Effectiveness of eye armor during blast loading.

Science.gov (United States)

Bailoor, Shantanu; Bhardwaj, Rajneesh; Nguyen, Thao D

2015-11-01

Ocular trauma is one of the most common types of combat injuries resulting from the interaction of military personnel with improvised explosive devices. Ocular blast injury mechanisms are complex, and trauma may occur through various injury mechanisms. However, primary blast injuries (PBI) are an important cause of ocular trauma that may go unnoticed and result in significant damage to internal ocular tissues and visual impairment. Further, the effectiveness of commonly employed eye armor, designed for ballistic and laser protection, in lessening the severity of adverse blast overpressures (BOP) is unknown. In this paper, we employed a three-dimensional (3D) fluid-structure interaction computational model for assessing effectiveness of the eye armor during blast loading on human eyes and validated results against free field blast measurements by Bentz and Grimm (2013). Numerical simulations show that the blast waves focused on the ocular region because of reflections from surrounding facial features and resulted in considerable increase in BOP. We evaluated the effectiveness of spectacles and goggles in mitigating the pressure loading using the computational model. Our results corroborate experimental measurements showing that the goggles were more effective than spectacles in mitigating BOP loading on the eye. Numerical results confirmed that the goggles significantly reduced blast wave penetration in the space between the armor and the eyes and provided larger clearance space for blast wave expansion after penetration than the spectacles. The spectacles as well as the goggles were more effective in reducing reflected BOP at higher charge mass because of the larger decrease in dynamic pressures after the impact. The goggles provided greater benefit of reducing the peak pressure than the spectacles for lower charge mass. However, the goggles resulted in moderate, sustained elevated pressure loading on the eye, that became 50-100% larger than the pressure loading

ALT-II armor tile design for upgraded TEXTOR operation

International Nuclear Information System (INIS)

Newberry, B.L.; McGrath, R.T.; Watson, R.D.; Kohlhaas, W.; Finken, K.H.

1994-01-01

The upgrade of the TEXTOR tokamak at KFA Juelich was recently completed. This upgrade extended the TEXTOR pulse length from 5 seconds to 10 seconds. The auxiliary heating was increased to a total of 8.0 MW through a combination of neutral beam injection and radio frequency heating. Originally, the inertially cooled armor tiles of the full toroidal belt Advanced Limiter Test -- II (ALT-II) were designed for a 5-second operation with total heating of 6.0 MW. The upgrade of TEXTOR will increase the energy deposited per pulse onto the ALT-II by about 300%. Consequently, the graphite armor tiles for the ALT-II had to be redesigned to avoid excessively high graphite armor surface temperatures that would lead to unacceptable contamination of the plasma. This redesign took the form of two major changes in the ALT-II armor tile geometry. The first design change was an increase of the armor tile thermal mass, primarily by increasing the radial thickness of each tile from 17 mm to 20 mm. This increase in the radial tile dimension reduces the overall pumping efficiency of the ALT-II pump limiter by about 30%. The reduction in exhaust efficiency is unfortunate, but could be avoided only by active cooling of the ALT-II armor tiles. The active cooling option was too complicated and expensive to be considered at this time. The second design change involved redefining the plasma facing surface of each armor tile in order to fully utilize the entire surface area. The incident charged particle heat flux was distributed uniformly over the armor tile surfaces by carefully matching the radial, poloidal and toroidal curvature of each tile to the plasma flow in the TEXTOR boundary layer. This geometry redefinition complicates the manufacturing of the armor tiles, but results in significant thermal performance gains. In addition to these geometry upgrades, several material options were analyzed and evaluated

Joining of Tungsten Armor Using Functional Gradients

International Nuclear Information System (INIS)

John Scott O'Dell

2006-01-01

The joining of low thermal expansion armor materials such as tungsten to high thermal expansion heat sink materials has been a major problem in plasma facing component (PFC) development. Conventional planar bonding techniques have been unable to withstand the high thermal induced stresses resulting from fabrication and high heat flux testing. During this investigation, innovative functional gradient joints produced using vacuum plasma spray forming techniques have been developed for joining tungsten armor to copper alloy heat sinks. A model was developed to select the optimum gradient architecture. Based on the modeling effort, a 2mm copper rich gradient was selected. Vacuum plasma pray parameters and procedures were then developed to produce the functional gradient joint. Using these techniques, dual cooling channel, medium scale mockups (32mm wide x 400mm length) were produced with vacuum plasma spray formed tungsten armor. The thickness of the tungsten armor was up to 5mm thick. No evidence of debonding at the interface between the heat sink and the vacuum plasma sprayed material was observed.

Mock-up test results of monoblock-type CFC divertor armor for JT-60SA

Energy Technology Data Exchange (ETDEWEB)

Higashijima, S. [Japan Atomic Energy Agency, 801-1 Mukoyama, Naka, Ibaraki 311-0193 (Japan)], E-mail: higashijima.satoru@jaea.go.jp; Sakurai, S.; Suzuki, S.; Yokoyama, K.; Kashiwa, Y.; Masaki, K.; Shibama, Y.K.; Takechi, M.; Shibanuma, K.; Sakasai, A.; Matsukawa, M.; Kikuchi, M. [Japan Atomic Energy Agency, 801-1 Mukoyama, Naka, Ibaraki 311-0193 (Japan)

2009-06-15

The JT-60 Super Advanced (JT-60SA) tokamak project starts under both the Japanese domestic program and the international program 'Broader Approach'. The maximum heat flux to JT-60SA divertor is estimated to {approx}15 MW/m{sup 2} for 100 s. Japan Atomic Energy Agency (JAEA) has developed a divertor armor facing high heat flux in the engineering R and D for ITER, and it is concluded that monoblock-type CFC divertor armor is promising for JT-60SA. The JT-60SA armor consists of CFC monoblocks, a cooling CuCrZr screw-tube, and a thin oxygen-free high conductivity copper (OFHC-Cu) buffer layer between the CFC monoblock and the screw-tube. CFC/OFHC-Cu and OFHC-Cu/CuCrZr joints are essential for the armor, and these interfaces are brazed. Needed improvements from ITER engineering R and D are good CFC/OFHC-Cu and OFHC-Cu/CuCrZr interfaces and suppression of CFC cracking. For these purposes, metalization inside CFC monoblock is applied, and we confirmed again that the mock-up has heat removal capability in excess of ITER requirement. For optimization of the fabrication method and understanding of the production yield, the mock-ups corresponding to quantity produced in one furnace at the same time is also produced, and the half of the mock-ups could remove 15 MW/m{sup 2} as required. This paper summarizes the recent progress of design and mock-up test results for JT-60SA divertor armor.

Improved Shaped Charge Armors

National Research Council Canada - National Science Library

Vodenicharov, Stefan

2003-01-01

.... The major activities that are carried out are design, fabrication and testing in proving ground conditions of armor samples of various characteristics, electron microscopic and X-ray structural...

Glass matrix armor

International Nuclear Information System (INIS)

Calkins, N.C.

1991-01-01

This patent describes an armor system which utilizes glass. A plurality of constraint cells are mounted on a surface of a substrate, which is metal armor plate or a similar tough material, such that the cells almost completely cover the surface of the substrate. Each constraint cell has a projectile receiving wall parallel to the substrate surface and has sides which are perpendicular to and surround the perimeter of the receiving wall. The cells are mounted such that, in one embodiment, the substrate surface serves as a sixth side or closure for each cell. Each cell has inside of it a plate, termed the front plate, which is parallel to and in contact with substantially all of the insides surface of the receiving wall. The balance of each cell is completely filled with a projectile-abrading material consisting of glass and a ceramic material and, in certain embodiments, a polymeric material

A Workshop for Planning the Efficient Transfer of Recent Ceramic Armor/Antiarmor Modeling Results to the Armor Design Community: Summary and Draft Plan

National Research Council Canada - National Science Library

Klopp, Richard

1999-01-01

In the mid-1980s DARPA began sponsoring several programs to develop ceramic armor for heavy armor applications, supported by DARPA and ARO funded technology base initiatives in modeling, experiments...

Armor breakup and reformation in a degradational laboratory experiment

OpenAIRE

Orrú, Clara; Blom, Astrid; Uijttewaal, Wim S. J.

2016-01-01

Armor breakup and reformation was studied in a laboratory experiment using a trimodal mixture composed of a 1mm sand fraction and two gravel fractions (6 and 10mm). The initial bed was characterized by a stepwise downstream fining pattern (trimodal reach) and a downstream sand reach, and the experiment was conducted under conditions without sediment supply. In the initial stage of the experiment an armor formed over the trimodal reach. The formation of the armor under partial transport condit...

Analysis of Terminal Metallic Armor Plate Free-Surface Bulging

National Research Council Canada - National Science Library

Rapacki, Jr, E. J

2008-01-01

An analysis of the bulge formed on the free-surface of the terminal metallic plate of an armor array is shown to lead to reasonable estimates of the armor array's remaining penetration/perforation resistance...

Negligible heat strain in armored vehicle officers wearing personal body armor

Directory of Open Access Journals (Sweden)

Hunt Andrew P

2011-07-01

Full Text Available Abstract Objectives This study evaluated the heat strain experienced by armored vehicle officers (AVOs wearing personal body armor (PBA in a sub-tropical climate. Methods Twelve male AVOs, aged 35-58 years, undertook an eight hour shift while wearing PBA. Heart rate and core temperature were monitored continuously. Urine specific gravity (USG was measured before and after, and with any urination during the shift. Results Heart rate indicated an intermittent and low-intensity nature of the work. USG revealed six AVOs were dehydrated from pre through post shift, and two others became dehydrated. Core temperature averaged 37.4 ± 0.3°C, with maximum's of 37.7 ± 0.2°C. Conclusions Despite increased age, body mass, and poor hydration practices, and Wet-Bulb Globe Temperatures in excess of 30°C; the intermittent nature and low intensity of the work prevented excessive heat strain from developing.

Development of the armoring technique for ITER Divertor Dome

Energy Technology Data Exchange (ETDEWEB)

Litunovsky, Nikolay, E-mail: nlitunovsky@sintez.niiefa.spb.su [D.V. Efremov Reseasch Institute, 3, Doroga na Metallostroy, Saint Petersburg (Russian Federation); Alekseenko, Evgeny; Makhankov, Alexey; Mazul, Igor [D.V. Efremov Reseasch Institute, 3, Doroga na Metallostroy, Saint Petersburg (Russian Federation)

2011-10-15

This paper describes the current status of the technique for armoring of Plasma Facing Units (PFUs) of the ITER Divertor Dome with flat tungsten tiles planned for application at the procurement stage. Application of high-temperature vacuum brazing for armoring of High Heat Flux (HHF) plasma facing components was traditionally developed at the Efremov Institute and successfully tried out at the ITER R and D stage by manufacturing and HHF testing of a number of W- and Be-armored mock-ups . Nevertheless, the so-called 'fast brazing' technique successfully applied in the past was abandoned at the stage of manufacturing of the Dome Qualification Prototypes (Dome QPs), as it failed to retain the mechanical properties of CuCrZr heat sink of the substrate. Another problem was a substantially increased number of armoring tiles brazed onto one substrate. Severe ITER requirements for the joints quality have forced us to refuse from production of W/Cu joints by brazing in favor of casting. These modifications have allowed us to produce ITER Divertor Dome QPs with high-quality tungsten armor, which then passed successfully the HHF testing. Further preparation to the procurement stage is in progress.

Humvee Armor Plate Drilling

National Research Council Canada - National Science Library

2004-01-01

When drilling holes in hard steel plate used in up-armor kits for Humvee light trucks, the Anniston Army Depot, Anniston, Alabama, requested the assistance of the National Center for Defense Manufacturing and Machining (NCDMM...

The Armored Infantry in the US Force Structure.

Science.gov (United States)

1985-12-02

armored infantry and tank integration occurred during the capture of the town of Troyes , France, in 1944, by Task Force West of the 4th Armored...Singling and Troyes . The same can not be said of the foot infantryman because normally he was not associated with tanks. Such was the case in the previously

Analysis of behind the armor ballistic trauma.

Science.gov (United States)

Wen, Yaoke; Xu, Cheng; Wang, Shu; Batra, R C

2015-05-01

The impact response of body armor composed of a ceramic plate with an ultrahigh molecular weight polyethylene (UHMWPE) fiber-reinforced composite and layers of UHMWPE fibers shielding a block of ballistic gelatin has been experimentally and numerically analyzed. It is a surrogate model for studying injuries to human torso caused by a bullet striking body protection armor placed on a person. Photographs taken with a high speed camera are used to determine deformations of the armor and the gelatin. The maximum depth of the temporary cavity formed in the ballistic gelatin and the peak pressure 40mm behind the center of the gelatin front face contacting the armor are found to be, respectively, ~34mm and ~15MPa. The Johnson-Holmquist material model has been used to simulate deformations and failure of the ceramic. The UHMWPE fiber-reinforced composite and the UHMWPE fiber layers are modeled as linear elastic orthotropic materials. The gelatin is modeled as a strain-rate dependent hyperelastic material. Values of material parameters are taken from the open literature. The computed evolution of the temporary cavity formed in the gelatin is found to qualitatively agree with that seen in experiments. Furthermore, the computed time histories of the average pressure at four points in the gelatin agree with the corresponding experimentally measured ones. The maximum pressure at a point and the depth of the temporary cavity formed in the gelatin can be taken as measures of the severity of the bodily injury caused by the impact; e.g. see the United States National Institute of Justice standard 0101.06-Ballistic Resistance of Body Armor. Copyright © 2015 Elsevier Ltd. All rights reserved.

Performance of the PDX neutral beam wall armor

International Nuclear Information System (INIS)

Kugel, H.W.; Eubank, H.P.; Kozub, T.A.; Williams, M.D.

1985-02-01

The PDX wall armor was designed to function as an inner wall thermal armor, a neutral beam diagnostic, and a large area inner toroidal plasma limiter. In this paper we discuss its thermal performance as wall armor during two years of PDX neutral beam heating experiments. During this period it provided sufficient inner wall protection to permit perpendicular heating injections into normal and disruptive plasmas as well as injections in the absence of plasma involving special experiments, calibrations, and tests important for the optimization and development of the PDX neutral beam injection system. Many of the design constraints and performance issues encountered in this work are relevant to the design of larger fusion devices

ALT-II armor tile design for upgraded TEXTOR operation

International Nuclear Information System (INIS)

Newberry, B.L.; McGrath, R.T.; Watson, R.D.

1994-01-01

The upgrade of the TEXTOR tokamak at KFA Julich will be completed in the spring of 1994. The upgrade will extend the TEXTOR pulse length from 5 seconds to 10 seconds. The auxiliary heating systems are also scheduled to be upgraded so that eventually a total of 8.0 MW auxiliary heating will be available through a combination of neutral beam injection and radio frequency heating. Originally, the inertially cooled armor tiles on the full toroidal belt Advanced Limiter Test - II (ALT-II) were designed for 5-second operation with a total heating power of 6.0 MW. The upgrade of TEXTOR will increase the energy deposited per pulse onto ALT-II by more than 300%. Consequently, the graphite armor tiles for ALT-II had to be redesigned in order to increase their thermal inertia and, thereby, avoid excessively high graphite armor surface temperatures that would lead to unacceptable contamination of the plasma. The armor tile thermal inertia had been increase primarily by expanding the radial thickness of the tiles from 17 mm to 20 mm. This increase in radial tile dimension will reduce the overall pumping efficiency of the ALT-II pump limiter by about 30%. The final armor tile design was a compromise between increasing the power handling capability and reducing the particle exhaust efficiency of ALT-II. The reduction in exhaust efficiency is unfortunate, but could only be avoided by active cooling of the ALT-II armor tiles. The active cooling option was too complicated and expensive to be considered at this time

76 FR 70165 - Ballistic-Resistant Body Armor Standard Workshop

Science.gov (United States)

2011-11-10

... DEPARTMENT OF JUSTICE Office of Justice Programs [OJP (NIJ) Docket No. 1573] Ballistic-Resistant Body Armor Standard Workshop AGENCY: National Institute of Justice, DOJ. ACTION: Notice. SUMMARY: The... jointly hosting a workshop focused on NIJ Standard-0101.06, Ballistic Resistance of Body Armor, and the...

Armored Composite Ammunition Pressure Vessel

National Research Council Canada - National Science Library

Clark, William

1999-01-01

...). This ammunition containment system must not only meet environmental and handling requirements but also provide armor protection against impacting threats and reduce the response of the stowed...

Physical Training for Armor Crewmen

National Research Council Canada - National Science Library

Baker, Shane

2003-01-01

.... The author concluded that if his sample population represented the entire population then armor leaders were neglecting muscular strength, muscular endurance and flexibility in their physical readiness programs...

Design study of an armor tile handling manipulator for the Fusion Experimental Reactor

International Nuclear Information System (INIS)

Shibanuma, K.; Honda, T.; Satoh, K.; Terakado, T.; Kondoh, M.; Sasaki, N.; Munakata, T.; Murakami, S.

1991-01-01

A conceptual design of the Fusion Experimental Reactor (FER), which is a D-T burning reactor following on JT-60 in Japan, has been developed by Japan Atomic Energy Research Institute (JAERI). In FER, a rail-mounted vehicle concept is planned to be adopted for in-vessel maintenance, such as maintenance of divertor plates and armor tiles. Advantages of this concept are the high stiffness of the rail as a base structure for maintenance and the high mobility of the vehicle along the rail. Twin armor tile handling manipulators installed on both sides of the vehicle have been designed. The respective manipulators for armor tile handling have 8 degrees of freedom in order to have access to any place of the first wall and to go through the horizontal port by operating manipulator joints. If the two types of manipulators for divertor plates and armor tiles are installed on the vehicle and the divertor handling manipulator carries a case filled with armor tiles, the replacement time of armor tiles will be reduced. In FER, moreover, maintenance of armor tiles, which is a scheduled maintenance, is planned to be carried out by the autonomous control using position sensors etc. In order to accumulate the data base for the development of the autonomous control of the manipulator in armor tile maintenance, the present paper describes basic mechanical characteristics (stress, deflection and natural frequency) of the armor tile handling manipulator calculated by static stress and dynamic eigenvalue analyses. (orig.)

Physical Training for Armor Crewmen

National Research Council Canada - National Science Library

Baker, Shane

2003-01-01

This thesis examines the physical requirements of armor crewmen and provides a method for training them to meet those requirements based on current Army doctrine and emerging fitness doctrine using...

Armor Plate Surface Roughness Measurements

National Research Council Canada - National Science Library

Stanton, Brian; Coburn, William; Pizzillo, Thomas J

2005-01-01

...., surface texture and coatings) that could become important at high frequency. We measure waviness and roughness of various plates to know the parameter range for smooth aluminum and rolled homogenous armor (RHA...

Transparent Armor Cost Benefit Study

National Research Council Canada - National Science Library

Prokurat Franks, Lisa; Holm, David; Barnak, Rick

2006-01-01

...; the increase in demand for transparent gun shields in Operation Iraqi Freedom (OIF) and early versions of jerry-rigged shields used in OIF, including Pope glass and Transparent Armored Gun Shields (TAGS...

Quantifying the effectiveness of shoreline armoring removal on coastal biota of Puget Sound.

Science.gov (United States)

Lee, Timothy S; Toft, Jason D; Cordell, Jeffery R; Dethier, Megan N; Adams, Jeffrey W; Kelly, Ryan P

2018-01-01

Shoreline armoring is prevalent around the world with unprecedented human population growth and urbanization along coastal habitats. Armoring structures, such as riprap and bulkheads, that are built to prevent beach erosion and protect coastal infrastructure from storms and flooding can cause deterioration of habitats for migratory fish species, disrupt aquatic-terrestrial connectivity, and reduce overall coastal ecosystem health. Relative to armored shorelines, natural shorelines retain valuable habitats for macroinvertebrates and other coastal biota. One question is whether the impacts of armoring are reversible, allowing restoration via armoring removal and related actions of sediment nourishment and replanting of native riparian vegetation. Armoring removal is targeted as a viable option for restoring some habitat functions, but few assessments of coastal biota response exist. Here, we use opportunistic sampling of pre- and post-restoration data for five biotic measures (wrack % cover, saltmarsh % cover, number of logs, and macroinvertebrate abundance and richness) from a set of six restored sites in Puget Sound, WA, USA. This broad suite of ecosystem metrics responded strongly and positively to armor removal, and these results were evident after less than one year. Restoration responses remained positive and statistically significant across different shoreline elevations and temporal trajectories. This analysis shows that removing shoreline armoring is effective for restoration projects aimed at improving the health and productivity of coastal ecosystems, and these results may be widely applicable.

Quantifying the effectiveness of shoreline armoring removal on coastal biota of Puget Sound

Directory of Open Access Journals (Sweden)

Timothy S. Lee

2018-02-01

Full Text Available Shoreline armoring is prevalent around the world with unprecedented human population growth and urbanization along coastal habitats. Armoring structures, such as riprap and bulkheads, that are built to prevent beach erosion and protect coastal infrastructure from storms and flooding can cause deterioration of habitats for migratory fish species, disrupt aquatic–terrestrial connectivity, and reduce overall coastal ecosystem health. Relative to armored shorelines, natural shorelines retain valuable habitats for macroinvertebrates and other coastal biota. One question is whether the impacts of armoring are reversible, allowing restoration via armoring removal and related actions of sediment nourishment and replanting of native riparian vegetation. Armoring removal is targeted as a viable option for restoring some habitat functions, but few assessments of coastal biota response exist. Here, we use opportunistic sampling of pre- and post-restoration data for five biotic measures (wrack % cover, saltmarsh % cover, number of logs, and macroinvertebrate abundance and richness from a set of six restored sites in Puget Sound, WA, USA. This broad suite of ecosystem metrics responded strongly and positively to armor removal, and these results were evident after less than one year. Restoration responses remained positive and statistically significant across different shoreline elevations and temporal trajectories. This analysis shows that removing shoreline armoring is effective for restoration projects aimed at improving the health and productivity of coastal ecosystems, and these results may be widely applicable.

Magnetic non-destructive evaluation of ruptures of tensile armor in oil risers

International Nuclear Information System (INIS)

Pérez-Benitez, J A; Padovese, L R

2012-01-01

Risers are flexible multilayered pipes formed by an inner flexible metal structure surrounded by polymer layers and spiral wound steel ligaments, also known as armor wires. Since these risers are used to link subsea pipelines to floating oil and gas production installations, and their failure could produce catastrophic consequences, some methods have been proposed to monitor the armor integrity. However, until now there is no practical method that allows the automatic non-destructive detection of individual armor wire rupture. In this work we show a method using magnetic Barkhausen noise that has shown high efficiency in the detection of armor wire rupture. The results are examined under the cyclic and static load conditions of the riser. This work also analyzes the theory behind the singular dependence of the magnetic Barkhausen noise on the applied tension in riser armor wires. (paper)

Transparent ceramics for armor and EM window applications

OpenAIRE

Patel, Parimal J.; Gilde, Gary A.; Dehmer, Peter G.; McCauley, James W.

2000-01-01

Recently, the U.S. Army Research Laboratory (ARL) has focused increased attention on the development of transparent armor material systems for a variety of applications. Future combat and non-combat environments will require lightweight, threat adjustable, multifunctional, and affordable armor. Current glass/polycarbonate technologies are not expected to meet the increased requirements. Results over the past few years indicate that the use of transparent crystalline ceramics greatly improve t...

27 CFR 478.148 - Armor piercing ammunition intended for sporting or industrial purposes.

Science.gov (United States)

2010-04-01

... 27 Alcohol, Tobacco Products and Firearms 3 2010-04-01 2010-04-01 false Armor piercing ammunition... AMMUNITION COMMERCE IN FIREARMS AND AMMUNITION Exemptions, Seizures, and Forfeitures § 478.148 Armor piercing ammunition intended for sporting or industrial purposes. The Director may exempt certain armor piercing...

Armored garment for protecting

Science.gov (United States)

Purvis, James W [Albuquerque, NM; Jones, II, Jack F.; Whinery, Larry D [Albuquerque, NM; Brazfield, Richard [Albuquerque, NM; Lawrie, Catherine [Tijeras, NM; Lawrie, David [Tijeras, NM; Preece, Dale S [Watkins, CO

2009-08-11

A lightweight, armored protective garment for protecting an arm or leg from blast superheated gases, blast overpressure shock, shrapnel, and spall from a explosive device, such as a Rocket Propelled Grenade (RPG) or a roadside Improvised Explosive Device (IED). The garment has a ballistic sleeve made of a ballistic fabric, such as an aramid fiber (e.g., KEVLAR.RTM.) cloth, that prevents thermal burns from the blast superheated gases, while providing some protection from fragments. Additionally, the garment has two or more rigid armor inserts that cover the upper and lower arm and protect against high-velocity projectiles, shrapnel and spall. The rigid inserts can be made of multiple plies of a carbon/epoxy composite laminate. The combination of 6 layers of KEVLAR.RTM. fabric and 28 plies of carbon/epoxy laminate inserts (with the inserts being sandwiched in-between the KEVLAR.RTM. layers), can meet the level IIIA fragmentation minimum V.sub.50 requirements for the US Interceptor Outer Tactical Vest.

’Stinger under Armor:’ An Analysis of Alternatives

Science.gov (United States)

1990-01-01

This paper examines a concept for employment of the Stinger Air Defense Artillery weapon system known as ’Stinger under Armor .’ It traces the...areas air defense in the pre-FAADS era. This broader deficiency ultimately drove the need for ’Stinger under Armor ’ as a short-term solution to a current battlefield vulnerability.

Ballistic protection performance of curved armor systems with or without debondings/delaminations

International Nuclear Information System (INIS)

Tan, Ping

2014-01-01

Highlights: • Influence of pre-existing defect in an armor system on its ballistic performance. • Development of finite element models for the ballistic performance of armor systems. • Prediction of the ballistic limit and back face deformation of curved armor systems. - Abstract: In order to discern how pre-existing defects such as single or multiple debondings/delaminations in a curved armor system may affect its ballistic protection performance, two-dimensional axial finite element models were generated using the commercial software ANSYS/Autodyn. The armor systems considered in this investigation are composed of boron carbide front component and Kevlar/epoxy backing component. They are assumed to be perfectly bonded at the interface without defects. The parametric study shows that for the cases considered, the maximum back face deformation of a curved armor system with or without defects is more sensitive to its curvature, material properties of the ceramic front component, and pre-existing defect size and location than the ballistic limit velocity. Additionally, both the ballistic limit velocity and maximum back face deformation are significantly affected by the backing component thickness, front/backing component thickness ratio and the number of delaminations

Blast-Resistant Improvement of Sandwich Armor Structure with Aluminum Foam Composite

OpenAIRE

Yang, Shu; Qi, Chang

2013-01-01

Sandwich armor structures with aluminum foam can be utilized to protect a military vehicle from harmful blast load such as a landmine explosion. In this paper, a system-level dynamic finite element model is developed to simulate the blast event and to evaluate the blast-resistant performance of the sandwich armor structure. It is found that a sandwich armor structure with only aluminum foam is capable of mitigating crew injuries under a moderate blast load. However, a severe blast load causes...

Advancing viral RNA structure prediction: measuring the thermodynamics of pyrimidine-rich internal loops.

Science.gov (United States)

Phan, Andy; Mailey, Katherine; Saeki, Jessica; Gu, Xiaobo; Schroeder, Susan J

2017-05-01

Accurate thermodynamic parameters improve RNA structure predictions and thus accelerate understanding of RNA function and the identification of RNA drug binding sites. Many viral RNA structures, such as internal ribosome entry sites, have internal loops and bulges that are potential drug target sites. Current models used to predict internal loops are biased toward small, symmetric purine loops, and thus poorly predict asymmetric, pyrimidine-rich loops with >6 nucleotides (nt) that occur frequently in viral RNA. This article presents new thermodynamic data for 40 pyrimidine loops, many of which can form UU or protonated CC base pairs. Uracil and protonated cytosine base pairs stabilize asymmetric internal loops. Accurate prediction rules are presented that account for all thermodynamic measurements of RNA asymmetric internal loops. New loop initiation terms for loops with >6 nt are presented that do not follow previous assumptions that increasing asymmetry destabilizes loops. Since the last 2004 update, 126 new loops with asymmetry or sizes greater than 2 × 2 have been measured. These new measurements significantly deepen and diversify the thermodynamic database for RNA. These results will help better predict internal loops that are larger, pyrimidine-rich, and occur within viral structures such as internal ribosome entry sites. © 2017 Phan et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Armoring confined bubbles in concentrated colloidal suspensions

Science.gov (United States)

Yu, Yingxian; Khodaparast, Sepideh; Stone, Howard

2016-11-01

Encapsulation of a bubble with microparticles is known to significantly improve the stability of the bubble. This phenomenon has recently gained increasing attention due to its application in a variety of technologies such as foam stabilization, drug encapsulation and colloidosomes. Nevertheless, the production of such colloidal armored bubble with controlled size and particle coverage ratio is still a great challenge industrially. We study the coating process of a long air bubble by microparticles in a circular tube filled with a concentrated microparticles colloidal suspension. As the bubble proceeds in the suspension of particles, a monolayer of micro-particles forms on the interface of the bubble, which eventually results in a fully armored bubble. We investigate the phenomenon that triggers and controls the evolution of the particle accumulation on the bubble interface. Moreover, we examine the effects of the mean flow velocity, the size of the colloids and concentration of the suspension on the dynamics of the armored bubble. The results of this study can potentially be applied to production of particle-encapsulated bubbles, surface-cleaning techniques, and gas-assisted injection molding.

Ballistic Application of Coir Fiber Reinforced Epoxy Composite in Multilayered Armor

OpenAIRE

Luz, Fernanda Santos da; Monteiro, Sergio Neves; Lima, Eduardo Sousa; Lima Júnior, Édio Pereira

2017-01-01

Multilayered armor systems (MAS) composed of relatively lighter materials with capacity to provide personal ballistic protection are being extensively investigated and used in armor vests. A typical MAS to stand high impact energy 7.62 mm bullet has a front ceramic followed by an aramid fabric laminate, such as Kevlar™. Since both the army and municipal police personnel might need to wear an armor vest, a large number of vests needs to be supplied. In the case of Kevlar™, one of the most expe...

77 FR 39259 - Agency Information Collection Activities; Proposed Collection; Comments Requested: Body Armor in...

Science.gov (United States)

2012-07-02

...: Establishment survey and initial approval of collection. (2) Title of Form/Collection: Body Armor in Correctional Institutions Survey. The collections include the forms Body Armor Administrative Agency-Level Survey and Body Armor Individual-level Correctional Officer Survey. (3) Agency form number, if any, and...

77 FR 22345 - Agency Information Collection Activities: Proposed Collection; Comments Requested; Body Armor in...

Science.gov (United States)

2012-04-13

... Collection: Establishment survey and initial approval of collection. (2) Title of Form/Collection: Body Armor... Agency-Level Survey and Body Armor Individual-level Correctional Officer Survey. (3) Agency form number... approaches to overcome those barriers. (a) For the Body Armor Administrative Agency-Level Survey, the chief...

7 CFR 1755.406 - Shield or armor ground resistance measurements.

Science.gov (United States)

2010-01-01

...) The insulation resistance test set should have an output voltage not to exceed 500 volts dc and may be... 7 Agriculture 11 2010-01-01 2010-01-01 false Shield or armor ground resistance measurements. 1755... MATERIALS, AND STANDARD CONTRACT FORMS § 1755.406 Shield or armor ground resistance measurements. (a) Shield...

Engineering model for body armor

NARCIS (Netherlands)

Roebroeks, G.H.J.J.; Carton, E.P.

2014-01-01

TNO has developed an engineering model for flexible body armor, as one of their energy based engineering models that describe the physics of projectile to target interactions (weaves, metals, ceramics). These models form the basis for exploring the possibilities for protection improvement. This

Imperfection analysis of flexible pipe armor wires in compression and bending

DEFF Research Database (Denmark)

Østergaard, Niels Højen; Lyckegaard, Anders; Andreasen, Jens H.

2012-01-01

The work presented in this paper is motivated by a specific failure mode known as lateral wire buckling occurring in the tensile armor layers of flexible pipes. The tensile armor is usually constituted by two layers of initially helically wound steel wires with opposite lay directions. During pipe...... ability of the wires. This may cause the wires to buckle in the circumferential pipe direction, when these are restrained against radial deformations by adjacent layers. In the present paper, a single armoring wire modeled as a long and slender curved beam embedded in a frictionless cylinder bent...

Expanding the Availability of Lightweight Aluminum Alloy Armor Plate Procured from Detailed Military Specifications

Science.gov (United States)

Doherty, Kevin; Squillacioti, Richard; Cheeseman, Bryan; Placzankis, Brian; Gallardy, Denver

For many years, the range of aluminum alloys for armor plate applications obtainable in accordance with detailed military specifications was very limited. However, the development of improved aluminum alloys for aerospace and other applications has provided an opportunity to modernize the Army portfolio for ground vehicle armor applications. While the benefits of offering additional alloy choices to vehicle designers is obvious, the process of creating detailed military specifications for armor plate applications is not trivial. A significant amount of material and testing is required to develop the details required by an armor plate specification. Due to the vast number of material programs that require standardization and with a limited amount of manpower and funds as a result of Standardization Reform in 1995, one typically requires a need statement from a vehicle program office to justify and sponsor the work. This presentation will focus on recent aluminum alloy armor plate specifications that have added capability to vehicle designers' selection of armor materials that offer possible benefits such as lower cost, higher strength, better ballistic and corrosion resistance, improved weldability, etc.

Mosaic Transparent Armor System Final Report CRADA No. TC02162.0

Energy Technology Data Exchange (ETDEWEB)

Kuntz, J. D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Breslin, M. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2017-08-29

This was a collaborative effort between Lawrence Livermore National Security, LLC as manager and operator of Lawrence Livermore National Laboratory (LLNL) and The Protective Group, Inc. (TPG) to improve the performance of the mosaic transparent armor system (MTAS) for transparent armor applications, military and civilian. LLNL was to provide the unique MTAS technology and designs to TPG for innovative construction and ballistic testing of improvements needed for current and near future application of the armor windows on vehicles and aircraft. The goal of the project was to advance the technology of MTAS to the point that these mosaic transparent windows would be introduced and commercially manufactured for military vehicles and aircraft.

Mapping Optimal Charge Density and Length of ROMP-Based PTDMs for siRNA Internalization.

Science.gov (United States)

Caffrey, Leah M; deRonde, Brittany M; Minter, Lisa M; Tew, Gregory N

2016-10-10

A fundamental understanding of how polymer structure impacts internalization and delivery of biologically relevant cargoes, particularly small interfering ribonucleic acid (siRNA), is of critical importance to the successful design of improved delivery reagents. Herein we report the use of ring-opening metathesis polymerization (ROMP) methods to synthesize two series of guanidinium-rich protein transduction domain mimics (PTDMs): one based on an imide scaffold that contains one guanidinium moiety per repeat unit, and another based on a diester scaffold that contains two guanidinium moieties per repeat unit. By varying both the degree of polymerization and, in effect, the relative number of cationic charges in each PTDM, the performances of the two ROMP backbones for siRNA internalization were evaluated and compared. Internalization of fluorescently labeled siRNA into Jurkat T cells demonstrated that fluorescein isothiocyanate (FITC)-siRNA internalization had a charge content dependence, with PTDMs containing approximately 40 to 60 cationic charges facilitating the most internalization. Despite this charge content dependence, the imide scaffold yielded much lower viabilities in Jurkat T cells than the corresponding diester PTDMs with similar numbers of cationic charges, suggesting that the diester scaffold is preferred for siRNA internalization and delivery applications. These developments will not only improve our understanding of the structural factors necessary for optimal siRNA internalization, but will also guide the future development of optimized PTDMs for siRNA internalization and delivery.

Embedded Fiber Optic Sensors for Integral Armor

National Research Council Canada - National Science Library

Fink, Bruce

2000-01-01

This report describes the work performed with Production Products Manufacturing & Sales (PPMS), Inc., under the "Liquid Molded Composite Armor Smart Structures Using Embedded Sensors" Small Business Innovative Research...

Patterned Armor Performance Evaluation for Multiple Impacts

National Research Council Canada - National Science Library

De

2003-01-01

.... Performance characteristics of an ideal patterned armor with respect to multiple hits are discussed, and the types of single-shot ballistic data needed to quantify that performance are presented...

Armor in Vietnam

Science.gov (United States)

1976-05-01

battles a-Riuot the insurgent enemy, especially with armor. French contingents were present in Tndo Chinh P-w early as 1852, but it was not until 1884...committed to Vietnam were straight infantry. These troons er•A tran -norted in hn4±{ copters and usually airlifted to the battle zone; however, once...0STAINf0 FROM VKTNAM NATIONAL MAP SERVICE (NOS) PHU-YEN OCTOBER 19665 OARLAC ......... KKAN1+ HOA QLWA- DUC TUYEN- DUC PHUOC- NINH_ C;ry OF -10 T CAM RANK TAY

Computed tomography of the ''armored brain''

International Nuclear Information System (INIS)

Ludwig, B.; Nix, W.; Lanksch, W.

1983-01-01

A classified chronic subdural hematoma may cover the surface of the cerebral hemispheres to such an extent that one can talk of an ''armored brain''. Pathogenesis, clinical course and treatment are discussed based on the computed tomograms of five cases. (orig.)

Report to the Attorney General on Body Armor Safety Initiative Testing and Activities

National Research Council Canada - National Science Library

2005-01-01

On November 17, 2003, Attorney General John Ashcroft announced the U.S. Department of Justice's Body Armor Safety Initiative in response to concerns from the law enforcement community regarding the effectiveness of body armor in use...

Effect of surface texture and structure on the development of stable fluvial armors

Science.gov (United States)

Bertin, Stephane; Friedrich, Heide

2018-04-01

Stable fluvial armors are found in river systems under conditions of partial sediment transport and limited sediment supply, a common occurrence in nature. Stable armoring is also readily recreated in experimental flumes. Initially, this bed stabilizing phenomenon was examined for different flow discharges and solely related to surface coarsening and bedload transport reduction. The models developed suggest a specific armor composition (i.e., texture) dependent on the parent bed material and formative discharge. Following developments in topographic remote sensing, recent research suggests that armor structure is an important control on bed stability and roughness. In this paper, replicated flume runs during which digital elevation models (DEMs) were collected from both exposed and flooded gravel beds are used to interpret armoring manifestations and to assess their replicability. A range of methodologies was used for the analysis, providing information on (i) surface grain size and orientation, (ii) bed-elevation distributions, (iii) the spatial coherence of the elevations at the grain-scale, (iv) surface slope and aspect, (v) grain imbrication and (vi) the spatial variability in DEM properties. The bed-surface topography was found to be more responsive than bed-material size to changes in flow strength. Our experimental results also provide convincing evidence that gravel-beds' response to water-work during parallel degradation is unique (i.e., replicable) given the formative parameters. Based on this finding, relationships between the armors' properties and formative parameters are proposed, and are supported by adding extensive data from previous research.

Functional trade-off between strength and thermal capacity of dermal armor: Insights from girdled lizards.

Science.gov (United States)

Broeckhoven, Chris; du Plessis, Anton; Hui, Cang

2017-10-01

The presence of dermal armor is often unambiguously considered the result of an evolutionary predator-prey arms-race. Recent studies focusing predominantly on osteoderms - mineralized elements embedded in the dermis layer of various extant and extinct vertebrates - have instead proposed that dermal armor might exhibit additional functionalities besides protection. Multiple divergent functionalities could impose conflicting demands on a phenotype, yet, functional trade-offs in dermal armor have rarely been investigated. Here, we use high-resolution micro-computed tomography and voxel-based simulations to test for a trade-off between the strength and thermal capacity of osteoderms using two armored cordylid lizards as model organisms. We demonstrate that high vascularization, associated with improved thermal capacity might limit the strength of osteoderms. These results call for a holistic, cautionary future approach to studies investigating dermal armor, especially those aiming to inspire artificial protective materials. Copyright © 2017 Elsevier Ltd. All rights reserved.

A numerical study on the disturbance of explosive reactive armors to jet penetration

Directory of Open Access Journals (Sweden)

Xiang-dong Li

2014-03-01

Full Text Available The disturbance of flat and V-shaped sandwich reactive armor configurations to shaped-charge jet is studied by a numerical approach. The disturbing and cutting effects of the two reactive armor configurations to the jet are successfully captured. The predicted disturbance characteristics and patterns are in fairly good agreement with the X-ray photographic observations. The residual depth of penetration into a semi-infinitive homogeneous steel target behind the reactive armor is computed for a series of jet/armor parameters. For the flat configuration, it is demonstrated that the residual penetration depth is not significantly reduced for a normal impact while it is reduced up to 75% for an oblique impact. In comparison, the V-shaped configuration reduces the penetration depth of the jet to 90%, and it is observed that the penetration depth is not sensitive to the V-shaped angle.

Acquisition of the Armored Medical Evacuation Vehicle

National Research Council Canada - National Science Library

2000-01-01

.... The platform for the AMEV is an upgraded M2A0 Bradley Fighting Vehicle variant, which has the turret removed, the roof squared off and raised 13 inches, a 600 horsepower engine, and additional armor...

Fracture mechanical analysis of tungsten armor failure of a water-cooled divertor target

Energy Technology Data Exchange (ETDEWEB)

Li, Muyuan; Werner, Ewald [Lehrstuhl für Werkstoffkunde und Werkstoffmechanik, Technische Universität München, Boltzmannstr. 15, 85748 Garching (Germany); You, Jeong-Ha, E-mail: you@ipp.mpg.de [Max-Planck-Institut für Plasmaphysik, Boltzmannstr. 2, 85748 Garching (Germany)

2014-11-15

Highlights: • The FEM-based VCE method and XFEM were employed for computing K{sub I} (or J-integral) and predicting progressive cracking, respectively. • The most probable pattern of crack formation is radial cracking in the tungsten armor block. • The most probable site of cracking is the upper interfacial region of the tungsten armor block adjacent to the top position of the copper interlayer. • The initiation of a major crack becomes likely, only when the strength of tungsten armor block is significantly reduced from its original strength. - Abstract: The inherent brittleness of tungsten at low temperature and the embrittlement by neutron irradiation are its most critical weaknesses for fusion applications. In the current design of the ITER and DEMO divertor, the high heat flux loads during the operation impose a strong constraint on the structure–mechanical performance of the divertor. Thus, the combination of brittleness and the thermally induced stress fields due to the high heat flux loads raises a serious reliability issue in terms of the structural integrity of tungsten armor. In this study, quantitative estimates of the vulnerability of the tungsten monoblock armor cracking under stationary high heat flux loads are presented. A comparative fracture mechanical investigation has been carried out by means of two different types of computational approaches, namely, the extended finite element method (XFEM) and the finite element method (FEM)-based virtual crack tip extension (VCE) method. The fracture analysis indicates that the most probable pattern of crack formation is radial cracking in the tungsten armor starting from the interface to tube and the most probable site of cracking is the upper interfacial region of the tungsten armor adjacent to the top position of the copper interlayer. The strength threshold for crack initiation and the high heat flux load threshold for crack propagation are evaluated based on XFEM simulations and computations

27 CFR 478.149 - Armor piercing ammunition manufactured or imported for the purpose of testing or experimentation.

Science.gov (United States)

2010-04-01

... 27 Alcohol, Tobacco Products and Firearms 3 2010-04-01 2010-04-01 false Armor piercing ammunition... Armor piercing ammunition manufactured or imported for the purpose of testing or experimentation. The provisions of §§ 478.37 and 478.99(d) with respect to the manufacture or importation of armor piercing...

Repair of manufacturing defects in the armor of plasma facing units of the ITER Divertor Dome

International Nuclear Information System (INIS)

Litunovsky, Nikolay; Alekseenko, Evgeny; Kuznetsov, Vladimir; Lyanzberg, Dmitriy; Makhankov, Aleksey; Rulev, Roman

2013-01-01

Highlights: • Sporadic manufacturing defects in ITER Divertor Dome PFUs may be repaired. • We have developed a repair technique for ITER Divertor Dome PFUs. • Armor repair technique for ITER Divertor Dome PFUs is successfully tested. -- Abstract: The paper describes the repair procedure developed for removal of manufacturing defects occurring sporadically during armoring of plasma facing units (PFUs) of the ITER Divertor Dome. Availability of armor repair technique is prescribed by the procurement arrangement for the ITER Divertor Dome concluded in 2009 between the ITER Organization and the ITER Domestic Agency of Russia. The paper presents the detailed description of the procedure, data on its effect on the joints of the rest part of the armor and on the grain structure of the PFU heat sink. The results of thermocycling of large-scale Dome PFU mock-ups manufactured with demonstration of armor repair are also given

Repair of manufacturing defects in the armor of plasma facing units of the ITER Divertor Dome

Energy Technology Data Exchange (ETDEWEB)

Litunovsky, Nikolay, E-mail: nlitunovsky@sintez.niiefa.spb.su; Alekseenko, Evgeny; Kuznetsov, Vladimir; Lyanzberg, Dmitriy; Makhankov, Aleksey; Rulev, Roman

2013-10-15

Highlights: • Sporadic manufacturing defects in ITER Divertor Dome PFUs may be repaired. • We have developed a repair technique for ITER Divertor Dome PFUs. • Armor repair technique for ITER Divertor Dome PFUs is successfully tested. -- Abstract: The paper describes the repair procedure developed for removal of manufacturing defects occurring sporadically during armoring of plasma facing units (PFUs) of the ITER Divertor Dome. Availability of armor repair technique is prescribed by the procurement arrangement for the ITER Divertor Dome concluded in 2009 between the ITER Organization and the ITER Domestic Agency of Russia. The paper presents the detailed description of the procedure, data on its effect on the joints of the rest part of the armor and on the grain structure of the PFU heat sink. The results of thermocycling of large-scale Dome PFU mock-ups manufactured with demonstration of armor repair are also given.

Numerical simulations of semi-armor-piercing warhead penetrating aircraft carrier target

OpenAIRE

Dong Sangqaing; Cai Xinghui; Wang Guoliang; Gao Yunliang; Lu Jiangren

2015-01-01

FEM models of semi-armor-piercing warhead penetrating aircraft carrier deck are established, which are validated by related experimental data. Base on the models, the process of semi-armor-piercing warhead penetrating aircraft carrier deck with different incidence angles and attack angles are carried out. The results show that incidence angles have no remarkable influence on penetration capability of the projectile under the circumstance of zero attack angle. Ductility reaming damage mode and...

Preparing soft-bodied arthropods for arthropods for microscope examination: Armored Scales (Insects: Hemiptera: Diaspididae)

Science.gov (United States)

Proper identification of armored scales (Hemiptera: Diaspididae) requires preparation of the specimen on a microscope slide. This training video provides visual instruction on how to prepare armored scales specimens on microscope slides for examination and identification. Steps ranging from collect...

Dragon Skin - How It Changed Body Armor Testing in the United States Army

Science.gov (United States)

2015-09-01

members of this committee who have their kids at one time or another wearing body armor in theater, either Iraq or Afghanistan. And that includes... YouTube has pictures of Dragon Skin body armor testing on the Internet and Wikipedia has posted a carefully documented description of the history of

Production and characterization of ceramics for armor application

International Nuclear Information System (INIS)

Alves, J.T.; Lopes, C.M.A.; Assis, J.M.K.; Melo, F.C.L.

2010-01-01

The fabrication of devices for ballistic protection as bullet proof vests and helmets and armored vehicles has been evolving over the past years along with the materials and models used for this specific application. The requirements for high efficient light-weight ballistic protection systems which not interfere in the user comfort and mobility has driven the research in this area. In this work we will present the results of characterization of two ceramics based on alumina and silicon carbide. The ceramics were produced in lab scale and the specific mass, scanning electron microscopy (SEM) microstructure, Vickers hardness, flexural resistance at room temperature and X-ray diffraction were evaluated. Ballistic tests performed in the selected materials showed that the ceramics present armor efficiency. (author)

Cost-Effective Manufacturing of Damage-Tolerant Integral Armor

National Research Council Canada - National Science Library

Fink, Bruce

2000-01-01

The U.S. Army Research Laboratory (ARL) and the University of Delaware (UD) have developed an enabling technology to produce a polymer matrix composite-based integral armor with improved multihit ballistic capability...

Thermal-stress analysis and testing of DIII-D armor tiles

International Nuclear Information System (INIS)

Baxi, C.B.; Anderson, P.M.; Reis, E.E.; Smith, J.P.; Smith, P.D.; Croesmann, C.; Watkins, J.; Whitley, J.

1987-10-01

It is planned to install about 1500 new armor tiles in the DIII-D tokamak. The armor tiles currently installed in DIII-D are made by brazing Poco AXF-5Q graphite onto Inconel X-750 stock. A small percentage of these have failed by breakage of graphite. These failures were believed to be related to significant residual stress remaining in graphite after brazing. Hence, an effort was undertaken to improve the design with all-graphite tiles. Three criteria must be satisfied by the armor tiles and the hardware used to attach the tiles to the vessel walls: tiles should not structurally fail, peak tile temperature must be less than 2500 K, and peak vessel stresses must be below acceptable levels. A number of alternate design concepts were first analyzed with the two-dimensional finite element codes TOPAZ2D and NIKE2D. Promising designs were optimized for best parameters such as thicknesses, etc. The two best designs were further analyzed for thermal stresses with the three-dimensional codes P/THERMAL and P/STRESS. Prototype tiles of a number of materials were fabricated by GA and tested at the Plasma Materials Test Facility of the Sandia National Laboratory at Albuquerque. The tests simulated the heat flux and cooling conditions in DIII-D. This paper describes the 2-D and 3-D thermal stress analyses, the test results and logic which led to the selected design of the DIII-D armor tiles. 5 refs., 7 figs., 3 tabs

Statistical description of flume experiments on mixed-size bed-load transport and bed armoring processes

Science.gov (United States)

Chen, D.; Zhang, Y.

2008-12-01

The objective of this paper is to describe the statistical properties of experiments on non-uniform bed-load transport as well as the mechanism of bed armoring processes. Despite substantial effort made over the last two decades, the ability to compute the bed-load flux in a turbulent system remains poor. The major obstacles include the poor understanding of the formation of armor lays on bed surfaces. Such a layer is much flow-resistible than the underlying material and therefore significantly inhibits sediment transport from the reach. To study the problem, we conducted a flume study for mixed sand/gravel sediments. We observed that aggregated sediment blocks were the most common characters in armor layers - the largest sizes resist hydraulic forces, while the smaller sizes add interlocking support and prevent loss of fine material through gaps between the larger particles. Fractional transport rates with the existing of armor layers were measured with time by sediment trapping method at the end of flume. To address the intermittent and time-varying behavior of bed-load transport during bed armoring processes, we investigated the probability distribution of the fractional bed-load transport rates, and the underlying dynamic model derived from the continuous time random walk framework. Results indicate that it is critical to consider the impact of armor layers when a flow is sufficient to move some of the finer particles and yet insufficient to move all the larger particles on a channel bed.

Optimal Hydrophobicity in Ring-Opening Metathesis Polymerization-Based Protein Mimics Required for siRNA Internalization.

Science.gov (United States)

deRonde, Brittany M; Posey, Nicholas D; Otter, Ronja; Caffrey, Leah M; Minter, Lisa M; Tew, Gregory N

2016-06-13

Exploring the role of polymer structure for the internalization of biologically relevant cargo, specifically siRNA, is of critical importance to the development of improved delivery reagents. Herein, we report guanidinium-rich protein transduction domain mimics (PTDMs) based on a ring-opening metathesis polymerization scaffold containing tunable hydrophobic moieties that promote siRNA internalization. Structure-activity relationships using Jurkat T cells and HeLa cells were explored to determine how the length of the hydrophobic block and the hydrophobic side chain compositions of these PTDMs impacted siRNA internalization. To explore the hydrophobic block length, two different series of diblock copolymers were synthesized: one series with symmetric block lengths and one with asymmetric block lengths. At similar cationic block lengths, asymmetric and symmetric PTDMs promoted siRNA internalization in the same percentages of the cell population regardless of the hydrophobic block length; however, with 20 repeat units of cationic charge, the asymmetric block length had greater siRNA internalization, highlighting the nontrivial relationships between hydrophobicity and overall cationic charge. To further probe how the hydrophobic side chains impacted siRNA internalization, an additional series of asymmetric PTDMs was synthesized that featured a fixed hydrophobic block length of five repeat units that contained either dimethyl (dMe), methyl phenyl (MePh), or diphenyl (dPh) side chains and varied cationic block lengths. This series was further expanded to incorporate hydrophobic blocks consisting of diethyl (dEt), diisobutyl (diBu), and dicyclohexyl (dCy) based repeat units to better define the hydrophobic window for which our PTDMs had optimal activity. High-performance liquid chromatography retention times quantified the relative hydrophobicities of the noncationic building blocks. PTDMs containing the MePh, diBu, and dPh hydrophobic blocks were shown to have superior

Manufacturing process scale-up of optical grade transparent spinel ceramic at ArmorLine Corporation

Science.gov (United States)

Spilman, Joseph; Voyles, John; Nick, Joseph; Shaffer, Lawrence

2013-06-01

While transparent Spinel ceramic's mechanical and optical characteristics are ideal for many Ultraviolet (UV), visible, Short-Wave Infrared (SWIR), Mid-Wave Infrared (MWIR), and multispectral sensor window applications, commercial adoption of the material has been hampered because the material has historically been available in relatively small sizes (one square foot per window or less), low volumes, unreliable supply, and with unreliable quality. Recent efforts, most notably by Technology Assessment and Transfer (TA and T), have scaled-up manufacturing processes and demonstrated the capability to produce larger windows on the order of two square feet, but with limited output not suitable for production type programs. ArmorLine Corporation licensed the hot-pressed Spinel manufacturing know-how of TA and T in 2009 with the goal of building the world's first dedicated full-scale Spinel production facility, enabling the supply of a reliable and sufficient volume of large Transparent Armor and Optical Grade Spinel plates. With over $20 million of private investment by J.F. Lehman and Company, ArmorLine has installed and commissioned the largest vacuum hot press in the world, the largest high-temperature/high-pressure hot isostatic press in the world, and supporting manufacturing processes within 75,000 square feet of manufacturing space. ArmorLine's equipment is capable of producing window blanks as large as 50" x 30" and the facility is capable of producing substantial volumes of material with its Lean configuration and 24/7 operation. Initial production capability was achieved in 2012. ArmorLine will discuss the challenges that were encountered during scale-up of the manufacturing processes, ArmorLine Optical Grade Spinel optical performance, and provide an overview of the facility and its capabilities.

Structural impact of armor monoblock dimensions on the failure behavior of ITER-type divertor target components: Size matters

Energy Technology Data Exchange (ETDEWEB)

Li, Muyuan; You, Jeong-Ha, E-mail: you@ipp.mpg.de

2016-12-15

Highlights: • Quantitative assessment of size effects was conducted numerically for W monoblock. • Decreasing the width of W monoblock leads to a lower risk of failure. • The Cu interlayer was not affected significantly by varying armor thickness. • The predicted trends were in line with the experimental observations. - Abstract: Plenty of high-heat-flux tests conducted on tungsten monoblock type divertor target mock-ups showed that the threshold heat flux density for cracking and fracture of tungsten armor seems to be related to the dimension of the monoblocks. Thus, quantitative assessment of such size effects is of practical importance for divertor target design. In this paper, a computational study about the thermal and structural impact of monoblock size on the plastic fatigue and fracture behavior of an ITER-type tungsten divertor target is reported. As dimensional parameters, the width and thickness of monoblock, the thickness of sacrificial armor, and the inner diameter of cooling tube were varied. Plastic fatigue lifetime was estimated for the loading surface of tungsten armor and the copper interlayer by use of a cyclic-plastic constitutive model. The driving force of brittle crack growth through the tungsten armor was assessed in terms of J-integral at the crack tip. Decrease of the monoblock width effectively reduced accumulation of plastic strain at the armor surface and the driving force of brittle cracking. Decrease of sacrificial armor thickness led to decrease of plastic deformation at the loading surface due to lower surface temperature, but the thermal and mechanical response of the copper interlayer was not affected by the variation of armor thickness. Monoblock with a smaller tube diameter but with the same armor thickness and shoulder thickness experienced lower fatigue load. The predicted trends were in line with the experimental observations.

Analysis of Terminal Metallic Armor Plate Free-Surface Bulging

National Research Council Canada - National Science Library

Rapacki, Jr, E. J

2008-01-01

.... Terminal ballistic performance evaluations of penetrators and armors are often performed via statistical analyses to obtain a velocity or obliquity at which the expected probability of perforation...

Soft Body Armor: An Overview of Materials, Manufacturing, Testing, and Ballistic Impact Dynamics

Science.gov (United States)

2011-08-01

Atlantic Treaty Organization NIJ National Institute of Justice OTV Outer tactical vest PBI Polybenzimidazole PBO Polybenzobisoxazole PET ...grenades and mortar rounds, is performed in accordance with the North Atlantic Treaty Organization (NATO) Standardization Agreement (STANAG) 2920.6...LEVELS IN SOFT BODY ARMOR The design of woven fabrics for armor applications is complex because it requires an understanding of the related

Development and Verification of Body Armor Target Geometry Created Using Computed Tomography Scans

Science.gov (United States)

2017-07-13

Computed Tomography Scans by Autumn R Kulaga, Kathryn L Loftis, and Eric Murray Approved for public release; distribution is...Army Research Laboratory Development and Verification of Body Armor Target Geometry Created Using Computed Tomography Scans by Autumn R Kulaga...Development and Verification of Body Armor Target Geometry Created Using Computed Tomography Scans 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c

Ballistic Resistance of Armored Passenger Vehicles: Test Protocols and Quality Methods

Energy Technology Data Exchange (ETDEWEB)

Jeffrey M. Lacy; Robert E. Polk

2005-07-01

This guide establishes a test methodology for determining the overall ballistic resistance of the passenger compartment of assembled nontactical armored passenger vehicles (APVs). Because ballistic testing of every piece of every component of an armored vehicle is impractical, if not impossible, this guide describes a testing scheme based on statistical sampling of exposed component surface areas. Results from the test of the sampled points are combined to form a test score that reflects the probability of ballistic penetration into the passenger compartment of the vehicle.

106-17 Telemetry Standards. Annex A.4. Asynchronous Recorder Multiplexer Output Re-Constructor (ARMOR)

Science.gov (United States)

2017-07-01

Output Re-Constructor 1. General This standard defines the recommended multiplexer format for single-channel data recording on small-format (1/2 in...which is 1-based, is determined by the position of the channel’s module in the ARMOR system . The first input channel found in the ARMOR system is

Fabrication, testing and modeling of a new flexible armor inspired from natural fish scales and osteoderms

International Nuclear Information System (INIS)

Chintapalli, Ravi Kiran; Mirkhalaf, Mohammad; Dastjerdi, Ahmad Khayer; Barthelat, Francois

2014-01-01

Crocodiles, armadillo, turtles, fish and many other animal species have evolved flexible armored skins in the form of hard scales or osteoderms, which can be described as hard plates of finite size embedded in softer tissues. The individual hard segments provide protection from predators, while the relative motion of these segments provides the flexibility required for efficient locomotion. In this work, we duplicated these broad concepts in a bio-inspired segmented armor. Hexagonal segments of well-defined size and shape were carved within a thin glass plate using laser engraving. The engraved plate was then placed on a soft substrate which simulated soft tissues, and then punctured with a sharp needle mounted on a miniature loading stage. The resistance of our segmented armor was significantly higher when smaller hexagons were used, and our bio-inspired segmented glass displayed an increase in puncture resistance of up to 70% compared to a continuous plate of glass of the same thickness. Detailed structural analyses aided by finite elements revealed that this extraordinary improvement is due to the reduced span of individual segments, which decreases flexural stresses and delays fracture. This effect can however only be achieved if the plates are at least 1000 stiffer than the underlying substrate, which is the case for natural armor systems. Our bio-inspired system also displayed many of the attributes of natural armors: flexible, robust with ‘multi-hit’ capabilities. This new segmented glass therefore suggests interesting bio-inspired strategies and mechanisms which could be systematically exploited in high-performance flexible armors. This study also provides new insights and a better understanding of the mechanics of natural armors such as scales and osteoderms. (paper)

Mechanisms of stability of armored bubbles: FY 1996 Final Report

International Nuclear Information System (INIS)

Rossen, W.R.; Kam, S.I.

1996-11-01

Theoretical and experimental studies examine how a coating, or open-quotes armor,close quotes of partially wetted solid particles can stabilize tiny bubbles against diffusion of gas into the surrounding liquid, in spite of the high capillary pressures normally associated with such bubbles. Experiments with polymethylmethacrylate (PNMA) beads and carbonated water demonstrate that armored bubbles can persist for weeks in liquid unsaturated with respect to the gas in the bubbles. This question is of concern regarding gas discharges from waste tanks at the Hanford reservation. The stresses on the solid-solid contacts between particles in such cases is large and could drive sintering of the particles into a rigid framework. Stability analysis suggests that a slightly shrunken bubble would not expel a solid particle from its armor to relieve stress and allow the bubble to shrink further. Expulsion of particles from more stressed bubbles at zero capillary pressure is energetically favored in some cases. It is not clear, however, whether this expulsion would proceed spontaneously from a small perturbation or require a large initial disturbance of the bubble. In some cases, it appears that a bubble would expel some particles and shrink, but the bubble would approach a final, stable size rather than disappear completely. This simplified analysis leaves out several factors. For instance, only one perturbation toward expelling a solid from the armor is considered; perhaps other perturbations would be more energetically favored than that tested. Other considerations (particle deformation, surface roughness, contact-angle hysteresis, and adhesion or physical bonding between adjacent particles) would make expelling solids more difficult than indicated by this theoretical study

Micro-engineered first wall tungsten armor for high average power laser fusion energy systems

Science.gov (United States)

Sharafat, Shahram; Ghoniem, Nasr M.; Anderson, Michael; Williams, Brian; Blanchard, Jake; Snead, Lance; HAPL Team

2005-12-01

The high average power laser program is developing an inertial fusion energy demonstration power reactor with a solid first wall chamber. The first wall (FW) will be subject to high energy density radiation and high doses of high energy helium implantation. Tungsten has been identified as the candidate material for a FW armor. The fundamental concern is long term thermo-mechanical survivability of the armor against the effects of high temperature pulsed operation and exfoliation due to the retention of implanted helium. Even if a solid tungsten armor coating would survive the high temperature cyclic operation with minimal failure, the high helium implantation and retention would result in unacceptable material loss rates. Micro-engineered materials, such as castellated structures, plasma sprayed nano-porous coatings and refractory foams are suggested as a first wall armor material to address these fundamental concerns. A micro-engineered FW armor would have to be designed with specific geometric features that tolerate high cyclic heating loads and recycle most of the implanted helium without any significant failure. Micro-engineered materials are briefly reviewed. In particular, plasma-sprayed nano-porous tungsten and tungsten foams are assessed for their potential to accommodate inertial fusion specific loads. Tests show that nano-porous plasma spray coatings can be manufactured with high permeability to helium gas, while retaining relatively high thermal conductivities. Tungsten foams where shown to be able to overcome thermo-mechanical loads by cell rotation and deformation. Helium implantation tests have shown, that pulsed implantation and heating releases significant levels of implanted helium. Helium implantation and release from tungsten was modeled using an expanded kinetic rate theory, to include the effects of pulsed implantations and thermal cycles. Although, significant challenges remain micro-engineered materials are shown to constitute potential

Micro-engineered first wall tungsten armor for high average power laser fusion energy systems

International Nuclear Information System (INIS)

Sharafat, Shahram; Ghoniem, Nasr M.; Anderson, Michael; Williams, Brian; Blanchard, Jake; Snead, Lance

2005-01-01

The high average power laser program is developing an inertial fusion energy demonstration power reactor with a solid first wall chamber. The first wall (FW) will be subject to high energy density radiation and high doses of high energy helium implantation. Tungsten has been identified as the candidate material for a FW armor. The fundamental concern is long term thermo-mechanical survivability of the armor against the effects of high temperature pulsed operation and exfoliation due to the retention of implanted helium. Even if a solid tungsten armor coating would survive the high temperature cyclic operation with minimal failure, the high helium implantation and retention would result in unacceptable material loss rates. Micro-engineered materials, such as castellated structures, plasma sprayed nano-porous coatings and refractory foams are suggested as a first wall armor material to address these fundamental concerns. A micro-engineered FW armor would have to be designed with specific geometric features that tolerate high cyclic heating loads and recycle most of the implanted helium without any significant failure. Micro-engineered materials are briefly reviewed. In particular, plasma-sprayed nano-porous tungsten and tungsten foams are assessed for their potential to accommodate inertial fusion specific loads. Tests show that nano-porous plasma spray coatings can be manufactured with high permeability to helium gas, while retaining relatively high thermal conductivities. Tungsten foams where shown to be able to overcome thermo-mechanical loads by cell rotation and deformation. Helium implantation tests have shown, that pulsed implantation and heating releases significant levels of implanted helium. Helium implantation and release from tungsten was modeled using an expanded kinetic rate theory, to include the effects of pulsed implantations and thermal cycles. Although, significant challenges remain micro-engineered materials are shown to constitute potential

Calculation of Equivalent Resistance for Ground Wires Twined with Armor Rods in Contact Terminals

Directory of Open Access Journals (Sweden)

Gang Liu

2018-03-01

Full Text Available Ground wire breakage accidents can destroy the stable operation of overhead lines. The excessive temperature increase arising from the contact resistance between the ground wire and armor rod in the contact terminal is one of the main reasons causing the breakage of ground wires. Therefore, it is necessary to calculate the equivalent resistance for ground wires twined with armor rods in contact terminals. According to the actual distribution characteristics of the contact points in the contact terminal, a three-dimensional electromagnetic field simulation model of the contact terminal was established. Based on the model, the current distribution in the contact terminal was obtained. Subsequently, the equivalent resistance of a ground wire twined with the armor rod in the contact terminal was calculated. The effects of the factors influencing the equivalent resistance were also discussed. The corresponding verification experiments were conducted on a real ground wire on a contact terminal. The measurement results of the equivalent resistance for the armor rod segment showed good agreement with the electromagnetic modeling results.

Damage Assessment in TiB2 Ceramic Armor Targets

National Research Council Canada - National Science Library

Rupert, Nevin

2001-01-01

The interaction between long rods and ceramics is only partially understood; however, this understanding is essential in the design of improved performance of impact-resistant materials and armor system design applications...

Mock-up development of new warship protective armor structure and feasibility analysis of ship installation

Directory of Open Access Journals (Sweden)

ZHENG Pan

2017-05-01

Full Text Available To ensure the installation of the new design of protective armor structure on larger warships,a study into the installation process of the structure of this armor is carried out to improve installation efficiency and ensure the protective effect. This paper proposes a typical composite armor structure design which is composed of ‘silicate aerogel/ballistic ceramic/high-strength polyethylene/silicate aerogel’. The study analyzes the modeling design,down-selection of materials and equipment,and real ship mock-up technical development. The reliability and application of high strength polyethylene in response to high temperatures in the real ship installation process is discussed. The results show that high-temperatures during welding have no negative impact on the high strength polyethylene of the armored structure. The design demonstrates that this installation process is feasible and can be provided as an alternative solution by virtues of its good maneuverability,controllable precision,checkable quality and high reliability.

Experimental studies on tungsten-armor impact on nuclear responses of solid breeding blanket

International Nuclear Information System (INIS)

Sato, S.; Nakao, M.; Verzilov, Y.; Ochiai, K.; Wada, M.; Kubota, N.; Kondo, K.; Yamauchi, M.; Enoeda, M.; Nishitani, T.

2005-01-01

In order to experimentally evaluate the tungsten armor impact on tritium production of the solid breeding blanket being developed by JAERI for tokamak-type DEMO reactors, neutronics integral experiments have been performed by using DT neutrons at Fusion Neutron Source (FNS) facility of JAERI. Solid breeding blanket mockups relevant to the DEMO blanket have been applied in this study. The mockups are constructed by a set of layers consisting of 0 - 25.2 mm thick tungsten, 16 mm thick F82H, 12 mm thick Li 2 TiO 3 and 100 - 200mm thick beryllium with cross-section of 660 x 660 mm in maximum. Pellets of Li 2 CO 3 are embedded inside the Li 2 TiO 3 layers to measure the tritium production rate. By installing the 5, 12.6 and 25.2 mm thick tungsten armors, sum of the integrated tritium productions at the pellets are reduced by about 2, 3 and 6 % relative to the case without the armor, respectively. Numerical calculations have been conducted using the Monte Carlo code. Calculation results for sum of the integrated tritium productions in the case with the tungsten armor agree well with the experiment data within 4% and 19% under condition without and with a neutron reflector, respectively. (author)

The Future Role of Armor in Central-Eastern Europe

National Research Council Canada - National Science Library

Lorincz, Gabor

2003-01-01

... attrition based military cultures. It seems since the end of the Cold War the armor community has had identity problems caused by the events and the triggered military solutions of the last ten years...

Composite treatment of ceramic tile armor

Science.gov (United States)

Hansen, James G. R. [Oak Ridge, TN; Frame, Barbara J [Oak Ridge, TN

2010-12-14

An improved ceramic tile armor has a core of boron nitride and a polymer matrix composite (PMC) facing of carbon fibers fused directly to the impact face of the tile. A polyethylene fiber composite backing and spall cover are preferred. The carbon fiber layers are cured directly onto the tile, not adhered using a separate adhesive so that they are integral with the tile, not a separate layer.

Friction Stir Weld Failure Mechanisms in Aluminum-Armor Structures Under Ballistic Impact Loading Conditions

Science.gov (United States)

2013-01-01

REPORT Friction Stir Weld Failure Mechanisms in Aluminum-Armor Structures Under Ballistic Impact Loading Conditions 14. ABSTRACT 16. SECURITY...properties and of the attendant ballistic-impact failure mechanisms in prototypical friction stir welding (FSW) joints found in armor structures made of high...mechanisms, friction stir welding M. Grujicic, B. Pandurangan, A. Arakere, C-F. Yen, B. A. Cheeseman Clemson University Office of Sponsored Programs 300

75 FR 25208 - Announcement of Body Armor Research Needs Meeting

Science.gov (United States)

2010-05-07

... manufacturing community (including fiber producers, fabric producers, and armor manufacturers) and government..., passport issuing country, passport number, city of birth, country of birth, date of birth, gender, title...

Co-Injection Resin Transfer Molding for Optimization of Integral Armor

National Research Council Canada - National Science Library

Fink, B

1998-01-01

... enhancement over existing defense industry practices. CIRTM was invented and developed for single-step manufacturing of integral armor by enabling simultaneous injection of multiple resins into multi-layer preform...

Highly deformable bones: unusual deformation mechanisms of seahorse armor.

Science.gov (United States)

Porter, Michael M; Novitskaya, Ekaterina; Castro-Ceseña, Ana Bertha; Meyers, Marc A; McKittrick, Joanna

2013-06-01

Multifunctional materials and devices found in nature serve as inspiration for advanced synthetic materials, structures and robotics. Here, we elucidate the architecture and unusual deformation mechanisms of seahorse tails that provide prehension as well as protection against predators. The seahorse tail is composed of subdermal bony plates arranged in articulating ring-like segments that overlap for controlled ventral bending and twisting. The bony plates are highly deformable materials designed to slide past one another and buckle when compressed. This complex plate and segment motion, along with the unique hardness distribution and structural hierarchy of each plate, provide seahorses with joint flexibility while shielding them against impact and crushing. Mimicking seahorse armor may lead to novel bio-inspired technologies, such as flexible armor, fracture-resistant structures or prehensile robotics. Copyright © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Designing an Innovative Composite Armor System for Affordable Ballistic Protection

National Research Council Canada - National Science Library

Ma, Zheng-Dong; Wang, Hui; Cui, Yushun; Rose, Douglas; Socks, Adria; Ostberg, Donald

2006-01-01

.... This paper focuses on the frontal armor plate and back plate design problems with demonstration examples, including both results of the virtual prototyping and ballistic testing for proof-of-concept...

Under the armor: X-ray computed tomographic reconstruction of the internal skeleton of Coahomasuchus chathamensis (Archosauria: Aetosauria) from the Upper Triassic of North Carolina, USA, and a phylogenetic analysis of Aetosauria.

Science.gov (United States)

Hoffman, Devin K; Heckert, Andrew B; Zanno, Lindsay E

2018-01-01

Aetosauria is a clade of heavily armored, quadrupedal omnivorous to herbivorous archosaurs known from the Late Triassic across what was the supercontinent of Pangea. Their abundance in many deposits relative to the paucity of other Triassic herbivores indicates that they were key components of Late Triassic ecosystems. However, their evolutionary relationships remain contentious due, in large part, to their extensive dermal armor, which often obstructs observation of internal skeletal anatomy and limits access to potentially informative characters. In an attempt to address this problem we reanalyzed the holotype of a recently described species of Coahomasuchus , C. chathamensis , from the Sanford sub-basin of North Carolina using computed tomography (CT). CT scans of the holotype specimen clarify preservation of the skeleton, revealing several articulated vertebrae and ribs, an isolated vertebra, left ulna, left scapula, and the right humerus, though none of the material resulted in updated phylogenetic scorings. Reexamination of aetosaur materials from the holotype locality also indicates that several isolated osteoderms and elements of the appendicular skeleton are newly referable. Based on these results, we update the Coahomasuchus chathamensis hypodigm and conduct a revised phylogenetic analysis with improved character scorings for Coahomasuchus and several other aetosaurs. Our study recovers Coahomasuchus in a polytomy with Aetosaurus and the Typothoracinae, in contrast with a recent analysis that recovered Coahomasuchus as a wild-card taxon.

Virtual Experiments to Determine Behind-Armor Debris for Survivability Analysis

National Research Council Canada - National Science Library

Prakash, Anand

2004-01-01

.... This data is currently generated by conducting laboratory experiments in a standard set-up in which each threat projectile is fired on the actual armor and the BAD pattern is captured on witness plates...

Testing method for ceramic armor and bare ceramic tiles

NARCIS (Netherlands)

Carton, E.P.; Roebroeks, G.H.J.J.

2014-01-01

TNO has developed an alternative, more configuration independent ceramic test method than the standard Depth-of-Penetration test method. In this test ceramic tiles and ceramic based armor are evaluated as target without a semi-infinite backing layer. An energy approach is chosen to evaluate and rank

Ceramic/polymer functionally graded material (FGM) lightweight armor system

Energy Technology Data Exchange (ETDEWEB)

Petrovic, J.J.; McClellan, K.J.

1998-12-31

This is the final report of a two-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). Functionally graded material is an enabling technology for lightweight body armor improvements. The objective was to demonstrate the ability to produce functionally graded ceramic-polymer and ceramic-metal lightweight armor materials. This objective involved two aspects. The first and key aspect was the development of graded-porosity boron-carbide ceramic microstructures. The second aspect was the development of techniques for liquid infiltration of lightweight metals and polymers into the graded-porosity ceramic. The authors were successful in synthesizing boron-carbide ceramic microstructures with graded porosity. These graded-porosity boron-carbide hot-pressed pieces were then successfully liquid-infiltrated in vacuum with molten aluminum at 1,300 C, and with liquid polymers at room temperature. Thus, they were able to demonstrate the feasibility of producing boron carbide-aluminum and boron carbide-polymer functionally graded materials.

Dynamic lift on an artificial static armor layer during highly unsteady open channel flow

OpenAIRE

Spiller, Stephan Mark; Ruther, Nils; Friedrich, Heide

2015-01-01

The dynamic lift acting on a 100 mm × 100 mm section of a static armor layer during unsteady flow is directly measured in a series of physical experiments. The static armor layer is represented by an artificial streambed mold, made from an actual gravel bed. Data from a total of 190 experiments are presented, undertaken in identical conditions. Results show that during rapid discharge increases, the dynamic lift on the streambed repeatedly exhibits three clear peaks. The magnitude of the obse...

Application of nondestructive ion beam analysis to measure variations in the elemental composition of armor materials

Energy Technology Data Exchange (ETDEWEB)

Pallone, Arthur. E-mail: art.pallone@murraystate.edu; Demaree, John; Adams, Jane. E-mail: jadams@arl.army.mil

2004-06-01

Lightweight, state-of-the-art armors rely on ceramics for their enhanced performance. One goal of the United States Army is to expand the industrial base of companies that provide the armors. A systematic study of armor performance as a function of ceramic stoichiometry will result in a better understanding of the fundamental relations between composition and mechanical performance. One ceramic of interest is aluminum oxynitride (AlON). The stoichiometries of representative samples of AlON were investigated with the nondestructive techniques of Rutherford backscattering spectrometry and resonant nuclear reaction analysis. Future tests of the performance of the AlON samples are to be correlated with the stoichiometries, and hence will lead to optimum, standardized processes for the manufacture of the AlON.

Front-facing fluoropolymer-coated armor composite

OpenAIRE

Gamache, Raymond M.; Roland, Charles M.; Fragiadakis, Daniel M.

2018-01-01

Patent A front-facing armor system utilizing a composite laminate backed by a high hardness substrate. The composite laminate comprises a series of first and second layers. The first layer of the bi-layer laminate system is a polymer with a density of at least 1.8 g/ᵌ and having both an amorphous and crystalline phase, and having phase transformation pressure of at least 0.5 GPa at a temperature of 20° C. The second layer of each bi-layer provides acoustic impedance ...

Hydroxyapatite-armored poly(ε-caprolactone) microspheres and hydroxyapatite microcapsules fabricated via a Pickering emulsion route.

Science.gov (United States)

Fujii, Syuji; Okada, Masahiro; Nishimura, Taiki; Maeda, Hayata; Sugimoto, Tatsuya; Hamasaki, Hiroyuki; Furuzono, Tsutomu; Nakamura, Yoshinobu

2012-05-15

Hydroxyapatite (HAp) nanoparticle-armored poly(ε-caprolactone) (PCL) microspheres were fabricated via a "Pickering-type" emulsion solvent evaporation method in the absence of any molecular surfactants. It was clarified that the interaction between carbonyl/carboxylic acid groups of PCL and the HAp nanoparticles at an oil-water interface played a crucial role in the preparation of the stable Pickering-type emulsions and the HAp nanoparticle-armored microspheres. The HAp nanoparticle-armored PCL microspheres were characterized in terms of size, size distribution, morphology, and chemical compositions using scanning electron microscopy, laser diffraction, energy dispersive X-ray microanalysis, and thermogravimetric analysis. The presence of HAp nanoparticles at the surface of the microspheres was confirmed by scanning electron microscopy and energy dispersive X-ray microanalysis. Pyrolysis of the PCL cores led to the formation of the corresponding HAp hollow microcapsules. Copyright © 2012 Elsevier Inc. All rights reserved.

Weldability and Impact Energy Properties of High-Hardness Armor Steel

Science.gov (United States)

Cabrilo, Aleksandar; Geric, Katarina; Jovanovic, Milos; Vukic, Lazic

2018-03-01

In this study, the weldability of high-hardness armor steel by the gas metal arc welding method has been investigated. The study was aimed at determining the weakness points of manual welding compared to automated welding through microhardness testing, the cooling rate, tensile characteristics and nondestructive analysis. Detailed studies were performed for automated welding on the impact energy and microhardness in the fusion line, as the most sensitive zone of the armor steel weld joint. It was demonstrated that the selection of the preheating and interpass temperature is important in terms of the cooling rate and quantity of diffusible and retained hydrogen in the weld joint. The tensile strength was higher than 800 MPa. The width of the heat-affected zone did not exceed 15.9 mm, measured from the weld centerline, while the impact energy results were 74 and 39 J at 20 and - 40 °C, respectively.

Armor of cermet with metal therein increasing with depth

Science.gov (United States)

Wilkins, M.L.; Holt, A.C.; Cline, C.F.; Foreschner, K.E.

1973-07-01

The system described consists of a ceramic matrix having a gradient of fine ductile metallic particles dispersed therein in an amount of from 0.0%, commencing at the front or impact surface of the armor, to about 2 to 15% by volume along the interface to the back of the system. (auth)

Function-Oriented Material Design of Joints for Advance Armors Under Ballistic Impact

National Research Council Canada - National Science Library

Ma, Zheng-Dong; Wang, Hui; Raju, Basavaraju

2004-01-01

The objective of this research is to develop a system of software tools based on a new design methodology for the efficient composite armor structural design under ballistic impact loading conditions...

Sensitization of Naturally Aged Aluminum 5083 Armor Plate

Science.gov (United States)

2015-07-29

5 - 1 - SENSITIZATION OF NATURALLY AGED ALUMINUM 5083 ARMOR PLATE INTRODUCTION Aluminum -magnesium alloys are important for both ship...boundaries [3,4]. The magnesium-rich phase (normally β-Al3Mg2) is highly anodic with respect to the surrounding aluminum phase, thus is susceptible... alloys , and with varying amounts of debris scattered about the surface consistent with corrosion product, Figure 2b, that often forms over time within

Effects of Body Armor Fit on Marksmanship Performance

Science.gov (United States)

2016-09-01

SIMULATORS SIZES(DIMENSIONS) IOTV(IMPROVED OUTER TACTICAL VEST ) U.S. Army Natick Soldier Research, Development and Engineering Center...configurations were counterbalanced to control for order effect. Body Armor. The U.S. Army, standard issue Improved Outer Tactical Vest (IOTV) Generation III...targets at that great of an arc (≥50°) was not operationally realistic. Fig. 2 Improved outer tactical vest (IOTV) Gen III Table 1 Distribution of

Miniaturized hand held microwave interference scanning system for NDE of dielectric armor and armor systems

International Nuclear Information System (INIS)

Schmidt, Karl F.; Little, Jack R.; Ellingson, William A.; Meitzler, Thomas J.; Green, William

2011-01-01

Inspection of ceramic-based armor has advanced through development of a microwave-based, portable, non-contact NDE system. Recently, this system was miniaturized and made wireless for maximum utility in field applications. The electronic components and functionality of the laboratory system are retained, with alternative means of position input for creation of scan images. Validation of the detection capability was recently demonstrated using specially fabricated surrogates and ballistic impact-damaged specimens. The microwave data results have been compared to data from laboratory-based microwave interferometry systems and digital x-ray imaging. The microwave interference scanning has been shown to reliably detect cracks, laminar features and material property variations. The authors present details of the system operation, descriptions of the test samples used and recent results obtained.

A parametric design of ceramic faced composite armor subject to air weapon threats

International Nuclear Information System (INIS)

Guo, Y N; Sun, Q

2015-01-01

By taking into consideration the two categories of military projectile threats to aircraft structures, an optimal layer configuration of ceramic faced composite armor was designed in this paper. Using numerical simulations and the same layer arrangement of ceramic, UHMWPE, and carbon fiber laminates, a parametric finite element model using LS-DYNA code was built. Several thickness combinations were analyzed in order to determine the final lightest configuration that is capable of supporting a high-speed impact load and HEI blast wave load, which implements a high anti-penetration design for aircraft armor. This configuration can be used to improve the anti-impact ability of aircraft structures as well as achieve a structure/function integration design that considers a lighter weight. (paper)

PELE侵彻复合装甲数值模拟%Numerical Simulation of PELE Penetrating Composite Armor

Institute of Scientific and Technical Information of China (English)

李干; 王志军; 王妍; 李硕

2016-01-01

为了探究横向增强型侵彻体(PELE)侵彻复合装甲后的毁伤效果,采用显式非线性动力分析软件AUTODYN,对装填特氟龙(聚四氟乙烯)的侵彻膨胀弹以900 m/s着靶速度侵彻复合靶板的过程进行了数值模拟,得到PELE弹对复合靶侵彻破坏效应及相关参数.结果表明:聚碳酸酯(玻璃纤维)、聚氨酯(泡沫塑料)与凯夫拉复合装甲的结构均被PELE的横向效应所破坏;复合装甲的夹心材料不同,靶板的破坏程度也不尽相同;复合装甲能对PELE的横向效应起到一定的抑制作用,而凯夫拉材料抑制作用较好.%In order to analyze the damage effect of the penetrator with enhanced lateral efficiency( PELE) penetrating composite armor, an explicit nonlinear dynamic analysis software AUTODYN was used to simulate the process of PELE filled with Teflon( polytetrafluoroethylene) penetrating composite target plate using the speed of 900 m/s, and the destructive effect and relevant parameters of PELE penetrating composite armor were obtained finally. The result shows that the composite armor constructed by polycarbonate( glass fibre) ,polyurethane and Kevlar is damaged seriously by lateral efficiency of PELE. The different composite-armors have different damage. The composite armor has definite inhibitory effect on lateral efficiency of PELE,and the inhibitory effect of Kevlar is better.

Defining the RNA Internal Loops Preferred by Benzimidazole Derivatives via Two-Dimensional Combinatorial Screening and Computational Analysis

Science.gov (United States)

Velagapudi, Sai Pradeep; Seedhouse, Steven J.; French, Jonathan

2011-01-01

RNA is an important therapeutic target, however, RNA targets are generally underexploited due to a lack of understanding of the small molecules that bind RNA and the RNA motifs that bind small molecules. Herein, we describe the identification of the RNA internal loops derived from a 4096-member 3×3 nucleotide loop library that are the most specific and highest affinity binders to a series of four designer, drug-like benzimidazoles. These studies establish a potentially general protocol to define the highest affinity and most specific RNA motif targets for heterocyclic small molecules. Such information could be used to target functionally important RNAs in genomic sequence. PMID:21604752

Flow and Turbulence at Rubble-Mound Breakwater Armor Layers under Solitary Wave

DEFF Research Database (Denmark)

Jensen, Bjarne; Christensen, Erik Damgaard; Sumer, B. Mutlu

2015-01-01

This paper presents the results of an experimental investigation of the flow and turbulence at the armor layer of rubble-mound breakwaters during wave action. The study focused on the details of the flow and turbulence in the armor layer and on the effect of the porous core on flow and stability....... To isolate the processes involved with the flow in the porous core, experiments were conducted with increasing complexity. Specifically, three parallel experiments were performed including (1) an impermeable smooth breakwater slope, (2) an impermeable breakwater slope with large roughness elements added...... to the breakwater, and (3) a porous breakwater where the porous core was added below the breakwater front. One breakwater slope of 1:1.5 was applied. In this paper the focus is on the details of a single sequence of wave approach, run-up, and rundown. To isolate this sequence the experiments were performed applying...

Transformation: Transition From a Heavy to a Lighter Family of Armored Fighting Vehicles

National Research Council Canada - National Science Library

Petty, Thomas

2001-01-01

Since the end of World War II, the single event with greatest impact on the development of armor was the war that did not happen-the expected conflict between the United States and the Soviet Union...

27 CFR 478.37 - Manufacture, importation and sale of armor piercing ammunition.

Science.gov (United States)

2010-04-01

... 27 Alcohol, Tobacco Products and Firearms 3 2010-04-01 2010-04-01 false Manufacture, importation... COMMERCE IN FIREARMS AND AMMUNITION Administrative and Miscellaneous Provisions § 478.37 Manufacture, importation and sale of armor piercing ammunition. No person shall manufacture or import, and no manufacturer...

The genetic architecture of parallel armor plate reduction in threespine sticklebacks.

Directory of Open Access Journals (Sweden)

Pamela F Colosimo

2004-05-01

Full Text Available How many genetic changes control the evolution of new traits in natural populations? Are the same genetic changes seen in cases of parallel evolution? Despite long-standing interest in these questions, they have been difficult to address, particularly in vertebrates. We have analyzed the genetic basis of natural variation in three different aspects of the skeletal armor of threespine sticklebacks (Gasterosteus aculeatus: the pattern, number, and size of the bony lateral plates. A few chromosomal regions can account for variation in all three aspects of the lateral plates, with one major locus contributing to most of the variation in lateral plate pattern and number. Genetic mapping and allelic complementation experiments show that the same major locus is responsible for the parallel evolution of armor plate reduction in two widely separated populations. These results suggest that a small number of genetic changes can produce major skeletal alterations in natural populations and that the same major locus is used repeatedly when similar traits evolve in different locations.

Armor systems including coated core materials

Science.gov (United States)

Chu, Henry S [Idaho Falls, ID; Lillo, Thomas M [Idaho Falls, ID; McHugh, Kevin M [Idaho Falls, ID

2012-07-31

An armor system and method involves providing a core material and a stream of atomized coating material that comprises a liquid fraction and a solid fraction. An initial layer is deposited on the core material by positioning the core material in the stream of atomized coating material wherein the solid fraction of the stream of atomized coating material is less than the liquid fraction of the stream of atomized coating material on a weight basis. An outer layer is then deposited on the initial layer by positioning the core material in the stream of atomized coating material wherein the solid fraction of the stream of atomized coating material is greater than the liquid fraction of the stream of atomized coating material on a weight basis.

Standard Methodology for Assessment of Range of Motion While Wearing Body Armor

Science.gov (United States)

2013-09-30

76 STANDING STATURE (with Footwear ...Thanks also to Natick Soldier Research, Development and Engineering Center and the Soldier Integrated Protection Team and those project officers who...being fit into their best body armor size for that configuration): • Standing Stature (with footwear ) • Seated Stature At the goniometer station

1st International Symposium on Stress-Associated RNA Granules in Human Disease and Viral Infection

Directory of Open Access Journals (Sweden)

Bruce W. Banfield

2014-09-01

Full Text Available In recent years, important linkages have been made between RNA granules and human disease processes. On June 8-10 of this year, we hosted a new symposium, dubbed the 1st International Symposium on Stress-Associated RNA Granules in Human Disease and Viral Infection. This symposium brought together experts from diverse research disciplines ranging from cancer and neuroscience to infectious disease. This report summarizes speaker presentations and highlights current challenges in the field.

Development of conductively cooled first wall armor and actively cooled divertor structure for ITER/FER

International Nuclear Information System (INIS)

Ioki, K.; Yamada, M.; Sakata, S.; Okada, K.; Toyoda, M.; Shimizu, K.; Tsujimura, S.; Iimura, M.; Akiba, M.; Araki, M.; Seki, M.

1991-01-01

Based on the design requirements for the plasma facing components in ITER/FER, we have performed design studies on the conductively cooled first wall armor and the divertor plate with sliding supports. The full-scale armor tiles were fabricated for heat load tests, and good thermal performances were obtained in heat load tests of 0.2-0.4 MW/m 2 . It is shown by the thermomechanical analysis on the divertor plate that thermal stresses and bending deformation are reduced significantly by using the sliding supports. The divertor test module with the sliding supports has been fabricated to investigate its fabricability and to verify the functions of the sliding supports during a high heat load of about 10 MW/m 2 . (orig.)

Modeling the Biodynamical Response of the Human Thorax with Body Armor from a Bullet Impact

National Research Council Canada - National Science Library

Lobuono, John

2001-01-01

.... The finite element model of the human thorax is validated by comparing the model's results to experimental data obtained from cadavers wearing a protective body armor system undergoing a projectile impact...

Modeling the Biodynamical Response of the Human Thorax With Body Armor From a Bullet Impact

National Research Council Canada - National Science Library

Lobuono, John

2001-01-01

.... The finite element model of the human thorax is validated by comparing the model's results to experimental data obtained from cadavers wearing a protective body armor system undergoing a projectile impact...

Laser-induced micro-jetting from armored droplets

KAUST Repository

Marston, J. O.

2015-06-23

We present findings from an experimental study of laser-induced cavitation within a liquid drop coated with a granular material, commonly referred to as “armored droplets” or “liquid marbles.” The cavitation event follows the formation of plasma after a nanosecond laser pulse. Using ultra-high-speed imaging up to 320,610 fps, we investigate the extremely rapid dynamics following the cavitation, which manifests itself in the form of a plethora of micro-jets emanating simultaneously from the spaces between particles on the surface of the drop. These fine jets break up into droplets with a relatively narrow diameter range, on the order of 10 μm. © 2015, Springer-Verlag Berlin Heidelberg.

Modeling the Biodynamical Response of the Human Thorax with Body Armor from a Bullet Impact

National Research Council Canada - National Science Library

Lobuono, John

2001-01-01

The objective of this study is to develop a finite element model of the human thorax with a protective body armor system so that the model can adequately determine the thorax's biodynamical response...

Modeling the Biodynamical Response of the Human Thorax With Body Armor From a Bullet Impact

National Research Council Canada - National Science Library

Lobuono, John

2001-01-01

The objective of this study is to develop a finite element model of the human thorax with a protective body armor system so that the model can adequately determine the thorax's biodynamical response...

Characteristics of behind armor blunt trauma produced by bullets with different structural materials: an experimental study

Directory of Open Access Journals (Sweden)

Ling-qing WANG

2013-07-01

Full Text Available Objective　To investigate the effect of structural materials of bullets on behind armor blunt trauma (BABT. Methods　Ten healthy male Landraces were randomly divided into two groups (5 each: 56 type 7.62-mm rifle bullet group and SS109 5.56-mm rifle bullet group. The kinetic energy of two types of bullets was adjusted to the same level (about 1880J by the way of grow downwards gunpowder. Then the animals as protected with both grade NIJ Ⅲ ceramic hard armor and grade Ⅱ police soft body armor, were shot at the left midclavicular line of fourth intercostal space (shooting distance was 25m. The damage to the animals was observed. Other 2 healthy male Landraces were selected, and biomechanical sensor was subcutaneously implanted into the soft tissue in precordium and intracalvarium to detect the pressure at the time point of bullet contact under the protection of armor, and the relationship between pressure and damage was analyzed. Results　Respiration, heart rate and systolic arterial pressure of animals in two groups were all elevated after injury, but there was no significant difference between the two groups. No obvious change was found on blood oxygen saturation of both groups. Gross anatomy showed the predominant local injury was cardiac and pulmonary contusions. The area of pulmonary hemorrhage of 7.62mm group was 6.00%±3.18%, significantly higher than that of 5.56mm group (3.59%±2.11%, P<0.05. Histopathological examination revealed acute injuries of lung tissues, myocardial tissue and cerebral cortical neurons. The contents of cardiac troponin T (TnT, creatine kinase (CK and creatine kinase-MB (CK-MB isoenzyme were all increased 3 hours after injury, and the rise was higher in 7.62mm group than in 5.56mm group (P<0.05. Biomechanical testing showed the pressure of precordium and intracalvarium was elevated at the moment of bullet contact, and the rise was higher in 7.62mm group than in 5.56mm group (P<0.05. Conclusions�

Physics and Technology of Transparent Ceramic Armor: Sintered Al2O3 vs Cubic Materials

National Research Council Canada - National Science Library

Krell, Andreas; Hutzler, Thomas; Klimke, Jens

2006-01-01

Sintered sub-micrometer alumina (alpha-Al2O3) is the hardest transparent armor. However, its trigonal structure gives rise to a strong thickness effect that makes thicker components translucent. Cubic ceramics (no birefringence...

Improving the Success of Light Armored Vehicle Drivers: A Qualitative Descriptive Narrative Study

Science.gov (United States)

Byrd, Dathan

2016-01-01

This qualitative descriptive narrative research was the first known study to collect participants' perceptions on the effectiveness of the Marine Corps' Light Armored Vehicle driver training. The general problem was the Marine Corps' vague guidance on curriculum development, instruction, and assessment for driver training of the Light armored…

Differential Regulation of rRNA and tRNA Transcription from the rRNA-tRNA Composite Operon in Escherichia coli.

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Hiraku Takada

Full Text Available Escherichia coli contains seven rRNA operons, each consisting of the genes for three rRNAs (16S, 23S and 5S rRNA in this order and one or two tRNA genes in the spacer between 16S and 23S rRNA genes and one or two tRNA genes in the 3' proximal region. All of these rRNA and tRNA genes are transcribed from two promoters, P1 and P2, into single large precursors that are afterward processed to individual rRNAs and tRNAs by a set of RNases. In the course of Genomic SELEX screening of promoters recognized by RNA polymerase (RNAP holoenzyme containing RpoD sigma, a strong binding site was identified within 16S rRNA gene in each of all seven rRNA operons. The binding in vitro of RNAP RpoD holoenzyme to an internal promoter, referred to the promoter of riRNA (an internal RNA of the rRNA operon, within each 16S rRNA gene was confirmed by gel shift assay and AFM observation. Using this riRNA promoter within the rrnD operon as a representative, transcription in vitro was detected with use of the purified RpoD holoenzyme, confirming the presence of a constitutive promoter in this region. LacZ reporter assay indicated that this riRNA promoter is functional in vivo. The location of riRNA promoter in vivo as identified using a set of reporter plasmids agrees well with that identified in vitro. Based on transcription profile in vitro and Northern blot analysis in vivo, the majority of transcript initiated from this riRNA promoter was estimated to terminate near the beginning of 23S rRNA gene, indicating that riRNA leads to produce the spacer-coded tRNA. Under starved conditions, transcription of the rRNA operon is markedly repressed to reduce the intracellular level of ribosomes, but the levels of both riRNA and its processed tRNAGlu stayed unaffected, implying that riRNA plays a role in the continued steady-state synthesis of tRNAs from the spacers of rRNA operons. We then propose that the tRNA genes organized within the spacers of rRNA-tRNA composite operons

Production and characterization of ceramics for armor application; Producao e caracterizacao de ceramicas para blindagem balistica

Energy Technology Data Exchange (ETDEWEB)

Alves, J.T.; Lopes, C.M.A. [Instituto Tecnologico de Aeronautica (ITA), Sao Jose dos Campos, SP (Brazil). Div. de Engenharia Mecanica-Aeronautica; Assis, J.M.K.; Melo, F.C.L., E-mail: cmoniz@iae.cta.b [Instituto de Aeronautica e Espaco (IAE), Sao Jose dos Campos, SP (Brazil). Div. de Materiais

2010-07-01

The fabrication of devices for ballistic protection as bullet proof vests and helmets and armored vehicles has been evolving over the past years along with the materials and models used for this specific application. The requirements for high efficient light-weight ballistic protection systems which not interfere in the user comfort and mobility has driven the research in this area. In this work we will present the results of characterization of two ceramics based on alumina and silicon carbide. The ceramics were produced in lab scale and the specific mass, scanning electron microscopy (SEM) microstructure, Vickers hardness, flexural resistance at room temperature and X-ray diffraction were evaluated. Ballistic tests performed in the selected materials showed that the ceramics present armor efficiency. (author)

β-glucuronidase use as a single internal control gene may confound analysis in FMR1 mRNA toxicity studies.

Science.gov (United States)

Kraan, Claudine M; Cornish, Kim M; Bui, Quang M; Li, Xin; Slater, Howard R; Godler, David E

2018-01-01

Relationships between Fragile X Mental Retardation 1 (FMR1) mRNA levels in blood and intragenic FMR1 CGG triplet expansions support the pathogenic role of RNA gain of function toxicity in premutation (PM: 55-199 CGGs) related disorders. Real-time PCR (RT-PCR) studies reporting these findings normalised FMR1 mRNA level to a single internal control gene called β-glucuronidase (GUS). This study evaluated FMR1 mRNA-CGG correlations in 33 PM and 33 age- and IQ-matched control females using three normalisation strategies in peripheral blood mononuclear cells (PBMCs): (i) GUS as a single internal control; (ii) the mean of GUS, Eukaryotic Translation Initiation Factor 4A2 (EIF4A2) and succinate dehydrogenase complex flavoprotein subunit A (SDHA); and (iii) the mean of EIF4A2 and SDHA (with no contribution from GUS). GUS mRNA levels normalised to the mean of EIF4A2 and SDHA mRNA levels and EIF4A2/SDHA ratio were also evaluated. FMR1mRNA level normalised to the mean of EIF4A2 and SDHA mRNA levels, with no contribution from GUS, showed the most significant correlation with CGG size and the greatest difference between PM and control groups (p = 10-11). Only 15% of FMR1 mRNA PM results exceeded the maximum control value when normalised to GUS, compared with over 42% when normalised to the mean of EIF4A2 and SDHA mRNA levels. Neither GUS mRNA level normalised to the mean RNA levels of EIF4A2 and SDHA, nor to the EIF4A2/SDHA ratio were correlated with CGG size. However, greater variability in GUS mRNA levels were observed for both PM and control females across the full range of CGG repeat as compared to the EIF4A2/SDHA ratio. In conclusion, normalisation with multiple control genes, excluding GUS, can improve assessment of the biological significance of FMR1 mRNA-CGG size relationships.

Myotonic Dystrophy Type 1 RNA Crystal Structures Reveal Heterogeneous 1 × 1 Nucleotide UU Internal Loop Conformations

Energy Technology Data Exchange (ETDEWEB)

Kumar, Amit; Park, HaJeung; Fang, Pengfei; Parkesh, Raman; Guo, Min; Nettles, Kendall W.; Disney, Matthew D. (Scripps)

2012-03-27

RNA internal loops often display a variety of conformations in solution. Herein, we visualize conformational heterogeneity in the context of the 5'CUG/3'GUC repeat motif present in the RNA that causes myotonic dystrophy type 1 (DM1). Specifically, two crystal structures of a model DM1 triplet repeating construct, 5'r[{und UU}GGGC(C{und U}G){sub 3}GUCC]{sub 2}, refined to 2.20 and 1.52 {angstrom} resolution are disclosed. Here, differences in the orientation of the 5' dangling UU end between the two structures induce changes in the backbone groove width, which reveals that noncanonical 1 x 1 nucleotide UU internal loops can display an ensemble of pairing conformations. In the 2.20 {angstrom} structure, CUGa, the 5' UU forms a one hydrogen-bonded pair with a 5' UU of a neighboring helix in the unit cell to form a pseudoinfinite helix. The central 1 x 1 nucleotide UU internal loop has no hydrogen bonds, while the terminal 1 x 1 nucleotide UU internal loops each form a one-hydrogen bond pair. In the 1.52 {angstrom} structure, CUGb, the 5' UU dangling end is tucked into the major groove of the duplex. While the canonically paired bases show no change in base pairing, in CUGb the terminal 1 x 1 nucleotide UU internal loops now form two hydrogen-bonded pairs. Thus, the shift in the major groove induced by the 5' UU dangling end alters noncanonical base patterns. Collectively, these structures indicate that 1 x 1 nucleotide UU internal loops in DM1 may sample multiple conformations in vivo. This observation has implications for the recognition of this RNA, and other repeating transcripts, by protein and small molecule ligands.

Extending the Operational Relevance of the Current Heavy Mechanized and Armor Force to 2020 and Beyond

National Research Council Canada - National Science Library

Boston, Gerald

2003-01-01

Can the U.S. Army's current heavy mechanized and armor force adapt emerging Joint Vision 2020 operational concepts, in order to remain relevant to the land power requirements of combatant commanders across...

Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas

Science.gov (United States)

Petrov, Anton I.; Zirbel, Craig L.; Leontis, Neocles B.

2013-01-01

The analysis of atomic-resolution RNA three-dimensional (3D) structures reveals that many internal and hairpin loops are modular, recurrent, and structured by conserved non-Watson–Crick base pairs. Structurally similar loops define RNA 3D motifs that are conserved in homologous RNA molecules, but can also occur at nonhomologous sites in diverse RNAs, and which often vary in sequence. To further our understanding of RNA motif structure and sequence variability and to provide a useful resource for structure modeling and prediction, we present a new method for automated classification of internal and hairpin loop RNA 3D motifs and a new online database called the RNA 3D Motif Atlas. To classify the motif instances, a representative set of internal and hairpin loops is automatically extracted from a nonredundant list of RNA-containing PDB files. Their structures are compared geometrically, all-against-all, using the FR3D program suite. The loops are clustered into motif groups, taking into account geometric similarity and structural annotations and making allowance for a variable number of bulged bases. The automated procedure that we have implemented identifies all hairpin and internal loop motifs previously described in the literature. All motif instances and motif groups are assigned unique and stable identifiers and are made available in the RNA 3D Motif Atlas (http://rna.bgsu.edu/motifs), which is automatically updated every four weeks. The RNA 3D Motif Atlas provides an interactive user interface for exploring motif diversity and tools for programmatic data access. PMID:23970545

Enhancement in ballistic performance of composite hard armor through carbon nanotubes

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Jason Gibson

2013-12-01

Full Text Available The use of carbon nanotubes in composite hard armor is discussed in this study. The processing techniques to make various armor composite panels consisting of Kevlar®29 woven fabric in an epoxy matrix and the subsequent V50 test results for both 44 caliber soft-point rounds and 30 caliber FSP (fragment simulated projectile threats are presented. A 6.5% improvement in the V50 test results was found for a combination of 1.65 wt% loading of carbon nanotubes and 1.65 wt% loading of milled fibers. The failure mechanism of carbon nanotubes during the ballistic event is discussed through scanning electron microscope images of the panels after the failure. Raman Spectroscopy was also utilized to evaluate the residual strain in the Kevlar®29 fibers post shoot. The Raman Spectroscopy shows a Raman shift of 25 cm−1 for the Kevlar®29 fiber utilized in the composite panel that had an enhancement in the V50 performance by using milled fiber and multi-walled carbon nanotubes. Evaluating both scenarios where an improvement was made and other panels without any improvement allows for understanding of how loading levels and synergistic effects between carbon nanotubes and milled fibers can further enhance ballistic performance.

Vacuum UV spectroscopy of armor erosion from plasma gun disruption simulation experiments

International Nuclear Information System (INIS)

Rockett, P.D.; Gahl, J.M.; Zhitlukhin, A.; Arkhipov, K.; Bakhtin, V.; Toporkov, D.; Ovchinnokov, I.; Kuznetsov, V.E.; Titov, V.A.

1995-01-01

Extensive simulations of tokamak disruptions have provided a picture of material erosion that is limited by the transfer of energy from the incident plasma to the armor solid surface through a dense vapor shield. Two transmission grating vacuum ultraviolet (VUV) spectrographs were designed and utilized to study the plasma-material interface in plasma gun simulation experiments. Target materials included POCO graphite, ATJ graphite, boron nitride and plasma-sprayed tungsten. Detailed spectra were recorded with a spatial resolution of ca. 0.7mm resolution on VIKA at Efremov and on 2MK-200 at Troitsk. Time-resolved data with 40-200ns resolution were then recorded along with the same spatial resolution on 2MK-200. The VIKA plasma gun directly illuminated a target with a high-intensity plasma pulse of 2-100MJm -2 with low-energy ions of ca. 100eV. The 2MK-200 plasma gun illuminated the target via a magnetic cusp that permitted only deuterium to pass with energies of ca. 1keV, but which produced a fairly low intensity of 2MJm -2 . Power densities on target ranged from 10 7 to 10 8 Wcm -2 . Emitted spectra were recorded from 15 to 450A over a distance from 0 to 7cm above the armor target surface. The data from both plasma gun facilities demonstrated that the hottest plasma region was sitting several millimeters above the armor tile surface. This apparently constituted the absorption region, which confirmed past computer simulations. Spectra indicated both the species and ionization level that were being ablated from the target, demonstrating impurity content, and showing plasma ablation velocity. Graphite samples clearly showed CV lines as well as impurity lines from O V and O VI. The BN tiles produced textbook examples of BIV and BV, and extensive NIV, V and VI lines. These are being compared with radiation-hydrodynamic calculations. (orig.)

High energy ballistic and fracture comparison between multilayered armor systems using non-woven curaua fabric composites and aramid laminates

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Fábio de Oliveira Braga

2017-10-01

Full Text Available For personal protection against high kinetic energy projectiles, multilayered armor systems (MAS are usually the best option. They combine synergistically the properties of different materials such as ceramics, composites and metals. In the present work, ballistic tests were performed to evaluate multilayered armor systems (MAS using curaua non-woven fabric epoxy composites as second layer. A comparison to a MAS using aramid (Kevlar™ fabric laminates was made. The results showed that the curaua non-woven fabric composites are suitable to the high ballistic applications, and are promising substitutes for aramid fabric laminates. Keywords: Composite, Natural fiber, Curaua fiber, Non-woven fabric, Aramid laminate, Ballistic test

The Armys Armored Multi Purpose Vehicle (AMPV): Background and Issues for Congress

Science.gov (United States)

2016-02-24

1 Information in this section is taken from Christopher F. Foss, Jane’s Armour and Artillery, 2011-2012...for the ABCT AMPV is 2,907 vehicles—a 10 vehicle increase over 2013 quantities. Discussions with the AMPV Program Manager revealed the 10 extra...Selected Weapon Programs, GAO-14-340SP, March 2014, p. 129. 14 CRS Meeting with AMPV Program Manager May 20, 2014. 15 Ibid. The Army’s Armored Multi

Development, installation, and initial operation of DIII-D graphite armor tiles

International Nuclear Information System (INIS)

Anderson, P.M.; Baxi, C.B.; Reis, E.E.; Smith, J.P.; Smith, P.D.

1988-04-01

An upgrade of the DIII-D vacuum vessel protection system has been completed. The ceiling, floor, and inner wall have been armored to enable operation of CIT-relevant doublenull diverted plasmas and to enable the use of the inner wall as a limiting surface. The all- graphite tiles replace the earlier partial coverage armor configuration which consisted of a combination of Inconel tiles and graphite brazed to Inconel tiles. A new all-graphite design concept was chosen for cost and reliability reasons. The 10 minute duration between plasma discharges required the tiles to be cooled by conduction to the water-cooled vessel wall. Using two and three- dimensional analyses, the tile design was optimized to minimize thermal stresses with uniform thermal loading on the plasma-facing surface. Minimizing the stresses around the tile hold-down feature and eliminating stress concentrators were emphasized in the design. The design of the tile fastener system resulted in sufficient hold-down forces for good thermal conductance to the vessel and for securing the tile against eddy current forces. The tiles are made of graphite, and a program to select a suitable grade of graphite was undertaken. Initially, graphites were compared based on published technical data. Graphite samples were then tested for thermal shock capacity in an electron beam test facility at the Sandia National Laboratory (SNLA) in Albuquerque, New Mexico, USA. 4 refs., 6 figs

Ni2+-binding RNA motifs with an asymmetric purine-rich internal loop and a G-A base pair.

Science.gov (United States)

Hofmann, H P; Limmer, S; Hornung, V; Sprinzl, M

1997-01-01

RNA molecules with high affinity for immobilized Ni2+ were isolated from an RNA pool with 50 randomized positions by in vitro selection-amplification. The selected RNAs preferentially bind Ni2+ and Co2+ over other cations from first series transition metals. Conserved structure motifs, comprising about 15 nt, were identified that are likely to represent the Ni2+ binding sites. Two conserved motifs contain an asymmetric purine-rich internal loop and probably a mismatch G-A base pair. The structure of one of these motifs was studied with proton NMR spectroscopy and formation of the G-A pair at the junction of helix and internal loop was demonstrated. Using Ni2+ as a paramagnetic probe, a divalent metal ion binding site near this G-A base pair was identified. Ni2+ ions bound to this motif exert a specific stabilization effect. We propose that small asymmetric purine-rich loops that contain a G-A interaction may represent a divalent metal ion binding site in RNA. PMID:9409620

Physiological, Biomechanical, and Maximal Performance Comparisons of Female Soldiers Carrying Loads Using Prototype U.S. Marine Corps Modular Lightweight Load-Carrying Equipment (MOLLE) with Interceptor Body Armor and U.S. Army All-Purpose Lightweight Individual Carrying Equipment (ALICE) with PASGT Body Armor

National Research Council Canada - National Science Library

Harman, Everett

1999-01-01

The experiment evaluated the physiological, biomechanical, and maximal performance responses of 12 female soldiers carrying loads with prototype Modular Lightweight Load-Carrying Equipment with Interceptor body armor (MOLLE...

Fugitive emissions control on dry copper tailing with crushed rock armor

International Nuclear Information System (INIS)

Haase, E.F.

1992-01-01

Four inactive copper tailing impoundments totalling 1,900 acres near Ajo in southwestern Arizona were covered on horizontal surfaces with a 2 in. nominal thickness of crushed rock to control particulate emissions. The tailings are typically dominated by sand-sized particles but may also include significant PM 10 fractions towards the centers of the impoundments. The technology was selected by Phelps Dodge Corporation, after investigation of several alternatives, as a permanent and practical cover that essentially eliminates fugitive emissions. It simulates the natural desert pavement that characterizes this arid area of the Sonoran Desert. Rocky overburden was crushed to minus 3 in. diameter and broadcast on dry surfaces of tailing impoundments with all-terrain, balloon-tired spreaders. Stony residues in the rock armor tend to cement together following rainfall, forming a crust that enhances surface stability and erosion control. Slopes with windblown tailing deposition were covered to a nominal 6 in. thickness by conventional dozer pushing and blading of minus 10 in. rock over the sides. Athel trees, planted extensively since 1970 on two of the four inactive impoundments, provided partial control of fugitives, but were subjected to harsh environmental conditions, including abrasion from saltating particles. The rock armor functions as a mulch which is expected to improve water relations for existing vegetation and areas seeded with native species. New surface microenvironments, and the virtual elimination of surface creep and saltation, are expected to support native plant growth under favorable climatic conditions

Nondestructive ultrasonic characterization of armor grade silicon carbide

Science.gov (United States)

Portune, Andrew Richard

Ceramic materials have traditionally been chosen for armor applications for their superior mechanical properties and low densities. At high strain rates seen during ballistic events, the behavior of these materials relies upon the total volumetric flaw concentration more so than any single anomalous flaw. In this context flaws can be defined as any microstructural feature which detriments the performance of the material, potentially including secondary phases, pores, or unreacted sintering additives. Predicting the performance of armor grade ceramic materials depends on knowledge of the absolute and relative concentration and size distribution of bulk heterogeneities. Ultrasound was chosen as a nondestructive technique for characterizing the microstructure of dense silicon carbide ceramics. Acoustic waves interact elastically with grains and inclusions in large sample volumes, and were well suited to determine concentration and size distribution variations for solid inclusions. Methodology was developed for rapid acquisition and analysis of attenuation coefficient spectra. Measurements were conducted at individual points and over large sample areas using a novel technique entitled scanning acoustic spectroscopy. Loss spectra were split into absorption and scattering dominant frequency regimes to simplify analysis. The primary absorption mechanism in polycrystalline silicon carbide was identified as thermoelastic in nature. Correlations between microstructural conditions and parameters within the absorption equation were established through study of commercial and custom engineered SiC materials. Nonlinear least squares regression analysis was used to estimate the size distributions of boron carbide and carbon inclusions within commercial SiC materials. This technique was shown to additionally be capable of approximating grain size distributions in engineered SiC materials which did not contain solid inclusions. Comparisons to results from electron microscopy

An international comparability study on quantification of mRNA gene expression ratios: CCQM-P103.1

Directory of Open Access Journals (Sweden)

Alison S. Devonshire

2016-06-01

Full Text Available Measurement of RNA can be used to study and monitor a range of infectious and non-communicable diseases, with profiling of multiple gene expression mRNA transcripts being increasingly applied to cancer stratification and prognosis. An international comparison study (Consultative Committee for Amount of Substance (CCQM-P103.1 was performed in order to evaluate the comparability of measurements of RNA copy number ratio for multiple gene targets between two samples. Six exogenous synthetic targets comprising of External RNA Control Consortium (ERCC standards were measured alongside transcripts for three endogenous gene targets present in the background of human cell line RNA. The study was carried out under the auspices of the Nucleic Acids (formerly Bioanalysis Working Group of the CCQM. It was coordinated by LGC (United Kingdom with the support of National Institute of Standards and Technology (USA and results were submitted from thirteen National Metrology Institutes and Designated Institutes. The majority of laboratories performed RNA measurements using RT-qPCR, with datasets also being submitted by two laboratories based on reverse transcription digital polymerase chain reaction and one laboratory using a next-generation sequencing method. In RT-qPCR analysis, the RNA copy number ratios between the two samples were quantified using either a standard curve or a relative quantification approach. In general, good agreement was observed between the reported results of ERCC RNA copy number ratio measurements. Measurements of the RNA copy number ratios for endogenous genes between the two samples were also consistent between the majority of laboratories. Some differences in the reported values and confidence intervals (‘measurement uncertainties’ were noted which may be attributable to choice of measurement method or quantification approach. This highlights the need for standardised practices for the calculation of fold change ratios and

Army Training Study: Training Effectiveness Analysis (TEA) Summary. Volume 1. Armor.

Science.gov (United States)

1978-08-08

c. r tf(e rx =r) rfs it ,, 0’( r’( r , a S’ f "’ u nn Ir Irf I I. * 222 ARM’- NN :TuDY TWANINC EFFCIUENEZ-: ANALISIS TEA : MMARY ’JLUM~ I ARMOR U...selected 5 ’.e o. 11 module clusters , read the objectives fr.r te firs. im’dule, studied whatever available Yesource mnatterial he wished, and reported...ambitious an undertaking, since the percentage of trainees who completed SrTh1 averaged 66% over all task clusters . A completion rate of 52% was reported

Nondestructive characterization of UHMWPE armor materials

Science.gov (United States)

Chiou, Chien-Ping; Margetan, Frank J.; Barnard, Daniel J.; Hsu, David K.; Jensen, Terrence; Eisenmann, David

2012-05-01

Ultra-high molecular weight polyethylene (UHMWPE) is a material increasingly used for fabricating helmet and body armor. In this work, plate specimens consolidated from thin fiber sheets in series 3124 and 3130 were examined with ultrasound, X-ray and terahertz radiation. Ultrasonic through-transmission scans using both air-coupled and immersion modes revealed that the 3130 series material generally had much lower attenuation than the 3124 series, and that certain 3124 plates had extremely high attenuation. Due to the relatively low inspection frequencies used, pulse-echo immersion ultrasonic testing could not detect distinct flaw echoes from the interior. To characterize the nature of the defective condition that was responsible for the high ultrasonic attenuation, terahertz radiation in the time-domain spectroscopy mode were used to image the flaws. Terahertz scan images obtained on the high attenuation samples clearly showed a distribution of a large number of defects, possibly small planar delaminations, throughout the volume of the interior. Their precise nature and morphology are to be verified by optical microscopy of the sectioned surface.

Nondestructive characterization of UHMWPE armor materials

International Nuclear Information System (INIS)

Chiou, Chien-Ping; Margetan, Frank J.; Barnard, Daniel J.; Hsu, David K.; Jensen, Terrence; Eisenmann, David

2012-01-01

Ultra-high molecular weight polyethylene (UHMWPE) is a material increasingly used for fabricating helmet and body armor. In this work, plate specimens consolidated from thin fiber sheets in series 3124 and 3130 were examined with ultrasound, X-ray and terahertz radiation. Ultrasonic through-transmission scans using both air-coupled and immersion modes revealed that the 3130 series material generally had much lower attenuation than the 3124 series, and that certain 3124 plates had extremely high attenuation. Due to the relatively low inspection frequencies used, pulse-echo immersion ultrasonic testing could not detect distinct flaw echoes from the interior. To characterize the nature of the defective condition that was responsible for the high ultrasonic attenuation, terahertz radiation in the time-domain spectroscopy mode were used to image the flaws. Terahertz scan images obtained on the high attenuation samples clearly showed a distribution of a large number of defects, possibly small planar delaminations, throughout the volume of the interior. Their precise nature and morphology are to be verified by optical microscopy of the sectioned surface.

Fragmentation of armor piercing steel projectiles upon oblique perforation of steel plates

Directory of Open Access Journals (Sweden)

Aizik F.

2012-08-01

Full Text Available In this study, a constitutive strength and failure model for a steel core of a14.5 mm API projectile was developed. Dynamic response of a projectile steel core was described by the Johnson-Cook constitutive model combined with principal tensile stress spall model. In order to obtain the parameters required for numerical description of projectile core material behavior, a series of planar impact experiments was done. The parameters of the Johnson-Cook constitutive model were extracted by matching simulated and experimental velocity profiles of planar impact. A series of oblique ballistic experiments with x-ray monitoring was carried out to study the effect of obliquity angle and armor steel plate thickness on shattering behavior of the 14.5 mm API projectile. According to analysis of x-ray images the fragmentation level increases with both steel plate thickness and angle of inclination. The numerical modeling of the ballistic experiments was done using commercial finite element code, LS-DYNA. Dynamic response of high hardness (HH armor steel was described using a modified Johnson-Cook strength and failure model. A series of simulations with various values of maximal principal tensile stress was run in order to capture the overall fracture behavior of the projectile’s core. Reasonable agreement between simulated and x-ray failure pattern of projectile core has been observed.

Pathways of cellular internalisation of liposomes delivered siRNA and effects on siRNA engagement with target mRNA and silencing in cancer cells.

Science.gov (United States)

Alshehri, Abdullah; Grabowska, Anna; Stolnik, Snow

2018-02-28

Design of an efficient delivery system is a generally recognised bottleneck in translation of siRNA technology into clinic. Despite research efforts, cellular processes that determine efficiency of siRNA silencing achieved by different delivery formulations remain unclear. Here, we investigated the mechanism(s) of cellular internalisation of a model siRNA-loaded liposome system in a correlation to the engagement of delivered siRNA with its target and consequent silencing by adopting siRNA molecular beacon technology. Probing of cellular internalisation pathways by a panel of pharmacological inhibitors indicated that clathrin-mediated (dynamin-dependent) endocytosis, macropinocytosis (dynamine independent), and cell membrane cholesterol dependent process(es) (clathrin and caveolea-independent) all play a role in the siRNA-liposomes internalization. The inhibition of either of these entry routes was, in general, mirrored by a reduction in the level of siRNA engagement with its target mRNA, as well as in a reduction of the target gene silencing. A dramatic increase in siRNA engagement with its target RNA was observed on disruption of endosomal membrane (by chloroquine), accompanied with an increased silencing. The work thus illustrates that employing molecular beacon siRNA technology one can start to assess the target RNA engagement - a stage between initial cellular internalization and final gene silencing of siRNA delivery systems.

Bone histology sheds light on the nature of the "dermal armor" of the enigmatic sauropod dinosaur Agustinia ligabuei Bonaparte, 1999

Science.gov (United States)

Bellardini, Flavio; Cerda, Ignacio A.

2017-02-01

Agustinia ligabuei is an Early Cretaceous sauropod dinosaur from the northwest of Patagonia that is currently the topic of debate with respect to its phylogenetic position and atypical dermal armor. The presence of four morphotypes of laminar and transversely elongated putative osteoderms was used to consider Agustinia as an armored sauropod. Regarding the different hypotheses about the identity of the bony structures of Agustinia (e.g., osteoderms, cervical or dorsal ribs, hypertrophied elements), a comparative histological analysis has been carried out. Histological evidence is presented herein and reveals that none of the morphotypes of Agustinia shows a primary bone tissue formed by structural fiber bundles as in other sauropod dinosaur osteoderms. Furthermore, on the basis of their gross morphology and microstructure, the bony structures originally classified as types 1 + 4 and 3 are more comparable respectively with dorsal and cervical ribs than any other kind of dermal or bony element. Due to poor preservation, the nature of the type 2 cannot be assessed but is here tentatively assigned to a pelvic girdle element. Although a phylogenetic reassessment of Agustinia is not the purpose of this paper, our paleohistological analyses have broader implications: by not supporting the dermal armor hypothesis for Agustinia, its inclusion in Lithostrotia is not justified in the absence of other diagnostic features.

The cis-acting replication signal at the 3' end of Flock House virus RNA2 is RNA3-dependent

International Nuclear Information System (INIS)

Albarino, Cesar G.; Eckerle, Lance D.; Ball, L. Andrew

2003-01-01

The nodavirus Flock House virus has a bipartite positive-sense RNA genome consisting of RNAs 1 and 2, which encode the viral RNA-dependent RNA polymerase (RdRp) and capsid protein precursor, respectively. The RdRp catalyzes replication of both genome segments and produces from RNA1 a subgenomic RNA (RNA3) that transactivates RNA2 replication. Here, we replaced internal sequences of RNAs 1 and 2 with a common heterologous core and were thereby able to test the RNA termini for compatibility in supporting the replication of chimeric RNAs. The results showed that the 3' 50 nt of RNA2 contained an RNA3-dependent cis-acting replication signal. Since covalent RNA dimers can direct the synthesis of monomeric replication products, the RdRp can evidently respond to cis-acting replication signals located internally. Accordingly, RNA templates containing the 3' termini of both RNAs 1 and 2 in tandem generated different replication products depending on the presence or absence of RNA3

Armor: An αβγ assembly for irradiated fuel analysis

International Nuclear Information System (INIS)

Beraud, M.

1967-04-01

The assembly ARMOR which was built with a view to carrying out research on irradiated fuels consists of an αβγ enclosure made up of 11 cells in line. After a general description of the assembly in its present form, the various functions are reviewed: introduction of the samples, chemical de-canning, dissolution of the irradiated uranium pellets, preparation of solutions for mass spectrometric analyses, disposal of the effluents and of the solid waste. The assembly-has been working since 1961. During the 5 to 6 years operation, various improvements have been made and a certain number of observations have been collected concerning the work. (author) [fr

Automated identification of RNA 3D modules with discriminative power in RNA structural alignments

DEFF Research Database (Denmark)

Theis, Corinna; Höner zu Siederdissen, Christian; Hofacker, Ivo L.

2013-01-01

Recent progress in predicting RNA structure is moving towards filling the 'gap' in 2D RNA structure prediction where, for example, predicted internal loops often form non-canonical base pairs. This is increasingly recognized with the steady increase of known RNA 3D modules. There is a general...... comparative evidence. Subsequently, the modules, initially represented by a graph, are turned into models for the RMDetect program, which allows to test their discriminative power using real and randomized Rfam alignments. An initial extraction of 22495 3D modules in all PDB files results in 977 internal loop...

Coated armor system and process for making the same

Science.gov (United States)

Chu, Henry S.; Lillo, Thomas M.; McHugh, Kevin M.

2010-11-23

An armor system and method involves providing a core material and a stream of atomized coating material that comprises a liquid fraction and a solid fraction. An initial layer is deposited on the core material by positioning the core material in the stream of atomized coating material wherein the solid fraction of the stream of atomized coating material is less than the liquid fraction of the stream of atomized coating material on a weight basis. An outer layer is then deposited on the initial layer by positioning the core material in the stream of atomized coating material wherein the solid fraction of the stream of atomized coating material is greater than the liquid fraction of the stream of atomized coating material on a weight basis.

Similarities in transcription factor IIIC subunits that bind to the posterior regions of internal promoters for RNA polymerase III

OpenAIRE

Matsutani Sachiko

2004-01-01

Abstract Background In eukaryotes, RNA polymerase III (RNAP III) transcribes the genes for small RNAs like tRNAs, 5S rRNA, and several viral RNAs, and short interspersed repetitive elements (SINEs). The genes for these RNAs and SINEs have internal promoters that consist of two regions. These two regions are called the A and B blocks. The multisubunit transcription factor TFIIIC is required for transcription initiation of RNAP III; in transcription of tRNAs, the B-block binding subunit of TFII...

Design of Vibration Absorber using Spring and Rubber for Armored Vehicle 5.56 mm Caliber Rifle

Directory of Open Access Journals (Sweden)

Aditya Sukma Nugraha

2014-12-01

Full Text Available This paper presents a design of vibration absorber using spring and rubber for 5.56 mm caliber rifle armored vehicle. Such a rifle is used in a Remote-Controlled Weapon System (RCWS or a turret where it is fixed using a two degree of freedom pan-tilt mechanism. A half car lumped mass dynamic model of armored vehicles was derived. Numerical simulation was conducted using fourth order Runge Kutta method. Various types of vibration absorbers using spring and rubber with different configurations are installed in the elevation element. Vibration effects on horizontal direction, vertical direction and angular deviation of the elevation element was investigated. Three modes of fire were applied i.e. single fire, semi-automatic fire and automatic fire. From simulation results, it was concluded that the parallel configuration of damping rubber type 3, which has stiffness of 980,356.04 (N/m2 and damping coefficient of 107.37 (N.s/m, and Carbon steel spring whose stiffness coefficient is 5.547 x 106 (N/m2 provides the best vibration absorption. 

The natural armors of fish: A comparison of the lamination pattern and structure of scales.

Science.gov (United States)

Murcia, Sandra; Lavoie, Ellen; Linley, Tim; Devaraj, Arun; Ossa, E Alex; Arola, D

2017-09-01

Fish scales exhibit a unique balance of flexibility, strength and toughness, which is essential to provide protection without encumbering locomotion. Although the mechanical behavior and structure of this natural armor are of recent interest, a comparison of these qualities from scales of different fish species has not been reported. In this investigation the armor of fish with different locomotion, size and protection needs were analyzed. Scales from the Arapaima gigas, the tarpon (Megalops atlanticus) and the carp (Cyprinus carpio) were compared in terms of the stacking sequence of individual plies and their microstructure. The scales were also compared with respect to anatomical position to distinguish site-specific functional differences. Results show that the lamination sequence of plies for the carp and tarpon exhibit a Bouligand structure with relative rotation of 75° between consecutive plies. The arapaima scales exhibit a cross-ply structure, with 90° rotation between adjacent plies. In addition, results indicate that the volume fraction of reinforcement, the number of plies and the variations in thickness with anatomical position are unique amongst the three fish. These characteristics should be considered in evaluations focused on the mechanical behavior. Copyright © 2016 Elsevier Ltd. All rights reserved.

The natural armors of fish: A comparison of the lamination pattern and structure of scales

Energy Technology Data Exchange (ETDEWEB)

Murcia, Sandra; Lavoie, Ellen; Linley, Tim; Devaraj, Arun; Ossa, E. Alex; Arola, D.

2017-09-01

Fish scales exhibit a unique balance of flexibility, strength and toughness, which is essential to provide protection without encumbering locomotion. Although the mechanical behavior and structure of this natural armor are of recent interest, a comparison of these qualities from scales of different fish species has not been reported. In this investigation the armor of fish with different locomotion, size and protection needs were analyzed. Scales from the Arapaima gigas, the tarpon (Megalops atlanticus) and the carp (Cyprinus carpio) were compared in terms of the stacking sequence of individual plies and their microstructure. The scales were also compared with respect to anatomical position to distinguish site-specific functional differences. Results show that the lamination sequence of plies for the carp and tarpon exhibit a Bouligand structure with relative rotation of 75° between consecutive plies. The arapaima scales exhibit a cross-ply structure, with 90° rotation between adjacent plies. In addition, results indicate that the volume fraction of reinforcement, the number of plies and the variations in thickness with anatomical position are unique amongst the three fish. These characteristics should be considered in evaluations focused on the mechanical behavior.

A Preliminary Report on the Strength and Metallography of a Bimetallic Friction Stir Weld Joint Between AA6061 and MIL-DTL-46100E High Hardness Steel Armor

Science.gov (United States)

2012-11-26

bimetallic friction stir weld joint between AA6061 and MIL-DTL-46100E High Hardness steel armor. ABSTRACT One half inch thick plates of 6061-T6 aluminum...alloy and High Hardness steel armor (MIL- STD-46100) were successfully joined by the friction stir welding (FSW) process using a tungsten-rhenium...4. TITLE AND SUBTITLE A preliminary report on the strength and metallography of a bimetallic friction stir weld joint between AA6061 and MIL-DTL

Artesunate Reduces Serum Lipopolysaccharide in Cecal Ligation/Puncture Mice via Enhanced LPS Internalization by Macrophages through Increased mRNA Expression of Scavenger Receptors

Directory of Open Access Journals (Sweden)

Bin Li

2014-01-01

Full Text Available Innate immunity is the first line of defense in human beings against pathogen infection; monocytes/macrophages are the primary cells of the innate immune system. Recently, macrophages/monocytes have been discovered to participate in LPS clearance, and the clearance efficiency determines the magnitude of the inflammatory response and subsequent organ injury. Previously, we reported that artesunate (AS protected sepsis mice against heat-killed E. coli challenge. Herein, we further confirmed that AS protected cecal ligation/puncture (CLP sepsis mice. Its protection on sepsis mice was related to not only reduction of pro-inflammatory cytokines and serum LPS levels but also improvement of liver function. Based on the fact that AS did not directly bind and neutralize LPS, we hypothesized that the reduction of serum LPS level might be related to enhancement of LPS internalization and subsequent detoxification. Our results showed that AS increased FITC-LPS internalization by peritoneal macrophage and liver Kupffer cell, but enhancement of LPS internalization by AS was not related to the clathrin-dependent pathway. However, AS induced mRNA expression of important scavenger receptors (SRs; SR-A and MARCO mRNA expression was upregulated, suggesting that AS enhancement of LPS internalization and inhibition of pro-inflammatory cytokines was related to changes in mRNA expression of SRs.

rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments

OpenAIRE

O?Connor, Patrick B. F.; Li, Gene-Wei; Weissman, Jonathan S.; Atkins, John F.; Baranov, Pavel V.

2013-01-01

Motivation: Ribosome profiling is a new technique that allows monitoring locations of translating ribosomes on mRNA at a whole transcriptome level. A recent ribosome profiling study demonstrated that internal Shine?Dalgarno (SD) sequences have a major global effect on translation rates in bacteria: ribosomes pause at SD sites in mRNA. Therefore, it is important to understand how SD sites effect mRNA movement through the ribosome and generation of ribosome footprints. Results: Here, we provide...

Ballistic Performance of Mallow and Jute Natural Fabrics Reinforced Epoxy Composites in Multilayered Armor

OpenAIRE

Nascimento, Lucio Fabio Cassiano; Louro, Luis Henrique Leme; Monteiro, Sergio Neves; Gomes, Alaelson Vieira; Marçal, Rubens Lincoln Santana Blazutti; Lima Júnior, Édio Pereira; Margem, Jean Igor

2017-01-01

Natural fiber reinforced polymer composites have recently been investigated as a component of multilayered armor system (MAS). These composites were found to present advantages when replacing conventional high strength synthetic aramid fabric laminate composite (KevlarTM, with same thickness, as MAS second layer. Continuous and loose natural fibers were up to now mostly used to reinforce these ballistic composites. Only two natural fabrics reinforced polymer composite were so far used with sa...

Activities of HIP joining of plasma-facing armors in the blanket first-wall in Korea

Energy Technology Data Exchange (ETDEWEB)

Jung, Yang-Il, E-mail: yijung@kaeri.re.kr [Korea Atomic Energy Research Institute, Daedeok-daero, Daejeon 34057 (Korea, Republic of); Park, Jeong-Yong; Choi, Byoung-Kwon; Lee, Jung-Suk; Kim, Hyun-Gil; Park, Dong-Jun; Park, Jung-Hwan; Kim, Suk-Kwon; Lee, Dong-Won [Korea Atomic Energy Research Institute, Daedeok-daero, Daejeon 34057 (Korea, Republic of); Cho, Seungyon [National Fusion Research Institute, Gwahak-ro, Yuseong, Daejeon 34133 (Korea, Republic of)

2016-11-01

Highlights: • HIP joints of Be/CuCrZr, Be/FMS, W/FMS were demonstrated. • The process conditions for HIP joining were developed. • For the joining of Be, coating interlayers as well as thick diffusion barrier was developed. • For the joining of W, double-staged HIP was applied for the joint integrity. • No significant defects nor a brittle failure were observed along the joint interface. - Abstract: Joining technology for dissimilar materials was developed for the fabrication of an ITER blanket first-wall, which consisted of Be, CuCrZr, and stainless steel (SS). The Be/CuCrZr/SS joint was fabricated using a hot isostatic pressing (HIP) method. Beryllium armor was joined to the CuCrZr/SS block at 580 °C under 100 MPa. The optimal interlayer coatings of Cr/Cu and Ti/Cr/Cu were developed using an ion-beam assisted physical vapor deposition. Beryllium is also a candidate armor material for the TBM first-wall. Successful joining of Be to ferritic-martensitic steel (FMS) was accomplished using an HIP method by introducing the thick diffusion barrier. A thick diffusion barrier of a Cu foil(10 μm) limited the excessive diffusion and prevented the formation of brittle phases at the Be/FMS interface. Be and FMS were bonded at 650–850 °C; however, a temperature of lower than 750 °C was recommended to avoid material degradation of FMS. In addition, the joining of W to FMS has been developed. Tungsten is another armor material applicable to more severe plasma conditions. The large difference in the thermal expansion between W and FMS was resolved by introducing the Ti interlayer and Mo separator. Moreover, the double-staged HIP (the first stage at 900 °C and 100 MPa and the second stage at 750 °C and 70 MPa) was applied to suppress the edge delamination of W/FMS joints during thermal history.

Assessing a Suitable Contribution of the French Armor Branch to the Doctrinal Development of Violence: Mastering Operations in the Urban Environment

National Research Council Canada - National Science Library

Millet, Jean-Michel

2003-01-01

.... This study analyzes the current state of the French Army doctrinal development of armor employment in the violence-mastering mode in the urban environment and compare it to the lessons learned...

Study of Nano Powder for Improvement the Mechanical Properties of Armor

Directory of Open Access Journals (Sweden)

Raid Salih Jawad

2016-03-01

Full Text Available During this research nano alumina particles are used as reinforce material to improve characterization of armor. The work involves use of polyester resin as matrix. The properties obtained of resulted samples showed clearly improvement. Where values show linear increases in hardness from low value 77.3 gf/mm of pure polyester to high value 81.6 of polystyrene - 30 wt % nano alumina. Values of thermal conductivity greatly influenced by amount of porosity and so on the density of the sample, where pure polyester has low value 0.0661 W/mk of thermal conductivity and polyester – 30 wt % nano aluminapossess conductivity 0.3411 W/mk.

RNA signal amplifier circuit with integrated fluorescence output.

Science.gov (United States)

Akter, Farhima; Yokobayashi, Yohei

2015-05-15

We designed an in vitro signal amplification circuit that takes a short RNA input that catalytically activates the Spinach RNA aptamer to produce a fluorescent output. The circuit consists of three RNA strands: an internally blocked Spinach aptamer, a fuel strand, and an input strand (catalyst), as well as the Spinach aptamer ligand 3,5-difluoro-4-hydroxylbenzylidene imidazolinone (DFHBI). The input strand initially displaces the internal inhibitory strand to activate the fluorescent aptamer while exposing a toehold to which the fuel strand can bind to further displace and recycle the input strand. Under a favorable condition, one input strand was able to activate up to five molecules of the internally blocked Spinach aptamer in 185 min at 30 °C. The simple RNA circuit reported here serves as a model for catalytic activation of arbitrary RNA effectors by chemical triggers.

An internal ribosome entry site directs translation of the 3'-gene from Pelargonium flower break virus genomic RNA: implications for infectivity.

Directory of Open Access Journals (Sweden)

Olga Fernández-Miragall

Full Text Available Pelargonium flower break virus (PFBV, genus Carmovirus has a single-stranded positive-sense genomic RNA (gRNA which contains five ORFs. The two 5'-proximal ORFs encode the replicases, two internal ORFs encode movement proteins, and the 3'-proximal ORF encodes a polypeptide (p37 which plays a dual role as capsid protein and as suppressor of RNA silencing. Like other members of family Tombusviridae, carmoviruses express ORFs that are not 5'-proximal from subgenomic RNAs. However, in one case, corresponding to Hisbiscus chlorotic ringspot virus, it has been reported that the 3'-proximal gene can be translated from the gRNA through an internal ribosome entry site (IRES. Here we show that PFBV also holds an IRES that mediates production of p37 from the gRNA, raising the question of whether this translation strategy may be conserved in the genus. The PFBV IRES was functional both in vitro and in vivo and either in the viral context or when inserted into synthetic bicistronic constructs. Through deletion and mutagenesis studies we have found that the IRES is contained within a 80 nt segment and have identified some structural traits that influence IRES function. Interestingly, mutations that diminish IRES activity strongly reduced the infectivity of the virus while the progress of the infection was favoured by mutations potentiating such activity. These results support the biological significance of the IRES-driven p37 translation and suggest that production of the silencing suppressor from the gRNA might allow the virus to early counteract the defence response of the host, thus facilitating pathogen multiplication and spread.

An internal ribosome entry site directs translation of the 3'-gene from Pelargonium flower break virus genomic RNA: implications for infectivity.

Science.gov (United States)

Fernández-Miragall, Olga; Hernández, Carmen

2011-01-01

Pelargonium flower break virus (PFBV, genus Carmovirus) has a single-stranded positive-sense genomic RNA (gRNA) which contains five ORFs. The two 5'-proximal ORFs encode the replicases, two internal ORFs encode movement proteins, and the 3'-proximal ORF encodes a polypeptide (p37) which plays a dual role as capsid protein and as suppressor of RNA silencing. Like other members of family Tombusviridae, carmoviruses express ORFs that are not 5'-proximal from subgenomic RNAs. However, in one case, corresponding to Hisbiscus chlorotic ringspot virus, it has been reported that the 3'-proximal gene can be translated from the gRNA through an internal ribosome entry site (IRES). Here we show that PFBV also holds an IRES that mediates production of p37 from the gRNA, raising the question of whether this translation strategy may be conserved in the genus. The PFBV IRES was functional both in vitro and in vivo and either in the viral context or when inserted into synthetic bicistronic constructs. Through deletion and mutagenesis studies we have found that the IRES is contained within a 80 nt segment and have identified some structural traits that influence IRES function. Interestingly, mutations that diminish IRES activity strongly reduced the infectivity of the virus while the progress of the infection was favoured by mutations potentiating such activity. These results support the biological significance of the IRES-driven p37 translation and suggest that production of the silencing suppressor from the gRNA might allow the virus to early counteract the defence response of the host, thus facilitating pathogen multiplication and spread.

Investigation of Fire-Vulnerability-Reduction Effectiveness of Fire-Resistant Diesel Fuel in Armored Vehicular Fuel Tanks

Science.gov (United States)

1980-09-30

FORT LEE VA 23801 ATTN DRXMD-MS LEXINGTON KY 40511 HQ, US ARHY ARMOR SCHOOL ATTN ATSB- TD HQ, US ARMY T&E COMMANI) FORT KNOX KY 40121 ATTN DRSTE-TO-O 1...CDM P 0 BOX 4005 FORT BELVOIR VA 22060 CHAMPAIGN IL 61820 CDR IHQ US ARMY INFANTRY SCHOOL , US ARMY TRAINING & DOCTRINE CMD ATTN ATSH-CD-MS-M ATTN ATCD

5S rRNA-derived and tRNA-derived SINEs in fruit bats.

Science.gov (United States)

Gogolevsky, Konstantin P; Vassetzky, Nikita S; Kramerov, Dmitri A

2009-05-01

Most short retroposons (SINEs) descend from cellular tRNA of 7SL RNA. Here, four new SINEs were found in megabats (Megachiroptera) but neither in microbats nor in other mammals. Two of them, MEG-RS and MEG-RL, descend from another cellular RNA, 5S rRNA; one (MEG-T2) is a tRNA-derived SINE; and MEG-TR is a hybrid tRNA/5S rRNA SINE. Insertion locus analysis suggests that these SINEs were active in the recent fruit bat evolution. Analysis of MEG-RS and MEG-RL in comparison with other few 5S rRNA-derived SINEs demonstrates that the internal RNA polymerase III promoter is their most invariant region, while the secondary structure is more variable. The mechanisms underlying the modular structure of these and other SINEs as well as their variation are discussed. The scenario of evolution of MEG SINEs is proposed.

Development of high conductive C/C composite tiles for plasma facing armor

International Nuclear Information System (INIS)

Ioki, K.; Namiki, K.; Tsujimura, S.; Toyoda, M.; Seki, M.; Takatsu, H.

1991-01-01

C/C composites with high thermal conductivity were developed in unidirectional, two-dimensional and felt types, and were fabricated as full-scale armor tile. Their thermal conductivity in the direction perpendicular to the plasma-side surface is 250∝550 W/mdeg C, that is comparable to that of pyrolytic graphite. It was shown by heat load tests that the C/C composites have low surface erosion characteristics and high thermal shock resistance. Various kinds of C/C composites were successfully bonded to metal substrate, and their mechanical strength and thermal shock resistance were tested. (orig.)

Sequence analysis of RNase MRP RNA reveals its origination from eukaryotic RNase P RNA

Science.gov (United States)

Zhu, Yanglong; Stribinskis, Vilius; Ramos, Kenneth S.; Li, Yong

2006-01-01

RNase MRP is a eukaryote-specific endoribonuclease that generates RNA primers for mitochondrial DNA replication and processes precursor rRNA. RNase P is a ubiquitous endoribonuclease that cleaves precursor tRNA transcripts to produce their mature 5′ termini. We found extensive sequence homology of catalytic domains and specificity domains between their RNA subunits in many organisms. In Candida glabrata, the internal loop of helix P3 is 100% conserved between MRP and P RNAs. The helix P8 of MRP RNA from microsporidia Encephalitozoon cuniculi is identical to that of P RNA. Sequence homology can be widely spread over the whole molecule of MRP RNA and P RNA, such as those from Dictyostelium discoideum. These conserved nucleotides between the MRP and P RNAs strongly support the hypothesis that the MRP RNA is derived from the P RNA molecule in early eukaryote evolution. PMID:16540690

Graphene-Armored Aluminum Foil with Enhanced Anticorrosion Performance as Current Collectors for Lithium-Ion Battery.

Science.gov (United States)

Wang, Mingzhan; Tang, Miao; Chen, Shulin; Ci, Haina; Wang, Kexin; Shi, Liurong; Lin, Li; Ren, Huaying; Shan, Jingyuan; Gao, Peng; Liu, Zhongfan; Peng, Hailin

2017-12-01

Aluminum (Al) foil, as the most accepted cathode current collector for lithium-ion batteries (LIBs), is susceptible to local anodic corrosions during long-term operations. Such corrosions could lead to the deterioration or even premature failure of the batteries and are generally believed to be a bottleneck for next-generation 5 V LIBs. Here, it is demonstrated that Al foil armored by conformal graphene coating exhibits significantly reinforced anodic corrosion resistance in both LiPF 6 and lithium bis(trifluoromethanesulphonyl) imide (LiTFSI) based electrolytes. Moreover, LiMn 2 O 4 cells using graphene-armored Al foil as current collectors (LMO/GA) demonstrate enhanced electrochemical performance in comparison with those using pristine Al foil (LMO/PA). The long-term discharge capacity retention of LMO/GA cell after ≈950 h straight operations at low rate (0.5 C) reaches up to 91%, remarkably superior to LMO/PA cell (75%). The self-discharge propensity of LMO/GA is clearly relieved and the rate/power performance is also improved with graphene mediations. This work not only contributes to the long-term stable operations of LIBs but also might catalyze the deployment of 5 V LIBs in the future. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Optimization and Validation of a Real Time Reverse Transcriptase Polymerase Chain Reaction with RNA Internal Control to Detect Rubella RNA

Directory of Open Access Journals (Sweden)

Winny Xie

2013-12-01

Full Text Available BACKGROUND: According to a report from WHO, cases of rubella infection in Indonesia has increased up to 10-fold from 2007 to 2011. Despite no data of congenital rubella syndrome in the report, there are approximately 45,000 cases of babies born with heart failure and 0.1-0.3% live births with congenital deafness in Indonesia. Allegedly, rubella infection during pregnancy may play a role in this condition. This study aimed to optimize and validate a real-time reverse transcriptase polymerase chain reaction (RT-qPCR method to detect rubella virus RNA as an aid for the diagnosis of congenital rubella infection. METHODS: Method optimization was conducted using nucleic acids extracted from Trimovax Merieux vaccine with the High Pure Viral Nucleic Acid Kit. One step RT-qPCR was performed with Quantifast Multiplex RTPCR+R Kit. Target synthetic DNA was designed and used to determine the sensitivity of the method. RNA internal control was synthesized to control the process of extraction and amplification. RESULTS: The analytical sensitivity of this method was as low as 5 copies target synthetic DNA/μl. The mean Coefficient of Variation (CV % of the critical threshold (Ct obtained were 2.71%, 1.20%, 1.62%, and 1.59% for within run, between run, between kit lots, and between operators, respectively. Recovery of the target synthetic DNA from amniotic fluid was 100.51% (by the log copies/μl at the concentration of 1,000,000 copies/μl. CONCLUSIONS: RT-qPCR is successfully used for the detection of rubella virus RNA in vaccine and synthetic nucleic acid. With its high sensitivity, good precision and recovery, this method offers a means to improve the diagnosis of congenital rubella infection in developing countries like Indonesia. KEYWORDS: congenital rubella, RT-qPCR, prenatal diagnosis, amniotic fluid.

Aging-associated changes in microRNA expression profile of internal anal sphincter smooth muscle: Role of microRNA-133a

Science.gov (United States)

Singh, Jagmohan; Boopathi, Ettickan; Addya, Sankar; Phillips, Benjamin; Rigoutsos, Isidore; Penn, Raymond B.

2016-01-01

A comprehensive genomic and proteomic, computational, and physiological approach was employed to examine the (previously unexplored) role of microRNAs (miRNAs) as regulators of internal anal sphincter (IAS) smooth muscle contractile phenotype and basal tone. miRNA profiling, genome-wide expression, validation, and network analyses were employed to assess changes in mRNA and miRNA expression in IAS smooth muscles from young vs. aging rats. Multiple miRNAs, including rno-miR-1, rno-miR-340-5p, rno-miR-185, rno-miR-199a-3p, rno-miR-200c, rno-miR-200b, rno-miR-31, rno-miR-133a, and rno-miR-206, were found to be upregulated in aging IAS. qPCR confirmed the upregulated expression of these miRNAs and downregulation of multiple, predicted targets (Eln, Col3a1, Col1a1, Zeb2, Myocd, Srf, Smad1, Smad2, Rhoa/Rock2, Fn1, Tagln v2, Klf4, and Acta2) involved in regulation of smooth muscle contractility. Subsequent studies demonstrated an aging-associated increase in the expression of miR-133a, corresponding decreases in RhoA, ROCK2, MYOCD, SRF, and SM22α protein expression, RhoA-signaling, and a decrease in basal and agonist [U-46619 (thromboxane A2 analog)]-induced increase in the IAS tone. Moreover, in vitro transfection of miR-133a caused a dose-dependent increase of IAS tone in strips, which was reversed by anti-miR-133a. Last, in vivo perianal injection of anti-miR-133a reversed the loss of IAS tone associated with age. This work establishes the important regulatory effect of miRNA-133a on basal and agonist-stimulated IAS tone. Moreover, reversal of age-associated loss of tone via anti-miR delivery strongly implicates miR dysregulation as a causal factor in the aging-associated decrease in IAS tone and suggests that miR-133a is a feasible therapeutic target in aging-associated rectoanal incontinence. PMID:27634012

NATO Advanced Research Workshop on Boron Rich Solids Sensors for Biological and Chemical Detection, Ultra High Temperature Ceramics, Thermoelectrics, Armor

CERN Document Server

Orlovskaya, Nina

2011-01-01

The objective of this book is to discuss the current status of research and development of boron-rich solids as sensors, ultra-high temperature ceramics, thermoelectrics, and armor. Novel biological and chemical sensors made of stiff and light-weight boron-rich solids are very exciting and efficient for applications in medical diagnoses, environmental surveillance and the detection of pathogen and biological/chemical terrorism agents. Ultra-high temperature ceramic composites exhibit excellent oxidation and corrosion resistance for hypersonic vehicle applications. Boron-rich solids are also promising candidates for high-temperature thermoelectric conversion. Armor is another very important application of boron-rich solids, since most of them exhibit very high hardness, which makes them perfect candidates with high resistance to ballistic impact. The following topical areas are presented: •boron-rich solids: science and technology; •synthesis and sintering strategies of boron rich solids; •microcantileve...

Armor stability of hardly (or partly) reshaping berm breakwaters

DEFF Research Database (Denmark)

Moghim, M. N.; Andersen, Thomas Lykke

2015-01-01

This paper deals with stability of hardly (or partly) reshaping berm breakwaters. A simple physical argument is used to derive a new stability formula based on the assumption that the maximum wave force causing damage of armor layer is proportional to the maximum wave momentum flux near...... the structure toe. The main goal of the present paper is to provide an estimation technique based on this physical principle to predict the deformation of the front slope in terms of the eroded area. The proposed method is verified by comparison with model test data. It is found that by using the maximum wave...... momentum flux approach the damage to the front slope (eroded area) can be very well predicted. Moreover, a simple method to estimate the eroded area based on measured or calculated berm recession (Rec) and depth of intersection of reshaped and initial profile (hf) is presented. The performance...

Perturbation of m6A Writers Reveals Two Distinct Classes of mRNA Methylation at Internal and 5′ Sites

Directory of Open Access Journals (Sweden)

Schraga Schwartz

2014-07-01

Full Text Available N6-methyladenosine (m6A is a common modification of mRNA with potential roles in fine-tuning the RNA life cycle. Here, we identify a dense network of proteins interacting with METTL3, a component of the methyltransferase complex, and show that three of them (WTAP, METTL14, and KIAA1429 are required for methylation. Monitoring m6A levels upon WTAP depletion allowed the definition of accurate and near single-nucleotide resolution methylation maps and their classification into WTAP-dependent and -independent sites. WTAP-dependent sites are located at internal positions in transcripts, topologically static across a variety of systems we surveyed, and inversely correlated with mRNA stability, consistent with a role in establishing “basal” degradation rates. WTAP-independent sites form at the first transcribed base as part of the cap structure and are present at thousands of sites, forming a previously unappreciated layer of transcriptome complexity. Our data shed light on the proteomic and transcriptional underpinnings of this RNA modification.

RNA-Based Vaccines in Cancer Immunotherapy

Directory of Open Access Journals (Sweden)

Megan A. McNamara

2015-01-01

Full Text Available RNA vaccines traditionally consist of messenger RNA synthesized by in vitro transcription using a bacteriophage RNA polymerase and template DNA that encodes the antigen(s of interest. Once administered and internalized by host cells, the mRNA transcripts are translated directly in the cytoplasm and then the resulting antigens are presented to antigen presenting cells to stimulate an immune response. Alternatively, dendritic cells can be loaded with either tumor associated antigen mRNA or total tumor RNA and delivered to the host to elicit a specific immune response. In this review, we will explain why RNA vaccines represent an attractive platform for cancer immunotherapy, discuss modifications to RNA structure that have been developed to optimize mRNA vaccine stability and translational efficiency, and describe strategies for nonviral delivery of mRNA vaccines, highlighting key preclinical and clinical data related to cancer immunotherapy.

RNA 3D modules in genome-wide predictions of RNA 2D structure

DEFF Research Database (Denmark)

Theis, Corinna; Zirbel, Craig L; Zu Siederdissen, Christian Höner

2015-01-01

. These modules can, for example, occur inside structural elements which in RNA 2D predictions appear as internal loops. Hence one question is if the use of such RNA 3D information can improve the prediction accuracy of RNA secondary structure at a genome-wide level. Here, we use RNAz in combination with 3D......Recent experimental and computational progress has revealed a large potential for RNA structure in the genome. This has been driven by computational strategies that exploit multiple genomes of related organisms to identify common sequences and secondary structures. However, these computational...... approaches have two main challenges: they are computationally expensive and they have a relatively high false discovery rate (FDR). Simultaneously, RNA 3D structure analysis has revealed modules composed of non-canonical base pairs which occur in non-homologous positions, apparently by independent evolution...

Biological armors under impact—effect of keratin coating, and synthetic bio-inspired analogues

International Nuclear Information System (INIS)

Achrai, B; Wagner, H D; Bar-On, B

2015-01-01

A number of biological armors, such as turtle shells, consist of a strong exoskeleton covered with a thin keratin coating. The mechanical role upon impact of this keratin coating has surprisingly not been investigated thus far. Low-velocity impact tests on the turtle shell reveal a unique toughening phenomenon attributed to the thin covering keratin layer, the presence of which noticeably improves the fracture energy and shell integrity. Synthetic substrate/coating analogues were subsequently prepared and exhibit an impact behavior similar to the biological ones. The results of the present study may improve our understanding, and even future designs, of impact-tolerant structures. (paper)

The Properties of Arc-Sprayed Aluminum Coatings on Armor-Grade Steel

Directory of Open Access Journals (Sweden)

Marcin Adamiak

2018-02-01

Full Text Available This article presents the results of an examination of the properties of arc-sprayed aluminum on alloyed armor-grade steel. Thermal arc spraying was conducted with a EuTronic Arc Spray 4 wire arc sprayer. Aluminum wire 1.6 mm in diameter was used to produce dense, abrasion- and erosion-resistant coatings approx. 1.0 mm thick with and without nickel/5% aluminum-buffered subcoating. Aluminum coatings were characterized in accordance with ASTM G 65-00 abrasion resistance test, ASTM G 76-95 erosion resistance tests, ASTM C 633-01 adhesion strength, HV0.1 hardness tests and metallographic analyses. Results demonstrate properties of arc-sprayed aluminum and aluminum-nickel material coatings that are especially promising in industrial applications where erosion-, abrasion- and corrosion-resistant coating properties are required.

Internal control for real-time polymerase chain reaction based on MS2 bacteriophage for RNA viruses diagnostics.

Science.gov (United States)

Zambenedetti, Miriam Ribas; Pavoni, Daniela Parada; Dallabona, Andreia Cristine; Dominguez, Alejandro Correa; Poersch, Celina de Oliveira; Fragoso, Stenio Perdigão; Krieger, Marco Aurélio

2017-05-01

Real-time reverse transcription polymerase chain reaction (RT-PCR) is routinely used to detect viral infections. In Brazil, it is mandatory the use of nucleic acid tests to detect hepatitis C virus (HCV), hepatitis B virus and human immunodeficiency virus in blood banks because of the immunological window. The use of an internal control (IC) is necessary to differentiate the true negative results from those consequent from a failure in some step of the nucleic acid test. The aim of this study was the construction of virus-modified particles, based on MS2 bacteriophage, to be used as IC for the diagnosis of RNA viruses. The MS2 genome was cloned into the pET47b(+) plasmid, generating pET47b(+)-MS2. MS2-like particles were produced through the synthesis of MS2 RNA genome by T7 RNA polymerase. These particles were used as non-competitive IC in assays for RNA virus diagnostics. In addition, a competitive control for HCV diagnosis was developed by cloning a mutated HCV sequence into the MS2 replicase gene of pET47b(+)-MS2, which produces a non-propagating MS2 particle. The utility of MS2-like particles as IC was evaluated in a one-step format multiplex real-time RT-PCR for HCV detection. We demonstrated that both competitive and non-competitive IC could be successfully used to monitor the HCV amplification performance, including the extraction, reverse transcription, amplification and detection steps, without compromising the detection of samples with low target concentrations. In conclusion, MS2-like particles generated by this strategy proved to be useful IC for RNA virus diagnosis, with advantage that they are produced by a low cost protocol. An attractive feature of this system is that it allows the construction of a multicontrol by the insertion of sequences from more than one pathogen, increasing its applicability for diagnosing different RNA viruses.

Internal control for real-time polymerase chain reaction based on MS2 bacteriophage for RNA viruses diagnostics

Directory of Open Access Journals (Sweden)

Miriam Ribas Zambenedetti

Full Text Available BACKGROUND Real-time reverse transcription polymerase chain reaction (RT-PCR is routinely used to detect viral infections. In Brazil, it is mandatory the use of nucleic acid tests to detect hepatitis C virus (HCV, hepatitis B virus and human immunodeficiency virus in blood banks because of the immunological window. The use of an internal control (IC is necessary to differentiate the true negative results from those consequent from a failure in some step of the nucleic acid test. OBJECTIVES The aim of this study was the construction of virus-modified particles, based on MS2 bacteriophage, to be used as IC for the diagnosis of RNA viruses. METHODS The MS2 genome was cloned into the pET47b(+ plasmid, generating pET47b(+-MS2. MS2-like particles were produced through the synthesis of MS2 RNA genome by T7 RNA polymerase. These particles were used as non-competitive IC in assays for RNA virus diagnostics. In addition, a competitive control for HCV diagnosis was developed by cloning a mutated HCV sequence into the MS2 replicase gene of pET47b(+-MS2, which produces a non-propagating MS2 particle. The utility of MS2-like particles as IC was evaluated in a one-step format multiplex real-time RT-PCR for HCV detection. FINDINGS We demonstrated that both competitive and non-competitive IC could be successfully used to monitor the HCV amplification performance, including the extraction, reverse transcription, amplification and detection steps, without compromising the detection of samples with low target concentrations. In conclusion, MS2-like particles generated by this strategy proved to be useful IC for RNA virus diagnosis, with advantage that they are produced by a low cost protocol. An attractive feature of this system is that it allows the construction of a multicontrol by the insertion of sequences from more than one pathogen, increasing its applicability for diagnosing different RNA viruses.

Fast flexible modeling of RNA structure using internal coordinates.

Science.gov (United States)

Flores, Samuel Coulbourn; Sherman, Michael A; Bruns, Christopher M; Eastman, Peter; Altman, Russ Biagio

2011-01-01

Modeling the structure and dynamics of large macromolecules remains a critical challenge. Molecular dynamics (MD) simulations are expensive because they model every atom independently, and are difficult to combine with experimentally derived knowledge. Assembly of molecules using fragments from libraries relies on the database of known structures and thus may not work for novel motifs. Coarse-grained modeling methods have yielded good results on large molecules but can suffer from difficulties in creating more detailed full atomic realizations. There is therefore a need for molecular modeling algorithms that remain chemically accurate and economical for large molecules, do not rely on fragment libraries, and can incorporate experimental information. RNABuilder works in the internal coordinate space of dihedral angles and thus has time requirements proportional to the number of moving parts rather than the number of atoms. It provides accurate physics-based response to applied forces, but also allows user-specified forces for incorporating experimental information. A particular strength of RNABuilder is that all Leontis-Westhof basepairs can be specified as primitives by the user to be satisfied during model construction. We apply RNABuilder to predict the structure of an RNA molecule with 160 bases from its secondary structure, as well as experimental information. Our model matches the known structure to 10.2 Angstroms RMSD and has low computational expense.

The Natural Armor of Fish: An Exploration of a Biological Composite

Science.gov (United States)

Murcia, Sandra C.

In the search for advanced structural materials, scientists are finding inspiration from materials in nature and biological composites. The need for lighter protective materials has directed attention to armored skins, which possess a combination of flexibility, puncture resistance and capacity for energy dissipation. This rare combination of properties is found in the armored skin of modern fish, and achieved by overlapping scales with exceptional specific strength and toughness. The main objectives of this research were to develop new understanding on the constituent layers and lamination patterns of elasmoid scales from teleost fish, and understand their importance to the mechanical properties relevant to armor performance. The investigation consists of five aims that address properties of the scales as a structural material, the spatial variations over the body of fish, the microstructure and properties of the individual layers, and the design and performance of the interface between these layers. An exploration of scales from Cyprinus carpio showed that the fracture resistance of elasmoid fish scales is largely dependent on the anatomical position and the corresponding microstructure. Elasmoid scales were found to consist of three principle layers, including the external highly mineralized limiting layer (LL), as well as the external (EE) and internal (IE) elasmodine, which consist of a number of lamina (or plies) of unidirectional type I collagen fibrils. While the fracture resistance increased with scale thickness, it was highly correlated with the number of plies in the elasmodine and ratio of mineralized plies in the EE. Furthermore, the hierarchical structure of the scales and the molecular level bonds were found to be of importance. Removal of the intra molecular water enabled inter-peptide bonding of the collagen fibrils, which increased the strength and elastic modulus. Furthermore, mineral crystals at the intra-fibrilar spaces impeded the formation of

Theranostic Niosomes for Efficient siRNA/microRNA Delivery and Activatable Near-Infrared Fluorescent Tracking of Stem Cells

DEFF Research Database (Denmark)

Yang, Chuanxu; Shan, Gao; Song, Ping

2018-01-01

RNA interference (RNAi) mediated gene regulation in stem cells offers great potential in regenerative medicine. In this study, we developed a theranostic platform for efficient delivery of small RNAs (siRNA/miRNA) to human mesenchymal stem cells (hMSCs) to promote differentiation, and meanwhile...... OFF/ON activatable fluorescence upon cellular internalization, resulting in efficient NIR labeling and the capability to dynamically monitor stem cells in mice. In addition, iSPN/siRNA achieved simultaneous long-term cell tracking and in vivo gene silencing after implantation in mice. These results...

Targeted siRNA Delivery and mRNA Knockdown Mediated by Bispecific Digoxigenin-binding Antibodies

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Britta Schneider

2012-01-01

Full Text Available Bispecific antibodies (bsAbs that bind to cell surface antigens and to digoxigenin (Dig were used for targeted small interfering RNA (siRNA delivery. They are derivatives of immunoglobulins G (IgGs that bind tumor antigens, such as Her2, IGF1-R, CD22, and LeY, with stabilized Dig-binding variable domains fused to the C-terminal ends of the heavy chains. siRNA that was digoxigeninylated at its 3′end was bound in a 2:1 ratio to the bsAbs. These bsAb–siRNA complexes delivered siRNAs specifically to cells that express the corresponding antigen as demonstrated by flow cytometry and confocal microscopy. The complexes internalized into endosomes and Dig-siRNAs separated from bsAbs, but Dig-siRNA was not released into the cytoplasm; bsAb-targeting alone was thus not sufficient for effective mRNA knockdown. This limitation was overcome by formulating the Dig-siRNA into nanoparticles consisting of dynamic polyconjugates (DPCs or into lipid-based nanoparticles (LNPs. The resulting complexes enabled bsAb-targeted siRNA-specific messenger RNA (mRNA knockdown with IC50 siRNA values in the low nanomolar range for a variety of bsAbs, siRNAs, and target cells. Furthermore, pilot studies in mice bearing tumor xenografts indicated mRNA knockdown in endothelial cells following systemic co-administration of bsAbs and siRNA formulated in LNPs that were targeted to the tumor vasculature.

Development of remote replacement system for armor tiles of first wall of FER

International Nuclear Information System (INIS)

Adachi, Junichi; Yoshizawa, Shunji; Nakano, Yasuo; Kuboyama, Takashi; Shibanuma, Kiyoshi; Kakudate, Satoshi; Oka, Kiyoshi.

1993-01-01

A remote system has been developed to replace automatically armor tiles of first walls with a single manipulator arm for the Fusion Experimental Reactor (FER). The system is composed of a manipulator arm and an end-effector (a tile replacement hand), which have a gripper of the tiles, a nutrunner to rotate attatching bolts of them and a vision sensor to measure positions of them. The system can replace the tiles by means of a visual feedback system using vision sensor, even if the positions of the tiles would have changed. As a result of tests, it has been proved that the end-effector is useful and the control system is practicable. (author)

One Dimension Analytical Model of Normal Ballistic Impact on Ceramic/Metal Gradient Armor

International Nuclear Information System (INIS)

Liu Lisheng; Zhang Qingjie; Zhai Pengcheng; Cao Dongfeng

2008-01-01

An analytical model of normal ballistic impact on the ceramic/metal gradient armor, which is based on modified Alekseevskii-Tate equations, has been developed. The process of gradient armour impacted by the long rod can be divided into four stages in this model. First stage is projectile's mass erosion or flowing phase, mushrooming phase and rigid phase; second one is the formation of comminuted ceramic conoid; third one is the penetration of gradient layer and last one is the penetration of metal back-up plate. The equations of third stage have been advanced by assuming the behavior of gradient layer as rigid-plastic and considering the effect of strain rate on the dynamic yield strength

One Dimension Analytical Model of Normal Ballistic Impact on Ceramic/Metal Gradient Armor

Science.gov (United States)

Liu, Lisheng; Zhang, Qingjie; Zhai, Pengcheng; Cao, Dongfeng

2008-02-01

An analytical model of normal ballistic impact on the ceramic/metal gradient armor, which is based on modified Alekseevskii-Tate equations, has been developed. The process of gradient armour impacted by the long rod can be divided into four stages in this model. First stage is projectile's mass erosion or flowing phase, mushrooming phase and rigid phase; second one is the formation of comminuted ceramic conoid; third one is the penetration of gradient layer and last one is the penetration of metal back-up plate. The equations of third stage have been advanced by assuming the behavior of gradient layer as rigid-plastic and considering the effect of strain rate on the dynamic yield strength.

ncRNA-class Web Tool: Non-coding RNA feature extraction and pre-miRNA classification web tool

KAUST Repository

Kleftogiannis, Dimitrios A.; Theofilatos, Konstantinos A.; Papadimitriou, Stergios; Tsakalidis, Athanasios K.; Likothanassis, Spiridon D.; Mavroudi, Seferina P.

2012-01-01

Until recently, it was commonly accepted that most genetic information is transacted by proteins. Recent evidence suggests that the majority of the genomes of mammals and other complex organisms are in fact transcribed into non-coding RNAs (ncRNAs), many of which are alternatively spliced and/or processed into smaller products. Non coding RNA genes analysis requires the calculation of several sequential, thermodynamical and structural features. Many independent tools have already been developed for the efficient calculation of such features but to the best of our knowledge there does not exist any integrative approach for this task. The most significant amount of existing work is related to the miRNA class of non-coding RNAs. MicroRNAs (miRNAs) are small non-coding RNAs that play a significant role in gene regulation and their prediction is a challenging bioinformatics problem. Non-coding RNA feature extraction and pre-miRNA classification Web Tool (ncRNA-class Web Tool) is a publicly available web tool ( http://150.140.142.24:82/Default.aspx ) which provides a user friendly and efficient environment for the effective calculation of a set of 58 sequential, thermodynamical and structural features of non-coding RNAs, plus a tool for the accurate prediction of miRNAs. © 2012 IFIP International Federation for Information Processing.

An Analysis Plan for the ARCOMS II (Armor Combat Operations Model Support II) Experiment.

Science.gov (United States)

1983-06-01

In order to facilitate Armor Combat Modeling, the data analysis shculd focus upon the methods which transform the data intc descriptive or predictive ...discussed in Chapter III tc predict the Farameter for probability of detection in time ŕt. This should be compared with the results of the N.4gh -t Vision...J 6A 46.) I-I 0 f U-CL 0~ z o -Z 06 09 03 v 0 0 SJldnYS 10 ON Ipgr Cp o LSTm n at emn itgas 4AA rI z ;A (AZ - 090.0 UlA0 -O ON 404 Fiur CAd &P CC

tRNA-like structure regulates translation of Brome mosaic virus RNA.

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Barends, Sharief; Rudinger-Thirion, Joëlle; Florentz, Catherine; Giegé, Richard; Pleij, Cornelis W A; Kraal, Barend

2004-04-01

For various groups of plant viruses, the genomic RNAs end with a tRNA-like structure (TLS) instead of the 3' poly(A) tail of common mRNAs. The actual function of these TLSs has long been enigmatic. Recently, however, it became clear that for turnip yellow mosaic virus, a tymovirus, the valylated TLS(TYMV) of the single genomic RNA functions as a bait for host ribosomes and directs them to the internal initiation site of translation (with N-terminal valine) of the second open reading frame for the polyprotein. This discovery prompted us to investigate whether the much larger TLSs of a different genus of viruses have a comparable function in translation. Brome mosaic virus (BMV), a bromovirus, has a tripartite RNA genome with a subgenomic RNA4 for coat protein expression. All four RNAs carry a highly conserved and bulky 3' TLS(BMV) (about 200 nucleotides) with determinants for tyrosylation. We discovered TLS(BMV)-catalyzed self-tyrosylation of the tyrosyl-tRNA synthetase but could not clearly detect tyrosine incorporation into any virus-encoded protein. We established that BMV proteins do not need TLS(BMV) tyrosylation for their initiation. However, disruption of the TLSs strongly reduced the translation of genomic RNA1, RNA2, and less strongly, RNA3, whereas coat protein expression from RNA4 remained unaffected. This aberrant translation could be partially restored by providing the TLS(BMV) in trans. Intriguingly, a subdomain of the TLS(BMV) could even almost fully restore translation to the original pattern. We discuss here a model with a central and dominant role for the TLS(BMV) during the BMV infection cycle.

[Correlation between RNA Expression Level and Early PMI in Human Brain Tissue].

Science.gov (United States)

Lü, Y H; Ma, K J; Li, Z H; Gu, J; Bao, J Y; Yang, Z F; Gao, J; Zeng, Y; Tao, L; Chen, L

2016-08-01

To explore the correlation between the expression levels of several RNA markers in human brain tissue and early postmortem interval （PMI）. Twelve individuals with known PMI （range from 4.3 to 22.5 h） were selected and total RNA was extracted from brain tissue. Eight commonly used RNA markers were chosen including β -actin, GAPDH, RPS29, 18S rRNA, 5S rRNA, U6 snRNA, miRNA-9 and miRNA-125b, and the expression levels were detected in brain tissue by real-time fluorescent quantitative PCR. The internal reference markers with stable expression in early PMI were screened using geNorm software and the relationship between its expression level and some relevant factors such as age, gender and cause of death were analyzed. RNA markers normalized by internal reference were inserted into the mathematic model established by previous research for PMI estimation using R software. Model quality was judged by the error rate calculated with estimated PMI. 5S rRNA, miRNA-9 and miRNA-125b showed quite stable expression and their expression levels had no relation with age, gender and cause of death. The error rate of estimated PMI using β -actin was 24.6%, while GAPDH was 41.0%. 5S rRNA, miRNA-9 and miRNA-125b are suitable as internal reference markers of human brain tissue owing to their stable expression in early PMI. The expression level of β -actin correlates well with PMI, which can be used as an additional index for early PMI estimation. Copyright© by the Editorial Department of Journal of Forensic Medicine

Use of Body Armor Protection Levels with Squad Automatic Weapon Fighting Load Impacts Soldier Performance, Mobility, and Postural Control

Science.gov (United States)

2015-05-01

Industrial Security Manual , Section ll-19 or DoD 5200.1-R, Information Security Program Regulation, Chapter IX. For Unclassified/Limited...accomplished using PSAW Statistics 18.0 ( SPSS Inc., Chicago, IL, USA). Separate analyses were performed to test each of the three hypotheses stated. However...the Soldier and diminish his/her lethality or survivability , which may be an area of consideration for future research. 4.2 Consequences of Body Armor

Armored kinorhynch-like scalidophoran animals from the early Cambrian.

Science.gov (United States)

Zhang, Huaqiao; Xiao, Shuhai; Liu, Yunhuan; Yuan, Xunlai; Wan, Bin; Muscente, A D; Shao, Tiequan; Gong, Hao; Cao, Guohua

2015-11-26

Morphology-based phylogenetic analyses support the monophyly of the Scalidophora (Kinorhyncha, Loricifera, Priapulida) and Nematoida (Nematoda, Nematomorpha), together constituting the monophyletic Cycloneuralia that is the sister group of the Panarthropoda. Kinorhynchs are unique among living cycloneuralians in having a segmented body with repeated cuticular plates, longitudinal muscles, dorsoventral muscles, and ganglia. Molecular clock estimates suggest that kinorhynchs may have diverged in the Ediacaran Period. Remarkably, no kinorhynch fossils have been discovered, in sharp contrast to priapulids and loriciferans that are represented by numerous Cambrian fossils. Here we describe several early Cambrian (~535 million years old) kinorhynch-like fossils, including the new species Eokinorhynchus rarus and two unnamed but related forms. E. rarus has characteristic scalidophoran features, including an introvert with pentaradially arranged hollow scalids. Its trunk bears at least 20 annuli each consisting of numerous small rectangular plates, and is armored with five pairs of large and bilaterally placed sclerites. Its trunk annuli are reminiscent of the epidermis segments of kinorhynchs. A phylogenetic analysis resolves E. rarus as a stem-group kinorhynch. Thus, the fossil record confirms that all three scalidophoran phyla diverged no later than the Cambrian Period.

Tactical Reconnaissance and Security for the Armor Battalion Commander: Is the Scout Platoon Combat Capable or Combat Ineffective?

Science.gov (United States)

1990-12-27

reconnaissance force back to a heavy ele ,._.it capable of security missions and limited 10 reconnaissance. Vletnam continued the platoon’s emphasis on...College, Fort Leavenworth, KS, 30 November 1988 (CARL Ref. AOR215860). JouroaI ~ el Bacevich, LTC A. J. "Training Scouts." Armor, September 1987, pp. 37...Swanson, Major Steven G. " Bronco Nine Speaks His Mind." MIlitaryInteigence, April-June 1990, pp. 8- 10, 12. "The Bustle Rack." Armo,; March-April 1990

Biochemical characterization of a recombinant Japanese encephalitis virus RNA-dependent RNA polymerase

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Kim Chan-Mi

2007-07-01

Full Text Available Abstract Background Japanese encephalitis virus (JEV NS5 is a viral nonstructural protein that carries both methyltransferase and RNA-dependent RNA polymerase (RdRp domains. It is a key component of the viral RNA replicase complex that presumably includes other viral nonstructural and cellular proteins. The biochemical properties of JEV NS5 have not been characterized due to the lack of a robust in vitro RdRp assay system, and the molecular mechanisms for the initiation of RNA synthesis by JEV NS5 remain to be elucidated. Results To characterize the biochemical properties of JEV RdRp, we expressed in Escherichia coli and purified an enzymatically active full-length recombinant JEV NS5 protein with a hexahistidine tag at the N-terminus. The purified NS5 protein, but not the mutant NS5 protein with an Ala substitution at the first Asp of the RdRp-conserved GDD motif, exhibited template- and primer-dependent RNA synthesis activity using a poly(A RNA template. The NS5 protein was able to use both plus- and minus-strand 3'-untranslated regions of the JEV genome as templates in the absence of a primer, with the latter RNA being a better template. Analysis of the RNA synthesis initiation site using the 3'-end 83 nucleotides of the JEV genome as a minimal RNA template revealed that the NS5 protein specifically initiates RNA synthesis from an internal site, U81, at the two nucleotides upstream of the 3'-end of the template. Conclusion As a first step toward the understanding of the molecular mechanisms for JEV RNA replication and ultimately for the in vitro reconstitution of viral RNA replicase complex, we for the first time established an in vitro JEV RdRp assay system with a functional full-length recombinant JEV NS5 protein and characterized the mechanisms of RNA synthesis from nonviral and viral RNA templates. The full-length recombinant JEV NS5 will be useful for the elucidation of the structure-function relationship of this enzyme and for the

Chimira: analysis of small RNA sequencing data and microRNA modifications.

Science.gov (United States)

Vitsios, Dimitrios M; Enright, Anton J

2015-10-15

Chimira is a web-based system for microRNA (miRNA) analysis from small RNA-Seq data. Sequences are automatically cleaned, trimmed, size selected and mapped directly to miRNA hairpin sequences. This generates count-based miRNA expression data for subsequent statistical analysis. Moreover, it is capable of identifying epi-transcriptomic modifications in the input sequences. Supported modification types include multiple types of 3'-modifications (e.g. uridylation, adenylation), 5'-modifications and also internal modifications or variation (ADAR editing or single nucleotide polymorphisms). Besides cleaning and mapping of input sequences to miRNAs, Chimira provides a simple and intuitive set of tools for the analysis and interpretation of the results (see also Supplementary Material). These allow the visual study of the differential expression between two specific samples or sets of samples, the identification of the most highly expressed miRNAs within sample pairs (or sets of samples) and also the projection of the modification profile for specific miRNAs across all samples. Other tools have already been published in the past for various types of small RNA-Seq analysis, such as UEA workbench, seqBuster, MAGI, OASIS and CAP-miRSeq, CPSS for modifications identification. A comprehensive comparison of Chimira with each of these tools is provided in the Supplementary Material. Chimira outperforms all of these tools in total execution speed and aims to facilitate simple, fast and reliable analysis of small RNA-Seq data allowing also, for the first time, identification of global microRNA modification profiles in a simple intuitive interface. Chimira has been developed as a web application and it is accessible here: http://www.ebi.ac.uk/research/enright/software/chimira. aje@ebi.ac.uk Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

RNA binding specificity of Ebola virus transcription factor VP30.

Science.gov (United States)

Schlereth, Julia; Grünweller, Arnold; Biedenkopf, Nadine; Becker, Stephan; Hartmann, Roland K

2016-09-01

The transcription factor VP30 of the non-segmented RNA negative strand Ebola virus balances viral transcription and replication. Here, we comprehensively studied RNA binding by VP30. Using a novel VP30:RNA electrophoretic mobility shift assay, we tested truncated variants of 2 potential natural RNA substrates of VP30 - the genomic Ebola viral 3'-leader region and its complementary antigenomic counterpart (each ∼155 nt in length) - and a series of other non-viral RNAs. Based on oligonucleotide interference, the major VP30 binding region on the genomic 3'-leader substrate was assigned to the internal expanded single-stranded region (∼ nt 125-80). Best binding to VP30 was obtained with ssRNAs of optimally ∼ 40 nt and mixed base composition; underrepresentation of purines or pyrimidines was tolerated, but homopolymeric sequences impaired binding. A stem-loop structure, particularly at the 3'-end or positioned internally, supports stable binding to VP30. In contrast, dsRNA or RNAs exposing large internal loops flanked by entirely helical arms on both sides are not bound. Introduction of a 5´-Cap(0) structure impaired VP30 binding. Also, ssDNAs bind substantially weaker than isosequential ssRNAs and heparin competes with RNA for binding to VP30, indicating that ribose 2'-hydroxyls and electrostatic contacts of the phosphate groups contribute to the formation of VP30:RNA complexes. Our results indicate a rather relaxed RNA binding specificity of filoviral VP30, which largely differs from that of the functionally related transcription factor of the Paramyxoviridae which binds to ssRNAs as short as 13 nt with a preference for oligo(A) sequences.

NCI RNA Biology 2017 symposium recap | Center for Cancer Research

Science.gov (United States)

The recent discovery of new classes of RNAs and the demonstration that alterations in RNA metabolism underlie numerous human cancers have resulted in enormous interest among CCR investigators in RNA biology. In order to share the latest research in this exciting field, the CCR Initiative in RNA Biology held its second international symposium April 23-24, 2017, in Natcher

mRNA processing in yeast

International Nuclear Information System (INIS)

Stevens, A.

1982-01-01

Investigations in this laboratory center on basic enzymatic reactions of RNA. Still undefined are reactions involved in the conversion of precursors of mRA (pre-mRNA) to mRNA in eukaryotes. The pre-mRNA is called heterogeneous nuclear RNA and is 2 to 6 times larger than mRNA. The conversion, called splicing, involves a removal of internal sequences called introns by endoribonuclease action followed by a rejoining of the 3'- and 5'-end fragments, called exons, by ligating activity. It has not been possible yet to study the enzymes involved in vitro. Also undefined are reactions involved in the turnover or discarding of certain of the pre-mRNA molecules. Yeast is a simple eukaryote and may be expected to have the same, but perhaps simpler, processing reactions as the higher eukaryotes. Two enzymes involved in the processing of pre-mRNA and mRNA in yeast are under investigation. Both enzymes have been partially purified from ribonucleoprotein particles of yeast. The first is a unique decapping enzyme which cleaves [ 3 H]m 7 Gppp [ 14 C]RNA-poly (A) of yeast, yielding [ 3 H]m 7 GDP and is suggested by the finding that the diphosphate product, m 7 GpppA(G), and UDP-glucose are not hydrolyzed. The second enzyme is an endoribonuclease which converts both the [ 3 H] and [ 14 C] labels of [ 3 H]m 7 Gppp[ 14 C]RNA-poly(A) from an oligo(dT)-cellulose bound form to an unbound, acid-insoluble form. Results show that the stimulation involves an interaction of the labeled RNA with the small nuclear RNA. The inhibition of the enzyme by ethidium bromide and its stimulation by small nuclear RNA suggest that it may be a processing ribonuclease, requiring specific double-stranded features in its substrate. The characterization of the unique decapping enzyme and endoribonuclease may help to understand reactions involved in the processing of pre-mRNA and mRNA in eukaryotes

Ground Vehicle System Integration (GVSI) and Design Optimization Model.

Science.gov (United States)

1996-07-30

number of stowed kills Same basic load lasts longer range Gun/ammo parameters impact system weight, under - armor volume requirements Round volume...internal volume is reduced, the model assumes that the crew’s ability to operate while under armor will be impaired. If the size of a vehicle crew is...changing swept volume will alter under armor volume requirements for the total system; if system volume is fixed, changing swept volume will

NCI RNA Biology 2017 symposium recap | Center for Cancer Research

Science.gov (United States)

The recent discovery of new classes of RNAs and the demonstration that alterations in RNA metabolism underlie numerous human cancers have resulted in enormous interest among CCR investigators in RNA biology. In order to share the latest research in this exciting field, the CCR Initiative in RNA Biology held its second international symposium April 23-24, 2017, in Natcher Auditorium. Learn more...

Similarities in transcription factor IIIC subunits that bind to the posterior regions of internal promoters for RNA polymerase III

Directory of Open Access Journals (Sweden)

Matsutani Sachiko

2004-08-01

Full Text Available Abstract Background In eukaryotes, RNA polymerase III (RNAP III transcribes the genes for small RNAs like tRNAs, 5S rRNA, and several viral RNAs, and short interspersed repetitive elements (SINEs. The genes for these RNAs and SINEs have internal promoters that consist of two regions. These two regions are called the A and B blocks. The multisubunit transcription factor TFIIIC is required for transcription initiation of RNAP III; in transcription of tRNAs, the B-block binding subunit of TFIIIC recognizes a promoter. Although internal promoter sequences are conserved in eukaryotes, no evidence of homology between the B-block binding subunits of vertebrates and yeasts has been reported previously. Results Here, I reported the results of PSI-BLAST searches using the B-block binding subunits of human and Shizosacchromyces pombe as queries, showing that the same Arabidopsis proteins were hit with low E-values in both searches. Comparison of the convergent iterative alignments obtained by these PSI-BLAST searches revealed that the vertebrate, yeast, and Arabidopsis proteins have similarities in their N-terminal one-third regions. In these regions, there were three domains with conserved sequence similarities, one located in the N-terminal end region. The N-terminal end region of the B-block binding subunit of Saccharomyces cerevisiae is tentatively identified as a HMG box, which is the DNA binding motif. Although I compared the alignment of the N-terminal end regions of the B-block binding subunits, and their homologs, with that of the HMG boxes, it is not clear whether they are related. Conclusion Molecular phylogenetic analyses using the small subunit rRNA and ubiquitous proteins like actin and α-tubulin, show that fungi are more closely related to animals than either is to plants. Interestingly, the results obtained in this study show that, with respect to the B-block binding subunits of TFIIICs, animals appear to be evolutionarily closer to plants

Similarities in transcription factor IIIC subunits that bind to the posterior regions of internal promoters for RNA polymerase III.

Science.gov (United States)

Matsutani, Sachiko

2004-08-09

In eukaryotes, RNA polymerase III (RNAP III) transcribes the genes for small RNAs like tRNAs, 5S rRNA, and several viral RNAs, and short interspersed repetitive elements (SINEs). The genes for these RNAs and SINEs have internal promoters that consist of two regions. These two regions are called the A and B blocks. The multisubunit transcription factor TFIIIC is required for transcription initiation of RNAP III; in transcription of tRNAs, the B-block binding subunit of TFIIIC recognizes a promoter. Although internal promoter sequences are conserved in eukaryotes, no evidence of homology between the B-block binding subunits of vertebrates and yeasts has been reported previously. Here, I reported the results of PSI-BLAST searches using the B-block binding subunits of human and Shizosacchromyces pombe as queries, showing that the same Arabidopsis proteins were hit with low E-values in both searches. Comparison of the convergent iterative alignments obtained by these PSI-BLAST searches revealed that the vertebrate, yeast, and Arabidopsis proteins have similarities in their N-terminal one-third regions. In these regions, there were three domains with conserved sequence similarities, one located in the N-terminal end region. The N-terminal end region of the B-block binding subunit of Saccharomyces cerevisiae is tentatively identified as a HMG box, which is the DNA binding motif. Although I compared the alignment of the N-terminal end regions of the B-block binding subunits, and their homologs, with that of the HMG boxes, it is not clear whether they are related. Molecular phylogenetic analyses using the small subunit rRNA and ubiquitous proteins like actin and alpha-tubulin, show that fungi are more closely related to animals than either is to plants. Interestingly, the results obtained in this study show that, with respect to the B-block binding subunits of TFIIICs, animals appear to be evolutionarily closer to plants than to fungi.

Development of a remote handling system for replacement of armor tiles in the Fusion Experimental Reactor

International Nuclear Information System (INIS)

Adachi, J.; Kakudate, S.; Oka, K.; Seki, M.

1995-01-01

The armor tiles of the Fusion Experimental Reactor (FER) planned by JAERI are categorized as scheduled maintenance components, since they are damaged by severe heat and particle loads from the plasma during operation. A remote handling system is thus required to replace a large number of tiles rapidly in the highly activated reactor. However, the simple teaching-playback method cannot be adapted to this system because of deflection of the tiles caused by thermal deformation and so on. We have developed a control system using visual feedback control to adapt to this deflection and an end-effector for a single arm. We confirm their performance in tests. (orig.)

2′-O Methylation of Internal Adenosine by Flavivirus NS5 Methyltransferase

Science.gov (United States)

Dong, Hongping; Chang, David C.; Hua, Maggie Ho Chia; Lim, Siew Pheng; Chionh, Yok Hian; Hia, Fabian; Lee, Yie Hou; Kukkaro, Petra; Lok, Shee-Mei; Dedon, Peter C.; Shi, Pei-Yong

2012-01-01

RNA modification plays an important role in modulating host-pathogen interaction. Flavivirus NS5 protein encodes N-7 and 2′-O methyltransferase activities that are required for the formation of 5′ type I cap (m7GpppAm) of viral RNA genome. Here we reported, for the first time, that flavivirus NS5 has a novel internal RNA methylation activity. Recombinant NS5 proteins of West Nile virus and Dengue virus (serotype 4; DENV-4) specifically methylates polyA, but not polyG, polyC, or polyU, indicating that the methylation occurs at adenosine residue. RNAs with internal adenosines substituted with 2′-O-methyladenosines are not active substrates for internal methylation, whereas RNAs with adenosines substituted with N6-methyladenosines can be efficiently methylated, suggesting that the internal methylation occurs at the 2′-OH position of adenosine. Mass spectroscopic analysis further demonstrated that the internal methylation product is 2′-O-methyladenosine. Importantly, genomic RNA purified from DENV virion contains 2′-O-methyladenosine. The 2′-O methylation of internal adenosine does not require specific RNA sequence since recombinant methyltransferase of DENV-4 can efficiently methylate RNAs spanning different regions of viral genome, host ribosomal RNAs, and polyA. Structure-based mutagenesis results indicate that K61-D146-K181-E217 tetrad of DENV-4 methyltransferase forms the active site of internal methylation activity; in addition, distinct residues within the methyl donor (S-adenosyl-L-methionine) pocket, GTP pocket, and RNA-binding site are critical for the internal methylation activity. Functional analysis using flavivirus replicon and genome-length RNAs showed that internal methylation attenuated viral RNA translation and replication. Polymerase assay revealed that internal 2′-O-methyladenosine reduces the efficiency of RNA elongation. Collectively, our results demonstrate that flavivirus NS5 performs 2′-O methylation of internal adenosine of

Mallow Fiber-Reinforced Epoxy Composites in Multilayered Armor for Personal Ballistic Protection

Science.gov (United States)

Nascimento, Lucio Fábio Cassiano; Louro, Luis Henrique Leme; Monteiro, Sergio Neves; Lima, Édio Pereira; da Luz, Fernanda Santos

2017-10-01

Lighter and less expensive polymer composites reinforced with natural fibers have been investigated as possible components of a multilayered armor system (MAS) for personal protection against high-velocity ammunition. Their ballistic performance was consistently found comparable with that of conventional Kevlar® synthetic aramid fiber. Among the numerous existing natural fibers with the potential for reinforcing polymer composites to replace Kevlar® in MAS, mallow fiber has not been fully investigated. Thus, the objective of this work is to evaluate the ballistic performance of epoxy composites reinforced with 30 vol.% of aligned mallow fibers as a second MAS layer backing a front ceramic plate. The results using high-velocity 7.62 ammunition show a similar indentation to a Kevlar® layer with the same thickness. An impedance matching calculation supports the similar ballistic performance of mallow fiber composite and Kevlar®. Reduced MAS costs associated with the mallow fiber composite are practical advantages over Kevlar®.

Dissolution of methane bubbles with hydrate armoring in deep ocean conditions

Science.gov (United States)

Kovalchuk, Margarita; Socolofsky, Scott

2017-11-01

The deep ocean is a storehouse of natural gas. Methane bubble moving upwards from marine sediments may become trapped in gas hydrates. It is uncertain precisely how hydrate armoring affects dissolution, or mass transfer from the bubble to the surrounding water column. The Texas A&M Oilspill Calculator was used to simulate a series of gas bubble dissolution experiments conducted in the United States Department of Energy National Energy Technology Laboratory High Pressure Water Tunnel. Several variations of the mass transfer coefficient were calculated based on gas or hydrate phase solubility and clean or dirty bubble correlations. Results suggest the mass transfer coefficient may be most closely modeled with gas phase solubility and dirty bubble correlation equations. Further investigation of hydrate bubble dissolution behavior will refine current numeric models which aid in understanding gas flux to the atmosphere and plumes such as oil spills. Research funded in part by the Texas A&M University 2017 Undergraduate Summer Research Grant and a Grant from the Methane Gas Hydrates Program of the US DOE National Energy Technology Laboratory.

An Investigation of Three Extremity Armor Systems: Determination of Physiological, Biomechanical, and Physical Performance Effects and Quantification of Body Area Coverage

Science.gov (United States)

2012-03-19

Fragmentation Protective Body Armor, had a filler made of ballistic nylon, which was sealed in a waterproof , vinyl envelope. As the name indicates...toe-off and peak braking and propulsive forces. GRF is a distributed force that acts over the entire surface of the foot or the shoe that is in...Catlin, M. J., & Dressendorfer, R. H. (1979). The effect of shoe weight on the energy cost of running [Abstract]. Medicine and Science in Sports

Imaging of RNA in situ hybridization by atomic force microscopy

NARCIS (Netherlands)

Kalle, W.H.J.; Macville, M.V.E.; van de Corput, M.P.C.; de Grooth, B.G.; Tanke, H.J.; Raap, A.K.

In this study we investigated the possibility of imaging internal cellular molecules after cytochemical detection with atomic force microscopy (AFM). To this end, rat 9G and HeLa cells were hybridized with haptenized probes for 28S ribosomal RNA, human elongation factor mRNA and cytomegalovirus

In vivo efficacy and off-target effects of locked nucleic acid (LNA) and unlocked nucleic acid (UNA) modified siRNA and small internally segmented interfering RNA (sisiRNA) in mice bearing human tumor xenografts

NARCIS (Netherlands)

Mook, O. R. F.; Vreijling, Jeroen; Wengel, Suzy L.; Wengel, Jesper; Zhou, Chuanzheng; Chattopadhyaya, Jyoti; Baas, Frank; Fluiter, Kees

2010-01-01

The clinical use of small interfering RNA (siRNA) is hampered by poor uptake by tissues and instability in circulation. In addition, off-target effects pose a significant additional problem for therapeutic use of siRNA. Chemical modifications of siRNA have been reported to increase stability and

Armored brain in patients with hydrocephalus after shunt surgery: review of the literatures.

Science.gov (United States)

Taha, Mahmoud M

2012-01-01

Armored brain or chronic calcified subdural hematoma is a rare complication of cerebrospinal fluid diversion with few cases reported in the literature. Seventeen patients with this pathology have been published. A complete review of the literatures regarding this topic has been collected and discussed. The author also presents a 12- year old boy with triventricular hydrocephalus who had undergone ventriculoperitoneal medium pressure shunt system since birth. The patient presented to our clinic with a 2-year history of seizures. The patient was conscious and without neurological deficits on examination. Computed tomography of the brain showed bilateral high density mass with surface calcification. X ray skull and MRI confirmed the calcified subdural hematoma bilaterally. We preferred conservative treatment and the patient continued his antiepileptic treatment. At one year follow up, the patient had the same neurological state. The case highlights the importance of frequent follow up CT brain after shunt surgery.

Preliminary in Vivo Evaluation of a Hybrid Armored Vascular Graft Combining Electrospinning and Additive Manufacturing Techniques

Directory of Open Access Journals (Sweden)

Cristiano Spadaccio

2016-01-01

Full Text Available In this study, we tested in vivo effectiveness of a previously developed poly-L-lactide/poly-8-caprolactone armored vascular graft releasing heparin. This bioprosthesis was designed in order to overcome the main drawbacks of tissue-engineered vascular grafts, mainly concerning poor mechanical properties, thrombogenicity, and endothelialization. The bioprosthesis was successfully implanted in an aortic vascular reconstruction model in rabbits. All grafts implanted were patent at four weeks postoperatively and have been adequately populated by endogenous cells without signs of thrombosis or structural failure and with no need of antiplatelet therapy. The results of this preliminary study might warrant for further larger controlled in vivo studies to further confirm these findings.

Reverse Evolution of Armor Plates in the Threespine Stickleback

Science.gov (United States)

Kitano, J.; Bolnick, D.I.; Beauchamp, D.A.; Mazur, M.M.; Mori, S.; Nakano, T.; Peichel, C.L.

2008-01-01

Faced with sudden environmental changes, animals must either adapt to novel environments or go extinct. Thus, study of the mechanisms underlying rapid adaptation is crucial not??only for the understanding of natural evolutionary processes but also for the understanding of human-induced evolutionary change, which is an increasingly important problem [1-8]. In the present study, we demonstrate that the frequency of completely plated threespine stickleback fish (Gasterosteus aculeatus) has increased in an urban freshwater lake (Lake Washington, Seattle, Washington) within the last 40 years. This is a dramatic example of "reverse evolution," [9] because the general evolutionary trajectory is toward armor-plate reduction in freshwater sticklebacks [10]. On the basis of our genetic studies and simulations, we propose that the most likely cause of reverse evolution is increased selection for the completely plated morph, which we suggest could result from higher levels of trout predation after a sudden increase in water transparency during the early 1970s. Rapid evolution was facilitated by the existence of standing allelic variation in Ectodysplasin (Eda), the gene that underlies the major plate-morph locus [11]. The Lake Washington stickleback thus provides a novel example of reverse evolution, which is probably caused by a change in allele frequency at the major plate locus in response to a changing predation regime. ?? 2008 Elsevier Ltd. All rights reserved.

75 FR 78268 - Draft NIJ Selection and Application Guide to Ballistic-Resistant Body Armor for Law Enforcement...

Science.gov (United States)

2010-12-15

...In an effort to obtain comments from interested parties, the U.S. Department of Justice, Office of Justice Programs, National Institute of Justice (NIJ) will make available to the general public the draft ``NIJ Selection and Application Guide to Ballistic-Resistant Body Armor for Law Enforcement, Corrections, and Public Safety.'' The opportunity to provide comments on this document is open to industry technical representatives, criminal justice agencies and organizations, research, development and scientific communities, and all other stakeholders and interested parties. Those individuals wishing to obtain and provide comments on the draft document under consideration are directed to the following Web site: http://www.justnet.org.

RNA secondary structure prediction using soft computing.

Science.gov (United States)

Ray, Shubhra Sankar; Pal, Sankar K

2013-01-01

Prediction of RNA structure is invaluable in creating new drugs and understanding genetic diseases. Several deterministic algorithms and soft computing-based techniques have been developed for more than a decade to determine the structure from a known RNA sequence. Soft computing gained importance with the need to get approximate solutions for RNA sequences by considering the issues related with kinetic effects, cotranscriptional folding, and estimation of certain energy parameters. A brief description of some of the soft computing-based techniques, developed for RNA secondary structure prediction, is presented along with their relevance. The basic concepts of RNA and its different structural elements like helix, bulge, hairpin loop, internal loop, and multiloop are described. These are followed by different methodologies, employing genetic algorithms, artificial neural networks, and fuzzy logic. The role of various metaheuristics, like simulated annealing, particle swarm optimization, ant colony optimization, and tabu search is also discussed. A relative comparison among different techniques, in predicting 12 known RNA secondary structures, is presented, as an example. Future challenging issues are then mentioned.

The internal initiation of translation in bovine viral diarrhea virus RNA depends on the presence of an RNA pseudoknot upstream of the initiation codon.

Science.gov (United States)

Moes, Lorin; Wirth, Manfred

2007-11-22

Bovine viral diarrhea virus (BVDV) is the prototype representative of the pestivirus genus in the Flaviviridae family. It has been shown that the initiation of translation of BVDV RNA occurs by an internal ribosome entry mechanism mediated by the 5' untranslated region of the viral RNA 1. The 5' and 3' boundaries of the IRES of the cytopathic BVDV NADL have been mapped and it has been suggested that the IRES extends into the coding of the BVDV polyprotein 2. A putative pseudoknot structure has been recognized in the BVDV 5'UTR in close proximity to the AUG start codon. A pseudoknot structure is characteristic for flavivirus IRESes and in the case of the closely related classical swine fever virus (CSFV) and the more distantly related Hepatitis C virus (HCV) pseudoknot function in translation has been demonstrated. To characterize the BVDV IRESes in detail, we studied the BVDV translational initiation by transfection of dicistronic expression plasmids into mammalian cells. A region coding for the amino terminus of the BVDV SD-1 polyprotein contributes considerably to efficient initiation of translation. The translation efficiency mediated by the IRES of BVDV strains NADL and SD-1 approximates the poliovirus type I IRES directed translation in BHK cells. Compared to the poliovirus IRES increased expression levels are mediated by the BVDV IRES of strain SD-1 in murine cell lines, while lower levels are observed in human cell lines. Site directed mutagenesis revealed that a RNA pseudoknot upstream of the initiator AUG is an important structural element for IRES function. Mutants with impaired ability to base pair in stem I or II lost their translational activity. In mutants with repaired base pairing either in stem 1 or in stem 2 full translational activity was restored. Thus, the BVDV IRES translation is dependent on the pseudoknot integrity. These features of the pestivirus IRES are reminiscent of those of the classical swine fever virus, a pestivirus, and the

The internal initiation of translation in bovine viral diarrhea virus RNA depends on the presence of an RNA pseudoknot upstream of the initiation codon

Directory of Open Access Journals (Sweden)

Moes Lorin

2007-11-01

Full Text Available Abstract Background Bovine viral diarrhea virus (BVDV is the prototype representative of the pestivirus genus in the Flaviviridae family. It has been shown that the initiation of translation of BVDV RNA occurs by an internal ribosome entry mechanism mediated by the 5' untranslated region of the viral RNA 1. The 5' and 3' boundaries of the IRES of the cytopathic BVDV NADL have been mapped and it has been suggested that the IRES extends into the coding of the BVDV polyprotein 2. A putative pseudoknot structure has been recognized in the BVDV 5'UTR in close proximity to the AUG start codon. A pseudoknot structure is characteristic for flavivirus IRESes and in the case of the closely related classical swine fever virus (CSFV and the more distantly related Hepatitis C virus (HCV pseudoknot function in translation has been demonstrated. Results To characterize the BVDV IRESes in detail, we studied the BVDV translational initiation by transfection of dicistronic expression plasmids into mammalian cells. A region coding for the amino terminus of the BVDV SD-1 polyprotein contributes considerably to efficient initiation of translation. The translation efficiency mediated by the IRES of BVDV strains NADL and SD-1 approximates the poliovirus type I IRES directed translation in BHK cells. Compared to the poliovirus IRES increased expression levels are mediated by the BVDV IRES of strain SD-1 in murine cell lines, while lower levels are observed in human cell lines. Site directed mutagenesis revealed that a RNA pseudoknot upstream of the initiator AUG is an important structural element for IRES function. Mutants with impaired ability to base pair in stem I or II lost their translational activity. In mutants with repaired base pairing either in stem 1 or in stem 2 full translational activity was restored. Thus, the BVDV IRES translation is dependent on the pseudoknot integrity. These features of the pestivirus IRES are reminiscent of those of the classical

Natural Mallow Fiber-Reinforced Epoxy Composite for Ballistic Armor Against Class III-A Ammunition

Science.gov (United States)

Nascimento, Lucio Fabio Cassiano; Holanda, Luane Isquerdo Ferreira; Louro, Luis Henrique Leme; Monteiro, Sergio Neves; Gomes, Alaelson Vieira; Lima, Édio Pereira

2017-10-01

Epoxy matrix composites reinforced with up to 30 vol pct of continuous and aligned natural mallow fibers were for the first time ballistic tested as personal armor against class III-A 9 mm FMJ ammunition. The ballistic efficiency of these composites was assessed by measuring the dissipated energy and residual velocity after the bullet perforation. The results were compared to those in similar tests of aramid fabric (Kevlar™) commonly used in vests for personal protections. Visual inspection and scanning electron microscopy analysis of impact-fractured samples revealed failure mechanisms associated with fiber pullout and rupture as well as epoxy cracking. As compared to Kevlar™, the mallow fiber composite displayed practically the same ballistic efficiency. However, there is a reduction in both weight and cost, which makes the mallow fiber composites a promising material for personal ballistic protection.

Thermal shock fracture of graphite armor plate under the heat load of plasma disruption

International Nuclear Information System (INIS)

Horie, Tomoyoshi; Seki, Masahiro; Ohmori, Junji

1989-01-01

Experiments on the thermal shock brittle fracture of graphite plates were performed. Thermal loading which simulated a plasma disruption was produced by an electron beam facility. Pre-cracks produced on the surface propagated to the inside of the specimen even if the thermal stress on the surface was compressive. Two mechanisms are possible to produce tensile stress around the crack tip under thermal shock conditions. Temperature, thermal stress, and the stress intensity factor for the specimen were analyzed based on the finite element method for various heating conditions. The trend of experimental results under the asymmetric heating agrees qualitatively with the analytical results. This phenomenon is important for the design of plasma facing components made of graphite. Establishment of a lifetime prediction procedure including fatigue, fatigue crack growth, and brittle fracture is needed for graphite armors. (orig.)

[Correlation between five RNA markers of rat's skin and PMI at different temperatures].

Science.gov (United States)

Pan, Hui; Zhang, Heng; Lü, Ye-hui; Ma, Jian-long; Ma, Kai-jun; Chen, Long

2014-08-01

To explore the correlation between postmortem interval (PMI) and five RNA markers of rat's skin--β-actin, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), 18S ribosomal RNA(18S rRNA), 5S ribosomal RNA (5S rRNA), and microRNA-203 (miR-203), at different temperatures. Eighteen SD rats were randomly divided into three environmental temperature groups: 4 °C, 15 °C and 35 °C, respectively. Skin samples were taken at 11 time points from 0 h to 120 h post-mortem. The total RNA was extracted from the skin samples and the five RNA levels were detected by real-time fluorescent quantitative PCR. Proper internal reference was selected by geNorm software. Regression analysis of the RNA markers was conducted by GraphPad software. 5S rRNA and miR-203 were most suitable internal references. A good linear relationship between PMI and RNA levels (β-actin and GAPDH) was observed in two groups (4 °C and 15 °C), whereas the S type curve relationship between the expression levels of the two markers (β-actin and GAPDH) and PMI was observed in the 35 °C group. The partial linear relationship between 18S rRNA and PMI was observed in the groups (15 °C and 35 °C). Skin could be a suitable material for extracting RNA. The RNA expression levels of β-actin and GAPDH correlate well with PMI, and these RNA markers of skin tissue could be additional indice for the estimation of PMI.

ITSoneDB: a comprehensive collection of eukaryotic ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences.

Science.gov (United States)

Santamaria, Monica; Fosso, Bruno; Licciulli, Flavio; Balech, Bachir; Larini, Ilaria; Grillo, Giorgio; De Caro, Giorgio; Liuni, Sabino; Pesole, Graziano

2018-01-04

A holistic understanding of environmental communities is the new challenge of metagenomics. Accordingly, the amplicon-based or metabarcoding approach, largely applied to investigate bacterial microbiomes, is moving to the eukaryotic world too. Indeed, the analysis of metabarcoding data may provide a comprehensive assessment of both bacterial and eukaryotic composition in a variety of environments, including human body. In this respect, whereas hypervariable regions of the 16S rRNA are the de facto standard barcode for bacteria, the Internal Transcribed Spacer 1 (ITS1) of ribosomal RNA gene cluster has shown a high potential in discriminating eukaryotes at deep taxonomic levels. As metabarcoding data analysis rely on the availability of a well-curated barcode reference resource, a comprehensive collection of ITS1 sequences supplied with robust taxonomies, is highly needed. To address this issue, we created ITSoneDB (available at http://itsonedb.cloud.ba.infn.it/) which in its current version hosts 985 240 ITS1 sequences spanning over 134 000 eukaryotic species. Each ITS1 is mapped on the NCBI reference taxonomy with its start and end positions precisely annotated. ITSoneDB has been developed in agreement to the FAIR guidelines by enabling the users to query and download its content through a simple web-interface and access relevant metadata by cross-linking to European Nucleotide Archive. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Beryllium armored mockups for fusion high flux application

International Nuclear Information System (INIS)

Gervash, A.; Giniyatulin, R.; Mazul, I.; Watson, R.

1998-01-01

One of the main requirements to use Be as a candidate for plasma facing component in ITER is providing a reliable joint between Be and Cu-alloy heat sink structure. In this work authors present the results of recent activity on this way. To create Be/CuCrZr joints the unique fast e-beam brazing technology was developed in Russia. The numbers of Be/CuCrZr mock-ups were manufactured in Efremov Institute by fast e-beam brazing using Cu-Sn-In-Ni brazing alloy. These mock-ups were tested by Sandia Laboratory at the EBTS electron beam facility. The goals of the tests were to define the allowable dimensions of the armour tiles for the heat loads of more than 10 MW/m 2 , to find the limit of bond strength for the Be/CuCrZr joint and response to heat loads and to estimate the life time of the brazed tiles by thermo-cyclic testing. The screening and thermal fatigue results are presented. With the aim to check the applicability of developed fast brazing process to DS-Cu alloy (GlidCop) the actively cooled mock-up produced by fast brazing Be onto GlidCop structure was manufactured and tested in Efremov Institute, main results are discussed. Summarizing testing data authors show that the CuCrZr or DS-Cu heat sink armored with beryllium can survive high heat fluxes (≥10 MW/m 2 ) during thousand heating/cooling cycles without serious damaging in the armour material and its joint. (author)

Viscoelastic shock wave in ballistic gelatin behind soft body armor.

Science.gov (United States)

Liu, Li; Fan, Yurun; Li, Wei

2014-06-01

Ballistic gelatins are widely used as a surrogate of biological tissue in blunt trauma tests. Non-penetration impact tests of handgun bullets on the 10wt% ballistic gelatin block behind soft armor were carried out in which a high-speed camera recorded the crater׳s movement and pressure sensors imbedded in the gelatin block recorded the pressure waves at different locations. The observed shock wave attenuation indicates the necessity of considering the gelatin׳s viscoelasticity. A three-element viscoelastic constitutive model was adopted, in which the relevant parameters were obtained via fitting the damping free oscillations at the beginning of the creep-mode of rheological measurement, and by examining the data of published split Hopkinson pressure bar (SHPB) experiments. The viscoelastic model is determined by a retardation time of 5.5×10(-5)s for high oscillation frequencies and a stress relaxation time of 2.0-4.5×10(-7)s for shock wave attenuation. Using the characteristic-line method and the spherical wave assumption, the propagation of impact pressure wave front and the subsequent unloading profile can be simulated using the experimental velocity boundary condition. The established viscoelastic model considerably improves the prediction of shock wave attenuation in the ballistic gelatin. Copyright © 2014 Elsevier Ltd. All rights reserved.

Accumulation of dsRNA in endosomes contributes to inefficient RNA interference in the fall armyworm, Spodoptera frugiperda.

Science.gov (United States)

Yoon, June-Sun; Gurusamy, Dhandapani; Palli, Subba Reddy

2017-11-01

RNA interference (RNAi) efficiency varies among insects studied. The barriers for successful RNAi include the presence of double-stranded ribonucleases (dsRNase) in the lumen and hemolymph that could potentially digest double-stranded RNA (dsRNA) and the variability in the transport of dsRNA into and within the cells. We recently showed that the dsRNAs are transported into lepidopteran cells, but they are not processed into small interference RNAs (siRNAs) because they are trapped in acidic bodies. In the current study, we focused on the identification of acidic bodies in which dsRNAs accumulate in Sf9 cells. Time-lapse imaging studies showed that dsRNAs enter Sf9 cells and accumulate in acidic bodies within 20 min after their addition to the medium. CypHer-5E-labeled dsRNA also accumulated in the midgut and fat body dissected from Spodoptera frugiperda larvae with similar patterns observed in Sf9 cells. Pharmacological inhibitor assays showed that the dsRNAs use clathrin mediated endocytosis pathway for transport into the cells. We investigated the potential dsRNA accumulation sites employing LysoTracker and double labeling experiments using the constructs to express a fusion of green fluorescence protein with early or late endosomal marker proteins and CypHer-5E-labeled dsRNA. Interestingly, CypHer-5E-labeled dsRNA accumulated predominantly in early and late endosomes. These data suggest that entrapment of internalized dsRNA in endosomes is one of the major factors contributing to inefficient RNAi response in lepidopteran insects. Copyright © 2017 Elsevier Ltd. All rights reserved.

Conference Scene: Advances in RNA nanotechnology promise to transform medicine.

Science.gov (United States)

Leontis, Neocles; Sweeney, Blake; Haque, Farzin; Guo, Peixuan

2013-07-01

The second International Conference on RNA Nanotechnology and Therapeutics was held on the 3-5 April in Lexington, (KY, USA). The focus of the conference was on leveraging the unique chemical and biological properties of RNA to promote transformative advances in medicine. The conference convened more than 200 researchers from 15 countries and many disciplines, roughly double the participants of the first conference. While many presentations focused on the design, assembly and characterization of RNA nanoparticles and their uses for in vivo and in vitro sensing, diagnosis and therapy, others covered a variety of relevant areas of RNA biology and chemistry.

Impact of the surface quality on the thermal shock performance of beryllium armor tiles for first wall applications

Energy Technology Data Exchange (ETDEWEB)

Spilker, B., E-mail: b.spilker@fz-juelich.de; Linke, J.; Pintsuk, G.; Wirtz, M.

2016-11-01

Highlights: • Different surface qualities of S-65 beryllium are tested under high heat flux conditions. • After 1000 thermal shocks, the loaded area exhibits a crucial destruction. • Stress accelerated grain boundary oxidation/dynamic embrittlement effects are linked to the thermal shock performance of beryllium. • Thermally induced cracks form between 1 and 10 pulses and grow wider and deeper between 10 and 100 pulses. • Thermally induced cracks form and propagate independently from surface grooves and the surface quality. - Abstract: Beryllium will be applied as first wall armor material in ITER. The armor has to sustain high steady state and transient power fluxes. For transient events like edge localized modes, these transient power fluxes rise up to 1.0 GW m{sup −2} with a duration of 0.5–0.75 ms in the divertor region and a significant fraction of this power flux is deposited on the first wall as well. In the present work, the reference beryllium grade for the ITER first wall application S-65 was prepared with various surface conditions and subjected to transient power fluxes (thermal shocks) with ITER relevant loading parameters. After 1000 thermal shocks, a crucial destruction of the entire loaded area was observed and linked to the stress accelerated grain boundary oxidation (SAGBO)/dynamic embrittlement (DE) effect. Furthermore, the study revealed that the majority of the thermally induced cracks formed between 1 and 10 pulses and then grew wider and deeper with increasing pulse number. The surface quality did not influence the cracking behavior of beryllium in any detectable way. However, the polished surface demonstrated the highest resistance against the observed crucial destruction mechanism.

Molecular mechanisms for the regulation of histone mRNA stem-loop-binding protein by phosphorylation

Energy Technology Data Exchange (ETDEWEB)

Zhang, Jun; Tan, Dazhi; DeRose, Eugene F.; Perera, Lalith; Dominski, Zbigniew; Marzluff, William F.; Tong, Liang; Tanaka Hall, Traci M. [NIH; (UNC); (Columbia)

2014-08-06

Replication-dependent histone mRNAs end with a conserved stem loop that is recognized by stem-loop–binding protein (SLBP). The minimal RNA-processing domain of SLBP is phosphorylated at an internal threonine, and Drosophila SLBP (dSLBP) also is phosphorylated at four serines in its 18-aa C-terminal tail. We show that phosphorylation of dSLBP increases RNA-binding affinity dramatically, and we use structural and biophysical analyses of dSLBP and a crystal structure of human SLBP phosphorylated on the internal threonine to understand the striking improvement in RNA binding. Together these results suggest that, although the C-terminal tail of dSLBP does not contact the RNA, phosphorylation of the tail promotes SLBP conformations competent for RNA binding and thereby appears to reduce the entropic penalty for the association. Increased negative charge in this C-terminal tail balances positively charged residues, allowing a more compact ensemble of structures in the absence of RNA.

Recent High Heat Flux Tests on W-Rod-Armored Mockups

International Nuclear Information System (INIS)

Nygren, Richard E.; Youchison, Dennis L.; McDonald, Jimmie M.; Lutz, Thomas J.; Miszkiel, Mark E.

2000-01-01

In the authors initial high heat flux tests on small mockups armored with W rods, done in the small electron beam facility (EBTS) at Sandia National Laboratories, the mockups exhibited excellent thermal performance. However, to reach high heat fluxes, they reduced the heated area to only a portion (approximately25%) of the sample. They have now begun tests in their larger electron beam facility, EB 1200, where the available power (1.2 MW) is more than enough to heat the entire surface area of the small mockups. The initial results indicate that, at a given power, the surface temperatures of rods in the EB 1200 tests is somewhat higher than was observed in the EBTS tests. Also, it appears that one mockup (PW-10) has higher surface temperatures than other mockups with similar height (10mm) W rods, and that the previously reported values of absorbed heat flux on this mockup were too high. In the tests in EB 1200 of a second mockup, PW-4, absorbed heat fluxes of approximately22MW/m 2 were reached but the corresponding surface temperatures were somewhat higher than in EBTS. A further conclusion is that the simple 1-D model initially used in evaluating some of the results from the EBTS testing was not adequate, and 3-D thermal modeling will be needed to interpret the results

MicroRNA-encoding long non-coding RNAs

Directory of Open Access Journals (Sweden)

Zhu Xiaopeng

2008-05-01

Full Text Available Abstract Background Recent analysis of the mouse transcriptional data has revealed the existence of ~34,000 messenger-like non-coding RNAs (ml-ncRNAs. Whereas the functional properties of these ml-ncRNAs are beginning to be unravelled, no functional information is available for the large majority of these transcripts. Results A few ml-ncRNA have been shown to have genomic loci that overlap with microRNA loci, leading us to suspect that a fraction of ml-ncRNA may encode microRNAs. We therefore developed an algorithm (PriMir for specifically detecting potential microRNA-encoding transcripts in the entire set of 34,030 mouse full-length ml-ncRNAs. In combination with mouse-rat sequence conservation, this algorithm detected 97 (80 of them were novel strong miRNA-encoding candidates, and for 52 of these we obtained experimental evidence for the existence of their corresponding mature microRNA by microarray and stem-loop RT-PCR. Sequence analysis of the microRNA-encoding RNAs revealed an internal motif, whose presence correlates strongly (R2 = 0.9, P-value = 2.2 × 10-16 with the occurrence of stem-loops with characteristics of known pre-miRNAs, indicating the presence of a larger number microRNA-encoding RNAs (from 300 up to 800 in the ml-ncRNAs population. Conclusion Our work highlights a unique group of ml-ncRNAs and offers clues to their functions.

Responses to Three USARIEM Job Analysis Questionnaires (JAQs) Conducted with Cavalry Scouts and Armor Crewmen (MOSs 19D and 19K)

Science.gov (United States)

2016-11-18

gun for one fire command 56 24 Boxes of rounds loaded for the .50 Cal Machine Gun on an Abrams Tank 56 25 Mean estimates of time spent by 19Ds...Number of rounds loaded for one fire command 55 22 Total boxes of rounds loaded for .50 cal machine gun on an Abrams tank 56 23 Number of Soldiers...and 19K MOSs, respectively). A total o f 8,580 Army calvary scouts and 6,613 armor crewmen in the USA Army as of May or June of 2014 were invited

A Sequence-Independent, Unstructured Internal Ribosome Entry Site Is Responsible for Internal Expression of the Coat Protein of Turnip Crinkle Virus.

Science.gov (United States)

May, Jared; Johnson, Philip; Saleem, Huma; Simon, Anne E

2017-04-15

To maximize the coding potential of viral genomes, internal ribosome entry sites (IRES) can be used to bypass the traditional requirement of a 5' cap and some/all of the associated translation initiation factors. Although viral IRES typically contain higher-order RNA structure, an unstructured sequence of about 84 nucleotides (nt) immediately upstream of the Turnip crinkle virus (TCV) coat protein (CP) open reading frame (ORF) has been found to promote internal expression of the CP from the genomic RNA (gRNA) both in vitro and in vivo An absence of extensive RNA structure was predicted using RNA folding algorithms and confirmed by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) RNA structure probing. Analysis of the IRES region in vitro by use of both the TCV gRNA and reporter constructs did not reveal any sequence-specific elements but rather suggested that an overall lack of structure was an important feature for IRES activity. The CP IRES is A-rich, independent of orientation, and strongly conserved among viruses in the same genus. The IRES was dependent on eIF4G, but not eIF4E, for activity. Low levels of CP accumulated in vivo in the absence of detectable TCV subgenomic RNAs, strongly suggesting that the IRES was active in the gRNA in vivo Since the TCV CP also serves as the viral silencing suppressor, early translation of the CP from the viral gRNA is likely important for countering host defenses. Cellular mRNA IRES also lack extensive RNA structures or sequence conservation, suggesting that this viral IRES and cellular IRES may have similar strategies for internal translation initiation. IMPORTANCE Cap-independent translation is a common strategy among positive-sense, single-stranded RNA viruses for bypassing the host cell requirement of a 5' cap structure. Viral IRES, in general, contain extensive secondary structure that is critical for activity. In contrast, we demonstrate that a region of viral RNA devoid of extensive secondary

Conceptual thermal-mechanical design of the TFTR first wall armor against neutral beam impingement

International Nuclear Information System (INIS)

Chi, J.W.H.; Flaherty, R.

1976-01-01

The Tokamak Fusion Test Reactor (TFTR) is designed to operate in a pulsed mode with relatively low duty cycles. Each pulse consists of a short plasma heat-up period, a reaction period, followed by a relatively long cooldown period. Plasma heating is accomplished by ohmic heating by a current induced change in the magnetically linked ohmic heating coils, followed by neutral beam injection for further preheat and the initiation of fusion reactions. During normal operation, the bulk of the neutral beam energy will be absorbed by the plasma, while the remainder will impinge on the vacuum vessel wall. The amount of thermal energy deposited on an unprotected wall is expected to be excessive, limiting the frequency of pulses and requiring frequent wall replacement. A faulted condition would cause penetration of an unprotected wall. As a consequence, a wall armoring (or liner) concept was developed to protect the vacuum vessel wall and to permit ease of liner replacement

The RNA gene information: retroelement-microRNA entangling as the RNA quantum code.

Science.gov (United States)

Fujii, Yoichi Robertus

2013-01-01

MicroRNA (miRNA) and retroelements may be a master of regulator in our life, which are evolutionally involved in the origin of species. To support the Darwinism from the aspect of molecular evolution process, it has tremendously been interested in the molecular information of naive RNA. The RNA wave model 2000 consists of four concepts that have altered from original idea of the miRNA genes for crosstalk among embryonic stem cells, their niche cells, and retroelements as a carrier vesicle of the RNA genes. (1) the miRNA gene as a mobile genetic element induces transcriptional and posttranscriptional silencing via networking-processes (no hierarchical architecture); (2) the RNA information supplied by the miRNA genes expands to intracellular, intercellular, intraorgan, interorgan, intraspecies, and interspecies under the cycle of life into the global environment; (3) the mobile miRNAs can self-proliferate; and (4) cells contain two types information as resident and genomic miRNAs. Based on RNA wave, we have developed an interest in investigation of the transformation from RNA information to quantum bits as physicochemical characters of RNA with the measurement of RNA electron spin. When it would have been given that the fundamental bases for the acquired characters in genetics can be controlled by RNA gene information, it may be available to apply for challenging against RNA gene diseases, such as stress-induced diseases.

ISEV position paper: extracellular vesicle RNA analysis and bioinformatics

Directory of Open Access Journals (Sweden)

Andrew F. Hill

2013-12-01

Full Text Available Extracellular vesicles (EVs are the collective term for the various vesicles that are released by cells into the extracellular space. Such vesicles include exosomes and microvesicles, which vary by their size and/or protein and genetic cargo. With the discovery that EVs contain genetic material in the form of RNA (evRNA has come the increased interest in these vesicles for their potential use as sources of disease biomarkers and potential therapeutic agents. Rapid developments in the availability of deep sequencing technologies have enabled the study of EV-related RNA in detail. In October 2012, the International Society for Extracellular Vesicles (ISEV held a workshop on “evRNA analysis and bioinformatics.” Here, we report the conclusions of one of the roundtable discussions where we discussed evRNA analysis technologies and provide some guidelines to researchers in the field to consider when performing such analysis.

Evaluation of dose attenuation factor of armored car against radiation accidents

International Nuclear Information System (INIS)

Sato, Tatsuhiko; Fujii, Katsutoshi; Murayama, Takashi

2002-03-01

The Tokyo Fire Department developed an armored car against radiation accidents. The car is covered by lead shields for attenuating dose from gamma rays. Dose from neutrons also can be attenuated by pouring water into tanks attached to the surface of the car. However, dose attenuation factors of the radiation shields had been determined by an estimation of single-layer shield, and more precise evaluation of multi-layer shield was required. By request from the Tokyo Fire Department, a precise evaluation of the dose attenuation in multi-layer shield was carried out. The evaluation was made by a Monte Carlo radiation transport simulation code MCNP4B for the shields used in the front, side and back of the car. Three types of the radiation sources ( 252 Cf as a neutron source, 60 Co as a gamma ray source, and radiation source corresponding to the JCO criticality accident) were considered in the calculation. Benchmark experiments using neutron and gamma ray sources were also performed for ensuring the evaluation method. As a result, it was found out that doses of neutron and gamma ray were attenuated to approximately 10% and 25% by the thickest shield, respectively. These values were close to the ones which had already obtained by the estimation of single-layer shield. (author)

Nonreplicative RNA Recombination of an Animal Plus-Strand RNA Virus in the Absence of Efficient Translation of Viral Proteins

Science.gov (United States)

Kleine Büning, Maximiliane; Meyer, Denise; Austermann-Busch, Sophia; Roman-Sosa, Gleyder; Rümenapf, Tillmann

2017-01-01

RNA recombination is a major driving force for the evolution of RNA viruses and is significantly implicated in the adaptation of viruses to new hosts, changes of virulence, as well as in the emergence of new viruses including drug-resistant and escape mutants. However, the molecular details of recombination in animal RNA viruses are only poorly understood. In order to determine whether viral RNA recombination depends on translation of viral proteins, a nonreplicative recombination system was established which is based on cotransfection of cells with synthetic bovine viral diarrhea virus (family Flaviviridae) RNA genome fragments either lacking the internal ribosome entry site required for cap-independent translation or lacking almost the complete polyprotein coding region. The emergence of a number of recombinant viruses demonstrated that IRES-mediated translation of viral proteins is dispensable for efficient recombination and suggests that RNA recombination can occur in the absence of viral proteins. Analyses of 58 independently emerged viruses led to the detection of recombinant genomes with duplications, deletions and insertions in the 5′ terminal region of the open reading frame, leading to enlarged core fusion proteins detectable by Western blot analysis. This demonstrates a remarkable flexibility of the pestivirus core protein. Further experiments with capped and uncapped genome fragments containing a luciferase gene for monitoring the level of protein translation revealed that even a ∼1,000-fold enhancement of translation of viral proteins did not increase the frequency of RNA recombination. Taken together, this study highlights that nonreplicative RNA recombination does not require translation of viral proteins. PMID:28338950

iDoRNA: An Interacting Domain-based Tool for Designing RNA-RNA Interaction Systems

Directory of Open Access Journals (Sweden)

Jittrawan Thaiprasit

2016-03-01

Full Text Available RNA-RNA interactions play a crucial role in gene regulation in living organisms. They have gained increasing interest in the field of synthetic biology because of their potential applications in medicine and biotechnology. However, few novel regulators based on RNA-RNA interactions with desired structures and functions have been developed due to the challenges of developing design tools. Recently, we proposed a novel tool, called iDoDe, for designing RNA-RNA interacting sequences by first decomposing RNA structures into interacting domains and then designing each domain using a stochastic algorithm. However, iDoDe did not provide an optimal solution because it still lacks a mechanism to optimize the design. In this work, we have further developed the tool by incorporating a genetic algorithm (GA to find an RNA solution with maximized structural similarity and minimized hybridized RNA energy, and renamed the tool iDoRNA. A set of suitable parameters for the genetic algorithm were determined and found to be a weighting factor of 0.7, a crossover rate of 0.9, a mutation rate of 0.1, and the number of individuals per population set to 8. We demonstrated the performance of iDoRNA in comparison with iDoDe by using six RNA-RNA interaction models. It was found that iDoRNA could efficiently generate all models of interacting RNAs with far more accuracy and required far less computational time than iDoDe. Moreover, we compared the design performance of our tool against existing design tools using forty-four RNA-RNA interaction models. The results showed that the performance of iDoRNA is better than RiboMaker when considering the ensemble defect, the fitness score and computation time usage. However, it appears that iDoRNA is outperformed by NUPACK and RNAiFold 2.0 when considering the ensemble defect. Nevertheless, iDoRNA can still be an useful alternative tool for designing novel RNA-RNA interactions in synthetic biology research. The source code of iDoRNA

Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme.

Science.gov (United States)

White, Neil A; Hoogstraten, Charles G

2017-09-01

The hairpin ribozyme consists of two RNA internal loops that interact to form the catalytically active structure. This docking transition is a rare example of intermolecular formation of RNA tertiary structure without coupling to helix annealing. We have used temperature-dependent surface plasmon resonance (SPR) to characterize the thermodynamics and kinetics of RNA tertiary structure formation for the junctionless form of the ribozyme, in which loops A and B reside on separate molecules. We find docking to be strongly enthalpy-driven and to be accompanied by substantial activation barriers for association and dissociation, consistent with the structural reorganization of both internal loops upon complex formation. Comparisons with the parallel analysis of a ribozyme variant carrying a 2'-O-methyl modification at the self-cleavage site and with published data in other systems reveal a surprising diversity of thermodynamic signatures, emphasizing the delicate balance of contributions to the free energy of formation of RNA tertiary structure. Copyright © 2017 Elsevier B.V. All rights reserved.

Nucleotide sequence of a human tRNA gene heterocluster

International Nuclear Information System (INIS)

Chang, Y.N.; Pirtle, I.L.; Pirtle, R.M.

1986-01-01

Leucine tRNA from bovine liver was used as a hybridization probe to screen a human gene library harbored in Charon-4A of bacteriophage lambda. The human DNA inserts from plaque-pure clones were characterized by restriction endonuclease mapping and Southern hybridization techniques, using both [3'- 32 P]-labeled bovine liver leucine tRNA and total tRNA as hybridization probes. An 8-kb Hind III fragment of one of these γ-clones was subcloned into the Hind III site of pBR322. Subsequent fine restriction mapping and DNA sequence analysis of this plasmid DNA indicated the presence of four tRNA genes within the 8-kb DNA fragment. A leucine tRNA gene with an anticodon of AAG and a proline tRNA gene with an anticodon of AGG are in a 1.6-kb subfragment. A threonine tRNA gene with an anticodon of UGU and an as yet unidentified tRNA gene are located in a 1.1-kb subfragment. These two different subfragments are separated by 2.8 kb. The coding regions of the three sequenced genes contain characteristic internal split promoter sequences and do not have intervening sequences. The 3'-flanking region of these three genes have typical RNA polymerase III termination sites of at least four consecutive T residues

Molecular Beacon-Based MicroRNA Imaging During Neurogenesis.

Science.gov (United States)

Lee, Jonghwan; Kim, Soonhag

2016-01-01

The fluorescence monitoring system for examining endogenous microRNA (miRNA) activity in cellular level provides crucial information on not only understanding a critical role of miRNA involving a variety of biological processes, but also evaluating miRNA expression patterns in a noninvasive manner. In this protocol, we report the details of a new procedure for a molecular beacon-based miRNA monitoring system, which includes the illustration scheme for miRNA detection strategy, exogenous miRNA detection, and measurement of endogenous miRNA expression level during neurogenesis. The fluorescence signal of miR-124a beacon quenched by BHQ2 was gradually recovered as increasing concentration of the miR-124a in tube. The functional work of miR-124a beacon was examined in intracellular environment, allowing for the internalization of the miR-124a beacon by lipofectamine, which resulted in activated fluorescent signals of the miR-124a beacon in the HeLa cells after the addition of synthetic miR-124a. The endogenous miR-124a expression level was detected by miR-124a beacon system during neurogenesis, showing brighter fluorescence intensity in cytoplasmic area of P19 cells after induction of neuronal differentiation by retinoic acid. The molecular beacon based-miRNA detection technique could be applicable to the simultaneous visualization of a variety of miRNA expression patterns using different fluorescence dyes. For the study of examining endogenous miRNA expression level using miRNA-beacon system, if cellular differentiation step is already prepared, transfection step of miR-124a beacon into P19 cells, and acquisition of activated fluorescence signal measured by confocal microscope can be conducted approximately within 6 h.

RNA-SSPT: RNA Secondary Structure Prediction Tools.

Science.gov (United States)

Ahmad, Freed; Mahboob, Shahid; Gulzar, Tahsin; Din, Salah U; Hanif, Tanzeela; Ahmad, Hifza; Afzal, Muhammad

2013-01-01

The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes.

Combinatorics of RNA-RNA interaction

DEFF Research Database (Denmark)

Li, Thomas J X; Reidys, Christian

2012-01-01

RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Here joint structure...... means that in a diagram representation the intramolecular bonds of each partner are pseudoknot-free, that the intermolecular binding pairs are noncrossing, and that there is no so-called "zigzag" configuration. This paper presents the combinatorics of RNA interaction structures including...

Fluorescence detection of natural RNA using rationally designed "clickable" oligonucleotide probes

DEFF Research Database (Denmark)

Okholm, Anders; Kjems, Jørgen; Astakhova, Kira

2014-01-01

Herein a reliable approach to the design of effective fluorescent probes for RNA detection is described. The fluorescence signalling of hybridization by internally positioned polyaromatic hydrocarbons and rhodamine dyes was achieved with a low fluorescence background signal, high fluorescence qua...... quantum yields at ambient and elevated temperature, high selectivity and signal specificity of the probes when binding to miR-7 and circRNA targets....

Viral tRNA Mimicry from a Biocommunicative Perspective

Directory of Open Access Journals (Sweden)

Ascensión Ariza-Mateos

2017-12-01

Full Text Available RNA viruses have very small genomes which limits the functions they can encode. One of the strategies employed by these viruses is to mimic key factors of the host cell so they can take advantage of the interactions and activities these factors typically participate in. The viral RNA genome itself was first observed to mimic cellular tRNA over 40 years ago. Since then researchers have confirmed that distinct families of RNA viruses are accessible to a battery of cellular factors involved in tRNA-related activities. Recently, potential tRNA-like structures have been detected within the sequences of a 100 mRNAs taken from human cells, one of these being the host defense interferon-alpha mRNA; these are then additional to the examples found in bacterial and yeast mRNAs. The mimetic relationship between tRNA, cellular mRNA, and viral RNA is the central focus of two considerations described below. These are subsequently used as a preface for a final hypothesis drawing on concepts relating to mimicry from the social sciences and humanities, such as power relations and creativity. Firstly, the presence of tRNA-like structures in mRNAs indicates that the viral tRNA-like signal could be mimicking tRNA-like elements that are contextualized by the specific carrier mRNAs, rather than, or in addition to, the tRNA itself, which would significantly increase the number of potential semiotic relations mediated by the viral signals. Secondly, and in particular, mimicking a host defense mRNA could be considered a potential new viral strategy for survival. Finally, we propose that mRNA’s mimicry of tRNA could be indicative of an ancestral intracellular conflict in which species of mRNAs invaded the cell, but from within. As the meaning of the mimetic signal depends on the context, in this case, the conflict that arises when the viral signal enters the cell can change the meaning of the mRNAs’ internal tRNA-like signals, from their current significance to that

Nonreplicative RNA Recombination of an Animal Plus-Strand RNA Virus in the Absence of Efficient Translation of Viral Proteins.

Science.gov (United States)

Kleine Büning, Maximiliane; Meyer, Denise; Austermann-Busch, Sophia; Roman-Sosa, Gleyder; Rümenapf, Tillmann; Becher, Paul

2017-04-01

RNA recombination is a major driving force for the evolution of RNA viruses and is significantly implicated in the adaptation of viruses to new hosts, changes of virulence, as well as in the emergence of new viruses including drug-resistant and escape mutants. However, the molecular details of recombination in animal RNA viruses are only poorly understood. In order to determine whether viral RNA recombination depends on translation of viral proteins, a nonreplicative recombination system was established which is based on cotransfection of cells with synthetic bovine viral diarrhea virus (family Flaviviridae) RNA genome fragments either lacking the internal ribosome entry site required for cap-independent translation or lacking almost the complete polyprotein coding region. The emergence of a number of recombinant viruses demonstrated that IRES-mediated translation of viral proteins is dispensable for efficient recombination and suggests that RNA recombination can occur in the absence of viral proteins. Analyses of 58 independently emerged viruses led to the detection of recombinant genomes with duplications, deletions and insertions in the 5' terminal region of the open reading frame, leading to enlarged core fusion proteins detectable by Western blot analysis. This demonstrates a remarkable flexibility of the pestivirus core protein. Further experiments with capped and uncapped genome fragments containing a luciferase gene for monitoring the level of protein translation revealed that even a ∼1,000-fold enhancement of translation of viral proteins did not increase the frequency of RNA recombination. Taken together, this study highlights that nonreplicative RNA recombination does not require translation of viral proteins. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

The characteristics and mechanism of apoptosis induced by internal irradiation

International Nuclear Information System (INIS)

Hong Chengjiao; Zhang Junning; Zhu Shoupeng

2001-01-01

Apoptosis in tumor cells induced by radionuclides is likely the most effective way to cure cancer. In order to explore the possibility in clinic application, the characteristics and mechanism of apoptosis induced by internal irradiation were investigated. The apoptosis and expressions of bcl-2mRNA, bcl-2 and bax of K 562 cells following internal exposure with different accumulated absorbed doses of strontium-89 were studied. 6 h after irradiation, the characteristics of apoptosis and necrosis appeared in K 562 cells. The apoptosis and necrosis enhanced with the prolongation of internally contaminated time at 6 h, 9 h, 12 h, 24 h and 48 h. The expressions of bcl-2mRNA decreased at 12 h, most remarkably at 24 h. The expressions of bcl-2 decreased after irradiation whereas bax had no obvious changes. The results suggest that the apoptosis induced by internal exposure may be regulated by lower expressions of bcl-2mRNA and bcl-2, lower bcl-2/bax value

The RAppArmor Package: Enforcing Security Policies in R Using Dynamic Sandboxing on Linux

Directory of Open Access Journals (Sweden)

Jeroen Ooms

2013-11-01

Full Text Available The increasing availability of cloud computing and scientific super computers brings great potential for making R accessible through public or shared resources. This allows us to efficiently run code requiring lots of cycles and memory, or embed R functionality into, e.g., systems and web services. However some important security concerns need to be addressed before this can be put in production. The prime use case in the design of R has always been a single statistician running R on the local machine through the interactive console. Therefore the execution environment of R is entirely unrestricted, which could result in malicious behavior or excessive use of hardware resources in a shared environment. Properly securing an R process turns out to be a complex problem. We describe various approaches and illustrate potential issues using some of our personal experiences in hosting public web services. Finally we introduce the RAppArmor package: a Linux based reference implementation for dynamic sandboxing in R on the level of the operating system.

Comprehensive characterization of lncRNA-mRNA related ceRNA network across 12 major cancers

Science.gov (United States)

Feng, Li; Li, Feng; Sun, Zeguo; Wu, Tan; Shi, Xinrui; Li, Jing; Li, Xia

2016-01-01

Recent studies indicate that long noncoding RNAs (lncRNAs) can act as competing endogenous RNAs (ceRNAs) to indirectly regulate mRNAs through shared microRNAs, which represents a novel layer of RNA crosstalk and plays critical roles in the development of tumor. However, the global regulation landscape and characterization of these lncRNA related ceRNA crosstalk in cancers is still largely unknown. Here, we systematically characterized the lncRNA related ceRNA interactions across 12 major cancers and the normal physiological states by integrating multidimensional molecule profiles of more than 5000 samples. Our study suggest the large difference of ceRNA regulation between normal and tumor states and the higher similarity across similar tissue origin of tumors. The ceRNA related molecules have more conserved features in tumor networks and they play critical roles in both the normal and tumorigenesis processes. Besides, lncRNAs in the pan-cancer ceRNA network may be potential biomarkers of tumor. By exploring hub lncRNAs, we found that these conserved key lncRNAs dominate variable tumor hallmark processes across pan-cancers. Network dynamic analysis highlights the critical roles of ceRNA regulation in tumorigenesis. By analyzing conserved ceRNA interactions, we found that miRNA mediate ceRNA regulation showed different patterns across pan-cancer; while analyzing the cancer specific ceRNA interactions reveal that lncRNAs synergistically regulated tumor driver genes of cancer hallmarks. Finally, we found that ceRNA modules have the potential to predict patient survival. Overall, our study systematically dissected the lncRNA related ceRNA networks in pan-cancer that shed new light on understanding the molecular mechanism of tumorigenesis. PMID:27580177

Comparison of protocols and RNA carriers for plasma miRNA isolation. Unraveling RNA carrier influence on miRNA isolation

Science.gov (United States)

Martos, Laura; Fernández-Pardo, Álvaro; Oto, Julia; Medina, Pilar; España, Francisco; Navarro, Silvia

2017-01-01

microRNAs are promising biomarkers in biological fluids in several diseases. Different plasma RNA isolation protocols and carriers are available, but their efficiencies have been scarcely compared. Plasma microRNAs were isolated using a phenol and column-based procedure and a column-based procedure, in the presence or absence of two RNA carriers (yeast RNA and MS2 RNA). We evaluated the presence of PCR inhibitors and the relative abundance of certain microRNAs by qRT-PCR. Furthermore, we analyzed the association between different isolation protocols, the relative abundance of the miRNAs in the sample, the GC content and the free energy of microRNAs. In all microRNAs analyzed, the addition of yeast RNA as a carrier in the different isolation protocols used gave lower raw Cq values, indicating higher microRNA recovery. Moreover, this increase in microRNAs recovery was dependent on their own relative abundance in the sample, their GC content and the free-energy of their own most stable secondary structure. Furthermore, the normalization of microRNA levels by an endogenous microRNA is more reliable than the normalization by plasma volume, as it reduced the difference in microRNA fold abundance between the different isolation protocols evaluated. Our thorough study indicates that a standardization of pre- and analytical conditions is necessary to obtain reproducible inter-laboratory results in plasma microRNA studies. PMID:29077772

Identification of Subtype Specific miRNA-mRNA Functional Regulatory Modules in Matched miRNA-mRNA Expression Data: Multiple Myeloma as a Case

Directory of Open Access Journals (Sweden)

Yunpeng Zhang

2015-01-01

Full Text Available Identification of miRNA-mRNA modules is an important step to elucidate their combinatorial effect on the pathogenesis and mechanisms underlying complex diseases. Current identification methods primarily are based upon miRNA-target information and matched miRNA and mRNA expression profiles. However, for heterogeneous diseases, the miRNA-mRNA regulatory mechanisms may differ between subtypes, leading to differences in clinical behavior. In order to explore the pathogenesis of each subtype, it is important to identify subtype specific miRNA-mRNA modules. In this study, we integrated the Ping-Pong algorithm and multiobjective genetic algorithm to identify subtype specific miRNA-mRNA functional regulatory modules (MFRMs through integrative analysis of three biological data sets: GO biological processes, miRNA target information, and matched miRNA and mRNA expression data. We applied our method on a heterogeneous disease, multiple myeloma (MM, to identify MM subtype specific MFRMs. The constructed miRNA-mRNA regulatory networks provide modular outlook at subtype specific miRNA-mRNA interactions. Furthermore, clustering analysis demonstrated that heterogeneous MFRMs were able to separate corresponding MM subtypes. These subtype specific MFRMs may aid in the further elucidation of the pathogenesis of each subtype and may serve to guide MM subtype diagnosis and treatment.

RNA polymerase of the killer virus of yeast

International Nuclear Information System (INIS)

Georgopoulos, D.E.; Leibowitz, M.J.

1984-01-01

The L/sub A/ and M double-stranded (ds) RNA segments of the cytoplasmically inherited killer virus of Saccharomyces cerevisiae are encapsidated in virions that contain a DNA-independent transcriptase activity. This enzyme catalyzes the synthesis of full-length (+) stranded copies of the genomic dsRNA segments, denoted l/sub A/ and m. The L/sub A/ dsRNA segment appears to encode the major capsid protein in which both dsRNA molecules are encapsidated, while M dsRNA encodes products responsible for the two killer phenotypes of toxin production and resistance to toxin. Proteins extracted from transcriptionally active virions fail to cross-react with antibody to yeast DNA-dependent RNA polymerases, suggesting that none of the subunits of the host cell polymerases are active in viral transcription. Sequence analysis of the in vitro transcripts reveals neither to be 3'-terminally polyadenylated, although m contains an apparent internal polyA-like tract. In the presence of any three ribonucleoside triphosphates (0.5 mM), the fourth ribonucleoside triphosphate shows an optimal rate of incorporation into transcript at a concentration of 20 μM. However, in a 3-hour reaction, the yield of a product RNA increases with the concentration of the limiting ribonucleotide up to 0.5 mM. Gel electrophoresis of the reaction products reveals that increasing the substrate concentration accelerates the appearance of radioactivity in full-length l/sub A/ and m transcripts

antaRNA: ant colony-based RNA sequence design.

Science.gov (United States)

Kleinkauf, Robert; Mann, Martin; Backofen, Rolf

2015-10-01

RNA sequence design is studied at least as long as the classical folding problem. Although for the latter the functional fold of an RNA molecule is to be found ,: inverse folding tries to identify RNA sequences that fold into a function-specific target structure. In combination with RNA-based biotechnology and synthetic biology ,: reliable RNA sequence design becomes a crucial step to generate novel biochemical components. In this article ,: the computational tool antaRNA is presented. It is capable of compiling RNA sequences for a given structure that comply in addition with an adjustable full range objective GC-content distribution ,: specific sequence constraints and additional fuzzy structure constraints. antaRNA applies ant colony optimization meta-heuristics and its superior performance is shown on a biological datasets. http://www.bioinf.uni-freiburg.de/Software/antaRNA CONTACT: backofen@informatik.uni-freiburg.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

High Thermal Dissipation of Al Heat Sink When Inserting Ceramic Powders by Ultrasonic Mechanical Coating and Armoring.

Science.gov (United States)

Tsai, Wei-Yu; Huang, Guan-Rong; Wang, Kuang-Kuo; Chen, Chin-Fu; Huang, J C

2017-04-26

Aluminum alloys, which serve as heat sink in light-emitting diode (LED) lighting, are often inherent with a high thermal conductivity, but poor thermal total emissivity. Thus, high emissive coatings on the Al substrate can enhance the thermal dissipation efficiency of radiation. In this study, the ultrasonic mechanical coating and armoring (UMCA) technique was used to insert various ceramic combinations, such as Al₂O₃, SiO₂, or graphite, to enhance thermal dissipation. Analytic models have been established to couple the thermal radiation and convection on the sample surface through heat flow equations. A promising match has been reached between the theoretical predictions and experimental measurements. With the adequate insertion of ceramic powders, the temperature of the Al heat sinks can be lowered by 5-11 °C, which is highly favorable for applications requiring cooling components.

From "Cellular" RNA to "Smart" RNA: Multiple Roles of RNA in Genome Stability and Beyond.

Science.gov (United States)

Michelini, Flavia; Jalihal, Ameya P; Francia, Sofia; Meers, Chance; Neeb, Zachary T; Rossiello, Francesca; Gioia, Ubaldo; Aguado, Julio; Jones-Weinert, Corey; Luke, Brian; Biamonti, Giuseppe; Nowacki, Mariusz; Storici, Francesca; Carninci, Piero; Walter, Nils G; Fagagna, Fabrizio d'Adda di

2018-03-30

Coding for proteins has been considered the main function of RNA since the "central dogma" of biology was proposed. The discovery of noncoding transcripts shed light on additional roles of RNA, ranging from the support of polypeptide synthesis, to the assembly of subnuclear structures, to gene expression modulation. Cellular RNA has therefore been recognized as a central player in often unanticipated biological processes, including genomic stability. This ever-expanding list of functions inspired us to think of RNA as a "smart" phone, which has replaced the older obsolete "cellular" phone. In this review, we summarize the last two decades of advances in research on the interface between RNA biology and genome stability. We start with an account of the emergence of noncoding RNA, and then we discuss the involvement of RNA in DNA damage signaling and repair, telomere maintenance, and genomic rearrangements. We continue with the depiction of single-molecule RNA detection techniques, and we conclude by illustrating the possibilities of RNA modulation in hopes of creating or improving new therapies. The widespread biological functions of RNA have made this molecule a reoccurring theme in basic and translational research, warranting it the transcendence from classically studied "cellular" RNA to "smart" RNA.

34A, miRNA-944, miRNA-101 and miRNA-218 in cervical cancer

African Journals Online (AJOL)

RNAs (21 - 24 nucleotides in length) that are critical for many important processes such as development, ... RNA extraction and reverse transcription. Total RNA was extracted from each of the experimental groups using ... used as an endogenous control to normalize the expression of miRNA-143, miRNA-34A, miRNA-.

Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding.

Science.gov (United States)

Wu, Johnny C; Gardner, David P; Ozer, Stuart; Gutell, Robin R; Ren, Pengyu

2009-08-28

The accurate prediction of the secondary and tertiary structure of an RNA with different folding algorithms is dependent on several factors, including the energy functions. However, an RNA higher-order structure cannot be predicted accurately from its sequence based on a limited set of energy parameters. The inter- and intramolecular forces between this RNA and other small molecules and macromolecules, in addition to other factors in the cell such as pH, ionic strength, and temperature, influence the complex dynamics associated with transition of a single stranded RNA to its secondary and tertiary structure. Since all of the factors that affect the formation of an RNAs 3D structure cannot be determined experimentally, statistically derived potential energy has been used in the prediction of protein structure. In the current work, we evaluate the statistical free energy of various secondary structure motifs, including base-pair stacks, hairpin loops, and internal loops, using their statistical frequency obtained from the comparative analysis of more than 50,000 RNA sequences stored in the RNA Comparative Analysis Database (rCAD) at the Comparative RNA Web (CRW) Site. Statistical energy was computed from the structural statistics for several datasets. While the statistical energy for a base-pair stack correlates with experimentally derived free energy values, suggesting a Boltzmann-like distribution, variation is observed between different molecules and their location on the phylogenetic tree of life. Our statistical energy values calculated for several structural elements were utilized in the Mfold RNA-folding algorithm. The combined statistical energy values for base-pair stacks, hairpins and internal loop flanks result in a significant improvement in the accuracy of secondary structure prediction; the hairpin flanks contribute the most.

Dual-functionalized graphene oxide for enhanced siRNA delivery to breast cancer cells.

Science.gov (United States)

Imani, Rana; Shao, Wei; Taherkhani, Samira; Emami, Shahriar Hojjati; Prakash, Satya; Faghihi, Shahab

2016-11-01

The aim of this study is to improve hydrocolloid stability and siRNA transfection ability of a reduced graphene oxide (rGO) based nano-carrier using a phospholipid-based amphiphilic polymer (PL-PEG) and cell penetrating peptide (CPPs). The dual functionalized nano-carrier is comprehensively characterized for its chemical structure, size, surface charge and morphology as well as thermal stability. The nano-carrier cytocompatibility, siRNA condensation ability both in the presence and absence of enzyme, endosomal buffering capacity, cellular uptake and intracellular localization are also assessed. The siRNA loaded nano-carrier is used for internalization to MCF-7 cells and its gene silencing ability is compared with AllStars Hs Cell Death siRNA as a model gene. The nano-carrier remains stable in biological solution, exhibits excellent cytocompatibility, retards the siRNA migration and protects it against enzyme degradation. The buffering capacity analysis shows that incorporation of the peptide in nano-carrier structure would increase the resistance to endo/lysosomal like acidic condition (pH 6-4) The functionalized nano-carrier which is loaded with siRNA in an optimal N:P ratio presents superior internalization efficiency (82±5.1% compared to HiPerFect(®)), endosomal escape quality and capable of inducing cell death in MCF-7 cancer cells (51±3.1% compared to non-treated cells). The success of siRNA-based therapy is largely dependent on the safe and efficient delivery system, therefore; the dual functionalized rGO introduced here could have a great potential to be used as a carrier for siRNA delivery with relevancy in therapeutics and clinical applications. Copyright © 2016 Elsevier B.V. All rights reserved.

Extracellular RNA Communication (ExRNA)

Data.gov (United States)

Federal Laboratory Consortium — Until recently, scientists believed RNA worked mostly inside the cell that produced it. Some types of RNA help translate genes into proteins that are necessary for...

RNA Crystallization

Science.gov (United States)

Golden, Barbara L.; Kundrot, Craig E.

2003-01-01

RNA molecules may be crystallized using variations of the methods developed for protein crystallography. As the technology has become available to syntheisize and purify RNA molecules in the quantities and with the quality that is required for crystallography, the field of RNA structure has exploded. The first consideration when crystallizing an RNA is the sequence, which may be varied in a rational way to enhance crystallizability or prevent formation of alternate structures. Once a sequence has been designed, the RNA may be synthesized chemically by solid-state synthesis, or it may be produced enzymatically using RNA polymerase and an appropriate DNA template. Purification of milligram quantities of RNA can be accomplished by HPLC or gel electrophoresis. As with proteins, crystallization of RNA is usually accomplished by vapor diffusion techniques. There are several considerations that are either unique to RNA crystallization or more important for RNA crystallization. Techniques for design, synthesis, purification, and crystallization of RNAs will be reviewed here.

Identifying microRNA/mRNA dysregulations in ovarian cancer.

Science.gov (United States)

Miles, Gregory D; Seiler, Michael; Rodriguez, Lorna; Rajagopal, Gunaretnam; Bhanot, Gyan

2012-03-27

MicroRNAs are a class of noncoding RNA molecules that co-regulate the expression of multiple genes via mRNA transcript degradation or translation inhibition. Since they often target entire pathways, they may be better drug targets than genes or proteins. MicroRNAs are known to be dysregulated in many tumours and associated with aggressive or poor prognosis phenotypes. Since they regulate mRNA in a tissue specific manner, their functional mRNA targets are poorly understood. In previous work, we developed a method to identify direct mRNA targets of microRNA using patient matched microRNA/mRNA expression data using an anti-correlation signature. This method, applied to clear cell Renal Cell Carcinoma (ccRCC), revealed many new regulatory pathways compromised in ccRCC. In the present paper, we apply this method to identify dysregulated microRNA/mRNA mechanisms in ovarian cancer using data from The Cancer Genome Atlas (TCGA). TCGA Microarray data was normalized and samples whose class labels (tumour or normal) were ambiguous with respect to consensus ensemble K-Means clustering were removed. Significantly anti-correlated and correlated genes/microRNA differentially expressed between tumour and normal samples were identified. TargetScan was used to identify gene targets of microRNA. We identified novel microRNA/mRNA mechanisms in ovarian cancer. For example, the expression level of RAD51AP1 was found to be strongly anti-correlated with the expression of hsa-miR-140-3p, which was significantly down-regulated in the tumour samples. The anti-correlation signature was present separately in the tumour and normal samples, suggesting a direct causal dysregulation of RAD51AP1 by hsa-miR-140-3p in the ovary. Other pairs of potentially biological relevance include: hsa-miR-145/E2F3, hsa-miR-139-5p/TOP2A, and hsa-miR-133a/GCLC. We also identified sets of positively correlated microRNA/mRNA pairs that are most likely result from indirect regulatory mechanisms. Our findings identify

Natural RNA circles function as efficient microRNA sponges

DEFF Research Database (Denmark)

Hansen, Thomas Birkballe; Jensen, Trine I; Clausen, Bettina Hjelm

2013-01-01

MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that act by direct base pairing to target sites within untranslated regions of messenger RNAs. Recently, miRNA activity has been shown to be affected by the presence of miRNA sponge transcripts, the so-called comp......MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that act by direct base pairing to target sites within untranslated regions of messenger RNAs. Recently, miRNA activity has been shown to be affected by the presence of miRNA sponge transcripts, the so......-called competing endogenous RNA in humans and target mimicry in plants. We previously identified a highly expressed circular RNA (circRNA) in human and mouse brain. Here we show that this circRNA acts as a miR-7 sponge; we term this circular transcript ciRS-7 (circular RNA sponge for miR-7). ciRS-7 contains more...... sponge, suggesting that miRNA sponge effects achieved by circRNA formation are a general phenomenon. This study serves as the first, to our knowledge, functional analysis of a naturally expressed circRNA....

Elucidating the role of free polycations in gene knockdown by siRNA polyplexes

DEFF Research Database (Denmark)

Klauber, Thomas Christopher Bogh; Søndergaard, Rikke Vicki; Sawant, Rupa R.

2016-01-01

capability, but are very different regarding siRNA decondensation, cellular internalization and induction of reporter gene knockdown. Lipid conjugation of bPEI 1.8. kDa improves the siRNA delivery properties, but with markedly different formulation requirements and mechanisms of action compared...... today.A major reason for the lack of progress is insufficient understanding of cell-polyplex interaction. We investigate siRNA delivery using polyethyleneimine (PEI) based vectors and examine how crucial formulation parameters determine the challenges associated with PEI as a delivery vector. We further...

RNA Origami

DEFF Research Database (Denmark)

Sparvath, Steffen Lynge

introducerede vores gruppe den enkeltstrengede RNA-origami metode, der giver mulighed for cotranscriptional foldning af veldefinerede nanostrukturer, og er en central del af arbejdet præsenteret heri. Denne ph.d.-afhandling udforsker potentielle anvendelser af RNA-origami nanostrukturer, som nanomedicin eller...... biosensorer. Afhandlingen består af en introduktion til RNA-nanoteknologi feltet, en introduktion af enkeltstrenget RNA-origami design, og fire studier, der beskriver design, produktion og karakterisering af både strukturelle og funktionelle RNA-origamier. Flere RNA-origami designs er blevet undersøgt, og...... projekterne, der indgår i denne afhandling, inkluderer de nyeste fremskridt indenfor strukturel RNA-nanoteknologi og udvikling af funktionelle RNA-baserede enheder. Det første studie beskriver konstruktion og karakterisering af en enkeltstrenget 6-helix RNA-origami stuktur, som er den første demonstration af...

Branched RNA: A New Architecture for RNA Interference

Directory of Open Access Journals (Sweden)

Anna Aviñó

2011-01-01

Full Text Available Branched RNAs with two and four strands were synthesized. These structures were used to obtain branched siRNA. The branched siRNA duplexes had similar inhibitory capacity as those of unmodified siRNA duplexes, as deduced from gene silencing experiments of the TNF-α protein. Branched RNAs are considered novel structures for siRNA technology, and they provide an innovative tool for specific gene inhibition. As the method described here is compatible with most RNA modifications described to date, these compounds may be further functionalized to obtain more potent siRNA derivatives and can be attached to suitable delivery systems.

Plant RNA Regulatory Network and RNA Granules in Virus Infection

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Kristiina Mäkinen

2017-12-01

Full Text Available Regulation of post-transcriptional gene expression on mRNA level in eukaryotic cells includes translocation, translation, translational repression, storage, mRNA decay, RNA silencing, and nonsense-mediated decay. These processes are associated with various RNA-binding proteins and cytoplasmic ribonucleoprotein complexes many of which are conserved across eukaryotes. Microscopically visible aggregations formed by ribonucleoprotein complexes are termed RNA granules. Stress granules where the translationally inactive mRNAs are stored and processing bodies where mRNA decay may occur present the most studied RNA granule types. Diverse RNP-granules are increasingly being assigned important roles in viral infections. Although the majority of the molecular level studies on the role of RNA granules in viral translation and replication have been conducted in mammalian systems, some studies link also plant virus infection to RNA granules. An increasing body of evidence indicates that plant viruses require components of stress granules and processing bodies for their replication and translation, but how extensively the cellular mRNA regulatory network is utilized by plant viruses has remained largely enigmatic. Antiviral RNA silencing, which is an important regulator of viral RNA stability and expression in plants, is commonly counteracted by viral suppressors of RNA silencing. Some of the RNA silencing suppressors localize to cellular RNA granules and have been proposed to carry out their suppression functions there. Moreover, plant nucleotide-binding leucine-rich repeat protein-mediated virus resistance has been linked to enhanced processing body formation and translational repression of viral RNA. Many interesting questions relate to how the pathways of antiviral RNA silencing leading to viral RNA degradation and/or repression of translation, suppression of RNA silencing and viral RNA translation converge in plants and how different RNA granules and

Plant RNA Regulatory Network and RNA Granules in Virus Infection.

Science.gov (United States)

Mäkinen, Kristiina; Lõhmus, Andres; Pollari, Maija

2017-01-01

Regulation of post-transcriptional gene expression on mRNA level in eukaryotic cells includes translocation, translation, translational repression, storage, mRNA decay, RNA silencing, and nonsense-mediated decay. These processes are associated with various RNA-binding proteins and cytoplasmic ribonucleoprotein complexes many of which are conserved across eukaryotes. Microscopically visible aggregations formed by ribonucleoprotein complexes are termed RNA granules. Stress granules where the translationally inactive mRNAs are stored and processing bodies where mRNA decay may occur present the most studied RNA granule types. Diverse RNP-granules are increasingly being assigned important roles in viral infections. Although the majority of the molecular level studies on the role of RNA granules in viral translation and replication have been conducted in mammalian systems, some studies link also plant virus infection to RNA granules. An increasing body of evidence indicates that plant viruses require components of stress granules and processing bodies for their replication and translation, but how extensively the cellular mRNA regulatory network is utilized by plant viruses has remained largely enigmatic. Antiviral RNA silencing, which is an important regulator of viral RNA stability and expression in plants, is commonly counteracted by viral suppressors of RNA silencing. Some of the RNA silencing suppressors localize to cellular RNA granules and have been proposed to carry out their suppression functions there. Moreover, plant nucleotide-binding leucine-rich repeat protein-mediated virus resistance has been linked to enhanced processing body formation and translational repression of viral RNA. Many interesting questions relate to how the pathways of antiviral RNA silencing leading to viral RNA degradation and/or repression of translation, suppression of RNA silencing and viral RNA translation converge in plants and how different RNA granules and their individual

Methylated nucleosides in tRNA and tRNA methyltransferases

Directory of Open Access Journals (Sweden)

Hiroyuki eHori

2014-05-01

Full Text Available To date, more than 90 modified nucleosides have been found in tRNA and the biosynthetic pathways of the majority of tRNA modifications include a methylation step(s. Recent studies of the biosynthetic pathways have demonstrated that the availability of methyl group donors for the methylation in tRNA is important for correct and efficient protein synthesis. In this review, I focus on the methylated nucleosides and tRNA methyltransferases. The primary functions of tRNA methylations are linked to the different steps of protein synthesis, such as the stabilization of tRNA structure, reinforcement of the codon–anticodon interaction, regulation of wobble base pairing, and prevention of frameshift errors. However, beyond these basic functions, recent studies have demonstrated that tRNA methylations are also involved in the RNA quality control system and regulation of tRNA localization in the cell. In a thermophilic eubacterium, tRNA modifications and the modification enzymes form a network that responses to temperature changes. Furthermore, several modifications are involved in genetic diseases, infections, and the immune response. Moreover, structural, biochemical, and bioinformatics studies of tRNA methyltransferases have been clarifying the details of tRNA methyltransferases and have enabled these enzymes to be classified. In the final section, the evolution of modification enzymes is discussed.

A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore

Energy Technology Data Exchange (ETDEWEB)

Huang, Hao; Suslov, Nikolai B.; Li, Nan-Sheng; Shelke, Sandip A.; Evans, Molly E.; Koldobskaya, Yelena; Rice, Phoebe A.; Piccirilli, Joseph A. [UC

2014-08-21

Spinach is an in vitro–selected RNA aptamer that binds a GFP-like ligand and activates its green fluorescence. Spinach is thus an RNA analog of GFP and has potentially widespread applications for in vivo labeling and imaging. We used antibody-assisted crystallography to determine the structures of Spinach both with and without bound fluorophore at 2.2-Å and 2.4-Å resolution, respectively. Spinach RNA has an elongated structure containing two helical domains separated by an internal bulge that folds into a G-quadruplex motif of unusual topology. The G-quadruplex motif and adjacent nucleotides comprise a partially preformed binding site for the fluorophore. The fluorophore binds in a planar conformation and makes extensive aromatic stacking and hydrogen bond interactions with the RNA. Our findings provide a foundation for structure-based engineering of new fluorophore-binding RNA aptamers.

RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts

International Nuclear Information System (INIS)

Bahrami, Arash; Clos, Lawrence J.; Markley, John L.; Butcher, Samuel E.; Eghbalnia, Hamid R.

2012-01-01

The significant biological role of RNA has further highlighted the need for improving the accuracy, efficiency and the reach of methods for investigating RNA structure and function. Nuclear magnetic resonance (NMR) spectroscopy is vital to furthering the goals of RNA structural biology because of its distinctive capabilities. However, the dispersion pattern in the NMR spectra of RNA makes automated resonance assignment, a key step in NMR investigation of biomolecules, remarkably challenging. Herein we present RNA Probabilistic Assignment of Imino Resonance Shifts (RNA-PAIRS), a method for the automated assignment of RNA imino resonances with synchronized verification and correction of predicted secondary structure. RNA-PAIRS represents an advance in modeling the assignment paradigm because it seeds the probabilistic network for assignment with experimental NMR data, and predicted RNA secondary structure, simultaneously and from the start. Subsequently, RNA-PAIRS sets in motion a dynamic network that reverberates between predictions and experimental evidence in order to reconcile and rectify resonance assignments and secondary structure information. The procedure is halted when assignments and base-parings are deemed to be most consistent with observed crosspeaks. The current implementation of RNA-PAIRS uses an initial peak list derived from proton-nitrogen heteronuclear multiple quantum correlation ( 1 H– 15 N 2D HMQC) and proton–proton nuclear Overhauser enhancement spectroscopy ( 1 H– 1 H 2D NOESY) experiments. We have evaluated the performance of RNA-PAIRS by using it to analyze NMR datasets from 26 previously studied RNAs, including a 111-nucleotide complex. For moderately sized RNA molecules, and over a range of comparatively complex structural motifs, the average assignment accuracy exceeds 90%, while the average base pair prediction accuracy exceeded 93%. RNA-PAIRS yielded accurate assignments and base pairings consistent with imino resonances for a

RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts

Energy Technology Data Exchange (ETDEWEB)

Bahrami, Arash; Clos, Lawrence J.; Markley, John L.; Butcher, Samuel E. [National Magnetic Resonance Facility at Madison (United States); Eghbalnia, Hamid R., E-mail: eghbalhd@uc.edu [University of Cincinnati, Department of Molecular and Cellular Physiology (United States)

2012-04-15

The significant biological role of RNA has further highlighted the need for improving the accuracy, efficiency and the reach of methods for investigating RNA structure and function. Nuclear magnetic resonance (NMR) spectroscopy is vital to furthering the goals of RNA structural biology because of its distinctive capabilities. However, the dispersion pattern in the NMR spectra of RNA makes automated resonance assignment, a key step in NMR investigation of biomolecules, remarkably challenging. Herein we present RNA Probabilistic Assignment of Imino Resonance Shifts (RNA-PAIRS), a method for the automated assignment of RNA imino resonances with synchronized verification and correction of predicted secondary structure. RNA-PAIRS represents an advance in modeling the assignment paradigm because it seeds the probabilistic network for assignment with experimental NMR data, and predicted RNA secondary structure, simultaneously and from the start. Subsequently, RNA-PAIRS sets in motion a dynamic network that reverberates between predictions and experimental evidence in order to reconcile and rectify resonance assignments and secondary structure information. The procedure is halted when assignments and base-parings are deemed to be most consistent with observed crosspeaks. The current implementation of RNA-PAIRS uses an initial peak list derived from proton-nitrogen heteronuclear multiple quantum correlation ({sup 1}H-{sup 15}N 2D HMQC) and proton-proton nuclear Overhauser enhancement spectroscopy ({sup 1}H-{sup 1}H 2D NOESY) experiments. We have evaluated the performance of RNA-PAIRS by using it to analyze NMR datasets from 26 previously studied RNAs, including a 111-nucleotide complex. For moderately sized RNA molecules, and over a range of comparatively complex structural motifs, the average assignment accuracy exceeds 90%, while the average base pair prediction accuracy exceeded 93%. RNA-PAIRS yielded accurate assignments and base pairings consistent with imino

MysiRNA-designer: a workflow for efficient siRNA design.

Directory of Open Access Journals (Sweden)

Mohamed Mysara

Full Text Available The design of small interfering RNA (siRNA is a multi factorial problem that has gained the attention of many researchers in the area of therapeutic and functional genomics. MysiRNA score was previously introduced that improves the correlation of siRNA activity prediction considering state of the art algorithms. In this paper, a new program, MysiRNA-Designer, is described which integrates several factors in an automated work-flow considering mRNA transcripts variations, siRNA and mRNA target accessibility, and both near-perfect and partial off-target matches. It also features the MysiRNA score, a highly ranked correlated siRNA efficacy prediction score for ranking the designed siRNAs, in addition to top scoring models Biopredsi, DISR, Thermocomposition21 and i-Score, and integrates them in a unique siRNA score-filtration technique. This multi-score filtration layer filters siRNA that passes the 90% thresholds calculated from experimental dataset features. MysiRNA-Designer takes an accession, finds conserved regions among its transcript space, finds accessible regions within the mRNA, designs all possible siRNAs for these regions, filters them based on multi-scores thresholds, and then performs SNP and off-target filtration. These strict selection criteria were tested against human genes in which at least one active siRNA was designed from 95.7% of total genes. In addition, when tested against an experimental dataset, MysiRNA-Designer was found capable of rejecting 98% of the false positive siRNAs, showing superiority over three state of the art siRNA design programs. MysiRNA is a freely accessible (Microsoft Windows based desktop application that can be used to design siRNA with a high accuracy and specificity. We believe that MysiRNA-Designer has the potential to play an important role in this area.

International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons

Science.gov (United States)

Olson, Nathan D.; Lund, Steven P.; Zook, Justin M.; Rojas-Cornejo, Fabiola; Beck, Brian; Foy, Carole; Huggett, Jim; Whale, Alexandra S.; Sui, Zhiwei; Baoutina, Anna; Dobeson, Michael; Partis, Lina; Morrow, Jayne B.

2015-01-01

This study presents the results from an interlaboratory sequencing study for which we developed a novel high-resolution method for comparing data from different sequencing platforms for a multi-copy, paralogous gene. The combination of PCR amplification and 16S ribosomal RNA gene (16S rRNA) sequencing has revolutionized bacteriology by enabling rapid identification, frequently without the need for culture. To assess variability between laboratories in sequencing 16S rRNA, six laboratories sequenced the gene encoding the 16S rRNA from Escherichia coli O157:H7 strain EDL933 and Listeria monocytogenes serovar 4b strain NCTC11994. Participants performed sequencing methods and protocols available in their laboratories: Sanger sequencing, Roche 454 pyrosequencing®, or Ion Torrent PGM®. The sequencing data were evaluated on three levels: (1) identity of biologically conserved position, (2) ratio of 16S rRNA gene copies featuring identified variants, and (3) the collection of variant combinations in a set of 16S rRNA gene copies. The same set of biologically conserved positions was identified for each sequencing method. Analytical methods using Bayesian and maximum likelihood statistics were developed to estimate variant copy ratios, which describe the ratio of nucleotides at each identified biologically variable position, as well as the likely set of variant combinations present in 16S rRNA gene copies. Our results indicate that estimated variant copy ratios at biologically variable positions were only reproducible for high throughput sequencing methods. Furthermore, the likely variant combination set was only reproducible with increased sequencing depth and longer read lengths. We also demonstrate novel methods for evaluating variable positions when comparing multi-copy gene sequence data from multiple laboratories generated using multiple sequencing technologies. PMID:27077030

International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons

Directory of Open Access Journals (Sweden)

Nathan D. Olson

2015-03-01

Full Text Available This study presents the results from an interlaboratory sequencing study for which we developed a novel high-resolution method for comparing data from different sequencing platforms for a multi-copy, paralogous gene. The combination of PCR amplification and 16S ribosomal RNA gene (16S rRNA sequencing has revolutionized bacteriology by enabling rapid identification, frequently without the need for culture. To assess variability between laboratories in sequencing 16S rRNA, six laboratories sequenced the gene encoding the 16S rRNA from Escherichia coli O157:H7 strain EDL933 and Listeria monocytogenes serovar 4b strain NCTC11994. Participants performed sequencing methods and protocols available in their laboratories: Sanger sequencing, Roche 454 pyrosequencing®, or Ion Torrent PGM®. The sequencing data were evaluated on three levels: (1 identity of biologically conserved position, (2 ratio of 16S rRNA gene copies featuring identified variants, and (3 the collection of variant combinations in a set of 16S rRNA gene copies. The same set of biologically conserved positions was identified for each sequencing method. Analytical methods using Bayesian and maximum likelihood statistics were developed to estimate variant copy ratios, which describe the ratio of nucleotides at each identified biologically variable position, as well as the likely set of variant combinations present in 16S rRNA gene copies. Our results indicate that estimated variant copy ratios at biologically variable positions were only reproducible for high throughput sequencing methods. Furthermore, the likely variant combination set was only reproducible with increased sequencing depth and longer read lengths. We also demonstrate novel methods for evaluating variable positions when comparing multi-copy gene sequence data from multiple laboratories generated using multiple sequencing technologies.

RNA binding and replication by the poliovirus RNA polymerase

International Nuclear Information System (INIS)

Oberste, M.S.

1988-01-01

RNA binding and RNA synthesis by the poliovirus RNA-dependent RNA polymerase were studied in vitro using purified polymerase. Templates for binding and RNA synthesis studies were natural RNAs, homopolymeric RNAs, or subgenomic poliovirus-specific RNAs synthesized in vitro from cDNA clones using SP6 or T7 RNA polymerases. The binding of the purified polymerase to poliovirion and other RNAs was studied using a protein-RNA nitrocellulose filter binding assay. A cellular poly(A)-binding protein was found in the viral polymerase preparations, but was easily separated from the polymerase by chromatography on poly(A) Sepharose. The binding of purified polymerase to 32 P-labeled ribohomopolymeric RNAs was examined, and the order of binding observed was poly(G) >>> poly(U) > poly(C) > poly(A). The K a for polymerase binding to poliovirion RNA and to a full-length negative strand transcript was about 1 x 10 9 M -1 . The polymerase binds to a subgenomic RNAs which contain the 3' end of the genome with a K a similar to that for virion RNA, but binds less well to 18S rRNA, globin mRNA, and subgenomic RNAs which lack portions of the 3' noncoding region

RNA.

Science.gov (United States)

Darnell, James E., Jr.

1985-01-01

Ribonucleic acid (RNA) converts genetic information into protein and usually must be processed to serve its function. RNA types, chemical structure, protein synthesis, translation, manufacture, and processing are discussed. Concludes that the first genes might have been spliced RNA and that humans might be closer than bacteria to primitive…

Identification of Subtype Specific miRNA-mRNA Functional Regulatory Modules in Matched miRNA-mRNA Expression Data: Multiple Myeloma as a Case

OpenAIRE

Zhang, Yunpeng; Liu, Wei; Xu, Yanjun; Li, Chunquan; Wang, Yingying; Yang, Haixiu; Zhang, Chunlong; Su, Fei; Li, Yixue; Li, Xia

2015-01-01

Identification of miRNA-mRNA modules is an important step to elucidate their combinatorial effect on the pathogenesis and mechanisms underlying complex diseases. Current identification methods primarily are based upon miRNA-target information and matched miRNA and mRNA expression profiles. However, for heterogeneous diseases, the miRNA-mRNA regulatory mechanisms may differ between subtypes, leading to differences in clinical behavior. In order to explore the pathogenesis of each subtype, it i...

microRNA-independent recruitment of Argonaute 1 to nanos mRNA through the Smaug RNA-binding protein.

Science.gov (United States)

Pinder, Benjamin D; Smibert, Craig A

2013-01-01

Argonaute (Ago) proteins are typically recruited to target messenger RNAs via an associated small RNA such as a microRNA (miRNA). Here, we describe a new mechanism of Ago recruitment through the Drosophila Smaug RNA-binding protein. We show that Smaug interacts with the Ago1 protein, and that Ago1 interacts with and is required for the translational repression of the Smaug target, nanos mRNA. The Ago1/nanos mRNA interaction does not require a miRNA, but it does require Smaug. Taken together, our data suggest a model whereby Smaug directly recruits Ago1 to nanos mRNA in a miRNA-independent manner, thereby repressing translation.

RNA epitranscriptomics: Regulation of infection of RNA and DNA viruses by N6 -methyladenosine (m6 A).

Science.gov (United States)

Tan, Brandon; Gao, Shou-Jiang

2018-04-26

N 6 -methyladenosine (m 6 A) was discovered 4 decades ago. However, the functions of m 6 A and the cellular machinery that regulates its changes have just been revealed in the last few years. m 6 A is an abundant internal mRNA modification on cellular RNA and is implicated in diverse cellular functions. Recent works have demonstrated the presence of m 6 A in the genomes of RNA viruses and transcripts of a DNA virus with either a proviral or antiviral role. Here, we first summarize what is known about the m 6 A "writers," "erasers," "readers," and "antireaders" as well as the role of m 6 A in mRNA metabolism. We then review how the replications of numerous viruses are enhanced and restricted by m 6 A with emphasis on the oncogenic DNA virus, Kaposi sarcoma-associated herpesvirus (KSHV), whose m 6 A epitranscriptome was recently mapped. In the context of KSHV, m 6 A and the reader protein YTHDF2 acts as an antiviral mechanism during viral lytic replication. During viral latency, KSHV alters m 6 A on genes that are implicated in cellular transformation and viral latency. Lastly, we discuss future studies that are important to further delineate the functions of m 6 A in KSHV latent and lytic replication and KSHV-induced oncogenesis. Copyright © 2018 John Wiley & Sons, Ltd.

RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database

Directory of Open Access Journals (Sweden)

Andronescu Mirela

2008-08-01

Full Text Available Abstract Background The ability to access, search and analyse secondary structures of a large set of known RNA molecules is very important for deriving improved RNA energy models, for evaluating computational predictions of RNA secondary structures and for a better understanding of RNA folding. Currently there is no database that can easily provide these capabilities for almost all RNA molecules with known secondary structures. Results In this paper we describe RNA STRAND – the RNA secondary STRucture and statistical ANalysis Database, a curated database containing known secondary structures of any type and organism. Our new database provides a wide collection of known RNA secondary structures drawn from public databases, searchable and downloadable in a common format. Comprehensive statistical information on the secondary structures in our database is provided using the RNA Secondary Structure Analyser, a new tool we have developed to analyse RNA secondary structures. The information thus obtained is valuable for understanding to which extent and with which probability certain structural motifs can appear. We outline several ways in which the data provided in RNA STRAND can facilitate research on RNA structure, including the improvement of RNA energy models and evaluation of secondary structure prediction programs. In order to keep up-to-date with new RNA secondary structure experiments, we offer the necessary tools to add solved RNA secondary structures to our database and invite researchers to contribute to RNA STRAND. Conclusion RNA STRAND is a carefully assembled database of trusted RNA secondary structures, with easy on-line tools for searching, analyzing and downloading user selected entries, and is publicly available at http://www.rnasoft.ca/strand.

MicroRNA from tuberculosis RNA: A bioinformatics study

OpenAIRE

Wiwanitkit, Somsri; Wiwanitkit, Viroj

2012-01-01

The role of microRNA in the pathogenesis of pulmonary tuberculosis is the interesting topic in chest medicine at present. Recently, it was proposed that the microRNA can be a useful biomarker for monitoring of pulmonary tuberculosis and might be the important part in pathogenesis of disease. Here, the authors perform a bioinformatics study to assess the microRNA within known tuberculosis RNA. The microRNA part can be detected and this can be important key information in further study of the p...

Nucleolin Mediates MicroRNA-directed CSF-1 mRNA Deadenylation but Increases Translation of CSF-1 mRNA*

Science.gov (United States)

Woo, Ho-Hyung; Baker, Terri; Laszlo, Csaba; Chambers, Setsuko K.

2013-01-01

CSF-1 mRNA 3′UTR contains multiple unique motifs, including a common microRNA (miRNA) target in close proximity to a noncanonical G-quadruplex and AU-rich elements (AREs). Using a luciferase reporter system fused to CSF-1 mRNA 3′UTR, disruption of the miRNA target region, G-quadruplex, and AREs together dramatically increased reporter RNA levels, suggesting important roles for these cis-acting regulatory elements in the down-regulation of CSF-1 mRNA. We find that nucleolin, which binds both G-quadruplex and AREs, enhances deadenylation of CSF-1 mRNA, promoting CSF-1 mRNA decay, while having the capacity to increase translation of CSF-1 mRNA. Through interaction with the CSF-1 3′UTR miRNA common target, we find that miR-130a and miR-301a inhibit CSF-1 expression by enhancing mRNA decay. Silencing of nucleolin prevents the miRNA-directed mRNA decay, indicating a requirement for nucleolin in miRNA activity on CSF-1 mRNA. Downstream effects followed by miR-130a and miR-301a inhibition of directed cellular motility of ovarian cancer cells were found to be dependent on nucleolin. The paradoxical effects of nucleolin on miRNA-directed CSF-1 mRNA deadenylation and on translational activation were explored further. The nucleolin protein contains four acidic stretches, four RNA recognition motifs (RRMs), and nine RGG repeats. All three domains in nucleolin regulate CSF-1 mRNA and protein levels. RRMs increase CSF-1 mRNA, whereas the acidic and RGG domains decrease CSF-1 protein levels. This suggests that nucleolin has the capacity to differentially regulate both CSF-1 RNA and protein levels. Our finding that nucleolin interacts with Ago2 indirectly via RNA and with poly(A)-binding protein C (PABPC) directly suggests a nucleolin-Ago2-PABPC complex formation on mRNA. This complex is in keeping with our suggestion that nucleolin may work with PABPC as a double-edged sword on both mRNA deadenylation and translational activation. Our findings underscore the complexity of

Studying RNA-protein interactions in vivo by RNA immunoprecipitation

DEFF Research Database (Denmark)

Selth, Luke A; Close, Pierre; Svejstrup, Jesper Q

2011-01-01

and have significant effects on gene expression. RNA immunoprecipitation (RIP) is a powerful technique used to detect direct and indirect interactions between individual proteins and specific RNA molecules in vivo. Here, we describe RIP methods for both yeast and mammalian cells.......The crucial roles played by RNA-binding proteins in all aspects of RNA metabolism, particularly in the regulation of transcription, have become increasingly evident. Moreover, other factors that do not directly interact with RNA molecules can nevertheless function proximally to RNA polymerases...

RNA SURVEILLANCE– AN EMERGING ROLE FOR RNA REGULATORY NETWORKS IN AGING

OpenAIRE

Montano, Monty; Long, Kimberly

2010-01-01

In this review, we describe recent advances in the field of RNA regulatory biology and relate these advances to aging science. We introduce a new term, RNA surveillance, an RNA regulatory process that is conserved in metazoans, and describe how RNA surveillance represents molecular cross-talk between two emerging RNA regulatory systems – RNA interference and RNA editing. We discuss how RNA surveillance mechanisms influence mRNA and microRNA expression and activity during lifespan. Additionall...

Long-term survivability of riprap for armoring uranium-mill tailings and covers: a literature review

International Nuclear Information System (INIS)

Lindsey, C.G.; Long, L.W.; Begej, C.W.

1982-06-01

Pacific Northwest Laboratory (PNL) is investigating the use of a rock armoring blanket (riprap) to mitigate wind and water erosion of an earthen radon suppression cover applied to uranium mill tailings. Because the radon suppression cover and the tailings must remain intact for up to 1000 years or longer, the riprap must withstand natural weathering forces. This report is a review of information on rock weathering and riprap durability. Chemical and physical weathering processes, rock characteristics related to durability, climatic conditions affecting the degree and rate of weathering, and testing procedures used to measure weathering susceptibilities have been reviewed. Sampling and testing techniques, as well as analyses of physical and chemical weathering susceptibilities, are necessary to evaluate rock durability. Many potential riprap materials may not be able to survive 1000 years of weathering. Available techniques for durability testing cannot adequately predict rock durability for the 1000-year period because they do not consider the issue of time (i.e., how long must riprap remain stable). This report includes an Appendix, which discusses rock weathering, written by Dr. Richard Jahns of Stanford University

Identification and association of novel lncRNA pouMU1 gene ...

Indian Academy of Sciences (India)

TUANHUI REN

2017-12-08

Dec 8, 2017 ... The GAPDH gene was used as an internal control: forward and ... was extracted using. Trizol, and RNA quality was assessed using electrophore- .... tistical Product and Service Solutions, IBM Corporation,. Armonk, USA).

Rapid Generation of MicroRNA Sponges for MicroRNA Inhibition

NARCIS (Netherlands)

Kluiver, Joost; Gibcus, Johan H.; Hettinga, Chris; Adema, Annelies; Richter, Mareike K. S.; Halsema, Nancy; Slezak-Prochazka, Izabella; Ding, Ye; Kroesen, Bart-Jan; van den Berg, Anke

2012-01-01

MicroRNA (miRNA) sponges are transcripts with repeated miRNA antisense sequences that can sequester miRNAs from endogenous targets. MiRNA sponges are valuable tools for miRNA loss-of-function studies both in vitro and in vivo. We developed a fast and flexible method to generate miRNA sponges and

The Role of Dynamic m6 A RNA Methylation in Photobiology.

Science.gov (United States)

Robinson, Myles; Shah, Palak; Cui, Yan-Hong; He, Yu-Ying

2018-05-04

N 6 -methyladenosine (m 6 A) is the most abundant internal RNA modification among numerous post-transcriptional modifications identified in eukaryotic mRNA. m 6 A modification of RNA is catalyzed by the "writer" m 6 A methyltransferase enzyme complex, consisting of METTL3, METTL14, WTAP and KIAA1429. The m 6 A modification is reversible and can be removed by "eraser" m 6 A demethylase enzymes, namely, FTO and ALKBH5. The biological function of m 6 A modification on RNA is carried out by RNA-binding effector proteins called "readers." Varied functions of the reader proteins regulate mRNA metabolism by affecting stability, translation, splicing or nuclear export. The epitranscriptomic gene regulation by m 6 A RNA methylation regulates various pathways, which contribute to basic cellular processes essential for cell maintenance, development and cell fate, and affect response to external stimuli and stressors. In this review, we summarize the recent advances in the regulation and function of m 6 A RNA methylation, with a focus on UV-induced DNA damage response and the circadian clock machinery. Insights into the mechanisms of m 6 A RNA regulation and post-transcriptional regulatory function in these biological processes may facilitate the development of new preventive and therapeutic strategies for various diseases related to dysregulation of UV damage response and circadian rhythm. © 2018 The American Society of Photobiology.

Correlation between RNA Degradation Patterns of Rat's Brain and Early PMI at Different Temperatures.

Science.gov (United States)

Lü, Y H; Li, Z H; Tuo, Y; Liu, L; Li, K; Bian, J; Ma, J L; Chen, L

2016-06-01

To explore the correlation between early postmortem interval （PMI） and eight RNA markers of rat's brain at different temperatures. Total 222 SD rats were randomly divided into control group （PMI=0 h） and four experimental groups. And the rats in the experimental groups were sacrificed by cervical dislocation and respectively kept at 5 ℃, 15 ℃, 25 ℃ and 35 ℃ in a controlled environment chamber. The RNA was extracted from brain tissues, which was taken at 9 time points from 1 h to 24 h postmortem. The expression levels of eight markers, β-actin, GAPDH, RPS29, 18S rRNA, 5S rRNA, U6 snRNA, miRNA-9 and miRNA-125b, were detected using real-time fluorescent quantitative PCR, respectively. Proper internal reference was selected by geNorm software. Regression analysis of normalized RNA markers was performed by SPSS software. Mathematical model for PMI estimation was established using R software. Another 6 SD rats with known PMI were used to verify the mathematical model. 5S rRNA, miR-9 and miR-125b were suitable as internal reference markers for their stable expression. Both β-actin and GAPDH had well time-dependent degradation patterns and degraded continually with prolongation of PMI in 24 h postmortem. The mathematical model of the variation of ΔCt values with PMI and temperature was set up by R software and the model could be used for PMI estimation. The average error rates of model validation using β-actin and GAPDH were 14.1% and 22.2%, respectively. The expression levels of β-actin and GAPDH are well correlated with PMI and environmental temperature. The mathematical model established in present study can provide references for estimating early PMI under various temperature conditions. Copyright© by the Editorial Department of Journal of Forensic Medicine

MicroRNA-directed siRNA biogenesis in Caenorhabditis elegans.

Science.gov (United States)

Corrêa, Régis L; Steiner, Florian A; Berezikov, Eugene; Ketting, René F

2010-04-08

RNA interference (RNAi) is a post-transcriptional silencing process, triggered by double-stranded RNA (dsRNA), leading to the destabilization of homologous mRNAs. A distinction has been made between endogenous RNAi-related pathways and the exogenous RNAi pathway, the latter being essential for the experimental use of RNAi. Previous studies have shown that, in Caenorhabditis elegans, a complex containing the enzymes Dicer and the Argonaute RDE-1 process dsRNA. Dicer is responsible for cleaving dsRNA into short interfering RNAs (siRNAs) while RDE-1 acts as the siRNA acceptor. RDE-1 then guides a multi-protein complex to homologous targets to trigger mRNA destabilization. However, endogenous role(s) for RDE-1, if any, have remained unexplored. We here show that RDE-1 functions as a scavenger protein, taking up small RNA molecules from many different sources, including the microRNA (miRNA) pathway. This is in striking contrast to Argonaute proteins functioning directly in the miRNA pathway, ALG-1 and ALG-2: these proteins exclusively bind miRNAs. While playing no significant role in the biogenesis of the main pool of miRNAs, RDE-1 binds endogenous miRNAs and triggers RdRP activity on at least one perfectly matching, endogenous miRNA target. The resulting secondary siRNAs are taken up by a set of Argonaute proteins known to act as siRNA acceptors in exogenous RNAi, resulting in strong mRNA destabilization. Our results show that RDE-1 in an endogenous setting is actively screening the transcriptome using many different small RNAs, including miRNAs, as a guide, with implications for the evolution of transcripts with a potential to be recognized by Dicer.

The design of the poloidal divertor experiment tokamak wall armor and inner limiter system

International Nuclear Information System (INIS)

Kugel, H.W.; Ulrickson, M.

1982-01-01

The inner wall protective plates for the Poloidal Divertor Experiment Tokamak are designed to absorb 8 MW of neutral deuterium beam power at maximum power densities of 3 kW/cm 2 for pulse lengths of 0.5 s. Preliminary studies indicate that the design could survive several pulses of l-s duration. The design consists of a tile and mounting plate structure. The mounting plates are water cooled to allow short duty cycles and beam calorimetry. The temperature and flow of the coolant are measured to obtain the injected power. A thermocouple array on the tiles provides beam position and power density profiles. Several material combinations for the tiles were subjected to thermal tests using both electron and neutral beams, and titanium-carbidecoated graphite was selected as the tile material. The heat transfer coefficient of the tile backing plate structure was measured to determine the maximum pulse rate allowable. The design of the armor system allows the structure to be used as a neutral beam power diagnostic and as an inner plasma limiter. The electrical and cooling systems external to the vacuum vessel are discussed

Characterization of dermal plates from armored catfish Pterygoplichthys pardalis reveals sandwich-like nanocomposite structure.

Science.gov (United States)

Ebenstein, Donna; Calderon, Carlos; Troncoso, Omar P; Torres, Fernando G

2015-05-01

Dermal plates from armored catfish are bony structures that cover their body. In this paper we characterized structural, chemical, and nanomechanical properties of the dermal plates from the Amazonian fish Pterygoplichthys pardalis. Analysis of the morphology of the plates using scanning electron microscopy (SEM) revealed that the dermal plates have a sandwich-like structure composed of an inner porous matrix surrounded by two external dense layers. This is different from the plywood-like laminated structure of elasmoid fish scales but similar to the structure of osteoderms found in the dermal armour of some reptiles and mammals. Chemical analysis performed using Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC) and X-ray diffraction (XRD) results revealed similarities between the composition of P. pardalis plates and the elasmoid fish scales of Arapaima gigas. Reduced moduli of P. pardalis plates measured using nanoindentation were also consistent with reported values for A. gigas scales, but further revealed that the dermal plate is an anisotropic and heterogeneous material, similar to many other fish scales and osteoderms. It is postulated that the sandwich-like structure of the dermal plates provides a lightweight and tough protective layer. Copyright © 2015 Elsevier Ltd. All rights reserved.

Plant RNA binding proteins for control of RNA virus infection

Directory of Open Access Journals (Sweden)

Sung Un eHuh

2013-12-01

Full Text Available Plant RNA viruses have effective strategies to infect host plants through either direct or indirect interactions with various host proteins, thus suppressing the host immune system. When plant RNA viruses enter host cells exposed RNAs of viruses are recognized by the host immune system through processes such as siRNA-dependent silencing. Interestingly, some host RNA binding proteins have been involved in the inhibition of RNA virus replication, movement, and translation through RNA-specific binding. Host plants intensively use RNA binding proteins for defense against viral infections in nature. In this mini review, we will summarize the function of some host RNA binding proteins which act in a sequence-specific binding manner to the infecting virus RNA. It is important to understand how plants effectively suppresses RNA virus infections via RNA binding proteins, and this defense system can be potentially developed as a synthetic virus defense strategy for use in crop engineering.

Effective Anti-miRNA Oligonucleotides Show High Releasing Rate of MicroRNA from RNA-Induced Silencing Complex.

Science.gov (United States)

Ariyoshi, Jumpei; Matsuyama, Yohei; Kobori, Akio; Murakami, Akira; Sugiyama, Hiroshi; Yamayoshi, Asako

2017-10-01

MicroRNAs (miRNAs) regulate gene expression by forming RNA-induced silencing complexes (RISCs) and have been considered as promising therapeutic targets. MiRNA is an essential component of RISC for the modulation of gene expression. Therefore, the release of miRNA from RISC is considered as an effective method for the inhibition of miRNA functions. In our previous study, we reported that anti-miRNA oligonucleotides (AMOs), which are composed of the 2'-O-methyl (2'-OMe) RNA, could induce the release of miRNA from RISC. However, the mechanisms underlying the miRNA-releasing effects of chemically modified AMOs, which are conventionally used as anti-cancer drugs, are still unclear. In this study, we investigated the relationship between the miRNA releasing rate from RISC and the inhibitory effect on RISC activity (IC 50 ) using conventional chemically modified AMOs. We demonstrated that the miRNA-releasing effects of AMOs are directly proportional to the IC 50 values, and AMOs, which have an ability to promote the release of miRNA from RISC, can effectively inhibit RISC activity in living cells.

Interactions between non-native armored suckermouth catfish (Loricariidae: Pterygoplichthys) and native Florida manatee (Trichechus manatus latirostris) in artesian springs

Science.gov (United States)

Nico, Leo G.; Loftus, William F.; Reid, James P.

2009-01-01

Non-native suckermouth armored catfishes (Loricariidae) of the genus Pterygoplichthys are now common throughout much of peninsular Florida. In this paper, we present preliminary observations on interactions between a Pterygoplichthys species, tentatively identified as P. disjunctivus (Weber, 1991), and endangered native Florida manatees, Trichechus manatus latirostris (Harlan, 1824), in artesian spring systems in Florida's St. Johns River drainage. The introduced catfish have become abundant in spring habitats, sites used by manatees as winter thermal refuges. In the spring runs, Pterygoplichthys regularly attaches to manatees and grazes the epibiota on their skin. On occasion, dozens of Pterygoplichthys congregate on individual manatees. Manatee responses varied widely; some did not react visibly to attached catfish whereas others appeared agitated and attempted to dislodge the fish. The costs and/or benefits of this interaction to manatees remain unclear.

Isolation of Microarray-Grade Total RNA, MicroRNA, and DNA from a Single PAXgene Blood RNA Tube

DEFF Research Database (Denmark)

Kruhøffer, Mogens; Andersen, Lars Dyrskjøt; Voss, Thorsten

2007-01-01

We have developed a procedure for isolation of microRNA and genomic DNA in addition to total RNA from whole blood stabilized in PAXgene Blood RNA tubes. The procedure is based on automatic extraction on a BioRobot MDx and includes isolation of DNA from a fraction of the stabilized blood...... and recovery of small RNA species that are otherwise lost. The procedure presented here is suitable for large-scale experiments and is amenable to further automation. Procured total RNA and DNA was tested using Affymetrix Expression and single-nucleotide polymorphism GeneChips, respectively, and isolated micro......RNA was tested using spotted locked nucleic acid-based microarrays. We conclude that the yield and quality of total RNA, microRNA, and DNA from a single PAXgene blood RNA tube is sufficient for downstream microarray analysis....

IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions.

Science.gov (United States)

Mann, Martin; Wright, Patrick R; Backofen, Rolf

2017-07-03

The IntaRNA algorithm enables fast and accurate prediction of RNA-RNA hybrids by incorporating seed constraints and interaction site accessibility. Here, we introduce IntaRNAv2, which enables enhanced parameterization as well as fully customizable control over the prediction modes and output formats. Based on up to date benchmark data, the enhanced predictive quality is shown and further improvements due to more restrictive seed constraints are highlighted. The extended web interface provides visualizations of the new minimal energy profiles for RNA-RNA interactions. These allow a detailed investigation of interaction alternatives and can reveal potential interaction site multiplicity. IntaRNAv2 is freely available (source and binary), and distributed via the conda package manager. Furthermore, it has been included into the Galaxy workflow framework and its already established web interface enables ad hoc usage. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Genetic relatedness of orbiviruses by RNA-RNA blot hybridization

International Nuclear Information System (INIS)

Bodkin, D.K.

1985-01-01

RNA-RNA blot hybridization was developed in order to identify type-specific genes among double-stranded (ds) RNA viruses, to assess the genetic relatedness of dsRNA viruses and to classify new strains. Viral dsRNA segments were electrophoresed through 10% polyacrylamide gels, transferred to membranes, and hybridized to [5' 32 P]-pCp labeled genomic RNA from a related strain. Hybridization was performed at 52 0 C, 50% formamide, 5X SSC. Under these conditions heterologous RNA species must share ≥ 74% sequence homology in order to form stable dsRNA hybrids. Cognate genes of nine members of the Palyam serogroup of orbiviruses were identified and their sequence relatedness to the prototype. Palyam virus, was determined. Reciprocal blot hybridizations were performed using radiolabeled genomic RNA of all members of the Palyam serogroup. Unique and variant genes were identified by lack of cross-homology or by weak homology between segments. Since genes 2 and 6 exhibited the highest degree of sequence variability, response to the vertebrate immune system may be a major cause of sequence divergence among members of a single serogroup. Changuinola serogroup isolates were compared by dot-blot hybridization, while Colorado tick fever (CTF) serogroup isolates were compared by the RNA-RNA blot hybridization procedure described for reovirus and Palyam serogroup isolates. Preliminary blot hybridization data were also obtained on the relatedness of members of different Orbivirus serogroups

Visualizing RNA Secondary Structure Base Pair Binding Probabilities using Nested Concave Hulls

OpenAIRE

Sansen , Joris; Bourqui , Romain; Thebault , Patricia; Allali , Julien; Auber , David

2015-01-01

International audience; The challenge 1 of the BIOVIS 2015 design contest consists in designing an intuitive visual depiction of base pairs binding probabilities for secondary structure of ncRNA. Our representation depicts the potential nucleotide pairs binding using nested concave hulls over the computed MFE ncRNA secondary structure. Thus, it allows to identify regions with a high level of uncertainty in the MFE computation and the structures which seem to match to reality.

An Integrated Approach for RNA-seq Data Normalization.

Science.gov (United States)

Yang, Shengping; Mercante, Donald E; Zhang, Kun; Fang, Zhide

2016-01-01

DNA copy number alteration is common in many cancers. Studies have shown that insertion or deletion of DNA sequences can directly alter gene expression, and significant correlation exists between DNA copy number and gene expression. Data normalization is a critical step in the analysis of gene expression generated by RNA-seq technology. Successful normalization reduces/removes unwanted nonbiological variations in the data, while keeping meaningful information intact. However, as far as we know, no attempt has been made to adjust for the variation due to DNA copy number changes in RNA-seq data normalization. In this article, we propose an integrated approach for RNA-seq data normalization. Comparisons show that the proposed normalization can improve power for downstream differentially expressed gene detection and generate more biologically meaningful results in gene profiling. In addition, our findings show that due to the effects of copy number changes, some housekeeping genes are not always suitable internal controls for studying gene expression. Using information from DNA copy number, integrated approach is successful in reducing noises due to both biological and nonbiological causes in RNA-seq data, thus increasing the accuracy of gene profiling.

RNA content in the nucleolus alters p53 acetylation via MYBBP1A

Science.gov (United States)

Kuroda, Takao; Murayama, Akiko; Katagiri, Naohiro; Ohta, Yu-mi; Fujita, Etsuko; Masumoto, Hiroshi; Ema, Masatsugu; Takahashi, Satoru; Kimura, Keiji; Yanagisawa, Junn

2011-01-01

A number of external and internal insults disrupt nucleolar structure, and the resulting nucleolar stress stabilizes and activates p53. We show here that nucleolar disruption induces acetylation and accumulation of p53 without phosphorylation. We identified three nucleolar proteins, MYBBP1A, RPL5, and RPL11, involved in p53 acetylation and accumulation. MYBBP1A was tethered to the nucleolus through nucleolar RNA. When rRNA transcription was suppressed by nucleolar stress, MYBBP1A translocated to the nucleoplasm and facilitated p53–p300 interaction to enhance p53 acetylation. We also found that RPL5 and RPL11 were required for rRNA export from the nucleolus. Depletion of RPL5 or RPL11 blocked rRNA export and counteracted reduction of nucleolar RNA levels caused by inhibition of rRNA transcription. As a result, RPL5 or RPL11 depletion inhibited MYBBP1A translocation and p53 activation. Our observations indicated that a dynamic equilibrium between RNA generation and export regulated nucleolar RNA content. Perturbation of this balance by nucleolar stress altered the nucleolar RNA content and modulated p53 activity. PMID:21297583

RNA interference for the control of whiteflies (Bemisia tabaci) by oral ...

Indian Academy of Sciences (India)

respective primers (table 2), and actin served as the internal control. Each reaction ..... emerged adults and variation in the quality and the quantity of siRNA synthesized ... Environment News Service, 21 August (countercurrents.org). Febvay G ...

Non-Watson Crick base pairs might stabilize RNA structural motifs in ...

Indian Academy of Sciences (India)

Watson Crick base pairs, internal loops and pseudoknots have been the highlighting feature of recent structural determination of RNAs. The recent crystal structure of group-I introns has demonstrated that these might constitute RNA structural ...

A discontinuous RNA platform mediates RNA virus replication: building an integrated model for RNA-based regulation of viral processes.

Directory of Open Access Journals (Sweden)

Baodong Wu

2009-03-01

Full Text Available Plus-strand RNA viruses contain RNA elements within their genomes that mediate a variety of fundamental viral processes. The traditional view of these elements is that of local RNA structures. This perspective, however, is changing due to increasing discoveries of functional viral RNA elements that are formed by long-range RNA-RNA interactions, often spanning thousands of nucleotides. The plus-strand RNA genomes of tombusviruses exemplify this concept by possessing different long-range RNA-RNA interactions that regulate both viral translation and transcription. Here we report that a third fundamental tombusvirus process, viral genome replication, requires a long-range RNA-based interaction spanning approximately 3000 nts. In vivo and in vitro analyses suggest that the discontinuous RNA platform formed by the interaction facilitates efficient assembly of the viral RNA replicase. This finding has allowed us to build an integrated model for the role of global RNA structure in regulating the reproduction of a eukaryotic RNA virus, and the insights gained have extended our understanding of the multifunctional nature of viral RNA genomes.

RNase MRP is required for entry of 35S precursor rRNA into the canonical processing pathway.

Science.gov (United States)

Lindahl, Lasse; Bommankanti, Ananth; Li, Xing; Hayden, Lauren; Jones, Adrienne; Khan, Miriam; Oni, Tolulope; Zengel, Janice M

2009-07-01

RNase MRP is a nucleolar RNA-protein enzyme that participates in the processing of rRNA during ribosome biogenesis. Previous experiments suggested that RNase MRP makes a nonessential cleavage in the first internal transcribed spacer. Here we report experiments with new temperature-sensitive RNase MRP mutants in Saccharomyces cerevisiae that show that the abundance of all early intermediates in the processing pathway is severely reduced upon inactivation of RNase MRP. Transcription of rRNA continues unabated as determined by RNA polymerase run-on transcription, but the precursor rRNA transcript does not accumulate, and appears to be unstable. Taken together, these observations suggest that inactivation of RNase MRP blocks cleavage at sites A0, A1, A2, and A3, which in turn, prevents precursor rRNA from entering the canonical processing pathway (35S > 20S + 27S > 18S + 25S + 5.8S rRNA). Nevertheless, at least some cleavage at the processing site in the second internal transcribed spacer takes place to form an unusual 24S intermediate, suggesting that cleavage at C2 is not blocked. Furthermore, the long form of 5.8S rRNA is made in the absence of RNase MRP activity, but only in the presence of Xrn1p (exonuclease 1), an enzyme not required for the canonical pathway. We conclude that RNase MRP is a key enzyme for initiating the canonical processing of precursor rRNA transcripts, but alternative pathway(s) might provide a backup for production of small amounts of rRNA.

Bifurcations in the interplay of messenger RNA, protein and nonprotein coding RNA

International Nuclear Information System (INIS)

Zhdanov, Vladimir P

2008-01-01

The interplay of messenger RNA (mRNA), protein, produced via translation of this RNA, and nonprotein coding RNA (ncRNA) may include regulation of the ncRNA production by protein and (i) ncRNA-protein association resulting in suppression of the protein regulatory activity or (ii) ncRNA-mRNA association resulting in degradation of the miRNA-mRNA complex. The kinetic models describing these two scenarios are found to predict bistability provided that protein suppresses the ncRNA formation

Internal ribosome entry site-mediated translation of a mammalian mRNA is regulated by amino acid availability

NARCIS (Netherlands)

Fernandez, J.; Yaman, I.; Mishra, R.; Merrick, W. C.; Snider, M. D.; Lamers, W. H.; Hatzoglou, M.

2001-01-01

The cationic amino acid transporter, Cat-1, facilitates the uptake of the essential amino acids arginine and lysine. Amino acid starvation causes accumulation and increased translation of cat-1 mRNA, resulting in a 58-fold increase in protein levels and increased arginine uptake. A bicistronic mRNA

Genetic recombination in plant-infecting messenger-sense RNA viruses: overview and research perspectives.

Science.gov (United States)

Bujarski, Jozef J

2013-01-01

RNA recombination is one of the driving forces of genetic variability in (+)-strand RNA viruses. Various types of RNA-RNA crossovers were described including crosses between the same or different viral RNAs or between viral and cellular RNAs. Likewise, a variety of molecular mechanisms are known to support RNA recombination, such as replicative events (based on internal or end-to-end replicase switchings) along with non-replicative joining among RNA fragments of viral and/or cellular origin. Such mechanisms as RNA decay or RNA interference are responsible for RNA fragmentation and trans-esterification reactions which are likely accountable for ligation of RNA fragments. Numerous host factors were found to affect the profiles of viral RNA recombinants and significant differences in recombination frequency were observed among various RNA viruses. Comparative analyses of viral sequences allowed for the development of evolutionary models in order to explain adaptive phenotypic changes and co-evolving sites. Many questions remain to be answered by forthcoming RNA recombination research. (1) How various factors modulate the ability of viral replicase to switch templates, (2) What is the intracellular location of RNA-RNA template switchings, (3) Mechanisms and factors responsible for non-replicative RNA recombination, (4) Mechanisms of integration of RNA viral sequences with cellular genomic DNA, and (5) What is the role of RNA splicing and ribozyme activity. From an evolutionary stand point, it is not known how RNA viruses parasitize new host species via recombination, nor is it obvious what the contribution of RNA recombination is among other RNA modification pathways. We do not understand why the frequency of RNA recombination varies so much among RNA viruses and the status of RNA recombination as a form of sex is not well documented.

Genetic recombination in plant-infecting messenger-sense RNA viruses: overview and research perspectives

Directory of Open Access Journals (Sweden)

Jozef Julian Bujarski

2013-03-01

Full Text Available RNA recombination is one of the driving forces of genetic variability in (+-strand RNA viruses. Various types of RNA-RNA crossovers were described including crosses between the same or different viral RNAs or between viral and cellular RNAs. Likewise, a variety of molecular mechanisms are known to support RNA recombination, such as replicative events (based on internal or end-to-end replicase switchings along with nonreplicative joining among RNA fragments of viral and/or cellular origin. Such mechanisms as RNA decay or RNA interference are responsible for RNA fragmentation and trans-esterification reactions which are likely accountable for ligation of RNA fragments. Numerous host factors were found to affect the profiles of viral RNA recombinants and significant differences in recombination frequency were observed among various RNA viruses. Comparative analyses of viral sequences allowed for the development of evolutionary models in order to explain adaptive phenotypic changes and co-evolving sites. Many questions remain to be answered by forthcoming RNA recombination research. (i How various factors modulate the ability of viral replicase to switch templates, (ii What is the intracellular location of RNA-RNA template switchings, (iii Mechanisms and factors responsible for non-replicative RNA recombination, (iv Mechanisms of integration of RNA viral sequences with cellular genomic DNA, and (v What is the role of RNA splicing and ribozyme activity. From an evolutionary stand point, it is not known how RNA viruses parasitize new host species via recombination, nor is it obvious what the contribution of RNA recombination is among other RNA modification pathways. We do not understand why the frequency of RNA recombination varies so much among RNA viruses and the status of RNA recombination as a form of sex is not well documented.

Standard NIJ 0115.00 za testiranje otpornosti zaštitnih prsluka na ubode nožem i predmetima sa oštrim vrhom / NIJ 0115.00 standard for testing stab resistance of body armor

Directory of Open Access Journals (Sweden)

Đuro Jovanić

2008-04-01

Full Text Available Standard NIJ 0115.00 (prema Nacionalnom institutu pravde SAD, namenjen je za utvrđivanje minimuma tehničkih zahteva i metoda ispitivanja otpornosti zaštitnih prsluka, koji treba da zaštite gornji deo tela od uboda nožem i predmetima sa oštrim vrhom. Područje primene ovog standarda ograničeno je samo na pretnje ubodima, a ne na balističke pretnje, poput onih koje su obuhvaćene standardom NIJ 0101.04 za testiranje balističke otpornosti zaštitnih prsluka. / In this work made presentation of NIJ 0115.04. (National Institute of Justice standard, witch purpose is to establish minimum performance requirements and methods of testing for the stab resistance of body armor intended to protect the torso against slash and stab threats. The scope of the standard is limited to stab resistance only; the standard does not address ballistic threats, as those are covered by NIJ Standard 0101.04. Ballistic Resistance of Personal Body Armor.

Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler.

Science.gov (United States)

Bindewald, Eckart; Grunewald, Calvin; Boyle, Brett; O'Connor, Mary; Shapiro, Bruce A

2008-10-01

One approach to designing RNA nanoscale structures is to use known RNA structural motifs such as junctions, kissing loops or bulges and to construct a molecular model by connecting these building blocks with helical struts. We previously developed an algorithm for detecting internal loops, junctions and kissing loops in RNA structures. Here we present algorithms for automating or assisting many of the steps that are involved in creating RNA structures from building blocks: (1) assembling building blocks into nanostructures using either a combinatorial search or constraint satisfaction; (2) optimizing RNA 3D ring structures to improve ring closure; (3) sequence optimisation; (4) creating a unique non-degenerate RNA topology descriptor. This effectively creates a computational pipeline for generating molecular models of RNA nanostructures and more specifically RNA ring structures with optimized sequences from RNA building blocks. We show several examples of how the algorithms can be utilized to generate RNA tecto-shapes.

Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler☆

Science.gov (United States)

Bindewald, Eckart; Grunewald, Calvin; Boyle, Brett; O’Connor, Mary; Shapiro, Bruce A.

2013-01-01

One approach to designing RNA nanoscale structures is to use known RNA structural motifs such as junctions, kissing loops or bulges and to construct a molecular model by connecting these building blocks with helical struts. We previously developed an algorithm for detecting internal loops, junctions and kissing loops in RNA structures. Here we present algorithms for automating or assisting many of the steps that are involved in creating RNA structures from building blocks: (1) assembling building blocks into nanostructures using either a combinatorial search or constraint satisfaction; (2) optimizing RNA 3D ring structures to improve ring closure; (3) sequence optimisation; (4) creating a unique non-degenerate RNA topology descriptor. This effectively creates a computational pipeline for generating molecular models of RNA nanostructures and more specifically RNA ring structures with optimized sequences from RNA building blocks. We show several examples of how the algorithms can be utilized to generate RNA tecto-shapes. PMID:18838281

Functional 5' UTR mRNA structures in eukaryotic translation regulation and how to find them.

Science.gov (United States)

Leppek, Kathrin; Das, Rhiju; Barna, Maria

2018-03-01

RNA molecules can fold into intricate shapes that can provide an additional layer of control of gene expression beyond that of their sequence. In this Review, we discuss the current mechanistic understanding of structures in 5' untranslated regions (UTRs) of eukaryotic mRNAs and the emerging methodologies used to explore them. These structures may regulate cap-dependent translation initiation through helicase-mediated remodelling of RNA structures and higher-order RNA interactions, as well as cap-independent translation initiation through internal ribosome entry sites (IRESs), mRNA modifications and other specialized translation pathways. We discuss known 5' UTR RNA structures and how new structure probing technologies coupled with prospective validation, particularly compensatory mutagenesis, are likely to identify classes of structured RNA elements that shape post-transcriptional control of gene expression and the development of multicellular organisms.

How the RNA isolation method can affect microRNA microarray results

DEFF Research Database (Denmark)

Podolska, Agnieszka; Kaczkowski, Bogumil; Litman, Thomas

2011-01-01

RNA microarray analysis on porcine brain tissue. One method is a phenol-guanidine isothiocyanate-based procedure that permits isolation of total RNA. The second method, miRVana™ microRNA isolation, is column based and recovers the small RNA fraction alone. We found that microarray analyses give different results...... that depend on the RNA fraction used, in particular because some microRNAs appear very sensitive to the RNA isolation method. We conclude that precautions need to be taken when comparing microarray studies based on RNA isolated with different methods.......The quality of RNA is crucial in gene expression experiments. RNA degradation interferes in the measurement of gene expression, and in this context, microRNA quantification can lead to an incorrect estimation. In the present study, two different RNA isolation methods were used to perform micro...

The integrated analysis of RNA-seq and microRNA-seq depicts miRNA-mRNA networks involved in Japanese flounder (Paralichthys olivaceus) albinism.

Science.gov (United States)

Wang, Na; Wang, Ruoqing; Wang, Renkai; Tian, Yongsheng; Shao, Changwei; Jia, Xiaodong; Chen, Songlin

2017-01-01

Albinism, a phenomenon characterized by pigmentation deficiency on the ocular side of Japanese flounder (Paralichthys olivaceus), has caused significant damage. Limited mRNA and microRNA (miRNA) information is available on fish pigmentation deficiency. In this study, a high-throughput sequencing strategy was employed to identify the mRNA and miRNAs involved in P. olivaceus albinism. Based on P. olivaceus genome, RNA-seq identified 21,787 know genes and 711 new genes by transcripts assembly. Of those, 235 genes exhibited significantly different expression pattern (fold change ≥2 or ≤0.5 and q-value≤0.05), including 194 down-regulated genes and 41 up-regulated genes in albino versus normally pigmented individuals. These genes were enriched to 81 GO terms and 9 KEGG pathways (p≤0.05). Among those, the pigmentation related pathways-Melanogenesis and tyrosine metabolism were contained. High-throughput miRNA sequencing identified a total of 475 miRNAs, including 64 novel miRNAs. Furthermore, 33 differentially expressed miRNAs containing 13 up-regulated and 20 down-regulated miRNAs were identified in albino versus normally pigmented individuals (fold change ≥1.5 or ≤0.67 and p≤0.05). The next target prediction discovered a variety of putative target genes, of which, 134 genes including Tyrosinase (TYR), Tyrosinase-related protein 1 (TYRP1), Microphthalmia-associated transcription factor (MITF) were overlapped with differentially expressed genes derived from RNA-seq. These target genes were significantly enriched to 254 GO terms and 103 KEGG pathways (p<0.001). Of those, tyrosine metabolism, lysosomes, phototransduction pathways, etc., attracted considerable attention due to their involvement in regulating skin pigmentation. Expression patterns of differentially expressed mRNA and miRNAs were validated in 10 mRNA and 10 miRNAs by qRT-PCR. With high-throughput mRNA and miRNA sequencing and analysis, a series of interested mRNA and miRNAs involved in fish

Switching off small RNA regulation with trap-mRNA

DEFF Research Database (Denmark)

Overgaard, Martin; Johansen, Jesper; Møller-Jensen, Jakob

2009-01-01

to operate at the level of transcription initiation. By employing a highly sensitive genetic screen we uncovered a novel RNA-based regulatory principle in which induction of a trap-mRNA leads to selective degradation of a small regulatory RNA molecule, thereby abolishing the sRNA-based silencing of its...

Morphological and hematological studies of Trypanosoma spp. infecting ornamental armored catfish from Guamá River-PA, Brazil

Directory of Open Access Journals (Sweden)

Rodrigo Y. Fujimoto

2013-09-01

Full Text Available A total of 281 specimens of freshwater armored ornamental fish species (Leporacanthicus galaxias, Lasiancistrus saetiger, Cochliodon sp., Hypostomus sp., Pseudacanthicus spinosus, Ancistrus sp. and Rineloricaria cf. lanceolata were captured at the hydrological basin of Guamá River, Pará, Brazil. The infection by Trypanosoma spp. was inspected. The morphological and morphometric characterization of the parasites and the hematological parameters were determined. Leporacanthicus galaxias and Pseudacanthicus spinosus presented 100% infection prevalence, and the other species showed a variable prevalence of infection. The parasites showed clearly different morphotypes and dimensions, and probably belong to different species. The hematological response to the infection varied with the host. Cochliodon sp. showed no differences between infected and not infected fish. In other species several modifications on some hematological parameters were found, but apparently without causing disease. It is emphasized the possibility of introduction of the parasites in new environments due to the artificial movements of these ornamental fish.

Functional characterization of the Drosophila MRP (mitochondrial RNA processing) RNA gene.

Science.gov (United States)

Schneider, Mary D; Bains, Anupinder K; Rajendra, T K; Dominski, Zbigniew; Matera, A Gregory; Simmonds, Andrew J

2010-11-01

MRP RNA is a noncoding RNA component of RNase mitochondrial RNA processing (MRP), a multi-protein eukaryotic endoribonuclease reported to function in multiple cellular processes, including ribosomal RNA processing, mitochondrial DNA replication, and cell cycle regulation. A recent study predicted a potential Drosophila ortholog of MRP RNA (CR33682) by computer-based genome analysis. We have confirmed the expression of this gene and characterized the phenotype associated with this locus. Flies with mutations that specifically affect MRP RNA show defects in growth and development that begin in the early larval period and end in larval death during the second instar stage. We present several lines of evidence demonstrating a role for Drosophila MRP RNA in rRNA processing. The nuclear fraction of Drosophila MRP RNA localizes to the nucleolus. Further, a mutant strain shows defects in rRNA processing that include a defect in 5.8S rRNA processing, typical of MRP RNA mutants in other species, as well as defects in early stages of rRNA processing.

Development of a novel recombinant encapsidated RNA particle: evaluation as an internal control for diagnostic RT-PCR

DEFF Research Database (Denmark)

King, Donald P.; Montague, Nick; Ebert, Katja

2007-01-01

-and-mouth disease virus (FMDV) and a set for swine vesicular disease virus (SVDV) was engineered into a full-length cDNA clone containing the RNA-2 segment of Cowpea Mosaic Virus (CPMV). After co-inoculation with a plasmid that expressed CPMV RNA-1, recombinant virus particles were rescued from cowpea plants (Vigna...

Cytoplasmic Z-RNA

International Nuclear Information System (INIS)

Zarling, D.A.; Calhoun, C.J.; Hardin, C.C.; Zarling, A.H.

1987-01-01

Specific immunochemical probes for Z-RNA were generated and characterized to search for possible Z-RNA-like double helices in cells. Z-RNA was detected in the cytoplasm of fixed protozoan cells by immunofluorescence microscopy using these anti-Z-RNA IgCs. In contrast, autoimmune or experimentally elicited anti-DNA antibodies, specifically reactive with B-DNA or Z-DNA, stained the nuclei. Pre-or nonimmune IgGs did not bind to the cells. RNase A or T1 digestion eliminated anti-Z-RNA IgG binding to cytoplasmic determinants; however, DNase I or mung bean nuclease had no effect. Doxorubicin and ethidium bromide prevented anti-Z-RNA antibody binding; however, actinomycin D, which does not bind double-stranded RNA, did not. Anti-Z-RNA immunofluorescence was specifically blocked in competition assays by synthetic Z-RNA but not Z-DNA, A-RNA, or single-stranded RNAs. Thus, some cytoplasmic sequences in fixed cells exist in the left-handed Z-RNA conformation

Turning limited experimental information into 3D models of RNA.

Science.gov (United States)

Flores, Samuel Coulbourn; Altman, Russ B

2010-09-01

Our understanding of RNA functions in the cell is evolving rapidly. As for proteins, the detailed three-dimensional (3D) structure of RNA is often key to understanding its function. Although crystallography and nuclear magnetic resonance (NMR) can determine the atomic coordinates of some RNA structures, many 3D structures present technical challenges that make these methods difficult to apply. The great flexibility of RNA, its charged backbone, dearth of specific surface features, and propensity for kinetic traps all conspire with its long folding time, to challenge in silico methods for physics-based folding. On the other hand, base-pairing interactions (either in runs to form helices or isolated tertiary contacts) and motifs are often available from relatively low-cost experiments or informatics analyses. We present RNABuilder, a novel code that uses internal coordinate mechanics to satisfy user-specified base pairing and steric forces under chemical constraints. The code recapitulates the topology and characteristic L-shape of tRNA and obtains an accurate noncrystallographic structure of the Tetrahymena ribozyme P4/P6 domain. The algorithm scales nearly linearly with molecule size, opening the door to the modeling of significantly larger structures.

RNA Interference - Towards RNA becoming a Medicine -42 ...

Indian Academy of Sciences (India)

research. A brief history of the development ofRNAi is shown in. Box 2. Mechanism of ... new RNA strand using target RNA as the template and thereby converting it ... thought to excise precursor stRNA from their -70 nt stem loop precursor to ...

Role of RNase MRP in viral RNA degradation and RNA recombination.

Science.gov (United States)

Jaag, Hannah M; Lu, Qiasheng; Schmitt, Mark E; Nagy, Peter D

2011-01-01

RNA degradation, together with RNA synthesis, controls the steady-state level of viral RNAs in infected cells. The endoribonucleolytic cleavage of viral RNA is important not only for viral RNA degradation but for RNA recombination as well, due to the participation of some RNA degradation products in the RNA recombination process. To identify host endoribonucleases involved in degradation of Tomato bushy stunt virus (TBSV) in a Saccharomyces cerevisiae model host, we tested eight known endoribonucleases. Here we report that downregulation of SNM1, encoding a component of the RNase MRP, and a temperature-sensitive mutation in the NME1 gene, coding for the RNA component of RNase MRP, lead to reduced production of the endoribonucleolytically cleaved TBSV RNA in yeast. We also show that the highly purified yeast RNase MRP cleaves the TBSV RNA in vitro, resulting in TBSV RNA degradation products similar in size to those observed in yeast cells. Knocking down the NME1 homolog in Nicotiana benthamiana also led to decreased production of the cleaved TBSV RNA, suggesting that in plants, RNase MRP is involved in TBSV RNA degradation. Altogether, this work suggests a role for the host endoribonuclease RNase MRP in viral RNA degradation and recombination.

Use of gamma camera for measurement of the internal contamination with depleted uranium

International Nuclear Information System (INIS)

Spaic, R.; Markovic, S.; Pavlovic, S.; Pavlovic, R.; Ajdinovic, B.; Baskot, B.; Djurovic, B.

2000-01-01

Depleted uranium from radioactive wastes is used for manufacturing bullets used in Iraq, Republic of Serbia and Yugoslavia. These bullets are extremely dense and capable of penetrating heavily armored vehicles. Their medical importance lies in the fact that the bullets contain seventy percent depleted uranium which creates aerosolized particles less than five microns in diameter, small enough to be inhaled, after spontaneous bullet burn at impact. Nuclear medicine scientists must be aware of this and be prepared to measure internal contamination of persons exposed to this radioactive material. Whole body counters (WBC) represent appropriate equipment for this purpose but their availability in developing countries is not sufficient. Gamma camera is an alternative. The minimum detectable activity (MDA) of depleted uranium, iodine and technetium for gamma cameras was measured in this paper. Low energy X-ray 100 KeV with 20% windows are used for the depleted uranium detection. About 40% gamma emissions from depleted uranium fall within these limits. The activities measured (50-100 Bq) are about ten times higher then on WBC (5 Bq). This does not limit the use of gamma cameras for measurement of lung or whole body internal contamination with depleted uranium. (author)

Real-time isothermal RNA amplification of toxic marine microalgae using preserved reagents on an integrated microfluidic platform.

Science.gov (United States)

Tsaloglou, Maria-Nefeli; Laouenan, Florian; Loukas, Christos-Moritz; Monsalve, Lisandro Gabriel; Thanner, Christine; Morgan, Hywel; Ruano-López, Jesus M; Mowlem, Matthew C

2013-01-21

Quantitation of specific RNA sequences is a useful technique in marine biology that can elucidate cell abundance, speciation and viability, especially for early detection of harmful algal blooms. We are thus developing an integrated microfluidic system for cell concentration and lysis, RNA extraction/purification and quantitative RNA detection for environmental applications. The portable system is based on a microfluidic cartridge, or "lab-card", using a low-cost injection moulded device, with a laminated lid. Here we present real-time isothermal RNA amplification using reagent master-mixes preserved on-chip in a gel at 4 °C for up to eight months. We demonstrate quantitation by reference to an internal control in a competitive assay with 500 cell equivalents of the toxic microalga Karenia brevis. Annealing of primers, amplification at 41 °C and real-time fluorescence detection of the internal control and target using sequence-specific molecular beacons were all performed on-chip.

Structure and Dynamics of RNA Repeat Expansions That Cause Huntington's Disease and Myotonic Dystrophy Type 1.

Science.gov (United States)

Chen, Jonathan L; VanEtten, Damian M; Fountain, Matthew A; Yildirim, Ilyas; Disney, Matthew D

2017-07-11

RNA repeat expansions cause a host of incurable, genetically defined diseases. The most common class of RNA repeats consists of trinucleotide repeats. These long, repeating transcripts fold into hairpins containing 1 × 1 internal loops that can mediate disease via a variety of mechanism(s) in which RNA is the central player. Two of these disorders are Huntington's disease and myotonic dystrophy type 1, which are caused by r(CAG) and r(CUG) repeats, respectively. We report the structures of two RNA constructs containing three copies of a r(CAG) [r(3×CAG)] or r(CUG) [r(3×CUG)] motif that were modeled with nuclear magnetic resonance spectroscopy and simulated annealing with restrained molecular dynamics. The 1 × 1 internal loops of r(3×CAG) are stabilized by one-hydrogen bond (cis Watson-Crick/Watson-Crick) AA pairs, while those of r(3×CUG) prefer one- or two-hydrogen bond (cis Watson-Crick/Watson-Crick) UU pairs. Assigned chemical shifts for the residues depended on the identity of neighbors or next nearest neighbors. Additional insights into the dynamics of these RNA constructs were gained by molecular dynamics simulations and a discrete path sampling method. Results indicate that the global structures of the RNA are A-form and that the loop regions are dynamic. The results will be useful for understanding the dynamic trajectory of these RNA repeats but also may aid in the development of therapeutics.

Simultaneous detection and identification of four cherry viruses by two step multiplex RT-PCR with an internal control of plant nad5 mRNA.

Science.gov (United States)

Noorani, Md Salik; Awasthi, Prachi; Sharma, Maheshwar Prasad; Ram, Raja; Zaidi, Aijaz Asgar; Hallan, Vipin

2013-10-01

A multiplex reverse transcription-polymerase chain reaction (mRT-PCR) was developed and standardized for the simultaneous detection of four cherry viruses: Cherry virus A (CVA, Genus; Capillovirus), Cherry necrotic rusty mottle virus (CNRMV, unassigned species of the Betaflexiviridae), Little cherry virus 1 (LChV-1, Genus; Closterovirus) and Prunus necrotic ringspot virus (PNRSV, Genus; Ilarvirus) with nad5 as plant internal control. A reliable and quick method for total plant RNA extraction from pome and stone fruit trees was also developed. To minimize primer dimer formation, a single antisense primer for CVA and CNRMV was used. A mixture of random hexamer and oligo (dT) primer was used for cDNA synthesis, which was highly suited and economic for multiplexing. All four viruses were detected successfully by mRT-PCR in artificially created viral RNA mixture and field samples of sweet cherry. The identity of the viruses was confirmed by sequencing. The assay could detect above viruses in diluted cDNA (10(-4)) and RNA (10(-3), except PNRSV which was detected only till ten times lesser dilution). The developed mRT-PCR will not only be useful for the detection of viruses from single or multiple infections of sweet cherry plants but also for other stone and pome fruits. The developed method will be therefore quite helpful for virus indexing, plant quarantine and certification programs. This is the first report for the simultaneous detection of four cherry viruses by mRT-PCR. Copyright © 2013 Elsevier B.V. All rights reserved.

De la motte au château d’artillerie, la fouille du château de Guingamp (Côtes-d’Armor

Directory of Open Access Journals (Sweden)

Laurent Beuchet

2010-02-01

Full Text Available L’opération d’archéologie préventive du château de Guingamp (Côtes-d’Armor a été réalisée dans le cadre d'un projet de création d'une salle culturelle sur le site du château. La fouille a été menée sur une superficie de 2000 m², sur une durée effective de cinq mois entre octobre 2004 et mars 2005, avec un effectif moyen de sept personnes.À l’issue de la fouille, trois phases principales d’occupation peuvent être identifiées :la motte des Comtes de Guingamp (XIe-XIIe s. ;une enceinte polygon...

RNA-Binding Proteins Revisited – The Emerging Arabidopsis mRNA Interactome

KAUST Repository

Köster, Tino

2017-04-13

RNA–protein interaction is an important checkpoint to tune gene expression at the RNA level. Global identification of proteins binding in vivo to mRNA has been possible through interactome capture – where proteins are fixed to target RNAs by UV crosslinking and purified through affinity capture of polyadenylated RNA. In Arabidopsis over 500 RNA-binding proteins (RBPs) enriched in UV-crosslinked samples have been identified. As in mammals and yeast, the mRNA interactomes came with a few surprises. For example, a plethora of the proteins caught on RNA had not previously been linked to RNA-mediated processes, for example proteins of intermediary metabolism. Thus, the studies provide unprecedented insights into the composition of the mRNA interactome, highlighting the complexity of RNA-mediated processes.

RNA-Binding Proteins Revisited – The Emerging Arabidopsis mRNA Interactome

KAUST Repository

Kö ster, Tino; Marondedze, Claudius; Meyer, Katja; Staiger, Dorothee

2017-01-01

RNA–protein interaction is an important checkpoint to tune gene expression at the RNA level. Global identification of proteins binding in vivo to mRNA has been possible through interactome capture – where proteins are fixed to target RNAs by UV crosslinking and purified through affinity capture of polyadenylated RNA. In Arabidopsis over 500 RNA-binding proteins (RBPs) enriched in UV-crosslinked samples have been identified. As in mammals and yeast, the mRNA interactomes came with a few surprises. For example, a plethora of the proteins caught on RNA had not previously been linked to RNA-mediated processes, for example proteins of intermediary metabolism. Thus, the studies provide unprecedented insights into the composition of the mRNA interactome, highlighting the complexity of RNA-mediated processes.

Design and optimization of a novel reverse transcription linear-after-the-exponential PCR for the detection of foot-and-mouth disease virus.

Science.gov (United States)

Pierce, K E; Mistry, R; Reid, S M; Bharya, S; Dukes, J P; Hartshorn, C; King, D P; Wangh, L J

2010-07-01

A novel molecular assay for the detection of foot-and-mouth disease virus (FMDV) was developed using linear-after-the-exponential polymerase chain reaction (LATE-PCR). Pilot experiments using synthetic DNA targets demonstrated the ability of LATE-PCR to quantify initial target concentration through endpoint detection. A two-step protocol involving reverse transcription (RT) followed by LATE-PCR was then used to confirm the ability of the assay to detect FMDV RNA. Finally, RT and LATE-PCR were combined in a one-step duplex assay for co-amplification of an FMDV RNA segment and an internal control comprised of an Armored RNA. In that form, each of the excess primers in the reaction mixture hybridize to their respective RNA targets during a short pre-incubation, then generate cDNA strands during a 3-min RT step at 60°C, and the resulting cDNA is amplified by LATE-PCR without intervening sample processing. The RT-LATE-PCR assay generates fluorescent signals at endpoint that are proportional to the starting number of RNA targets and can detect a range of sequence variants using a single mismatch-tolerant probe. In addition to offering improvements over current laboratory-based molecular diagnostic assays for FMDV, this new assay is compatible with a novel portable ('point-of-care') device, the BioSeeq II, designed for the rapid diagnosis of FMD in the field. © 2009 The Authors. Journal compilation © 2009 The Society for Applied Microbiology.

Using information theory to assess the communicative capacity of circulating microRNA.

Science.gov (United States)

Finn, Nnenna A; Searles, Charles D

2013-10-11

The discovery of extracellular microRNAs (miRNAs) and their transport modalities (i.e., microparticles, exosomes, proteins and lipoproteins) has sparked theories regarding their role in intercellular communication. Here, we assessed the information transfer capacity of different miRNA transport modalities in human serum by utilizing basic principles of information theory. Zipf Statistics were calculated for each of the miRNA transport modalities identified in human serum. Our analyses revealed that miRNA-mediated information transfer is redundant, as evidenced by negative Zipf's Statistics with magnitudes greater than one. In healthy subjects, the potential communicative capacity of miRNA in complex with circulating proteins was significantly lower than that of miRNA encapsulated in circulating microparticles and exosomes. Moreover, the presence of coronary heart disease significantly lowered the communicative capacity of all circulating miRNA transport modalities. To assess the internal organization of circulating miRNA signals, Shannon's zero- and first-order entropies were calculated. Microparticles (MPs) exhibited the lowest Shannon entropic slope, indicating a relatively high capacity for information transfer. Furthermore, compared to the other miRNA transport modalities, MPs appeared to be the most efficient at transferring miRNA to cultured endothelial cells. Taken together, these findings suggest that although all transport modalities have the capacity for miRNA-based information transfer, MPs may be the simplest and most robust way to achieve miRNA-based signal transduction in sera. This study presents a novel method for analyzing the quantitative capacity of miRNA-mediated information transfer while providing insight into the communicative characteristics of distinct circulating miRNA transport modalities. Published by Elsevier Inc.

RNA-dependent RNA polymerases from cowpea mosaic virus-infected cowpea leaves

NARCIS (Netherlands)

Dorssers, L.

1983-01-01

The aim of the research described in this thesis was the purification and identification of the RNA-dependent RNA polymerase engaged in replicating viral RNA in cowpea mosaic virus (CPMV)- infected cowpea leaves.

Previously, an RNA-dependent RNA polymerase produced upon infection of

Lipoprotein Lipase mRNA expression in different tissues of farm ...

African Journals Online (AJOL)

Lipoprotein lipase (LPL) controls triacylglycerol partitioning between adipose tissues and muscles, so it is important enzyme for fattening of animals .The present work was planned to clarify the use of polymerase chain reaction (PCR) for detection of LPL mRNA expression in different tissues representing internal organs of ...

Cyclophilin B stimulates RNA synthesis by the HCV RNA dependent RNA polymerase.

Science.gov (United States)

Heck, Julie A; Meng, Xiao; Frick, David N

2009-04-01

Cyclophilins are cellular peptidyl isomerases that have been implicated in regulating hepatitis C virus (HCV) replication. Cyclophilin B (CypB) is a target of cyclosporin A (CsA), an immunosuppressive drug recently shown to suppress HCV replication in cell culture. Watashi et al. recently demonstrated that CypB is important for efficient HCV replication, and proposed that it mediates the anti-HCV effects of CsA through an interaction with NS5B [Watashi K, Ishii N, Hijikata M, Inoue D, Murata T, Miyanari Y, et al. Cyclophilin B is a functional regulator of hepatitis C virus RNA polymerase. Mol Cell 2005;19:111-22]. We examined the effects of purified CypB proteins on the enzymatic activity of NS5B. Recombinant CypB purified from insect cells directly stimulated NS5B-catalyzed RNA synthesis. CypB increased RNA synthesis by NS5B derived from genotype 1a, 1b, and 2a HCV strains. Stimulation appears to arise from an increase in productive RNA binding. NS5B residue Pro540, a previously proposed target of CypB peptidyl-prolyl isomerase activity, is not required for stimulation of RNA synthesis.

Picornavirus RNA is protected from cleavage by ribonuclease during virion uncoating and transfer across cellular and model membranes.

Science.gov (United States)

Groppelli, Elisabetta; Levy, Hazel C; Sun, Eileen; Strauss, Mike; Nicol, Clare; Gold, Sarah; Zhuang, Xiaowei; Tuthill, Tobias J; Hogle, James M; Rowlands, David J

2017-02-01

Picornaviruses are non-enveloped RNA viruses that enter cells via receptor-mediated endocytosis. Because they lack an envelope, picornaviruses face the challenge of delivering their RNA genomes across the membrane of the endocytic vesicle into the cytoplasm to initiate infection. Currently, the mechanism of genome release and translocation across membranes remains poorly understood. Within the enterovirus genus, poliovirus, rhinovirus 2, and rhinovirus 16 have been proposed to release their genomes across intact endosomal membranes through virally induced pores, whereas one study has proposed that rhinovirus 14 releases its RNA following disruption of endosomal membranes. For the more distantly related aphthovirus genus (e.g. foot-and-mouth disease viruses and equine rhinitis A virus) acidification of endosomes results in the disassembly of the virion into pentamers and in the release of the viral RNA into the lumen of the endosome, but no details have been elucidated as how the RNA crosses the vesicle membrane. However, more recent studies suggest aphthovirus RNA is released from intact particles and the dissociation to pentamers may be a late event. In this study we have investigated the RNase A sensitivity of genome translocation of poliovirus using a receptor-decorated-liposome model and the sensitivity of infection of poliovirus and equine-rhinitis A virus to co-internalized RNase A. We show that poliovirus genome translocation is insensitive to RNase A and results in little or no release into the medium in the liposome model. We also show that infectivity is not reduced by co-internalized RNase A for poliovirus and equine rhinitis A virus. Additionally, we show that all poliovirus genomes that are internalized into cells, not just those resulting in infection, are protected from RNase A. These results support a finely coordinated, directional model of viral RNA delivery that involves viral proteins and cellular membranes.

Picornavirus RNA is protected from cleavage by ribonuclease during virion uncoating and transfer across cellular and model membranes.

Directory of Open Access Journals (Sweden)

Elisabetta Groppelli

2017-02-01

Full Text Available Picornaviruses are non-enveloped RNA viruses that enter cells via receptor-mediated endocytosis. Because they lack an envelope, picornaviruses face the challenge of delivering their RNA genomes across the membrane of the endocytic vesicle into the cytoplasm to initiate infection. Currently, the mechanism of genome release and translocation across membranes remains poorly understood. Within the enterovirus genus, poliovirus, rhinovirus 2, and rhinovirus 16 have been proposed to release their genomes across intact endosomal membranes through virally induced pores, whereas one study has proposed that rhinovirus 14 releases its RNA following disruption of endosomal membranes. For the more distantly related aphthovirus genus (e.g. foot-and-mouth disease viruses and equine rhinitis A virus acidification of endosomes results in the disassembly of the virion into pentamers and in the release of the viral RNA into the lumen of the endosome, but no details have been elucidated as how the RNA crosses the vesicle membrane. However, more recent studies suggest aphthovirus RNA is released from intact particles and the dissociation to pentamers may be a late event. In this study we have investigated the RNase A sensitivity of genome translocation of poliovirus using a receptor-decorated-liposome model and the sensitivity of infection of poliovirus and equine-rhinitis A virus to co-internalized RNase A. We show that poliovirus genome translocation is insensitive to RNase A and results in little or no release into the medium in the liposome model. We also show that infectivity is not reduced by co-internalized RNase A for poliovirus and equine rhinitis A virus. Additionally, we show that all poliovirus genomes that are internalized into cells, not just those resulting in infection, are protected from RNase A. These results support a finely coordinated, directional model of viral RNA delivery that involves viral proteins and cellular membranes.

Fast prediction of RNA-RNA interaction using heuristic algorithm.

Science.gov (United States)

Montaseri, Soheila

2015-01-01

Interaction between two RNA molecules plays a crucial role in many medical and biological processes such as gene expression regulation. In this process, an RNA molecule prohibits the translation of another RNA molecule by establishing stable interactions with it. Some algorithms have been formed to predict the structure of the RNA-RNA interaction. High computational time is a common challenge in most of the presented algorithms. In this context, a heuristic method is introduced to accurately predict the interaction between two RNAs based on minimum free energy (MFE). This algorithm uses a few dot matrices for finding the secondary structure of each RNA and binding sites between two RNAs. Furthermore, a parallel version of this method is presented. We describe the algorithm's concurrency and parallelism for a multicore chip. The proposed algorithm has been performed on some datasets including CopA-CopT, R1inv-R2inv, Tar-Tar*, DIS-DIS, and IncRNA54-RepZ in Escherichia coli bacteria. The method has high validity and efficiency, and it is run in low computational time in comparison to other approaches.

The RNA synthesis machinery of negative-stranded RNA viruses

International Nuclear Information System (INIS)

Ortín, Juan; Martín-Benito, Jaime

2015-01-01

The group of Negative-Stranded RNA Viruses (NSVs) includes many human pathogens, like the influenza, measles, mumps, respiratory syncytial or Ebola viruses, which produce frequent epidemics of disease and occasional, high mortality outbreaks by transmission from animal reservoirs. The genome of NSVs consists of one to several single-stranded, negative-polarity RNA molecules that are always assembled into mega Dalton-sized complexes by association to many nucleoprotein monomers. These RNA-protein complexes or ribonucleoproteins function as templates for transcription and replication by action of the viral RNA polymerase and accessory proteins. Here we review our knowledge on these large RNA-synthesis machines, including the structure of their components, the interactions among them and their enzymatic activities, and we discuss models showing how they perform the virus transcription and replication programmes. - Highlights: • Overall organisation of NSV RNA synthesis machines. • Structure and function of the ribonucleoprotein components: Atomic structure of the RNA polymerase complex. • Commonalities and differences between segmented- and non-segmented NSVs. • Transcription versus replication programmes

The RNA synthesis machinery of negative-stranded RNA viruses

Energy Technology Data Exchange (ETDEWEB)

Ortín, Juan, E-mail: jortin@cnb.csic.es [Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CSIC) and CIBER de Enfermedades Respiratorias (ISCIII), Madrid (Spain); Martín-Benito, Jaime, E-mail: jmartinb@cnb.csic.es [Department of Macromolecular Structures, Centro Nacional de Biotecnología (CSIC), Madrid (Spain)

2015-05-15

The group of Negative-Stranded RNA Viruses (NSVs) includes many human pathogens, like the influenza, measles, mumps, respiratory syncytial or Ebola viruses, which produce frequent epidemics of disease and occasional, high mortality outbreaks by transmission from animal reservoirs. The genome of NSVs consists of one to several single-stranded, negative-polarity RNA molecules that are always assembled into mega Dalton-sized complexes by association to many nucleoprotein monomers. These RNA-protein complexes or ribonucleoproteins function as templates for transcription and replication by action of the viral RNA polymerase and accessory proteins. Here we review our knowledge on these large RNA-synthesis machines, including the structure of their components, the interactions among them and their enzymatic activities, and we discuss models showing how they perform the virus transcription and replication programmes. - Highlights: • Overall organisation of NSV RNA synthesis machines. • Structure and function of the ribonucleoprotein components: Atomic structure of the RNA polymerase complex. • Commonalities and differences between segmented- and non-segmented NSVs. • Transcription versus replication programmes.

Structural studies on an internal loop from a hairpin ribozyme

Energy Technology Data Exchange (ETDEWEB)

Cai, Z.; SantaLucia, J. Jr.; Tinoco, I. Jr. [Univ. of California, Berkeley, CA (United States)

1994-12-01

Ribozymes, RNA enzymes, catalyze site-specific RNA cleavage and ligation reactions. We are studying the three-dimensional structure of a hairpin ribozyme derived from the minus strand of tobacco ring spot virus satellite RNA ((-)sTRSV), which has been engineering to specifically cleave the HIV-1 RNA. The minimum structure for the catalytic reaction involves a 50-nucleotide ribozyme and a 14-nucleotide substrate. The proposed secondary structure of the ribozyme-substrate complex consists of four short helices separated by two internal loops. The relatively large size (64-nucleotide) of the ribozyme-substrate complex presents formidable problems in solving the structure using NMR. Therefore we are studying smaller structural subunits of the complex. We are determining the high resolution structure of the symmetric internal loop involving the cleavage site and the flanking helices. One strand of the internal loop was selectively {sup 13}C-labeled at C8 of each purine and C6 of each pyrimidine. By using {sup 13}C-edited two-dimensional NMR, the proton NOESY spectrum was greatly simplified. This allowed unambiguous sequential proton resonance assignments along each strand. Three-dimensional {sup 1}-{sup 13}C HMQC-NOESY was used to further facilitate resonance assignments. We are also enzymatically synthesizing the entire 50-nucleotide ribozyme and will combine it with the {sup 13}C-labeled substrate. Through comparison of the NOE connectivities of the labeled nucleotides from the internal loop alone with those from the entire complex, the differences between the two structures can be elucidated.

Clinical significance of LUNX mRNA, CK19 mRNA, CEA mRNA expression in detecting micrometastasis from lung cancer

International Nuclear Information System (INIS)

Zhu Guangying; Liu Delin; Chen Jie

2003-01-01

Objective: To evaluate the sensitivity, specificity and clinical significance of CK19 mRNA, CEA mRNA and LUNX mRNA for detecting micrometastasis by sampling the peripheral blood and regional lymph nodes of lung cancer patients. Methods: Reverse transcriptase chain reaction (RT-PCR) was used to detect LUNX mRNA, CK19 mRNA, CEA mRNA for micrometastasis by sampling the peripheral blood of 48 lung cancer patients and 44 regional lymph nodes of such patients treated by curative resection. Peripheral blood of 30 patients with pulmonary benign lesions and 10 normal healthy volunteers and lymph nodes of 6 patients with benign pulmonary diseases served as control. Results: 1) LUNX mRNA, CK19 mRNA, CEA mRNA were expressed in all (35/35) lung cancer tissues. 2) In the peripheral blood from 48 lung cancer patients, 30 (62.5%) were positive for LUNX mRNA, 24 (50.0%) positive for CK19 mRNA and 32(66.7%) positive for CEA mRNA. The positive detection rates of micrometastasis in 44 lymph nodes from lung cancer patients were 36.4% (16 out of 44) for LUNX mRNA, 27.3% (12 out of 44) for CK19 mRNA and 40.9% (18 out of 44) for CEA mRNA. 3) In the 30 blood samples from patients with pulmonary benign diseases, 2 (6.7%) expressed CK19 mRNA, but none expressed LUNX mRNA or CEA mRNA. All the 3 molecular markers were negative in the 10 blood samples from healthy volunteers. In 11 lymph nodes from patients with pulmonary benign lesions, none was positive for any of the three markers. 4) In 44 regional lymph nodes from lung cancer patients, 6 (13.6%) were positive for metastasis by histopathological examination, with a positive rate significantly lower than that of the RT-PCR (P<0.05). 5) The micrometastatic positive rate in the peripheral blood of 40 non-small cell lung cancer (NSCLC) patients was significantly related to TNM stage (P=0.01). Conclusions: LUNX mRNA, CK19 MRNA, CEA mRNA are all appropriate target genes for the detection of micrometastasis from lung cancer. LUNX mRNA and CEA mRNA

Integrated structural biology to unravel molecular mechanisms of protein-RNA recognition.

Science.gov (United States)

Schlundt, Andreas; Tants, Jan-Niklas; Sattler, Michael

2017-04-15

Recent advances in RNA sequencing technologies have greatly expanded our knowledge of the RNA landscape in cells, often with spatiotemporal resolution. These techniques identified many new (often non-coding) RNA molecules. Large-scale studies have also discovered novel RNA binding proteins (RBPs), which exhibit single or multiple RNA binding domains (RBDs) for recognition of specific sequence or structured motifs in RNA. Starting from these large-scale approaches it is crucial to unravel the molecular principles of protein-RNA recognition in ribonucleoprotein complexes (RNPs) to understand the underlying mechanisms of gene regulation. Structural biology and biophysical studies at highest possible resolution are key to elucidate molecular mechanisms of RNA recognition by RBPs and how conformational dynamics, weak interactions and cooperative binding contribute to the formation of specific, context-dependent RNPs. While large compact RNPs can be well studied by X-ray crystallography and cryo-EM, analysis of dynamics and weak interaction necessitates the use of solution methods to capture these properties. Here, we illustrate methods to study the structure and conformational dynamics of protein-RNA complexes in solution starting from the identification of interaction partners in a given RNP. Biophysical and biochemical techniques support the characterization of a protein-RNA complex and identify regions relevant in structural analysis. Nuclear magnetic resonance (NMR) is a powerful tool to gain information on folding, stability and dynamics of RNAs and characterize RNPs in solution. It provides crucial information that is complementary to the static pictures derived from other techniques. NMR can be readily combined with other solution techniques, such as small angle X-ray and/or neutron scattering (SAXS/SANS), electron paramagnetic resonance (EPR), and Förster resonance energy transfer (FRET), which provide information about overall shapes, internal domain

The microRNA and messengerRNA profile of the RNA-induced silencing complex in human primary astrocyte and astrocytoma cells.

Science.gov (United States)

Moser, Joanna J; Fritzler, Marvin J

2010-10-18

GW/P bodies are cytoplasmic ribonucleoprotein-rich foci involved in microRNA (miRNA)-mediated messenger RNA (mRNA) silencing and degradation. The mRNA regulatory functions within GW/P bodies are mediated by GW182 and its binding partner hAgo2 that bind miRNA in the RNA-induced silencing complex (RISC). To date there are no published reports of the profile of miRNA and mRNA targeted to the RISC or a comparison of the RISC-specific miRNA/mRNA profile differences in malignant and non-malignant cells. RISC mRNA and miRNA components were profiled by microarray analysis of malignant human U-87 astrocytoma cells and its non-malignant counterpart, primary human astrocytes. Total cell RNA as well as RNA from immunoprecipitated RISC was analyzed. The novel findings were fourfold: (1) miRNAs were highly enriched in astrocyte RISC compared to U-87 astrocytoma RISC, (2) astrocytoma and primary astrocyte cells each contained unique RISC miRNA profiles as compared to their respective cellular miRNA profiles, (3) miR-195, 10b, 29b, 19b, 34a and 455-3p levels were increased and the miR-181b level was decreased in U-87 astrocytoma RISC as compared to astrocyte RISC, and (4) the RISC contained decreased levels of mRNAs in primary astrocyte and U-87 astrocytoma cells. The observation that miR-34a and miR-195 levels were increased in the RISC of U-87 astrocytoma cells suggests an oncogenic role for these miRNAs. Differential regulation of mRNAs by specific miRNAs is evidenced by the observation that three miR34a-targeted mRNAs and two miR-195-targeted mRNAs were downregulated while one miR-195-targeted mRNA was upregulated. Biological pathway analysis of RISC mRNA components suggests that the RISC plays a pivotal role in malignancy and other conditions. This study points to the importance of the RISC and ultimately GW/P body composition and function in miRNA and mRNA deregulation in astrocytoma cells and possibly in other malignancies.

The microRNA and messengerRNA profile of the RNA-induced silencing complex in human primary astrocyte and astrocytoma cells.

Directory of Open Access Journals (Sweden)

Joanna J Moser

2010-10-01

Full Text Available GW/P bodies are cytoplasmic ribonucleoprotein-rich foci involved in microRNA (miRNA-mediated messenger RNA (mRNA silencing and degradation. The mRNA regulatory functions within GW/P bodies are mediated by GW182 and its binding partner hAgo2 that bind miRNA in the RNA-induced silencing complex (RISC. To date there are no published reports of the profile of miRNA and mRNA targeted to the RISC or a comparison of the RISC-specific miRNA/mRNA profile differences in malignant and non-malignant cells.RISC mRNA and miRNA components were profiled by microarray analysis of malignant human U-87 astrocytoma cells and its non-malignant counterpart, primary human astrocytes. Total cell RNA as well as RNA from immunoprecipitated RISC was analyzed. The novel findings were fourfold: (1 miRNAs were highly enriched in astrocyte RISC compared to U-87 astrocytoma RISC, (2 astrocytoma and primary astrocyte cells each contained unique RISC miRNA profiles as compared to their respective cellular miRNA profiles, (3 miR-195, 10b, 29b, 19b, 34a and 455-3p levels were increased and the miR-181b level was decreased in U-87 astrocytoma RISC as compared to astrocyte RISC, and (4 the RISC contained decreased levels of mRNAs in primary astrocyte and U-87 astrocytoma cells.The observation that miR-34a and miR-195 levels were increased in the RISC of U-87 astrocytoma cells suggests an oncogenic role for these miRNAs. Differential regulation of mRNAs by specific miRNAs is evidenced by the observation that three miR34a-targeted mRNAs and two miR-195-targeted mRNAs were downregulated while one miR-195-targeted mRNA was upregulated. Biological pathway analysis of RISC mRNA components suggests that the RISC plays a pivotal role in malignancy and other conditions. This study points to the importance of the RISC and ultimately GW/P body composition and function in miRNA and mRNA deregulation in astrocytoma cells and possibly in other malignancies.

Cancer-Related Triplets of mRNA-lncRNA-miRNA Revealed by Integrative Network in Uterine Corpus Endometrial Carcinoma

Directory of Open Access Journals (Sweden)

Chenglin Liu

2017-01-01

Full Text Available The regulation of transcriptome expression level is a complex process involving multiple-level interactions among molecules such as protein coding RNA (mRNA, long noncoding RNA (lncRNA, and microRNA (miRNA, which are essential for the transcriptome stability and maintenance and regulation of body homeostasis. The availability of multilevel expression data enables a comprehensive view of the regulatory network. In this study, we analyzed the coding and noncoding gene expression profiles of 301 patients with uterine corpus endometrial carcinoma (UCEC. A new method was proposed to construct a genome-wide integrative network based on variance inflation factor (VIF regression method. The cross-regulation relations of mRNA, lncRNA, and miRNA were then selected based on clique-searching algorithm from the network, when any two molecules of the three were shown as interacting according to the integrative network. Such relation, which we call the mRNA-lncRNA-miRNA triplet, demonstrated the complexity in transcriptome regulation process. Finally, six UCEC-related triplets were selected in which the mRNA participates in endometrial carcinoma pathway, such as CDH1 and TP53. The multi-type RNAs are proved to be cross-regulated as to each of the six triplets according to literature. All the triplets demonstrated the association with the initiation and progression of UCEC. Our method provides a comprehensive strategy for the investigation of transcriptome regulation mechanism.

Viral RNA polymerase scanning and the gymnastics of Sendai virus RNA synthesis

International Nuclear Information System (INIS)

Kolakofsky, Daniel; Le Mercier, Philippe; Iseni, Frederic; Garcin, Dominique

2004-01-01

mRNA synthesis from nonsegmented negative-strand RNA virus (NNV) genomes is unique in that the genome RNA is embedded in an N protein assembly (the nucleocapsid) and the viral RNA polymerase does not dissociate from the template after release of each mRNA, but rather scans the genome RNA for the next gene-start site. A revised model for NNV RNA synthesis is presented, in which RNA polymerase scanning plays a prominent role. Polymerase scanning of the template is known to occur as the viral transcriptase negotiates gene junctions without falling off the template

On RNA-RNA interaction structures of fixed topological genus.

Science.gov (United States)

Fu, Benjamin M M; Han, Hillary S W; Reidys, Christian M

2015-04-01

Interacting RNA complexes are studied via bicellular maps using a filtration via their topological genus. Our main result is a new bijection for RNA-RNA interaction structures and a linear time uniform sampling algorithm for RNA complexes of fixed topological genus. The bijection allows to either reduce the topological genus of a bicellular map directly, or to lose connectivity by decomposing the complex into a pair of single stranded RNA structures. Our main result is proved bijectively. It provides an explicit algorithm of how to rewire the corresponding complexes and an unambiguous decomposition grammar. Using the concept of genus induction, we construct bicellular maps of fixed topological genus g uniformly in linear time. We present various statistics on these topological RNA complexes and compare our findings with biological complexes. Furthermore we show how to construct loop-energy based complexes using our decomposition grammar. Copyright © 2015 Elsevier Inc. All rights reserved.

Solid nano-in-nanoparticles for potential delivery of siRNA.

Science.gov (United States)

Amsalem, Orit; Nassar, Taher; Benhamron, Sandrine; Lazarovici, Philip; Benita, Simon; Yavin, Eylon

2017-07-10

siRNA-based therapeutics possess great potential to treat a wide variety of genetic disorders. However, they suffer from low cellular uptake and short half-lives in blood circulation; issues that remain to be addressed. This work is, to the best of our knowledge, the first to report the production of solid nano-in-nanoparticles, termed double nano carriers (DNCs) by means of the innovative technology of nano spray drying. DNCs (with a median size of 580-770nm) were produced by spraying at low temperatures (50°C) to prevent damage to heat-sensitive biomacromolecules like siRNA. DNCs consisting of Poly (d,l-lactide-co-glycolide) used as a wall material, encapsulating 20% human serum albumin primary nanoparticles (PNPs) loaded with siRNA, were obtained as a dry nanoparticulate powder with smooth spherical surfaces and a unique inner morphology. Incubation of pegylated or non-pegylated DNCs under sink conditions at 37°C, elicited a controlled release profile of the siRNA for up to 12 or 24h, respectively, with a minimal burst effect. Prolonged incubation of pegylated DNCs loaded with active siRNA (anti EGFR) in an A549 epithelial cell culture monolayer did not induce any apparent cytotoxicity. A slow degradation of the internalized DNCs by the cells was also observed resulting in the progressive release of the siRNA for up to 6days, as corroborated by laser confocal microscopy. The structural integrity and silencing activity of the double encapsulated siRNA were fully preserved, as demonstrated by HPLC, gel electrophoresis, and potent RNAi activity of siRNA extracted from DNCs. These results demonstrate the potential use of DNCs as a nano drug delivery system for systemic administration and controlled release of siRNA and potentially other sensitive bioactive macromolecules. Copyright © 2016 Elsevier B.V. All rights reserved.

Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them

Science.gov (United States)

Leppek, Kathrin; Das, Rhiju; Barna, Maria

2017-01-01

RNA molecules can fold into intricate shapes that can provide an additional layer of control of gene expression beyond that of their sequence. In this Review, we discuss the current mechanistic understanding of structures in 5′ untranslated regions (UTRs) of eukaryotic mRNAs and the emerging methodologies used to explore them. These structures may regulate cap-dependent translation initiation through helicase-mediated remodelling of RNA structures and higher-order RNA interactions, as well as cap-independent translation initiation through internal ribosome entry sites (IRESs), mRNA modifications and other specialized translation pathways. We discuss known 5′ UTR RNA structures and how new structure probing technologies coupled with prospective validation, particularly compensatory mutagenesis, are likely to identify classes of structured RNA elements that shape post-transcriptional control of gene expression and the development of multicellular organisms. PMID:29165424

Changes in rRNA levels during stress invalidates results from mRNA blotting: Fluorescence in situ rRNA hybridization permits renormalization for estimation of cellular mRNA levels

DEFF Research Database (Denmark)

Hansen, M.C.; Nielsen, A.K.; Molin, Søren

2001-01-01

obtained by these techniques are compared between experiments in which differences in growth rates, strains, or stress treatments occur, the normalization procedure may have a significant impact on the results. In this report we present a solution to the normalization problem in RNA slot blotting...... the relative level of rRNA per cell, and slot blotting to rRNA probes, which estimates the level of rRNA per extracted total RNA, the amount of RNA per cell was calculated in a series of heat shock experiments with the gram-positive bacterium Lactococcus lactis. It was found that the level of rRNA per cell...... decreased to 30% in the course of the heat shock. This lowered ribosome level led to a decrease in the total RNA content, resulting in a gradually increasing overestimation of the mRNA levels throughout the experiment. Using renormalized cellular mRNA levels, the HrcA-mediated regulation of the genes...

Towards annotating the plant epigenome: the Arabidopsis thaliana small RNA locus map.

Science.gov (United States)

Hardcastle, Thomas J; Müller, Sebastian Y; Baulcombe, David C

2018-04-20

Based on 98 public and internal small RNA high throughput sequencing libraries, we mapped small RNAs to the genome of the model organism Arabidopsis thaliana and defined loci based on their expression using an empirical Bayesian approach. The resulting loci were subsequently classified based on their genetic and epigenetic context as well as their expression properties. We present the results of this classification, which broadly conforms to previously reported divisions between transcriptional and post-transcriptional gene silencing small RNAs, and to PolIV and PolV dependencies. However, we are able to demonstrate the existence of further subdivisions in the small RNA population of functional significance. Moreover, we present a framework for similar analyses of small RNA populations in all species.

RNA-Catalyzed Polymerization and Replication of RNA

Science.gov (United States)

Horning, D. P.; Samantha, B.; Tjhung, K. F.; Joyce, G. F.

2017-07-01

In an effort to reconstruct RNA-based life, in vitro evolution was used to obtain an RNA polymerase ribozyme that can synthesize a variety of complex functional RNAs and can catalyze the exponential amplification of short RNAs.

microRNA-independent recruitment of Argonaute 1 to nanos mRNA through the Smaug RNA-binding protein

OpenAIRE

Pinder, Benjamin D; Smibert, Craig A

2012-01-01

Argonaute 1 directly interacts with the RNA binding protein Smaug in Drosophila, is thereby recruited to the Smaug target nanos mRNA and is required for Smaug-mediated translational repression of the nanos mRNA.

5S rRNA gene arrangements in protists: a case of nonadaptive evolution.

Science.gov (United States)

Drouin, Guy; Tsang, Corey

2012-06-01

Given their high copy number and high level of expression, one might expect that both the sequence and organization of eukaryotic ribosomal RNA genes would be conserved during evolution. Although the organization of 18S, 5.8S and 28S ribosomal RNA genes is indeed relatively well conserved, that of 5S rRNA genes is much more variable. Here, we review the different types of 5S rRNA gene arrangements which have been observed in protists. This includes linkages to the other ribosomal RNA genes as well as linkages to ubiquitin, splice-leader, snRNA and tRNA genes. Mapping these linkages to independently derived phylogenies shows that these diverse linkages have repeatedly been gained and lost during evolution. This argues against such linkages being the primitive condition not only in protists but also in other eukaryote species. Because the only characteristic the diverse genes with which 5S rRNA genes are found linked with is that they are tandemly repeated, these arrangements are unlikely to provide any selective advantage. Rather, the observed high variability in 5S rRNA genes arrangements is likely the result of the fact that 5S rRNA genes contain internal promoters, that these genes are often transposed by diverse recombination mechanisms and that these new gene arrangements are rapidly homogenized by unequal crossingovers and/or by gene conversions events in species with short generation times and frequent founder events.

TargetRNA: a tool for predicting targets of small RNA action in bacteria

OpenAIRE

Tjaden, Brian

2008-01-01

Many small RNA (sRNA) genes in bacteria act as posttranscriptional regulators of target messenger RNAs. Here, we present TargetRNA, a web tool for predicting mRNA targets of sRNA action in bacteria. TargetRNA takes as input a genomic sequence that may correspond to an sRNA gene. TargetRNA then uses a dynamic programming algorithm to search each annotated message in a specified genome for mRNAs that evince basepair-binding potential to the input sRNA sequence. Based on the calculated basepair-...

The modification of siRNA with 3' cholesterol to increase nuclease protection and suppression of native mRNA by select siRNA polyplexes.

Science.gov (United States)

Ambardekar, Vishakha V; Han, Huai-Yun; Varney, Michelle L; Vinogradov, Serguei V; Singh, Rakesh K; Vetro, Joseph A

2011-02-01

Polymer-siRNA complexes (siRNA polyplexes) are being actively developed to improve the therapeutic application of siRNA. A major limitation for many siRNA polyplexes, however, is insufficient mRNA suppression. Given that modifying the sense strand of siRNA with 3' cholesterol (chol-siRNA) increases the activity of free nuclease-resistant siRNA in vitro and in vivo, we hypothesized that complexation of chol-siRNA can increase mRNA suppression by siRNA polyplexes. In this study, the characteristics and siRNA activity of self assembled polyplexes formed with chol-siRNA or unmodified siRNA were compared using three types of conventional, positively charged polymers: (i) biodegradable, cross-linked nanogels (BDNG) (ii) graft copolymers (PEI-PEG), and (iii) linear block copolymers (PLL10-PEG, and PLL50-PEG). Chol-siRNA did not alter complex formation or the resistance of polyplexes to siRNA displacement by heparin but increased nuclease protection by BDNG, PLL10-PEG, and PLL50-PEG polyplexes over polyplexes with unmodified siRNA. Chol-CYPB siRNA increased suppression of native CYPB mRNA in mammary microvascular endothelial cells (MVEC) by BDNG polyplexes (35%) and PLL10-PEG polyplexes (69%) over comparable CYPB siRNA polyplexes but had no effect on PEI-PEG or PLL50-PEG polyplexes. Overall, these results indicate that complexation of chol-siRNA increases nuclease protection and mRNA suppression by select siRNA polyplexes. These results also suggest that polycationic block length is an important factor in increasing mRNA suppression by PLL-PEG chol-siRNA polyplexes in mammary MVEC. Copyright © 2010 Elsevier Ltd. All rights reserved.

RNA versatility, flexibility, and thermostability for practice in RNA nanotechnology and biomedical applications.

Science.gov (United States)

Haque, Farzin; Pi, Fengmei; Zhao, Zhengyi; Gu, Shanqing; Hu, Haibo; Yu, Hang; Guo, Peixuan

2018-01-01

In recent years, RNA has attracted widespread attention as a unique biomaterial with distinct biophysical properties for designing sophisticated architectures in the nanometer scale. RNA is much more versatile in structure and function with higher thermodynamic stability compared to its nucleic acid counterpart DNA. Larger RNA molecules can be viewed as a modular structure built from a combination of many 'Lego' building blocks connected via different linker sequences. By exploiting the diversity of RNA motifs and flexibility of structure, varieties of RNA architectures can be fabricated with precise control of shape, size, and stoichiometry. Many structural motifs have been discovered and characterized over the years and the crystal structures of many of these motifs are available for nanoparticle construction. For example, using the flexibility and versatility of RNA structure, RNA triangles, squares, pentagons, and hexagons can be constructed from phi29 pRNA three-way-junction (3WJ) building block. This review will focus on 2D RNA triangles, squares, and hexamers; 3D and 4D structures built from basic RNA building blocks; and their prospective applications in vivo as imaging or therapeutic agents via specific delivery and targeting. Methods for intracellular cloning and expression of RNA molecules and the in vivo assembly of RNA nanoparticles will also be reviewed. WIREs RNA 2018, 9:e1452. doi: 10.1002/wrna.1452 This article is categorized under: RNA Methods > RNA Nanotechnology RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA in Disease and Development > RNA in Disease Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs. © 2017 Wiley Periodicals, Inc.

MicroRNA-target binding structures mimic microRNA duplex structures in humans.

Directory of Open Access Journals (Sweden)

Xi Chen

Full Text Available Traditionally, researchers match a microRNA guide strand to mRNA sequences using sequence comparisons to predict its potential target genes. However, many of the predictions can be false positives due to limitations in sequence comparison alone. In this work, we consider the association of two related RNA structures that share a common guide strand: the microRNA duplex and the microRNA-target binding structure. We have analyzed thousands of such structure pairs and found many of them share high structural similarity. Therefore, we conclude that when predicting microRNA target genes, considering just the microRNA guide strand matches to gene sequences may not be sufficient--the microRNA duplex structure formed by the guide strand and its companion passenger strand must also be considered. We have developed software to translate RNA binding structure into encoded representations, and we have also created novel automatic comparison methods utilizing such encoded representations to determine RNA structure similarity. Our software and methods can be utilized in the other RNA secondary structure comparisons as well.

TruSeq Stranded mRNA and Total RNA Sample Preparation Kits

Science.gov (United States)

Total RNA-Seq enabled by ribosomal RNA (rRNA) reduction is compatible with formalin-fixed paraffin embedded (FFPE) samples, which contain potentially critical biological information. The family of TruSeq Stranded Total RNA sample preparation kits provides a unique combination of unmatched data quality for both mRNA and whole-transcriptome analyses, robust interrogation of both standard and low-quality samples and workflows compatible with a wide range of study designs.

Primer-dependent and primer-independent initiation of double stranded RNA synthesis by purified arabidopsis RNA-dependent RNA polymerases RDR2 and RDR6

DEFF Research Database (Denmark)

Devert, Anthony; Fabre, Nicolas; Floris, Maina Huguette Joséphine

2015-01-01

) targeted by RNA silencing. The dsRNA is subsequently cleaved by the ribonuclease DICER-like into secondary small interfering RNAs (siRNAs) that reinforce and/or maintain the silenced state of the target RNA. Models of RNA silencing propose that RDRs could use primer-independent and primer......Cellular RNA-dependent RNA polymerases (RDRs) are fundamental components of RNA silencing in plants and many other eukaryotes. In Arabidopsis thaliana genetic studies have demonstrated that RDR2 and RDR6 are involved in the synthesis of double stranded RNA (dsRNA) from single stranded RNA (ssRNA......-dependent initiation to generate dsRNA from a transcript targeted by primary siRNA or microRNA (miRNA). However, the biochemical activities of RDR proteins are still partly understood. Here, we obtained active recombinant RDR2 and RDR6 in a purified form. We demonstrate that RDR2 and RDR6 have primer...

A Method to Predict the Structure and Stability of RNA/RNA Complexes.

Science.gov (United States)

Xu, Xiaojun; Chen, Shi-Jie

2016-01-01

RNA/RNA interactions are essential for genomic RNA dimerization and regulation of gene expression. Intermolecular loop-loop base pairing is a widespread and functionally important tertiary structure motif in RNA machinery. However, computational prediction of intermolecular loop-loop base pairing is challenged by the entropy and free energy calculation due to the conformational constraint and the intermolecular interactions. In this chapter, we describe a recently developed statistical mechanics-based method for the prediction of RNA/RNA complex structures and stabilities. The method is based on the virtual bond RNA folding model (Vfold). The main emphasis in the method is placed on the evaluation of the entropy and free energy for the loops, especially tertiary kissing loops. The method also uses recursive partition function calculations and two-step screening algorithm for large, complicated structures of RNA/RNA complexes. As case studies, we use the HIV-1 Mal dimer and the siRNA/HIV-1 mutant (T4) to illustrate the method.

Spontaneous reverse movement of mRNA-bound tRNA through the ribosome.

Science.gov (United States)

Konevega, Andrey L; Fischer, Niels; Semenkov, Yuri P; Stark, Holger; Wintermeyer, Wolfgang; Rodnina, Marina V

2007-04-01

During the translocation step of protein synthesis, a complex of two transfer RNAs bound to messenger RNA (tRNA-mRNA) moves through the ribosome. The reaction is promoted by an elongation factor, called EF-G in bacteria, which, powered by GTP hydrolysis, induces an open, unlocked conformation of the ribosome that allows for spontaneous tRNA-mRNA movement. Here we show that, in the absence of EF-G, there is spontaneous backward movement, or retrotranslocation, of two tRNAs bound to mRNA. Retrotranslocation is driven by the gain in affinity when a cognate E-site tRNA moves into the P site, which compensates the affinity loss accompanying the movement of peptidyl-tRNA from the P to the A site. These results lend support to the diffusion model of tRNA movement during translocation. In the cell, tRNA movement is biased in the forward direction by EF-G, which acts as a Brownian ratchet and prevents backward movement.

Long-term survivability of riprap for armoring uranium-mill tailings and covers: a literature review. [203 references

Energy Technology Data Exchange (ETDEWEB)

Lindsey, C.G.; Long, L.W.; Begej, C.W.

1982-06-01

Pacific Northwest Laboratory (PNL) is investigating the use of a rock armoring blanket (riprap) to mitigate wind and water erosion of an earthen radon suppression cover applied to uranium mill tailings. Because the radon suppression cover and the tailings must remain intact for up to 1000 years or longer, the riprap must withstand natural weathering forces. This report is a review of information on rock weathering and riprap durability. Chemical and physical weathering processes, rock characteristics related to durability, climatic conditions affecting the degree and rate of weathering, and testing procedures used to measure weathering susceptibilities have been reviewed. Sampling and testing techniques, as well as analyses of physical and chemical weathering susceptibilities, are necessary to evaluate rock durability. Many potential riprap materials may not be able to survive 1000 years of weathering. Available techniques for durability testing cannot adequately predict rock durability for the 1000-year period because they do not consider the issue of time (i.e., how long must riprap remain stable). This report includes an Appendix, which discusses rock weathering, written by Dr. Richard Jahns of Stanford University.

A New Class of SINEs with snRNA Gene-Derived Heads.

Science.gov (United States)

Kojima, Kenji K

2015-05-27

Eukaryotic genomes are colonized by various transposons including short interspersed elements (SINEs). The 5' region (head) of the majority of SINEs is derived from one of the three types of RNA genes--7SL RNA, transfer RNA (tRNA), or 5S ribosomal RNA (rRNA)--and the internal promoter inside the head promotes the transcription of the entire SINEs. Here I report a new group of SINEs whose heads originate from either the U1 or U2 small nuclear RNA gene. These SINEs, named SINEU, are distributed among crocodilians and classified into three families. The structures of the SINEU-1 subfamilies indicate the recurrent addition of a U1- or U2-derived sequence onto the 5' end of SINEU-1 elements. SINEU-1 and SINEU-3 are ancient and shared among alligators, crocodiles, and gharials, while SINEU-2 is absent in the alligator genome. SINEU-2 is the only SINE family that was active after the split of crocodiles and gharials. All SINEU families, especially SINEU-3, are preferentially inserted into a family of Mariner DNA transposon, Mariner-N4_AMi. A group of Tx1 non-long terminal repeat retrotransposons designated Tx1-Mar also show target preference for Mariner-N4_AMi, indicating that SINEU was mobilized by Tx1-Mar. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Platelet RNA as a circulating biomarker trove for cancer diagnostics.

Science.gov (United States)

Best, M G; Vancura, A; Wurdinger, T

2017-07-01

Platelets are multifunctional cell fragments, circulating in blood in high abundance. Platelets assist in thrombus formation, sensing of pathogens entering the blood stream, signaling to immune cells, releasing vascular remodeling factors, and, negatively, enhancing cancer metastasis. Platelets are 'educated' by their environment, including in patients with cancer. Cancer cells appear to initiate intraplatelet signaling, resulting in splicing of platelet pre-mRNAs, and enhance secretion of cytokines. Platelets can induce leukocyte and endothelial cell modeling factors, for example, through adenine nucleotides (ATP), thereby facilitating extravasation of cancer cells. Besides releasing factors, platelets can also sequester RNAs and proteins released by cancer cells. Thus, platelets actively respond to queues from local and systemic conditions, thereby altering their transcriptome and molecular content. Platelets contain a rich repertoire of RNA species, including mRNAs, small non-coding RNAs and circular RNAs; although studies regarding the functionality of the various platelet RNA species require more attention. Recent advances in high-throughput characterization of platelet mRNAs revealed 10 to > 1000 altered mRNAs in platelets in the presence of disease. Hence, platelet RNA appears to be dynamically affected by pathological conditions, thus possibly providing opportunities to use platelet RNA as diagnostic, prognostic, predictive, or monitoring biomarkers. In this review, we cover the literature regarding the platelet RNA families, processing of platelet RNAs, and the potential application of platelet RNA as disease biomarkers. © 2017 International Society on Thrombosis and Haemostasis.

RNA processing and ribonucleoprotein assembly studied in vivo by RNA transfection

International Nuclear Information System (INIS)

Kleinschmidt, A.M.; Pederson, T.

1990-01-01

The authors present a method for studying RNA processing and ribonucleoprotein assembly in vivo, by using RNA synthesized in vitro. SP6-transcribed 32 P-labeled U2 small nuclear RNA precursor molecules were introduced into cultured human 293 cells by calcium phosphate-mediated uptake, as in standard DNA transfection experiments. RNase protection mapping demonstrated that the introduced pre-U2 RNA underwent accurate 3' end processing. The introduced U2 RNA was assembled into ribonucleoprotein particles that reacted with an antibody specific for proteins known to be associated with the U2 small nuclear ribonucleoprotein particle. The 3' end-processed, ribonucleoprotein-assembled U2 RNA accumulated in the nuclear fraction. When pre-U2 RNA with a 7-methylguanosine group at the 5' end was introduced into cells, it underwent conversion to a 2,2,7-trimethylguanosine cap structure, a characteristic feature of the U-small nuclear RNAs. Pre-U2 RNA introduced with an adenosine cap (Ap-ppG) also underwent processing, small nuclear ribonucleoprotein assembly, and nuclear accumulation, establishing that a methylated guanosine cap structure is not required for these steps in U2 small nuclear ribonucleprotein biosynthesis. Beyond its demonstrated usefulness in the study of small nuclear ribonucleoprotein biosynthesis, RNA transfection may be of general applicability to the investigation of eukaryotic RNA processing in vivo and may also offer opportunities for introducing therapeutically targeted RNAs (ribozymes or antisense RNA) into cells

RNA precursor pool metabolism and RNA synthesis in X-irradiated Tetrahymena

International Nuclear Information System (INIS)

Stephens, R.E.; Paul, I.J.; Zimmerman, A.M.

1976-01-01

The incorporation of a radioactive RNA precursor ( 3 H-uridine) has been used in many studies as an index for measuring the synthesis of RNA, yet there is a distinct possibility that the results so obtained were significantly influenced by radiation-induced effects on the metabolism of this precursor into UTP (the primary immediate precursor of RNA) before its incorporation into RNA. A direct examination was therefore undertaken of the effects of X-irradiation on the metabolism of 3 H-uridine and its relationship to RNA synthesis as determined by incorporation. X-irradiation of logarithmically growing Tetrahymena pyriformis caused a dose-dependent depression of total cellular RNA synthesis. Ribosomal RNA (which comprises about 80 per cent of total cellular RNA) synthesis was also depressed by X-irradiation in a dose-dependent manner. Measurements of the levels of radioactivity present in the UTP precursor pool of both irradiated and unirradiated cells were obtained by means of DEAE-cellulose column chromatography of the extracted free nucleotides. Metabolism of 3 H-uridine into UMP, UDP and UTP was depressed by 40%, 26% and 27% respectively, whereas incorporation of 3 H-uridine into RNA was depressed by 77%. The results show that about one-third of the observed (apparent) depression in RNA synthesis was due to radiation-induced effects on the precursor pool, and the remaining two-thirds due to some definite effect of radiation at the transcription level leading to depressed synthesis of RNA. (U.K.)

Combining miRNA and mRNA Expression Profiles in Wilms Tumor Subtypes

Directory of Open Access Journals (Sweden)

Nicole Ludwig

2016-03-01

Full Text Available Wilms tumor (WT is the most common childhood renal cancer. Recent findings of mutations in microRNA (miRNA processing proteins suggest a pivotal role of miRNAs in WT genesis. We performed miRNA expression profiling of 36 WTs of different subtypes and four normal kidney tissues using microarrays. Additionally, we determined the gene expression profile of 28 of these tumors to identify potentially correlated target genes and affected pathways. We identified 85 miRNAs and 2107 messenger RNAs (mRNA differentially expressed in blastemal WT, and 266 miRNAs and 1267 mRNAs differentially expressed in regressive subtype. The hierarchical clustering of the samples, using either the miRNA or mRNA profile, showed the clear separation of WT from normal kidney samples, but the miRNA pattern yielded better separation of WT subtypes. A correlation analysis of the deregulated miRNA and mRNAs identified 13,026 miRNA/mRNA pairs with inversely correlated expression, of which 2844 are potential interactions of miRNA and their predicted mRNA targets. We found significant upregulation of miRNAs-183, -301a/b and -335 for the blastemal subtype, and miRNAs-181b, -223 and -630 for the regressive subtype. We found marked deregulation of miRNAs regulating epithelial to mesenchymal transition, especially in the blastemal subtype, and miRNAs influencing chemosensitivity, especially in regressive subtypes. Further research is needed to assess the influence of preoperative chemotherapy and tumor infiltrating lymphocytes on the miRNA and mRNA patterns in WT.

dPORE-miRNA: Polymorphic regulation of microRNA genes

KAUST Repository

Schmeier, Sebastian; Schaefer, Ulf; MacPherson, Cameron R.; Bajic, Vladimir B.

2011-01-01

Background: MicroRNAs (miRNAs) are short non-coding RNA molecules that act as post-transcriptional regulators and affect the regulation of protein-coding genes. Mostly transcribed by PolII, miRNA genes are regulated at the transcriptional level similarly to protein-coding genes. In this study we focus on human miRNAs. These miRNAs are involved in a variety of pathways and can affect many diseases. Our interest is on possible deregulation of the transcription initiation of the miRNA encoding genes, which is facilitated by variations in the genomic sequence of transcriptional control regions (promoters). Methodology: Our aim is to provide an online resource to facilitate the investigation of the potential effects of single nucleotide polymorphisms (SNPs) on miRNA gene regulation. We analyzed SNPs overlapped with predicted transcription factor binding sites (TFBSs) in promoters of miRNA genes. We also accounted for the creation of novel TFBSs due to polymorphisms not present in the reference genome. The resulting changes in the original TFBSs and potential creation of new TFBSs were incorporated into the Dragon Database of Polymorphic Regulation of miRNA genes (dPORE-miRNA). Conclusions: The dPORE-miRNA database enables researchers to explore potential effects of SNPs on the regulation of miRNAs. dPORE-miRNA can be interrogated with regards to: a/miRNAs (their targets, or involvement in diseases, or biological pathways), b/SNPs, or c/transcription factors. dPORE-miRNA can be accessed at http://cbrc.kaust.edu.sa/dpore and http://apps.sanbi.ac.za/dpore/. Its use is free for academic and non-profit users. © 2011 Schmeier et al.

dPORE-miRNA: Polymorphic regulation of microRNA genes

KAUST Repository

Schmeier, Sebastian

2011-02-04

Background: MicroRNAs (miRNAs) are short non-coding RNA molecules that act as post-transcriptional regulators and affect the regulation of protein-coding genes. Mostly transcribed by PolII, miRNA genes are regulated at the transcriptional level similarly to protein-coding genes. In this study we focus on human miRNAs. These miRNAs are involved in a variety of pathways and can affect many diseases. Our interest is on possible deregulation of the transcription initiation of the miRNA encoding genes, which is facilitated by variations in the genomic sequence of transcriptional control regions (promoters). Methodology: Our aim is to provide an online resource to facilitate the investigation of the potential effects of single nucleotide polymorphisms (SNPs) on miRNA gene regulation. We analyzed SNPs overlapped with predicted transcription factor binding sites (TFBSs) in promoters of miRNA genes. We also accounted for the creation of novel TFBSs due to polymorphisms not present in the reference genome. The resulting changes in the original TFBSs and potential creation of new TFBSs were incorporated into the Dragon Database of Polymorphic Regulation of miRNA genes (dPORE-miRNA). Conclusions: The dPORE-miRNA database enables researchers to explore potential effects of SNPs on the regulation of miRNAs. dPORE-miRNA can be interrogated with regards to: a/miRNAs (their targets, or involvement in diseases, or biological pathways), b/SNPs, or c/transcription factors. dPORE-miRNA can be accessed at http://cbrc.kaust.edu.sa/dpore and http://apps.sanbi.ac.za/dpore/. Its use is free for academic and non-profit users. © 2011 Schmeier et al.

Alterations in messenger RNA and small nuclear RNA metabolism resulting from fluorouracil incorporation

International Nuclear Information System (INIS)

Armstrong, R.D.; Cadman, E.C.

1985-01-01

Studies were completed to examine the effect of 5-fluorouracil (FUra) incorporation on messenger RNA (mRNA) and small molecular weight nuclear RNA (SnRNA) metabolism. Studies of mRNA were completed using cDNA-mRNA hybridization methods to specifically examine dihydrofolate reductase (DHFR) mRNA. C 3 -L5178Y murine leukemia cells which are gene-amplified for DHFR, were exposed to FUra for 6, 12 or 24 hr, and the nuclear and cytoplasmic levels of DHFR-mRNA determined by hybridization with 32 P-DHFR-cDNA. FUra produced a dose-dependent increase in nuclear DHFR-mRNA levels, while total cytoplasmic DHFR-mRNA levels appeared to be unchanged. To examine only mRNA synthesized during FUra exposure, cells were also treated concurrently with [ 3 H] cytidine, and the [ 3 H]mRNA-cDNA hybrids measured following S 1 -nuclease treatment. FUra produced a concentration-dependent increase in nascent nuclear DHFR-mRNA levels, and a decrease in nascent cytoplasmic DHFR-mRNAs levels. These results suggest that FUra produces either an inhibition of mRNA processing, or an inhibition of nuclear-cytoplasmic transport. Preliminary experiments to examine ATP-dependent mRNA transport were completed with isolated nuclei from cells treated with FUra for 1 or 24 hr and then pulse-labeled for 1 hr with [ 3 H] cytidine. The results demonstrate a FUra-concentration and time-dependent inhibition of ATP-mediated mRNA efflux

RNA decay by messenger RNA interferases

DEFF Research Database (Denmark)

Christensen-Dalsgaard, Mikkel; Overgaard, Martin; Winther, Kristoffer Skovbo

2008-01-01

Two abundant toxin-antitoxin (TA) gene families, relBE and mazEF, encode mRNA cleaving enzymes whose ectopic overexpression abruptly inhibits translation and thereby induces a bacteriostatic condition. Here we describe and discuss protocols for the overproduction, purification, and analysis of mR...... cleaving enzymes such as RelE of Escherichia coli and the corresponding antitoxin RelB. In particular, we describe a set of plasmid vectors useful for the detailed analysis of cleavage sites in model mRNAs.......Two abundant toxin-antitoxin (TA) gene families, relBE and mazEF, encode mRNA cleaving enzymes whose ectopic overexpression abruptly inhibits translation and thereby induces a bacteriostatic condition. Here we describe and discuss protocols for the overproduction, purification, and analysis of mRNA...

Thermal Stability of siRNA Modulates Aptamer- conjugated siRNA Inhibition

Directory of Open Access Journals (Sweden)

Alexey Berezhnoy

2012-01-01

Full Text Available Oligonucleotide aptamer-mediated in vivo cell targeting of small interfering RNAs (siRNAs is emerging as a useful approach to enhance the efficacy and reduce the adverse effects resulting from siRNA-mediated genetic interference. A current main impediment in aptamer-mediated siRNA targeting is that the activity of the siRNA is often compromised when conjugated to an aptamer, often requiring labor intensive and time consuming design and testing of multiple configurations to identify a conjugate in which the siRNA activity has not been significantly reduced. Here, we show that the thermal stability of the siRNA is an important parameter of siRNA activity in its conjugated form, and that siRNAs with lower melting temperature (Tm are not or are minimally affected when conjugated to the 3′ end of 2′F-pyrimidine-modified aptamers. In addition, the configuration of the aptamer-siRNA conjugate retains activity comparable with the free siRNA duplex when the passenger strand is co-transcribed with the aptamer and 3′ overhangs on the passenger strand are removed. The approach described in this paper significantly reduces the time and effort necessary to screening siRNA sequences that retain biological activity upon aptamer conjugation, facilitating the process of identifying candidate aptamer-siRNA conjugates suitable for in vivo testing.

Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures

Science.gov (United States)

Sloma, Michael F.; Mathews, David H.

2016-01-01

RNA secondary structure prediction is widely used to analyze RNA sequences. In an RNA partition function calculation, free energy nearest neighbor parameters are used in a dynamic programming algorithm to estimate statistical properties of the secondary structure ensemble. Previously, partition functions have largely been used to estimate the probability that a given pair of nucleotides form a base pair, the conditional stacking probability, the accessibility to binding of a continuous stretch of nucleotides, or a representative sample of RNA structures. Here it is demonstrated that an RNA partition function can also be used to calculate the exact probability of formation of hairpin loops, internal loops, bulge loops, or multibranch loops at a given position. This calculation can also be used to estimate the probability of formation of specific helices. Benchmarking on a set of RNA sequences with known secondary structures indicated that loops that were calculated to be more probable were more likely to be present in the known structure than less probable loops. Furthermore, highly probable loops are more likely to be in the known structure than the set of loops predicted in the lowest free energy structures. PMID:27852924

Cellular localization of transforming growth factor-alpha mRNA in rat forebrain.

Science.gov (United States)

Seroogy, K B; Lundgren, K H; Lee, D C; Guthrie, K M; Gall, C M

1993-05-01

The cellular localization of transforming growth factor-alpha (TGF alpha) mRNA in juvenile and adult rat forebrain was examined using in situ hybridization with a 35S-labeled cRNA probe. TGF alpha cRNA-labeled neuronal perikarya were distributed across many forebrain regions including the olfactory bulb, caudate-putamen, nucleus accumbens, olfactory tubercle, ventral pallidum, amygdala, hippocampal stratum granulosum and CA3 stratum pyramidale, and piriform, entorhinal, and retrosplenial cortices. TGF alpha cRNA-hybridizing cells were also localized to several thalamic nuclei and to the suprachiasmatic, dorsomedial, and ventromedial nuclei of the hypothalamus. In addition, labeled cells were present in regions of white matter including the corpus callosum, anterior commissure, internal and external capsules, optic tract, and lateral olfactory tract. Thus, both neurons and glia appear to synthesize TGF alpha in normal brain. Hybridization densities were greater in neuronal fields at 2 weeks of age compared with the adult, suggesting a role for TGF alpha in the development of several forebrain systems. Our results demonstrating the prominent and wide-spread expression of TGF alpha mRNA in forebrain, combined with the extremely low abundance of epidermal growth factor mRNA in brain, support the argument that TGF alpha is the principal endogenous ligand for the epidermal growth factor receptor in normal brain.

Update on Pneumocystis carinii f. sp. hominis Typing Based on Nucleotide Sequence Variations in Internal Transcribed Spacer Regions of rRNA Genes

Science.gov (United States)

Lee, Chao-Hung; Helweg-Larsen, Jannik; Tang, Xing; Jin, Shaoling; Li, Baozheng; Bartlett, Marilyn S.; Lu, Jang-Jih; Lundgren, Bettina; Lundgren, Jens D.; Olsson, Mats; Lucas, Sebastian B.; Roux, Patricia; Cargnel, Antonietta; Atzori, Chiara; Matos, Olga; Smith, James W.

1998-01-01

Pneumocystis carinii f. sp. hominis isolates from 207 clinical specimens from nine countries were typed based on nucleotide sequence variations in the internal transcribed spacer regions I and II (ITS1 and ITS2, respectively) of rRNA genes. The number of ITS1 nucleotides has been revised from the previously reported 157 bp to 161 bp. Likewise, the number of ITS2 nucleotides has been changed from 177 to 192 bp. The number of ITS1 sequence types has increased from 2 to 15, and that of ITS2 has increased from 3 to 14. The 15 ITS1 sequence types are designated types A through O, and the 14 ITS2 types are named types a through n. A total of 59 types of P. carinii f. sp. hominis were found in this study. PMID:9508304

Disruption of Specific RNA-RNA Interactions in a Double-Stranded RNA Virus Inhibits Genome Packaging and Virus Infectivity.

Science.gov (United States)

Fajardo, Teodoro; Sung, Po-Yu; Roy, Polly

2015-12-01

Bluetongue virus (BTV) causes hemorrhagic disease in economically important livestock. The BTV genome is organized into ten discrete double-stranded RNA molecules (S1-S10) which have been suggested to follow a sequential packaging pathway from smallest to largest segment during virus capsid assembly. To substantiate and extend these studies, we have investigated the RNA sorting and packaging mechanisms with a new experimental approach using inhibitory oligonucleotides. Putative packaging signals present in the 3'untranslated regions of BTV segments were targeted by a number of nuclease resistant oligoribonucleotides (ORNs) and their effects on virus replication in cell culture were assessed. ORNs complementary to the 3' UTR of BTV RNAs significantly inhibited virus replication without affecting protein synthesis. Same ORNs were found to inhibit complex formation when added to a novel RNA-RNA interaction assay which measured the formation of supramolecular complexes between and among different RNA segments. ORNs targeting the 3'UTR of BTV segment 10, the smallest RNA segment, were shown to be the most potent and deletions or substitution mutations of the targeted sequences diminished the RNA complexes and abolished the recovery of viable viruses using reverse genetics. Cell-free capsid assembly/RNA packaging assay also confirmed that the inhibitory ORNs could interfere with RNA packaging and further substitution mutations within the putative RNA packaging sequence have identified the recognition sequence concerned. Exchange of 3'UTR between segments have further demonstrated that RNA recognition was segment specific, most likely acting as part of the secondary structure of the entire genomic segment. Our data confirm that genome packaging in this segmented dsRNA virus occurs via the formation of supramolecular complexes formed by the interaction of specific sequences located in the 3' UTRs. Additionally, the inhibition of packaging in-trans with inhibitory ORNs

The Modification of siRNA with 3′ Cholesterol to Increase Nuclease Protection and Suppression of Native mRNA by Select siRNA Polyplexes

Science.gov (United States)

Ambardekar, Vishakha V.; Han, Huai-Yun; Varney, Michelle L.; Vinogradov, Serguei V.; Singh, Rakesh K.; Vetro, Joseph A.

2010-01-01

Polymer-siRNA complexes (siRNA polyplexes) are being actively developed to improve the therapeutic application of siRNA. A major limitation for many siRNA polyplexes, however, is insufficient mRNA suppression. Given that modifying the sense strand of siRNA with 3′ cholesterol (chol-siRNA) increases the activity of free nuclease-resistant siRNA in vitro and in vivo, we hypothesized that complexation of chol-siRNA can increase mRNA suppression by siRNA polyplexes. In this study, the characteristics and siRNA activity of self assembled polyplexes formed with chol-siRNA or unmodified siRNA were compared using three types of conventional, positively charged polymers: (i) biodegradable, cross-linked nanogels (BDNG) (ii) graft copolymers (PEI-PEG), and (iii) linear block copolymers (PLL10-PEG, and PLL50-PEG). Chol-siRNA did not alter complex formation or the resistance of polyplexes to siRNA displacement by heparin but increased nuclease protection by BDNG, PLL10-PEG, and PLL50-PEG polyplexes over polyplexes with unmodified siRNA. Chol-CYPB siRNA increased suppression of native CYPB mRNA in mammary microvascular endothelial cells (MVEC) by BDNG polyplexes (35%) and PLL10-PEG polyplexes (69%) over comparable CYPB siRNA polyplexes but had no effect on PEI-PEG or PLL50-PEG polyplexes. Overall, these results indicate that complexation of chol-siRNA increases nuclease protection and mRNA suppression by select siRNA polyplexes. These results also suggest that polycationic block length is an important factor in increasing mRNA suppression by PLL-PEG chol-siRNA polyplexes in mammary MVEC. PMID:21047680

RAID: a comprehensive resource for human RNA-associated (RNA–RNA/RNA–protein) interaction

Science.gov (United States)

Zhang, Xiaomeng; Wu, Deng; Chen, Liqun; Li, Xiang; Yang, Jinxurong; Fan, Dandan; Dong, Tingting; Liu, Mingyue; Tan, Puwen; Xu, Jintian; Yi, Ying; Wang, Yuting; Zou, Hua; Hu, Yongfei; Fan, Kaili; Kang, Juanjuan; Huang, Yan; Miao, Zhengqiang; Bi, Miaoman; Jin, Nana; Li, Kongning; Li, Xia; Xu, Jianzhen; Wang, Dong

2014-01-01

Transcriptomic analyses have revealed an unexpected complexity in the eukaryote transcriptome, which includes not only protein-coding transcripts but also an expanding catalog of noncoding RNAs (ncRNAs). Diverse coding and noncoding RNAs (ncRNAs) perform functions through interaction with each other in various cellular processes. In this project, we have developed RAID (http://www.rna-society.org/raid), an RNA-associated (RNA–RNA/RNA–protein) interaction database. RAID intends to provide the scientific community with all-in-one resources for efficient browsing and extraction of the RNA-associated interactions in human. This version of RAID contains more than 6100 RNA-associated interactions obtained by manually reviewing more than 2100 published papers, including 4493 RNA–RNA interactions and 1619 RNA–protein interactions. Each entry contains detailed information on an RNA-associated interaction, including RAID ID, RNA/protein symbol, RNA/protein categories, validated method, expressing tissue, literature references (Pubmed IDs), and detailed functional description. Users can query, browse, analyze, and manipulate RNA-associated (RNA–RNA/RNA–protein) interaction. RAID provides a comprehensive resource of human RNA-associated (RNA–RNA/RNA–protein) interaction network. Furthermore, this resource will help in uncovering the generic organizing principles of cellular function network. PMID:24803509

Seryl-tRNA Synthetases in Translation and Beyond

Directory of Open Access Journals (Sweden)

Marko Močibob

2016-06-01

Full Text Available For a long time seryl-tRNA synthetases (SerRSs stood as an archetypal, canonical aminoacyl-tRNA synthetases (aaRS, exhibiting only basic tRNA aminoacylation activity and with no moonlighting functions beyond protein biosynthesis. The picture has changed substantially in recent years after the discovery that SerRSs play an important role in antibiotic production and resistance and act as a regulatory factor in vascular development, as well as after the discovery of mitochondrial morphogenesis factor homologous to SerRS in insects. In this review we summarize the recent research results from our laboratory, which advance the understanding of seryl-tRNA synthetases and further paint the dynamic picture of unexpected SerRS activities. SerRS from archaeon Methanothermobacter thermautotrophicus was shown to interact with the large ribosomal subunit and it was postulated to contribute to a more efficient translation by the"tRNA channeling" hypothesis. Discovery of the atypical SerRS in a small number of methanogenic archaea led to the discovery of a new family of enzymes in numerous bacteria - amino acid:[carrier protein] ligases (aa:CP ligases. These SerRS homologues resigned tRNA aminoacylation activity, and instead adopted carrier proteins as the acceptors of activated amino acids. The crystal structure of the aa:CP ligase complex with the carrier protein revealed that the interactions between two macromolecules are incomparable to tRNA binding by the aaRS and consequently represent a true evolutionary invention. Kinetic investigations of SerRSs and the accuracy of amino acid selection revealed that SerRSs possess pre-transfer proofreading activity, challenging the widely accepted presumption that hydrolytic proofreading activity must reside in an additional, separate editing domain, not present in SerRSs. Finally, the plant tRNA serylation system is discussed, which is particularly interesting due to the fact that protein biosynthesis takes place

MicroRNA Expression Profiles in Cultured Human Fibroblasts in Space

Science.gov (United States)

Wu, Honglu; Lu, Tao; Jeevarajan, John; Rohde, Larry; Zhang, Ye

2014-01-01

Microgravity, or an altered gravity environment from the static 1g, has been shown to influence global gene expression patterns and protein levels in living organisms. However, it is unclear how these changes in gene and protein expressions are related to each other or are related to other factors regulating such changes. A different class of RNA, the small non-coding microRNA (miRNA), can have a broad effect on gene expression networks by mainly inhibiting the translation process. Previously, we investigated changes in the expression of miRNA and related genes under simulated microgravity conditions on the ground using the NASA invented bioreactor. In comparison to static 1 g, simulated microgravity altered a number of miRNAs in human lymphoblastoid cells. Pathway analysis with the altered miRNAs and RNA expressions revealed differential involvement of cell communication and catalytic activity, as well as immune response signaling and NGF activation of NF-kB pathways under simulated microgravity condition. The network analysis also identified several projected networks with c- Rel, ETS1 and Ubiquitin C as key factors. In a flight experiment on the International Space Station (ISS), we will investigate the effects of actual spaceflight on miRNA expressions in nondividing human fibroblast cells in mostly G1 phase of the cell cycle. A fibroblast is a type of cell that synthesizes the extracellular matrix and collagen, the structural framework for tissues, and plays a critical role in wound healing and other functions. In addition to miRNA expressions, we will investigate the effects of spaceflight on the cellular response to DNA damages from bleomycin treatment.

An armored-cable-based fiber Bragg grating sensor array for perimeter fence intrusion detection

Science.gov (United States)

Hao, Jianzhong; Dong, Bo; Varghese, Paulose; Phua, Jiliang; Foo, Siang Fook

2012-01-01

In this paper, an armored-cable-based optical fiber Bragg grating (FBG) sensor array, for perimeter fence intrusion detection, is demonstrated and some of the field trial results are reported. The field trial was conducted at a critical local installation in Singapore in December 2010. The sensor array was put through a series of both simulated and live intrusion scenarios to test the stability and suitability of operation in the local environmental conditions and to determine its capabilities in detecting and reporting these intrusions accurately to the control station. Such a sensor array can provide perimeter intrusion detection with fine granularity and preset pin-pointing accuracy. The various types of intrusions included aided or unaided climbs, tampering and cutting of the fence, etc. The unique sensor packaging structure provides high sensitivity, crush resistance and protection against rodents. It is also capable of resolving nuisance events such as rain, birds sitting on the fence or seismic vibrations. These sensors are extremely sensitive with a response time of a few seconds. They can be customized for a desired spatial resolution and pre-determined sensitivity. Furthermore, it is easy to cascade a series of such sensors to monitor and detect intrusion events over a long stretch of fence line. Such sensors can be applied to real-time intrusion detection for perimeter security, pipeline security and communications link security.

RegRNA: an integrated web server for identifying regulatory RNA motifs and elements

OpenAIRE

Huang, Hsi-Yuan; Chien, Chia-Hung; Jen, Kuan-Hua; Huang, Hsien-Da

2006-01-01

Numerous regulatory structural motifs have been identified as playing essential roles in transcriptional and post-transcriptional regulation of gene expression. RegRNA is an integrated web server for identifying the homologs of regulatory RNA motifs and elements against an input mRNA sequence. Both sequence homologs and structural homologs of regulatory RNA motifs can be recognized. The regulatory RNA motifs supported in RegRNA are categorized into several classes: (i) motifs in mRNA 5′-untra...

Establishment of lipofection for studying miRNA function in human adipocytes.

Science.gov (United States)

Enlund, Eveliina; Fischer, Simon; Handrick, René; Otte, Kerstin; Debatin, Klaus-Michael; Wabitsch, Martin; Fischer-Posovszky, Pamela

2014-01-01

miRNA dysregulation has recently been linked to human obesity and its related complications such as type 2 diabetes. In order to study miRNA function in human adipocytes, we aimed for the modulation of mature miRNA concentration in these cells. Adipocytes, however, tend to be resistant to transfection and there is often a need to resort to viral transduction or electroporation. Our objective therefore was to identify an efficient, non-viral transfection reagent capable of delivering small RNAs into these cells. To achieve this, we compared the efficiencies of three transfection agents, Lipofectamine 2000, ScreenFect A and BPEI 1.2 k in delivering fluorescent-labelled siRNA into human Simpson-Golabi-Behmel syndrome (SGBS) preadipocytes and adipocytes. Downregulation of a specific target gene in response to miRNA mimic overexpression was assayed in SGBS cells and also in ex vivo differentiated primary human adipocytes. Our results demonstrated that while all three transfection agents were able to internalize the oligos, only lipofection resulted in the efficient downregulation of a specific target gene both in SGBS cells and in primary human adipocytes. Lipofectamine 2000 outperformed ScreenFect A in preadipocytes, but in adipocytes the two reagents gave comparable results making ScreenFect A a notable new alternative for the gold standard Lipofectamine 2000.

Hydrophobically Modified siRNAs Silence Huntingtin mRNA in Primary Neurons and Mouse Brain

Directory of Open Access Journals (Sweden)

Julia F Alterman

2015-01-01

Full Text Available Applications of RNA interference for neuroscience research have been limited by a lack of simple and efficient methods to deliver oligonucleotides to primary neurons in culture and to the brain. Here, we show that primary neurons rapidly internalize hydrophobically modified siRNAs (hsiRNAs added directly to the culture medium without lipid formulation. We identify functional hsiRNAs targeting the mRNA of huntingtin, the mutation of which is responsible for Huntington's disease, and show that direct uptake in neurons induces potent and specific silencing in vitro. Moreover, a single injection of unformulated hsiRNA into mouse brain silences Htt mRNA with minimal neuronal toxicity. Thus, hsiRNAs embody a class of therapeutic oligonucleotides that enable simple and straightforward functional studies of genes involved in neuronal biology and neurodegenerative disorders in a native biological context.

Strategies underlying RNA silencing suppression by negative strand RNA viruses

NARCIS (Netherlands)

Hemmes, J.C.

2007-01-01

The research described in this thesis focused on the strategies of negative strand RNA viruses to counteract antiviral RNA silencing. In plants and insects, RNA silencing has been shown to act as a sequence specific antiviral defence mechanism that is characterised by the processing of double

Experimental study of thermal comfort on stab resistant body armor.

Science.gov (United States)

Ji, Tingchao; Qian, Xinming; Yuan, Mengqi; Jiang, Jinhui

2016-01-01

This research aims to investigate the impacts of exercise intensity and sequence on human physiology parameters and subjective thermal sensation when wearing stab resistant body armor under daily working conditions in China [26 and 31 °C, 45-50 % relative humidity (RH)], and to investigate on the relationship between subjective judgments and objective parameters. Eight male volunteers were recruited to complete 3 terms of exercises with different velocity set on treadmill for 90 min at 26 °C and 31 °C, 45-50 % RH. In Exercise 1 volunteers were seated during the test. In Exercise 2, volunteers walked with the velocity of 3 km/h in the first 45 min and 6 km/h in the left 45 min. In Exercise 3, volunteers walked with the velocity of 6 km/h in the first 45 min and 3 km/h in the left 45 min. The body core temperature, skin temperature and subjective judgments were recorded during the whole process. Analysis of variance was performed among all the tests. Individual discrepancy of Exercise 1 is larger than that of Exercise 2 and 3. On the premise of the same walking distance and environmental conditions, core temperature in Exercise 3 is about 0.2 °C lower than that in Exercise 2 in the end; and with the velocity decrease from 6 km/h to 3 km/h in the end, thermal tolerance of Exercise 3 is about 1 degree lower than that in Exercise 2. Skin temperatures of human trunk were at least 1 °C higher than that of limbs. Activity narrows the individual discrepancy on core temperature. Within experimental conditions, decreasing of intensity at last stage makes the core temperature lower and the whole process much tolerable. The core temperature is more sensitive to the external disturbance on the balance of the whole body, and it can reflect the subjective thermal sensation and physical exertion.

Diverging affinity of tospovirus RNA silencing suppressor proteins, NSs, for various RNA duplex molecules.

Science.gov (United States)

Schnettler, Esther; Hemmes, Hans; Huismann, Rik; Goldbach, Rob; Prins, Marcel; Kormelink, Richard

2010-11-01

The tospovirus NSs protein was previously shown to suppress the antiviral RNA silencing mechanism in plants. Here the biochemical analysis of NSs proteins from different tospoviruses, using purified NSs or NSs containing cell extracts, is described. The results showed that all tospoviral NSs proteins analyzed exhibited affinity to small double-stranded RNA molecules, i.e., small interfering RNAs (siRNAs) and micro-RNA (miRNA)/miRNA* duplexes. Interestingly, the NSs proteins from tomato spotted wilt virus (TSWV), impatiens necrotic spot virus (INSV), and groundnut ringspot virus (GRSV) also showed affinity to long double-stranded RNA (dsRNA), whereas tomato yellow ring virus (TYRV) NSs did not. The TSWV NSs protein was shown to be capable of inhibiting Dicer-mediated cleavage of long dsRNA in vitro. In addition, it suppressed the accumulation of green fluorescent protein (GFP)-specific siRNAs during coinfiltration with an inverted-repeat-GFP RNA construct in Nicotiana benthamiana. In vivo interference of TSWV NSs in the miRNA pathway was shown by suppression of an enhanced GFP (eGFP) miRNA sensor construct. The ability to stabilize miRNA/miRNA* by different tospovirus NSs proteins in vivo was demonstrated by increased accumulation and detection of both miRNA171c and miRNA171c* in tospovirus-infected N. benthamiana. All together, these data suggest that tospoviruses interfere in the RNA silencing pathway by sequestering siRNA and miRNA/miRNA* molecules before they are uploaded into their respective RNA-induced silencing complexes. The observed affinity to long dsRNA for only a subset of the tospoviruses studied is discussed in light of evolutional divergence and their ancestral relation to the animal-infecting members of the Bunyaviridae.

Initiation of translation in bacteria by a structured eukaryotic IRES RNA.

Science.gov (United States)

Colussi, Timothy M; Costantino, David A; Zhu, Jianyu; Donohue, John Paul; Korostelev, Andrei A; Jaafar, Zane A; Plank, Terra-Dawn M; Noller, Harry F; Kieft, Jeffrey S

2015-03-05

The central dogma of gene expression (DNA to RNA to protein) is universal, but in different domains of life there are fundamental mechanistic differences within this pathway. For example, the canonical molecular signals used to initiate protein synthesis in bacteria and eukaryotes are mutually exclusive. However, the core structures and conformational dynamics of ribosomes that are responsible for the translation steps that take place after initiation are ancient and conserved across the domains of life. We wanted to explore whether an undiscovered RNA-based signal might be able to use these conserved features, bypassing mechanisms specific to each domain of life, and initiate protein synthesis in both bacteria and eukaryotes. Although structured internal ribosome entry site (IRES) RNAs can manipulate ribosomes to initiate translation in eukaryotic cells, an analogous RNA structure-based mechanism has not been observed in bacteria. Here we report our discovery that a eukaryotic viral IRES can initiate translation in live bacteria. We solved the crystal structure of this IRES bound to a bacterial ribosome to 3.8 Å resolution, revealing that despite differences between bacterial and eukaryotic ribosomes this IRES binds directly to both and occupies the space normally used by transfer RNAs. Initiation in both bacteria and eukaryotes depends on the structure of the IRES RNA, but in bacteria this RNA uses a different mechanism that includes a form of ribosome repositioning after initial recruitment. This IRES RNA bridges billions of years of evolutionary divergence and provides an example of an RNA structure-based translation initiation signal capable of operating in two domains of life.

Evaluation of two main RNA-seq approaches for gene quantification in clinical RNA sequencing: polyA+ selection versus rRNA depletion.

Science.gov (United States)

Zhao, Shanrong; Zhang, Ying; Gamini, Ramya; Zhang, Baohong; von Schack, David

2018-03-19

To allow efficient transcript/gene detection, highly abundant ribosomal RNAs (rRNA) are generally removed from total RNA either by positive polyA+ selection or by rRNA depletion (negative selection) before sequencing. Comparisons between the two methods have been carried out by various groups, but the assessments have relied largely on non-clinical samples. In this study, we evaluated these two RNA sequencing approaches using human blood and colon tissue samples. Our analyses showed that rRNA depletion captured more unique transcriptome features, whereas polyA+ selection outperformed rRNA depletion with higher exonic coverage and better accuracy of gene quantification. For blood- and colon-derived RNAs, we found that 220% and 50% more reads, respectively, would have to be sequenced to achieve the same level of exonic coverage in the rRNA depletion method compared with the polyA+ selection method. Therefore, in most cases we strongly recommend polyA+ selection over rRNA depletion for gene quantification in clinical RNA sequencing. Our evaluation revealed that a small number of lncRNAs and small RNAs made up a large fraction of the reads in the rRNA depletion RNA sequencing data. Thus, we recommend that these RNAs are specifically depleted to improve the sequencing depth of the remaining RNAs.

Application of Live-Cell RNA Imaging Techniques to the Study of Retroviral RNA Trafficking

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Darrin V. Bann

2012-06-01

Full Text Available Retroviruses produce full-length RNA that serves both as a genomic RNA (gRNA, which is encapsidated into virus particles, and as an mRNA, which directs the synthesis of viral structural proteins. However, we are only beginning to understand the cellular and viral factors that influence trafficking of retroviral RNA and the selection of the RNA for encapsidation or translation. Live cell imaging studies of retroviral RNA trafficking have provided important insight into many aspects of the retrovirus life cycle including transcription dynamics, nuclear export of viral RNA, translational regulation, membrane targeting, and condensation of the gRNA during virion assembly. Here, we review cutting-edge techniques to visualize single RNA molecules in live cells and discuss the application of these systems to studying retroviral RNA trafficking.

RDE-4 preferentially binds long dsRNA and its dimerization is necessary for cleavage of dsRNA to siRNA.

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Parker, Greg S; Eckert, Debra M; Bass, Brenda L

2006-05-01

In organisms ranging from Arabidopsis to humans, Dicer requires dsRNA-binding proteins (dsRBPs) to carry out its roles in RNA interference (RNAi) and micro-RNA (miRNA) processing. In Caenorhabditis elegans, the dsRBP RDE-4 acts with Dicer during the initiation of RNAi, when long dsRNA is cleaved to small interfering RNAs (siRNAs). RDE-4 is not required in subsequent steps, and how RDE-4 distinguishes between long dsRNA and short siRNA is unclear. We report the first detailed analysis of RDE-4 binding, using purified recombinant RDE-4 and various truncated proteins. We find that, similar to other dsRBPs, RDE-4 is not sequence-specific. However, consistent with its in vivo roles, RDE-4 binds with higher affinity to long dsRNA. We also observe that RDE-4 is a homodimer in solution, and that the C-terminal domain of the protein is required for dimerization. Using extracts from wild-type and rde-4 mutant C. elegans, we show that the C-terminal dimerization domain is required for the production of siRNA. Our findings suggest a model for RDE-4 function during the initiation of RNAi.

Reconstruction and analysis of the lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in rheumatoid arthritis.

Science.gov (United States)

Jiang, Hui; Ma, Rong; Zou, Shubiao; Wang, Yongzhong; Li, Zhuqing; Li, Weiping

2017-06-01

Rheumatoid arthritis (RA) is an autoimmune disease with an unknown etiology, occurring in approximately 1.0% of general population. More and more studies have suggested that long non-coding RNAs (lncRNAs) could play important roles in various biological processes and be associated with the pathogenesis of different kinds of diseases including RA. Although a large number of lncRNAs have been found, our knowledge of their function and physiological/pathological significance is still in its infancy. In order to reveal functional lncRNAs and identify the key lncRNAs in RA, we reconstructed a global triple network based on the competitive endogenous RNA (ceRNA) theory using the data from National Center for Biotechnology Information Gene Expression Omnibus and our previous paper. Meanwhile, Gene Ontology (GO) and pathway analysis were performed using Cytoscape plug-in BinGO and Database for Annotation, Visualization, and Integration Discovery (DAVID), respectively. We found that the lncRNA-miRNA-mRNA network was composed of 7 lncRNA nodes, 90 mRNA nodes, 24 miRNA nodes, and 301 edges. The functional assay showed that 147 GO terms and 23 pathways were enriched. In addition, three lncRNAs (S5645.1, XR_006437.1, J01878) were highly related to RA, and therefore, were selected as key lncRNAs. This study suggests that specific lncRNAs are associated with the development of RA, and three lncRNAs (S5645.1, XR_006437.1, J01878) could be used as potential diagnostic biomarkers and therapeutic targets.

Cap-independent translation mechanism of red clover necrotic mosaic virus RNA2 differs from that of RNA1 and is linked to RNA replication.

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Mizumoto, Hiroyuki; Iwakawa, Hiro-Oki; Kaido, Masanori; Mise, Kazuyuki; Okuno, Tetsuro

2006-04-01

The genome of Red clover necrotic mosaic virus (RCNMV) in the genus Dianthovirus is divided into two RNA molecules of RNA1 and RNA2, which have no cap structure at the 5' end and no poly(A) tail at the 3' end. The 3' untranslated region (3' UTR) of RCNMV RNA1 contains an essential RNA element (3'TE-DR1), which is required for cap-independent translation. In this study, we investigated a cap-independent translational mechanism of RNA2 using a firefly luciferase (Luc) gene expression assay system in cowpea protoplasts and a cell-free lysate (BYL) prepared from evacuolated tobacco BY2 protoplasts. We were unable to detect cis-acting RNA sequences in RNA2 that can replace the function of a cap structure, such as the 3'TE-DR1 of RNA1. However, the uncapped reporter RNA2, RNA2-Luc, in which the Luc open reading frame (ORF) was inserted between the 5' UTR and the movement protein ORF, was effectively translated in the presence of p27 and p88 in protoplasts in which RNA2-Luc was replicated. Time course experiments in protoplasts showed that the translational activity of RNA2-Luc did not reflect the amount of RNA2. Mutations in cis-acting RNA replication elements of RNA2 abolished the cap-independent translational activity of RNA2-Luc, suggesting that the translational activity of RNA2-Luc is coupled to RNA replication. Our results show that the translational mechanism differs between two segmented genomic RNAs of RCNMV. We present a model in which only RNA2 that is generated de novo through the viral RNA replication machinery functions as mRNA for translation.

Analysis of RNA binding by the dengue virus NS5 RNA capping enzyme.

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Brittney R Henderson

Full Text Available Flaviviruses are small, capped positive sense RNA viruses that replicate in the cytoplasm of infected cells. Dengue virus and other related flaviviruses have evolved RNA capping enzymes to form the viral RNA cap structure that protects the viral genome and directs efficient viral polyprotein translation. The N-terminal domain of NS5 possesses the methyltransferase and guanylyltransferase activities necessary for forming mature RNA cap structures. The mechanism for flavivirus guanylyltransferase activity is currently unknown, and how the capping enzyme binds its diphosphorylated RNA substrate is important for deciphering how the flavivirus guanylyltransferase functions. In this report we examine how flavivirus NS5 N-terminal capping enzymes bind to the 5' end of the viral RNA using a fluorescence polarization-based RNA binding assay. We observed that the K(D for RNA binding is approximately 200 nM Dengue, Yellow Fever, and West Nile virus capping enzymes. Removal of one or both of the 5' phosphates reduces binding affinity, indicating that the terminal phosphates contribute significantly to binding. RNA binding affinity is negatively affected by the presence of GTP or ATP and positively affected by S-adensyl methoninine (SAM. Structural superpositioning of the dengue virus capping enzyme with the Vaccinia virus VP39 protein bound to RNA suggests how the flavivirus capping enzyme may bind RNA, and mutagenesis analysis of residues in the putative RNA binding site demonstrate that several basic residues are critical for RNA binding. Several mutants show differential binding to 5' di-, mono-, and un-phosphorylated RNAs. The mode of RNA binding appears similar to that found with other methyltransferase enzymes, and a discussion of diphosphorylated RNA binding is presented.

The Mounting process and dielectric tests of the Parque Caballero armored substation in SF6(220 Kv); Montaje y pruebas dielectricas de la estacion blindada en gas SF6 (220 kV) 'Parque Caballero'

Energy Technology Data Exchange (ETDEWEB)

Decoud, Carlos; Bobadilla, Alberto [ANDE - Administracion Nacional de Electricidad, Assuncion (Paraguay)

2001-07-01

This document approaches the aspects referring to the mounting and also dielectric tests for the Parque Caballero armored substation in SF6. This type of installation represents a innovation regarding substations in urban centres. The most relevant items in relation to the mounting process are shown in a summarized way, as well as the aspects related to dielectric tests executed during the substation commissioning.

Overview of methods in RNA nanotechnology: synthesis, purification, and characterization of RNA nanoparticles.

Science.gov (United States)

Haque, Farzin; Guo, Peixuan

2015-01-01

RNA nanotechnology encompasses the use of RNA as a construction material to build homogeneous nanostructures by bottom-up self-assembly with defined size, structure, and stoichiometry; this pioneering concept demonstrated in 1998 (Guo et al., Molecular Cell 2:149-155, 1998; featured in Cell) has emerged as a new field that also involves materials engineering and synthetic structural biology (Guo, Nature Nanotechnology 5:833-842, 2010). The field of RNA nanotechnology has skyrocketed over the last few years, as evidenced by the burst of publications in prominent journals on RNA nanostructures and their applications in nanomedicine and nanotechnology. Rapid advances in RNA chemistry, RNA biophysics, and RNA biology have created new opportunities for translating basic science into clinical practice. RNA nanotechnology holds considerable promise in this regard. Increased evidence also suggests that substantial part of the 98.5 % of human genome (Lander et al. Nature 409:860-921, 2001) that used to be called "junk DNA" actually codes for noncoding RNA. As we understand more on how RNA structures are related to function, we can fabricate synthetic RNA nanoparticles for the diagnosis and treatment of diseases. This chapter provides a brief overview of the field regarding the design, construction, purification, and characterization of RNA nanoparticles for diverse applications in nanotechnology and nanomedicince.

Molecular recognition of pyr mRNA by the Bacillus subtilis attenuation regulatory protein PyrR

Science.gov (United States)

Bonner, Eric R.; D’Elia, John N.; Billips, Benjamin K.; Switzer, Robert L.

2001-01-01

The pyrimidine nucleotide biosynthesis (pyr) operon in Bacillus subtilis is regulated by transcriptional attenuation. The PyrR protein binds in a uridine nucleotide-dependent manner to three attenuation sites at the 5′-end of pyr mRNA. PyrR binds an RNA-binding loop, allowing a terminator hairpin to form and repressing the downstream genes. The binding of PyrR to defined RNA molecules was characterized by a gel mobility shift assay. Titration indicated that PyrR binds RNA in an equimolar ratio. PyrR bound more tightly to the binding loops from the second (BL2 RNA) and third (BL3 RNA) attenuation sites than to the binding loop from the first (BL1 RNA) attenuation site. PyrR bound BL2 RNA 4–5-fold tighter in the presence of saturating UMP or UDP and 150- fold tighter with saturating UTP, suggesting that UTP is the more important co-regulator. The minimal RNA that bound tightly to PyrR was 28 nt long. Thirty-one structural variants of BL2 RNA were tested for PyrR binding affinity. Two highly conserved regions of the RNA, the terminal loop and top of the upper stem and a purine-rich internal bulge and the base pairs below it, were crucial for tight binding. Conserved elements of RNA secondary structure were also required for tight binding. PyrR protected conserved areas of the binding loop in hydroxyl radical footprinting experiments. PyrR likely recognizes conserved RNA sequences, but only if they are properly positioned in the correct secondary structure. PMID:11726695

The ViennaRNA web services.

Science.gov (United States)

Gruber, Andreas R; Bernhart, Stephan H; Lorenz, Ronny

2015-01-01

The ViennaRNA package is a widely used collection of programs for thermodynamic RNA secondary structure prediction. Over the years, many additional tools have been developed building on the core programs of the package to also address issues related to noncoding RNA detection, RNA folding kinetics, or efficient sequence design considering RNA-RNA hybridizations. The ViennaRNA web services provide easy and user-friendly web access to these tools. This chapter describes how to use this online platform to perform tasks such as prediction of minimum free energy structures, prediction of RNA-RNA hybrids, or noncoding RNA detection. The ViennaRNA web services can be used free of charge and can be accessed via http://rna.tbi.univie.ac.at.

RNA-SeQC: RNA-seq metrics for quality control and process optimization.

Science.gov (United States)

DeLuca, David S; Levin, Joshua Z; Sivachenko, Andrey; Fennell, Timothy; Nazaire, Marc-Danie; Williams, Chris; Reich, Michael; Winckler, Wendy; Getz, Gad

2012-06-01

RNA-seq, the application of next-generation sequencing to RNA, provides transcriptome-wide characterization of cellular activity. Assessment of sequencing performance and library quality is critical to the interpretation of RNA-seq data, yet few tools exist to address this issue. We introduce RNA-SeQC, a program which provides key measures of data quality. These metrics include yield, alignment and duplication rates; GC bias, rRNA content, regions of alignment (exon, intron and intragenic), continuity of coverage, 3'/5' bias and count of detectable transcripts, among others. The software provides multi-sample evaluation of library construction protocols, input materials and other experimental parameters. The modularity of the software enables pipeline integration and the routine monitoring of key measures of data quality such as the number of alignable reads, duplication rates and rRNA contamination. RNA-SeQC allows investigators to make informed decisions about sample inclusion in downstream analysis. In summary, RNA-SeQC provides quality control measures critical to experiment design, process optimization and downstream computational analysis. See www.genepattern.org to run online, or www.broadinstitute.org/rna-seqc/ for a command line tool.

Therapeutic miRNA and siRNA: Moving from Bench to Clinic as Next Generation Medicine

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Chiranjib Chakraborty

2017-09-01

Full Text Available In the past few years, therapeutic microRNA (miRNA and small interfering RNA (siRNA are some of the most important biopharmaceuticals that are in commercial space as future medicines. This review summarizes the patents of miRNA- and siRNA-based new drugs, and also provides a snapshot about significant biopharmaceutical companies that are investing for the therapeutic development of miRNA and siRNA molecules. An insightful view about individual siRNA and miRNA drugs has been depicted with their present status, which is gaining attention in the therapeutic landscape. The efforts of the biopharmaceuticals are discussed with the status of their preclinical and/or clinical trials. Here, some of the setbacks have been highlighted during the biopharmaceutical development of miRNA and siRNA as individual therapeutics. Finally, a snapshot is illustrated about pharmacokinetics, pharmacodynamics with absorption, distribution, metabolism, and excretion (ADME, which is the fundamental development process of these therapeutics, as well as the delivery system for miRNA- and siRNA-based drugs. Keywords: miRNA, siRNA, drug development

Expressed microRNA associated with high rate of egg production in chicken ovarian follicles.

Science.gov (United States)

Wu, N; Gaur, U; Zhu, Q; Chen, B; Xu, Z; Zhao, X; Yang, M; Li, D

2017-04-01

MicroRNA (miRNA) is a highly conserved class of small noncoding RNA about 19-24 nucleotides in length that function in a specific manner to post-transcriptionally regulate gene expression in organisms. Tissue miRNA expression studies have discovered a myriad of functions for miRNAs in various aspects, but a role for miRNAs in chicken ovarian tissue at 300 days of age has not hitherto been reported. In this study, we performed the first miRNA analysis of ovarian tissues in chickens with low and high rates of egg production using high-throughput sequencing. By comparing low rate of egg production chickens with high rate of egg production chickens, 17 significantly differentially expressed miRNAs were found (P chickens with high rates of egg production, suggesting that these miRNAs have an important role in ovary development and reproductive management of chicken. Furthermore, we uncovered that a significantly up-regulated miRNA-gga-miR-200a-3p-is ubiquitous in reproduction-regulation-related pathways. This miRNA may play a special central role in the reproductive management of chicken, and needs to be further studied for confirmation. © 2016 Stichting International Foundation for Animal Genetics.

Fragment-based modelling of single stranded RNA bound to RNA recognition motif containing proteins

Science.gov (United States)

de Beauchene, Isaure Chauvot; de Vries, Sjoerd J.; Zacharias, Martin

2016-01-01

Abstract Protein-RNA complexes are important for many biological processes. However, structural modeling of such complexes is hampered by the high flexibility of RNA. Particularly challenging is the docking of single-stranded RNA (ssRNA). We have developed a fragment-based approach to model the structure of ssRNA bound to a protein, based on only the protein structure, the RNA sequence and conserved contacts. The conformational diversity of each RNA fragment is sampled by an exhaustive library of trinucleotides extracted from all known experimental protein–RNA complexes. The method was applied to ssRNA with up to 12 nucleotides which bind to dimers of the RNA recognition motifs (RRMs), a highly abundant eukaryotic RNA-binding domain. The fragment based docking allows a precise de novo atomic modeling of protein-bound ssRNA chains. On a benchmark of seven experimental ssRNA–RRM complexes, near-native models (with a mean heavy-atom deviation of <3 Å from experiment) were generated for six out of seven bound RNA chains, and even more precise models (deviation < 2 Å) were obtained for five out of seven cases, a significant improvement compared to the state of the art. The method is not restricted to RRMs but was also successfully applied to Pumilio RNA binding proteins. PMID:27131381

Deep Sequencing Insights in Therapeutic shRNA Processing and siRNA Target Cleavage Precision.

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Denise, Hubert; Moschos, Sterghios A; Sidders, Benjamin; Burden, Frances; Perkins, Hannah; Carter, Nikki; Stroud, Tim; Kennedy, Michael; Fancy, Sally-Ann; Lapthorn, Cris; Lavender, Helen; Kinloch, Ross; Suhy, David; Corbau, Romu

2014-02-04

TT-034 (PF-05095808) is a recombinant adeno-associated virus serotype 8 (AAV8) agent expressing three short hairpin RNA (shRNA) pro-drugs that target the hepatitis C virus (HCV) RNA genome. The cytosolic enzyme Dicer cleaves each shRNA into multiple, potentially active small interfering RNA (siRNA) drugs. Using next-generation sequencing (NGS) to identify and characterize active shRNAs maturation products, we observed that each TT-034-encoded shRNA could be processed into as many as 95 separate siRNA strands. Few of these appeared active as determined by Sanger 5' RNA Ligase-Mediated Rapid Amplification of cDNA Ends (5-RACE) and through synthetic shRNA and siRNA analogue studies. Moreover, NGS scrutiny applied on 5-RACE products (RACE-seq) suggested that synthetic siRNAs could direct cleavage in not one, but up to five separate positions on targeted RNA, in a sequence-dependent manner. These data support an on-target mechanism of action for TT-034 without cytotoxicity and question the accepted precision of substrate processing by the key RNA interference (RNAi) enzymes Dicer and siRNA-induced silencing complex (siRISC).Molecular Therapy-Nucleic Acids (2014) 3, e145; doi:10.1038/mtna.2013.73; published online 4 February 2014.

Characterization of an internal ribosomal entry segment within the 5' leader of avian reticuloendotheliosis virus type A RNA and development of novel MLV-REV-based retroviral vectors.

Science.gov (United States)

López-Lastra, M; Gabus, C; Darlix, J L

1997-11-01

The murine leukemia virus (MLV)-related type C viruses constitute a major class of retroviruses that includes numerous endogenous and exogenous mammalian viruses and the related avian spleen necrosis virus (SNV). The MLV-related viruses possess a long and multifunctional 5' untranslated leader involved in key steps of the viral life cycle--splicing, translation, RNA dimerization, encapsidation, and reverse transcription. Recent studies have shown that the 5' leader of Friend murine leukemia virus and Moloney murine leukemia virus can direct cap independent translation of gag precursor proteins (Berlioz et al., 1995; Vagner et al., 1995b). These data, together with structural homology studies (Koning et al., 1992), prompted us to undertake a search for new internal ribosome entry segment (IRES) of retroviral origin. Here we describe an IRES element within the 5' leader of avian reticuloendotheliosis virus type A (REV-A) genomic RNA. Data show that the REV-A 5' IRES element maps downstream of the packaging/dimerization (E/DLS) sequence (Watanabe and Temin, 1982; Darlix et al., 1992) and the minimal IRES sequence appears to be within a 129 nt fragment (nucleotides 452-580) of the 5' leader, immediately upstream of the gag AUG codon. The REV-A IRES has been successfully utilized in the construction of novel high titer MLV-based retroviral vectors, containing one or more IRES elements of retroviral origin. These retroviral constructs, which represent a starting point for the design of novel vectors suitable for gene therapy, are also of interest as a model system of internal translation initiation and its possible regulation during development, cancer, or virus infection.

Efficient replication of the in vitro transcripts from cloned cDNA of tomato black ring virus satellite RNA requires the 48K satellite RNA-encoded protein.

Science.gov (United States)

Hemmer, O; Oncino, C; Fritsch, C

1993-06-01

Tomato black ring virus isolate L supports the multiplication of a large satellite RNA of 1376 nt which has no common features with the two genomic RNAs except for the terminal motif 5' VPg UUGAAAA and a 3' poly(A) tail. The TBRV sat-RNA contains an ORF for a protein of 48K which is translated both in vitro and in vivo. To determine the function of the 48K protein we have studied the effect of different mutations introduced in the ORF of the cDNA clone on the capacity of transcripts to multiply in Chenopodium quinoa plants or protoplasts when inoculated along with the genomic RNAs. Transcripts in which nucleotides have been substituted within the 5' proximal region of the ORF multiplied poorly even when the modification conserved the 48K protein sequence, suggesting that this portion of the ORF contains cis-acting RNA sequences. Transcripts with alterations in the internal region of the ORF retained their multiplication capacity provided the mutation did not destroy the ORF or modify the length of the protein expressed. The absence of multiplication in plants of transcripts unable to express the 48K protein and their inability to replicate in protoplasts suggest strongly that the sat-RNA translation product itself is implicated in the replication of sat-RNA.

Chitosan/Hyaluronic Acid Nanoparticles: Rational Design Revisited for RNA Delivery.

Science.gov (United States)

Lallana, Enrique; Rios de la Rosa, Julio M; Tirella, Annalisa; Pelliccia, Maria; Gennari, Arianna; Stratford, Ian J; Puri, Sanyogitta; Ashford, Marianne; Tirelli, Nicola

2017-07-03

Chitosan/hyaluronic acid (HA) nanoparticles can be used to deliver an RNA/DNA cargo to cells overexpressing HA receptors such as CD44. For these systems, unequivocal links have not been established yet between chitosan macromolecular (molecular weight; degree of deacetylation, i.e., charge density) and nanoparticle variables (complexation strength, i.e., stability; nucleic acid protection; internalization rate) on one hand, and transfection efficiency on the other hand. Here, we have focused on the role of avidity on transfection efficiency in the CD44-expressing HCT-116 as a cellular model; we have employed two differently sized payloads (a large luciferase-encoding mRNA and a much smaller anti-Luc siRNA), and a small library of chitosans (variable molecular weight and degree of deactylation). The RNA avidity for chitosan showed-as expected-an inverse relationship: higher avidity-higher polyplex stability-lower transfection efficiency. The avidity of chitosan for RNA appears to lead to opposite effects: higher avidity-higher polyplex stability but also higher transfection efficiency. Surprisingly, the best transfecting particles were those with the lowest propensity for RNA release, although this might be a misleading relationship: for example, the same macromolecular parameters that increase avidity can also boost chitosan's endosomolytic activity, with a strong enhancement in transfection. The performance of these nonviral vectors appears therefore difficult to predict simply on the basis of carrier- or payload-related variables, and a more holistic consideration of the journey of the nanoparticle, from cell uptake to cytosolic bioavailability of payload, is needed. It is also noteworthy that the nanoparticles used in this study showed optimal performance under slightly acidic conditions (pH 6.4), which is promising for applications in a tumoral extracellular environment. It is also worth pointing out that under these conditions we have for the first time

Saint-André-des-Eaux (Côtes-d’Armor : étude archéologique d’une église paroissiale et de ses peintures murales

Directory of Open Access Journals (Sweden)

Mathias Dupuis

2008-07-01

Full Text Available Le petit village de Saint-André-des-Eaux se situe dans les Côtes-d’Armor, à une dizaine de kilomètres au sud-est de Dinan. Les vestiges de l’ancienne église paroissiale et de son cimetière prennent place quelques centaines de mètres à l’écart du bourg (fig. 1, sur les abords boisés de l’étang de Bétineuc, un vaste plan d’eau artificiel créé dans les années 1970 afin d’assainir cette zone autrefois marécageuse. En effet, le contexte de plaine, la proximité de la Rance et le maillage resserré ...

Lowering the quantification limit of the QubitTM RNA HS assay using RNA spike-in.

Science.gov (United States)

Li, Xin; Ben-Dov, Iddo Z; Mauro, Maurizio; Williams, Zev

2015-05-06

RNA quantification is often a prerequisite for most RNA analyses such as RNA sequencing. However, the relatively low sensitivity and large sample consumption of traditional RNA quantification methods such as UV spectrophotometry and even the much more sensitive fluorescence-based RNA quantification assays, such as the Qubit™ RNA HS Assay, are often inadequate for measuring minute levels of RNA isolated from limited cell and tissue samples and biofluids. Thus, there is a pressing need for a more sensitive method to reliably and robustly detect trace levels of RNA without interference from DNA. To improve the quantification limit of the Qubit™ RNA HS Assay, we spiked-in a known quantity of RNA to achieve the minimum reading required by the assay. Samples containing trace amounts of RNA were then added to the spike-in and measured as a reading increase over RNA spike-in baseline. We determined the accuracy and precision of reading increases between 1 and 20 pg/μL as well as RNA-specificity in this range, and compared to those of RiboGreen(®), another sensitive fluorescence-based RNA quantification assay. We then applied Qubit™ Assay with RNA spike-in to quantify plasma RNA samples. RNA spike-in improved the quantification limit of the Qubit™ RNA HS Assay 5-fold, from 25 pg/μL down to 5 pg/μL while maintaining high specificity to RNA. This enabled quantification of RNA with original concentration as low as 55.6 pg/μL compared to 250 pg/μL for the standard assay and decreased sample consumption from 5 to 1 ng. Plasma RNA samples that were not measurable by the Qubit™ RNA HS Assay were measurable by our modified method. The Qubit™ RNA HS Assay with RNA spike-in is able to quantify RNA with high specificity at 5-fold lower concentration and uses 5-fold less sample quantity than the standard Qubit™ Assay.

The early history of tRNA recognition by aminoacyl-tRNA synthetases

Indian Academy of Sciences (India)

Madhu

2006-10-04

Oct 4, 2006 ... Discovery of aminoacyl-tRNA synthetases and importance ... The pioneering work of Fritz Lipmann on the high-energy ... the peculiar structural and functional relationships tRNAs ... a bulk of only 20 families of tRNA molecules in contrast ...... balance of tRNA and aminoacyl-tRNA synthetase; Science 242.

Construction of RNA nanocages by re-engineering the packaging RNA of Phi29 bacteriophage

Science.gov (United States)

Hao, Chenhui; Li, Xiang; Tian, Cheng; Jiang, Wen; Wang, Guansong; Mao, Chengde

2014-05-01

RNA nanotechnology promises rational design of RNA nanostructures with wide array of structural diversities and functionalities. Such nanostructures could be used in applications such as small interfering RNA delivery and organization of in vivo chemical reactions. Though having impressive development in recent years, RNA nanotechnology is still quite limited and its programmability and complexity could not rival the degree of its closely related cousin: DNA nanotechnology. Novel strategies are needed for programmed RNA self-assembly. Here, we have assembled RNA nanocages by re-engineering a natural, biological RNA motif: the packaging RNA of phi29 bacteriophage. The resulting RNA nanostructures have been thoroughly characterized by gel electrophoresis, cryogenic electron microscopy imaging and dynamic light scattering.

Site-Specific Covalent Conjugation of Modified mRNA by tRNA Guanine Transglycosylase.

Science.gov (United States)

Ehret, Fabian; Zhou, Cun Yu; Alexander, Seth C; Zhang, Dongyang; Devaraj, Neal K

2018-03-05

Modified mRNA (mod-mRNA) has recently been widely studied as the form of RNA useful for therapeutic applications due to its high stability and lowered immune response. Herein, we extend the scope of the recently established RNA-TAG (transglycosylation at guanosine) methodology, a novel approach for genetically encoded site-specific labeling of large mRNA transcripts, by employing mod-mRNA as substrate. As a proof of concept, we covalently attached a fluorescent probe to mCherry encoding mod-mRNA transcripts bearing 5-methylcytidine and/or pseudouridine substitutions with high labeling efficiencies. To provide a versatile labeling methodology with a wide range of possible applications, we employed a two-step strategy for functionalization of the mod-mRNA to highlight the therapeutic potential of this new methodology. We envision that this novel and facile labeling methodology of mod-RNA will have great potential in decorating both coding and noncoding therapeutic RNAs with a variety of diagnostic and functional moieties.

A path-based measurement for human miRNA functional similarities using miRNA-disease associations

Science.gov (United States)

Ding, Pingjian; Luo, Jiawei; Xiao, Qiu; Chen, Xiangtao

2016-09-01

Compared with the sequence and expression similarity, miRNA functional similarity is so important for biology researches and many applications such as miRNA clustering, miRNA function prediction, miRNA synergism identification and disease miRNA prioritization. However, the existing methods always utilized the predicted miRNA target which has high false positive and false negative to calculate the miRNA functional similarity. Meanwhile, it is difficult to achieve high reliability of miRNA functional similarity with miRNA-disease associations. Therefore, it is increasingly needed to improve the measurement of miRNA functional similarity. In this study, we develop a novel path-based calculation method of miRNA functional similarity based on miRNA-disease associations, called MFSP. Compared with other methods, our method obtains higher average functional similarity of intra-family and intra-cluster selected groups. Meanwhile, the lower average functional similarity of inter-family and inter-cluster miRNA pair is obtained. In addition, the smaller p-value is achieved, while applying Wilcoxon rank-sum test and Kruskal-Wallis test to different miRNA groups. The relationship between miRNA functional similarity and other information sources is exhibited. Furthermore, the constructed miRNA functional network based on MFSP is a scale-free and small-world network. Moreover, the higher AUC for miRNA-disease prediction indicates the ability of MFSP uncovering miRNA functional similarity.

A ribonuclease coordinates siRNA amplification and mRNA cleavage during RNAi.

Science.gov (United States)

Tsai, Hsin-Yue; Chen, Chun-Chieh G; Conte, Darryl; Moresco, James J; Chaves, Daniel A; Mitani, Shohei; Yates, John R; Tsai, Ming-Daw; Mello, Craig C

2015-01-29

Effective silencing by RNA-interference (RNAi) depends on mechanisms that amplify and propagate the silencing signal. In some organisms, small-interfering RNAs (siRNAs) are amplified from target mRNAs by RNA-dependent RNA polymerase (RdRP). Both RdRP recruitment and mRNA silencing require Argonaute proteins, which are generally thought to degrade RNAi targets by directly cleaving them. However, in C. elegans, the enzymatic activity of the primary Argonaute, RDE-1, is not required for silencing activity. We show that RDE-1 can instead recruit an endoribonuclease, RDE-8, to target RNA. RDE-8 can cleave RNA in vitro and is needed for the production of 3' uridylated fragments of target mRNA in vivo. We also find that RDE-8 promotes RdRP activity, thereby ensuring amplification of siRNAs. Together, our findings suggest a model in which RDE-8 cleaves target mRNAs to mediate silencing, while generating 3' uridylated mRNA fragments to serve as templates for the RdRP-directed amplification of the silencing signal. Copyright © 2015 Elsevier Inc. All rights reserved.

Layer-by-layer nanoparticles as an efficient siRNA delivery vehicle for SPARC silencing.

Science.gov (United States)

Tan, Yang Fei; Mundargi, Raghavendra C; Chen, Min Hui Averil; Lessig, Jacqueline; Neu, Björn; Venkatraman, Subbu S; Wong, Tina T

2014-05-14

Efficient and safe delivery systems for siRNA therapeutics remain a challenge. Elevated secreted protein, acidic, and rich in cysteine (SPARC) protein expression is associated with tissue scarring and fibrosis. Here we investigate the feasibility of encapsulating SPARC-siRNA in the bilayers of layer-by-layer (LbL) nanoparticles (NPs) with poly(L-arginine) (ARG) and dextran (DXS) as polyelectrolytes. Cellular binding and uptake of LbL NPs as well as siRNA delivery were studied in FibroGRO cells. siGLO-siRNA and SPARC-siRNA were efficiently coated onto hydroxyapatite nanoparticles. The multilayered NPs were characterized with regard to particle size, zeta potential and surface morphology using dynamic light scattering and transmission electron microscopy. The SPARC-gene silencing and mRNA levels were analyzed using ChemiDOC western blot technique and RT-PCR. The multilayer SPARC-siRNA incorporated nanoparticles are about 200 nm in diameter and are efficiently internalized into FibroGRO cells. Their intracellular fate was also followed by tagging with suitable reporter siRNA as well as with lysotracker dye; confocal microscopy clearly indicates endosomal escape of the particles. Significant (60%) SPARC-gene knock down was achieved by using 0.4 pmole siRNA/μg of LbL NPs in FibroGRO cells and the relative expression of SPARC mRNA reduced significantly (60%) against untreated cells. The cytotoxicity as evaluated by xCelligence real-time cell proliferation and MTT cell assay, indicated that the SPARC-siRNA-loaded LbL NPs are non-toxic. In conclusion, the LbL NP system described provides a promising, safe and efficient delivery platform as a non-viral vector for siRNA delivery that uses biopolymers to enhance the gene knock down efficiency for the development of siRNA therapeutics. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

How Severely Is DNA Quantification Hampered by RNA Co-extraction?

Science.gov (United States)

Sanchez, Ignacio; Remm, Matthieu; Frasquilho, Sonia; Betsou, Fay; Mathieson, William

2015-10-01

The optional RNase digest that is part of many DNA extraction protocols is often omitted, either because RNase is not provided in the kit or because users do not want to risk contaminating their laboratory. Consequently, co-eluting RNA can become a "contaminant" of unknown magnitude in a DNA extraction. We extracted DNA from liver, lung, kidney, and heart tissues and established that 28-52% of the "DNA" as assessed by spectrophotometry is actually RNA (depending on tissue type). Including an RNase digest in the extraction protocol reduced 260:280 purity ratios. Co-eluting RNA drives an overestimation of DNA yield when quantification is carried out using OD 260 nm spectrophotometry, or becomes an unquantified contaminant when spectrofluorometry is used for DNA quantification. This situation is potentially incompatible with the best practice guidelines for biobanks issued by organizations such as the International Society for Biological and Environmental Repositories, which state that biospecimens should be accurately characterized in terms of their identity, purity, concentration, and integrity. Consequently, we conclude that an RNase digest must be included in DNA extractions if pure DNA is required. We also discuss the implications of unquantified RNA contamination in DNA samples in the context of laboratory accreditation schemes.

RNase-assisted RNA chromatography

Science.gov (United States)

Michlewski, Gracjan; Cáceres, Javier F.

2010-01-01

RNA chromatography combined with mass spectrometry represents a widely used experimental approach to identify RNA-binding proteins that recognize specific RNA targets. An important drawback of most of these protocols is the high background due to direct or indirect nonspecific binding of cellular proteins to the beads. In many cases this can hamper the detection of individual proteins due to their low levels and/or comigration with contaminating proteins. Increasing the salt concentration during washing steps can reduce background, but at the cost of using less physiological salt concentrations and the likely loss of important RNA-binding proteins that are less stringently bound to a given RNA, as well as the disassembly of protein or ribonucleoprotein complexes. Here, we describe an improved RNA chromatography method that relies on the use of a cocktail of RNases in the elution step. This results in the release of proteins specifically associated with the RNA ligand and almost complete elimination of background noise, allowing a more sensitive and thorough detection of RNA-binding proteins recognizing a specific RNA transcript. PMID:20571124

RNA modifications by oxidation

DEFF Research Database (Denmark)

Poulsen, Henrik E; Specht, Elisabeth; Broedbaek, Kasper

2012-01-01