaction of the (Pt)G with guanines adjacent to the homopurine TFO binding site in the target. The extent of cross-linking is greatest when the (Pt)G is located on the 3' end of the TFO and the target guanine is on the same strand as the TFO binding site. Multiple, contiguous deoxyguanosines in the TFO binding site or a cytosine adjacent to the G(Pt) of the TFO significantly reduce cross-linking. DNA reporter plasmids in which platinated TFOs were cross-linked at a site in the transcribed region between a CMV promoter and a luciferase reporter gene were transfected into Chinese hamster ovary cells, and luciferase expression was compared with that for the corresponding non-cross-linked plasmid. Luciferase expression was inhibited 95 % when TFO-G(Pt) was bound and cross-linked to the transcribed strand, demonstrating that the cross-linked TFO was able to block transcription elongation. Further inhibition (99 %) was observed in nucleotide excision repair (NER) deficient cells, suggesting that NER may repair this lesion. The 3'-G(Pt) group of TFO-G(Pt) protects the TFO from degradation by exonucleases found in mammalian serum. Taken together, these results suggest that platinated TFOs of the type TFO-G(Pt) may find applications as agents for suppressing DNA transcription and consequently inhibiting gene expression in mammalian cells. PMID:22965663

  7. Molecular Cloning of MAPK Gene Family Using Synthetic Oligonucleotide Probe.

    Science.gov (United States)

    Zhou, Song; Wang, Qin; Chen, Jing; Chen, Jiang-Ye

    1999-01-01

    MAPK(mitogen activated protein kinase) is a kind of Ser/Thr protein kinase. The MAPKs play an important role in several different signal transduction pathways. The MAPKs may also have a role in morphorgenesis of Candida albicans. An oligonucleotide probe was used to screen novel MAPKs in C. albicans. All MAPKs shared high homogeneity in their eleven kinase subdomains, especially subdoman VII and VIII. In subdomain VII, nearly all MAPKs have the same KIDFGLAR sequence, and the two known MAPKs in C. albicans CEK1 and MKC1 have only one different nucleotide in that DNA sequence. This probe was hybridized with C. albicans genomic DNA. Under stringent conditions, the probe could only hybridize with CEK1 and MKC1 gene fragment. But when hybridized at 40 degrees in non-SDS solution, two novel bands appeared. This condition was used to screen SC5314 DNA library, and many positive clones with different hybridization density were obtained. The strongest hybridization clones were identified to contain CEK1 and MKC1 gene. From the stronger positive hybridization clones, two novel genes were identified. The first gene, named CRK1(CDC2-related protein kinase 1), shared high homogeneity to MAPKs, but was not of them. It is closest to SGV1 from S. cerevisiae (with homology 47%) and PITALRE from human (with homology 41%), both of which are CDC2-related protein kinases. The second gene called CEK2(Candida albicans extracelluar signal-regulated kinase 2) is a novel MAPK of Candida albicans, which shares the highest identity with CEK1 and its S. cerevisiae homologs, FUS3 and KSS1, two redundant MAPKs in yeast pheromone response and morphogenesis. PMID:12114967

  8. Diffusion of Oligonucleotides from within Iron-Crosslinked Polyelectrolyte-Modified Alginate Beads: A Model System for Drug Release

    CERN Document Server

    Privman, Vladimir; Luz, Roberto A S; Guz, Nataliia; Glasser, M Lawrence; Katz, Evgeny

    2016-01-01

    We developed and experimentally verified an analytical model to describe diffusion of oligonucleotides from stable hydrogel beads. The synthesized alginate beads are Fe3+-cross-linked as well as polyelectrolyte-doped for uniformity and stability at physiological pH. Data on diffusion of oligonucleotides from inside the beads provide physical insights into the volume nature of the immobilization of a fraction of oligonucleotides due to polyelectrolyte cross-linking, i.e., the absence of the surface-layer barrier in this case. Furthermore, our results suggest a new simple approach to measuring the diffusion coefficient of the mobile oligonucleotide molecules inside hydrogel. The considered alginate beads provide a model for a well-defined component in drug release systems and for the oligonucleotide-release transduction steps in drug-delivering and biocomputing applications. This is illustrated by destabilizing the beads with citrate that induces full oligonucleotide release with non-diffusional kinetics.

  9. 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.

  10. A large-aperture low-cost hydrophone array for tracking whales from small boats.

    Science.gov (United States)

    Miller, B; Dawson, S

    2009-11-01

    A passive sonar array designed for tracking diving sperm whales in three dimensions from a single small vessel is presented, and the advantages and limitations of operating this array from a 6 m boat are described. The system consists of four free floating buoys, each with a hydrophone, built-in recorder, and global positioning system receiver (GPS), and one vertical stereo hydrophone array deployed from the boat. Array recordings are post-processed onshore to obtain diving profiles of vocalizing sperm whales. Recordings are synchronized using a GPS timing pulse recorded onto each track. Sensitivity analysis based on hyperbolic localization methods is used to obtain probability distributions for the whale's three-dimensional location for vocalizations received by at least four hydrophones. These localizations are compared to those obtained via isodiachronic sequential bound estimation. Results from deployment of the system around a sperm whale in the Kaikoura Canyon in New Zealand are shown. PMID:19894806

  11. Transport Canada : navigable water protection technical paper on boating safety at dams

    Energy Technology Data Exchange (ETDEWEB)

    Putt, B. [Transport Canada, Sarnia, ON (Canada); Di Censo, V.M. [Transport Canada, Ottawa, ON (Canada)

    2009-07-01

    The Navigable Waters Protection Act (NWPA) was designed to ensure a balance between public rights of navigation and the need to build bridges, dams, and other structures. This paper discussed an owner's guide to navigation safety around water control structures. Developed by Transport Canada, the guide was intended to help owners of water control structures address boating safety matters and assist owners in making applications under the NWPA. The guide was prepared to address amendments made to the NWPA in 2009 as well as to assist owners in identifying potential hazards and interactions by the boating public at water control structures. The guide included information related to signage; navigation aids; barriers and booms; warning alerts and alarms; portage and access around structures; and application requirements. It was concluded that the guide will also provide a summary of legislation that may affect owners of water control structures.

  12. Basics of Bayesian Learning - Basically Bayes

    DEFF Research Database (Denmark)

    Larsen, Jan

    Tutorial presented at the IEEE Machine Learning for Signal Processing Workshop 2006, Maynooth, Ireland, September 8, 2006. The tutorial focuses on the basic elements of Bayesian learning and its relation to classical learning paradigms. This includes a critical discussion of the pros and cons...

  13. Modified oligonucleotides for triple helix studies and for the obtention of structures with biomedical and technological interest

    OpenAIRE

    Alvira Torre, Margarita

    2010-01-01

    [eng] Oligonucleotides are short fragments of DNA (10-100nt) which are of great interest because their applications in molecular biology, biomedicine and nanotechnology. As a result of their ability to base pairing, oligonucleotides can be used as primers, hybridization probes in biosensors, agents for controlling gene expression, structural material in nanotechnology or as substrates for a variety of biochemical and biophysical studies. Chemical modification of oligonucleotides as well as co...

  14. Boat Pumpout Locations, Fresh Water Boat Ramps in Rhode Island; Rs44ofr95; Public ramps and launching areas for boats and small craft on fresh water rivers streams lakes and ponds, Published in 1995, 1:24000 (1in=2000ft) scale, State of Rhode Island and Providence Plantations.

    Data.gov (United States)

    NSGIC GIS Inventory (aka Ramona) — This Boat Pumpout Locations dataset, published at 1:24000 (1in=2000ft) scale, was produced all or in part from Hardcopy Maps information as of 1995. It is described...

  15. A life cycle assessment method for alternative material selection strategies in boat structures

    OpenAIRE

    Bardet, Raphaël Régis

    2010-01-01

    In general the use of composites results in shorter production time, lightweight and lower maintenance costs to the marine industry in the leisure, fast and fishing boats sectors. The social and economic benefits of using composite materials have made users complacent about the pollution and the health and safety issues associated with these materials. As the perception of environmental problems changes with time, alternatives with lower emissions allowing for cleaner production and easier di...

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

    Science.gov (United States)

    Sasano, Masahiko; Imasato, Motonobu; Yamano, Hiroya; Oguma, Hiroyuki

    2016-06-01

    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.

  17. Finding an Export Market for a Small Finnish Boating Accessories Web-Shop : A case study

    OpenAIRE

    Nylund, Thomas

    2015-01-01

    Technological developments and regional integration have increased the amount of inter-national business transactions. Organizations of all sizes now have a possibility to take advantage of international business opportunities. By internationalizing firms can find new sources of growth and innovation, and escape unfavorable home market conditions. This thesis is an empirical study of potential export markets. The thesis is a case study of a small Finnish boating accessories web-shop. The thes...

  18. 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. 

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

    OpenAIRE

    Aulia Widyandari; Dedy Wahyudi

    2012-01-01

    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, auxili...

  20. 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.

  1. 2'-O-[2-(guanidinium)ethyl]-modified oligonucleotides: stabilizing effect on duplex and triplex structures

    Energy Technology Data Exchange (ETDEWEB)

    Prakash, T.P.; Puschl, A.; Lesnik, E.; Mohan, V.; Tereshko, V.; Egli, M.; Manoharan, M. (Vanderbilt); (UC)

    2010-03-08

    Oligonucleotides with a novel 2'-O-[2-(guanidinium)ethyl] (2'-O-GE) modification have been synthesized using a novel protecting group strategy for the guanidinium group. This modification enhances the binding affinity of oligonucleotides to RNA as well as duplex DNA ({Delta}T{sub m} 3.2 C per modification). The 2'-O-GE modified oligonucleotides exhibited exceptional resistance to nuclease degradation. The crystal structure of a palindromic duplex formed by a DNA oligonucleotide with a single 2'-O-GE modification was solved at 1.16 {angstrom} resolution.

  2. 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.

  3. 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.

  4. Boat ramp locations within the Columbia River Basin with associated recreational use, water quality measurements, and risk assessment data for zebra and quagga mussels

    Science.gov (United States)

    Hardiman, Jill M.; Holmberg, Glen S.; Elder, Nancy E.

    2015-01-01

    Aquatic invasive species are often transported between water bodies on boats or boat trailers, thus they are considered one of the primary vectors for new introductions of invasive species to a water body. This data set contains geographic positioning system locational data for boater access points, use data (i.e. recreational, fishing), water quality measurements (e.g. calcium concentrations, pH), risk assessment data, and other physical attributes (i.e. size, elevation) where available within the Columbia and Snake Rivers and throughout the Columbia River Basin. This work builds on an earlier body of work by Wells et al. 2011, Prioritizing Zebra and Quagga Mussel Monitoring in the Columbia River Basin (PDF link below), which provided much of the initial water quality, use information, and risk assessment data (categorical values for the risk of introduction and the risk of establishment). Updated information has been added by collecting additional data on use of water bodies, as well as combined categorical ranking methodology for identifying water bodies that may be high risk for both introduction and establishment of zebra and quagga mussels. This data is also related to a regional effort to contribute to the coordination of monitoring efforts for early detection of zebra and quagga mussels in the context of risk assessment data (CRBAIS weblink below). Data sets provided here include a service definition file, provided with a few reference layers within the region for viewing and an online map ( http://arcg.is/1LrNmBj) with some query options, a GIS shapefile (Child Item), and a tabular data set (csv file; Child Item). It is recommended that all users of this data thoroughly read the metadata files for data definitions, sources, and data limitations. It is recommended to use the online map link ( http://arcg.is/1LrNmBj) for a quick view of the data set and some basic query options.  Once on the ArcGIS online map, to view all the data layers click the show

  5. A facile inhibitor screening of SARS coronavirus N protein using nanoparticle-based RNA oligonucleotide

    Directory of Open Access Journals (Sweden)

    Roh C

    2012-05-01

    Full Text Available Changhyun RohDivision of Biotechnology, Advanced Radiation Technology Institute (ARTI, Korea Atomic Energy Research Institute (KAERI, Jeongeup, Republic of KoreaAbstract: Hundreds of million people worldwide have been infected with severe acute respiratory syndrome (SARS, and the rate of global death from SARS has remarkably increased. Hence, the development of efficient drug treatments for the biological effects of SARS is highly needed. We have previously shown that quantum dots (QDs-conjugated RNA oligonucleotide is sensitive to the specific recognition of the SARS-associated coronavirus (SARS-CoV nucleocapsid (N protein. In this study, we found that a designed biochip could analyze inhibitors of the SARS-CoV N protein using nanoparticle-based RNA oligonucleotide. Among the polyphenolic compounds examined, (--catechin gallate and (--gallocatechin gallate demonstrated a remarkable inhibition activity on SARS-CoV N protein. (--catechin gallate and (--gallocatechin gallate attenuated the binding affinity in a concentrated manner as evidenced by QDs-conjugated RNA oligonucleotide on a designed biochip. At a concentration of 0.05 µg mL–1, (--catechin gallate and (--gallocatechin gallate showed more than 40% inhibition activity on a nanoparticle-based RNA oligonucleotide biochip system.Keywords: SARS, RNA oligonucleotide, quantum dots, inhibitor, screening

  6. Efficient gene silencing by delivery of locked nucleic acid antisense oligonucleotides, unassisted by transfection reagents.

    Science.gov (United States)

    Stein, C A; Hansen, J Bo; Lai, Johnathan; Wu, SiJian; Voskresenskiy, Anatoliy; Høg, Anja; Worm, Jesper; Hedtjärn, Maj; Souleimanian, Naira; Miller, Paul; Soifer, Harris S; Castanotto, Daniella; Benimetskaya, Luba; Ørum, Henrik; Koch, Troels

    2010-01-01

    For the past 15-20 years, the intracellular delivery and silencing activity of oligodeoxynucleotides have been essentially completely dependent on the use of a delivery technology (e.g. lipofection). We have developed a method (called 'gymnosis') that does not require the use of any transfection reagent or any additives to serum whatsoever, but rather takes advantage of the normal growth properties of cells in tissue culture in order to promote productive oligonucleotide uptake. This robust method permits the sequence-specific silencing of multiple targets in a large number of cell types in tissue culture, both at the protein and mRNA level, at concentrations in the low micromolar range. Optimum results were obtained with locked nucleic acid (LNA) phosphorothioate gap-mers. By appropriate manipulation of oligonucleotide dosing, this silencing can be continuously maintained with little or no toxicity for >240 days. High levels of oligonucleotide in the cell nucleus are not a requirement for gene silencing, contrary to long accepted dogma. In addition, gymnotic delivery can efficiently deliver oligonucleotides to suspension cells that are known to be very difficult to transfect. Finally, the pattern of gene silencing of in vitro gymnotically delivered oligonucleotides correlates particularly well with in vivo silencing. The establishment of this link is of particular significance to those in the academic research and drug discovery and development communities.

  7. Oligonucleotide delivery with cell surface binding and cell penetrating Peptide amphiphile nanospheres.

    Science.gov (United States)

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

    2015-05-01

    A drug delivery system designed specifically for oligonucleotide therapeutics can ameliorate the problems associated with the in vivo delivery of these molecules. The internalization of free oligonucleotides is challenging, and cytotoxicity is the main obstacle for current transfection vehicles. To develop nontoxic delivery vehicles for efficient transfection of oligonucleotides, we designed a self-assembling peptide amphiphile (PA) nanosphere delivery system decorated with cell penetrating peptides (CPPs) containing multiple arginine residues (R4 and R8), and a cell surface binding peptide (KRSR), and report the efficiency of this system in delivering G-3129, a Bcl-2 antisense oligonucleotide (AON). PA/AON (peptide amphiphile/antisense oligonucleotide) complexes were characterized with regards to their size and secondary structure, and their cellular internalization efficiencies were evaluated. The effect of the number of arginine residues on the cellular internalization was investigated by both flow cytometry and confocal imaging, and the results revealed that uptake efficiency improved as the number of arginines in the sequence increased. The combined effect of cell penetration and surface binding property on the cellular internalization and its uptake mechanism was also evaluated by mixing R8-PA and KRSR-PA. R8 and R8/KRSR decorated PAs were found to drastically increase the internalization of AONs compared to nonbioactive PA control. Overall, the KRSR-decorated self-assembled PA nanospheres were demonstrated to be noncytotoxic delivery vectors with high transfection rates and may serve as a promising delivery system for AONs. PMID:25828697

  8. Conjugates of Phthalocyanines With Oligonucleotides as Reagents for Sensitized or Catalytic DNA Modification

    Directory of Open Access Journals (Sweden)

    2006-01-01

    Full Text Available Several conjugates of metallophthalocyanines with deoxyribooligonucleotides were synthesized to investigate sequence-specific modification of DNA by them. Oligonucleotide parts of these conjugates were responsible for the recognition of selected complementary sequences on the DNA target. Metallophthalocyanines were able to induce the DNA modification: phthalocyanines of Zn(II and Al(III were active as photosensitizers in the generation of singlet oxygen 1 O 2 , while phthalocyanine of Co(II promoted DNA oxidation by molecular oxygen through the catalysis of formation of reactive oxygen species ( ⋅ O 2 − , O 2 H 2 , OH. Irradiation of the reaction mixture containing either Zn(II- or Al(III-tetracarboxyphthalocyanine conjugates of oligonucleotide pd(TCTTCCCA with light of > 340 nm wavelength (Hg lamp or He/Ne laser resulted in the modification of the 22-nucleotide target d(TGAATGGGAAGAGGGTCAGGTT. A conjugate of Co(II-tetracarboxyphthalocyanine with the oligonucleotide was found to modify the DNA target in the presence of O 2 and 2-mercaptoethanol or in the presence of O 2 H 2 . Under both sensitized and catalyzed conditions, the nucleotides G 13 – G 15 were mainly modified, providing evidence that the reaction proceeded in the double-stranded oligonucleotide. These results suggest the possible use of phthalocyanine-oligonucleotide conjugates as novel artificial regulators of gene expression and therapeutic agents for treatment of cancer.

  9. LNA-modified isothermal oligonucleotide microarray for differentiating bacilli of similar origin

    Indian Academy of Sciences (India)

    Jing Yan; Ying Yuan; Runqing Mu; Hong Shang; Yifu Guan

    2014-12-01

    Oligonucleotide microarray has been one of the most powerful tools in the ‘Post-Genome Era’ for its high sensitivity, high throughput and parallel processing capability. To achieve high detection specificity, we fabricated an isothermal microarray using locked nucleic acid (LNA)-modified oligonucleotide probes, since LNA has demonstrated the advanced ability to enhance the binding affinity toward their complementary nucleotides. After designing the nucleotide sequences of these oligonucleotide probes for gram-positive bacilli of similar origin (Bacillus subtilis, Bacillus licheniformis, Bacillus pumilus, Bacillus megaterium and Bacillus circulans), we unified the melting temperatures of these oligonucleotide probes by modifying some nucleotides using LNA. Furthermore, we optimized the experimental procedures of hydrating microarray slides, blocking side surface as well as labelling the PCR products. Experimental results revealed that KOD Dash DNA polymerase could efficiently incorporate Cy3-dCTP into the PCR products, and the LNA-isothermal oligonucleotide microarray were able to distinguish the bacilli of similar origin with a high degree of accuracy and specificity under the optimized experimental condition.

  10. 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.

  11. Emissions in the exhaust of fishing boats after adding viscous agents into fuel oils.

    Science.gov (United States)

    Hsieh, Lien-Te; Shih, Shun-I; Lin, Sheng-Lun; Yang, Tsun-Lirng; Wu, Tser-Son; Hung, Chung-Hsien

    2009-12-20

    In order to avoid the illegal use of fishing boat fuel A (FBFA) by traveling diesel vehicles (TDVs) in Taiwan, alternatives that are easily distinguished from premium diesel fuel (PDF) were prepared to evaluate their suitability. Two new ingredients, pyrolysis fuel oil (PFO) and residue of desulfurization unit (RDS), were added into FBFA and formed PFO0.5 and RDS0.5, respectively. Along with FBFA, these three fuels were analyzed for their chemical and physical properties. Furthermore, they were used by three fishing boats with different sizes, output powers, and weights. The engine performances and pollutant emissions were examined and monitored. Experimental results show that there are significant differences in appearance between PDF and the two new blended fuels (PFO0.5 and RDS0.5), and thus misuse or illegal use of FBFA could be substantially reduced. The fuel consumption, which is negatively related to the heating value of fuels, is in order of FBFAfishing boats, using RDS0.5 resulted in a decrease in CO and NO(x) emissions, while the PM emission factors (g bhp(-1) h(-1) and g L(-1)-fuel) were reduced by approximately 36% and 33%, respectively. Owing to the higher total aromatic content in PFO0.5 and RDS0.5, total-PAH concentrations in the exhausts from the three fishing boats using PFO0.5 and RDS0.5 were slightly (1.2 and 1.1 times, respectively) higher than for those using FBFA. Nevertheless, the estimated total BaP(eq) from the three fishing boats using RDS0.5 was 27.5, 19.5, and 8.25% lower than those using FBFA. With using PFO0.5, they were totally different, at 23.5, 2.79, and 2.58% higher. With regard to looking different to PDF, RDS0.5 is superior to PFO0.5, and is thus recommended as a better alternative to FBFA, particularly because it can help lower more emissions of CO, NO(x), PM and BaP(eq).

  12. Influence of boat material on the structure, stoichiometry and optical properties of gallium sulphide films prepared by thermal evaporation

    Energy Technology Data Exchange (ETDEWEB)

    Rao, Pritty [National Centre for Compositional Characterization of Materials, Bhabha Atomic Research Centre, ECIL Post, Hyderabad 500062 (India); Kumar, Sanjiv, E-mail: sanjucccm@rediffmail.com [National Centre for Compositional Characterization of Materials, Bhabha Atomic Research Centre, ECIL Post, Hyderabad 500062 (India); Sahoo, N.K. [Atomic and Molecular Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India)

    2015-01-15

    The paper describes the deposition of thin films of gallium sulphide on soda-lime glass substrates by thermal evaporation of chemically synthesized powders consisting of gallium sulphide and gallium oxyhydroxide from a Mo or Ta boat and the evolution of their compositional, structural and optical properties on vacuum annealing. The films deposited from Mo or Ta boats possessed distinctly different properties. The Mo-boat evaporated pristine films were amorphous, transparent (α ∼ 10{sup 3} cm{sup −1}) in visible region and had a direct band gap of about 3.2 eV. Vacuum annealing at 723 K brought about their crystallization predominantly into cubic γ-Ga{sub 2}S{sub 3} and a blue shift by about 0.2 eV. The Ta-boat evaporated pristine films were also amorphous but were absorbing (α ∼ 10{sup 4} cm{sup −1}) and had a direct band gap of about 2.1 eV. These crystallized into hexagonal GaS and experienced a blue shift by more than 1.0 eV on vacuum annealing at 723 K. The dissimilar properties of the two kinds of films arose mainly from their different atomic compositions. The Mo-boat evaporated pristine films contained Ga and S in ∼1:1 atomic proportions while those prepared using Ta-boat were Ga rich which impaired their transmission characteristics. The former composition favoured the stabilization of S rich gallium sulphide (Ga{sub 2}S{sub 3}) phase while the latter stabilised S deficient species, GaS. Besides inducing crystallization, vacuum annealing at 723 K also caused the diffusion of Ga in excess of atomic composition of the phase formed, into soda-lime glass which improved the optical transmission of the films. Gallium oxyhydroxide, an inevitable co-product of the chemical synthetic process, in the evaporant introduced oxygen and hydrogen impurities in the films which do not seem to significantly influence their optical properties. - Highlights: • Gallium sulphide films are prepared by thermal evaporation from a Mo or Ta boat. • Mo-boat

  13. 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

  14. 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

  15. Delivery of antisense oligonucleotide to the cornea by iontophoresis.

    Science.gov (United States)

    Berdugo, M; Valamanesh, F; Andrieu, C; Klein, C; Benezra, D; Courtois, Y; Behar-Cohen, F

    2003-04-01

    We wished to evaluate the potential of iontophoresis to promote the delivery of antisense oligonucleotides (ODN) directed at the vascular endothelial growth factor (VEGF)-R2 receptor (KDR/Flk) to the cornea of the rat eye. Fluorescence (CY5)-labeled ODNs in phosphate-buffered saline (PBS) (20 microM) were locally administered to rat eyes, and their fate within the anterior segment was studied. Thirty-four male, 5-week-old Wistar rats were used for all experiments. The rats were divided in four groups. In group I (12 rats, 12 eyes), the ODNs (20 microM) were delivered by iontophoresis (300 microA for 5 minutes) using a specially designed corneal applicator. In group II (12 rats, 12 eyes), the ODNs (20 microM) were delivered using the same applicator, but no electrical current was applied. In group III (6 rats, 6 eyes), a corneal neovascular reaction was induced prior to the application of ODNs (20 microM), and iontophoresis electrical current was delivered as for group I rats. Group IV (4 rats, 4 eyes) received ODN (60 microM) iontophoresis application (300 microA for 5 minutes) and were used for ODN integrity studies. The animals were killed 5 minutes, 90 minutes, and 24 hours after a single ODN application and studied. Topically applied ODNs using the same iontophoresis applicator but without current do not penetrate the cornea and remain confined to the superficial epithelial layer. ODNs delivered with transcorneoscleral iontophoresis penetrate into all corneal layers and are also detected in the iris. In corneas with neovascularization, ODNs were particularly localized within the vascular endothelial cells of the stroma. ODNs extracted from eye tissues 24 hours after iontophoresis remained unaltered. The iontophoresis current did not cause any detectable ocular damage under these conditions. Iontophoresis promotes the delivery of ODNs to the anterior segment of the eye, including all corneal layers. Iontophoresis of ODNs directed at VEGF-R2 may be used for the

  16. Basic Science Training Program.

    Science.gov (United States)

    Brummel, Clete

    These six learning modules were developed for Lake Michigan College's Basic Science Training Program, a workshop to develop good study skills while reviewing basic science. The first module, which was designed to provide students with the necessary skills to study efficiently, covers the following topics: time management; an overview of a study…

  17. Basic Research Objectives Reaffirmed

    Institute of Scientific and Technical Information of China (English)

    Guo Haiyan; Zhao Baohua

    2002-01-01

    @@ As a national institution for scientific research and a component of the national innovation system, CAS should and must make key contributions to the great national rejuvenation of the country. Keeping this in mind, CAS has developed four developmental targets for its basic research. This was revealed at a CAS conference on basic research held June 11-12 in Beijing.

  18. Bracken Basic Concept Scale.

    Science.gov (United States)

    Naglieri, Jack A.; Bardos, Achilles N.

    1990-01-01

    The Bracken Basic Concept Scale, for use with preschool and primary-aged children, determines a child's school readiness and knowledge of English-language verbal concepts. The instrument measures 258 basic concepts in such categories as comparisons, time, quantity, and letter identification. This paper describes test administration, scoring and…

  19. Exponentiation: A New Basic?

    Science.gov (United States)

    Davis, Brent

    2015-01-01

    For centuries, the basic operations of school mathematics have been identified as addition, subtraction, multiplication, and division. Notably, these operations are "basic," not because they are foundational to mathematics knowledge, but because they were vital to a newly industrialized and market-driven economy several hundred years…

  20. Cellular uptake of antisense oligonucleotides after complexing or conjugation with cell-penetrating model peptides.

    Science.gov (United States)

    Oehlke, J; Birth, P; Klauschenz, E; Wiesner, B; Beyermann, M; Oksche, A; Bienert, M

    2002-08-01

    The uptake by mammalian cells of phosphorothioate oligonucleotides was compared with that of their respective complexes or conjugates with cationic, cell-penetrating model peptides of varying helix-forming propensity and amphipathicity. An HPLC-based protocol for the synthesis and purification of disulfide bridged conjugates in the 10-100 nmol range was developed. Confocal laser scanning microscopy (CLSM) in combination with gel-capillary electrophoresis and laser induced fluorescence detection (GCE-LIF) revealed cytoplasmic and nuclear accumulationin all cases. The uptake differences between naked oligonucleotides and their respective peptide complexes or conjugates were generally confined to one order of magnitude. No significant influence of the structural properties of the peptide components upon cellular uptake was found. Our results question the common belief that the increased biological activity of oligonucleotides after derivatization with membrane permeable peptides may be primarily due to improved membrane translocation.

  1. Study of the simultaneous preparation of oligopeptides and oligonucleotides under prebiotic conditions

    Energy Technology Data Exchange (ETDEWEB)

    Caroon, J.M.

    1975-08-01

    The effect of imidazole in promoting the formation of biopolymers under chemical evolutionary conditions was investigated. At the onset of this work, it was known that short-chain oligonucleotides formed in aqueous solutions of ATP, imidazole, and MgCl/sub 2/; in addition, short peptides had been shown to form in aqueous solutions of aminoacylimidazolides and MgCl/sub 2/. The products formed in an aqueous solution of ATP, imidazole, alanine, and MgCl/sub 2/ was investigated and it was found that, under plausible prebiotic conditions, the formation of representatives of both peptides and oligonucleotides could be demonstrated. Furthermore, it was shown that the simultaneous formation of peptides increased the formation of oligonucleotides. A preliminary study was made on the possibility of inducing asymmetry in the clay catalyzed polymerization of peptides, but the results were discouraging. (auth)

  2. 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.

  3. Repair of Thalassemic Human β -globin mRNA in Mammalian Cells by Antisense Oligonucleotides

    Science.gov (United States)

    Sierakowska, Halina; Sambade, Maria J.; Agrawal, Sudhir; Kole, Ryszard

    1996-11-01

    In one form of β -thalassemia, a genetic blood disorder, a mutation in intron 2 of the β -globin gene (IVS2-654) causes aberrant splicing of β -globin pre-mRNA and, consequently, β -globin deficiency. Treatment of mammalian cells stably expressing the IVS2-654 human β -globin gene with antisense oligonucleotides targeted at the aberrant splice sites restored correct splicing in a dose-dependent fashion, generating correct human β -globin mRNA and polypeptide. Both products persisted for up to 72 hr posttreatment. The oligonucleotides modified splicing by a true antisense mechanism without overt unspecific effects on cell growth and splicing of other pre-mRNAs. This novel approach in which antisense oligonucleotides are used to restore rather than to down-regulate the activity of the target gene is applicable to other splicing mutants and is of potential clinical interest.

  4. Potent triple helix stabilization by 5',3'-modified triplex-forming oligonucleotides.

    Science.gov (United States)

    Ben Gaied, Nouha; Zhao, Zhengyun; Gerrard, Simon R; Fox, Keith R; Brown, Tom

    2009-07-20

    Anthraquinone and pyrene analogues attached to the 3' and/or 5' termini of triplex-forming oligonucleotides (TFOs) by various linkers increased the stability of parallel triple helices. The modifications are simple to synthesize and can be introduced during standard solid-phase oligonucleotide synthesis. Potent triplex stability was achieved by using doubly modified TFOs, which in the most favourable cases gave an increase in melting temperature of 30 degrees C over the unmodified counterparts and maintained their selectivity for the correct target duplex. Such TFOs can produce triplexes with melting temperatures of 40 degrees C at pH 7 even though they do not contain any triplex-stabilizing base analogues. These studies have implications for the design of triplex-forming oligonucleotides for use in biology and nanotechnology. PMID:19554592

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

    International Nuclear Information System (INIS)

    The dynamics of the human oligonucleotide AG3(T2AG3)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

  6. Dynamics of human telomerase RNA structure revealed by antisense oligonucleotide technique.

    Science.gov (United States)

    Vasilkova, Daria V; Azhibek, Dulat M; Zatsepin, Timofei S; Naraikina, Yulia V; Prassolov, Vladimir S; Prokofjeva, Maria M; Zvereva, Maria I; Rubtsova, Maria P

    2013-12-01

    Telomeres are the nucleoprotein complexes that cap the linear chromosome ends. Telomerase is a ribonucleoprotein that maintains telomere length in stem, embryonic and cancer cells. Somatic cells don't contain active telomerase and telomere function as mitotic clock and telomere length determines the number of cell divisions. Telomerase RNA (TER) contains the template for telomere synthesis and serves as a structural scaffold for holoenzyme assembly. We compared different oligonucleotide based methods for telomerase RNA inhibition, such as antisense oligonucleotides, knockdown by transient siRNA transfection and silencing by miRNA derived from short expressed RNA hairpin in HEK293 cells. All of these methods were applied to different TER regions. Our results revealed that CR2/CR3 domain of TER is accessible in vitro and in vivo and could serve as an optimal site for oligonucleotide-based telomerase silencing.

  7. Mechanical properties and fabrication of small boat using woven glass/sugar palm fibres reinforced unsaturated polyester hybrid composite

    Energy Technology Data Exchange (ETDEWEB)

    Misri, S; Leman, Z; Sapuan, S M; Ishak, M R, E-mail: sairizal_misri@yahoo.com [Department of Mechanical and Manufacturing Engineering, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor (Malaysia)

    2010-05-15

    In recent years, sugar palm fibre has been found to have great potential to be used as fibre reinforcement in polymer matrix composites. This research investigates the mechanical properties of woven glass/sugar palm fibres reinforced unsaturated polyester hybrid composite. The composite specimens made of different layer of fibres such as strand mat, natural and hand woven of sugar palm fibres. The composites were fabricated using a compression moulding technique. The tensile and impact test was carried out in accordance to ASTM 5083 and ASTM D256 standard. The fibre glass boat is a familiar material used in boat industry. A lot of research on fabrication process such as lay-up, vacuum infusion mould and resin transfer mould has been conducted. Hybrid material of sugar palm fibre and fibre glass was used in fabricating the boat. This research investigates the method selection for fabrication of small boat application of natural fibre composites. The composite specimens made of different layer of fibres; woven glass fibre, strand mat, natural and hand woven of woven sugar palm fibres were prepared. The small boat were fabricated using a compression moulding and lay up technique. The results of the experiment showed that the tensile strength, tensile modulus, elongation at break value and impact strength were higher than the natural woven sugar palm fibre. The best method for fabricating the small boat was compression moulding technique. As a general conclusion, the usage of glass fibre had improved the tensile properties sugar palm fibre composites and compression moulding technique is suitable to be used in making a small boat application of natural fibre composites.

  8. Mechanical properties and fabrication of small boat using woven glass/sugar palm fibres reinforced unsaturated polyester hybrid composite

    International Nuclear Information System (INIS)

    In recent years, sugar palm fibre has been found to have great potential to be used as fibre reinforcement in polymer matrix composites. This research investigates the mechanical properties of woven glass/sugar palm fibres reinforced unsaturated polyester hybrid composite. The composite specimens made of different layer of fibres such as strand mat, natural and hand woven of sugar palm fibres. The composites were fabricated using a compression moulding technique. The tensile and impact test was carried out in accordance to ASTM 5083 and ASTM D256 standard. The fibre glass boat is a familiar material used in boat industry. A lot of research on fabrication process such as lay-up, vacuum infusion mould and resin transfer mould has been conducted. Hybrid material of sugar palm fibre and fibre glass was used in fabricating the boat. This research investigates the method selection for fabrication of small boat application of natural fibre composites. The composite specimens made of different layer of fibres; woven glass fibre, strand mat, natural and hand woven of woven sugar palm fibres were prepared. The small boat were fabricated using a compression moulding and lay up technique. The results of the experiment showed that the tensile strength, tensile modulus, elongation at break value and impact strength were higher than the natural woven sugar palm fibre. The best method for fabricating the small boat was compression moulding technique. As a general conclusion, the usage of glass fibre had improved the tensile properties sugar palm fibre composites and compression moulding technique is suitable to be used in making a small boat application of natural fibre composites.

  9. Mechanical properties and fabrication of small boat using woven glass/sugar palm fibres reinforced unsaturated polyester hybrid composite

    Science.gov (United States)

    Misri, S.; Leman, Z.; Sapuan, S. M.; Ishak, M. R.

    2010-05-01

    In recent years, sugar palm fibre has been found to have great potential to be used as fibre reinforcement in polymer matrix composites. This research investigates the mechanical properties of woven glass/sugar palm fibres reinforced unsaturated polyester hybrid composite. The composite specimens made of different layer of fibres such as strand mat, natural and hand woven of sugar palm fibres. The composites were fabricated using a compression moulding technique. The tensile and impact test was carried out in accordance to ASTM 5083 and ASTM D256 standard. The fibre glass boat is a familiar material used in boat industry. A lot of research on fabrication process such as lay-up, vacuum infusion mould and resin transfer mould has been conducted. Hybrid material of sugar palm fibre and fibre glass was used in fabricating the boat. This research investigates the method selection for fabrication of small boat application of natural fibre composites. The composite specimens made of different layer of fibres; woven glass fibre, strand mat, natural and hand woven of woven sugar palm fibres were prepared. The small boat were fabricated using a compression moulding and lay up technique. The results of the experiment showed that the tensile strength, tensile modulus, elongation at break value and impact strength were higher than the natural woven sugar palm fibre. The best method for fabricating the small boat was compression moulding technique. As a general conclusion, the usage of glass fibre had improved the tensile properties sugar palm fibre composites and compression moulding technique is suitable to be used in making a small boat application of natural fibre composites.

  10. A highly sensitive and selective viral protein detection method based on RNA oligonucleotide nanoparticle

    Science.gov (United States)

    Roh, Changhyun; Lee, Ho-Young; Kim, Sang-Eun; Jo, Sung-Kee

    2010-01-01

    Globally, approximately 170 million people (representing approximately 3% of the population worldwide), are infected with hepatitis C virus (HCV) and at risk of serious liver disease, including chronic hepatitis. We propose a new quantum dots (QDs)-supported RNA oligonucleotide approach for the specific and sensitive detection of viral protein using a biochip. This method was developed by immobilizing a HCV nonstructural protein 5B (NS5B) on the surface of a glass chip via the formation of a covalent bond between an amine protein group and a ProLinker™ glass chip. The QDs-supported RNA oligonucleotide was conjugated via an amide formation reaction from coupling of a 5′-end-amine-modified RNA oligonucleotide on the surface of QDs displaying carboxyl groups via standard EDC coupling. The QDs-conjugated RNA oligonucleotide was interacted to immobilized viral protein NS5B on the biochip. The detection is based on the variation of signal of QDs-supported RNA oligonucleotide bound on an immobilized biochip. It was demonstrated that the value of the signal has a linear relationship with concentrations of the HCV NS5B viral protein in the 1 μg mL−1 to 1 ng mL−1 range with a detection limit of 1 ng mL−1. The major advantages of this RNA-oligonucleotide nanoparticle assay are its good specificity, ease of performance, and ability to perform one-spot monitoring. The proposed method could be used as a general method of HCV detection and is expected to be applicable to other types of diseases as well. PMID:20517476

  11. Bolaamphiphile-based nanocomplex delivery of phosphorothioate gapmer antisense oligonucleotides as a treatment for Clostridium difficile

    Science.gov (United States)

    Hegarty, John P; Krzeminski, Jacek; Sharma, Arun K; Guzman-Villanueva, Diana; Weissig, Volkmar; Stewart, David B

    2016-01-01

    Despite being a conceptually appealing alternative to conventional antibiotics, a major challenge toward the successful implementation of antisense treatments for bacterial infections is the development of efficient oligonucleotide delivery systems. Cationic vesicles (bolasomes) composed of dequalinium chloride (“DQAsomes”) have been used to deliver plasmid DNA across the cardiolipin-rich inner membrane of mitochondria. As cardiolipin is also a component of many bacterial membranes, we investigated the application of cationic bolasomes to bacteria as an oligonucleotide delivery system. Antisense sequences designed in silico to target the expression of essential genes of the bacterial pathogen, Clostridium difficile, were synthesized as 2′-O-methyl phosphorothioate gapmer antisense oligonucleotides (ASO). These antisense gapmers were quantitatively assessed for their ability to block mRNA translation using luciferase reporter and C. difficile protein expression plasmid constructs in a coupled transcription–translation system. Cationic bolaamphiphile compounds (dequalinium derivatives) of varying alkyl chain length were synthesized and bolasomes were prepared via probe sonication of an aqueous suspension. Bolasomes were characterized by particle size distribution, zeta potential, and binding capacities for anionic oligonucleotide. Bolasomes and antisense gapmers were combined to form antisense nanocomplexes. Anaerobic C. difficile log phase cultures were treated with serial doses of gapmer nanocomplexes or equivalent amounts of empty bolasomes for 24 hours. Antisense gapmers for four gene targets achieved nanomolar minimum inhibitory concentrations for C. difficile, with the lowest values observed for oligonucleotides targeting polymerase genes rpoB and dnaE. No inhibition of bacterial growth was observed from treatments at matched dosages of scrambled gapmer nanocomplexes or plain, oligonucleotide-free bolasomes compared to untreated control cultures. We

  12. Oligonucleotide Fingerprinting of rRNA Genes for Analysis of Fungal Community Composition

    OpenAIRE

    Valinsky, Lea; Della Vedova, Gianluca; Jiang, Tao; Borneman, James

    2002-01-01

    Thorough assessments of fungal diversity are currently hindered by technological limitations. Here we describe a new method for identifying fungi, oligonucleotide fingerprinting of rRNA genes (OFRG). ORFG sorts arrayed rRNA gene (ribosomal DNA [rDNA]) clones into taxonomic clusters through a series of hybridization experiments, each using a single oligonucleotide probe. A simulated annealing algorithm was used to design an OFRG probe set for fungal rDNA. Analysis of 1,536 fungal rDNA clones d...

  13. Customized oligonucleotide microchips that convert multiple genetic information to simple patterns, are portable and reusable

    Science.gov (United States)

    Mirzabekov, Andrei; Guschin, Dmitry Y.; Chik, Valentine; Drobyshev, Aleksei; Fotin, Alexander; Yershov, Gennadiy; Lysov, Yuri

    2002-01-01

    This invention relates to using customized oligonucleotide microchips as biosensors for the detection and identification of nucleic acids specific for different genes, organisms and/or individuals in the environment, in food and in biological samples. The microchips are designed to convert multiple bits of genetic information into simpler patterns of signals that are interpreted as a unit. Because of an improved method of hybridizing oligonucleotides from samples to microchips, microchips are reusable and transportable. For field study, portable laser or bar code scanners are suitable.

  14. Effects of HSP70 Antisense Oligonucleotide on the Proliferation and Apoptosis of Human Hepatocellular Carcinoma Cells

    Institute of Scientific and Technical Information of China (English)

    杨雪; 贺海斌; 杨威; 宋涛; 郭成; 郑鑫; 刘青光

    2010-01-01

    The study investigated the effects of heat shock protein 70(HSP70) antisense oligonucleotide(ASODN) on the proliferation and apoptosis of a human hepatocellular carcinoma cell line(SMMC-7721 cells) in vitro.HSP70 oligonucleotide was transfected into SMMC-7721 cells by the mediation of SofastTM transfection reagent.Inhibition rate of SMMC-7721 cells was determined by using MTT method.Apoptosis rate and cell cycle distribution were measured by flow cytometry.Immunocytochemistry staining was used to observe th...

  15. Sequence selective naked-eye detection of DNA harnessing extension of oligonucleotide-modified nucleotides.

    Science.gov (United States)

    Verga, Daniela; Welter, Moritz; Marx, Andreas

    2016-02-01

    DNA polymerases can efficiently and sequence selectively incorporate oligonucleotide (ODN)-modified nucleotides and the incorporated oligonucleotide strand can be employed as primer in rolling circle amplification (RCA). The effective amplification of the DNA primer by Φ29 DNA polymerase allows the sequence-selective hybridisation of the amplified strand with a G-quadruplex DNA sequence that has horse radish peroxidase-like activity. Based on these findings we develop a system that allows DNA detection with single-base resolution by naked eye.

  16. Directed basic research

    International Nuclear Information System (INIS)

    In its execution, and in the requirement of no other deliverables than knowledge generation, directed basic research is no different from conventional (self-directed) basic research. The selected areas are determined in a national perspective. Directed Basic Research may be in an area where the knowledge generation would benefit Indian Society in the long term, or it may be in an area where the results of the research would benefit Indian Industry or our strategic interests in the long term. India can become a global innovation leader provided we have technology foresight to make the right technology choices, provided we introduce coherent synergy (a phrase I coined a few years back in this context) in our science and technology related activities and provided we establish an effective innovation ecosystem. We must also selectively promote some technology areas through directed basic research. Sustainable economic development in the future requires strong and increased funding of basic research. While directed basic research should be encouraged, self-directed basic research should also receive substantially increased support. (author)

  17. 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

  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. Studies on the Syntheses and Properties of 5'-Branched-sugar Isonucleosides and the Related Oligonucleotides

    Institute of Scientific and Technical Information of China (English)

    TianXiaobing; ZhangLihe; MinJimei

    2001-01-01

    The chemistry of nucleosides and oligonucleotides is an actively investigated field in the search for new drugs. Thesyntheses and the properties of isonucleosides and oligonucleotides have been investigated to improve their stability,antitumor and antiviral activities, and to reduce their toxicity.

  20. FLUORESCENT OLIGONUCLEOTIDES CONTAINING A NOVEL PERYLENE 2 '-AMINO-alpha-L-LNA MONOMER: SYNTHESIS AND ANALYTICAL POTENTIAL

    DEFF Research Database (Denmark)

    Astakhova, I. V.; Kumar, T. S.; Wengel, J.

    2011-01-01

    efficiency of the resulting perylene-2'-amino-alpha-L-LNA monomer (T*) into synthetic oligonucleotides was significantly improved by replacement of the typically used 1H-tetrazole activator with pyridine hydrochloride. Generally, oligonucleotides containing monomer T* showed high binding affinity towards...

  1. The Effect of Organic Modifiers on Electrospray Ionization Charge-State Distribution and Desorption Efficiency for Oligonucleotides

    Science.gov (United States)

    Chen, Buyun; Mason, Sadie F.; Bartlett, Michael G.

    2013-02-01

    The chemical composition of the solution has a critical impact on the electrospray desorption efficiency of oligonucleotides. Several physiochemical properties of various organic modifiers were investigated with respect to their role in the desorption process of oligonucleotides. The Henry's Law Constant, which reflects the volatility of alkylamines, was found to have a prominent effect on both the electrospray charge state distribution and desorption efficiency of oligonucleotides. Alkylamines with higher k_{H,cc}( {aq/gas} ) values such as hexylamine, piperidine, and imidazole reduced the charge state distribution by forming complexes with the oligonucleotide and dissociating from it in the gas phase, while alkylamines with extremely low k_{H,cc}( {aq/gas} ) values reduced the electrospray charge state distribution by facilitating ion emission at an earlier stage of the electrospray desorption process. Ion-pairing agents with moderate k_{H,cc}( {aq/gas} ) values do not alter the electrospray charge state distribution of oligonucleotides and their ability to enhance oligonucleotide ionization followed the order of decreasing k_{H,cc}( {aq/gas} ) values. The Henry's Law Constant also correlated to the impact of the acidic modifiers on oligonucleotide ionization efficiency. Ionization enhancement effects were observed with hexafluoroisopropanol, and this effect was attributed to its low k_{H,cc}( {aq/gas} ) and moderate acidity. The comprehensive effects of both alkylamine and hexafluoroisoproapnol on the electrospray ionization desorption of oligonucleotides were also evaluated, and acid-base equilibrium was found to play a critical role in determining these effects.

  2. HIV Treatment: The Basics

    Science.gov (United States)

    HIV Treatment HIV Treatment: The Basics (Last updated 3/1/2016; last reviewed 3/1/2016) Key Points Antiretroviral therapy (ART) ... reduces the risk of HIV transmission . How do HIV medicines work? HIV attacks and destroys the infection- ...

  3. Understanding Infertility - The Basics

    Medline Plus

    Full Text Available ... here . Basic Infertility Evaluation 450 x 274 | Running Time: 3 min 40 sec Dr. Roger Lobo of ... Causes of Female Infertility 450 x 274 | Running Time: 2 min 35 sec Dr. Roger Lobo, of ...

  4. Basic Information about Mercury

    Science.gov (United States)

    ... Twitter Google+ Pinterest Contact Us 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 ...

  5. Brain Basics: Preventing Stroke

    Science.gov (United States)

    ... free mailed brochure Cómo Prevenir un Accidente Cerebrovascular Brain Basics: Preventing Stroke Request free mailed brochure Table ... Americans are protecting their most important asset—their brain. Are you? Stroke ranks as the fourth leading ...

  6. Understanding Infertility - The Basics

    Medline Plus

    Full Text Available ... Smoking Cessation Links to Professional Societies and Organizations Home › Understanding Infertility - The Basics A series of patient ... Find a Health Care Provider Back to Top Home | About Us | Reproductive Health Topics | News & Publications | Resources ...

  7. EHR/PHR Basics

    Science.gov (United States)

    Skip Navigation Bar Home Current Issue Past Issues EHR EHR/PHR Basics Past Issues / Summer 2009 Table of ... information to it. With an electronic health record (EHR) or electronic medical record (EMR), your doctor (or ...

  8. Understanding Infertility - The Basics

    Medline Plus

    Full Text Available ... Basic Infertility Evaluation 450 x 274 | Running Time: 3 min 40 sec Dr. Roger Lobo of the ... Coping With Infertility 450 x 274 | Running Time: 3 min 31 sec Dr. Roger Lobo of the ...

  9. 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.

  10. 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...

  11. 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.

  12. 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.

  13. 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.

  14. Quantification of Boat Visitation Rates at Artificial and Natural Reefs in the Eastern Gulf of Mexico Using Acoustic Recorders.

    Science.gov (United States)

    Simard, Peter; Wall, Kara R; Mann, David A; Wall, Carrie C; Stallings, Christopher D

    2016-01-01

    Artificial reefs are commonly used as a management tool, in part to provide ecosystem services, including opportunities for recreational fishing and diving. Quantifying the use of artificial reefs by recreational boaters is essential for determining their value as ecosystem services. In this study, four artificial-natural reef pairs in the eastern Gulf of Mexico (off western Florida) were investigated for boat visitation rates using autonomous acoustic recorders. Digital SpectroGram (DSG) recorders were used to collect sound files from April 2013 to March 2015. An automatic detection algorithm was used to identify boat noise in individual files using the harmonic peaks generated by boat engines, and by comparing the sound amplitude of each file with surrounding files. In all four pairs, visitation rates were significantly higher at the artificial reef than the natural reef. This increase in boat visitation was likely due to actual or perceived increased quality of fishing and diving at the artificial reefs, or to lack of knowledge of the presence or locations of the natural reefs. Inshore reefs (25 m depth). This study appears to be the first to use acoustic data to measure participant use of boating destinations, and highlights the utility of acoustic monitoring for the valuation of this important ecosystem service provided by artificial reefs.

  15. Quantification of Boat Visitation Rates at Artificial and Natural Reefs in the Eastern Gulf of Mexico Using Acoustic Recorders

    Science.gov (United States)

    Simard, Peter; Wall, Kara R.; Mann, David A.; Wall, Carrie C.; Stallings, Christopher D.

    2016-01-01

    Artificial reefs are commonly used as a management tool, in part to provide ecosystem services, including opportunities for recreational fishing and diving. Quantifying the use of artificial reefs by recreational boaters is essential for determining their value as ecosystem services. In this study, four artificial–natural reef pairs in the eastern Gulf of Mexico (off western Florida) were investigated for boat visitation rates using autonomous acoustic recorders. Digital SpectroGram (DSG) recorders were used to collect sound files from April 2013 to March 2015. An automatic detection algorithm was used to identify boat noise in individual files using the harmonic peaks generated by boat engines, and by comparing the sound amplitude of each file with surrounding files. In all four pairs, visitation rates were significantly higher at the artificial reef than the natural reef. This increase in boat visitation was likely due to actual or perceived increased quality of fishing and diving at the artificial reefs, or to lack of knowledge of the presence or locations of the natural reefs. Inshore reefs (25 m depth). This study appears to be the first to use acoustic data to measure participant use of boating destinations, and highlights the utility of acoustic monitoring for the valuation of this important ecosystem service provided by artificial reefs. PMID:27500533

  16. Basics of Quantum Computation

    OpenAIRE

    Vedral, Vlatko; Martin B. Plenio

    1998-01-01

    Quantum computers require quantum logic, something fundamentally different to classical Boolean logic. This difference leads to a greater efficiency of quantum computation over its classical counter-part. In this review we explain the basic principles of quantum computation, including the construction of basic gates, and networks. We illustrate the power of quantum algorithms using the simple problem of Deutsch, and explain, again in very simple terms, the well known algorithm of Shor for fac...

  17. 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....

  18. 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.

  19. 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

  20. A Global Approach for the Design of a Rim- Driven Marine Turbine Generator for Sail Boat

    OpenAIRE

    Drouen, Laurent; CHARPENTIER, Jean-Frederic; Clenet, Stéphane; SEMAIL, Eric

    2012-01-01

    Development of new ways to provide clean onboard electric energy is a key feature for the sailing boat industry and sail race teams. This is why marine turbines (MT), are considered to provide onboard energy. These turbines can be used to harness kinetic energy of the water flow related to the ship motion. In this paper we propose to study an unconventional design of such a turbine where the electrical generator is located in the periphery of the blades and where the magnetic gap is water fil...

  1. Don’t Rock the Boat: How Antiphase Crew Coordination Affects Rowing

    OpenAIRE

    de Brouwer, Anouk J.; De Poel, Harjo J.; Mathijs J Hofmijster

    2013-01-01

    It is generally accepted that crew rowing requires perfect synchronization between the movements of the rowers. However, a long-standing and somewhat counterintuitive idea is that out-of-phase crew rowing might have benefits over in-phase (i.e., synchronous) rowing. In synchronous rowing, 5 to 6% of the power produced by the rower(s) is lost to velocity fluctuations of the shell within each rowing cycle. Theoretically, a possible way for crews to increase average boat velocity is to reduce th...

  2. Phosphorothioate anti-sense oligonucleotides: the kinetics and mechanism of the generation of the sulfurising agent from phenylacetyl disulfide (PADS).

    Science.gov (United States)

    Scotson, James L; Andrews, Benjamin I; Laws, Andrew P; Page, Michael I

    2016-09-21

    The synthesis of phosphorothioate oligonucleotides is often accomplished in the pharmaceutical industry by the sulfurisation of the nucleotide-phosphite using phenylacetyl disulfide (PADS) which has an optimal combination of properties. This is best achieved by an initial 'ageing' of PADS for 48 h in acetonitrile with 3-picoline to generate polysulfides. The initial base-catalysed degradation of PADS occurs by an E1cB-type elimination to generate a ketene and acyldisulfide anion. Proton abstraction to reversibly generate a carbanion is demonstrated by H/D exchange, the rate of which is greatly increased by electron-withdrawing substituents in the aromatic ring of PADS. The ketene can be trapped intramolecularly by an o-allyl group. The disulfide anion generated subsequently attacks unreacted PADS on sulfur to give polysulfides, the active sulfurising agent. The rate of degradation of PADS is decreased by less basic substituted pyridines and is only first order in PADS indicating that the rate-limiting step is formation of the disulfide anion from the carbanion. PMID:27531007

  3. 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...

  4. Prophylactic vaccines mimic synthetic CpG oligonucleotides in their ability to modulate immune responses

    NARCIS (Netherlands)

    Vries, I.J.M. de; Tel, J.; Benitez-Ribas, D.; Torensma, R.; Figdor, C.G.

    2011-01-01

    Synthetic oligonucleotide ligands that bind to toll-like receptors are known to modulate the immune response via the activation of antigen presenting cells, and were therefore proposed as a novel form of vaccine adjuvant. Clinical-grade they are, however, not readily available. Here, we show that co

  5. Refinement of antisense oligonucleotide mediated exon skipping as therapy for Duchenne muscular dystrophy

    NARCIS (Netherlands)

    Heemskerk, Johannes Antonius

    2011-01-01

    In recent years, modulation of mRNA has emerged as a promising therapeutic tool. For instance, in the field of neuromuscular disorders therapeutic strategies are being developed for several diseases, including antisense oligonucleotide (AON) mediated exon skipping for Duchenne Muscular Dystrophy (DM

  6. Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays

    NARCIS (Netherlands)

    Urakawa, H.; Fantroussi, El S.; Smidt, H.; Smoot, J.C.; Tribou, E.H.; Kelly, J.J.; Noble, P.A.; Stahl, D.A.

    2003-01-01

    The discrimination between perfect-match and single-base-pair-mismatched nucleic acid duplexes was investigated by using oligonucleotide DNA microarrays and nonequilibrium dissociation rates (melting profiles). DNA and RNA versions of two synthetic targets corresponding to the 16S rRNA sequences of

  7. 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 2'-O-met

  8. Oligo switches: photoresponsive oligonucleotide conjugates by solid-supported click chemistry

    OpenAIRE

    Freeman, Colin; Vyle, Joseph S; Heaney, Frances

    2013-01-01

    Photoresponsive oligonucleotides (ONs) incorporating isoxazole-linked azobenzene (AB) moieties were prepared by resin-supported nitrile oxide-alkyne cycloaddition (NOAC) chemistry. The thermal and photochromic properties of the modified ONs were significantly influenced by the extent of π-conjugation between the isoxazole and the AB modules

  9. Cell penetrating peptide delivery of splice directing oligonucleotides as a treatment for Duchenne muscular dystrophy.

    Science.gov (United States)

    Betts, Corinne A; Wood, Matthew J A

    2013-01-01

    Duchenne muscular dystrophy is a severe, X-linked muscle wasting disorder caused by the absence of an integral structural protein called dystrophin. This is caused by mutations or deletions in the dystrophin gene which disrupt the reading frame, thereby halting the production of a functional protein. A number of potential therapies have been investigated for the treatment of this disease including utrophin upregulation, 'stop-codon read through' aminoglycosides and adeno-associated virus gene replacement as well as stem cell therapy. However, the most promising treatment to date is the use of antisense oligonucleotides which cause exon skipping by binding to a specific mRNA sequence, skipping the desired exon, thereby restoring the reading frame and producing a truncated yet functional protein. The results from recent 2'OMePS and morpholino clinical trials have renewed hope for Duchenne patients; however in vivo studies in a mouse model, mdx, have revealed low systemic distribution and poor delivery of oligonucleotides to affected tissues such as the brain and heart. However a variety of cell penetrating peptides directly conjugated to antisense oligonucleotides have been shown to enhance delivery in Duchenne model systems with improved systemic distribution and greater efficacy compared to 'naked' antisense oligonucleotides. These cell penetrating peptides, combined with an optimised dose and dosing regimen, as well as thorough toxicity profile have the potential to be developed into a promising treatment which may be progressed to clinical trial. PMID:23140454

  10. An oral oligonucleotide delivery system based on a thiolated polymer: Development and in vitro evaluation.

    Science.gov (United States)

    Martien, Ronny; Hoyer, Herbert; Perera, Glen; Schnürch, Andreas Bernkop

    2011-08-01

    The purpose of this study was to develop and evaluate an oral oligonucleotide delivery system based on a thiolated polymer/reduced glutathione (GSH) system providing a protective effect toward nucleases and permeation enhancement. A polycarbophil-cysteine conjugate (PCP-Cys) was synthesized. Enzymatic degradation of a model oligonucleotide by DNase I and within freshly collected intestinal fluid was investigated in the absence and presence of PCP-Cys. Permeation studies with PCP-Cys/GSH versus control were performed in vitro on Caco-2 cell monolayers and ex vivo on rat intestinal mucosa. PCP-Cys displayed 223 ± 13.8 μmol thiol groups per gram polymer. After 4h, 61% of the free oligonucleotides were degraded by DNase I and 80% within intestinal fluid. In contrast, less than 41% (DNase I) and 60% (intestinal fluid) were degraded in the presence of 0.02% (m/v) PCP-Cys. Permeation studies revealed an 8-fold (Caco-2) and 10-fold (intestinal mucosa) increase in apparent permeability compared to buffer control. Hence, this PCP-Cys/GSH system might be a promising tool for the oral administration of oligonucleotides as it allows a significant protection toward degrading enzymes and facilitates their transport across intestinal membranes.

  11. Pd0-Catalyzed Methyl Transfer on Nucleosides and Oligonucleotides, Envisaged as a PET Tracer

    Directory of Open Access Journals (Sweden)

    Eric Fouquet

    2013-11-01

    Full Text Available The methyl transfer reaction from activated monomethyltin, via a modified Stille coupling reaction, was studied under “ligandless” conditions on fully deprotected 5'-modified nucleosides and one dinucleotide. The reaction was optimized to proceed in a few minutes and quantitative yield, even under dilute conditions, thus affording a rapid and efficient new method for oligonucleotide labelling with carbon-11.

  12. 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. PMID:22914677

  13. 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 incorporat...

  14. Stable gene targeting in human cells using single-strand oligonucleotides with modified bases.

    Directory of Open Access Journals (Sweden)

    Xavier Rios

    Full Text Available Recent advances allow multiplexed genome engineering in E. coli, employing easily designed oligonucleotides to edit multiple loci simultaneously. A similar technology in human cells would greatly expedite functional genomics, both by enhancing our ability to test how individual variants such as single nucleotide polymorphisms (SNPs are related to specific phenotypes, and potentially allowing simultaneous mutation of multiple loci. However, oligo-mediated targeting of human cells is currently limited by low targeting efficiencies and low survival of modified cells. Using a HeLa-based EGFP-rescue reporter system we show that use of modified base analogs can increase targeting efficiency, in part by avoiding the mismatch repair machinery. We investigate the effects of oligonucleotide toxicity and find a strong correlation between the number of phosphorothioate bonds and toxicity. Stably EGFP-corrected cells were generated at a frequency of ~0.05% with an optimized oligonucleotide design combining modified bases and reduced number of phosphorothioate bonds. We provide evidence from comparative RNA-seq analysis suggesting cellular immunity induced by the oligonucleotides might contribute to the low viability of oligo-corrected cells. Further optimization of this method should allow rapid and scalable genome engineering in human cells.

  15. 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.

  16. Effects of antisense oligonucleotides on the expression of macrophage migration inhibitory factor on macrophages

    Institute of Scientific and Technical Information of China (English)

    WEIYINGCHEN; GUANGRANLI; XUEQINGYU; XIAOYANLI; XIAOYANG

    2005-01-01

    To investigate the effects of antisense oligonucleotides on the expression of macrophage migration inhibitory factor (MIF) on macrophages, the mouse phosphorothioate oligonucleotides were designed and synthesized with the sequences of antisense, 5'-TACGGATACAAGTAGCAC-3';Sense, 5'-ATGC-CTATGTTCATCGTG-3';Missense, 5'-CTCTCAGACTCGATCTGT-3'. These phosphorothioate oligonucleotides were then transfected into cultured macrophages (RAW264.7) by luciferase vector, and the transfected macrophages were incubated with Lipopolysaccharide (LPS) (1 ng/ml) for various periods of times and collected afterwards. The content of MIF protein in the cultural supernatants was determined by ELISA, cellular RNA extracted and the expression of MIF mRNA was examined by RT-PCR analysis.The experimental results showed that LPS could induce a time-dependent specific expression of MIF on macrophages, in which the MIF mRNA in cells and the MIF protein in cultural supernatants appeared after 3 h and reached their highest concentration at 9-12 h after LPS stimulation. The levels of mRNA and proteins in the macrophages treated with antisense olignucleotides were decreased significantly after stimulation with LPS in comparison with that of stimulation with LPS alone or with that with LPS plus sense or missense oligonucleotides.There were no differences among those without LPS stimulation. It is concluded that macrophages stimulated with LPS express MIF, and the antisense olignucleotides of MIF inhibitthe expression of MIF mRNA as well as the secretion of MIF proteins in macrophages.

  17. PCSK9 LNA antisense oligonucleotides induce sustained reduction of LDL cholesterol in nonhuman primates.

    Science.gov (United States)

    Lindholm, Marie W; Elmén, Joacim; Fisker, Niels; Hansen, Henrik F; Persson, Robert; Møller, Marianne R; Rosenbohm, Christoph; Ørum, Henrik; Straarup, Ellen M; Koch, Troels

    2012-02-01

    Proprotein convertase subtilisin/kexin type 9 (PCSK9) has emerged as a therapeutic target for the reduction of low-density lipoprotein cholesterol (LDL-C). PCSK9 increases the degradation of the LDL receptor, resulting in high LDL-C in individuals with high PCSK9 activity. Here, we show that two locked nucleic acid (LNA) antisense oligonucleotides targeting PCSK9 produce sustained reduction of LDL-C in nonhuman primates after a loading dose (20 mg/kg) and four weekly maintenance doses (5 mg/kg). PCSK9 messenger RNA (mRNA) and serum PCSK9 protein were reduced by 85% which resulted in a 50% reduction in circulating LDL-C. Serum total cholesterol (TC) levels were reduced to the same extent as LDL-C with no reduction in high-density lipoprotein levels, demonstrating a specific pharmacological effect on LDL-C. The reduction in hepatic PCSK9 mRNA correlated with liver LNA oligonucleotide content. This verified that anti-PCSK9 LNA oligonucleotides regulated LDL-C through an antisense mechanism. The compounds were well tolerated with no observed effects on toxicological parameters (liver and kidney histology, alanine aminotransferase, aspartate aminotransferase, urea, and creatinine). The pharmacologic evidence and initial safety profile of the compounds used in this study indicate that LNA antisense oligonucleotides targeting PCSK9 provide a viable therapeutic strategy and are potential complements to statins in managing high LDL-C.

  18. Oligonucleotide array outperforms SNP array on formalin-fixed paraffin-embedded clinical samples.

    Science.gov (United States)

    Nasri, Soroush; Anjomshoaa, Ahmad; Song, Sarah; Guilford, Parry; McNoe, Les; Black, Michael; Phillips, Vicky; Reeve, Anthony; Humar, Bostjan

    2010-04-01

    Compromised quality of formalin-fixed paraffin-embedded (FFPE)-derived DNA has compounded the use of archival specimens for array-based genomic studies. Recent technological advances have led to first successes in this field; however, there is currently no general agreement on the most suitable platform for the array-based analysis of FFPE DNA. In this study, FFPE and matched fresh-frozen (FF) specimens were separately analyzed with Affymetrix single nucleotide polymorphism (SNP) 6.0 and Agilent 4x44K oligonucleotide arrays to compare the genomic profiles from the two tissue sources and to assess the relative performance of the two platforms on FFPE material. Genomic DNA was extracted from matched FFPE-FF pairs of normal intestinal epithelium from four patients and were applied to the SNP and oligonucleotide platforms according to the manufacturer-recommended protocols. On the Affymetrix platform, a substantial increase in apparent copy number alterations was observed in all FFPE tissues relative to their matched FF counterparts. In contrast, FFPE and matched FF genomic profiles obtained via the Agilent platform were very similar. Both the SNP and the oligonucleotide platform performed comparably on FF material. This study demonstrates that Agilent oligonucleotide array comparative genomic hybridization generates reliable results from FFPE extracted DNA, whereas the Affymetrix SNP-based array seems less suitable for the analysis of FFPE material.

  19. Tetrahedron-structured DNA and functional oligonucleotide for construction of an electrochemical DNA-based biosensor.

    Science.gov (United States)

    Bu, Nan-Nan; Tang, Chun-Xia; He, Xi-Wen; Yin, Xue-Bo

    2011-07-21

    Tetrahedron-structured DNA (ts-DNA) in combination with a functionalized oligonucleotide was used to develop a "turn-on" biosensor for Hg(2+) ions. The ts-DNA provided an improved sensitivity and was used to block the active sites.

  20. In situ entry of oligonucleotides into brain cells can occur through a nucleic acid channel

    NARCIS (Netherlands)

    Shi, Fuxin; Gounko, Natasha V.; Wang, Xiaoqin; Ronken, Eric; Hoekstra, Dick

    2007-01-01

    Brain tissue has become a challenging therapeutic target, in part because of failure of conventional treatments of brain tumors and a gradually increasing number of neurodegenerative diseases. Because antisense oligonucleotides are readily internalized by neuronal cells in culture, these compounds c

  1. Obstructive Effects of Ultrasonic Microbubble Intensifier on CHG-5 Cell with Survivin Antisense Oligonucleotides Transfection

    Institute of Scientific and Technical Information of China (English)

    CAO Hong-ying; CAO You-de; WANG Zhi-gang; LI Pan

    2008-01-01

    Objective:To study the effects on human glioma cell line CHG-5 by ultrasonic microbubble intensifier with survivin antisense oligonucleotides (ASODN)transfection. Methods: Antisense oligonucleotides targeting survivin mRNA was designed and synthesized.Four regimen groups were designed,group A:survivin antisense oligonucleotides transfected with ultrasonic microbubble intensifier combined with ultrasound irradiation,group B: survivin antisense oligonucleotides transfected with lipofectamine combined with ultrasound irradiation,group C:survivin antisense oligonucelotides with lipofectamine transfection.group D:blank control.The expression changes of surviving protein were measured by immunohistochemical staining and Western blotting,and MTr assay was used to measure the changes of proliferation.Results:Survivin protein expression in group A was decreased significantly in human glioma cell line CHG-5 than other groups(P<0.05),and the proliferating rate of CHG-5 in group A was also significantly inhibited(P<0.05).Conclusion:Ultrasonic microbubble intensifier transfection combined with ultrasound irradiation is a promising method in gene transfection effectively and noninvasively.

  2. A highly sensitive and selective viral protein detection method based on RNA oligonucleotide nanoparticle

    Directory of Open Access Journals (Sweden)

    Changhyun Roh

    2010-04-01

    Full Text Available Changhyun Roh1, Ho-Young Lee2, Sang-Eun Kim2, Sung-Kee Jo11Radiation Research Division for Biotechnology, Advanced Radiation Technology Institute (ARTI, Korea Atomic Energy Research Institute (KAERI, Sinjeong-dong, Jeongeup, Jeonbuk, South Korea; 2Department of Nuclear Medicine, College of Medicine, Seoul National University, South KoreaAbstract: Globally, approximately 170 million people (representing approximately 3% of the population worldwide, are infected with hepatitis C virus (HCV and at risk of serious liver disease, including chronic hepatitis. We propose a new quantum dots (QDs-supported RNA oligonucleotide approach for the specific and sensitive detection of viral protein using a biochip. This method was developed by immobilizing a HCV nonstructural protein 5B (NS5B on the surface of a glass chip via the formation of a covalent bond between an amine protein group and a ProLinkerTM glass chip. The QDs-supported RNA oligonucleotide was conjugated via an amide formation reaction from coupling of a 5′-end-amine-modified RNA oligonucleotide on the surface of QDs displaying carboxyl groups via standard EDC coupling. The QDs-conjugated RNA oligonucleotide was interacted to immobilized viral protein NS5B on the biochip. The detection is based on the variation of signal of QDs-supported RNA oligonucleotide bound on an immobilized biochip. It was demonstrated that the value of the signal has a linear relationship with concentrations of the HCV NS5B viral protein in the 1 μg mL-1 to 1 ng mL-1 range with a detection limit of 1 ng mL-1. The major advantages of this RNA-oligonucleotide nanoparticle assay are its good specificity, ease of performance, and ability to perform one-spot monitoring. The proposed method could be used as a general method of HCV detection and is expected to be applicable to other types of diseases as well.Keywords: hepatitis C virus, viral protein, RNA oligonucleotide, quantum dots, biochip

  3. Internal conflicts of Emily Dickinson-A study of the images of boat and sea in Dickinson’s poems

    Institute of Scientific and Technical Information of China (English)

    WAN Hai-yan

    2014-01-01

    The peculiar images, the boat and the sea, often recur in the poems of Emily Dickinson, the great American poet, which well reflect her internal conflicts, the conflicts between being an autonomous woman and being a passionate yet submissive wom-an. In her poems, the sea is a symbol of the male-dominated society or an individual man. While the little boat is the epitome of Dickinson:sometimes it wants to be strong-willed and clear of its destination, sometimes it just wants to moor in the sea and en-joy the calmness. The paper tends to reveal the psychological struggle of Emily Dickinson and show the whole image of her as an individual through the analysis of the images of boat and sea in Dickinson’s poems.

  4. Modified technique of using conventional slider boat for liquid phase epitaxy of silicon for solar cell application

    Indian Academy of Sciences (India)

    D Majumdar; S Chatterjee; U Gangopadhyay; H Saha

    2003-10-01

    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 silicon substrate resulting in poor nucleation, melt removal from the growth substrate and saturation wafer associated with LPE in this technique are practically eliminated using sandwich method with simple modifications of the boat and the method of growth. Some experimental studies on the effect of different surface preparations of growth substrate are also reported. Growth results are shown and discussed. Further, improvization of slider boat to facilitate better study of growth parameters is suggested in the line of modification already carried out.

  5. Influence of boat noises on escape behaviour of white-spotted eagle ray Aetobatus ocellatus at Moorea Island (French Polynesia).

    Science.gov (United States)

    Berthe, Cecile; Lecchini, David

    2016-02-01

    The present study tested different sounds that could disturb eagle rays (Aetobatus ocellatus) during their foraging activities at Moorea, French Polynesia. Results showed that artificial white sound and single-frequency tones (40 Hz, 600 Hz or 1 kHz) did not have an effect on rays (at least 90% of rays continued to forage over sand), while playbacks of boat motor sound significantly disturbed rays during foraging activity (60% exhibited an escape behaviour). Overall, our study highlighted the negative effect of boat noises on the foraging activity of eagle rays. These noises produced by boat traffic could, however, have some positive effects for marine aquaculture if they could be used as a deterrent to repel the eagle rays, main predators of the pearl oysters.

  6. 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.)

  7. Influence of boat noises on escape behaviour of white-spotted eagle ray Aetobatus ocellatus at Moorea Island (French Polynesia).

    Science.gov (United States)

    Berthe, Cecile; Lecchini, David

    2016-02-01

    The present study tested different sounds that could disturb eagle rays (Aetobatus ocellatus) during their foraging activities at Moorea, French Polynesia. Results showed that artificial white sound and single-frequency tones (40 Hz, 600 Hz or 1 kHz) did not have an effect on rays (at least 90% of rays continued to forage over sand), while playbacks of boat motor sound significantly disturbed rays during foraging activity (60% exhibited an escape behaviour). Overall, our study highlighted the negative effect of boat noises on the foraging activity of eagle rays. These noises produced by boat traffic could, however, have some positive effects for marine aquaculture if they could be used as a deterrent to repel the eagle rays, main predators of the pearl oysters. PMID:26857089

  8. 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.

  9. Coupling strategies for the synthesis of Peptide-oligonucleotide conjugates for patterned synthetic biomineralization.

    Science.gov (United States)

    Carter, Joshua D; Labean, Thomas H

    2011-01-01

    This work describes preparation strategies for peptide-oligonucleotide conjugates that combine the self-assembling behavior of DNA oligonucleotides with the molecular recognition capabilities of peptides. The syntheses include a solution-phase fragment coupling reaction and a solid-phase fragment coupling strategy where the oligonucleotide has been immobilized on DEAE Sepharose. The yield of four coupling reagents is evaluated, two reagents in water, EDC (1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride) and DMTMM (4-(4,6-dimethoxy[1,3,5]triazin-2-yl)-4-methyl-morpholinium chloride), and two in dimethylformamide (DMF), PyBOP ((Benzotriazol-1-yloxy) tripyrrolidinophosphonium hexafluorophosphate) and HBTU (O-benzotriazole-N,N,N',N'-tetramethyluronium hexafluorophosphate), while the oligonucleotide fragment is either in solution or immobilized on DEAE. These coupling strategies rely on an unprotected 5' amino linker on the oligonucleotide reacting with the peptide C-terminus. The peptide, selected from a combinatorial library for its gold-binding behavior, was 12 amino acids long with an N-terminus acetyl cap. Formation of the conjugates was confirmed by gel electrophoresis and mass spectrometry while molecular recognition functionality of the peptide portion was verified using atomic force microscopy. Solution-phase yields were superior to their solid-phase counterparts. EDC resulted in the highest yield for both solution-phase (95%) and solid-phase strategies (24%), while the DMF-based reagents, PyBOP and HBTU, resulted in low yields with reduced recovery. All recoverable conjugates demonstrated gold nanoparticle templating capability. PMID:22007290

  10. Coupling Strategies for the Synthesis of Peptide-Oligonucleotide Conjugates for Patterned Synthetic Biomineralization

    Directory of Open Access Journals (Sweden)

    Joshua D. Carter

    2011-01-01

    Full Text Available This work describes preparation strategies for peptide-oligonucleotide conjugates that combine the self-assembling behavior of DNA oligonucleotides with the molecular recognition capabilities of peptides. The syntheses include a solution-phase fragment coupling reaction and a solid-phase fragment coupling strategy where the oligonucleotide has been immobilized on DEAE Sepharose. The yield of four coupling reagents is evaluated, two reagents in water, EDC (1-ethyl-3-(3-dimethylaminopropyl carbodiimide hydrochloride and DMTMM (4-(4,6-dimethoxy[1,3,5]triazin-2-yl-4-methyl-morpholinium chloride, and two in dimethylformamide (DMF, PyBOP ((Benzotriazol-1-yloxy tripyrrolidinophosphonium hexafluorophosphate and HBTU (O-benzotriazole-N,N,N′,N′-tetramethyluronium hexafluorophosphate, while the oligonucleotide fragment is either in solution or immobilized on DEAE. These coupling strategies rely on an unprotected 5′ amino linker on the oligonucleotide reacting with the peptide C-terminus. The peptide, selected from a combinatorial library for its gold-binding behavior, was 12 amino acids long with an N-terminus acetyl cap. Formation of the conjugates was confirmed by gel electrophoresis and mass spectrometry while molecular recognition functionality of the peptide portion was verified using atomic force microscopy. Solution-phase yields were superior to their solid-phase counterparts. EDC resulted in the highest yield for both solution-phase (95% and solid-phase strategies (24%, while the DMF-based reagents, PyBOP and HBTU, resulted in low yields with reduced recovery. All recoverable conjugates demonstrated gold nanoparticle templating capability.

  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. Nuclear multifragmentation: Basic concepts

    Indian Academy of Sciences (India)

    G Chaudhuri; S Mallik; S Das Gupta

    2014-05-01

    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 multiplicity, isotopic distribution and isoscaling. Extension of canonical thermodynamical model to a projectile fragmentation model is outlined. Application of the projectile fragmentation model for calculating average number of intermediate mass fragments and the average size of the largest cluster at different bound, differential charge distribution and cross-section of neutron-rich nuclei of different projectile fragmentation reactions at different energies are described. Application of nuclear multifragmentation reaction in basic research as well as in other domains is outlined.

  15. 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...

  16. Comparative analysis of structure of sporting preparation in a boat-racing, rowing on kayaks and canoe

    Directory of Open Access Journals (Sweden)

    Zhirnov A.V.

    2011-07-01

    Full Text Available In the article information of expert estimation of different types of preparation is presented in boating. On the basis of analysis of literary sources the structure of the sporting training is certain. Principles of application of quantitative methods of estimation of quality are considered in sport. The most priority types of sporting preparation are exposed in different disciplines of rowing. On the basis of opinions of experts the comparative analysis of influence on the sporting result of different types of preparation is conducted in a boat-racing and rowing on kayaks and canoe.

  17. Decontamination: back to basics.

    Science.gov (United States)

    Meredith, Susan J; Sjorgen, Geoff

    2008-07-01

    My invitation from this Journal's Editor, Felicia Cox, to provide a paper for this themed issue, included the sentence 'I was wondering if you or a colleague would like to contribute a back to basics article on the relevant standards and guidelines for decontamination, including what is compliance?'. The reason it is so interesting to me is that the term 'back to basics' implies reverting to a simpler time in life - when by just sticking to the rules, life became easier. However, with decontamination this is not actually true.

  18. 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

  19. 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

  20. 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''.

  1. A regional waterway management system for balancing recreational boating and resource protection.

    Science.gov (United States)

    Swett, Robert A; Listowski, Charles; Fry, Douglas; Boutelle, Stephen; Fann, David

    2009-06-01

    Florida's coasts have been transformed over the past three decades as population growth and unprecedented demand for individual shore access to bays and estuaries led to the creation of residential canal developments. Thousands of miles of channels and basins were dredged as a by-product of this urbanization process. The navigable waterways that resulted are now being stressed by increasing boat traffic and canal-side activities. Recognizing their common goal to preserve the recreational and ecological value of southwest Florida waterways, the Florida Department of Environmental Protection, the four-county West Coast Inland Navigation District, and the University of Florida Sea Grant College Program signed a Memorandum of Agreement. The signatories agreed to develop a science-based Regional Waterway Management System (RWMS), which is a new approach to waterway planning and permitting based on carefully mapped channel depths, a census of actual boat populations, and the spatial extent of natural resources. The RWMS provides a comprehensive, regional overview of channel conditions and the geographic distribution and severity of existing impediments to safe navigation and resource protection. RWMS information and analyses result in regional-scale permitting to accommodate water-dependent uses while minimizing environmental impacts and reducing public expenditures. Compared with traditional approaches to waterway management, the science-based RWMS is relatively unbiased, objective, transparent, ecologically sound, and fiscally prudent. PMID:19020927

  2. 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.

  3. 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.

  4. Conformation of hindered piperidines: Spectroscopic evidence for contribution of boat conformations

    Indian Academy of Sciences (India)

    A Thangamani; J Jayabharathi; A Manimekalai

    2010-07-01

    High resolution 1H and 13C NMR resonance assignments and conformational assignments were carried out for four (3)-benzyl-(2),(6)-bis(aryl)piperidin-4-ones 1-4 and their four -nitroso-(3)-benzyl-(2),(6)-bis(aryl)piperidin-4-ones 5-8. In addition to conventional 1D NMR methods, 2D shiftcorrelated NMR techniques (1H-1H COSY and 1H-13C COSY) were used for signal assignments. At room temperature the (3)-benzyl-(2),(6)-bis(aryl)piperidin-4-ones 1-4 exist in only one isomeric form whereas their -nitroso derivatives 5-8 exist in two isomeric forms. The preferred conformations of both the isomeric forms of nitrosamines were determined by comparison of the spectral data with those of the corresponding parent amines 1-4 and with the aid of substituent parameters. The results indicate the presence of an equilibrium mixture of boat forms B1 and B2 for Z isomers of 5-8. For the E isomers of 5-8, boat form B1 is predicted to be the major conformer. The piperidin-4-ones 1-4 exist in normal chair conformations with equatorial orientations of all the substituents.

  5. Hydrodynamics of a self-propelled camphor boat at the air-water interface

    Science.gov (United States)

    Akella, Sathish; Singh, Dhiraj; Singh, Ravi; Bandi, Mahesh

    2015-11-01

    A camphor tablet, when placed at the air-water interface undergoes sublimation and camphor vapour spreads radially outwards across the surface due to Marangoni forces. This steady camphor influx from tablet onto the air-water interface is balanced by the camphor outflux due to evaporation. When spontaneous fluctuations in evaporation break the axial symmetry of Marangoni force acting radially outwards, the camphor tablet is propelled like a boat along the water surface. We report experiments on the hydrodynamics of a self-propelled camphor boat at air-water interfaces. We observe three different modes of motion, namely continuous, harmonic and periodic, due to the volatile nature of camphor. We explain these modes in terms of ratio of two time-scales: the time-scale over which viscous forces are dominant over the Marangoni forces (τη) and the time-scale over which Marangoni forces are dominant over the viscous forces (τσ). The continuous, harmonic and periodic motions are observed when τη /τσ ~ 1 , τη /τσ >= 1 and τη /τσ >> 1 respectively. Experimentally, the ratio of the time scales is varied by changing the interfacial tension of the air-water interface using Sodium Dodecyl Sulfate. This work was supported by the Collective Interactions Unit, OIST Graduate University.

  6. Effect of CD44 Suppression by Antisense Oligonucleotide on Attachment of Human Trabecular Meshwork Cells to HA

    Institute of Scientific and Technical Information of China (English)

    李中国; 张虹

    2004-01-01

    The effects of suppression of CD44 by CD44-specific antisense oligonucleotide on attachment of human trabecular meshwork cells to hyaluronic acid (HA) were observed and the possible relationship between CD44 and primary open-angle glaucoma (POAG) investigated. CD44-specific antisense oligonucleotide was delivered with cationic lipid to cultured human trabecular meshwork cells. The expression of CD44 suppressed by CD44-specific antisense oligonucleotide was detected by RT-PCR and Western blotting. The effect of CD44 suppression by specific antisense oligonucleotide on attachment of trabecular meshwork cells to HA was measured by MTT assay. Results showed that expression of CD44 was suppressed by CD4, specific antisense oligonucleotide. Antisense oligonucleotide also suppressed the adhesion of human trabecular meshwork cells to HA in a concentration dependent manner. It was concluded that attachment of human trabecular meshwork cells to HA was decreased when CD44 was suppressed by specific antisense oligonucleotide. CD44might play a role in pathogenesis of POAG by affecting the adhesion of trabecular meshwork cells to HA.

  7. 红船精神在中国革命精神系统中的地位和作用%Position and Function of the Red Boat Spirit in China's Revolutionary Spirit System

    Institute of Scientific and Technical Information of China (English)

    钟昌斌

    2015-01-01

    红船精神是中国革命精神之源,在中国革命精神系统中具有独特的地位和作用。从构成上看,红船精神把马克思主义科学理论因子作为思想内核,为推动中国革命精神始终走在先进思想前列提供了前提条件;继承并纳入中华传统文化的优良成分,奠定了先进的中国革命精神系统的保障基础。从作用看,红船精神是流淌在中国共产党血管中的基本能量,在当今不断发展的中国革命精神研究中充分体现出其特点,为推进中国革命精神系统化研究做出了贡献。从结果看,红船精神在推动中国革命精神建设和中国革命发展中谱写了恢弘的篇章。%The “Red Boat Spirit”,the source of the spirit of the Chinese revolution,holds a unique position in China's revolutionary spirit system.In view of its constitution ,the “Red Boat Spirit”,with the scientific theory of Marxism as its ideological core,provided preconditions to secure the Chinese revolutionary spirit in an advanced state;it inherited and brought in fine ingredients of traditional Chinese culture,and laid a guarantee foundation for the advanced Chinese revolutionary spirit system.In view of its function,the Red Boat Spirit is the basic energy flowing in the blood vessels of the CPC,fully reflecting its characteristics in today's evolving re-search of the Chinese revolution spirit,and contributing to the research of Chinese revolutionary spirit system. Concerning the consequence, the Red Boat Spirit has composed a grand chapter in promoting China's revolutionary spirit construction and the development of Chinese revolution.

  8. Designing a Two-Phase BLDC Motor and Finite-Element Analysis of Designing a Controller in Order to Manoeuvre High-Speed Boats in Marine Turbulences

    Directory of Open Access Journals (Sweden)

    Mehrdad Jafarboland

    2014-01-01

    Full Text Available High speed boats are small kind of boats which are piloted with boatman.These boats are usually used in strategic commissions like military which fast speeds and good manoeuvrability are of essential importance.Rough sea path, marine turbulences and multi input multi output nonlinear dynamical model of this boats,make it very difficult to pilot and manoeuvre them.in this paper,.two controller are designed and proposed for pursuing desired path and manoeuvring fast speeds.Fuzzy controller is compared with the result of PID controller. Simulation results also indicate that these proposed controllers have suitable responses and can pilot the boat in the best manner.

  9. Simple Method To Prepare Oligonucleotide-Conjugated Antibodies and Its Application in Multiplex Protein Detection in Single Cells.

    Science.gov (United States)

    Gong, Haibiao; Holcomb, Ilona; Ooi, Aik; Wang, Xiaohui; Majonis, Daniel; Unger, Marc A; Ramakrishnan, Ramesh

    2016-01-20

    The diversity of nucleic acid sequences enables genomics studies in a highly multiplexed format. Since multiplex protein detection is still a challenge, it would be useful to use genomics tools for this purpose. This can be accomplished by conjugating specific oligonucleotides to antibodies. Upon binding of the oligonucleotide-conjugated antibodies to their targets, the protein levels can be converted to oligonucleotide levels. In this report we describe a simple method for preparing oligonucleotide-conjugated antibodies and discuss this method's application in oligonucleotide extension reaction (OER) for multiplex protein detection. Conjugation is based on strain-promoted alkyne-azide cycloaddition (the Cu-free click reaction), in which the antibody is activated with a dibenzocyclooctyne (DBCO) moiety and subsequently linked covalently with an azide-modified oligonucleotide. In the functional test, the reaction conditions and purification processes were optimized to achieve maximum yield and best performance. The OER assay employs a pair of antibody binders (two antibodies, each conjugated with its own oligonucleotide) developed for each protein target. The two oligonucleotides contain unique six-base complementary regions at their 3' prime ends to allow annealing and extension by DNA synthesis enzymes to form a DNA template. Following preamplification, the DNA template is detected by qPCR. Distinct oligonucleotide sequences are assigned to different antibody binders to enable multiplex protein detection. When tested using recombinant proteins, some antibody binders, such as those specific to CSTB, MET, EpCAM, and CASP3, had dynamic ranges of 5-6 logs. The antibody binders were also used in a multiplexed format in OER assays, and the binders successfully detected their protein targets in cell lysates, and in single cells in combination with the C1 system. This click reaction-based antibody conjugation procedure is cost-effective, needs minimal hands-on time, and

  10. Basic Drafting: Book Two.

    Science.gov (United States)

    Davis, Ronald; And Others

    The second of a two-book course in drafting, this manual consists of 12 topics in the following units: sketching techniques, geometric constructions, orthographic views, dimensioning procedures, basic tolerancing, auxiliary views, sectional views, inking tools and techniques, axonometrics, oblique, perspective, and computer-aided drafting.…

  11. Basic Drafting: Book One.

    Science.gov (United States)

    Davis, Ronald; And Others

    The first of a two-book course in drafting, this manual consists of 13 topics in the following units: introduction to drafting, general safety, basic tools and lines, major equipment, applying for a job, media, lettering, reproduction, drawing sheet layout, architect's scale usage, civil engineer's scale usage, mechanical engineer's scale usage,…

  12. Basic Microfluidics Theory

    DEFF Research Database (Denmark)

    Svendsen, Winnie Edith

    2015-01-01

    ,000 m−1, which is a huge difference and has a large impact on flow behavior. In this chapter the basic microfluidic theory will be presented, enabling the reader to gain a comprehensive understanding of how liquids behave at the microscale, enough to be able to engage in design of micro systems...

  13. 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.

  14. 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.

  15. Hindi Basic Reader.

    Science.gov (United States)

    Harter, J. Martin; And Others

    This reader is intended to accompany the Basic Course in Spoken Hindi. Following an outline of the Devanagari script, 20 lessons are presented. Each consists of a reading selection, several illustrative sentences in English and Hindi, and a series of questions. Most of the reading selections were adapted from the magazine "Bal-Bharati." (RM)

  16. FULA BASIC COURSE.

    Science.gov (United States)

    SWIFT, LLOYD B.; AND OTHERS

    THIS BEGINNING COURSE IS AN INTRODUCTION TO FULA (KNOWN VARIOUSLY AS FULANI, FUL, PEUL, OR PHEUL), A NIGER-CONGO LANGUAGE SPOKEN THROUGHOUT THE GRASSLAND AREAS OF WEST AFRICA FROM THE ATLANTIC TO CAMEROUN. THE TEXT IS ONE OF A SERIES OF SHORT BASIC COURSES IN SELECTED AFRICAN LANGUAGES BEING PREPARED BY THE FOREIGN SERVICE INSTITUTE. IT IS…

  17. Basic bioreactor design.

    NARCIS (Netherlands)

    Riet, van 't K.; Tramper, J.

    1991-01-01

    Based on a graduate course in biochemical engineering, provides the basic knowledge needed for the efficient design of bioreactors and the relevant principles and data for practical process engineering, with an emphasis on enzyme reactors and aerated reactors for microorganisms. Includes exercises.

  18. Portuguese Basic Courses.

    Science.gov (United States)

    Defense Language Inst., Washington, DC.

    This basic course in Brazilian Portuguese consists of 75 lessons in six volumes. Volume I is in two parts, with the dialogs, questions and exercises presented in Portuguese in the first part, and the intonation patterns and English translations presented in the second. The general format follows the Defense Language Institute format, employing…

  19. IGBO, BASIC COURSE.

    Science.gov (United States)

    SWIFT, LLOYD B.; AND OTHERS

    A BASIC COURSE WAS PREPARED ON THE SPEECH OF TWO MEMBERS OF THE EZINEHITE GROUP OF IGBOS IN EASTERN NIGERIA. THE ESSENTIAL PHONOLOGICAL AND GRAMMATICAL STRUCTURES OF IGBO ARE PRESENTED WITHIN A SMALL VOCABULARY OF APPROXIMATELY 600 ITEMS. THE COURSE MATERIALS CONSIST OF (1) TONE DRILLS, (2) 24 UNITS OF DIALOGS, NOTES, AND DRILLS, (3) SIX UNITS OF…

  20. 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.