Science.gov

Sample records for armored rna internal

  1. A novel duplex real time quantitative reverse transcription polymerase chain reaction for rubella virus with armored RNA as a noncompetitive internal positive control.

    PubMed

    Zhao, Lihong; Li, Ruiying; Liu, Aihua; Zhao, Shuping

    2015-07-01

    The objective of this study was to build and apply a duplex real time quantitative reverse transcription-polymerase chain reaction (RT-PCR) for rubella virus. Firstly, a 60-bp-long armored RV RNA was constructed in the laboratory. Secondly, a duplex real time RT-PCR assay was established. Thirdly, the 60-bp-long armored RV RNA was used as an internal positive control (IPC) for the duplex real time RT-PCR. And finally the duplex real time RT-PCR assay was applied to detect RV RNA in clinical specimens. The in-house assay has a high amplification efficiency (0.99), a high analytical sensitivity (200 copies/mL), and a good reproducibility. The diagnostic specificity and sensitivity of the in-house assay were both 100%, due to the monitoring of the armored RV RNA IPC. Therefore, the in-house duplex real time quantitative RT-PCR assay is a specific, sensitive, reproducible and accurate assay for quantitation of RV RNA in clinical specimens. And noncompetitive armored RV RNA IPC can monitor RT-PCR inhibition and prevent false-negative and inaccurate results in the real time detection system.

  2. Use of armored RNA as a standard to construct a calibration curve for real-time RT-PCR.

    PubMed

    Donia, D; Divizia, M; Pana', A

    2005-06-01

    Armored Enterovirus RNA was used to standardize a real-time reverse transcription (RT)-PCR for environmental testing. Armored technology is a system to produce a robust and stable RNA standard, trapped into phage proteins, to be used as internal control. The Armored Enterovirus RNA protected sequence includes 263 bp of highly conserved sequences in 5' UTR region. During these tests, Armored RNA has been used to produce a calibration curve, comparing three different fluorogenic chemistry: TaqMan system, Syber Green I and Lux-primers. The effective evaluation of three amplifying commercial reagent kits, in use to carry out real-time RT-PCR, and several extraction procedures of protected viral RNA have been carried out. The highest Armored RNA recovery was obtained by heat treatment while chemical extraction may decrease the quantity of RNA. The best sensitivity and specificity was obtained using the Syber Green I technique since it is a reproducible test, easy to use and the cheapest one. TaqMan and Lux-primer assays provide good RT-PCR efficiency in relationship to the several extraction methods used, since labelled probe or primer request in these chemistry strategies, increases the cost of testing.

  3. Composite armor, armor system and vehicle including armor system

    DOEpatents

    Chu, Henry S.; Jones, Warren F.; Lacy, Jeffrey M.; Thinnes, Gary L.

    2013-01-01

    Composite armor panels are disclosed. Each panel comprises a plurality of functional layers comprising at least an outermost layer, an intermediate layer and a base layer. An armor system incorporating armor panels is also disclosed. Armor panels are mounted on carriages movably secured to adjacent rails of a rail system. Each panel may be moved on its associated rail and into partially overlapping relationship with another panel on an adjacent rail for protection against incoming ordnance from various directions. The rail system may be configured as at least a part of a ring, and be disposed about a hatch on a vehicle. Vehicles including an armor system are also disclosed.

  4. Armored spring-core superconducting cable and method of construction

    DOEpatents

    McIntyre, Peter M.; Soika, Rainer H.

    2002-01-01

    An armored spring-core superconducting cable (12) is provided. The armored spring-core superconducting cable (12) may include a spring-core (20), at least one superconducting strand (24) wound onto the spring-core (20), and an armored shell (22) that encases the superconducting strands (24). The spring-core (20) is generally a perforated tube that allows purge gases and cryogenic liquids to be circulated through the armored superconducting cable (12), as well as managing the internal stresses within the armored spring-core superconducting cable (12). The armored shell (22) manages the external stresses of the armored spring-core superconducting cable (12) to protect the fragile superconducting strands (24). The armored spring-core superconducting cable (12) may also include a conductive jacket (34) formed outwardly of the armored shell (22).

  5. Armor structures

    DOEpatents

    Chu, Henry Shiu-Hung [Idaho Falls, ID; Lacy, Jeffrey M [Idaho Falls, ID

    2008-04-01

    An armor structure includes first and second layers individually containing a plurality of i-beams. Individual i-beams have a pair of longitudinal flanges interconnected by a longitudinal crosspiece and defining opposing longitudinal channels between the pair of flanges. The i-beams within individual of the first and second layers run parallel. The laterally outermost faces of the flanges of adjacent i-beams face one another. One of the longitudinal channels in each of the first and second layers faces one of the longitudinal channels in the other of the first and second layers. The channels of the first layer run parallel with the channels of the second layer. The flanges of the first and second layers overlap with the crosspieces of the other of the first and second layers, and portions of said flanges are received within the facing channels of the i-beams of the other of the first and second layers.

  6. Shock destruction armor system

    DOEpatents

    Froeschner, Kenneth E.

    1993-01-01

    A shock destruction armor system is constructed and arranged to destroy the force of impact of a projectile by shock hydrodynamics. The armor system is designed to comprise a plurality of superimposed armor plates each preferably having a thickness less than five times the projectile's diameter and are preferably separated one-from-another by a distance at least equal to one-half of the projectile's diameter. The armor plates are effective to hydrodynamically and sequentially destroy the projectile. The armor system is particularly adapted for use on various military vehicles, such as tanks, aircraft and ships.

  7. Imaging body armor.

    PubMed

    Harcke, H Theodore; Schauer, David A; Harris, Robert M; Campman, Steven C; Lonergan, Gael J

    2002-04-01

    This study examined the feasibility of performing radiographic studies on patients wearing standard-issue body armor. The Kevlar helmet, fragmentation vest, demining suit sleeve, and armor plate were studied with plain film and computed tomography in a simulated casualty situation. We found that the military helmet contains metal screws and metal clips in the headband, but diagnostic computed tomographic images can be obtained. Kevlar, the principal component of soft armor, has favorable photon attenuation characteristics. Plate armor of composite material also did not limit radiographic studies. Therefore, when medically advantageous, patients can be examined radiographically while wearing standard military body armor. Civilian emergency rooms should be aware of these observations because law enforcement officers wear similar protective armor. PMID:11977874

  8. Natural flexible dermal armor.

    PubMed

    Yang, Wen; Chen, Irene H; Gludovatz, Bernd; Zimmermann, Elizabeth A; Ritchie, Robert O; Meyers, Marc A

    2013-01-01

    Fish, reptiles, and mammals can possess flexible dermal armor for protection. Here we seek to find the means by which Nature derives its protection by examining the scales from several fish (Atractosteus spatula, Arapaima gigas, Polypterus senegalus, Morone saxatilis, Cyprinius carpio), and osteoderms from armadillos, alligators, and leatherback turtles. Dermal armor has clearly been developed by convergent evolution in these different species. In general, it has a hierarchical structure with collagen fibers joining more rigid units (scales or osteoderms), thereby increasing flexibility without significantly sacrificing strength, in contrast to rigid monolithic mineral composites. These dermal structures are also multifunctional, with hydrodynamic drag (in fish), coloration for camouflage or intraspecies recognition, temperature and fluid regulation being other important functions. The understanding of such flexible dermal armor is important as it may provide a basis for new synthetic, yet bioinspired, armor materials. PMID:23161399

  9. M113: Armored Rescuer

    NASA Video Gallery

    The space shuttle required a unique rescue vehicle, one strong enough to bull its way into a launch pad and carry a flight crew and firefighters to safety. The answer is a group of M113 armored per...

  10. Laminate armor and related methods

    SciTech Connect

    Chu, Henry S; Lillo, Thomas M; Zagula, Thomas M

    2013-02-26

    Laminate armor and methods of manufacturing laminate armor. Specifically, laminate armor plates comprising a commercially pure titanium layer and a titanium alloy layer bonded to the commercially pure titanium outer layer are disclosed, wherein an average thickness of the titanium alloy inner layer is about four times an average thickness of the commercially pure titanium outer layer. In use, the titanium alloy layer is positioned facing an area to be protected. Additionally, roll-bonding methods for manufacturing laminate armor plates are disclosed.

  11. Flexible Dermal Armor in Nature

    NASA Astrophysics Data System (ADS)

    Yang, Wen; Chen, Irene H.; Mckittrick, Joanna; Meyers, Marc A.

    2012-04-01

    Many animals possess dermal armor, which acts primarily as protection against predators. We illustrate this through examples from both our research and the literature: alligator, fish (alligator gar, arapaima, and Senegal bichir), armadillo, leatherback turtle, and a lizard, the Gila monster. The dermal armor in these animals is flexible and has a hierarchical structure with collagen fibers joining mineralized units (scales, tiles, or plates). This combination significantly increases the strength and flexibility in comparison with a simple monolithic mineral composite or rigid dermal armor. This dermal armor is being studied for future bioinspired armor applications providing increased mobility.

  12. Embedded-monolith armor

    DOEpatents

    McElfresh, Michael W.; Groves, Scott E; Moffet, Mitchell L.; Martin, Louis P.

    2016-07-19

    A lightweight armor system utilizing a face section having a multiplicity of monoliths embedded in a matrix supported on low density foam. The face section is supported with a strong stiff backing plate. The backing plate is mounted on a spall plate.

  13. Glass matrix armor

    SciTech Connect

    Calkins, N.C.

    1991-09-03

    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.

  14. AC-130H Gunship Armor Upgrade Project

    SciTech Connect

    Shell, T.E.; Landingham, R.L.

    1990-09-19

    This report covers the test methods and equipment for testing aircraft armor both hard and soft. The hard armor are the typical ceramic type while the soft armor are various types of layered composite materials. 10 figs. (JEF)

  15. Glass matrix armor

    DOEpatents

    Calkins, Noel C.

    1991-01-01

    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 inside 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. The glass may be in monolithic form or particles of ceramic may be dispersed in a glass matrix. The ceramic material may be in monolithic form or may be in the form of particles dispersed in glass or dispersed in said polymer.

  16. Armored garment for protecting

    DOEpatents

    Purvis, James W.; Jones, II, Jack F.; Whinery, Larry D.; Brazfield, Richard; Lawrie, Catherine; Lawrie, David; Preece, Dale S.

    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.

  17. Armored long non-coding RNA MEG3 targeting EGFR based on recombinant MS2 bacteriophage virus-like particles against hepatocellular carcinoma

    PubMed Central

    Chang, Le; Wang, Guojing; Jia, Tingting; Zhang, Lei; Li, Yulong; Han, Yanxi; Zhang, Kuo; Lin, Guigao; Zhang, Rui; Li, Jinming; Wang, Lunan

    2016-01-01

    Hepatocellular carcinoma (HCC) is one of the most frequently diagnosed cancers worldwide. However, the treatment of patients with HCC is particularly challenging. Long non-coding RNA maternally expressed gene 3 (MEG3) has been identified as a potential suppressor of several types of tumors, but the delivery of long RNA remains problematic, limiting its applications. In the present study, we designed a novel delivery system based on MS2 virus-like particles (VLPs) crosslinked with GE11 polypeptide. This vector was found to be fast, effective and safe for the targeted delivery of lncRNA MEG3 RNA to the epidermal growth factor receptor (EGFR)-positive HCC cell lines without the activation of EGFR downstream pathways, and significantly attenuated both in vitro and in vivo tumor cell growth. Our study also revealed that the targeted delivery was mainly dependent on clathrin-mediated endocytosis and MEG3 RNA suppresses tumor growth mainly via increasing the expression of p53 and its downstream gene GDF15, but decreasing the expression of MDM2. Thus, this vector is promising as a novel delivery system and may facilitate a new approach to lncRNA based cancer therapy. PMID:26992211

  18. Armored long non-coding RNA MEG3 targeting EGFR based on recombinant MS2 bacteriophage virus-like particles against hepatocellular carcinoma.

    PubMed

    Chang, Le; Wang, Guojing; Jia, Tingting; Zhang, Lei; Li, Yulong; Han, Yanxi; Zhang, Kuo; Lin, Guigao; Zhang, Rui; Li, Jinming; Wang, Lunan

    2016-04-26

    Hepatocellular carcinoma (HCC) is one of the most frequently diagnosed cancers worldwide. However, the treatment of patients with HCC is particularly challenging. Long non-coding RNA maternally expressed gene 3 (MEG3) has been identified as a potential suppressor of several types of tumors, but the delivery of long RNA remains problematic, limiting its applications. In the present study, we designed a novel delivery system based on MS2 virus-like particles (VLPs) crosslinked with GE11 polypeptide. This vector was found to be fast, effective and safe for the targeted delivery of lncRNA MEG3 RNA to the epidermal growth factor receptor (EGFR)-positive HCC cell lines without the activation of EGFR downstream pathways, and significantly attenuated both in vitro and in vivo tumor cell growth. Our study also revealed that the targeted delivery was mainly dependent on clathrin-mediated endocytosis and MEG3 RNA suppresses tumor growth mainly via increasing the expression of p53 and its downstream gene GDF15, but decreasing the expression of MDM2. Thus, this vector is promising as a novel delivery system and may facilitate a new approach to lncRNA based cancer therapy. PMID:26992211

  19. Armor and Anesthesia

    PubMed Central

    MacLeish, Kenneth T.

    2013-01-01

    For many civilians, the high-tech weapons, armor, and military medicine with which U.S. soldiers are equipped present an image of lethal capacity and physical invulnerability. But, as this article explores, soldiers themselves just as often associate the life-sustaining technology of modern warfare with feelings that range from a pragmatic ambivalence about exposure to harm all the way to profoundly unsettling vulnerability. This article, based on fieldwork among soldiers and military families at the U.S. Army’s Ft. Hood, examines sensory and affective dimensions of soldiers’ intimate bodily relationships with the technologies that alternately or even simultaneously keep them alive and expose them to harm. I argue that modern military discipline and technology conspire to cultivate soldiers as highly durable, capable, unfeeling, interchangeable bodies, or what might be called, after Susan Buck-Morss (1992), anesthetic subjects. But for soldiers themselves, their training, combat environment, protective gear, and weapons are a rich font of both emotional and bodily feeling that exists in complex tension with the also deeply felt military imperative to carry on in the face of extreme discomfort and danger. PMID:22574391

  20. RNAcentral: an international database of ncRNA sequences

    DOE PAGES

    Williams, Kelly Porter

    2014-10-28

    The field of non-coding RNA biology has been hampered by the lack of availability of a comprehensive, up-to-date collection of accessioned RNA sequences. Here we present the first release of RNAcentral, a database that collates and integrates information from an international consortium of established RNA sequence databases. The initial release contains over 8.1 million sequences, including representatives of all major functional classes. A web portal (http://rnacentral.org) provides free access to data, search functionality, cross-references, source code and an integrated genome browser for selected species.

  1. Internal guide RNA interactions interfere with Cas9-mediated cleavage.

    PubMed

    Thyme, Summer B; Akhmetova, Laila; Montague, Tessa G; Valen, Eivind; Schier, Alexander F

    2016-01-01

    The CRISPR/Cas system uses guide RNAs (gRNAs) to direct sequence-specific DNA cleavage. Not every gRNA elicits cleavage and the mechanisms that govern gRNA activity have not been resolved. Low activity could result from either failure to form a functional Cas9-gRNA complex or inability to recognize targets in vivo. Here we show that both phenomena influence Cas9 activity by comparing mutagenesis rates in zebrafish embryos with in vitro cleavage assays. In vivo, our results suggest that genomic factors such as CTCF inhibit mutagenesis. Comparing near-identical gRNA sequences with different in vitro activities reveals that internal gRNA interactions reduce cleavage. Even though gRNAs containing these structures do not yield cleavage-competent complexes, they can compete with active gRNAs for binding to Cas9. These results reveal that both genomic context and internal gRNA interactions can interfere with Cas9-mediated cleavage and illuminate previously uncharacterized features of Cas9-gRNA complex formation. PMID:27282953

  2. Internal guide RNA interactions interfere with Cas9-mediated cleavage

    PubMed Central

    Thyme, Summer B.; Akhmetova, Laila; Montague, Tessa G.; Valen, Eivind; Schier, Alexander F.

    2016-01-01

    The CRISPR/Cas system uses guide RNAs (gRNAs) to direct sequence-specific DNA cleavage. Not every gRNA elicits cleavage and the mechanisms that govern gRNA activity have not been resolved. Low activity could result from either failure to form a functional Cas9–gRNA complex or inability to recognize targets in vivo. Here we show that both phenomena influence Cas9 activity by comparing mutagenesis rates in zebrafish embryos with in vitro cleavage assays. In vivo, our results suggest that genomic factors such as CTCF inhibit mutagenesis. Comparing near-identical gRNA sequences with different in vitro activities reveals that internal gRNA interactions reduce cleavage. Even though gRNAs containing these structures do not yield cleavage-competent complexes, they can compete with active gRNAs for binding to Cas9. These results reveal that both genomic context and internal gRNA interactions can interfere with Cas9-mediated cleavage and illuminate previously uncharacterized features of Cas9–gRNA complex formation. PMID:27282953

  3. Internal RNA Replication Elements are Prevalent in Tombusviridae

    PubMed Central

    Nicholson, Beth L.; Lee, Pui Kei K.; White, K. A.

    2012-01-01

    Internal replication elements (IREs) are RNA structures that are present at internal positions in the genomes of different types of plus-strand RNA viruses. Members of the genus Tombusvirus (family Tombusviridae) contain an IRE within the polymerase coding region of their genomes and this RNA element participates in both genome targeting to sites of replication and replicase complex assembly. Here we propose that other members of the virus family Tombusviridae also possess comparable IREs. Through sequence and structural analyses, candidate IREs in several genera of this family were identified, including aureusviruses, necroviruses, carmoviruses, and pelarspoviruses. The results from subsequent mutational analysis of selected proposed IREs were consistent with a critical role for these structures in viral genome accumulation during infections. Our study supports the existence of IREs in several genera in Tombusviridae and points to previously unappreciated similarities in genome replication strategies between members of this virus family. PMID:22888327

  4. Effectiveness of eye armor during blast loading.

    PubMed

    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

  5. Effectiveness of eye armor during blast loading.

    PubMed

    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

  6. BASELINE UT MEASUREMENTS FOR ARMOR INSPECTION

    SciTech Connect

    Margetan, Frank J.; Richter, Nate; Barnard, Dan; Hsu, David; Gray, Tim; Brasche, Lisa; Bruce Thompson, R.

    2010-02-22

    Some prototype armor panels are fabricated from several layers of dissimilar material bonded together. These may include ceramics, graphite composites, fiberglass composites and rubber. The ultrasonic properties of these layers influence inspections for armor defects. In this paper we describe measurements of ultrasonic velocity, attenuation, sound beam distortion and signal fluctuations for the individual layers comprising one armor prototype. We then discuss how knowledge of these properties can be used when choosing an optimum frequency for an ultrasonic pitch/catch immersion inspection. In our case an effective inspection frequency near 1.5 MHz affords: (1) adequate strength of through-transmitted signals in unflawed armor; (2) adequate lateral resolution for detecting small disbonds at interfaces; and (3) low levels of UT signal fluctuations due to the natural inhomogeneity of certain armor layers. The utility of this approach is demonstrated using armor panels containing artificial disbonds at selected interfaces.

  7. RNA--protein interactions within the internal translation initiation region of encephalomyocarditis virus RNA.

    PubMed Central

    Borovjagin, A V; Ezrokhi, M V; Rostapshov, V M; Ugarova TYu; Bystrova, T F; Shatsky, I N

    1991-01-01

    Various derivatives of the internal ribosomal entry site (IRES) of encephalomyocarditis virus (EMCV) RNA have been used to analyze by UV-cross-linking its interaction with mRNA binding proteins from ascites carcinoma Krebs-2 cells. A doublet of proteins with Mr 58 and 60 kD bound to two regions of the IRES. One site is centered at nt 420-421 of EMCV RNA whereas the other is located between nt 315-377. Both sites form hairpin structures, the loops of which contain UCUUU motif, conserved among cardio- and aphthoviruses. The interaction of p58 and p60 with IRES is affected by the integrity of the stem-loop structure proximal to the start AUG codon (nts 680-787), although, under similar conditions, cross-linking of these proteins to this region was not detected. Deletions in the main recognition site of p58 strongly reduce the initiation activity of the IRES in vitro. However, elimination of p58 (p60) binding by these mutations does not completely abolish the ability of the IRES to direct polypeptide synthesis starting from the authentic AUG codon. The IRES can be assembled in vitro from two covalently unlinked transcripts, one containing the target site for p58 and the other encompassing the remaining part of the IRES fused to a reporter gene, resulting in considerable restoration of its activity. Implications of these findings for the mechanism of initiation resulting from internal entry of ribosomes are discussed. Images PMID:1656384

  8. Internal initiation is responsible for synthesis of Wuhan nodavirus subgenomic RNA.

    PubMed

    Qiu, Yang; Cai, Dawei; Qi, Nan; Wang, Zhaowei; Zhou, Xi; Zhang, Jiamin; Hu, Yuanyang

    2011-05-01

    Nodaviruses are small nonenveloped spherical viruses with a bipartite genome of RNAs. In nodaviruses, subgenomic RNA3 (sgRNA3) plays a critical role in viral replication and survival, as it coordinates the replication of two viral genomic RNAs (RNA1 and RNA2) and encodes protein B2, which is a potent RNA-silencing inhibitor. Despite its importance, the molecular mechanism of nodaviral sgRNA3 synthesis is still poorly understood. Here, we propose that sgRNA3 of Wuhan nodavirus (WhNV) is internally initiated from a promoter on the negative template of genomic RNA1. Serial deletion and mutation analyses further revealed that the core promoter of WhNV sgRNA3 is between nucleotide positions -22 and +6 of its transcription start site. Besides, a stem-loop structure of WhNV sgRNA3 was computationally predicted upstream of sgRNA3's transcription start site. Both the secondary structure and the primary sequence were determined to be required for promoter activity. Furthermore, our results show that the synthesis of WhNV sgRNA3 is counterregulated by the replication of WhNV genomic RNA2, which encodes a viral capsid precursor protein. And this sgRNA3 synthesis is also able to trans-activate the replication of RNA2. Altogether, findings in this study indicate that there is a newly discovered internal initiation model for the synthesis of nodaviral sgRNA. PMID:21325414

  9. Composite structural armor for combat vehicle applications

    NASA Technical Reports Server (NTRS)

    Haskell, William E., III; Alesi, A. L.; Parsons, G. R.

    1990-01-01

    Several projects that have demonstrated the advantages of using thick composite armor technology for structural applications in armored combat vehicles are discussed. The first involved composite cargo doors for the Marine Corps LVTP-7 amphibious landing vehicle. Another was a demonstration composite turret that offered a weight reduction of 15.5 percent. The advantages of this composite armor compared to metallic armors used for combat vehicle hull and turret applications are reduced weight at equal ballistic protection; reduced back armor spall; excellent corrosion resistance; reduced production costs by parts consolidation; and inherent thermal and acoustic insulative properties. Based on the encouraging results of these past programs, the Demonstration Composite Hull Program was started in September 1986. To demonstrate this composite armor technology, the Army's newest infantry fighting vehicle, the Bradley Fighting Vehicle (BFV), was selected as a model. A composite infantry fighting vehicle, designated the CIFV for this program, has been designed and fabricated and is currently undergoing a 6000 mile field endurance test. The CIFV demonstration vehicle uses the BFV engine, transmission, suspension, track and other equipment.

  10. NDE of hybrid armor structures using acoustography

    SciTech Connect

    Sandhu, Jaswinder S.; Pergantis, Charles G.

    2011-06-23

    The US Army is investigating the use of composite materials to deliver lightweight and more effective armor protection systems to soldiers and other army assets. However, widespread use of such hybrid armor will require a reliable but fast NDE methodology to ensure integrity of these components during manufacturing and while in service. Traditional ultrasonic inspection of such hybrid armor structures may prove to be very effective, but point-by-point ultrasonic scanning is inherently time-consuming and manufacturing slowdowns could develop in high-volume production of such armor systems. In this paper, we report on the application of acoustography for the NDE of hybrid armor structures. Acoustography differs from conventional ultrasonic testing in that test objects are inspected in full field, analogously to real time x-ray imaging. The approach uses a novel, super high resolution large area acousto-optic (AO) sensor, which allows image formation through simple ultrasound shadow casting, analogous to x-ray image formation. This NDE approach offers significant inspection speed advantage over conventional point-by-point ultrasonic scanning procedures and is well-suited for high volume production. We will report initial results on a number of hybrid armor plate specimens employing composite materials that are being investigated by the US Army. Acoustography NDE results will also be verified using other complimentary NDE methods.

  11. Spliced synthetic genes as internal controls in RNA sequencing experiments.

    PubMed

    Hardwick, Simon A; Chen, Wendy Y; Wong, Ted; Deveson, Ira W; Blackburn, James; Andersen, Stacey B; Nielsen, Lars K; Mattick, John S; Mercer, Tim R

    2016-09-01

    RNA sequencing (RNA-seq) can be used to assemble spliced isoforms, quantify expressed genes and provide a global profile of the transcriptome. However, the size and diversity of the transcriptome, the wide dynamic range in gene expression and inherent technical biases confound RNA-seq analysis. We have developed a set of spike-in RNA standards, termed 'sequins' (sequencing spike-ins), that represent full-length spliced mRNA isoforms. Sequins have an entirely artificial sequence with no homology to natural reference genomes, but they align to gene loci encoded on an artificial in silico chromosome. The combination of multiple sequins across a range of concentrations emulates alternative splicing and differential gene expression, and it provides scaling factors for normalization between samples. We demonstrate the use of sequins in RNA-seq experiments to measure sample-specific biases and determine the limits of reliable transcript assembly and quantification in accompanying human RNA samples. In addition, we have designed a complementary set of sequins that represent fusion genes arising from rearrangements of the in silico chromosome to aid in cancer diagnosis. RNA sequins provide a qualitative and quantitative reference with which to navigate the complexity of the human transcriptome. PMID:27502218

  12. Investigation on Ballistic Performance of Armor Ceramics against Long-Rod Penetration

    NASA Astrophysics Data System (ADS)

    Huang, Feng-Lei; Zhang, Lian-Sheng

    2007-12-01

    A series of depth-of-penetration (DOF) tests are carried out to investigate the ballistic performance of armor ceramics. Based on the experimental results, an improved differential efficiency factor (DEF) is presented, which demonstrates that the general ballistic efficiency index is independent of the ceramic thickness. It is also shown that the density, internal friction, and compression strength of ceramics are crucial factors that affect the ballistic performance of ceramics significantly through the interaction between the long-rod projectiles and thick-tile armor.

  13. Collaborative study for the calibration of HCV RNA, HBV DNA and HIV RNA reference preparations against the relative international standards.

    PubMed

    Pisani, Giulio; Marino, Francesco; Cristiano, Karen; Bisso, Guillermo Mario; Mele, Caludio; Luciani, Francesca; Wirz, Maria; Gentili, Giuliano

    2007-01-01

    We organised a collaborative study to calibrate three new ISS reference preparations (ISS: Istituto Superiore di Sanità), one for HCV RNA, one for HIV RNA and one for HBV DNA, to be used for nucleic acid amplification techniques (NAT) in blood testing. Serial dilution of the ISS reference preparations and the respective international standards were tested in different days by each participating laboratory using two commercial NAT assays. Data were collected by the ISS for statistical analysis. Based on the mean potency of the HCV RNA and HIV RNA preparations, calculated from the results provided by the 12 participating laboratories, a definitive concentrations of 5700 IU/mL and 4000 IU/mL, respectively, were assigned to the reference materials. On the contrary, it was not possible to obtain a consensus titre for the HBV DNA reference material. These new Italian reference preparations (HCV RNA ISS/1005 and HIV RNA ISS/1005) calibrated against the respective international standards are available free of charge to any laboratory upon request.

  14. Joining of Tungsten Armor Using Functional Gradients

    SciTech Connect

    John Scott O'Dell

    2006-12-31

    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.

  15. Promoting Improved Ballistic Resistance of Transparent Armor

    SciTech Connect

    Wereszczak, Andrew A; Patel, P; Templeton, D W

    2011-01-01

    Transparent armor is a material or system of materials designed to be optically transparent, yet protect from fragmentation or ballistic impacts. Although engineered to defeat specific threats, or a range of threats, there are general requirements common to all of these designs. The primary requirement for a transparent armor system is to not only defeat the designated threat but also provide a multi-hit capability with minimized distortion of surrounding areas. Ground platforms have several parameters that must be optimized, such as weight, space efficiency, and cost versus performance. Glass exhibits tensile failure stress that is very much dependent on the amount of material being stressed, the side being tensile-stressed (i.e., air-versus tin-side if a float glass), and where it is being tensile stressed (i.e., in the middle or near an edge). An axiom arising from those effects is a greater amount of allowable deflection (i.e., higher failure stress) of a ballistically impacted transparent armor will result in improved ballistic resistance. Therefore, the interpretation and management of those tensile-failure-stress dependencies shall ultimately improve ballistic resistance and its predictability of transparent armor. Each of those three dependencies (size, side, and location) in a soda-lime silicate glass is described.

  16. Analysis of behind the armor ballistic trauma.

    PubMed

    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. PMID:25676500

  17. Proceedings of the international workshop on Ribosomal RNA technology, April 7-9, 2008, Bremen, Germany.

    PubMed

    Amaral-Zettler, Linda; Peplies, Jörg; Ramette, Alban; Fuchs, Bernhard; Ludwig, Wolfgang; Glöckner, Frank Oliver

    2008-09-01

    Thirty years have passed since Carl Woese proposed three primary domains of life based on the phylogenetic analysis of ribosomal RNA (rRNA) genes. Adopted by researchers worldwide, rRNA has become the "gold-standard" for molecular taxonomy, biodiversity analysis and the identification of microorganisms. The more than 700,000 rRNA sequences in public databases constitute an unprecedented hallmark of the richness of microbial biodiversity on earth. The International Workshop on Ribosomal RNA Technology convened on April 7-9, 2008 in Bremen, Germany (http://www.arb-silva.de/rrna-workshop) to summarize the current status of the field and strategize on the best ways of proceeding on both biological and technological fronts. In five sessions, 26 leading international speakers and approximately 120 participants representing diverse disciplines discussed new technological approaches to address three basic ecological questions: "Who is out there?" "How many are there?" and "What are they doing?".

  18. The formation of internal 6-methyladenine residues in eucaryotic messenger RNA.

    PubMed

    Tuck, M T

    1992-03-01

    1. The formation of internal 6-methyladenine (m6A) residues in eucaryotic messenger RNA (mRNA) is a postsynthetic modification in which S-adenosyl-L-methionine (SAM) serves as the methyl donor. 2. Of the methyl groups incorporated into mature mRNA 30-50% occur in m6A residues. 3. Although most cellular and certain viral mRNAs contain at least one m6A residue, some transcripts such as those coding for histone and globin are completely lacking in this modification. 4. 6-Methyladenine residues have also been localized to heterogeneous nuclear RNA (HnRNA), and for the most part these residues are conserved during mRNA processing. 5. In all known cases, the m6A residues are also found in a strict consensus sequence, Gm6AC or Am6AC, within the transcript. 6. Although the biological significance of internal adenine methylation in eucaryotic mRNA remains unclear, a great deal of research has indicated that this modification may be required for mRNA transport to the cytoplasm, the selection of splice sites or other RNA processing reactions. PMID:1551452

  19. From surface to subsurface and back again: the contribution of subsurface particle motion to surface armoring

    NASA Astrophysics Data System (ADS)

    Ferdowsi, B.; Jerolmack, D. J.; Ortiz, C. P.; Houssais, M.

    2015-12-01

    Armoring is the development of a coarse surface layer of sediments on a river bed, which overlies a smaller and typically more heterogeneous substrate. All existing models for this phenomenon are predicated on the idea that armoring develops due to size-selective transport and kinetic sieving at the surface of the granular bed. Here examine the development of armoring in the absence of size-selective surface transport, and demonstrate that subsurface particle movement can create an armored surface layer. We first conduct experiments in a laminar and annular flume, over a range of Shields stresses, with bimodal and refractive index-matched spherical sediments; this allows us to image the internal motion of the granular bed that is sheared from above by a viscous oil. Fluid-driven particle motion of the surface layer results in granular shear, that drives motion deep into the bed. This subsurface motion causes an upward migration of coarser particles, at a rate that is proportional to the granular shear rate. Comparison of experimental results to an existing continuum-granular flow model suggest that armoring in our bed-load exeriments is entirely consistent with shear-induced segregation in dry avalanches - but is slower. There is no size-selective transport at the surface in the experiments, as the annular flume is mass conserving and all particles move as bed load; this was confirmed by observation. To probe the granular physics of armor development further, we perform numerical simulations using a discrete element model (DEM) of granular flow, with and without damping. Simulations reproduce salient features of the experiments, and indicate that armoring is robust but that the rate of segregation is related to the degree of viscous damping. We posit that subsurface granular flow is an important and perhaps dominant contributor to surface armoring in rivers. More generally, this work shows how information is transferred from the surface to the subsurface and back

  20. Constrained ceramic-filled polymer armor

    DOEpatents

    Sandstrom, Donald J.; Calkins, Noel C.; Gac, Frank D.

    1990-01-01

    An armor system in which 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 inside surface of the receiving wall. The balance of each cell is completely filled with a projectile-abrading material, which is a ceramic material in particulate form dispersed in a polymeric matrix.

  1. CD28z CARs and Armored CARs

    PubMed Central

    Pegram, Hollie J.; Park, Jae H.; Brentjens, Renier J.

    2015-01-01

    CD19-targeted chimeric antigen receptor (CAR) T cells are currently being tested in the clinic with very promising outcomes. However, limitations to CAR T cell therapy exist. These include lack of efficacy against some tumors, specific targeting of tumor cells without affecting normal tissue and retaining activity within the suppressive tumor microenvironment. Whilst promising clinical trials are in progress, preclinical development is focused on optimizing CAR design, to generate “armored CAR T cells” which are protected from the inhibitory tumor microenvironment. Studies investigating the expression of cytokine transgenes, combination therapy with small molecule inhibitors or monoclonal antibodies are aimed at improving the anti-tumor efficacy of CAR T cell therapy. Other strategies aimed at improving CAR T cell therapy include utilizing dual CARs and chemokine receptors to more specifically target tumor cells. This review will describe the current clinical data and some novel “armored CAR T cell” approaches for improving anti-tumor efficacy therapy. PMID:24667958

  2. Constrained ceramic-filled polymer armor

    SciTech Connect

    Sandstrom, D.J.; Calkins, N.C.; Gac, F.D.

    1990-11-13

    An armor system is disclosed in which 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 inside surface of the receiving wall. The balance of each cell is completely filled with a projectile-abrading material, which is a ceramic material in particulate form dispersed in a polymeric matrix. 5 figs.

  3. Composite treatment of ceramic tile armor

    DOEpatents

    Hansen, James G. R.; Frame, Barbara J.

    2012-01-02

    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.

  4. Composite treatment of ceramic tile armor

    DOEpatents

    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.

  5. Analysis and in vitro localization of internal methylated adenine residues in dihydrofolate reductase mRNA.

    PubMed

    Rana, A P; Tuck, M T

    1990-08-25

    A T7 RNA transcript coding for mouse dihydrofolate reductase (DHFR) was utilized as a substrate for the N6-methyladenosine mRNA methyltransferase isolated from HeLa cell nuclei. This transcript acted as a 3 fold better substrate than either prolactin mRNA or a synthetic RNA substrate which contained multiple methylation consensus sequences. Formation of internal N6-methyladenine (m6A) residues in the DHFR transcript was shown to increase slightly by the absence of a 7-methylguanine-2'-O-methyl cap structure. Using T7 transcripts from different regions of the DHFR gene, the majority of the m6A residues were localized to the coding region and a segment of the transcript just 3' to the coding region. This data suggests that DHFR mRNA contains multiple methylation sites with most of these sites concentrated in the coding region of the transcript. PMID:2395644

  6. STS-113 crew during M-113 armored personnel carrier training

    NASA Technical Reports Server (NTRS)

    2002-01-01

    KENNEDY SPACE CENTER, FLA. -- Expedition 6 crew member Donald Pettit concentrates on driving an M-113 armored personnel carrier during emergency egress training at the pad. The crew is preparing for the mission aboard Space Shuttle Endeavour, which is scheduled to launch Nov. 10, by taking part in Terminal Countdown Demonstration Test activities. The TCDT includes a simulated launch countdown.. The Expedition 6 crew will travel on Space Shuttle Endeavour to the International Space Station to replace Expedition 5, returning to Earth after 4 months. The primary payloads on mission STS-113 are the first port truss segment, P1, and the Crew and Equipment Translation Aid (CETA) Cart B. Once delivered, the P1 truss will remain stowed until flight 12A.1 in 2003 when it will be attached to the central truss segment, S0, on the Space Station. Launch is scheduled for Nov. 10, 2002.

  7. STS-113 crew during M-113 armored personnel carrier training

    NASA Technical Reports Server (NTRS)

    2002-01-01

    KENNEDY SPACE CENTER, FLA. -- The Expedition 6 crew pauses for a photo after emergency egress training at the pad, which included driving the M-113 armored personnel carrier behind them. The crew is preparing for the mission aboard Space Shuttle Endeavour, which is scheduled to launch Nov. 10, by taking part in Terminal Countdown Demonstration Test activities. The TCDT includes a simulated launch countdown.. The Expedition 6 crew will travel on Space Shuttle Endeavour to the International Space Station to replace Expedition 5, returning to Earth after 4 months. The primary payloads on mission STS-113 are the first port truss segment, P1, and the Crew and Equipment Translation Aid (CETA) Cart B. Once delivered, the P1 truss will remain stowed until flight 12A.1 in 2003 when it will be attached to the central truss segment, S0, on the Space Station. Launch is scheduled for Nov. 10, 2002.

  8. STS-113 crew during M-113 armored personnel carrier training

    NASA Technical Reports Server (NTRS)

    2002-01-01

    KENNEDY SPACE CENTER, FLA. -- Expedition 6 crew member Nikolai Budarin takes his turn driving an M-113 armored personnel carrier during emergency egress training at the pad. The crew is preparing for the mission aboard Space Shuttle Endeavour, which is scheduled to launch Nov. 10, by taking part in Terminal Countdown Demonstration Test activities. The TCDT includes a simulated launch countdown.. The Expedition 6 crew will travel on Space Shuttle Endeavour to the International Space Station to replace Expedition 5, returning to Earth after 4 months. The primary payloads on mission STS-113 are the first port truss segment, P1, and the Crew and Equipment Translation Aid (CETA) Cart B. Once delivered, the P1 truss will remain stowed until flight 12A.1 in 2003 when it will be attached to the central truss segment, S0, on the Space Station. Launch is scheduled for Nov. 10, 2002.

  9. Armor breakup and reformation in a degradational laboratory experiment

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

    Armor breakup and reformation was studied in a laboratory experiment using a trimodal mixture composed of a 1 mm sand fraction and two gravel fractions (6 and 10 mm). 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 conditions led to an abrupt spatial transition in the bed slope and in the mean grain size of the bed surface, as such showing similar results to a previous laboratory experiment conducted with a bimodal mixture. The focus of the current analysis is to study the mechanisms of armor breakup. After an increase in flow rate the armor broke up and a new coarser armor quickly formed. The breakup initially induced a bed surface fining due to the exposure of the finer substrate, which was accompanied by a sudden increase in the sediment transport rate, followed by the formation of an armor that was coarser than the initial one. The reformation of the armor was enabled by the supply of coarse material from the upstream degrading reach and the presence of gravel in the original substrate sediment. Here armor breakup and reformation enabled slope adjustment such that the new steady state was closer to normal flow conditions.

  10. Cell-Internalization SELEX: Method for Identifying Cell-Internalizing RNA Aptamers for Delivering siRNAs to Target Cells

    PubMed Central

    Thiel, William H.; Thiel, Kristina W.; Flenker, Katie S.; Bair, Tom; Dupuy, Adam J.; McNamara, James O.; Miller, Francis J.; Giangrande, Paloma H.

    2015-01-01

    After a decade of work to address cellular uptake, the principal obstacle to RNAi-based therapeutics, there is now well-deserved, renewed optimism about RNAi-based drugs. Phase I and II studies have shown safe, strong, and durable-gene knockdown (80–90 %, lasting for a month after a single injection) and/or clinical benefit in treating several liver pathologies. Although promising, these studies have also highlighted the need for robust delivery techniques to develop RNAi therapeutics for treating other organ systems and diseases. Conjugation of siRNAs to cell-specific, synthetic RNA ligands (aptamers) is being proposed as a viable solution to this problem. While encouraging, the extended use of RNA aptamers as a delivery tool for siRNAs awaits the identification of RNA aptamer sequences capable of targeting and entering the cytoplasm of many different cell types. We describe a cell-based selection process for the rapid identification and characterization of RNA aptamers suited for delivering siRNA drugs into the cytoplasm of target cells. This process, termed “cell-internalization SELEX (Systematic Evolution of Ligands by Exponential Enrichment),” entails the combination of multiple sophisticated technologies, including cell culture-based SELEX procedures, next-generation sequencing (NGS), and novel bioinformatics tools. PMID:25319652

  11. World Health Organization International Standard to Harmonize Assays for Detection of Hepatitis E Virus RNA

    PubMed Central

    Blümel, Johannes; Mizusawa, Saeko; Matsubayashi, Keiji; Sakata, Hidekatsu; Okada, Yoshiaki; Nübling, C. Micha; Hanschmann, Kay-Martin O.

    2013-01-01

    Nucleic acid amplification technique–based assays are a primary method for the detection of acute hepatitis E virus (HEV) infection, but assay sensitivity can vary widely. To improve interlaboratory results for the detection and quantification of HEV RNA, a candidate World Health Organization (WHO) International Standard (IS) strain was evaluated in a collaborative study involving 23 laboratories from 10 countries. The IS, code number 6329/10, was formulated by using a genotype 3a HEV strain from a blood donation, diluted in pooled human plasma and lyophilized. A Japanese national standard, representing a genotype 3b HEV strain, was prepared and evaluated in parallel. The potencies of the standards were determined by qualitative and quantitative assays. Assay variability was substantially reduced when HEV RNA concentrations were expressed relative to the IS. Thus, WHO has established 6329/10 as the IS for HEV RNA, with a unitage of 250,000 International Units per milliliter. PMID:23647659

  12. Nuclear rRNA transcript processing versus internal transcribed spacer secondary structure.

    PubMed

    Coleman, Annette W

    2015-03-01

    rRNA is one of the few universal features of life, making it uniquely suited to assess phylogenetic relationships. The processing of the initial polycistronic rRNA transcript is also a conserved process, involving numerous cleavage events and the generation of secondary structures. The secondary structure of the internal transcribed spacer (ITS) regions of nuclear rRNA transcripts are well known for a wide variety of eukaryotes and have been used to aid in the alignment of these sequences for phylogenetic comparisons. By contrast, study of the processing of the initial rRNA transcripts has been largely limited to yeast, mice, rats, and humans. Here I examine the known cleavage sites in the two ITS regions and their positions relative to the secondary structure. A better understanding of the conservation of secondary structures and cleavage sites within the ITS regions will improve evolutionary inferences based on these sequences.

  13. Internal 6-methyladenine residues increase the in vitro translation efficiency of dihydrofolate reductase messenger RNA.

    PubMed

    Heilman, K L; Leach, R A; Tuck, M T

    1996-07-01

    N6-Methyladenosine (m6A) is found internally in a number of mRNA molecules from higher eucaryotic cells. In these investigations, it was found that the presence of m6A residues increase the in vitro translation efficiency of capped T7 transcripts of mouse dihydrofolate reductase (DHFR) mRNA. Using an in vitro rabbit reticulocyte translation system, the formation of internal m6A residues in the DHFR transcripts resulted in a 1.5-fold increase in translated DHFR compared to transcripts void of internal m6A residues. Translation in a wheat germ system, however, resulted in no increase in translation efficiency upon m6A formation, suggesting that the mechanism may be species-specific. PMID:8925412

  14. Light armored vehicle reconnaissance and surveillance system

    NASA Astrophysics Data System (ADS)

    Barbeau, Nicolas R.

    1994-10-01

    The Canadian Department of National Defence (DND) has established a requirement for a fleet of reconnaissance vehicles equipped with a modern surveillance system to be used in a wide variety of scenarios. This includes conventional operations within NATO, contingency operations in troubled areas as well as UN peacekeeping missions. As such, the Light Armored Vehicles Reconnaissance and Surveillance System will be the first 24 hour all- weather reconnaissance system integrated into a combat vehicle. This paper intends to describe how the operational requirements defined by DND were translated into sensor and system requirements. After a summary of the current configuration, it focuses on product pre-planned improvements and future needs.

  15. Partial purification of a 6-methyladenine mRNA methyltransferase which modifies internal adenine residues.

    PubMed Central

    Tuck, M T

    1992-01-01

    Two forms of a 6-methyladenine mRNA methyltransferase have been partially purified using a T7 transcript coding for mouse dihydrofolate reductase as an RNA substrate. Both enzyme forms modify internal adenine residues within the RNA substrate. The enzymes were purified 357- and 37-fold respectively from nuclear salt extracts prepared from HeLa cells using DEAE-cellulose and phosphocellulose chromatography. The activity of the first form of the enzyme eluted from DEAE-cellulose (major form) was at least 3-fold greater than that of the second (minor form). H.p.l.c. analysis of the hydrolysed, methylated mRNA substrates demonstrated that both forms of the enzyme produced only 6-methyladenine. The two forms of the enzyme differed in their RNA substrate specificity as well as in the dependence for a 5' cap structure. The 6-methyladenine mRNA methyltransferase activity was found to be elevated in HeLa nuclei as compared with nuclear extracts from rat kidney and brain. Enzymic activity could not be detected in nuclei from either normal rat liver or regenerating rat liver. In the case of the HeLa cell, activity could only be detected in nuclear extracts, with a small amount in the ribosomal fraction. Other HeLa subcellular fractions were void of activity. PMID:1445268

  16. 77 FR 22345 - Agency Information Collection Activities: Proposed Collection; Comments Requested; Body Armor in...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-13

    ... Information Collection Activities: Proposed Collection; Comments Requested; Body Armor in Correctional... 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...

  17. High-throughput chemiluminometric determination of prostate-specific membrane antigen mRNA in peripheral blood by RT-PCR using a synthetic RNA internal standard.

    PubMed

    Emmanouilidou, Evaggelia; Ioannou, Penelope C; Christopoulos, Theodore K

    2004-09-01

    A quantitative reverse transcriptase polymerase chain reaction (RT-PCR) method, employing internal standard (IS) RNA and a simplified chemiluminometric hybridization assay, is described for the determination of prostate-specific membrane antigen (PSMA) mRNA. The recombinant RNA IS has the same binding sites and size as the amplified PSMA mRNA. Biotinylated PCR products (263 bp) from PSMA mRNA and RNA IS are captured in microtiter wells coated with streptavidin, and hybridized with alkaline phosphatase-conjugated probes. The bound alkaline phosphatase (AP) is measured by using a chemiluminogenic substrate. The ratio of the luminescence values obtained for PSMA mRNA and the RNA IS is a linear function of the initial amount of PSMA mRNA present in the sample before RT-PCR. The linear range extends from 500 to 5,000,000 PSMA mRNA copies and the overall reproducibility of the assay, including RT-PCR and hybridization, ranges from 7.4 to 16.6%. Samples containing total RNA from PSMA-expressing LNCaP cells give luminescence ratios linearly related to the number of cells in the range 0.5-5,000 cells.

  18. Statistical Potentials for Hairpin and Internal Loops Improve the Accuracy of the Predicted RNA Structure

    PubMed Central

    Gardner, David P.; Ren, Pengyu; Ozer, Stuart; Gutell, Robin R.

    2011-01-01

    RNA is directly associated with a growing number of functions within the cell. The accurate prediction of different RNAs higher-order structure from their nucleic acid sequences will provide insight into their functions and molecular mechanics. We have been determining statistical potentials for a collection of structural elements that is larger than the number of structural elements determined with experimentally determined energy values. The experimentally derived free-energies and the statistical potentials for canonical base pair stacks are analogous, demonstrating that statistical potentials derived from comparative data can be used as an alternative energetic parameter. A new computational infrastructure - RNA Comparative Analysis Database (rCAD) - that utilizes a relational database was developed to manipulate and analyze very large sequence alignments and secondary structure datasets. Using rCAD, a richer set of energetic parameters for RNA fundamental structural elements including hairpin and internal loops was determined. A new version of RNAfold was developed to utilize these statistical potentials. Overall, these new statistical potentials for hairpin and internal loops integrated into the new version of RNAfold demonstrated significant improvements in the prediction accuracy of RNA secondary structure. PMID:21889515

  19. RNA.

    ERIC Educational Resources Information Center

    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…

  20. Armor systems including coated core materials

    DOEpatents

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

    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.

  1. Armor systems including coated core materials

    DOEpatents

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

    2013-10-08

    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.

  2. Composite armored vehicle advanced technology demonstator

    SciTech Connect

    Ostberg, D.T.; Dunfee, R.S.; Thomas, G.E.

    1996-12-31

    Composite structures are a key technology needed to develop future lightweight combat vehicles that are both deployable and survivable. The Composite Armored Vehicle Advanced Technology Demonstrator Program that started in fiscal year 1994 will continue through 1998 to verily that composite structures are a viable solution for ground combat vehicles. Testing thus far includes material characterization, structural component tests and full scale quarter section tests. Material and manufacturing considerations, tests, results and changes, and the status of the program will be described. The structural component tests have been completed successfully, and quarter section testing is in progress. Upon completion of the critical design review, the vehicle demonstrator will be Fabricated and undergo government testing.

  3. Rapid molecular identification of armored scale insects (Hemiptera: Diaspididae) on Mexican 'Hass' avocado.

    PubMed

    Rugman-Jones, Paul F; Morse, Joseph G; Stouthamer, Richard

    2009-10-01

    'Hass' avocado, Persea americana Mill., fruit imported into California from Mexico are infested with high levels of armored scale insects (Hemiptera: Diaspididae), constituting several species. The paucity and delicate nature of morphological characters traditionally used to diagnose armored scales often require careful preparation of slide-mounted specimens and expert knowledge of the group, for their accurate identification. Here, we present a simple, quick, and accurate means to identify armored scales on Mexican avocados, based on amplification of the internal transcribed spacer two of ribosomal DNA, by using the polymerase chain reaction (PCR). This region seems to show a high level of intraspecific conformity among scale specimens originating from different localities. A suite of species-specific reverse PCR primers are combined in a single reaction, with a universal forward primer, and produce a PCR product of a unique size, that after standard gel electrophoresis, allows the direct diagnosis of six diaspidid species: Abgrallaspis aguacatae Evans, Watson & Miller; Hemiberlesia lataniae (Signoret); Hemiberlesia sp. near latania; Hemiberlesia rapax (Comstock); Acutaspis albopicta (Cockerell); and Pinnaspis strachani (Cooley). Two additional species, Diaspis miranda (Cockerell) and Diaspis sp. near miranda, also are separated from the others by using this method and are subsequently diagnosed by secondary digestion of the PCR product with the restriction endonuclease smaI.

  4. Design of armor for protection against blast and impact

    NASA Astrophysics Data System (ADS)

    Rahimzadeh, Tanaz; Arruda, Ellen M.; Thouless, M. D.

    2015-12-01

    The features of blast and impact that can damage a delicate target supported by a structure include both the peak pressure and the impulse delivered to the structure. This study examines how layers of elastic and visco-elastic materials may be assembled to mitigate these features. The impedance mismatch between two elastic layers is known to reduce the pressure, but dissipation is required to mitigate the transmitted impulse in light-weight armor. A novel design concept called impact or blast tuning is introduced in which a multi-layered armor is used to tune the stress waves resulting from an impact or blast to specific frequencies that match the damping frequencies of visco-elastic layers. The material and geometrical parameters controlling the viscous dissipation of the energy within the armor are identified for a simplified one-dimensional system, to provide insight into how the optimal design of multi-use armor might be based on this concept.

  5. 75 FR 25208 - Announcement of Body Armor Research Needs Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-07

    ... the examination of such issues as material longevity, new materials, and improved testing... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF COMMERCE National Institute of Standards and Technology Announcement of Body Armor Research Needs Meeting...

  6. OPTIMIZING TRANSPARENT ARMOR DESIGN SUBJECT TO PROJECTILE IMPACT CONDITIONS

    SciTech Connect

    Sun, Xin; Lai, Canhai; Gorsich, Tara; Templeton, Douglas W.

    2009-03-01

    Design and manufacturing of transparent armor have been historically carried out using experimental approaches. In this study, we use advanced computational modeling tools to perform virtual design evaluations of transparent armor systems under different projectile impact conditions. AHPCRC developed modeling software EPIC’06 [1] is used in predicting the penetration resistance of transparent armor systems. LaGrangian-based finite element analyses combined with particle dynamics are used to simulate the damage initiation and propagation process for the armor system under impact conditions. It is found that a 1-parameter single state model can be used to predict the impact penetration depth with relatively good accuracy, suggesting that the finely comminuted glass particles follow the behavior similar to a viscous fluid. Even though the intact strength of borosilicate and soda lime glass are different, the same fractured strength can be used for both glasses to capture the penetration depth.

  7. Minimizing base loss and internal fragmentation in collisionally activated dissociation of multiply deprotonated RNA.

    PubMed

    Taucher, Monika; Rieder, Ulrike; Breuker, Kathrin

    2010-02-01

    In recent years, new classes of nonprotein-coding ribonucleic acids (ncRNAs) with important cellular functions have been discovered. Of particular interest for biomolecular research and pharmaceutical developments are small ncRNAs that are involved in gene regulation, such as small interfering RNAs (21-28 nt), pre-microRNAs (70-80 nt), or riboswitches (34-200 nt). De novo sequencing of RNA by top-down mass spectrometry has so far been limited to RNA consisting of up to approximately 20 nt. We report here complete sequence coverage for 34 nt RNA (10.9 kDa), along with 30 out of 32 possible complementary ion pairs from collisionally activated dissociation (CAD) experiments. The key to minimizing undesired base loss and internal fragmentation is to minimize the internal energy of fragment ions from primary backbone cleavage. This can be achieved by collisional cooling of primary fragment ions and selection of precursor ions of relatively low negative net charge (about -0.2/nt).

  8. Methods for Evaluating Cell-Specific, Cell-Internalizing RNA Aptamers

    PubMed Central

    Hernandez, Luiza I.; Flenker, Katie S.; Hernandez, Frank J.; Klingelhutz, Aloysius J.; II, James O. McNamara; Giangrande, Paloma H.

    2013-01-01

    Recent clinical trials of small interfering RNAs (siRNAs) highlight the need for robust delivery technologies that will facilitate the successful application of these therapeutics to humans. Arguably, cell targeting by conjugation to cell-specific ligands provides a viable solution to this problem. Synthetic RNA ligands (aptamers) represent an emerging class of pharmaceuticals with great potential for targeted therapeutic applications. For targeted delivery of siRNAs with aptamers, the aptamer-siRNA conjugate must be taken up by cells and reach the cytoplasm. To this end, we have developed cell-based selection approaches to isolate aptamers that internalize upon binding to their cognate receptor on the cell surface. Here we describe methods to monitor for cellular uptake of aptamers. These include: (1) antibody amplification microscopy, (2) microplate-based fluorescence assay, (3) a quantitative and ultrasensitive internalization method (“QUSIM”) and (4) a way to monitor for cytoplasmic delivery using the ribosome inactivating protein-based (RNA-RIP) assay. Collectively, these methods provide a toolset that can expedite the development of aptamer ligands to target and deliver therapeutic siRNAs in vivo. PMID:23894227

  9. The human insulin receptor mRNA contains a functional internal ribosome entry segment

    PubMed Central

    Spriggs, Keith A.; Cobbold, Laura C.; Ridley, Simon H.; Coldwell, Mark; Bottley, Andrew; Bushell, Martin; Willis, Anne E.; Siddle, Kenneth

    2009-01-01

    Regulation of mRNA translation is an important mechanism determining the level of expression of proteins in eukaryotic cells. Translation is most commonly initiated by cap-dependent scanning, but many eukaryotic mRNAs contain internal ribosome entry segments (IRESs), providing an alternative means of initiation capable of independent regulation. Here, we show by using dicistronic luciferase reporter vectors that the 5′-UTR of the mRNA encoding human insulin receptor (hIR) contains a functional IRES. RNAi-mediated knockdown showed that the protein PTB was required for maximum IRES activity. Electrophoretic mobility shift assays confirmed that PTB1, PTB2 and nPTB, but not unr or PTB4, bound to hIR mRNA, and deletion mapping implicated a CCU motif 448 nt upstream of the initiator AUG in PTB binding. The IR-IRES was functional in a number of cell lines, and most active in cells of neuronal origin, as assessed by luciferase reporter assays. The IRES was more active in confluent than sub-confluent cells, but activity did not change during differentiation of 3T3-L1 fibroblasts to adipocytes. IRES activity was stimulated by insulin in sub-confluent cells. The IRES may function to maintain expression of IR protein in tissues such as the brain where mRNA translation by cap-dependent scanning is less effective. PMID:19654240

  10. Molecular architecture of the ribosome-bound Hepatitis C Virus internal ribosomal entry site RNA.

    PubMed

    Yamamoto, Hiroshi; Collier, Marianne; Loerke, Justus; Ismer, Jochen; Schmidt, Andrea; Hilal, Tarek; Sprink, Thiemo; Yamamoto, Kaori; Mielke, Thorsten; Bürger, Jörg; Shaikh, Tanvir R; Dabrowski, Marylena; Hildebrand, Peter W; Scheerer, Patrick; Spahn, Christian M T

    2015-12-14

    Internal ribosomal entry sites (IRESs) are structured cis-acting RNAs that drive an alternative, cap-independent translation initiation pathway. They are used by many viruses to hijack the translational machinery of the host cell. IRESs facilitate translation initiation by recruiting and actively manipulating the eukaryotic ribosome using only a subset of canonical initiation factor and IRES transacting factors. Here we present cryo-EM reconstructions of the ribosome 80S- and 40S-bound Hepatitis C Virus (HCV) IRES. The presence of four subpopulations for the 80S•HCV IRES complex reveals dynamic conformational modes of the complex. At a global resolution of 3.9 Å for the most stable complex, a derived atomic model reveals a complex fold of the IRES RNA and molecular details of its interaction with the ribosome. The comparison of obtained structures explains how a modular architecture facilitates mRNA loading and tRNA binding to the P-site. This information provides the structural foundation for understanding the mechanism of HCV IRES RNA-driven translation initiation. PMID:26604301

  11. Mechanical unfolding of RNA: from hairpins to structures with internal multiloops.

    PubMed

    Hyeon, Changbong; Thirumalai, D

    2007-02-01

    Mechanical unfolding of RNA structures, ranging from hairpins to ribozymes, using laser optical tweezer experiments have begun to reveal the features of the energy landscape that cannot be easily explored using conventional experiments. Upon application of constant force (f), RNA hairpins undergo cooperative transitions from folded to unfolded states whereas subdomains of ribozymes unravel one at a time. Here, we use a self-organized polymer model and Brownian dynamics simulations to probe mechanical unfolding at constant force and constant-loading rate of four RNA structures of varying complexity. For simple hairpins, such as P5GA, application of constant force or constant loading rate results in bistable cooperative transitions between folded and unfolded states without populating any intermediates. The transition state location (DeltaxFTS) changes dramatically as the loading rate is varied. At loading rates comparable to those used in laser optical tweezer experiments, the hairpin is plastic, with DeltaxFTS being midway between folded and unfolded states; whereas at high loading rates, DeltaxFTS moves close to the folded state, i.e., RNA is brittle. For the 29-nucleotide TAR RNA with the three-nucleotide bulge, unfolding occurs in a nearly two-state manner with an occasional pause in a high free energy metastable state. Forced unfolding of the 55 nucleotides of the Hepatitis IRES domain IIa, which has a distorted L-shaped structure, results in well-populated stable intermediates. The most stable force-stabilized intermediate represents straightening of the L-shaped structure. For these structures, the unfolding pathways can be predicted using the contact map of the native structures. Unfolding of a RNA motif with internal multiloop, namely, the 109-nucleotide prohead RNA that is part of the 29 DNA packaging motor, at constant value of rf occurs with three distinct rips that represent unraveling of the paired helices. The rips represent kinetic barriers to

  12. Defensive aids suite prototype for light armored vehicles

    NASA Astrophysics Data System (ADS)

    Cantin, Andre; Fortin, Jean; Venter, Johan; Philip, Brian G.; Hagen, Russell; Krieger, Dietmar; Greenley, Mike

    2001-09-01

    The Defence Research Establishment Valcartier has initiated in 1998 R&D work to investigate and to demonstrate key technologies required for future Defensive Aid Suite to protect Light Armoured Vehicles. A basic Defensive Aid Suite demonstrator (Phase I) was built and integrated into the LAV vetronics by Litton Systems Canada and his consortium. The Defensive Aid Suite consisted of a 2-band HARLIDTM-based laser detection head, a processor capable to control and deploy countermeasures and a DAS touch-screen display all integrated in a Light Armored Vehicle. The crew was able to select the operation mode for direct fire or smoke deployment by pushing one of the pair of buttons available at the bottom of the display. This system was successfully demonstrated in October 1999 during an international trial. This article gives an overview of the results obtained in the field as well as some of the lessons learnt. It also describes laboratory and field measurements made on the Laser Warning Receiver unit itself. The results of the DAS tactical use and of Human factor evaluation will illustrate its performance within typical laser threat scenarios. This work will serve as the basis for the recommendation of a future DAS demonstrator (Phase II) integrating more sensors and countermeasures.

  13. Numerical simulation of armor capability of AI2O3 and SiC armor tiles

    NASA Astrophysics Data System (ADS)

    Rashid, T.; Aleem, M. A.; Akbar, S.; Rauf, A.; Shuaib, M.

    2016-08-01

    Alumina and Silicon Carbide armor plates have been tested numerically against 7.62x51 (mm x mm) armor piercing (AP) projectiles. A 2-D problem with axial symmetry has been designedand the simulations were carried out using commercial software ANSYS AUTODYN. Experiments were modeled for Alumina (99.5%), Alumina (99.7%) and SiC with a range of tile thicknesses (5, 10, 15 and 20 mm). The projectile was chosen as 7.62 x 51AP bullet (initial velocity 810 m/sec)with two different core materials Steel 4340 and WC, however, casing material was copper for both cores. SiC showed better defense against AP bullet as compared to Al2O3. The residual velocity and momentum of the bullet were found to decrease with increasing tile thickness. SiC tiles with thickness 15mm and 20 mm successfully sustained penetration against steel 4340 and WC core bullets, respectively. However none of the Alumina targets succeeded in stopping the bullet.

  14. Toroidal midplane neutral beam armor and plasma limiter

    DOEpatents

    Kugel, Henry W.; Hand Jr, Samuel W.; Ksayian, Haig

    1986-02-04

    For use in a tokamak fusion reactor having a midplane magnetic coil on the inner wall of an evacuated toriodal chamber within which a neutral beam heated, fusing plasma is magnetically confined, a neutral beam armor shield and plasma limiter is provided on the inner wall of the toroidal chamber to shield the midplane coil from neutral beam shine-thru and plasma deposition. The armor shield/plasma limiter forms a semicircular enclosure around the midplane coil with the outer surface of the armor shield/plasma limiter shaped to match, as closely as practical, the inner limiting magnetic flux surface of the toroidally confined, indented, bean-shaped plasma. The armor shield/plasma limiter includes a plurality of semicircular graphite plates each having a pair of coupled upper and lower sections with each plate positioned in intimate contact with an adjacent plate on each side thereof so as to form a closed, planar structure around the entire outer periphery of the circular midplane coil. The upper and lower plate sections are adapted for coupling to heat sensing thermocouples and to a circulating water conduit system for cooling the armor shield/plasma limiter.The inner center portion of each graphite plate is adapted to receive and enclose a section of a circular diagnostic magnetic flux loop so as to minimize the power from the plasma confinement chamber incident upon the flux loop.

  15. Toroidal midplane neutral beam armor and plasma limiter

    DOEpatents

    Kugel, Henry W.; Hand, Jr, Samuel W.; Ksayian, Haig

    1986-01-01

    For use in a tokamak fusion reactor having a midplane magnetic coil on the inner wall of an evacuated toriodal chamber within which a neutral beam heated, fusing plasma is magnetically confined, a neutral beam armor shield and plasma limiter is provided on the inner wall of the toroidal chamber to shield the midplane coil from neutral beam shine-thru and plasma deposition. The armor shield/plasma limiter forms a semicircular enclosure around the midplane coil with the outer surface of the armor shield/plasma limiter shaped to match, as closely as practical, the inner limiting magnetic flux surface of the toroidally confined, indented, bean-shaped plasma. The armor shield/plasma limiter includes a plurality of semicircular graphite plates each having a pair of coupled upper and lower sections with each plate positioned in intimate contact with an adjacent plate on each side thereof so as to form a closed, planar structure around the entire outer periphery of the circular midplane coil. The upper and lower plate sections are adapted for coupling to heat sensing thermocouples and to a circulating water conduit system for cooling the armor shield/plasma limiter.The inner center portion of each graphite plate is adapted to receive and enclose a section of a circular diagnostic magnetic flux loop so as to minimize the power from the plasma confinement chamber incident upon the flux loop.

  16. The complete mitochondrial genome of the armored catfish, Hypostomus plecostomus (Siluriformes: Loricariidae).

    PubMed

    Liu, Shikai; Zhang, Jiaren; Yao, Jun; Liu, Zhanjiang

    2016-05-01

    The complete mitochondrial genome of the armored catfish, Hypostomus plecostomus, was determined by next generation sequencing of genomic DNA without prior sample processing or primer design. Bioinformatics analysis resulted in the entire mitochondrial genome sequence with length of 16,523 bp. The H. plecostomus mitochondrial genome is consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region, showing typical circular molecule structure of mitochondrial genome as in other vertebrates. The whole genome base composition was estimated to be 31.8% A, 27.0% T, 14.6% G, and 26.6% C, with A/T bias of 58.8%. This work provided the H. plecostomus mitochondrial genome sequence which should be valuable for species identification, phylogenetic analysis and conservation genetics studies in catfishes.

  17. Training incidents in armored vehicles in the Singapore Armed Forces.

    PubMed

    Seng, Kok-Yong; Ng, Yih-Yng; Ying, Meng-Fai

    2003-02-01

    Training in armored vehicles presents occupational hazards. Since the inception of armored units in the Singapore Armed Forces in 1969, there has been no scientific study of the demographics of the trauma patterns. A review of existing literature also indicated a paucity of data on this subject. This article qualified and quantified the proportion of trauma during peacetime armored vehicle training during a 5-year period. Most of the 100 documented incidences of injuries occurred on the head and body limbs. Many injuries were caused by minor lacerations, abrasions, and crush injuries. Although fractures accounted for 24%, 65% of the total injury count could be classified as "minor." A diurnal pattern of injuries was noted in the study. The injury patterns could be used to analyze morbidity and mortality trends and facilitate subsequent evaluation of efficacy of affirmative action. New challenges facing further research in training injuries were also discussed. PMID:12636148

  18. Performance of the PDX neutral beam wall armor

    SciTech Connect

    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.

  19. Crystal structure of a c-di-AMP riboswitch reveals an internally pseudo-dimeric RNA.

    PubMed

    Jones, Christopher P; Ferré-D'Amaré, Adrian R

    2014-11-18

    Cyclic diadenosine monophosphate (c-di-AMP) is a second messenger that is essential for growth and homeostasis in bacteria. A recently discovered c-di-AMP-responsive riboswitch controls the expression of genes in a variety of bacteria, including important pathogens. To elucidate the molecular basis for specific binding of c-di-AMP by a gene-regulatory mRNA domain, we have determined the co-crystal structure of this riboswitch. Unexpectedly, the structure reveals an internally pseudo-symmetric RNA in which two similar three-helix-junction elements associate head-to-tail, creating a trough that cradles two c-di-AMP molecules making quasi-equivalent contacts with the riboswitch. The riboswitch selectively binds c-di-AMP and discriminates exquisitely against other cyclic dinucleotides, such as c-di-GMP and cyclic-AMP-GMP, via interactions with both the backbone and bases of its cognate second messenger. Small-angle X-ray scattering experiments indicate that global folding of the riboswitch is induced by the two bound cyclic dinucleotides, which bridge the two symmetric three-helix domains. This structural reorganization likely couples c-di-AMP binding to gene expression. PMID:25271255

  20. 46 CFR 111.05-7 - Armored and metallic sheathed cable.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... Armored and metallic sheathed cable. When installed, the metallic armor or sheath must meet the installation requirements of Section 25 of IEEE 45-2002 (incorporated by reference; see 46 CFR 110.10-1). ... 46 Shipping 4 2010-10-01 2010-10-01 false Armored and metallic sheathed cable. 111.05-7...

  1. 48 CFR 252.225-7030 - Restriction on Acquisition of Carbon, Alloy, and Armor Steel Plate.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... of Carbon, Alloy, and Armor Steel Plate. 252.225-7030 Section 252.225-7030 Federal Acquisition... Acquisition of Carbon, Alloy, and Armor Steel Plate. As prescribed in 225.7011-3, use the following clause: Restriction on Acquisition of Carbon, Alloy, and Armor Steel Plate (DEC 2006) (a) Carbon, alloy, and...

  2. 48 CFR 252.225-7030 - Restriction on Acquisition of Carbon, Alloy, and Armor Steel Plate.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... of Carbon, Alloy, and Armor Steel Plate. 252.225-7030 Section 252.225-7030 Federal Acquisition... Acquisition of Carbon, Alloy, and Armor Steel Plate. As prescribed in 225.7011-3, use the following clause: Restriction on Acquisition of Carbon, Alloy, and Armor Steel Plate (DEC 2006) (a) Carbon, alloy, and...

  3. 48 CFR 252.225-7030 - Restriction on Acquisition of Carbon, Alloy, and Armor Steel Plate.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... of Carbon, Alloy, and Armor Steel Plate. 252.225-7030 Section 252.225-7030 Federal Acquisition... Acquisition of Carbon, Alloy, and Armor Steel Plate. As prescribed in 225.7011-3, use the following clause: Restriction on Acquisition of Carbon, Alloy, and Armor Steel Plate (DEC 2006) (a) Carbon, alloy, and...

  4. 48 CFR 252.225-7030 - Restriction on Acquisition of Carbon, Alloy, and Armor Steel Plate.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... of Carbon, Alloy, and Armor Steel Plate. 252.225-7030 Section 252.225-7030 Federal Acquisition... Acquisition of Carbon, Alloy, and Armor Steel Plate. As prescribed in 225.7011-3, use the following clause: Restriction on Acquisition of Carbon, Alloy, and Armor Steel Plate (DEC 2006) (a) Carbon, alloy, and...

  5. 48 CFR 252.225-7030 - Restriction on Acquisition of Carbon, Alloy, and Armor Steel Plate.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... of Carbon, Alloy, and Armor Steel Plate. 252.225-7030 Section 252.225-7030 Federal Acquisition... Acquisition of Carbon, Alloy, and Armor Steel Plate. As prescribed in 225.7011-3, use the following clause: Restriction on Acquisition of Carbon, Alloy, and Armor Steel Plate (DEC 2006) (a) Carbon, alloy, and...

  6. Methods of producing armor systems, and armor systems produced using such methods

    DOEpatents

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

    2013-02-19

    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.

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

    SciTech Connect

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

    2011-06-23

    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.

  8. Internal polyadenylation of parvoviral precursor mRNA limits progeny virus production.

    PubMed

    Huang, Qinfeng; Deng, Xuefeng; Best, Sonja M; Bloom, Marshall E; Li, Yi; Qiu, Jianming

    2012-05-10

    Aleutian Mink Disease Virus (AMDV) is the only virus in the genus Amdovirus of family Parvoviridae. In adult mink, AMDV causes a persistent infection associated with severe dysfunction of the immune system. Cleavage of AMDV capsid proteins has been previously shown to play a role in regulating progeny virus production (Fang Cheng et al., J. Virol. 84:2687-2696, 2010). The present study shows that AMDV has evolved a second strategy to limit expression of capsid proteins by preventing processing of the full-length capsid protein-encoding mRNA transcripts. Characterization of the cis-elements of the proximal polyadenylation site [(pA)p] in the infectious clone of AMDV revealed that polyadenylation at the (pA)p site is controlled by an upstream element (USE) of 200 nts in length, the AAUAAA signal, and a downstream element (DSE) of 40 nts. A decrease in polyadenylation at the (pA)p site, either by mutating the AAUAAA signal or the DSE, which does not affect the encoding of amino acids in the infectious clone, increased the expression of capsid protein VP1/VP2 and thereby increased progeny virus production approximately 2-3-fold. This increase was accompanied by enhanced replication of the AMDV genome. Thus, this study reveals correlations among internal polyadenylation, capsid production, viral DNA replication and progeny virus production of AMDV, indicating that internal polyadenylation is a limiting step for parvovirus replication and progeny virus production. PMID:22361476

  9. Internal Polyadenylation of Parvoviral Precursor mRNA Limits Progeny Virus Production

    PubMed Central

    Huang, Qinfeng; Deng, Xuefeng; Best, Sonja M.; Bloom, Marshall E.; Li, Yi; Qiu, Jianming

    2012-01-01

    Aleutian Mink Disease Virus (AMDV) is the only virus in the genus Amdovirus of family Parvoviridae. In adult mink, AMDV causes a persistent infection associated with severe dysfunction of the immune system. Cleavage of AMDV capsid proteins has been previously shown to play a role in regulating progeny virus production (Fang Cheng et al, J. Virol. 84:2687–2696, 2010). The present study shows that AMDV has evolved a second strategy to limit expression of capsid proteins by preventing processing of the full-length capsid protein-encoding mRNA transcripts. Characterization of the cis-elements of the proximal polyadenylation site [(pA)p] in the infectious clone of AMDV revealed that polyadenylation at the (pA)p site is controlled by an upstream element (USE) of 200 nts in length, the AAUAAA signal, and a downstream element (DSE) of 40 nts. A decrease in polyadenylation at the (pA)p site, either by mutating the AAUAAA signal or the DSE, which does not affect the encoding of amino acids in the infectious clone, increased the expression of capsid protein VP1/VP2 and thereby increased progeny virus production approximately 2-3-fold. This increase was accompanied by enhanced replication of the AMDV genome. Thus, this study reveals correlations among internal polyadenylation, capsid production, viral DNA replication and progeny virus production of AMDV, indicating that internal polyadenylation is a limiting step for parvovirus replication and progeny virus production. PMID:22361476

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

    PubMed

    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

  11. Multifunctionality of chiton biomineralized armor with an integrated visual system

    DOE PAGES

    Li, Ling; Connors, Matthew; Kolle, Mathias; England, Grant; Speiser, Daniel; Xiao, Xianghui; Aizenberg, Joanna; Ortiz, Christine

    2015-11-20

    Nature provides a multitude of examples of multifunctional structural materials. There are often trade-offs in these materials because few of them are equally well suited for multiple tasks. One such example is the biomineralized armor of the chiton Acanthopleura granulata, which incorporates an integrated sensory system that includes hundreds of eyes with aragonite-based lens. Here, we used optical experiments to demonstrate directly, for the first time, that these microscopic, mineralized lenses are able to form images. Furthermore, our experiments revealed that the optical performance of these polycrystalline lenses is enhanced by the reduction of spherical aberration through the shape ofmore » the lens and that birefringence scattering is minimized by the use of relatively large, co-aligned grains (~10 μm as compared to ~1 μm in the non-eye regions). Additionally, we used multi-scale mechanical testing techniques to show that A. granulata’s lenses are an integral component of its biomineralized armor, but that both the intrinsic and overall mechanical properties of the lenses are compromised as compared to the primary solid regions of the armor plates. Our results demonstrate that as the size, complexity, and functionality of the integrated sensory elements increases, the local mechanical performance of the armor decreases. But, A. granulata has evolved several strategies to compensate for its local mechanical vulnerabilities to form a multifunctional system with co-optimized overall optical and structural functions.« less

  12. 75 FR 25884 - NIJ Body Armor Compliance Testing Program Workshop

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-10

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF JUSTICE Office of Justice Programs NIJ Body Armor Compliance Testing Program Workshop AGENCY: National Institute of Justice. ACTION: Notice of meeting. SUMMARY: The National Institute of Justice (NIJ) is hosting a...

  13. Lightcurve Analsyis of 774 Armor and 3161 Beadell

    NASA Astrophysics Data System (ADS)

    Oey, Julian; Han, Xianming L.; Gipson, Kevin

    2013-04-01

    Photometric studies of the asteroids 774 Armor and 3161 Beadell and were carried out by observers from Australia and USA. The data were combined and the following periods were obtained: 774 Amor, 25.107 ± 0.005 h; 3161 Beadell, 36.253 ± 0.004 h.

  14. Multifunctionality of chiton biomineralized armor with an integrated visual system

    SciTech Connect

    Li, Ling; Connors, Matthew; Kolle, Mathias; England, Grant; Speiser, Daniel; Xiao, Xianghui; Aizenberg, Joanna; Ortiz, Christine

    2015-11-20

    Nature provides a multitude of examples of multifunctional structural materials. There are often trade-offs in these materials because few of them are equally well suited for multiple tasks. One such example is the biomineralized armor of the chiton Acanthopleura granulata, which incorporates an integrated sensory system that includes hundreds of eyes with aragonite-based lens. Here, we used optical experiments to demonstrate directly, for the first time, that these microscopic, mineralized lenses are able to form images. Furthermore, our experiments revealed that the optical performance of these polycrystalline lenses is enhanced by the reduction of spherical aberration through the shape of the lens and that birefringence scattering is minimized by the use of relatively large, co-aligned grains (~10 μm as compared to ~1 μm in the non-eye regions). Additionally, we used multi-scale mechanical testing techniques to show that A. granulata’s lenses are an integral component of its biomineralized armor, but that both the intrinsic and overall mechanical properties of the lenses are compromised as compared to the primary solid regions of the armor plates. Our results demonstrate that as the size, complexity, and functionality of the integrated sensory elements increases, the local mechanical performance of the armor decreases. But, A. granulata has evolved several strategies to compensate for its local mechanical vulnerabilities to form a multifunctional system with co-optimized overall optical and structural functions.

  15. Natural Curaua Fiber-Reinforced Composites in Multilayered Ballistic Armor

    NASA Astrophysics Data System (ADS)

    Monteiro, Sergio Neves; Louro, Luis Henrique Leme; Trindade, Willian; Elias, Carlos Nelson; Ferreira, Carlos Luiz; de Sousa Lima, Eduardo; Weber, Ricardo Pondé; Miguez Suarez, João Carlos; da Silva Figueiredo, André Ben-Hur; Pinheiro, Wagner Anacleto; da Silva, Luis Carlos; Lima, Édio Pereira

    2015-10-01

    The performance of a novel multilayered armor in which the commonly used plies of aramid fabric layer were replaced by an equal thickness layer of distinct curaua fiber-reinforced composites with epoxy or polyester matrices was assessed. The investigated armor, in addition to its polymeric layer (aramid fabric or curaua composite), was also composed of a front Al2O3 ceramic tile and backed by an aluminum alloy sheet. Ballistic impact tests were performed with actual 7.62 caliber ammunitions. Indentation in a clay witness, simulating human body behind the back layer, attested the efficacy of the curaua-reinforced composite as an armor component. The conventional aramid fabric display a similar indentation as the curaua/polyester composite but was less efficient (deeper indentation) than the curaua/epoxy composite. This advantage is shown to be significant, especially in favor of the lighter and cheaper epoxy composite reinforced with 30 vol pct of curaua fiber, as possible substitute for aramid fabric in multilayered ballistic armor for individual protection. Scanning electron microscopy revealed the mechanism associated with the curaua composite ballistic performance.

  16. Site-specific labeling of RNA at internal ribose hydroxyl groups: terbium-assisted deoxyribozymes at work.

    PubMed

    Büttner, Lea; Javadi-Zarnaghi, Fatemeh; Höbartner, Claudia

    2014-06-01

    A general and efficient single-step method was established for site-specific post-transcriptional labeling of RNA. Using Tb(3+) as accelerating cofactor for deoxyribozymes, various labeled guanosines were site-specifically attached to 2'-OH groups of internal adenosines in in vitro transcribed RNA. The DNA-catalyzed 2',5'-phosphodiester bond formation proceeded efficiently with fluorescent, spin-labeled, biotinylated, or cross-linker-modified guanosine triphosphates. The sequence context of the labeling site was systematically analyzed by mutating the nucleotides flanking the targeted adenosine. Labeling of adenosines in a purine-rich environment showed the fastest reactions and highest yields. Overall, practically useful yields >70% were obtained for 13 out of 16 possible nucleotide (nt) combinations. Using this approach, we demonstrate preparative labeling under mild conditions for up to ~160-nt-long RNAs, including spliceosomal U6 small nuclear RNA and a cyclic-di-AMP binding riboswitch RNA.

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

    PubMed

    Devonshire, Alison S; Sanders, Rebecca; Whale, Alexandra S; Nixon, Gavin J; Cowen, Simon; Ellison, Stephen L R; Parkes, Helen; Pine, P Scott; Salit, Marc; McDaniel, Jennifer; Munro, Sarah; Lund, Steve; Matsukura, Satoko; Sekiguchi, Yuji; Kawaharasaki, Mamoru; Granjeiro, José Mauro; Falagan-Lotsch, Priscila; Saraiva, Antonio Marcos; Couto, Paulo; Yang, Inchul; Kwon, Hyerim; Park, Sang-Ryoul; Demšar, Tina; Žel, Jana; Blejec, Andrej; Milavec, Mojca; Dong, Lianhua; Zhang, Ling; Sui, Zhiwei; Wang, Jing; Viroonudomphol, Duangkamol; Prawettongsopon, Chaiwat; Partis, Lina; Baoutina, Anna; Emslie, Kerry; Takatsu, Akiko; Akyurek, Sema; Akgoz, Muslum; Vonsky, Maxim; Konopelko, L A; Cundapi, Edna Matus; Urquiza, Melina Pérez; Huggett, Jim F; Foy, Carole A

    2016-06-01

    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 uncertainties in the

  18. One RNA plays three roles to provide catalytic activity to a group I intron lacking an endogenous internal guide sequence.

    PubMed

    Vaidya, Nilesh; Lehman, Niles

    2009-07-01

    Catalytic RNA molecules possess simultaneously a genotype and a phenotype. However, a single RNA genotype has the potential to adopt two or perhaps more distinct phenotypes as a result of differential folding and/or catalytic activity. Such multifunctionality would be particularly significant if the phenotypes were functionally inter-related in a common biochemical pathway. Here, this phenomenon is demonstrated by the ability of the Azoarcus group I ribozyme to function when its canonical internal guide sequence (GUG) has been removed from the 5' end of the molecule, and added back exogenously in trans. The presence of GUG triplets in non-covalent fragments of the ribozyme allow trans-splicing to occur in both a reverse splicing assay and a covalent self-assembly assay in which the internal guide sequence (IGS)-less ribozyme can put itself together from two of its component pieces. Analysis of these reactions indicates that a single RNA fragment can perform up to three distinct roles in a reaction: behaving as a portion of a catalyst, behaving as a substrate, and providing an exogenous IGS. This property of RNA to be multifunctional in a single reaction pathway bolsters the probability that a system of self-replicating molecules could have existed in an RNA world during the origins of life on the Earth. PMID:19406926

  19. In vivo footprint of a picornavirus internal ribosome entry site reveals differences in accessibility to specific RNA structural elements.

    PubMed

    Fernández-Miragall, Olga; Martínez-Salas, Encarnación

    2007-11-01

    Internal ribosome entry site (IRES) elements were described in picornaviruses as an essential region of the viral RNA. Understanding of IRES function requires a detailed knowledge of each step involved in the internal initiation process, from RNA folding and IRES-protein interaction to ribosome recruitment. Thus, deciphering IRES accessibility to external agents due to RNA structural features, as well as RNA-protein protection within living cells, is of primary importance. In this study, two chemical reagents, dimethylsulfate (DMS) and aminomethylpsoralen, have been used to footprint the entire IRES of foot-and-mouth disease virus (FMDV) in living cells; these reagents enter the cell membrane and interact with nucleic acids in a structure-dependent manner. For FMDV, as in other picornaviruses, viral infection is dependent on the correct function of the IRES; therefore, the IRES region itself constitutes a useful target of antiviral drugs. Here, the in vivo footprint of a picornavirus IRES element in the context of a biologically active mRNA is shown for the first time. The accessibility of unpaired adenosine and cytosine nucleotides in the entire FMDV IRES was first obtained in vitro by DMS probing; subsequently, this information was used to interpret the footprint data obtained in vivo for the mRNA encompassing the IRES element in the intercistronic space. The results of DMS accessibility and UV-psoralen cross-linking studies in the competitive cellular environment provided evidence for differences in RNA structure from data obtained in vitro, and provided essential information to identify appropriate targets within the FMDV IRES aimed at combating this important pathogen.

  20. Multiscale impacts of armoring on Salish Sea shorelines: Evidence for cumulative and threshold effects

    NASA Astrophysics Data System (ADS)

    Dethier, Megan N.; Raymond, Wendel W.; McBride, Aundrea N.; Toft, Jason D.; Cordell, Jeffery R.; Ogston, Andrea S.; Heerhartz, Sarah M.; Berry, Helen D.

    2016-06-01

    Shoreline armoring is widespread in many parts of the protected inland waters of the Pacific Northwest, U.S.A, but impacts on physical and biological features of local nearshore ecosystems have only recently begun to be documented. Armoring marine shorelines can alter natural processes at multiple spatial and temporal scales; some, such as starving the beach of sediments by blocking input from upland bluffs may take decades to become visible, while others such as placement loss of armoring construction are immediate. We quantified a range of geomorphic and biological parameters at paired, nearby armored and unarmored beaches throughout the inland waters of Washington State to test what conditions and parameters are associated with armoring. We gathered identical datasets at a total of 65 pairs of beaches: 6 in South Puget Sound, 23 in Central Puget Sound, and 36 pairs North of Puget Sound proper. At this broad scale, demonstrating differences attributable to armoring is challenging given the high natural variability in measured parameters among beaches and regions. However, we found that armoring was consistently associated with reductions in beach width, riparian vegetation, numbers of accumulated logs, and amounts and types of beach wrack and associated invertebrates. Armoring-related patterns at lower beach elevations (further vertically from armoring) were progressively harder to detect. For some parameters, such as accumulated logs, there was a distinct threshold in armoring elevation that was associated with increased impacts. This large dataset for the first time allowed us to identify cumulative impacts that appear when increasing proportions of shorelines are armored. At large spatial and temporal scales, armoring much of a sediment drift cell may result in reduction of the finer grain-size fractions on beaches, including those used by spawning forage fish. Overall we have shown that local impacts of shoreline armoring can scale-up to have cumulative and

  1. Alternate pathways for processing in the internal transcribed spacer 1 in pre-rRNA of Saccharomyces cerevisiae.

    PubMed Central

    Lindahl, L; Archer, R H; Zengel, J M

    1994-01-01

    We have extended the system of Nogi et al. (Proc. Natl. Acad. Sci. USA 88, 1991, 3962-3966) for transcription of rRNA from an RNA polymerase II promoter in strains lacking functional RNA polymerase I. In our strains two differentially marked rRNA transcription units can be expressed alternately. Using this system we have shown that the A2 processing site in the internal transcribed spacer 1 (ITS1) of the pre-rRNA is dispensable. According to the accepted processing scheme, the A2 site serves to separate the parts of the primary rRNA transcript that are destined for incorporation into the two ribosomal subunits. However, we have found that, when A2 is impaired, separation of the small and large subunit rRNAs occurs at a processing site further downstream in ITS1, indicating that alternate pathways for ITS1 processing exist. Short deletions in the A2 region still allow residual processing at the A2 site. Mapping of the cleavage sites in such deletion transcripts suggests that sequences downstream of the A2 site are used for determining the position of the cleavage. Images PMID:7816631

  2. Armoring a droplet: soft jamming of a dense granular interface.

    PubMed

    Lagubeau, Guillaume; Rescaglio, Antonella; Melo, Francisco

    2014-09-01

    Droplets and bubbles protected by armors of particles have found vast applications in encapsulation, stabilization of emulsions and foams, or flotation processes. The liquid phase stores capillary energy, while concurrently the solid contacts of the granular network induce friction and energy dissipation, leading to hybrid interfaces of combined properties. By means of nonintrusive tensiometric methods and structural measurements, we distinguish three surface phases of increasing rigidity during the evaporation of armored droplets. The emergence of surface rigidity is reminiscent of jamming of granular matter, but it occurs differently since it is marked by a step by step hardening under surface compression. These results show that the concept of the effective surface tension remains useful only below the first jamming transition. Beyond this point, the surface stresses become anisotropic.

  3. Armor corrosion monitoring of a submarine AC cable

    SciTech Connect

    Genesca, J.; Perez, T.; Lara, C.

    1997-12-01

    After the hurricane Gilberto flattened (devastated) Cancun in September 1988, the submarine cables which supplied electricity to Isla Mjueres Island remained very damaged, and it was decided to install the new ones. In 1989, four new submarine cables were installed from Punta Sam, Cancun to Isla Mujeres. Such cables, of nominal tension 34.5 KV, were manufactures with a galvanized steel armor coated with asphalt, and began operation during 1990. The object of this communication is to present the experimental procedure that gave place to the armor corrosion monitoring procedure carried out in this particular case and to compare the results with those obtained on the field. Results of the cathodic protection system applied are also presented.

  4. Highly deformable bones: unusual deformation mechanisms of seahorse armor.

    PubMed

    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.

  5. Multifunctionality of chiton biomineralized armor with an integrated visual system.

    PubMed

    Li, Ling; Connors, Matthew J; Kolle, Mathias; England, Grant T; Speiser, Daniel I; Xiao, Xianghui; Aizenberg, Joanna; Ortiz, Christine

    2015-11-20

    Nature provides a multitude of examples of multifunctional structural materials in which trade-offs are imposed by conflicting functional requirements. One such example is the biomineralized armor of the chiton Acanthopleura granulata, which incorporates an integrated sensory system that includes hundreds of eyes with aragonite-based lenses. We use optical experiments to demonstrate that these microscopic lenses are able to form images. Light scattering by the polycrystalline lenses is minimized by the use of relatively large, crystallographically aligned grains. Multiscale mechanical testing reveals that as the size, complexity, and functionality of the integrated sensory elements increase, the local mechanical performance of the armor decreases. However, A. granulata has evolved several strategies to compensate for its mechanical vulnerabilities to form a multipurpose system with co-optimized optical and structural functions.

  6. Armoring and vertical sorting in aeolian dune fields

    NASA Astrophysics Data System (ADS)

    Gao, Xin; Narteau, Clément; Rozier, Olivier

    2016-04-01

    Unlike ripples, there are only few numerical studies on grain-size segregation at the scale of dunes in aeolian environments. Here we use a cellular automaton model to analyze vertical sorting in granular mixtures under steady unidirectional flow conditions. We investigate the feedbacks between dune growth and the segregation mechanisms by varying the size of coarse grains and their proportion within the bed. We systematically observe the development of a horizontal layer of coarse grains at the top of which sorted bed forms may grow by amalgamation. The formation of such an armor layer controls the overall sediment transport and availability. The emergence of dunes and the transition from barchan to transverse dune fields depend only on the grain size distribution of the initial sediment layer. As confirmed by observation, this result indicates that armor layers should be present in most arid deserts, where they are likely to control dune morphodynamics.

  7. Plastic deformation enabled energy dissipation in a bionanowire structured armor.

    PubMed

    Li, Haoze; Yue, Yonghai; Han, Xiaodong; Li, Xiaodong

    2014-05-14

    It has been challenging to simultaneously achieve high strength and toughness in engineered materials because of the trade-off relation between the two distinct properties. Nature, however, has elegantly solved this problem. Seashells, commonly referred to as nature's armors, exhibit an unusual resilience against predatory attacks. In this letter, we report an unexpected phenomenon in a bionanowire structured armor-conch shell where the shell's basic building blocks, i.e., the third-order lamellae, exhibit an exceptional plasticity with a maximum strain of 0.7% upon mechanical loading. We attribute such a plastic deformation behavior to the lamella's unique nanoparticle-biopolymer architecture, in which the biopolymer mediates the rotation of aragonite nanoparticles in response to external attacks. We also found that electron beam irradiation facilitates the lamella's plasticity. These findings advance our understanding of seashell's energy dissipating strategy and provide new design guidelines for developing high performance bioinspired materials and sensors.

  8. Multifunctionality of chiton biomineralized armor with an integrated visual system.

    PubMed

    Li, Ling; Connors, Matthew J; Kolle, Mathias; England, Grant T; Speiser, Daniel I; Xiao, Xianghui; Aizenberg, Joanna; Ortiz, Christine

    2015-11-20

    Nature provides a multitude of examples of multifunctional structural materials in which trade-offs are imposed by conflicting functional requirements. One such example is the biomineralized armor of the chiton Acanthopleura granulata, which incorporates an integrated sensory system that includes hundreds of eyes with aragonite-based lenses. We use optical experiments to demonstrate that these microscopic lenses are able to form images. Light scattering by the polycrystalline lenses is minimized by the use of relatively large, crystallographically aligned grains. Multiscale mechanical testing reveals that as the size, complexity, and functionality of the integrated sensory elements increase, the local mechanical performance of the armor decreases. However, A. granulata has evolved several strategies to compensate for its mechanical vulnerabilities to form a multipurpose system with co-optimized optical and structural functions. PMID:26586760

  9. Plastic deformation enabled energy dissipation in a bionanowire structured armor.

    PubMed

    Li, Haoze; Yue, Yonghai; Han, Xiaodong; Li, Xiaodong

    2014-05-14

    It has been challenging to simultaneously achieve high strength and toughness in engineered materials because of the trade-off relation between the two distinct properties. Nature, however, has elegantly solved this problem. Seashells, commonly referred to as nature's armors, exhibit an unusual resilience against predatory attacks. In this letter, we report an unexpected phenomenon in a bionanowire structured armor-conch shell where the shell's basic building blocks, i.e., the third-order lamellae, exhibit an exceptional plasticity with a maximum strain of 0.7% upon mechanical loading. We attribute such a plastic deformation behavior to the lamella's unique nanoparticle-biopolymer architecture, in which the biopolymer mediates the rotation of aragonite nanoparticles in response to external attacks. We also found that electron beam irradiation facilitates the lamella's plasticity. These findings advance our understanding of seashell's energy dissipating strategy and provide new design guidelines for developing high performance bioinspired materials and sensors. PMID:24745628

  10. Lightweight armor system and process for producing the same

    SciTech Connect

    Chu, Henry S.; Bruck, H. Alan; Strempek, Gary C.; Varacalle, Jr., Dominic J.

    2004-01-20

    A lightweight armor system may comprise a substrate having a graded metal matrix composite layer formed thereon by thermal spray deposition. The graded metal matrix composite layer comprises an increasing volume fraction of ceramic particles imbedded in a decreasing volume fraction of a metal matrix as a function of a thickness of the graded metal matrix composite layer. A ceramic impact layer is affixed to the graded metal matrix composite layer.

  11. Mechanisms of stability of armored bubbles: FY 1996 Final Report

    SciTech Connect

    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.

  12. The AMINO experiment: RNA stability under solar radiation studied on the EXPOSE-R facility of the International Space Station

    NASA Astrophysics Data System (ADS)

    Vergne, Jacques; Cottin, Hervé; da Silva, Laura; Brack, André; Chaput, Didier

    2015-01-01

    Careful examination of the present metabolism and in vitro selection of various catalytic RNAs strongly support the RNA world hypothesis as a crucial step of the origins and early life evolution. Small functional RNAs were exposed from 10 March 2009 to 21 January 2011 to space conditions on board the International Space Station in the EXPOSE-R mission. The aim of this study was to investigate the preservation or modification properties such as integrity of RNAs after space exposition. The exposition to the solar radiation has a strong degradation effect on the size distribution of RNA. Moreover, the comparison between the in-flight samples, exposed to the Sun and not exposed, indicates that the solar radiation degrades RNA bases.

  13. Toroidal midplane neutral beam armor and plasma limiter

    DOEpatents

    Kugel, H.W.; Hand, S.W. Jr.; Ksayian, H.

    1985-05-31

    This invention contemplates an armor shield/plasma limiter positioned upon the inner wall of a toroidal vacuum chamber within which is magnetically confined an energetic plasma in a tokamak nuclear fusion reactor. The armor shield/plasma limiter is thus of a general semi-toroidal shape and is comprised of a plurality of adjacent graphite plates positioned immediately adjacent to each other so as to form a continuous ring upon and around the toroidal chamber's inner wall and the reactor's midplane coil. Each plate has a generally semi-circular outer circumference and a recessed inner portion and is comprised of upper and lower half sections positioned immediately adjacent to one another along the midplane of the plate. With the upper and lower half sections thus joined, a channel or duct is provided within the midplane of the plate in which a magnetic flux loop is positioned. The magnetic flux loop is thus positioned immediately adjacent to the fusing toroidal plasma and serves as a diagnostic sensor with the armor shield/plasma limiter minimizing the amount of power from the energetic plasma as well as from the neutral particle beams heating the plasma incident upon the flux loop.

  14. Transparent ceramics for armor and EM window applications

    NASA Astrophysics Data System (ADS)

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

    2000-10-01

    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 the performance of a system. These results coupled with recent processing and manufacturing advances have revitalized the interest in using transparent ceramics for armor systems. The materials currently under investigation at ARL are magnesium aluminate spinel (MgAl2O4), aluminum oxynitride spinel (AlON), single crystal sapphire (Al2O3), glasses, and glass-ceramics. The polymers under investigation are polycarbonate (PC) and polyurethane (PU). An overview of current ARL efforts in these areas, including the motivation for using transparent ceramics, the requirements, the potential applications, and the ongoing processing research will be reviewed.

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

    SciTech Connect

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

    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.

  16. Myotonic dystrophy type 1 RNA crystal structures reveal heterogeneous 1 × 1 nucleotide UU internal loop conformations.

    PubMed

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

    2011-11-15

    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[UUGGGC(CUG)(3)GUCC](2), refined to 2.20 and 1.52 Å 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 × 1 nucleotide UU internal loops can display an ensemble of pairing conformations. In the 2.20 Å 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 × 1 nucleotide UU internal loop has no hydrogen bonds, while the terminal 1 × 1 nucleotide UU internal loops each form a one-hydrogen bond pair. In the 1.52 Å 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 × 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 × 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.

  17. Effect of Liposome Size on Internal RNA Replication Coupled with Replicase Translation.

    PubMed

    Sunami, Takeshi; Ichihashi, Norikazu; Nishikawa, Takehiro; Kazuta, Yasuaki; Yomo, Tetsuya

    2016-07-01

    Cell membranes inhibit the diffusion of intracellular materials, and compartment size can strongly affect the intracellular biochemical reactions. To assess the effect of the size of microcompartments on intracellular reactions, we constructed a primitive cell model consisting of giant liposomes and a translation-coupled RNA replication (TcRR) system. The RNA was replicated by Qβ replicase, which was translated from the RNA in giant liposomes encapsulating the cell-free translation system. A reporter RNA encoding the antisense strand of β-glucuronidase was introduced into the system to yield a TcRR read-out (green fluorescence). We demonstrate that TcRR was hardly detectable in larger liposomes (230 fL) but was more effective in smaller (7.7 fL) liposomes. Our experimental and theoretical results show that smaller microcompartments considerably enhance TcRR because the synthesized molecules, such as RNA and replicases, are more concentrated in smaller liposomes. PMID:27037959

  18. Shell-armored wood cobbles as a potential criterion for detrital coal deposits

    SciTech Connect

    DiMarco, M.J.; Nummedal, D.

    1986-01-01

    Shell-armored wood cobbles occur on detrital-peat beaches along the seaward edge of the Mississippi Delta. Shell material consists exclusively of Mulinia lateralis, a dwarf surf clam. Soft, heavy, waterlogged wood fragments are abraded and become armored by hard shells in response to wave activity on the beach. Although their preservation potential is suspect, fossilized shell-armored wood clasts would probably be recognized as a type of coal ball and might indicate an allochthonous origin for the host coal.

  19. Global shape mimicry of tRNA within a viral internal ribosome entry site mediates translational reading frame selection

    PubMed Central

    Au, Hilda H.; Cornilescu, Gabriel; Mouzakis, Kathryn D.; Ren, Qian; Burke, Jordan E.; Lee, Seonghoon; Butcher, Samuel E.; Jan, Eric

    2015-01-01

    The dicistrovirus intergenic region internal ribosome entry site (IRES) adopts a triple-pseudoknotted RNA structure and occupies the core ribosomal E, P, and A sites to directly recruit the ribosome and initiate translation at a non-AUG codon. A subset of dicistrovirus IRESs directs translation in the 0 and +1 frames to produce the viral structural proteins and a +1 overlapping open reading frame called ORFx, respectively. Here we show that specific mutations of two unpaired adenosines located at the core of the three-helical junction of the honey bee dicistrovirus Israeli acute paralysis virus (IAPV) IRES PKI domain can uncouple 0 and +1 frame translation, suggesting that the structure adopts distinct conformations that contribute to 0 or +1 frame translation. Using a reconstituted translation system, we show that ribosomes assembled on mutant IRESs that direct exclusive 0 or +1 frame translation lack reading frame fidelity. Finally, a nuclear magnetic resonance/small-angle X-ray scattering hybrid approach reveals that the PKI domain of the IAPV IRES adopts an RNA structure that resembles a complete tRNA. The tRNA shape-mimicry enables the viral IRES to gain access to the ribosome tRNA-binding sites and form intermolecular contacts with the ribosome that are necessary for initiating IRES translation in a specific reading frame. PMID:26554019

  20. Global shape mimicry of tRNA within a viral internal ribosome entry site mediates translational reading frame selection.

    PubMed

    Au, Hilda H; Cornilescu, Gabriel; Mouzakis, Kathryn D; Ren, Qian; Burke, Jordan E; Lee, Seonghoon; Butcher, Samuel E; Jan, Eric

    2015-11-24

    The dicistrovirus intergenic region internal ribosome entry site (IRES) adopts a triple-pseudoknotted RNA structure and occupies the core ribosomal E, P, and A sites to directly recruit the ribosome and initiate translation at a non-AUG codon. A subset of dicistrovirus IRESs directs translation in the 0 and +1 frames to produce the viral structural proteins and a +1 overlapping open reading frame called ORFx, respectively. Here we show that specific mutations of two unpaired adenosines located at the core of the three-helical junction of the honey bee dicistrovirus Israeli acute paralysis virus (IAPV) IRES PKI domain can uncouple 0 and +1 frame translation, suggesting that the structure adopts distinct conformations that contribute to 0 or +1 frame translation. Using a reconstituted translation system, we show that ribosomes assembled on mutant IRESs that direct exclusive 0 or +1 frame translation lack reading frame fidelity. Finally, a nuclear magnetic resonance/small-angle X-ray scattering hybrid approach reveals that the PKI domain of the IAPV IRES adopts an RNA structure that resembles a complete tRNA. The tRNA shape-mimicry enables the viral IRES to gain access to the ribosome tRNA-binding sites and form intermolecular contacts with the ribosome that are necessary for initiating IRES translation in a specific reading frame. PMID:26554019

  1. Global shape mimicry of tRNA within a viral internal ribosome entry site mediates translational reading frame selection.

    PubMed

    Au, Hilda H; Cornilescu, Gabriel; Mouzakis, Kathryn D; Ren, Qian; Burke, Jordan E; Lee, Seonghoon; Butcher, Samuel E; Jan, Eric

    2015-11-24

    The dicistrovirus intergenic region internal ribosome entry site (IRES) adopts a triple-pseudoknotted RNA structure and occupies the core ribosomal E, P, and A sites to directly recruit the ribosome and initiate translation at a non-AUG codon. A subset of dicistrovirus IRESs directs translation in the 0 and +1 frames to produce the viral structural proteins and a +1 overlapping open reading frame called ORFx, respectively. Here we show that specific mutations of two unpaired adenosines located at the core of the three-helical junction of the honey bee dicistrovirus Israeli acute paralysis virus (IAPV) IRES PKI domain can uncouple 0 and +1 frame translation, suggesting that the structure adopts distinct conformations that contribute to 0 or +1 frame translation. Using a reconstituted translation system, we show that ribosomes assembled on mutant IRESs that direct exclusive 0 or +1 frame translation lack reading frame fidelity. Finally, a nuclear magnetic resonance/small-angle X-ray scattering hybrid approach reveals that the PKI domain of the IAPV IRES adopts an RNA structure that resembles a complete tRNA. The tRNA shape-mimicry enables the viral IRES to gain access to the ribosome tRNA-binding sites and form intermolecular contacts with the ribosome that are necessary for initiating IRES translation in a specific reading frame.

  2. [Search for optimal combinations of the hygienic and protective characteristics of body armors].

    PubMed

    Logatkin, S M

    2008-01-01

    The protective composition of a body armor is generally characterized by two major parameters--the area and level of protection, i.e. resistance to bullets and fragments. These characteristics directly depend on the mass of a body armor and the sizes of the body's screening. The positive protective characteristics simultaneously have a negative impact on the most important hygienic indices of a body armor, such as convenience and easiness-to-use. The optimum combination of protective and performance characteristics of body armors makes a compromise between their mass and the level of protection.

  3. Characterizing the interaction among bullet, body armor, and human and surrogate targets.

    PubMed

    Shen, Weixin; Niu, Yuqing; Bykanova, Lucy; Laurence, Peter; Link, Norman

    2010-12-01

    This study used a combined experimental and modeling approach to characterize and quantify the interaction among bullet, body armor, and human surrogate targets during the 10-1000 μs range that is crucial to evaluating the protective effectiveness of body armor against blunt injuries. Ballistic tests incorporating high-speed flash X-ray measurements were performed to acquire the deformations of bullets and body armor samples placed against ballistic clay and gelatin targets with images taken between 10 μs and 1 ms of the initial impact. Finite element models (FEMs) of bullet, armor, and gelatin and clay targets were developed with material parameters selected to best fit model calculations to the test measurements. FEMs of bullet and armor interactions were then assembled with a FEM of a human torso and FEMs of clay and gelatin blocks in the shape of a human torso to examine the effects of target material and geometry on the interaction. Test and simulation results revealed three distinct loading phases during the interaction. In the first phase, the bullet was significantly slowed in about 60 μs as it transferred a major portion of its energy into the body armor. In the second phase, fibers inside the armor were pulled toward the point of impact and kept on absorbing energy until about 100 μs after the initial impact when energy absorption reached its peak. In the third phase, the deformation on the armor's back face continued to grow and energies inside both armor and targets redistributed through wave propagation. The results indicated that armor deformation and energy absorption in the second and third phases were significantly affected by the material properties (density and stiffness) and geometrical characteristics (curvature and gap at the armor-target interface) of the targets. Valid surrogate targets for testing the ballistic resistance of the armor need to account for these factors and produce the same armor deformation and energy absorption as on a

  4. Characterizing the interaction among bullet, body armor, and human and surrogate targets.

    PubMed

    Shen, Weixin; Niu, Yuqing; Bykanova, Lucy; Laurence, Peter; Link, Norman

    2010-12-01

    This study used a combined experimental and modeling approach to characterize and quantify the interaction among bullet, body armor, and human surrogate targets during the 10-1000 μs range that is crucial to evaluating the protective effectiveness of body armor against blunt injuries. Ballistic tests incorporating high-speed flash X-ray measurements were performed to acquire the deformations of bullets and body armor samples placed against ballistic clay and gelatin targets with images taken between 10 μs and 1 ms of the initial impact. Finite element models (FEMs) of bullet, armor, and gelatin and clay targets were developed with material parameters selected to best fit model calculations to the test measurements. FEMs of bullet and armor interactions were then assembled with a FEM of a human torso and FEMs of clay and gelatin blocks in the shape of a human torso to examine the effects of target material and geometry on the interaction. Test and simulation results revealed three distinct loading phases during the interaction. In the first phase, the bullet was significantly slowed in about 60 μs as it transferred a major portion of its energy into the body armor. In the second phase, fibers inside the armor were pulled toward the point of impact and kept on absorbing energy until about 100 μs after the initial impact when energy absorption reached its peak. In the third phase, the deformation on the armor's back face continued to grow and energies inside both armor and targets redistributed through wave propagation. The results indicated that armor deformation and energy absorption in the second and third phases were significantly affected by the material properties (density and stiffness) and geometrical characteristics (curvature and gap at the armor-target interface) of the targets. Valid surrogate targets for testing the ballistic resistance of the armor need to account for these factors and produce the same armor deformation and energy absorption as on a

  5. Intragenomic heterogeneity of the 16S rRNA-23S rRNA internal transcribed spacer among Pseudomonas syringae and Pseudomonas fluorescens strains.

    PubMed

    Milyutina, Irina A; Bobrova, Vera K; Matveeva, Eugenia V; Schaad, Norman W; Troitsky, Alexey V

    2004-10-01

    The 16S-23S rRNA internal transcribed spacer regions (ITS1) from 14 strains of Pseudomonas syringae and P. fluorescens were sequenced. ITS1 exhibited significant sequence variability among different operons within a single genome. From 1 to 4 types of ITS1 were found in individual genomes of the P. syringae and P. fluorescens strains. A total of eight ITS1 types were identified among strains studied. The ITS1 nucleotide sequences consisted of conserved blocks including, among others, a stem-forming region of box B, tRNAIle and tRNAAla genes and several variable blocks. The differences in the variable regions were mostly due to insertions and/or deletions of nucleotide blocks. The intragenomic heterogeneity of ITS1 was brought about by different combinations of variable blocks, which possibly have resulted from recombination and horizontal transfer.

  6. Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites.

    PubMed

    Schwartz, Schraga; Mumbach, Maxwell R; Jovanovic, Marko; Wang, Tim; Maciag, Karolina; Bushkin, G Guy; Mertins, Philipp; Ter-Ovanesyan, Dmitry; Habib, Naomi; Cacchiarelli, Davide; Sanjana, Neville E; Freinkman, Elizaveta; Pacold, Michael E; Satija, Rahul; Mikkelsen, Tarjei S; Hacohen, Nir; Zhang, Feng; Carr, Steven A; Lander, Eric S; Regev, Aviv

    2014-07-10

    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. PMID:24981863

  7. Development of a dual-internal-reference technique to improve accuracy when determining bacterial 16S rRNA:16S rRNA gene ratio with application to Escherichia coli liquid and aerosol samples.

    PubMed

    Zhen, Huajun; Krumins, Valdis; Fennell, Donna E; Mainelis, Gediminas

    2015-10-01

    Accurate enumeration of rRNA content in microbial cells, e.g. by using the 16S rRNA:16S rRNA gene ratio, is critical to properly understand its relationship to microbial activities. However, few studies have considered possible methodological artifacts that may contribute to the variability of rRNA analysis results. In this study, a technique utilizing genomic DNA and 16S rRNA from an exogenous species (Pseudomonas fluorescens) as dual internal references was developed to improve accuracy when determining the 16S rRNA:16S rRNA gene ratio of a target organism, Escherichia coli. This technique was able to adequately control the variability in sample processing and analysis procedures due to nucleic acid (DNA and RNA) losses, inefficient reverse transcription of RNA, and inefficient PCR amplification. The measured 16S rRNA:16S rRNA gene ratio of E. coli increased by 2-3 fold when E. coli 16S rRNA gene and 16S rRNA quantities were normalized to the sample-specific fractional recoveries of reference (P. fluorescens) 16S rRNA gene and 16S rRNA, respectively. In addition, the intra-sample variation of this ratio, represented by coefficients of variation from replicate samples, decreased significantly after normalization. This technique was applied to investigate the temporal variation of 16S rRNA:16S rRNA gene ratio of E. coli during its non-steady-state growth in a complex liquid medium, and to E. coli aerosols when exposed to particle-free air after their collection on a filter. The 16S rRNA:16S rRNA gene ratio of E. coli increased significantly during its early exponential phase of growth; when E. coli aerosols were exposed to extended filtration stress after sample collection, the ratio also increased. In contrast, no significant temporal trend in E. coli 16S rRNA:16S rRNA gene ratio was observed when the determined ratios were not normalized based on the recoveries of dual references. The developed technique could be widely applied in studies of relationship between

  8. Development of a dual-internal-reference technique to improve accuracy when determining bacterial 16S rRNA:16S rRNA gene ratio with application to Escherichia coli liquid and aerosol samples.

    PubMed

    Zhen, Huajun; Krumins, Valdis; Fennell, Donna E; Mainelis, Gediminas

    2015-10-01

    Accurate enumeration of rRNA content in microbial cells, e.g. by using the 16S rRNA:16S rRNA gene ratio, is critical to properly understand its relationship to microbial activities. However, few studies have considered possible methodological artifacts that may contribute to the variability of rRNA analysis results. In this study, a technique utilizing genomic DNA and 16S rRNA from an exogenous species (Pseudomonas fluorescens) as dual internal references was developed to improve accuracy when determining the 16S rRNA:16S rRNA gene ratio of a target organism, Escherichia coli. This technique was able to adequately control the variability in sample processing and analysis procedures due to nucleic acid (DNA and RNA) losses, inefficient reverse transcription of RNA, and inefficient PCR amplification. The measured 16S rRNA:16S rRNA gene ratio of E. coli increased by 2-3 fold when E. coli 16S rRNA gene and 16S rRNA quantities were normalized to the sample-specific fractional recoveries of reference (P. fluorescens) 16S rRNA gene and 16S rRNA, respectively. In addition, the intra-sample variation of this ratio, represented by coefficients of variation from replicate samples, decreased significantly after normalization. This technique was applied to investigate the temporal variation of 16S rRNA:16S rRNA gene ratio of E. coli during its non-steady-state growth in a complex liquid medium, and to E. coli aerosols when exposed to particle-free air after their collection on a filter. The 16S rRNA:16S rRNA gene ratio of E. coli increased significantly during its early exponential phase of growth; when E. coli aerosols were exposed to extended filtration stress after sample collection, the ratio also increased. In contrast, no significant temporal trend in E. coli 16S rRNA:16S rRNA gene ratio was observed when the determined ratios were not normalized based on the recoveries of dual references. The developed technique could be widely applied in studies of relationship between

  9. Metagenomic data of fungal internal transcribed Spacer and 18S rRNA gene sequences from Lonar lake sediment, India.

    PubMed

    Dudhagara, Pravin; Ghelani, Anjana; Bhavsar, Sunil; Bhatt, Shreyas

    2015-09-01

    The data in this article contains the sequences of fungal Internal Transcribed Spacer (ITS) and 18S rRNA gene from a metagenome of Lonar soda lake, India. Sequences were amplified using fungal specific primers, which amplified the amplicon lined between the 18S and 28S rRNA genes. Data were obtained using Fungal tag-encoded FLX amplicon pyrosequencing (fTEFAP) technique and used to analyze fungal profile by the culture-independent method. Primary analysis using PlutoF 454 pipeline suggests the Lonar lake mycobiome contained the 29 different fungal species. The raw sequencing data used to perform this analysis along with FASTQ file are located in the NCBI Sequence Read Archive (SRA) under accession No. SRX889598 (http://www.ncbi.nlm.nih.gov/sra/SRX889598).

  10. 76 FR 35024 - National Institute of Justice Stab-Resistant Body Armor Standard Workshop

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-15

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF JUSTICE Office of Justice Programs National Institute of Justice Stab-Resistant Body Armor Standard Workshop AGENCY: National Institute of Justice, DOJ. ACTION: Notice of Meeting of the Stab-Resistant Body Armor...

  11. 48 CFR 225.7011 - Restriction on carbon, alloy, and armor steel plate.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 3 2011-10-01 2011-10-01 false Restriction on carbon, alloy, and armor steel plate. 225.7011 Section 225.7011 Federal Acquisition Regulations System DEFENSE... on carbon, alloy, and armor steel plate....

  12. 48 CFR 225.7011 - Restriction on carbon, alloy, and armor steel plate.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 48 Federal Acquisition Regulations System 3 2013-10-01 2013-10-01 false Restriction on carbon, alloy, and armor steel plate. 225.7011 Section 225.7011 Federal Acquisition Regulations System DEFENSE... on carbon, alloy, and armor steel plate....

  13. 48 CFR 225.7011 - Restriction on carbon, alloy, and armor steel plate.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 3 2014-10-01 2014-10-01 false Restriction on carbon, alloy, and armor steel plate. 225.7011 Section 225.7011 Federal Acquisition Regulations System DEFENSE... on carbon, alloy, and armor steel plate....

  14. 48 CFR 225.7011 - Restriction on carbon, alloy, and armor steel plate.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 48 Federal Acquisition Regulations System 3 2012-10-01 2012-10-01 false Restriction on carbon, alloy, and armor steel plate. 225.7011 Section 225.7011 Federal Acquisition Regulations System DEFENSE... on carbon, alloy, and armor steel plate....

  15. 48 CFR 225.7011 - Restriction on carbon, alloy, and armor steel plate.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 3 2010-10-01 2010-10-01 false Restriction on carbon, alloy, and armor steel plate. 225.7011 Section 225.7011 Federal Acquisition Regulations System DEFENSE... on carbon, alloy, and armor steel plate....

  16. HIGH FREQUENCY ULTRASOUND OF ARMOR-GRADE ALUMINA CERAMICS

    SciTech Connect

    Bottiglieri, S.; Haber, R. A.

    2009-03-03

    Different lots of high density, commercial, armor-grade alumina (Al{sub 2}O{sub 3}) were tested using high frequency ultrasound in order to determine any correlation between measured properties and ballistic performance. C-scan images were taken using a 15 MHz ultrasonic transducer in order to form attenuation coefficient and elastic property maps. These samples were further characterized by using quantitative analysis. The results indicate that attenuation coefficient values appear to have the strongest correlation, of every property measured, to ballistic classifications.

  17. Simulation of armor penetration by tungsten rods: ALEGRA validation report

    SciTech Connect

    Carroll, D.E.; Hertel, E.S. Jr.; Trucano, T.G.

    1997-11-01

    Results from simulations of the impact and penetration of tungsten alloy rods into thick rolled armor plates are presented. The calculations were performed with the CTH and ALEGRA computer codes using the DOE massively parallel TFLOPS computer co-developed by Sandia National Laboratory and Intel Corporation. Comparisons with experimental results are presented. Agreement of the two codes with each other and with the empirical results for penetration channel depth and radius is very close. Other shock physics and penetration features are also compared to simulation results.

  18. Laser-induced micro-jetting from armored droplets

    NASA Astrophysics Data System (ADS)

    Marston, J. O.; Thoroddsen, S. T.

    2015-07-01

    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.

  19. Screening for plant viruses by next generation sequencing using a modified double strand RNA extraction protocol with an internal amplification control.

    PubMed

    Kesanakurti, Prasad; Belton, Mark; Saeed, Hanaa; Rast, Heidi; Boyes, Ian; Rott, Michael

    2016-10-01

    The majority of plant viruses contain RNA genomes. Detection of viral RNA genomes in infected plant material by next generation sequencing (NGS) is possible through the extraction and sequencing of total RNA, total RNA devoid of ribosomal RNA, small RNA interference (RNAi) molecules, or double stranded RNA (dsRNA). Plants do not typically produce high molecular weight dsRNA, therefore the presence of dsRNA makes it an attractive target for plant virus diagnostics. The sensitivity of NGS as a diagnostic method demands an effective dsRNA protocol that is both representative of the sample and minimizes sample cross contamination. We have developed a modified dsRNA extraction protocol that is more efficient compared to traditional protocols, requiring reduced amounts of starting material, that is less prone to sample cross contamination. This was accomplished by using bead based homogenization of plant material in closed, disposable 50ml tubes. To assess the quality of extraction, we also developed an internal control by designing a real-time (quantitative) PCR (qPCR) assay that targets endornaviruses present in Phaseolus vulgaris cultivar Black Turtle Soup (BTS). PMID:27387642

  20. Screening for plant viruses by next generation sequencing using a modified double strand RNA extraction protocol with an internal amplification control.

    PubMed

    Kesanakurti, Prasad; Belton, Mark; Saeed, Hanaa; Rast, Heidi; Boyes, Ian; Rott, Michael

    2016-10-01

    The majority of plant viruses contain RNA genomes. Detection of viral RNA genomes in infected plant material by next generation sequencing (NGS) is possible through the extraction and sequencing of total RNA, total RNA devoid of ribosomal RNA, small RNA interference (RNAi) molecules, or double stranded RNA (dsRNA). Plants do not typically produce high molecular weight dsRNA, therefore the presence of dsRNA makes it an attractive target for plant virus diagnostics. The sensitivity of NGS as a diagnostic method demands an effective dsRNA protocol that is both representative of the sample and minimizes sample cross contamination. We have developed a modified dsRNA extraction protocol that is more efficient compared to traditional protocols, requiring reduced amounts of starting material, that is less prone to sample cross contamination. This was accomplished by using bead based homogenization of plant material in closed, disposable 50ml tubes. To assess the quality of extraction, we also developed an internal control by designing a real-time (quantitative) PCR (qPCR) assay that targets endornaviruses present in Phaseolus vulgaris cultivar Black Turtle Soup (BTS).

  1. Origin of the 44-mm behind-armor blunt trauma standard.

    PubMed

    Hanlon, Erin; Gillich, Patrick

    2012-03-01

    A number of armed assaults on public officials occurred in the early 1970s, which prompted the Lightweight Soft Body Armor Program to develop modern, concealable, soft body armor. Methodology needed to be developed to (1) determine the effectiveness of the soft body armor to stop bullet penetration and (2) assess the potential injury from nonpenetrating blunt impacts to the body. Extensive research was performed under the program to develop methodologies to assess soft body armor, including behind-armor blunt trauma (BABT) evaluation. This methodology is still used today, and it has been applied extensively beyond the original intent. However, the origin of this methodology is not well understood by many researchers in the various fields in which it is being applied because the original documentation is difficult to obtain. Therefore, the purpose of this article is to provide a comprehensive review of the BABT to offer researchers information about its history and limitations.

  2. TAP1, a yeast gene that activates the expression of a tRNA gene with a defective internal promoter.

    PubMed Central

    Di Segni, G; McConaughy, B L; Shapiro, R A; Aldrich, T L; Hall, B D

    1993-01-01

    We developed a genetic selection system based on nonsense suppression in Saccharomyces cerevisiae to identify mutations in proteins involved in transcription initiation by RNA polymerase III. A SUP4 tRNA(Tyr) internal promoter mutation (A53T61) that was unable to suppress ochre mutations in vivo and was incapable of binding TFIIIC in vitro was used as the target for selection of trans-acting compensatory mutations. We identified two such mutations in the same gene, which we named TAP1 (for transcription activation protein). The level of the SUP4A53T61 transcript was threefold higher in the tap1-1 mutant than in the wild type. The tap1-1 mutant strain was also temperature sensitive for growth. The thermosensitive character cosegregated with the restorer of suppression activity, as shown by meiotic linkage analysis and coreversion of the two traits. At 1 to 2 h after a shift to the restrictive temperature, RNA synthesis was strongly inhibited in the tap1-1 mutant, preceding any effect upon protein synthesis or growth. A marked decrease in tRNA and 5S rRNA synthesis was seen, and shortly after that, rRNA synthesis was inhibited. By complementation of the ts- growth defect, we cloned the wild-type TAP1 gene. It is essential for yeast growth. We show in the accompanying report (T. L. Aldrich, G. Di Segni, B. L. McConaughy, N. J. Keen, S. Whelen, and B. D. Hall, Mol. Cell. Biol. 13:3434-3444, 1993) that TAP1 is identical to RAT1, a yeast gene implicated in poly(A)+ RNA export and that the TAP1/RAT1 gene product has extensive sequence similarity to the protein encoded by another yeast gene (variously named DST2, KEM1, RAR5, SEP1, or XRN1) having exonuclease and DNA strand transfer activity (reviewed by Kearsey and Kipling [Trends Cell Biol. 1:110-112, 1991]). Images PMID:8497259

  3. Superelement Analysis of Tile-Reinforced Composite Armor

    NASA Technical Reports Server (NTRS)

    Davila, Carlos G.

    1998-01-01

    Super-elements can greatly improve the computational efficiency of analyses of tile-reinforced structures such as the hull of the Composite Armored Vehicle. By taking advantage of the periodicity in this type of construction, super-elements can be used to simplify the task of modeling, to virtually eliminate the time required to assemble the stiffness matrices, and to reduce significantly the analysis solution time. Furthermore, super-elements are fully transferable between analyses and analysts, so that they provide a consistent method to share information and reduce duplication. This paper describes a methodology that was developed to model and analyze large upper hull components of the Composite Armored Vehicle. The analyses are based on two types of superelement models. The first type is based on element-layering, which consists of modeling a laminate by using several layers of shell elements constrained together with compatibility equations. Element layering is used to ensure the proper transverse shear deformation in the laminate rubber layer. The second type of model uses three-dimensional elements. Since no graphical pre-processor currently supports super-elements, a special technique based on master-elements was developed. Master-elements are representations of super-elements that are used in conjunction with a custom translator to write the superelement connectivities as input decks for ABAQUS.

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

    SciTech Connect

    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.

  5. Numerical simulation of armored vehicles subjected to undercarriage landmine blasts

    NASA Astrophysics Data System (ADS)

    Erdik, A.; Kilic, S. A.; Kilic, N.; Bedir, S.

    2016-07-01

    Landmine threats play a crucial role in the design of armored personnel carriers. Therefore, a reliable blast simulation methodology is valuable to the vehicle design development process. The first part of this study presents a parametric approach for the quantification of the important factors such as the incident overpressure, the reflected overpressure, the incident impulse, and the reflected impulse for the blast simulations that employ the Arbitrary Lagrangian-Eulerian formulation. The effects of mesh resolution, mesh topology, and fluid-structure interaction (FSI) parameters are discussed. The simulation results are compared with the calculations of the more established CONventional WEaPons (CONWEP) approach based on the available experimental data. The initial findings show that the spherical topology provides advantages over the Cartesian mesh domains. Furthermore, the FSI parameters play an important role when coarse Lagrangian finite elements are coupled with fine Eulerian elements at the interface. The optimum mesh topology and the mesh resolution of the parametric study are then used in the landmine blast simulation. The second part of the study presents the experimental blast response of an armored vehicle subjected to a landmine explosion under the front left wheel in accordance with the NATO AEP-55 Standard. The results of the simulations show good agreement with the experimental measurements.

  6. Computational model for armor penetration. Annual report No. 3, October 1980-April 1983

    SciTech Connect

    Erlich, D.C.; Seaman, L.; Cooper, T.; Caligiuri, R.D.; Curran, D.R.

    1987-10-01

    This is the first volume of a two-volume series comprising the third annual report for the program Computational Model for Armor Penetration. The objective of the program was to develop a phenomenologically sound material-disintegration model for computationally simulating armor penetration by projectile impact. The model would provide the capability to predict the ballistic limit and downrange fragment size and velocity distributions and would eventually be used by the DoD for armor and penetrator design. The materials studied in the program were 4340 steel and depleted uranium alloy, (DU) for the penetrators, and rolled homogeneous armor (RHA) for the target. This Volume reports on the experimental and analytical work performed during the third year to conclude the development of a computational model, SHEAR3, that describes the dominant material failure and fragmentation process (adiabatic shear banding) responsible for long-rod penetrator erosion and thick armor plate plugging and fragmentation. Volume 1 also describes application of SHEAR3 with the Lagrangian wave propagation code C-HEMP to computationally simulate penetration of armor plate by normally impacting long rods both near the ballistic limit and at higher velocities sufficient to produce significant back-of-the-armor fragmentation.

  7. The effects of exercise and body armor on cognitive function in healthy volunteers.

    PubMed

    Roberts, Aaron P J; Cole, Jon C

    2013-05-01

    Police officers routinely wear body armor to protect themselves against the threat posed by firearms and edged weapons, yet little is known of the cognitive effects of doing so. Two studies investigated the effects of exercise and body armor on working memory function in healthy volunteers. In study 1, male undergraduates were assigned to one of four groups: (i) brief exercise, (ii) brief exercise wearing body armor, (iii) extended exercise, and (iv) extended exercise wearing body armor. In study 2, university gym members were assigned to one of two groups: (i) wearing body armor and (ii) not wearing body armor. In both studies, heart rate and oral temperature were measured before, immediately after, and 5 minutes after exercise. The phonemic verbal fluency task and digits backward test were administered at the same time points. In both studies, a mixed analysis of variance revealed statistically significant changes to the cognitive functioning of participants. A change in cognitive strategy was observed, reflected by a decrease in executive function (switches) and an increase in nonexecutive function (cluster size). These data suggest that the cognitive effects of exercise and body armor may have profound implications for police officers' ability to make tactical decisions. PMID:23756004

  8. Analysis of Tile-Reinforced Composite Armor. Part 1; Advanced Modeling and Strength Analyses

    NASA Technical Reports Server (NTRS)

    Davila, C. G.; Chen, Tzi-Kang; Baker, D. J.

    1998-01-01

    The results of an analytical and experimental study of the structural response and strength of tile-reinforced components of the Composite Armored Vehicle are presented. The analyses are based on specialized finite element techniques that properly account for the effects of the interaction between the armor tiles, the surrounding elastomers, and the glass-epoxy sublaminates. To validate the analytical predictions, tests were conducted with panels subjected to three-point bending loads. The sequence of progressive failure events for the laminates is described. This paper describes the results of Part 1 of a study of the response and strength of tile-reinforced composite armor.

  9. [To the hygienic standardization of the stroke of shock elements through the armored clothes].

    PubMed

    Logatkin, S M

    2008-01-01

    The author considers major criteria for assessing the armored clothes by the armored dynamic force in the impenetrability of shocking elements. The used material simulators and the methods of studies are critically analyzed. The analysis has led to the conclusion that deformity depth of human soft tissue stimulators (clay, plasticine, gelatin blocks), used to evaluate the quality of armored clothes) may not be an indicator for the hygienic standardization of the stroke of shock elements through a barrier if the time of interaction is not taken into account. PMID:18368708

  10. STS-113 crew during M-113 armored personnel carrier training

    NASA Technical Reports Server (NTRS)

    2002-01-01

    KENNEDY SPACE CENTER, FLA. -- STS-113 Mission Commander James Wetherbee practices driving an M-113 armored personnel carrier, part of emergency egress training during Terminal Countdown Demonstration Test activities. He and the rest of the crew are preparing for the mission aboard Space Shuttle Endeavour, which is scheduled to launch Nov. 10. The TCDT includes a launch countdown. The primary payloads on mission STS-113 are the first port truss segment, P1, and the Crew and Equipment Translation Aid (CETA) Cart B. Once delivered, the P1 truss will remain stowed until flight 12A.1 in 2003 when it will be attached to the central truss segment, S0, on the Space Station. Also onboard Space Shuttle Endeavour will be the Expedition 6 crew who will replace Expedition 5, returning to Earth after 4 months.

  11. STS-113 crew during M-113 armored personnel carrier training

    NASA Technical Reports Server (NTRS)

    2002-01-01

    KENNEDY SPACE CENTER, FLA. -- The STS-113 crew pause for a photo after test drives in the M-113 armored personnel carrier behind them. From left are Mission Specialist Michael Lopez-Alegria, Pilot Paul Lockhart, Commander James Wetherbee and Mission Specialist John Herrington. Driving the M-113 is part of emergency egress training at the pad, one of the Terminal Countdown Demonstration Test activities in preparation for launch. The TCDT also includes a simulated launch countdown. The primary payloads on mission STS-113 are the first port truss segment, P1, and the Crew and Equipment Translation Aid (CETA) Cart B. Once delivered, the P1 truss will remain stowed until flight 12A.1 in 2003 when it will be attached to the central truss segment, S0, on the Space Station. Also onboard Space Shuttle Endeavour will be the Expedition 6 crew who will replace Expedition 5, returning to Earth after 4 months.

  12. STS-113 crew during M-113 armored personnel carrier training

    NASA Technical Reports Server (NTRS)

    2002-01-01

    KENNEDY SPACE CENTER, FLA. - STS-113 Mission Specialist Michael Lopez-Alegria is ready to begin a test drive behind the wheel of an M-113 armored personnel carrier during emergency egress training at the pad. He and the rest of the crew are preparing for the mission aboard Space Shuttle Endeavour, which is scheduled to launch Nov. 10, by taking part in Terminal Countdown Demonstration Test activities. The TCDT includes a simulated launch countdown. The primary payloads on mission STS-113 are the first port truss segment, P1, and the Crew and Equipment Translation Aid (CETA) Cart B. Once delivered, the P1 truss will remain stowed until flight 12A.1 in 2003 when it will be attached to the central truss segment, S0, on the Space Station. Also onboard Space Shuttle Endeavour will be the Expedition 6 crew who will replace Expedition 5, returning to Earth after 4 months.

  13. STS-113 crew during M-113 armored personnel carrier training

    NASA Technical Reports Server (NTRS)

    2002-01-01

    KENNEDY SPACE CENTER, FLA. -- STS-113 Pilot Paul Lockhart test drives an M-113 armored personnel carrier, part of emergency egress training during Terminal Countdown Demonstration Test activities. He is accompanied by several other crew members, seen at left, Mission Specialist Michael Lopez-Alegria and Commander James Wetherbee. The crew is preparing for the mission aboard Space Shuttle Endeavour, which is scheduled to launch Nov. 10. The TCDT includes a simulated launch countdown. The primary payloads on mission STS-113 are the first port truss segment, P1, and the Crew and Equipment Translation Aid (CETA) Cart B. Once delivered, the P1 truss will remain stowed until flight 12A.1 in 2003 when it will be attached to the central truss segment, S0, on the Space Station. Also onboard Space Shuttle Endeavour will be the Expedition 6 crew who will replace Expedition 5, returning to Earth after 4 months.

  14. STS-113 crew during M-113 armored personnel carrier training

    NASA Technical Reports Server (NTRS)

    2002-01-01

    KENNEDY SPACE CENTER, FLA. -- STS-113 Mission Specialist Michael Lopez-Alegria concentrates on driving an M-113 armored personnel carrier during emergency egress training at the pad. He is accompanied by (far left) Mission Specialist John Herrington and Commander James Wetherbee. Behind Lopez-Alegria is Pilot Paul Lockhart. The crew is preparing for the mission aboard Space Shuttle Endeavour, which is scheduled to launch Nov. 10, by taking part in Terminal Countdown Demonstration Test activities. The TCDT includes a simulated launch countdown.. The primary payloads on mission STS-113 are the first port truss segment, P1, and the Crew and Equipment Translation Aid (CETA) Cart B. Once delivered, the P1 truss will remain stowed until flight 12A.1 in 2003 when it will be attached to the central truss segment, S0, on the Space Station. Also onboard Space Shuttle Endeavour will be the Expedition 6 crew who will replace Expedition 5, returning to Earth after 4 months.

  15. Coated armor system and process for making the same

    DOEpatents

    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.

  16. Estimated radiactive and shock loading of fusion reactor armor

    SciTech Connect

    Swift, D C

    2008-11-25

    Inertial confinement fusion (ICF) is of interest as a source of neutrons for proliferation-resistant and high burn-up fission reactor designs. ICF is a transient process, each implosion leading to energy release over a short period, with a continuous series of ICF operations needed to drive the fission reactor. ICF yields energy in the form of MeV-range neutrons and ions, and thermal x-rays. These radiations, particularly the thermal x-rays, can deposit a pulse of energy in the wall of the ICF chamber, inducing loading by isochoric heating (i.e. at constant volume before the material can expand) or by ablation of material from the surface. The explosion of the hot ICF system, and the compression of any fill material in the chamber, may also result in direct mechanical loading by a blast wave (decaying shock) reaching the chamber wall. The chamber wall must be able to survive the repetitive loading events for long enough for the reactor to operate economically. It is thus necessary to understand the loading induced by ICF systems in possible chamber wall designs, and to predict the response and life time of the wall. Estimates are given for the loading induced in the wall armor of the fusion chamber caused by ablative thermal radiation from the fusion plasma and by the hydrodynamic shock. Taking a version of the LIFE design as an example, the ablation pressure was estimated to be {approx}0.6 GPa with an approximately exponential decay with time constant {approx}0.6 ns. Radiation hydrodynamics simulations suggested that ablation of the W armor should be negligible.

  17. Use of body armor protection with fighting load impacts soldier performance and kinematics.

    PubMed

    Loverro, Kari L; Brown, Tyler N; Coyne, Megan E; Schiffman, Jeffrey M

    2015-01-01

    The purpose of this evaluation was to examine how increasing body armor protection with and without a fighting load impacted soldiers' performance and mobility. Thirteen male soldiers performed one performance (repeated 30-m rushing) and three mobility tasks (walk, walk over and walk under) with three different body armor configurations and an anterior fighting load. Increasing body armor protection, decreased soldier performance, as individual and total 30-m rush times were significantly longer with greater protection. While increasing body armor protection had no impact on mobility, i.e. significant effect on trunk and lower limb biomechanics, during the walk and walk over tasks, greater protection did significantly decrease maximum trunk flexion during the walk under task. Adding fighting load may negatively impact soldier mobility, as greater maximum trunk extension was evident during the walk and walk over tasks, and decreased maximum trunk flexion exhibited during the walk under task with the fighting load.

  18. 76 FR 22920 - Stab Resistance of Personal Body Armor (2000) Standard Special Technical Committee Request for...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-25

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF JUSTICE Office of Justice Programs Stab Resistance of Personal Body Armor (2000) Standard Special Technical... Justice, DOJ. ACTION: Request for Proposals for Certification and Testing Expertise. SUMMARY: The...

  19. Shock imprint and rolling direction influence upon the breaking tenacity for 2P armor steel

    NASA Astrophysics Data System (ADS)

    Zichil, V.; Coseru, A.; Schnakovszky, C.; Herghelegiu, E.; Radu, C.

    2016-08-01

    The state of art in present literature shows that the breaking tenacity of a material is influenced by the integrity of the structure. Since armors used in aviation and to protect military vehicles are frequently impact loaded, through the contact between armor sheet and projectiles, or other foreign bodies, the authors have proposed to study the dependence between the breaking tenacity of 2P armor steel depending on the direction of the rolling of the armor plate, of the geometry (spherical imprint, pyramidal and linear imprint) and the depth of the deformation that results after impact. Tests were conducted upon CT (ASTM E- 399) specimen type, using the critical factor of stress intensity during the state of planar strain.

  20. Modeling gunshot bruises in soft body armor with an adaptive fuzzy system.

    PubMed

    Lee, Ian; Kosko, Bart; Anderson, W French

    2005-12-01

    Gunshots produce bruise patterns on persons who wear soft body armor when shot even though the armor stops the bullets. An adaptive fuzzy system modeled these bruise patterns based on the depth and width of the deformed armor given a projectile's mass and momentum. The fuzzy system used rules with sinc-shaped if-part fuzzy sets and was robust against random rule pruning: Median and mean test errors remained low even after removing up to one fifth of the rules. Handguns shot different caliber bullets at armor that had a 10%-ordnance gelatin backing. The gelatin blocks were tissue simulants. The gunshot data tuned the additive fuzzy function approximator. The fuzzy system's conditional variance V[Y/X = x] described the second-order uncertainty of the function approximation. Handguns with different barrel lengths shot bullets over a fixed distance at armor-clad gelatin blocks that we made with Type 250 A Ordnance Gelatin. The bullet-armor experiments found that a bullet's weight and momentum correlated with the depth of its impact on armor-clad gelatin (R2 = 0.881 and p-value < 0.001 for the null hypothesis that the regression line had zero slope). Related experiments on plumber's putty showed that highspeed baseball impacts compared well to bullet-armor impacts for large-caliber handguns. A baseball's momentum correlated with its impact depth in putty (R2 = 0.93 and p-value < 0.001). A bullet's momentum similarly correlated with its armor-impact in putty (R2 = 0.97 and p-value < 0.001). A Gujarati-Chow test showed that the two putty-impact regression lines had statistically indistinguishable slopes for p-value = 0.396. Baseball impact depths were comparable to bullet-armor impact depths: Getting shot with a .22 caliber bullet when wearing soft body armor resembles getting hit in the chest with a 40-mph baseball. Getting shot with a .45 caliber bullet resembles getting hit with a 90-mph baseball.

  1. Modeling gunshot bruises in soft body armor with an adaptive fuzzy system.

    PubMed

    Lee, Ian; Kosko, Bart; Anderson, W French

    2005-12-01

    Gunshots produce bruise patterns on persons who wear soft body armor when shot even though the armor stops the bullets. An adaptive fuzzy system modeled these bruise patterns based on the depth and width of the deformed armor given a projectile's mass and momentum. The fuzzy system used rules with sinc-shaped if-part fuzzy sets and was robust against random rule pruning: Median and mean test errors remained low even after removing up to one fifth of the rules. Handguns shot different caliber bullets at armor that had a 10%-ordnance gelatin backing. The gelatin blocks were tissue simulants. The gunshot data tuned the additive fuzzy function approximator. The fuzzy system's conditional variance V[Y/X = x] described the second-order uncertainty of the function approximation. Handguns with different barrel lengths shot bullets over a fixed distance at armor-clad gelatin blocks that we made with Type 250 A Ordnance Gelatin. The bullet-armor experiments found that a bullet's weight and momentum correlated with the depth of its impact on armor-clad gelatin (R2 = 0.881 and p-value < 0.001 for the null hypothesis that the regression line had zero slope). Related experiments on plumber's putty showed that highspeed baseball impacts compared well to bullet-armor impacts for large-caliber handguns. A baseball's momentum correlated with its impact depth in putty (R2 = 0.93 and p-value < 0.001). A bullet's momentum similarly correlated with its armor-impact in putty (R2 = 0.97 and p-value < 0.001). A Gujarati-Chow test showed that the two putty-impact regression lines had statistically indistinguishable slopes for p-value = 0.396. Baseball impact depths were comparable to bullet-armor impact depths: Getting shot with a .22 caliber bullet when wearing soft body armor resembles getting hit in the chest with a 40-mph baseball. Getting shot with a .45 caliber bullet resembles getting hit with a 90-mph baseball. PMID:16366262

  2. Fluorescence detection of KRAS2 mRNA hybridization in lung cancer cells with PNA-peptides containing an internal thiazole orange.

    PubMed

    Sonar, Mahesh V; Wampole, Matthew E; Jin, Yuan-Yuan; Chen, Chang-Po; Thakur, Mathew L; Wickstrom, Eric

    2014-09-17

    We previously developed reporter-peptide nucleic acid (PNA)-peptides for sequence-specific radioimaging and fluorescence imaging of particular mRNAs in cells and tumors. However, a direct test for PNA-peptide hybridization with RNA in the cytoplasm would be desirable. Thiazole orange (TO) dye at the 5' end of a hybridization agent shows a strong increase in fluorescence quantum yield when stacked upon a 5' terminal base pair, in solution and in cells. We hypothesized that hybridization agents with an internal TO could distinguish a single base mutation in RNA. Thus, we designed KRAS2 PNA-IGF1 tetrapeptide agents with an internal TO adjacent to the middle base of the 12th codon, a frequent site of cancer-initiating mutations. Our molecular dynamics calculations predicted a disordered bulge with weaker hybridization resulting from a single RNA mismatch. We observed that single-stranded PNA-IGF1 tetrapeptide agents with an internal TO showed low fluorescence, but fluorescence escalated 5-6-fold upon hybridization with KRAS2 RNA. Circular dichroism melting curves showed ∼10 °C higher Tm for fully complementary vs single base mismatch TO-PNA-peptide agent duplexes with KRAS2 RNA. Fluorescence measurements of treated human lung cancer cells similarly showed elevated cytoplasmic fluorescence intensity with fully complementary vs single base mismatch agents. Sequence-specific elevation of internal TO fluorescence is consistent with our hypothesis of detecting cytoplasmic PNA-peptide:RNA hybridization if a mutant agent encounters the corresponding mutant mRNA.

  3. Fluorescence Detection of KRAS2 mRNA Hybridization in Lung Cancer Cells with PNA-Peptides Containing an Internal Thiazole Orange

    PubMed Central

    2015-01-01

    We previously developed reporter-peptide nucleic acid (PNA)-peptides for sequence-specific radioimaging and fluorescence imaging of particular mRNAs in cells and tumors. However, a direct test for PNA-peptide hybridization with RNA in the cytoplasm would be desirable. Thiazole orange (TO) dye at the 5′ end of a hybridization agent shows a strong increase in fluorescence quantum yield when stacked upon a 5′ terminal base pair, in solution and in cells. We hypothesized that hybridization agents with an internal TO could distinguish a single base mutation in RNA. Thus, we designed KRAS2 PNA-IGF1 tetrapeptide agents with an internal TO adjacent to the middle base of the 12th codon, a frequent site of cancer-initiating mutations. Our molecular dynamics calculations predicted a disordered bulge with weaker hybridization resulting from a single RNA mismatch. We observed that single-stranded PNA-IGF1 tetrapeptide agents with an internal TO showed low fluorescence, but fluorescence escalated 5–6-fold upon hybridization with KRAS2 RNA. Circular dichroism melting curves showed ∼10 °C higher Tm for fully complementary vs single base mismatch TO-PNA-peptide agent duplexes with KRAS2 RNA. Fluorescence measurements of treated human lung cancer cells similarly showed elevated cytoplasmic fluorescence intensity with fully complementary vs single base mismatch agents. Sequence-specific elevation of internal TO fluorescence is consistent with our hypothesis of detecting cytoplasmic PNA-peptide:RNA hybridization if a mutant agent encounters the corresponding mutant mRNA. PMID:25180641

  4. Characterization of vibration and noise exposure in Canadian Forces armored vehicles

    NASA Astrophysics Data System (ADS)

    Nakashima, Ann M.; Borland, Matthew J.; Abel, Sharon M.

    2005-09-01

    A study to characterize the vibration and noise exposure in several Canadian Forces (CF) armored vehicles is in progress. Measurements of whole-body vibration and ambient noise levels are being made in the LAV III, Bison, Coyote, and M113 vehicles at three different positions: driver, crew commander, and passenger bench (or navigator seat in the case of the Coyote). The measurements are being made while the vehicles are idling, driven over rough terrain, and driven at a high speed on paved highways. There are several standards that provide guidance on the measurement and assessment of whole-body vibration, but they are difficult to implement in practice, particularly in adverse environments. The whole-body vibration measurements in this study are particularly difficult to interpret in the case of the crew commander, who often stands on the seat, and the passenger, who is seated but unrestrained by a seatbelt. The preliminary results-suggest, that according to the International Organization for Standardization guidelines (ISO 2631-1:1997), there may be potential health risks for the driver and passenger after driving on rough terrain for less than 10 min. Noise levels were as high as 100 dBA during high-speed highway driving.

  5. Bedload Transport Processes in Armored, Gravel-bed Channels: Impacts of Hydrograph Form

    NASA Astrophysics Data System (ADS)

    Kenworthy, M.; Yager, E.; Yarnell, S. M.

    2014-12-01

    Accurately predicting bed load transport rates remains challenging, with many influential factors still poorly understood, including unsteady flows and stream bed armoring. Nearly all natural channels experience unsteady flows, and hydrograph form varies significantly from gradually (i.e. snowmelt) to rapidly changing flows (i.e. rain driven or many regulated flows). However, most predictive methods neglect hydrograph impacts, and nearly all bedload transport experiments use steady flows. Stream bed armoring likely influences bedload transport rates as well, with the coarser surface limiting the availability of the finer, more mobile grain sizes in the subsurface. It remains uncertain whether armor persists, breaks up, or exchanges particles with bedload during high flow events. Coupled effects of hydrograph form and armor may also be significant, and previous work indicates that more gradual changes in flow promote more significant armoring compared to rapid changes in flow. To better understand the impacts of hydrograph form and armoring on bedload transport processes in gravel-bed rivers, flume experiments were conducted at the University of Idaho's Stream Lab. An armored, equilibrium bed was established as the initial condition for all experiments, which included steady-state discharges and a variety of hydrograph forms from gradually to rapidly changing. Steady-state runs allowed for comparison of bedload transport for a given discharge run singularly and in the context of various hydrographs. Though hydrograph form varied, minimum and peak flow rates and the total estimated transport capacity were held constant between runs. Armor ratios were estimated before and after runs by sampling the surface and subsurface separately. Armor behavior during runs was tracked by spray-painting the bed surface in three cross-sections that were repeatedly photographed then excavated after runs. Additional data collection during runs included photos for bed grain size

  6. Armored kinorhynch-like scalidophoran animals from the early Cambrian.

    PubMed

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

    2015-01-01

    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. PMID:26610151

  7. Reverse evolution of armor plates in the threespine stickleback.

    PubMed

    Kitano, Jun; Bolnick, Daniel I; Beauchamp, David A; Mazur, Michael M; Mori, Seiichi; Nakano, Takanori; Peichel, Catherine L

    2008-05-20

    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. PMID:18485710

  8. Armored kinorhynch-like scalidophoran animals from the early Cambrian.

    PubMed

    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.

  9. Viscoelastic shock wave in ballistic gelatin behind soft body armor.

    PubMed

    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. PMID:24607758

  10. Reverse Evolution of Armor Plates in the Threespine Stickleback

    USGS Publications Warehouse

    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.

  11. Armored kinorhynch-like scalidophoran animals from the early Cambrian

    PubMed Central

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

    2015-01-01

    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. PMID:26610151

  12. Viscoelastic shock wave in ballistic gelatin behind soft body armor.

    PubMed

    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.

  13. Unlocking Function of Aramid Fibers in Multilayered Ballistic Armor

    NASA Astrophysics Data System (ADS)

    Monteiro, Sergio N.; Lima, Édio P.; Louro, Luis Henrique L.; da Silva, Luis Carlos; Drelich, Jaroslaw W.

    2015-01-01

    Aramid fabric plies were ballistic tested using high impact 7.62 × 51 mm ammunition in two distinct conditions: (1) as a common multilayered armor system (MAS) component backing a front Al2O3-based tile, and (2) with the same plies thickness, as a single target. Single targets of the ceramic tile and the aluminum sheet (MAS third layer) were also tested. In the MAS, the aramid dissipated more than 36 pct of the impact energy during the test compared with only ~2 pct when separated from the MAS. Microscopic examination of aramid fabric revealed many ceramic fragments with a size of a few micrometers that coated surfaces of fibers. It is shown for the first time that, in addition to already reported fabric rupture, debonding, and stretching, a massive incrustation of ceramic fragments onto the fabric fibers might be responsible for the comparatively high aramid ballistic performance as the MAS component. Besides the mechanical incrustation and van der Waals forces on the harder ceramic fragments, it is proposed that short-living surface static charges generated on the aramid fibers could contribute to the capturing process.

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

    PubMed

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

    2014-09-01

    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. PMID:24613857

  15. Structural properties of mobile armors formed at different flow strengths in gravel-bed rivers

    NASA Astrophysics Data System (ADS)

    Powell, D. Mark; Ockelford, Annie; Rice, Stephen P.; Hillier, John K.; Nguyen, Thao; Reid, Ian; Tate, Nicholas J.; Ackerley, David

    2016-08-01

    Differences in the structure of mobile armors formed at three different flow strengths have been investigated in a laboratory flume. The temporal evolution of the bed surfaces and the properties of the final beds were compared using metrics of surface grain size, microtopography, and bed organization at both grain and mesoscales. Measurements of the bed condition were obtained on nine occasions during each experiment to describe the temporal evolution of the beds. Structured mobile armors formed quickly in each experiment. At the grain scale (1-45 mm; 9 ≤ Ds50 ≤ 17 mm where Ds50 is the median surface particle size), surface complexity decreased and bed roughness increased in response to surface coarsening and the development of the mobile armor. Particles comprising the armor also became flow aligned and developed imbrication. At a larger scale (100-200 mm), the surface developed a mesoscale topography through the development of bed patches with lower and higher elevations. Metrics of mobile armor structure showed remarkable consistency over prolonged periods of near-constant transport, demonstrating for the first time that actively transporting surfaces maintain an equilibrium bed structure. Bed structuring was least developed in the experiments conducted at the lowest flow strength. However, little difference was observed in the structural metrics of the mobile armors generated at higher flows. Although the range of transport rates studied was limited, the results suggest that the structure of mobile armors is insensitive to the formative transport rate except when rates are low (τ* ≈ 0.03 where τ* is the dimensionless shear stress).

  16. Additional data for a new Theileria sp. from China based on the sequences of ribosomal RNA internal transcribed spacers.

    PubMed

    Liu, Junlong; Guan, Guiquan; Liu, Zhijie; Liu, Aihong; Ma, Miling; Bai, Qi; Yin, Hong; Luo, Jianxun

    2013-02-01

    Theileria sinensis was recently isolated and named as an independent Theileria species that infects cattle in China. To date, this parasite has been described based on its morphology, transmission and molecular studies, indicating that it should be classified as a distinct species. To test the validity of this taxon, the two internal transcribed spacers (ITS1 and ITS2) and the 5.8S rRNA gene were cloned and sequenced from three T. sinensis isolates. The complete ITS sequences were compared with those of other Theileria sp. available in GenBank. Phylogenetic analyses based on sequence data for the complete ITS sequences indicate that T. sinensis lies in a distinct clade that is separate from that of T. buffeli/orientalis and T. annulata. Sequence comparisons indicate that different T. sinensis isolates possess unique sizes of ITS1 and ITS2 as well as species-specific nucleotide sequences. This analysis provides new molecular data to support the classification of T. sinensis as a distinct species from other known Theileria spp. based on ITS sequences.

  17. The addition of body armor diminishes dynamic postural stability in military soldiers.

    PubMed

    Sell, Timothy C; Pederson, Jonathan J; Abt, John P; Nagai, Takashi; Deluzio, Jennifer; Wirt, Michael D; McCord, Larry J; Lephart, Scott M

    2013-01-01

    Poor postural stability has been identified as a risk factor for lower extremity musculoskeletal injury. The additional weight of body armor carried by Soldiers alters static postural stability and may predispose Soldiers to lower extremity musculoskeletal injuries. However, static postural stability tasks poorly replicate the dynamic military environment, which places considerable stress on the postural control system during tactical training and combat. Therefore, the purpose of this study was to examine the effects of body armor on dynamic postural stability during single-leg jump landings. Thirty-six 101st Airborne Division (Air Assault) Soldiers performed single-leg jump landings in the anterior direction with and without wearing body armor. The dynamic postural stability index and the individual stability indices (medial-lateral stability index, anterior-posterior stability index, and vertical stability index) were calculated for each condition. Paired sample t-tests were performed to determine differences between conditions. Significant differences existed for the medial-lateral stability index, anterior-posterior stability index, vertical stability index, and dynamic postural stability index (p < 0.05). The addition of body armor resulted in diminished dynamic postural stability, which may result in increased lower extremity injuries. Training programs should address the altered dynamic postural stability while wearing body armor in attempts to promote adaptations that will result in safer performance during dynamic tasks.

  18. ALON optical ceramic transparencies for window, dome, and transparent armor applications

    NASA Astrophysics Data System (ADS)

    Goldman, Lee M.; Twedt, Rich; Balasubramanian, Sreeram; Sastri, Suri

    2011-06-01

    Surmet continues to invest in and expand its manufacturing capability for ALON® Optical Ceramic, as the market demand for this material increases. The biggest demand and opportunity continues to be in the area of transparent armor, however, the market for sensor domes and windows, made from ALON, continues to grow at an impressive rate as well. ALON® Transparent Armor's unsurpassed ballistic performance, combined with the robustness of ALON's manufacturing process and reproducibly high material quality make ALON the leading candidate for many future armor systems. Recent results for ALON armor windows will be presented. Advances being made in Surmet's production capability to support the very large quantities of material required by the transparent armor market also benefit the sensor market. Improvements in quality, quantity and manufacturability of ALON material, combined with improvements being made in optical quality, ensure a robust supply of high quality material for high volume window and dome applications. Recent advancement in ALON® window and dome blanks, as well as in optical fabrication will be presented.

  19. Identification of fundamental deformation and failure mechanisms in armor ceramics

    NASA Astrophysics Data System (ADS)

    Muller, Andrea Marie

    Indentation of a surface with a hard sphere can be used to examine micromechanical response of a wide range of materials and has been shown to generate loading conditions resembling early stages of ballistic impact events. Cracking morphologies also show similarities, particularly with formation of cone cracks at the contact site. The approach in this thesis is to use this indentation technique to characterize contact damage and deformation processes in armor ceramics, as well as identify the role of cone cracking and inelastic behavior. To accomplish these objectives, an instrumented indentation system was designed and fabricated, extending depth-sensing capabilities originally developed for nano-indentation to higher forces. This system is also equipped with an acoustic emission system to detect onset of cone cracking and subsequent failure. Once calibrated and verified the system was used to evaluate elastic modulus and cone crack initiation forces of two commercial float glasses. As-received air and tin surfaces of soda-lime-silica and borosilicate float glass were tested to determine differences in elastic and fracture behavior. Information obtained from load--displacement curves and visual inspection of indentation sites were used to determine elastic modulus, and conditions for onset of cone cracking as a function of surface roughness. No difference in reduced modulus or cone cracking loads on as-received air and tin surfaces were observed. Abraded surfaces showed the tin surface to be slightly more resistant to cone cracking. A study focusing on the transition from elastic to inelastic deformation in two transparent fine-grained polycrystalline spinels with different grain sizes was then conducted. Congruent experiments included observations on evolution of damage, examinations of sub-surface damage and inspection of remnant surface profiles. Indentation stress--strain behavior obtained from load--displacement curves revealed a small difference in yielding

  20. Biophysical Assessment and Predicted Thermophysiologic Effects of Body Armor

    PubMed Central

    Potter, Adam W.; Gonzalez, Julio A.; Karis, Anthony J.; Xu, Xiaojiang

    2015-01-01

    Introduction Military personnel are often required to wear ballistic protection in order to defend against enemies. However, this added protection increases mass carried and imposes additional thermal burden on the individual. Body armor (BA) is known to reduce combat casualties, but the effects of BA mass and insulation on the physical performance of soldiers are less well documented. Until recently, the emphasis has been increasing personal protection, with little consideration of the adverse impacts on human performance. Objective The purpose of this work was to use sweating thermal manikin and mathematical modeling techniques to quantify the tradeoff between increased BA protection, the accompanying mass, and thermal effects on human performance. Methods Using a sweating thermal manikin, total insulation (IT, clo) and vapor permeability indexes (im) were measured for a baseline clothing ensemble with and without one of seven increasingly protective U.S. Army BA configurations. Using mathematical modeling, predictions were made of thermal impact on humans wearing each configuration while working in hot/dry (desert), hot/humid (jungle), and temperate environmental conditions. Results In nearly still air (0.4 m/s), IT ranged from 1.57 to 1.63 clo and im from 0.35 to 0.42 for the seven BA conditions, compared to IT and im values of 1.37 clo and 0.45 respectively, for the baseline condition (no BA). Conclusion Biophysical assessments and predictive modeling show a quantifiable relationship exists among increased protection and increased thermal burden and decreased work capacity. This approach enables quantitative analysis of the tradeoffs between ballistic protection, thermal-work strain, and physical work performance. PMID:26200906

  1. 75 FR 78268 - Draft NIJ Selection and Application Guide to Ballistic-Resistant Body Armor for Law Enforcement...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-15

    ... of Justice Programs Draft NIJ Selection and Application Guide to Ballistic-Resistant Body Armor for... of Draft NIJ Selection and Application Guide to Ballistic-Resistant Body Armor for Law Enforcement... the general public the draft ``NIJ Selection and Application Guide to Ballistic-Resistant Body...

  2. MESA 3-D calculations of armor penetration by projectiles with combined obliquity and yaw

    SciTech Connect

    Cagliostro, D.J.; Mandell, D.A.; Schwalbe, L.A.; Adams, T.F.; Chapyak, E.J. )

    1989-01-01

    We introduce and briefly describe MESA, a new 3-D hydrodynamic code, developed specifically for simulations of armor and anti-armor systems. The code's current capabilities an its planned model improvements and additions are discussed. An Eulerian code using state-of-the-art numerical methods, MESA runs faster and is less affected by spurious numerical diffusion than older codes. It models hydrodynamic flow and the dynamic deformation of solid materials. It uses simple elastic-perfectly plastic material strength models as well as models with strain and strainrate hardening and thermal softening. Future versions will incorporate advanced fracture models. It treats detonations in explosives using a programmed burn. The code's current capabilities are illustrated with simulations of experiments on yawed rods obliquely impacting armor plates at 1.29 km/s. 12 refs., 14 figs.

  3. Porosity Detection in Ceramic Armor Tiles via Ultrasonic Time-Of

    NASA Astrophysics Data System (ADS)

    Margetan, Frank J.; Richter, Nathaniel; Jensen, Terrence

    2011-06-01

    Some multilayer armor panels contain ceramic tiles as one constituent, and porosity in the tiles can affect armor performance. It is well known that porosity in ceramic materials leads to a decrease in ultrasonic velocity. We report on a feasibility study exploring the use of ultrasonic time-of-flight (TOF) to locate and characterize porous regions in armor tiles. The tiles in question typically have well-controlled thickness, thus simplifying the translation of TOF data into velocity data. By combining UT velocity measurements and X-ray absorption measurements on selected specimens, one can construct a calibration curve relating velocity to porosity. That relationship can then be used to translate typical ultrasonic C-scans of TOF-versus-position into C-scans of porosity-versus-position. This procedure is demonstrated for pulse/echo, focused-transducer inspections of silicon carbide (SiC) ceramic tiles.

  4. Porosity detection in ceramic armor tiles via ultrasonic time-of-flight

    SciTech Connect

    Margetan, Frank J.; Richter, Nathaniel; Jensen, Terrence

    2011-06-23

    Some multilayer armor panels contain ceramic tiles as one constituent, and porosity in the tiles can affect armor performance. It is well known that porosity in ceramic materials leads to a decrease in ultrasonic velocity. We report on a feasibility study exploring the use of ultrasonic time-of-flight (TOF) to locate and characterize porous regions in armor tiles. The tiles in question typically have well-controlled thickness, thus simplifying the translation of TOF data into velocity data. By combining UT velocity measurements and X-ray absorption measurements on selected specimens, one can construct a calibration curve relating velocity to porosity. That relationship can then be used to translate typical ultrasonic C-scans of TOF-versus-position into C-scans of porosity-versus-position. This procedure is demonstrated for pulse/echo, focused-transducer inspections of silicon carbide (SiC) ceramic tiles.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    SciTech Connect

    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.

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

    PubMed

    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.

  8. NMR reveals the absence of hydrogen bonding in adjacent UU and AG mismatches in an isolated internal loop from ribosomal RNA.

    PubMed

    Shankar, Neelaabh; Xia, Tianbing; Kennedy, Scott D; Krugh, Thomas R; Mathews, David H; Turner, Douglas H

    2007-11-01

    NMR studies provide insights into structural features of internal loops. These insights can be combined with thermodynamic studies to generate models for predicting structure and energetics. The tandem mismatch internal loop, 5'GUGG3'(3'CUAC5'), has been studied by NMR. The NMR structure reveals an internal loop with no hydrogen bonding between the loop bases and with the G in the AG mismatch flipped out of the helix. The sequence of this internal loop is highly conserved in rRNA. The loop is located in the large ribosomal subunit and is part of a conserved 58-nt fragment that is the binding domain of ribosomal protein L11. Structural comparisons between variants of this internal loop in crystal structures of the 58-nt domain complexed with L11 protein and of the large ribosomal subunit (LSU) suggest that this thermodynamically destabilizing internal loop is partially preorganized for tertiary interactions and for binding L11. A model for predicting the base pairing and free energy of 2 x 2 nucleotide internal loops with a purine-purine mismatch next to a pyrimidine-pyrimidine mismatch is proposed on the basis of the present NMR structure and previously reported thermodynamics.

  9. 7 CFR 1755.406 - Shield or armor ground resistance measurements.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... plant and fiber optic cable plant. (b) Method of measurement. (1) The shield or armor ground resistance measurement shall be made between the copper cable and wire shield and ground and between the fiber optic... instructions. (d) Applicable results. (1) For all new copper cable and wire facilities and all new fiber...

  10. 27 CFR 478.148 - Armor piercing ammunition intended for sporting or industrial purposes.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... intended for sporting or industrial purposes. 478.148 Section 478.148 Alcohol, Tobacco Products, and... ammunition intended for sporting or industrial purposes. The Director may exempt certain armor piercing... for any such ammunition which is primarily intended for sporting purposes or intended for...

  11. 27 CFR 478.148 - Armor piercing ammunition intended for sporting or industrial purposes.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... intended for sporting or industrial purposes. 478.148 Section 478.148 Alcohol, Tobacco Products, and... ammunition intended for sporting or industrial purposes. The Director may exempt certain armor piercing... for any such ammunition which is primarily intended for sporting purposes or intended for...

  12. 27 CFR 478.148 - Armor piercing ammunition intended for sporting or industrial purposes.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... intended for sporting or industrial purposes. 478.148 Section 478.148 Alcohol, Tobacco Products, and... ammunition intended for sporting or industrial purposes. The Director may exempt certain armor piercing... for any such ammunition which is primarily intended for sporting purposes or intended for...

  13. 27 CFR 478.148 - Armor piercing ammunition intended for sporting or industrial purposes.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... intended for sporting or industrial purposes. 478.148 Section 478.148 Alcohol, Tobacco Products, and... ammunition intended for sporting or industrial purposes. The Director may exempt certain armor piercing... for any such ammunition which is primarily intended for sporting purposes or intended for...

  14. 27 CFR 478.148 - Armor piercing ammunition intended for sporting or industrial purposes.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... intended for sporting or industrial purposes. 478.148 Section 478.148 Alcohol, Tobacco Products, and... ammunition intended for sporting or industrial purposes. The Director may exempt certain armor piercing... for any such ammunition which is primarily intended for sporting purposes or intended for...

  15. 27 CFR 478.92 - How must licensed manufacturers and licensed importers identify firearms, armor piercing...

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 19 CFR part 134. (2) Firearm frames or receivers. A firearm frame or receiver that is not a component... 27 Alcohol, Tobacco Products and Firearms 3 2012-04-01 2010-04-01 true How must licensed manufacturers and licensed importers identify firearms, armor piercing ammunition, and large capacity...

  16. Further testing and development of simulation models for UT inspections of armor

    NASA Astrophysics Data System (ADS)

    Margetan, Frank J.; Richter, Nathaniel; Thompson, R. Bruce

    2012-05-01

    In previous work we introduced an approach for simulating ultrasonic pulse/echo immersion inspections of multi-layer armor panels. Model inputs include the thickness, density, velocity and attenuation of each armor layer, the focal properties of the transducer, and a measured calibration signal. The basic model output is a response-versus-time waveform (ultrasonic A-scan) which includes echoes from all interfaces including those arising from reverberations within layers. Such A-scans can be predicted both for unflawed panels and panels containing a large disbond at any given interface. In this paper we continue our testing of the simulation software, applying it now to an armor panel consisting of SiC ceramic tiles fully embedded in a titanium-alloy matrix. An interesting specimen of such armor became available in which some tile/metal interfaces appear to be well bonded, while others have disbonded areas of various sizes. We compare measured and predicted A-scans for UT inspections, and also demonstrate an extension of the model to predict ultrasonic C-scans over regions containing a small, isolated disbond.

  17. 7 CFR 1755.406 - Shield or armor ground resistance measurements.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... plant and fiber optic cable plant. (b) Method of measurement. (1) The shield or armor ground resistance measurement shall be made between the copper cable and wire shield and ground and between the fiber optic... instructions. (d) Applicable results. (1) For all new copper cable and wire facilities and all new fiber...

  18. 7 CFR 1755.406 - Shield or armor ground resistance measurements.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... plant and fiber optic cable plant. (b) Method of measurement. (1) The shield or armor ground resistance measurement shall be made between the copper cable and wire shield and ground and between the fiber optic... instructions. (d) Applicable results. (1) For all new copper cable and wire facilities and all new fiber...

  19. 7 CFR 1755.406 - Shield or armor ground resistance measurements.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... plant and fiber optic cable plant. (b) Method of measurement. (1) The shield or armor ground resistance measurement shall be made between the copper cable and wire shield and ground and between the fiber optic... instructions. (d) Applicable results. (1) For all new copper cable and wire facilities and all new fiber...

  20. 7 CFR 1755.406 - Shield or armor ground resistance measurements.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... plant and fiber optic cable plant. (b) Method of measurement. (1) The shield or armor ground resistance measurement shall be made between the copper cable and wire shield and ground and between the fiber optic... instructions. (d) Applicable results. (1) For all new copper cable and wire facilities and all new fiber...

  1. Calculation of stresses and slips in flexible armor layers with layers interaction

    SciTech Connect

    Feret, J.; Leroy, J.M.; Estrier, P.

    1995-12-31

    This paper deals with stress and displacement calculation in dynamically bent unbonded flexible pipes. The presented method is original in that movements and stresses of both armor layers are coupled. Good correlations between strain measurements and the theory have been found, as shown in the paper.

  2. 27 CFR 478.37 - Manufacture, importation and sale of armor piercing ammunition.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 3 2012-04-01 2010-04-01 true 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...

  3. 27 CFR 478.37 - Manufacture, importation and sale of armor piercing ammunition.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 3 2014-04-01 2014-04-01 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...

  4. 27 CFR 478.37 - Manufacture, importation and sale of armor piercing ammunition.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 3 2011-04-01 2010-04-01 true 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...

  5. 27 CFR 478.37 - Manufacture, importation and sale of armor piercing ammunition.

    Code of Federal Regulations, 2010 CFR

    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...

  6. 27 CFR 478.37 - Manufacture, importation and sale of armor piercing ammunition.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 3 2013-04-01 2013-04-01 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...

  7. 77 FR 39259 - Agency Information Collection Activities; Proposed Collection; Comments Requested: Body Armor in...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-02

    ... the proportion who have body armor, the rate of use, the decision-making factors which inform use, and... Management Division, Policy and Planning Staff, Two Constitution Square, 145 N Street NE., Room 2E-508...), will be submitting the following information collection request to the Office of Management and...

  8. Skeletal histology of the dermal armor of Placodontia: the occurrence of 'postcranial fibro-cartilaginous bone' and its developmental implications.

    PubMed

    Scheyer, Torsten M

    2007-12-01

    Placodontia (Reptilia: Sauropterygia) is a group of enigmatic armored marine reptiles restricted to the Triassic time period. Only a single row of osteoderms dorsal to the spine is present in the basal placodontoid Placodus gigas, whereas derived cyamodontoids superficially resemble turtles in enclosing their body in an armor shell. Despite the extensive occurrence of the dermal armor in the derived cyamodontoid group, little research has focused on its bone histology and development. Here, I present an overview of the bone microstructures that reveals the unique presence of cartilaginous tissue in the postcranial armor plates. Placodont armor plates stand in contrast to osteoderms of other tetrapods that develop intramembraneously or through metaplastic ossification without cartilaginous preformation. The different developmental pathways leading to this 'postcranial fibro-cartilaginous bone' tissue found in placodont plates compared to the dermal bone tissues of most other tetrapod osteoderms indicate the non-homology of these structures. A resulting morphogenetic model of histogenesis is given to exemplify how the derived armor morphologies (i.e. spiked, flat polygonal and hexagonal, and rhomboidal shapes) together with the peculiar bone histologies could have developed through differential growth. In accordance with the pachyostotic limb bones of placodonts, the presence of the compact 'postcranial fibro-cartilaginous bone' is interpreted as an osteosclerotic trend in the armor plates which aids in buoyancy control and affects maneuverability and swimming speed.

  9. Skeletal histology of the dermal armor of Placodontia: the occurrence of 'postcranial fibro-cartilaginous bone' and its developmental implications.

    PubMed

    Scheyer, Torsten M

    2007-12-01

    Placodontia (Reptilia: Sauropterygia) is a group of enigmatic armored marine reptiles restricted to the Triassic time period. Only a single row of osteoderms dorsal to the spine is present in the basal placodontoid Placodus gigas, whereas derived cyamodontoids superficially resemble turtles in enclosing their body in an armor shell. Despite the extensive occurrence of the dermal armor in the derived cyamodontoid group, little research has focused on its bone histology and development. Here, I present an overview of the bone microstructures that reveals the unique presence of cartilaginous tissue in the postcranial armor plates. Placodont armor plates stand in contrast to osteoderms of other tetrapods that develop intramembraneously or through metaplastic ossification without cartilaginous preformation. The different developmental pathways leading to this 'postcranial fibro-cartilaginous bone' tissue found in placodont plates compared to the dermal bone tissues of most other tetrapod osteoderms indicate the non-homology of these structures. A resulting morphogenetic model of histogenesis is given to exemplify how the derived armor morphologies (i.e. spiked, flat polygonal and hexagonal, and rhomboidal shapes) together with the peculiar bone histologies could have developed through differential growth. In accordance with the pachyostotic limb bones of placodonts, the presence of the compact 'postcranial fibro-cartilaginous bone' is interpreted as an osteosclerotic trend in the armor plates which aids in buoyancy control and affects maneuverability and swimming speed. PMID:17944862

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

    PubMed

    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

    2015-03-01

    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

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

    PubMed

    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

    2015-03-01

    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.

  12. Short Internal Sequences Involved in Replication and Virion Accumulation in a Subviral RNA of Turnip Crinkle Virus

    PubMed Central

    Sun, Xiaoping; Zhang, Guohua; Simon, Anne E.

    2005-01-01

    cis-acting sequences and structural elements in untranslated regions of viral genomes allow viral RNA-dependent RNA polymerases to correctly initiate and transcribe asymmetric levels of plus and minus strands during replication of plus-sense RNA viruses. Such elements include promoters, enhancers, and transcriptional repressors that may require interactions with distal RNA sequences for function. We previously determined that a non-sequence-specific hairpin (M1H) in the interior of a subviral RNA (satC) associated with Turnip crinkle virus is required for fitness and that its function might be to bridge flanking sequences (X. Sun and A. E. Simon, J. Virol. 77:7880-7889, 2003). To establish the importance of the flanking sequences in replication and satC-specific virion repression, segments on both sides of M1H were randomized and subjected to in vivo functional selection (in vivo SELEX). Analyses of winning (functional) sequences revealed three different conserved elements within the segments that could be specifically assigned roles in replication, virion repression, or both. One of these elements was also implicated in the molecular switch that releases the 3′ end from its interaction with the repressor hairpin H5, which is possibly involved in controlling the level of minus-strand synthesis. PMID:15596844

  13. The vhs1 mutant form of herpes simplex virus virion host shutoff protein retains significant internal ribosome entry site-directed RNA cleavage activity.

    PubMed

    Lu, P; Saffran, H A; Smiley, J R

    2001-01-01

    The virion host shutoff (vhs) protein of herpes simplex virus (HSV) triggers global shutoff of host protein synthesis and accelerated turnover of host and viral mRNAs during HSV infection. As well, it induces endoribonucleolytic cleavage of RNA substrates when produced in a rabbit reticulocyte lysate (RRL) in vitro translation system. The vhs1 point mutation (Thr 214-->Ile) eliminates vhs function during virus infection and in transiently transfected mammalian cells and was therefore previously considered to abolish vhs activity. Here we demonstrate that the vhs1 mutant protein induces readily detectable endoribonuclease activity on RNA substrates bearing the internal ribosome entry site of encephalomyocarditis virus in the RRL assay system. These data document that the vhs1 mutation does not eliminate catalytic activity and raise the possibility that the vhs-dependent endoribonuclease employs more than one mode of substrate recognition.

  14. DNA authentication of Plantago Herb based on nucleotide sequences of 18S-28S rRNA internal transcribed spacer region.

    PubMed

    Sahin, Fatma Pinar; Yamashita, Hiromi; Guo, Yahong; Terasaka, Kazuyoshi; Kondo, Toshiya; Yamamoto, Yutaka; Shimada, Hiroshi; Fujita, Masao; Kawasaki, Takeshi; Sakai, Eiji; Tanaka, Toshihiro; Goda, Yukihiro; Mizukami, Hajime

    2007-07-01

    Internal transcribed spacer (ITS) regions of nuclear ribosomal RNA gene were amplified from 23 plant- and herbarium specimens belonging to eight Plantago species (P. asiatica, P. depressa, P. major, P. erosa, P. hostifolia, P. camtschatica, P. virginica and P. lanceolata). Sequence comparison indicated that these Plantago species could be identified based on the sequence type of the ITS locus. Sequence analysis of the ITS regions amplified from the crude drug Plantago Herb obtained in the markets indicated that all the drugs from Japan were derived from P. asiatica whereas the samples obtained in China were originated from various Plantago species including P. asiatica, P. depressa, P. major and P. erosa.

  15. Probing the Mechanical Strength of an Armored Bubble and Its Implication to Particle-Stabilized Foams

    NASA Astrophysics Data System (ADS)

    Taccoen, Nicolas; Lequeux, François; Gunes, Deniz Z.; Baroud, Charles N.

    2016-01-01

    Bubbles are dynamic objects that grow and rise or shrink and disappear, often on the scale of seconds. This conflicts with their uses in foams where they serve to modify the properties of the material in which they are embedded. Coating the bubble surface with solid particles has been demonstrated to strongly enhance the foam stability, although the mechanisms for such stabilization remain mysterious. In this paper, we reduce the problem of foam stability to the study of the behavior of a single spherical bubble coated with a monolayer of solid particles. The behavior of this armored bubble is monitored while the ambient pressure around it is varied, in order to simulate the dissolution stress resulting from the surrounding foam. We find that above a critical stress, localized dislocations appear on the armor and lead to a global loss of the mechanical stability. Once these dislocations appear, the armor is unable to prevent the dissolution of the gas into the surrounding liquid, which translates into a continued reduction of the bubble volume, even for a fixed overpressure. The observed route to the armor failure therefore begins from localized dislocations that lead to large-scale deformations of the shell until the bubble completely dissolves. The critical value of the ambient pressure that leads to the failure depends on the bubble radius, with a scaling of Δ Pcollapse∝R-1 , but does not depend on the particle diameter. These results disagree with the generally used elastic models to describe particle-covered interfaces. Instead, the experimental measurements are accounted for by an original theoretical description that equilibrates the energy gained from the gas dissolution with the capillary energy cost of displacing the individual particles. The model recovers the short-wavelength instability, the scaling of the collapse pressure with bubble radius, and the insensitivity to particle diameter. Finally, we use this new microscopic understanding to predict

  16. Persistence of 10-year old Exxon Valdez oil on Gulf of Alaska beaches: The importance of boulder-armoring

    USGS Publications Warehouse

    Irvine, G.V.; Mann, D.H.; Short, J.W.

    2006-01-01

    Oil stranded as a result of the 1989 Exxon Valdez spill has persisted for >10 years at study sites on Gulf of Alaska shores distant from the spill's origin. These sites were contaminated by "oil mousse", which persists in these settings due to armoring of underlying sediments and their included oil beneath boulders. The boulder-armored beaches that we resampled in 1999 showed continued contamination by subsurface oil, despite their exposure to moderate to high wave energies. Significant declines in surface oil cover occurred at all study sites. In contrast, mousse has persisted under boulders in amounts similar to what was present in 1994 and probably in 1989. Especially striking is the general lack of weathering of this subsurface oil over the last decade. Oil at five of the six armored-beach sites 10 years after the spill is compositionally similar to 11-day old Exxon Valdez oil. Analysis of movements in the boulder-armor that covers the study beaches reveals that only minor shifts have occurred since 1994, suggesting that over the last five, and probably over the last 10 years, boulder-armors have remained largely unmoved at the study sites. These findings emphasize the importance of particular geomorphic parameters in determining stranded oil persistence. Surface armoring, combined with stranding of oil mousse, results in the unexpectedly lengthy persistence of only lightly to moderately weathered oil within otherwise high-energy wave environments. ?? 2006 Elsevier Ltd. All rights reserved.

  17. Persistence of 10-year old Exxon Valdez oil on Gulf of Alaska beaches: the importance of boulder-armoring.

    PubMed

    Irvine, Gail V; Mann, Daniel H; Short, Jeffrey W

    2006-09-01

    Oil stranded as a result of the 1989 Exxon Valdez spill has persisted for >10 years at study sites on Gulf of Alaska shores distant from the spill's origin. These sites were contaminated by "oil mousse", which persists in these settings due to armoring of underlying sediments and their included oil beneath boulders. The boulder-armored beaches that we resampled in 1999 showed continued contamination by subsurface oil, despite their exposure to moderate to high wave energies. Significant declines in surface oil cover occurred at all study sites. In contrast, mousse has persisted under boulders in amounts similar to what was present in 1994 and probably in 1989. Especially striking is the general lack of weathering of this subsurface oil over the last decade. Oil at five of the six armored-beach sites 10 years after the spill is compositionally similar to 11-day old Exxon Valdez oil. Analysis of movements in the boulder-armor that covers the study beaches reveals that only minor shifts have occurred since 1994, suggesting that over the last five, and probably over the last 10 years, boulder-armors have remained largely unmoved at the study sites. These findings emphasize the importance of particular geomorphic parameters in determining stranded oil persistence. Surface armoring, combined with stranding of oil mousse, results in the unexpectedly lengthy persistence of only lightly to moderately weathered oil within otherwise high-energy wave environments. PMID:16524600

  18. Persistence of 10-year old Exxon Valdez oil on Gulf of Alaska beaches: the importance of boulder-armoring.

    PubMed

    Irvine, Gail V; Mann, Daniel H; Short, Jeffrey W

    2006-09-01

    Oil stranded as a result of the 1989 Exxon Valdez spill has persisted for >10 years at study sites on Gulf of Alaska shores distant from the spill's origin. These sites were contaminated by "oil mousse", which persists in these settings due to armoring of underlying sediments and their included oil beneath boulders. The boulder-armored beaches that we resampled in 1999 showed continued contamination by subsurface oil, despite their exposure to moderate to high wave energies. Significant declines in surface oil cover occurred at all study sites. In contrast, mousse has persisted under boulders in amounts similar to what was present in 1994 and probably in 1989. Especially striking is the general lack of weathering of this subsurface oil over the last decade. Oil at five of the six armored-beach sites 10 years after the spill is compositionally similar to 11-day old Exxon Valdez oil. Analysis of movements in the boulder-armor that covers the study beaches reveals that only minor shifts have occurred since 1994, suggesting that over the last five, and probably over the last 10 years, boulder-armors have remained largely unmoved at the study sites. These findings emphasize the importance of particular geomorphic parameters in determining stranded oil persistence. Surface armoring, combined with stranding of oil mousse, results in the unexpectedly lengthy persistence of only lightly to moderately weathered oil within otherwise high-energy wave environments.

  19. Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5’ sites

    PubMed Central

    Schwartz, Schraga; Mumbach, Maxwell R.; Jovanovic, Marko; Wang, Tim; Maciag, Karolina; Bushkin, G. Guy; Mertins, Philipp; Ter-Ovanesyan, Dmitry; Habib, Naomi; Cacchiarelli, Davide; Sanjana, Neville E.; Freinkman, Elizaveta; Pacold, Michael E.; Satija, Rahul; Mikkelsen, Tarjei S.; Hacohen, Nir; Zhang, Feng; Carr, Steven A.; Lander, Eric S.; Regev, Aviv

    2014-01-01

    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, are topologically static across a variety of systems we surveyed, and are 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 sheds new light on proteomic and transcriptional underpinnings of this epitranscriptomic modification. PMID:24981863

  20. A magnesium-induced RNA conformational switch at the internal ribosome entry site of hepatitis C virus genome visualized by atomic force microscopy

    PubMed Central

    García-Sacristán, Ana; Moreno, Miguel; Ariza-Mateos, Ascensión; López-Camacho, Elena; Jáudenes, Rosa M.; Vázquez, Luis; Gómez, Jordi; Martín-Gago, José Ángel; Briones, Carlos

    2015-01-01

    The 5′ untranslated region of hepatitis C virus (HCV) genomic RNA contains an internal ribosome entry site (IRES) element, composed of domains II–IV, which is required for cap-independent translation initiation. Little information on the 3D structure of the whole functional HCV IRES is still available. Here, we use atomic force microscopy to visualize the HCV IRES conformation in its natural sequence context, which includes the upstream domain I and the essential, downstream domains V and VI. The 574 nt-long molecule analyzed underwent an unexpected, Mg2+-induced switch between two alternative conformations: from ‘open’, elongated morphologies at 0–2 mM Mg2+ concentration to a ‘closed’, comma-shaped conformation at 4–6 mM Mg2+. This sharp transition, confirmed by gel-shift analysis and partial RNase T1 cleavage, was hindered by the microRNA miR-122. The comma-shaped IRES-574 molecules visualized at 4–6 mM Mg2+ in the absence of miR-122 showed two arms. Our data support that the first arm would contain domain III, while the second one would be composed of domains (I–II)+(V–VI) thanks to a long-range RNA interaction between the I-II spacer and the basal region of domain VI. This reinforces the previously described structural continuity between the HCV IRES and its flanking domains I, V and VI. PMID:25510496

  1. Internal Transcribed Spacer rRNA Gene-Based Phylogenetic Reconstruction Using Algorithms with Local and Global Sequence Alignment for Black Yeasts and Their Relatives

    PubMed Central

    Caligiorne, R. B.; Licinio, P.; Dupont, J.; de Hoog, G. S.

    2005-01-01

    Sequences of rRNA gene internal transcribed spacer (ITS) of a standard set of black yeast-like fungal pathogens were compared using two methods: local and global alignments. The latter is based on DNA-walk divergence analysis. This method has become recently available as an algorithm (DNAWD program) which converts sequences into three-dimensional walks. The walks are compared with, or fit to, each other generating global alignments. The DNA-walk geometry defines a proper metric used to create a distance matrix appropriated for phylogenetic reconstruction. In this work, the analyses were carried out for species currently classified in Capronia, Cladophialophora, Exophiala, Fonsecaea, Phialophora, and Ramichloridium. Main groups were verified by small-subunit rRNA gene data. DNAWD applied to ITS2 alone enabled species recognition as well as phylogenetic reconstruction reflecting clades discriminated in small-subunit rRNA gene phylogeny, which was not possible with any other algorithm using local alignment for the same data set. It is concluded that DNAWD provides rapid insight into broader relationships between groups using genes that otherwise would be hardly usable for this purpose. PMID:15956403

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

    PubMed

    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.

  3. Advanced Modeling Strategies for the Analysis of Tile-Reinforced Composite Armor

    NASA Technical Reports Server (NTRS)

    Davila, Carlos G.; Chen, Tzi-Kang

    1999-01-01

    A detailed investigation of the deformation mechanisms in tile-reinforced armored components was conducted to develop the most efficient modeling strategies for the structural analysis of large components of the Composite Armored Vehicle. The limitations of conventional finite elements with respect to the analysis of tile-reinforced structures were examined, and two complementary optimal modeling strategies were developed. These strategies are element layering and the use of a tile-adhesive superelement. Element layering is a technique that uses stacks of shear deformable shell elements to obtain the proper transverse shear distributions through the thickness of the laminate. The tile-adhesive superelement consists of a statically condensed substructure model designed to take advantage of periodicity in tile placement patterns to eliminate numerical redundancies in the analysis. Both approaches can be used simultaneously to create unusually efficient models that accurately predict the global response by incorporating the correct local deformation mechanisms.

  4. Armor Development from Decapitated Flash Flood Bores in Supply-Limited Flume Experiments

    NASA Astrophysics Data System (ADS)

    Goodwin, K.; Rhodes, R.; Johnson, J. P.

    2013-12-01

    In rivers assumed to have quasi-normal flow, three main processes have been used to explain bed surface armoring: i) selective entrainment and transport of smaller grains, ii) limited supply of smaller grain sizes, and iii) equal mobility of grains of different sizes, which develops through natural feedbacks such that larger, less mobile grains are enriched on the surface relative to smaller grains. Flash flood-dominated river channels in arid environments often completely lack surface armoring, yet it is unclear whether increased sediment supply or transport of all grain sizes prevents armor development. In order to examine armor development in an end-member case of non-normal flow, we conducted a series of laboratory experiments using flash flood bores. The flume is 33.5 m long, 0.5 m wide, 0.8 m tall, and capable of creating reproducible flood bores by raising a high-speed computerized lift gate and releasing impounded water. For each experiment, the gate was quickly lowered as soon as the flood bore traveled the length of the flume, 'decapitating' the bore from subsequent flow, to better isolate the effects of the bore alone on entrainment and transport. Sediment was not fed into the upstream end of the flume and only sourced from the gravel bed (2 mm to 40 mm), resulting in supply-limited experimental conditions. In response to repeated flood bores, the surface grain size distribution rapidly coarsened. We interpret that kinetic sieving was the dominant cause of surface armoring in these experiments. LiDAR scans of the bed topography from before and after each bore show increased surface roughness due to grain size changes, but small surface elevation changes due to relatively limited erosion. Digital gravelometry from photographs taken after each bore show increased armoring, while sediment transported out the downstream end of the flume tended to be as coarse or coarser than the bed surface. Travel distances of three sizes of RFID-tagged tracer clasts show

  5. Protection mechanisms of the iron-plated armor of a deep-sea hydrothermal vent gastropod

    PubMed Central

    Yao, Haimin; Dao, Ming; Imholt, Timothy; Huang, Jamie; Wheeler, Kevin; Bonilla, Alejandro; Suresh, Subra; Ortiz, Christine

    2010-01-01

    Biological exoskeletons, in particular those with unusually robust and multifunctional properties, hold enormous potential for the development of improved load-bearing and protective engineering materials. Here, we report new materials and mechanical design principles of the iron-plated multilayered structure of the natural armor of Crysomallon squamiferum, a recently discovered gastropod mollusc from the Kairei Indian hydrothermal vent field, which is unlike any other known natural or synthetic engineered armor. We have determined through nanoscale experiments and computational simulations of a predatory attack that the specific combination of different materials, microstructures, interfacial geometries, gradation, and layering are advantageous for penetration resistance, energy dissipation, mitigation of fracture and crack arrest, reduction of back deflections, and resistance to bending and tensile loads. The structure-property-performance relationships described are expected to be of technological interest for a variety of civilian and defense applications. PMID:20133823

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

    NASA Astrophysics Data System (ADS)

    Guo, Y. N.; Sun, Q.

    2015-12-01

    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.

  7. Macrocomposite mechanical design, modeling, and behavior of physical models of bioinspired fish armor

    NASA Astrophysics Data System (ADS)

    Browning, Ashley; Ortiz, Christine; Boyce, Mary C.

    2012-02-01

    The macrocomposite design of flexible biological exoskeletons, consisting of overlapping mineralized armor units embedded in a compliant tissue, is a key determinant of their mechanical function (e.g penetration resistance and biomechanical flexibility). Here, we investigate the role of macrocomposite structure, composition, geometric orientation, and spatial distribution in a flexible model natural armor system present in the majority of teleost fish species. Physical multi-material composite models are fabricated using a combination of 3-D printing and molding methods. Mechanical experiments using digital image correlation enable measurement of both the macroscopic response and underlying deformation mechanisms during various loading scenarios. Finite element-based mechanical models yield detailed insights into the roles and the tradeoffs of the composite structure providing constraint, shear, and bending mechanisms to impart protection and flexibility.

  8. Development of an automated fuzing station for the future armored resupply vehicle

    SciTech Connect

    Chesser, J.B.; Jansen, J.F.; Lloyd, P.D.; Varma, V.K.

    1995-03-01

    The US Army is developing the Advanced Field Artillery System (SGSD), a next generation armored howitzer. The Future Armored Resupply Vehicle (FARV) will be its companion ammunition resupply vehicle. The FARV with automate the supply of ammunition and fuel to the AFAS which will increase capabilities over the current system. One of the functions being considered for automation is ammunition processing. Oak Ridge National Laboratory is developing equipment to demonstrate automated ammunition processing. One of the key operations to be automated is fuzing. The projectiles are initially unfuzed, and a fuze must be inserted and threaded into the projectile as part of the processing. A constraint on the design solution is that the ammunition cannot be modified to simplify automation. The problem was analyzed to determine the alignment requirements. Using the results of the analysis, ORNL designed, built, and tested a test stand to verify the selected design solution.

  9. The effect of ceramic/metal gradient armor's components characteristic on its impact-resistant characteristic

    SciTech Connect

    Liu Lisheng; Zhang Qingjie; Zhai Pengcheng; Cao Dongfeng

    2008-02-15

    The effect of ceramic/metal gradient armor's components characteristic on its impact-resistant characteristic has been investigated by a new modified Alekseevskii-Tate equation. The following researching work is done by the former model [1]: the effect of ceramic layer on the impact-resistant characteristic, the effect of gradient layer on the impact-resistant characteristic and the effect of metal layer on the impact-resistant characteristic.

  10. Stability of hard plates on soft substrates and application to the design of bioinspired segmented armor

    NASA Astrophysics Data System (ADS)

    Martini, R.; Barthelat, F.

    2016-07-01

    Flexible natural armors from fish, alligators or armadillo are attracting an increasing amount of attention from their unique and attractive combinations of hardness, flexibility and light weight. In particular, the extreme contrast of stiffness between hard plates and surrounding soft tissues give rise to unusual and attractive mechanisms, which now serve as model for the design of bio-inspired armors. Despite a growing interest in bio-inspired flexible protection, there is little guidelines as to the choice of materials, optimum thickness, size, shape and arrangement for the protective plates. In this work, we focus on a failure mode we recently observed on natural and bio-inspired scaled armors: the unstable tilting of individual scales subjected to off-centered point forces. We first present a series of experiments on this system, followed by a model based on contact mechanics and friction. We condense the result into a single stability diagram which capture the key parameters that govern the onset of plate tilting from a localized force. We found that the stability of individual plates is governed by the location of the point force on the plate, by the friction at the surface of the plate, by the size of the plate and by the stiffness of the substrate. We finally discuss how some of these parameters can be optimized at the design stage to produce bio-inspired protective systems with desired combination of surface hardness, stability and flexural compliance.

  11. The performance of the poloidal divertor experiment neutral beam wall armor

    SciTech Connect

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

    1986-05-01

    During 2 yr of experimental operations, the Poloidal Divertor Experiment (PDX) inner wall neutral beam graphite armor provided protection for perpendicular heating injections into normal and disruptive plasmas as well as injection in the absence of plasma for special experiments, calibrations, and tests involving the optimization and development of the PDX neutral beam injection system. About 80 to 100 heating injections occurred per operating day, at a 360-s duty cycle, into plasmas of various densities, and typically approx. =5 to 50% of the injected neutral beam power was transmitted to the armor. More than 10/sup 3/ neutral beam pulses of 100- to 300-ms duration were injected in the absence of plasma at peak power densities of 1.5 to 3 kW/cm/sup 2/, yielding peak surface temperatures of 950 to 1550/sup 0/C. There was no significant impurity production attributable to beam heating of the armor, and no observed beam-induced, macroscopic surface damage. Many of the design constraints and performance issues encountered in this work are relevant to the design of larger fusion devices.

  12. New low-temperature processing for boron carbide/aluminum-based composite armor. Final report

    SciTech Connect

    Pyzik, A.J.; Williams, P.D.; McCombs, A.

    1990-06-01

    The developed Boron Carbide/Aluminum based materials are a promising alternative for the use in lightweight armor application. The advantage of B4C/A1 composite over the traditional metal armor is its ballistic limit of 80 to 90% of that for hot pressed B4C, thus similar to ceramics such as A1N or SiC. The advantage of B4C/A1 over monolithic ceramic armor is its higher toughness. The ballistic efficiency of B4C materials, relative to hot-pressed boron carbide, was found to be directly related to the initial boron carbide content, the B-C-A1 phases formed in situ, and their continuity. The highest improvement of ballistic efficiency was associated with increasing contents of B4C and A1B2 in the system. The Rapid Omnidirectional Compaction process is a suitable technique to produce nearly dense B4C/A1 cermet at the low temperature. Dense, but soft, cermets can be near-net shaped and then changed into hard, ceramic-like structure through heat-treatment. Mechanical properties of B4C/A1 cermet depend mostly on the concentration and continuity of the boron carbide phase. Colloidal processing and post densification heat-treatment can be used to further modify properties for the application at hand.

  13. Ambient air cooling for concealed soft body armor in a hot environment.

    PubMed

    Ryan, Greg A; Bishop, Stacy H; Herron, Robert L; Katica, Charles P; Elbon, Bre'anna L; Bosak, Andrew M; Bishop, Phillip

    2014-01-01

    Concealed soft body armor inhibits convective and evaporative heat loss and increases heat storage, especially in hot environments. One option to potentially mitigate heat storage is to promote airflow under the soft body armor. The purpose of this study was to evaluate the effect of ambient air induction (∼100 liters per minute) on heat strain while wearing concealed soft body armor in a hot environment (wet bulb globe temperature = 30°C). A counter-balanced, repeated measures protocol was performed with nine healthy male volunteers. Participants were fitted with either a traditional or modified Level II concealed soft body armor. Participants performed cycles of 12 min of walking (1.25 liters per minute) and 3 min of arm curls (0.6 liters per minute) for a total of 60 min. Two-way repeated measures ANOVA was used to assess the mean differences in physiological measures (rectal temperature, heart rate, micro-environment [temperature and relative humidity]). Post hoc Bonferroni analysis and paired samples t-tests (alpha = 0.01) were conducted on omnibus significant findings. Perceptual measures (perceived exertion, thermal comfort) were analyzed using Wilcoxon Signed Ranks Tests. Modification led to an improvement in perceived exertion at 45 min (MOD: 10 ± 1; CON: 11 ± 2; p ≤ 0.001) and 60 min (MOD: 10 ± 2; CON: 12 ± 2; p ≤ 0.001) and a reduction in micro-environment temperature in MOD (1.0 ± 0.2°C, p = 0.03) compared to CON. Modification did not attenuate change in rectal temperature or heart rate (p < 0.01) during 60-min work bout. Change in rectal temperature approached significance between MOD and CON at the end of the work bout (MOD: 0.4 ± 0.2°C; CON: 0.7 ± 0.3°C; p = 0.048). The slope of rectal temperature was significantly greater (p = 0.04) under CON compared to MOD. These data suggest that air induction may provide small benefits while wearing concealed soft body armor, though improvements are needed to lessen physiological strain.

  14. Functional and Structural Analysis of the Internal Ribosome Entry Site Present in the mRNA of Natural Variants of the HIV-1

    PubMed Central

    Vallejos, Maricarmen; Carvajal, Felipe; Pino, Karla; Navarrete, Camilo; Ferres, Marcela; Huidobro-Toro, Juan Pablo; Sargueil, Bruno; López-Lastra, Marcelo

    2012-01-01

    The 5′untranslated regions (UTR) of the full length mRNA of the HIV-1 proviral clones pNL4.3 and pLAI, harbor an internal ribosomal entry site (IRES). In this study we extend this finding by demonstrating that the mRNA 5′UTRs of natural variants of HIV-1 also exhibit IRES-activity. Cap-independent translational activity was demonstrated using bicistronic mRNAs in HeLa cells and in Xenopus laevis oocytes. The possibility that expression of the downstream cistron in these constructs was due to alternative splicing or to cryptic promoter activity was ruled out. The HIV-1 variants exhibited significant 5′UTR nucleotide diversity with respect to the control sequence recovered from pNL4.3. Interestingly, translational activity from the 5′UTR of some of the HIV-1 variants was enhanced relative to that observed for the 5′UTR of pNL4.3. In an attempt to explain these findings we probed the secondary structure of the variant HIV-1 5′UTRs using enzymatic and chemical approaches. Yet subsequent structural analyses did not reveal significant variations when compared to the pNL4.3-5′UTR. Thus, the increased IRES-activity observed for some of the HIV-1 variants cannot be ascribed to a specific structural modification. A model to explain these findings is proposed. PMID:22496887

  15. Development of refractory armored silicon carbide by infrared transient liquid phase processing

    NASA Astrophysics Data System (ADS)

    Hinoki, Tatsuya; Snead, Lance L.; Blue, Craig A.

    2005-12-01

    Tungsten (W) and molybdenum (Mo) were coated on silicon carbide (SiC) for use as a refractory armor using a high power plasma arc lamp at powers up to 23.5 MW/m 2 in an argon flow environment. Both tungsten powder and molybdenum powder melted and formed coating layers on silicon carbide within a few seconds. The effect of substrate pre-treatment (vapor deposition of titanium (Ti) and tungsten, and annealing) and sample heating conditions on microstructure of the coating and coating/substrate interface were investigated. The microstructure was observed by scanning electron microscopy (SEM) and optical microscopy (OM). The mechanical properties of the coated materials were evaluated by four-point flexural tests. A strong tungsten coating was successfully applied to the silicon carbide substrate. Tungsten vapor deposition and pre-heating at 5.2 MW/m 2 made for a refractory layer containing no cracks propagating into the silicon carbide substrate. The tungsten coating was formed without the thick reaction layer. For this study, small tungsten carbide grains were observed adjacent to the interface in all conditions. In addition, relatively large, widely scattered tungsten carbide grains and a eutectic structure of tungsten and silicon were observed through the thickness in the coatings formed at lower powers and longer heating times. The strength of the silicon carbide substrate was somewhat decreased as a result of the processing. Vapor deposition of tungsten prior to powder coating helped prevent this degradation. In contrast, molybdenum coating was more challenging than tungsten coating due to the larger coefficient of thermal expansion (CTE) mismatch as compared to tungsten and silicon carbide. From this work it is concluded that refractory armoring of silicon carbide by Infrared Transient Liquid Phase Processing is possible. The tungsten armored silicon carbide samples proved uniform, strong, and capable of withstanding thermal fatigue testing.

  16. An assessment of the cost of microwave sintering ceramic tiles for armor applications: Phase 2 report

    SciTech Connect

    Das, S.; Curlee, T.R.

    1995-03-01

    This report documents the findings of the second phase of work to assess the costs of microwave sintering ceramic tiles for armor applications. In the first phase of work, the cost of microwave sintering and preliminary estimates of the total cost of microwave-sintered tiles under two microwave frequencies (i.e., 2.45 GHz and 28 GHz) for alumina and silicon carbide materials were reported. The second phase of work extends to the previous work to include all pre- and post-sintering manufacturing steps and considers process and cost variations in these steps that may result from the adoption of microwave sintering. Two separate models were developed for two different materials. As before, a process-cost approach was utilized within a spreadsheet environment. When compared to conventional sintering, the manufacturing of microwave-sintered alumina armor tiles will require an additional binder removal step prior to microwave sintering. The base-case cost of microwave-sintered alumina tiles is estimated to be $46.80/part and $50.50/part, given the use of 2.45 GHz and 28 GHz microwave power sources, respectively. In the case of microwave sintering of silicon carbide armor tiles, the material preparation step will be significantly different from conventional sintering. Instead of a binder removal step, there will be a green machining step. The base-case cost of microwave-sintered silicon carbide tiles is estimated to be $324.50/part and $327.50/part for 2.45 GHz and 28 GHz microwave power sources, respectively--compared to $235/part for conventionally-sintered tiles. Several sensitivity analyses of the impacts of variations in key economic and technical parameters on the costs of microwave-sintered tiles were conducted. Those analyses indicate that costs are quite sensitive to changes in the quantity of energy required during sintering.

  17. Placoderms (Armored Fish): Dominant Vertebrates of the Devonian Period

    NASA Astrophysics Data System (ADS)

    Young, Gavin C.

    2010-05-01

    Placoderms, the most diverse group of Devonian fishes, were globally distributed in all habitable freshwater and marine environments, like teleost fishes in the modern fauna. Their known evolutionary history (Early Silurian-Late Devonian) spanned at least 70 million years. Known diversity (335 genera) will increase when diverse assemblages from new areas are described. Placoderms first occur in the Early Silurian of China, but their diversity remained low until their main evolutionary radiation in the Early Devonian, after which they became the dominant vertebrates of Devonian seas. Most current placoderm data are derived from the second half of the group's evolutionary history, and recent claims that they form a paraphyletic group are based on highly derived Late Devonian forms; 16 shared derived characters are proposed here to support placoderm monophyly. Interrelationships of seven placoderm orders are unresolved because Silurian forms from China are still poorly known. The relationship of placoderms to the two major extant groups of jawed fishes—osteichthyans (bony fishes) and chondrichthyans (cartilaginous sharks, rays, and chimaeras)—remains uncertain, but the detailed preservation of placoderm internal braincase structures provides insights into the ancestral gnathostome (jawed vertebrate) condition. Placoderms provide the most complex morphological and biogeographic data set for the Middle Paleozoic; marked discrepancies in stratigraphic occurrence between different continental regions indicate strongly endemic faunas that were probably constrained by marine barriers until changes in paleogeography permitted range enlargement into new areas. Placoderm distributions in time and space indicate major faunal interchange between Gondwana and Laurussia near the Frasnian-Famennian boundary; closure of the Devonian equatorial ocean is a possible explanation.

  18. Preliminary In Vivo Evaluation of a Hybrid Armored Vascular Graft Combining Electrospinning and Additive Manufacturing Techniques.

    PubMed

    Spadaccio, Cristiano; Nappi, Francesco; De Marco, Federico; Sedati, Pietro; Sutherland, Fraser W H; Chello, Massimo; Trombetta, Marcella; Rainer, Alberto

    2016-01-01

    In this study, we tested in vivo effectiveness of a previously developed poly-l-lactide/poly-ε-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.

  19. Determination of influence factors and accident rates for the Armored Tractor/Safe Secure Trailer

    SciTech Connect

    Phillips, J.S.; Clauss, D.B.; Blower, D.F.

    1994-04-01

    Operating environments, such as road type, road location, and time of day, play an important role in the observed accident rates of heavy trucks used in general commerce. These same factors influence the accident rate of the Armored Tractor/Safe Secure Trailer (AT/SST) used by the Department of Energy to transport hazardous cargos within the continental United States. This report discusses the development of accident rate influence factors. These factors, based on heavy trucks used in general commerce, are used to modify the observed overall AT/SST accident rate to account for the different operating environments.

  20. Ultrasonic Characterization of Custom Engineered Armor Grade Alumina (Al2O3)

    NASA Astrophysics Data System (ADS)

    Bottiglieri, S.; Haber, R. A.

    2010-02-01

    High frequency ultrasonic characterization was performed on a series of alumina samples of varying degrees of density. These samples were specifically fired to temperatures below and above what is considered to be appropriate for the sintering of alumina. Ultrasound attenuation coefficient and Young's modulus C-scan mapping and acoustic spectroscopy were employed in order to establish a baseline fingerprint for each temperature type. Characterization was performed using 20 MHz and 75 MHz planar transducers. This study showed the veracity of high frequency ultrasound as a diagnostic tool in characterizing the effect of densification on material properties for armor-grade alumina.

  1. Simple go/no-go test for subcritical damage in body armor panels

    SciTech Connect

    Fisher, Jason; Chimenti, D. E.

    2011-06-23

    The development of a simple test for subcritical damage in body armor panels using pressure-sensitive dye-indicator film has been performed and demonstrated effective. Measurements have shown that static indicator levels are accurately reproduced in dynamic loading events. Impacts from hard blunt impactors instrumented with an accelerometer and embedded force transducer were studied. Reliable correlations between the indicator film and instrumented impact force are shown for a range of impact energies. Force and acceleration waveforms with corresponding indicator film results are presented for impact events onto damaged and undamaged panels. We find that panel damage can occur at impact levels far below the National Institute of Justice acceptance test standard.

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

    NASA Astrophysics Data System (ADS)

    Paris, V.; Weiss, A.; Vizel, A.; Ran, E.; Aizik, F.

    2012-08-01

    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.

  3. Structure and mechanical behaviors of protective armored pangolin scales and effects of hydration and orientation.

    PubMed

    Liu, Z Q; Jiao, D; Weng, Z Y; Zhang, Z F

    2016-03-01

    As natural flexible dermal armor, pangolin scales provide effective protection against predatory threats and possess other notable properties such as anti-adhesion and wear-resistance. In this study, the structure, mechanical properties, deformation and damage behaviors of pangolin scales were systematically investigated with the effects of hydration and orientation evaluated. The scales are divided into three macro-layers constituted by overlapping keratin tiles with distinct lamellar arrangements which are further composed of lower-ordered lamellae. Both hardness and strength are significantly decreased by hydration; while the plasticity is markedly improved concomitantly, and as such, the mechanical damages are mitigated. The tensile strength invariably approximates to one third of hardness in value. The tensile deformation is dominated by lamellae stretching and pulling out under wet condition, which is distinct from the trans-lamellar fracture in dry samples. The compressive behaviors are featured by pronounced plasticity in both dry and wet scales; and notable strain-hardening capacity is introduced by hydration, especially along the thickness direction wherein kinking occurs. Inter-lamellar cracking is effectively alleviated in wet samples compared with the dry ones and both of them deform by macroscopic buckling. This study may help stimulate possible inspiration for the design of high-performance synthetic armor materials by mimicking pangolin scales. PMID:26703230

  4. Constitutive Modeling of Hot Deformation Behavior of High-Strength Armor Steel

    NASA Astrophysics Data System (ADS)

    Bobbili, Ravindranadh; Madhu, Vemuri

    2016-05-01

    The hot isothermal compression tests of high-strength armor steel under a wide range of deformation temperatures (1100-1250 °C) and strain rates of (0.001-1/s) were performed. Based on the experimental data, constitutive models were established using the original Johnson-Cook (JC) model, modified JC model, and strain-compensated Arrhenius model, respectively. The modified JC model considers the coupled effects of strain hardening, strain rate hardening, and thermal softening. Moreover, the prediction accuracy of these developed models was determined by estimating the correlation coefficient ( R) and average absolute relative error (AARE). The results demonstrate that the flow behavior of high-strength armor steel is considerably influenced by the strain rate and temperature. The original JC model is inadequate to provide good description on the flow stress at evaluated temperatures. The modified JC model and strain-compensated Arrhenius model significantly enhance the predictability. It is also observed from the microstructure study that at low strain rates (0.001-0.01/s) and high temperatures (1200-1250 °C), a typical dynamic recrystallization (DRX) occurs.

  5. VUV spectroscopy of armor erosion from plasma gun disruption simulation experiments

    SciTech Connect

    Rockett, P.D.; Hunter, J.A.

    1994-12-31

    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. The authors have designed and utilized two transmission grating vacuum ultraviolet (VUV) spectrographs 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 {approximately}0.7 mm resolution on VIKA at Efremov and on 2MK-200 at Troitsk. Time-resolved data with 40-200 ns resolution was then recorded along with the same spatial resolution on 2MK-200. 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 C V lines as well as impurity lines from O V and O VI. The BN tiles produced textbook examples of B IV and B V, and extensive N IV, V, and VI lines. These are being compared to radiation-hydrodynamic calculations.

  6. Structure and mechanical behaviors of protective armored pangolin scales and effects of hydration and orientation.

    PubMed

    Liu, Z Q; Jiao, D; Weng, Z Y; Zhang, Z F

    2016-03-01

    As natural flexible dermal armor, pangolin scales provide effective protection against predatory threats and possess other notable properties such as anti-adhesion and wear-resistance. In this study, the structure, mechanical properties, deformation and damage behaviors of pangolin scales were systematically investigated with the effects of hydration and orientation evaluated. The scales are divided into three macro-layers constituted by overlapping keratin tiles with distinct lamellar arrangements which are further composed of lower-ordered lamellae. Both hardness and strength are significantly decreased by hydration; while the plasticity is markedly improved concomitantly, and as such, the mechanical damages are mitigated. The tensile strength invariably approximates to one third of hardness in value. The tensile deformation is dominated by lamellae stretching and pulling out under wet condition, which is distinct from the trans-lamellar fracture in dry samples. The compressive behaviors are featured by pronounced plasticity in both dry and wet scales; and notable strain-hardening capacity is introduced by hydration, especially along the thickness direction wherein kinking occurs. Inter-lamellar cracking is effectively alleviated in wet samples compared with the dry ones and both of them deform by macroscopic buckling. This study may help stimulate possible inspiration for the design of high-performance synthetic armor materials by mimicking pangolin scales.

  7. ANALYSES OF VARIOUS DAMAGE MECHANISMS IN TRANSPARENT ARMOR SUBJECT TO PROJECTILE IMPACT

    SciTech Connect

    Lai, Canhai; Sun, Xin; Templeton, Douglas W.

    2009-01-23

    Design and manufacturing of transparent armor have been historically carried out using experimental approaches. In this study, we use advanced computational modeling tools to study the various stress components during the impact event and to identify the different crack/damage driving mechanisms for the different cracking patterns. Experimentally observed damage patterns for a thick glass laminate under fragmentation simulation projectile (FSP) impact are used to compare with the modeling results. AHPCRC developed modeling software EPIC’06 [1] is used in predicting the penetration resistance of transparent armor systems. It is found that a 1-parameter single state model can be used to predict the impact penetration depth with relatively good accuracy. In addition, hoop stress and circumferential stresses are found to produce ripple cracks, needle cracks and radial cracks. It is also found that a region of high hoop stress and circumferential stress is produced by the impact at the back side of the target plate, causing the floret damage region possibly leading to higher penetration depth for thinner laminates or higher velocity impact.

  8. RNA Interference

    MedlinePlus

    ... NIGMS Home > Science Education > RNA Interference Fact Sheet RNA Interference Fact Sheet Tagline (Optional) Middle/Main Content Area What is RNA interference? RNA interference (RNAi) is a natural process ...

  9. Silencing of hepatitis C virus replication by a non-viral vector based on solid lipid nanoparticles containing a shRNA targeted to the internal ribosome entry site (IRES).

    PubMed

    Torrecilla, Josune; Del Pozo-Rodríguez, Ana; Solinís, María Ángeles; Apaolaza, Paola S; Berzal-Herranz, Beatriz; Romero-López, Cristina; Berzal-Herranz, Alfredo; Rodríguez-Gascón, Alicia

    2016-10-01

    Gene silencing mediated by RNAi has gained increasing interest as an alternative for the treatment of infectious diseases such as refractory hepatitis C virus (HCV) infection. In this work we have designed and evaluated a non-viral vector based on solid lipid nanoparticles (SLN) bearing hyaluronic acid, protamine and a short hairpin RNA (shRNA74) targeted to the Internal Ribosome Entry Site (IRES) of the HCV. The vector was able to inhibit the expression of the HCV IRES in Huh-7 cells, with the inhibition level dependent on the shRNA74 to SLN ratio and on the shRNA74 dose added to the culture cells. The nanocarrier was also able to inhibit the replication in human hepatoma cells supporting a subgenomic HCV replicon (Huh-7 NS3-3'). The vector was quickly and efficiently internalized by the cells, and endocytosis was the most productive uptake mechanism for silencing. Clathrin-mediated endocytosis and to a lesser extent caveolae/lipid raft-mediated endocytosis were identified as endocytic mechanisms involved in the cell uptake. Internalization via the CD44 receptor was also involved, although this entry route seems to be less productive for silencing than endocytosis. The vector did not induce either hemolysis or agglutination of red cells in vitro, which was indicative of good biocompatibility. In summary, we have shown for the first time the ability of a non-viral SLN-based vector to silence a HCV replicon.

  10. Silencing of hepatitis C virus replication by a non-viral vector based on solid lipid nanoparticles containing a shRNA targeted to the internal ribosome entry site (IRES).

    PubMed

    Torrecilla, Josune; Del Pozo-Rodríguez, Ana; Solinís, María Ángeles; Apaolaza, Paola S; Berzal-Herranz, Beatriz; Romero-López, Cristina; Berzal-Herranz, Alfredo; Rodríguez-Gascón, Alicia

    2016-10-01

    Gene silencing mediated by RNAi has gained increasing interest as an alternative for the treatment of infectious diseases such as refractory hepatitis C virus (HCV) infection. In this work we have designed and evaluated a non-viral vector based on solid lipid nanoparticles (SLN) bearing hyaluronic acid, protamine and a short hairpin RNA (shRNA74) targeted to the Internal Ribosome Entry Site (IRES) of the HCV. The vector was able to inhibit the expression of the HCV IRES in Huh-7 cells, with the inhibition level dependent on the shRNA74 to SLN ratio and on the shRNA74 dose added to the culture cells. The nanocarrier was also able to inhibit the replication in human hepatoma cells supporting a subgenomic HCV replicon (Huh-7 NS3-3'). The vector was quickly and efficiently internalized by the cells, and endocytosis was the most productive uptake mechanism for silencing. Clathrin-mediated endocytosis and to a lesser extent caveolae/lipid raft-mediated endocytosis were identified as endocytic mechanisms involved in the cell uptake. Internalization via the CD44 receptor was also involved, although this entry route seems to be less productive for silencing than endocytosis. The vector did not induce either hemolysis or agglutination of red cells in vitro, which was indicative of good biocompatibility. In summary, we have shown for the first time the ability of a non-viral SLN-based vector to silence a HCV replicon. PMID:27451369

  11. Differential distribution of U6 (RNU6-1) expression in human carcinoma tissues demonstrates the requirement for caution in the internal control gene selection for microRNA quantification.

    PubMed

    Lou, Ge; Ma, Ning; Xu, Ya; Jiang, Lei; Yang, Jing; Wang, Chuxuan; Jiao, Yufei; Gao, Xu

    2015-11-01

    Alterations in microRNA (miRNA) expression patterns have been associated with a number of human diseases. Accurate quantitation of miRNA levels is important for their use as biomarkers and in determining their functions. Although the issue of proper miRNA detection was solved with the introduction of standard reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR) assays, numerous issues with the selection of appropriate internal control genes remain. U6 (RNU6‑1) snRNA, the most commonly used internal control gene in miRNA RT‑qPCR assays, was shown to be unstable in clinical samples, particularly cancer tissues. Identification of the distribution of U6 in different tissues is the premise of more accurate quantification of miRNAs. However, the distribution of U6 in human carcinoma tissues and corresponding normal tissues is unknown. In the present study, U6 levels were significantly higher in human breast carcinoma tissues compared with the corresponding normal tissues by RT‑qPCR. In the carcinoma or corresponding adjacent normal tissues, the expression levels of U6 in epithelial cells were higher than those in the mesenchymal cells. Furthermore, the expression levels of U6 in the carcinoma tissues of the liver and intrahepatic bile ducts were higher than those in the adjacent normal tissues. These results suggest that the expression and distribution of U6 exhibits a high degree of variability among several types of human cells. Therefore, caution is required when selecting U6 as an internal control gene for evaluating expression profiles of miRNAs in patients with carcinoma, particularly carcinoma of the liver and intrahepatic bile ducts.

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

    PubMed

    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.

  13. Finite Element Modeling of the Behavior of Armor Materials Under High Strain Rates and Large Strains

    NASA Astrophysics Data System (ADS)

    Polyzois, Ioannis

    For years high strength steels and alloys have been widely used by the military for making armor plates. Advances in technology have led to the development of materials with improved resistance to penetration and deformation. Until recently, the behavior of these materials under high strain rates and large strains has been primarily based on laboratory testing using the Split Hopkinson Pressure Bar apparatus. With the advent of sophisticated computer programs, computer modeling and finite element simulations are being developed to predict the deformation behavior of these metals for a variety of conditions similar to those experienced during combat. In the present investigation, a modified direct impact Split Hopkinson Pressure Bar apparatus was modeled using the finite element software ABAQUS 6.8 for the purpose of simulating high strain rate compression of specimens of three armor materials: maraging steel 300, high hardness armor (HHA), and aluminum alloy 5083. These armor materials, provided by the Canadian Department of National Defence, were tested at the University of Manitoba by others. In this study, the empirical Johnson-Cook visco-plastic and damage models were used to simulate the deformation behavior obtained experimentally. A series of stress-time plots at various projectile impact momenta were produced and verified by comparison with experimental data. The impact momentum parameter was chosen rather than projectile velocity to normalize the initial conditions for each simulation. Phenomena such as the formation of adiabatic shear bands caused by deformation at high strains and strain rates were investigated through simulations. It was found that the Johnson-Cook model can accurately simulate the behavior of body-centered cubic (BCC) metals such as steels. The maximum shear stress was calculated for each simulation at various impact momenta. The finite element model showed that shear failure first occurred in the center of the cylindrical specimen and

  14. Carbide-Free Bainitic Weld Metal: A New Concept in Welding of Armor Steels

    NASA Astrophysics Data System (ADS)

    Krishna Murthy, N.; Janaki Ram, G. D.; Murty, B. S.; Reddy, G. M.; Rao, T. J. P.

    2014-12-01

    Carbide-free bainite, a fine mixture of bainitic ferrite and austenite, is a relatively recent development in steel microstructures. Apart from being very strong and tough, the microstructure is hydrogen-tolerant. These characteristics make it well-suited for weld metals. In the current work, an armor-grade quenched and tempered steel was welded such that the fusion zone developed a carbide-free bainitic microstructure. These welds showed very high joint efficiency and ballistic performance compared to those produced, as per the current industrial practice, using austenitic stainless steel fillers. Importantly, these welds showed no vulnerability to cold cracking, as verified using oblique Y-groove tests. The concept of carbide-free bainitic weld metal thus promises many useful new developments in welding of high-strength steels.

  15. Preliminary In Vivo Evaluation of a Hybrid Armored Vascular Graft Combining Electrospinning and Additive Manufacturing Techniques

    PubMed Central

    Spadaccio, Cristiano; Nappi, Francesco; De Marco, Federico; Sedati, Pietro; Sutherland, Fraser W.H.; Chello, Massimo; Trombetta, Marcella; Rainer, Alberto

    2016-01-01

    In this study, we tested in vivo effectiveness of a previously developed poly-l-lactide/poly-ε-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. PMID:26949333

  16. DNA barcodes for two scale insect families, mealybugs (Hemiptera: Pseudococcidae) and armored scales (Hemiptera: Diaspididae).

    PubMed

    Park, D-S; Suh, S-J; Hebert, P D N; Oh, H-W; Hong, K-J

    2011-08-01

    Although DNA barcode coverage has grown rapidly for many insect orders, there are some groups, such as scale insects, where sequence recovery has been difficult. However, using a recently developed primer set, we recovered barcode records from 373 specimens, providing coverage for 75 species from 31 genera in two families. Overall success was >90% for mealybugs and >80% for armored scale species. The G·C content was very low in most species, averaging just 16.3%. Sequence divergences (K2P) between congeneric species averaged 10.7%, while intra-specific divergences averaged 0.97%. However, the latter value was inflated by high intra-specific divergence in nine taxa, cases that may indicate species overlooked by current taxonomic treatments. Our study establishes the feasibility of developing a comprehensive barcode library for scale insects and indicates that its construction will both create an effective system for identifying scale insects and reveal taxonomic situations worthy of deeper analysis.

  17. Surface damage in TiC coating layers on PDX wall armor tiles

    NASA Astrophysics Data System (ADS)

    Gotoh, Y.; Hoven, H.; Koizlik, K.; Linke, J.; Wallura, E.; Nickel, H.; Kugel, H.; Ulrickson, M.

    1987-02-01

    Surface damage and material redepositions are investigated on 17 graphite tile surface of the PDX wall armor exposed to more than 6500 shots of neutral beam injection (NBI) shine-through and more than 700 shots of direct NBI. Titanium deposition layers, from 0.1 to 7 μm in thickness, redeposited metal droplets, or micro-projections with diameters of less than 2-3 μm and a number density at around 10 8/cm 2, are observed on the tile front faces. Aligned wedge-shaped pits are observed at all micro-projections, which are likely due to shadowed Ti-deposition at redeposited metal droplets by Ti-getter evaporation. Blistering observed in both the TiC coating and Ti-deposition layers is due to plasma shine-through D 0 beam irradiations to a fluence of more than 2 × 10 19 at./cm 2.

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

    SciTech Connect

    Liu Lisheng; Zhang Qingjie; Zhai Pengcheng; Cao Dongfeng

    2008-02-15

    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.

  19. DNA diagnostics of three armored scale species on kiwifruit in New Zealand.

    PubMed

    Edwards, Robert; Carraher, Colm; Poulton, Joanne; Sandanayaka, Manoharie; Todd, Jacqui H; Dobson, Shirley; Mauchline, Nicola; Hill, Garry; McKenna, Cathy; Newcomb, Richard D

    2008-12-01

    Three species of armored scale (Hemiptera: Diaspididae) are found on kiwifruit (Actinidia spp.) in New Zealand orchards: latania scale, Hemiberlesia lataniae (Signoret); greedy scale, Hemiberlesia rapax (Comstock); and oleander scale, Aspidiotus nerii (Bouché). Each of them is a quarantine pest in some of the markets to which New Zealand kiwifruit are exported. Adult females of the three species can be distinguished morphologically; however, the task is laborious when large numbers must be identified. Furthermore, it is not possible to distinguish among the immature stages. A DNA-based diagnostic using a multiplex polymerase chain reaction (PCR) method based on differences in the cytochrome oxidase I and II genes was developed to distinguish the three species. The test relies on the rapid isolation of amplifiable DNA by using a protease (prepGEM), followed by multiplex PCR using primers that distinguish the species at three or more nucleotide positions within cytochrome oxidase I and II, resulting in PCR products of characteristic size for each species. The test was validated in a double-blind experiment and then used to determine the relative distribution and abundance of the three species on leaves and fruit of 'Hayward' and 'Hortl6A' kiwifruit across the dominant growing regions throughout New Zealand during the 2007 season. In total, 3,418 scale insects were identified to species level: 1,904 (56%) were latania scale; 1,473 (43%) were greedy scale; and 41 (1%) were oleander scale. Since the last survey in 1988, latania scale has displaced greedy scale as the dominant species of armored scale on Hayward kiwifruit in the North Island and was found for the first time in the South Island. Only a single latania scale was found on Hortl6A fruit, consistent with previous reports of reduced rates of settlement on the fruit of this cultivar by latania scale compared with greedy scale. PMID:19133478

  20. Relationships between 16S-23S rRNA gene internal transcribed spacer DNA and genomic DNA similarities in the taxonomy of phototrophic bacteria

    NASA Astrophysics Data System (ADS)

    Okamura, K.; Hisada, T.; Takata, K.; Hiraishi, A.

    2013-04-01

    Rapid and accurate identification of microbial species is essential task in microbiology and biotechnology. In prokaryotic systematics, genomic DNA-DNA hybridization is the ultimate tool to determine genetic relationships among bacterial strains at the species level. However, a practical problem in this assay is that the experimental procedure is laborious and time-consuming. In recent years, information on the 16S-23S rRNA gene internal transcribed spacer (ITS) region has been used to classify bacterial strains at the species and intraspecies levels. It is unclear how much information on the ITS region can reflect the genome that contain it. In this study, therefore, we evaluate the quantitative relationship between ITS DNA and entire genomic DNA similarities. For this, we determined ITS sequences of several species of anoxygenic phototrophic bacteria belonging to the order Rhizobiales, and compared with DNA-DNA relatedness among these species. There was a high correlation between the two genetic markers. Based on the regression analysis of this relationship, 70% DNA-DNA relatedness corresponded to 92% ITS sequence similarity. This suggests the usefulness of the ITS sequence similarity as a criterion for determining the genospecies of the phototrophic bacteria. To avoid the effects of polymorphism bias of ITS on similarities, PCR products from all loci of ITS were used directly as genetic probes for comparison. The results of ITS DNA-DNA hybridization coincided well with those of genomic DNA-DNA relatedness. These collective data indicate that the whole ITS DNA-DNA similarity can be used as an alternative to genomic DNA-DNA similarity.

  1. From genus to phylum: large-subunit and internal transcribed spacer rRNA operon regions show similar classification accuracies influenced by database composition.

    PubMed

    Porras-Alfaro, Andrea; Liu, Kuan-Liang; Kuske, Cheryl R; Xie, Gary

    2014-02-01

    We compared the classification accuracy of two sections of the fungal internal transcribed spacer (ITS) region, individually and combined, and the 5' section (about 600 bp) of the large-subunit rRNA (LSU), using a naive Bayesian classifier and BLASTN. A hand-curated ITS-LSU training set of 1,091 sequences and a larger training set of 8,967 ITS region sequences were used. Of the factors evaluated, database composition and quality had the largest effect on classification accuracy, followed by fragment size and use of a bootstrap cutoff to improve classification confidence. The naive Bayesian classifier and BLASTN gave similar results at higher taxonomic levels, but the classifier was faster and more accurate at the genus level when a bootstrap cutoff was used. All of the ITS and LSU sections performed well (>97.7% accuracy) at higher taxonomic ranks from kingdom to family, and differences between them were small at the genus level (within 0.66 to 1.23%). When full-length sequence sections were used, the LSU outperformed the ITS1 and ITS2 fragments at the genus level, but the ITS1 and ITS2 showed higher accuracy when smaller fragment sizes of the same length and a 50% bootstrap cutoff were used. In a comparison using the larger ITS training set, ITS1 and ITS2 had very similar accuracy classification for fragments between 100 and 200 bp. Collectively, the results show that any of the ITS or LSU sections we tested provided comparable classification accuracy to the genus level and underscore the need for larger and more diverse classification training sets.

  2. A new species of armored scale, Mycetaspis ailynaomi (Hemiptera, Diaspididae, Aspidiotinae), associated with Mammea americana L. (Malpighiales, Calophyllaceae) from Puerto Rico

    PubMed Central

    Dones, Ramón A.; Evans, Gregory A.

    2011-01-01

    Abstract A new species of armored scale, Mycetaspis ailynaomi Dones and Evans is described and illustrated from specimens collected on mamey (Mammea americana) from Puerto Rico. A key to the species of Mycetaspis is provided. PMID:21852924

  3. Biochemical responses, morphometric changes, genotoxic effects and CYP1A expression in the armored catfish Pterygoplichthys anisitsi after 15 days of exposure to mineral diesel and biodiesel.

    PubMed

    Arantes Felício, Andréia; Martins Parente, Thiago Estevam; Regina Maschio, Lucilene; Nogueira, Lílian; Rodrigues Venancio, Larissa Paola; de Freitas Rebelo, Mauro; Schlenk, Daniel; de Almeida, Eduardo Alves

    2015-05-01

    Despite being considered friendlier to the environment, biodiesel fuel can be harmful to aquatic organisms, especially when combined with petroleum diesel fuel. In this work we evaluated the effects of mineral diesel fuel containing increasing concentrations of biodiesel (5% and 20%, namely B5 and B20) and pure biodiesel (B100), at concentrations of 0.001 and 0.01mLL(-1), after 15 days of exposure, in armored catfish (Pterygoplichtys anisitsi). Toxicity tests were also performed to estimate LC50 values (96h) for each compound. Biotransformation enzymes [ethoxyresorufin-O-deethylase (EROD), and glutathione S-transferase (GST)] as well as oxidative stress markers (superoxide dismutase, SOD, catalase, CAT, glutathione peroxidase, GPx, and the level of lipid peroxidation) were measured in liver and gills after treatment. Genotoxic effects were also accessed in erythrocytes using the comet assay and by evaluating the frequency of micronuclei formation. Further, the mRNA of cytochrome P450 1A (CYP1A) was also measured in liver. Mortality was not observed even exposure to concentrations as high as 6.0mLL(-1). EROD and GST activities were increased after B5 and B20 treatments; however, CYP1A mRNA induction was not observed. SOD and CAT activities were decreased, but GPx was significantly higher for all treatments in gills. There were no significant changes in lipid peroxidation, but genotoxicity markers revealed that all treatments increased comet scores. Fuels B5 and B20 increased micronuclei frequency. Our results indicate that despite being less toxic, biodiesel may cause sublethal alterations in fish that may alter long term health.

  4. ARC-1, a sequence element complementary to an internal 18S rRNA segment, enhances translation efficiency in plants when present in the leader or intercistronic region of mRNAs

    PubMed Central

    Akbergenov, R. Zh.; Zhanybekova, S. Sh.; Kryldakov, R. V.; Zhigailov, A.; Polimbetova, N. S.; Hohn, T.; Iskakov, B. K.

    2004-01-01

    The sequences of different plant viral leaders with known translation enhancer ability show partial complementarity to the central region of 18S rRNA. Such complementarity might serve as a means to attract 40S ribosomal subunits and explain in part the translation-enhancing property of these sequences. To verify this notion, we designed β-glucuronidase (GUS) mRNAs differing only in the nature of 10 nt inserts in the center of their 41 base leaders. These were complementary to consecutive domains of plant 18S rRNA. Sucrose gradient analysis revealed that leaders with inserts complementary to regions 1105–1114 and 1115–1124 (‘ARC-1’) of plant 18S rRNA bound most efficiently to the 40S ribosomal subunit after dissociation from 80S ribosomes under conditions of high ionic strength, a treatment known to remove translation initiation factors. Using wheat germ cell-free extracts, we could demonstrate that mRNAs with these leaders were translated more than three times more efficiently than a control lacking such a complementarity. Three linked copies of the insert enhanced translation of reporter mRNA to levels comparable with those directed by the natural translation enhancing leaders of tobacco mosaic virus and potato virus Y RNAs. Moreover, inserting the same leaders as intercistronic sequences in dicistronic mRNAs substantially increased translation of the second cistron, thereby revealing internal ribosome entry site activity. Thus, for plant systems, the complementary interaction between mRNA leader and the central region of 18S rRNA allows cap-independent binding of mRNA to the 43S pre-initiation complex without assistance of translation initiation factors. PMID:14718549

  5. Controls on and effects of armoring and vertical sorting in aeolian dune fields: A numerical simulation study

    NASA Astrophysics Data System (ADS)

    Gao, Xin; Narteau, Clément; Rozier, Olivier

    2016-03-01

    Unlike ripples, there are only few numerical studies on grain size segregation at the scale of dunes in aeolian environments. Here we use a cellular automaton model to analyze vertical sorting in granular mixtures under steady unidirectional flow conditions. We investigate the feedbacks between dune growth and the segregation mechanisms by varying the size of coarse grains and their proportion within the bed. We systematically observe the development of a horizontal layer of coarse grains at the top of which sorted bed forms may grow by amalgamation. The formation of such an armor layer controls the overall sediment transport and availability. The emergence of dunes and the transition from barchan to transverse dune fields depend only on the grain size distribution of the initial sediment layer. As confirmed by observation, this result indicates that armor layers should be present in most arid deserts, where they are likely to control dune morphodynamics.

  6. A checklist of Indian armored spiders (Araneae, Tetrablemmidae) with the description of a new species from the Western Ghats.

    PubMed

    Sankaran, Pradeep M; Sebastian, Pothalil A

    2016-01-01

    The Oriental armored spider genus Shearella Lehtinen, 1981 is recorded for the first time from India. Detailed description and illustrations of both sexes of Shearella alii sp. nov. are given. The geographic distribution of the genus is updated. Sinamma sanya (Lin & Li, 2010) is transferred back to Shearella, and Shearella browni (Shear, 1978) back to Monoblemma Gertsch, 1941. A checklist of all Indian tetrablemmid species currently known and a distribution map of all known Shearella spp. are presented. PMID:27394275

  7. High levels of exotic armored scales on imported avocados raise concerns regarding USDA-APHIS' phytosanitary risk assessment.

    PubMed

    Morse, J G; Rugman-Jones, P F; Watson, G W; Robinson, L J; Bi, J L; Stouthamer, R

    2009-06-01

    Between 1914 and 2007, a quarantine protected California avocado, Persea americana Mill., groves from pests that might be introduced into the state along with fresh, imported avocados. Soon after Mexican avocados were first allowed entry on 1 February 2007, live specimens of several species of armored scales (Hemiptera: Diaspididae) not believed to be present in California were detected on 'Hass' avocados entering the state from Mexico. Initially, the California Department of Food and Agriculture (CDFA) prevented avocados infested with these scales from entering the state or required that they be fumigated with an approved treatment such as methyl bromide. After a Science Advisory Panel meeting in May 2007, U.S. Department of Agriculture-Animal and Plant Health Inspection Service (USDA-APHIS) reaffirmed its position that armored scales on shipments of fruit for consumption (including avocados) pose a "low risk" for pest establishment. In compliance with APHIS protocols, as of 18 July 2007, CDFA altered its policy to allow shipments of scale-infested avocados into the state without treatment. Here, we report on sampling Mexican avocados over an 8-mo period, September 2007-April 2008. An estimated 67 million Mexican Hass avocados entered California over this period. Based on samples from 140 trucks containing approximately 15.6% of this volume of fruit, we estimate that approximately 47.6 million live, sessile armored scales and an additional 20.1 million live eggs and crawlers were imported. We found eight probable species of armored scales in the samples, seven of these are not believed to occur in California; 89.3% of the live scales were Abgrallaspis aguacatae Evans, Watson and Miller, a recently described species. In contrast to the USDA-APHIS opinion, we believe the volume of shipments and levels of live scales they contain present a significant risk to California's US$300 million avocado industry and to other crops that might become infested by one or more of

  8. A recurrent regulatory change underlying altered expression and Wnt response of the stickleback armor plates gene EDA

    PubMed Central

    O'Brown, Natasha M; Summers, Brian R; Jones, Felicity C; Brady, Shannon D; Kingsley, David M

    2015-01-01

    Armor plate changes in sticklebacks are a classic example of repeated adaptive evolution. Previous studies identified ectodysplasin (EDA) gene as the major locus controlling recurrent plate loss in freshwater fish, though the causative DNA alterations were not known. Here we show that freshwater EDA alleles have cis-acting regulatory changes that reduce expression in developing plates and spines. An identical T → G base pair change is found in EDA enhancers of divergent low-plated fish. Recreation of the T → G change in a marine enhancer strongly reduces expression in posterior armor plates. Bead implantation and cell culture experiments show that Wnt signaling strongly activates the marine EDA enhancer, and the freshwater T → G change reduces Wnt responsiveness. Thus parallel evolution of low-plated sticklebacks has occurred through a shared DNA regulatory change, which reduces the sensitivity of an EDA enhancer to Wnt signaling, and alters expression in developing armor plates while preserving expression in other tissues. DOI: http://dx.doi.org/10.7554/eLife.05290.001 PMID:25629660

  9. Puget Sound Shorelines and the Impacts of Armoring-Proceedings of a State of the Science Workshop, May 2009

    USGS Publications Warehouse

    : Shipman, Hugh; Dethier, Megan N.; Gelfenbaum, Guy; Fresh, Kurt L.; Dinicola, Richard S.

    2010-01-01

    The widespread extent and continued construction of seawalls and bulkheads on Puget Sound's beaches has emerged as a significant issue in shoreline management and coastal restoration in the region. Concerns about the impacts of shoreline armoring and managing the potential risks to coastal property are in many ways similar to those in other places, but Puget Sound also poses unique challenges related to its sheltered setting, glacially formed geology, rich estuarine ecology, and historical development pattern. The effects of armoring on shorelines are complex, involving both physical and biological science and requiring consideration of the cumulative impacts of small-scale activities over large scales of space and time. In addition, the issue is controversial, as it often places strongly held private interests in protecting shoreline property against broad public mandates to preserve shorelines for public uses and to protect environmental resources. Communities making difficult decisions about regulating shoreline activities and prioritizing restoration projects need to be informed by the best science available. To address these issues, a scientific workshop was convened in May 2009, specifically to bring local and national experts together to review the state of the science regarding the physical and biological impacts of armoring on sheltered shorelines such as those of Puget Sound.

  10. Efficient translation initiation directed by the 900-nucleotide-long and GC-rich 5' untranslated region of the human retrotransposon LINE-1 mRNA is strictly cap dependent rather than internal ribosome entry site mediated.

    PubMed

    Dmitriev, Sergey E; Andreev, Dmitri E; Terenin, Ilya M; Olovnikov, Ivan A; Prassolov, Vladimir S; Merrick, William C; Shatsky, Ivan N

    2007-07-01

    Retrotransposon L1 is a mobile genetic element of the LINE family that is extremely widespread in the mammalian genome. It encodes a dicistronic mRNA, which is exceptionally rare among eukaryotic cellular mRNAs. The extremely long and GC-rich L1 5' untranslated region (5'UTR) directs synthesis of numerous copies of RNA-binding protein ORF1p per mRNA. One could suggest that the 5'UTR of L1 mRNA contained a powerful internal ribosome entry site (IRES) element. Using transfection of cultured cells with the polyadenylated monocistronic (L1 5'UTR-Fluc) or bicistronic (Rluc-L1 5'UTR-Fluc) RNA constructs, capped or uncapped, it has been firmly established that the 5'UTR of L1 does not contain an IRES. Uncapping reduces the initiation activity of the L1 5'UTR to that of background. Moreover, the translation is inhibited by upstream AUG codons in the 5'UTR. Nevertheless, this cap-dependent initiation activity of the L1 5'UTR was unexpectedly high and resembles that of the beta-actin 5'UTR (84 nucleotides long). Strikingly, the deletion of up to 80% of the nucleotide sequence of the L1 5'UTR, with most of its stem loops, does not significantly change its translation initiation efficiency. These data can modify current ideas on mechanisms used by 40S ribosomal subunits to cope with complex 5'UTRs and call into question the conception that every long GC-rich 5'UTR working with a high efficiency has to contain an IRES. Our data also demonstrate that the ORF2 translation initiation is not directed by internal initiation, either. It is very inefficient and presumably based on a reinitiation event.

  11. Efficient Translation Initiation Directed by the 900-Nucleotide-Long and GC-Rich 5′ Untranslated Region of the Human Retrotransposon LINE-1 mRNA Is Strictly Cap Dependent Rather than Internal Ribosome Entry Site Mediated▿

    PubMed Central

    Dmitriev, Sergey E.; Andreev, Dmitri E.; Terenin, Ilya M.; Olovnikov, Ivan A.; Prassolov, Vladimir S.; Merrick, William C.; Shatsky, Ivan N.

    2007-01-01

    Retrotransposon L1 is a mobile genetic element of the LINE family that is extremely widespread in the mammalian genome. It encodes a dicistronic mRNA, which is exceptionally rare among eukaryotic cellular mRNAs. The extremely long and GC-rich L1 5′ untranslated region (5′UTR) directs synthesis of numerous copies of RNA-binding protein ORF1p per mRNA. One could suggest that the 5′UTR of L1 mRNA contained a powerful internal ribosome entry site (IRES) element. Using transfection of cultured cells with the polyadenylated monocistronic (L1 5′UTR-Fluc) or bicistronic (Rluc-L1 5′UTR-Fluc) RNA constructs, capped or uncapped, it has been firmly established that the 5′UTR of L1 does not contain an IRES. Uncapping reduces the initiation activity of the L1 5′UTR to that of background. Moreover, the translation is inhibited by upstream AUG codons in the 5′UTR. Nevertheless, this cap-dependent initiation activity of the L1 5′UTR was unexpectedly high and resembles that of the beta-actin 5′UTR (84 nucleotides long). Strikingly, the deletion of up to 80% of the nucleotide sequence of the L1 5′UTR, with most of its stem loops, does not significantly change its translation initiation efficiency. These data can modify current ideas on mechanisms used by 40S ribosomal subunits to cope with complex 5′UTRs and call into question the conception that every long GC-rich 5′UTR working with a high efficiency has to contain an IRES. Our data also demonstrate that the ORF2 translation initiation is not directed by internal initiation, either. It is very inefficient and presumably based on a reinitiation event. PMID:17470553

  12. Radiator Heat Pipes with Carbon-Carbon Fins and Armor for Space Nuclear Reactor Power Systems

    NASA Astrophysics Data System (ADS)

    Tournier, Jean-Michel; El-Genk, Mohamed

    2005-02-01

    Technologies for Space Reactor Power Systems are being developed to enable future NASA's missions early next decade to explore the farthest planets in the solar system. The choices of the energy conversion technology for these power systems require radiator temperatures that span a wide range, from 350 K to 800 K. Heat pipes with carbon-carbon fins and armor are the preferred choice for these radiators because of inherent redundancy and efficient spreading and rejection of waste heat into space at a relatively small mass penalty. The performance results and specific masses of radiator heat pipes with cesium, rubidium, and potassium working fluids are presented and compared in this paper. The heat pipes operate at 40% of the prevailing operation limit (a design margin of 60%), typically the sonic and/or capillary limit. The thickness of the carbon-carbon fins is 0.5 mm but the width is varied, and the evaporator and condenser sections are 0.15 and 1.35 m long, respectively. The 400-mesh wick and the heat pipe thin metal wall are titanium, and the carbon-carbon armor (~ 2 mm-thick) provides both structural strength and protection against meteoroids impacts. The cross-section area of the D-shaped radiator heat pipes is optimized for minimum mass. Because of the low vapor pressure of potassium and its very high Figure-Of-Merit (FOM), radiator potassium heat pipes are the best performers at temperatures above 800 K, where the sonic limit is no longer an issue. On the other hand, rubidium heat pipes are limited by the sonic limit below 762 K and by the capillary limit at higher temperature. The transition temperature between these two limits for the cesium heat pipes occurs at a lower temperature of 724 K, since cesium has lower FOM than rubidium. The present results show that with a design margin of 60%, the cesium heat pipes radiator is best at 680-720 K, the rubidium heat pipes radiator is best at 720-800 K, while the potassium heat pipes radiator is the best

  13. Radiator Heat Pipes with Carbon-Carbon Fins and Armor for Space Nuclear Reactor Power Systems

    SciTech Connect

    Tournier, Jean-Michel; El-Genk, Mohamed

    2005-02-06

    Technologies for Space Reactor Power Systems are being developed to enable future NASA's missions early next decade to explore the farthest planets in the solar system. The choices of the energy conversion technology for these power systems require radiator temperatures that span a wide range, from 350 K to 800 K. Heat pipes with carbon-carbon fins and armor are the preferred choice for these radiators because of inherent redundancy and efficient spreading and rejection of waste heat into space at a relatively small mass penalty. The performance results and specific masses of radiator heat pipes with cesium, rubidium, and potassium working fluids are presented and compared in this paper. The heat pipes operate at 40% of the prevailing operation limit (a design margin of 60%), typically the sonic and/or capillary limit. The thickness of the carbon-carbon fins is 0.5 mm but the width is varied, and the evaporator and condenser sections are 0.15 and 1.35 m long, respectively. The 400-mesh wick and the heat pipe thin metal wall are titanium, and the carbon-carbon armor ({approx} 2 mm-thick) provides both structural strength and protection against meteoroids impacts. The cross-section area of the D-shaped radiator heat pipes is optimized for minimum mass. Because of the low vapor pressure of potassium and its very high Figure-Of-Merit (FOM), radiator potassium heat pipes are the best performers at temperatures above 800 K, where the sonic limit is no longer an issue. On the other hand, rubidium heat pipes are limited by the sonic limit below 762 K and by the capillary limit at higher temperature. The transition temperature between these two limits for the cesium heat pipes occurs at a lower temperature of 724 K, since cesium has lower FOM than rubidium. The present results show that with a design margin of 60%, the cesium heat pipes radiator is best at 680-720 K, the rubidium heat pipes radiator is best at 720-800 K, while the potassium heat pipes radiator is the best

  14. Grain velocity of bedload movement in an armored non-uniform mobile bed

    NASA Astrophysics Data System (ADS)

    Liu, C.

    2015-12-01

    The velocity of bedload particles, which directly reflects the interaction between flow and sediment, is one of the important parameters to predict sediment transport rate, is also one of the fundamental problems for sediment transport. Many excellent works have been accomplished in this filed. However, the existing researches are mostly based on the artificial fixed bed, few moveable bed studies are focus on uniform sediment bed, these boundary conditions are different from a real river. In this research, an experiment on non-uniform sediment with an armored, moveable bed were carried out in a flume, the range of bed material is from 0.2mm to 20mm. With a special hanging glass and illumination system, the motion particles in the bed were clearly shoot on top of the flume by a video camera, avoiding the interference of waves at the flow surface. The speed of the camera is 50 frames per second. About 7000 unique coordinates of moving particles were determined from 3000 frames of successive pictures, the particle velocity of longitudinal and crosswise directions were obtained from the coordinates. The results show that, the probability density distribution of grain velocities of both directions are similar to that in the uniform sediment, which have an exponent decay trend, whereas the value of cross velocity of particles is clearly greater than that in the uniform sediment condition. Negative particle velocity was recognized in the experiment, it is shown that these negative may occur at two conditions, one is the backflow of fine particles behind the coarser particles, and the other is a state of movement change, such as a particle from static state to motion or vice versa. Furthermore, the particle movement was strongly affected by the arrangement of local coarse particles. The influence of coarser particles to the movement of fine particles also identified by two opposite effects, one is the acceleration effects in a 'tunnel' between pair of series particles, the

  15. Variations in the 16S-23S rRNA internal transcribed spacer of fibrolytic Butyrivibrio isolates from the reindeer rumen.

    PubMed

    Præsteng, Kirsti E; Mackie, Roderick I; Cann, Isaac K O; Mathiesen, Svein D; Sundset, Monica A

    2011-07-01

    Strains of Butyrivibrio are principal cellulytic bacteria in the rumen of the High Arctic Svalbard reindeer ( Rangifer tarandus platyrhynchus ). According to phylogenetic analysis based on 16S rRNA gene sequencing, Butyrivibrio can be divided into three subgroups within the Clostridia class of the phylum Firmicutes, but the current phenotypic and genotypic differentiation within the family Lachnospiraceae is insufficient. This current study describes the sequence diversity of the 16S-23S rRNA intergenic transcribed spacer (ITS) region of Butyrivibrio isolates from reindeer. A total of 17 different ITS sequences with sizes between 449 and 784 nt were obtained. Genes encoding tRNA(Ile) and tRNA(Ala) were identified in four of the sequences. Phylogenetic neighbor-joining trees were constructed based on the ITS sequence and compared with a phylogenetic neighbor-joining tree based on 16S rRNA gene sequences previously obtained for the same isolates. These comparisons indicated a better differentiation between strains in the ITS sequence than the 16S rRNA gene based tree. Through this study, a better means for identifying and tracking fibrolytic and potentially probiotic Butyrivibrio strains in reindeer and other ruminants has been provided.

  16. RNA Crystallization

    NASA Technical Reports Server (NTRS)

    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.

  17. Influences on Bed Sorting and Armoring in an Upland Gravel-Cobble Bed River, Middle Fork John Day River, Oregon

    NASA Astrophysics Data System (ADS)

    McDowell, P. F.

    2014-12-01

    The Middle Fork is an unconfined to partly confined upland river with channel length of 34 km, drainage area of 250-850 km2, and channel gradients of 0.004 to 0.006 in the study area. Geology is dominated by Tertiary volcanic and volcaniclastic rocks that yield abundant coarse clasts. Surface and subsurface bed material was sampled volumetrically at twenty-five sites. The textural types range from gravelly cobbles to sandy cobbly gravels, sand content is low (2 to 13%), mud content is very low, and sorting is poor to very poor. Generally the surface layer is an open framework gravel or cobble, while the subsurface layer is a filled or partially filled framework gravel or cobble. Despite an armored appearance, only 20% of the sites are armored using the standard armor ratio (surface D50/subsurface D50). While surface layers are not coarser than their subsurface layers in terms of the median or coarse end of the distribution, they are coarser in terms of fines (ratios based on D25, D16, % sand), suggesting that alternatives to the D50armor ratio might be useful. Multivariate analysis of size fraction data reveals four distinct groups of samples, distinguished mainly by differences in proportions of coarse to fine gravels, and in abundance of sand. While one group comprises only surface samples and another subsurface samples, two of the groups are mixed. One goal of the project is to evaluate the effects of land use history on bed material characteristics and mobility. Sediment characteristics were examined in relation to distance downstream, geology, relation to debris-flow sources, land use history, and other potential influences. There are no geologic associations or downstream trends in fining or other grain size parameters. Differences in land use history, such as former dredged-mined reaches and reaches with recent restoration projects also do not explain patterns of armoring or other sediment characteristics. High variability within each reach suggests that

  18. RNA helicases

    PubMed Central

    Owttrim, George W.

    2013-01-01

    Similar to proteins, RNA molecules must fold into the correct conformation and associate with protein complexes in order to be functional within a cell. RNA helicases rearrange RNA secondary structure and RNA-protein interactions in an ATP-dependent reaction, performing crucial functions in all aspects of RNA metabolism. In prokaryotes, RNA helicase activity is associated with roles in housekeeping functions including RNA turnover, ribosome biogenesis, translation and small RNA metabolism. In addition, RNA helicase expression and/or activity are frequently altered during cellular response to abiotic stress, implying they perform defined roles during cellular adaptation to changes in the growth environment. Specifically, RNA helicases contribute to the formation of cold-adapted ribosomes and RNA degradosomes, implying a role in alleviation of RNA secondary structure stabilization at low temperature. A common emerging theme involves RNA helicases acting as scaffolds for protein-protein interaction and functioning as molecular clamps, holding RNA-protein complexes in specific conformations. This review highlights recent advances in DEAD-box RNA helicase association with cellular response to abiotic stress in prokaryotes. PMID:23093803

  19. SIRE (sight-integrated ranging equipment): an eyesafe laser rangefinder for armored vehicle fire control systems

    NASA Astrophysics Data System (ADS)

    Keeter, Howard S.; Gudmundson, Glen A.; Woodall, Milton A., II

    1991-04-01

    The Sight Integrated Ranging Equipment (SIRE) incorporates an eyesafe laser rangefinder into the M-36 periscope used in tactical armored vehicles, such as the Commando Stingray light tank. The SIRE unit provides crucial range data simultaneously to the gunner and fire control computer. This capability greatly reduces 'time-to-fire', improves first-round hit probability, and increases the overall effectiveness of the vehicle under actual and simulated battlefield conditions. The SIRE can provide target range up to 10-km, with an accuracy of 10-meters. The key advantage of the SIRE over similar laser rangefinder systems is that it uses erbium:glass as the active lasing medium. With a nominal output wavelength of 1.54-microns, the SIRE can produce sufficient peak power to penetrate long atmospheric paths (even in the presence of obscurants), while remaining completely eyesafe under all operating conditions. The SIRE is the first eyesafe vehicle-based system to combine this level of accuracy, maximum range capability, and fire control interface. It simultaneously improves the accuracy and confidence of the operator, and eliminates the ocular hazard issues typically encountered with laser rangefinder devices.

  20. Armoring, stability, and transport driven by fluid flow over a granular bed

    NASA Astrophysics Data System (ADS)

    Allen, Benjamin; Kudrolli, Arshad

    2015-03-01

    We discuss experiments investigating the evolution of a granular bed by a fluid flow as a function of shear rate at the fluid-bed interface. This is a model system to investigate a variety of physical examples including wind blowing over sand, sediment transport in rivers, tidal flows interacting with beaches, flows in slurry pipelines, and sand proppants in hydraulic fracturing. In order to examine the onset and entrainment of the granular bed under steady state conditions, we have constructed a novel conical rheometer system which allows a variable amount of shear to be applied to the granular bed. The grain-fluid system is index matched so that we can visualize the grains away from the sides as well as visualize the fluid flow above and below the interface by using fluorescent tracer particles. We demonstrate that the onset of erosion arises as particles rotate out of their stable position highlighting the importance of torque balance to onset. We find significant armoring of the bed, as the bed is sheared by the fluid flow. Above onset, at least three distinct regions of bed mobility can be found. We will discuss the measured integrated granular flux as a function of shear rate and compare them with empirical laws found in the geophysical literature. Supported by NSF Grant Number CBET 1335928.

  1. Combat body armor and injuries to the head, face, and neck region: a systematic review.

    PubMed

    Tong, Darryl; Beirne, Ross

    2013-04-01

    There has been a reported increase in combat-related head, face, and neck (HFN) injuries among service personnel wearing combat body armor (CBA) that have deployed to Iraq and Afghanistan. Modern ceramic plate CBA has decreased the incidence of fatal-penetrating injuries to the torso but offers no protection to the limbs and face which remain exposed to gunshot wounds and fragments from explosive devices. The aim of this review was to systematically summarize the literature reporting on HFN injuries sustained by combat personnel wearing CBA and to highlight recommendations for increased protection to the facial region. Three major contributing factors were identified with this proportional increase in HFN injuries, namely the increased survivability of soldiers because of CBA, fragments injuries from explosive devices, and the lack of protection to the face and limbs. There appears to be no evidence to suggest that by virtue of wearing CBA the likelihood of sustaining an HFN injury increases as such, but a higher incidence of fragment injuries to the HFN region may be due to the more common use of improvised explosive devicess and other explosive devices. Further development of lightweight protection for the face is needed. PMID:23707828

  2. Structure and fracture resistance of alligator gar (Atractosteus spatula) armored fish scales.

    PubMed

    Yang, Wen; Gludovatz, Bernd; Zimmermann, Elizabeth A; Bale, Hrishikesh A; Ritchie, Robert O; Meyers, Marc A

    2013-04-01

    The alligator gar is a large fish with flexible armor consisting of ganoid scales. These scales contain a thin layer of ganoine (microhardness ~2.5 GPa) and a bony body (microhardness ~400 MPa), with jagged edges that provide effective protection against predators. We describe here the structure of both ganoine and bony foundation and characterize the mechanical properties and fracture mechanisms. The bony foundation is characterized by two components: a mineralized matrix and parallel arrays of tubules, most of which contain collagen fibers. The spacing of the empty tubules is ~60 μm; the spacing of those filled with collagen fibers is ~7 μm. Using micromechanical testing of such scales in a variable-pressure scanning electron microscope, we identify interactions between propagating cracks and the microstructure, and show that the toughness of the scales increases with crack extension in a classical resistance-curve response from the activation of extrinsic toughening mechanisms. We demonstrate how mechanical damage evolves in these structures, and further identify that the reinforcement of the mineral by the network of collagen fibers is the principal toughening mechanism resisting such damage. Additionally, we define the anisotropy of the toughness of the scales and relate this to the collagen fiber orientation. PMID:23274521

  3. Structure and fracture resistance of alligator gar (Atractosteus spatula) armored fish scales.

    PubMed

    Yang, Wen; Gludovatz, Bernd; Zimmermann, Elizabeth A; Bale, Hrishikesh A; Ritchie, Robert O; Meyers, Marc A

    2013-04-01

    The alligator gar is a large fish with flexible armor consisting of ganoid scales. These scales contain a thin layer of ganoine (microhardness ~2.5 GPa) and a bony body (microhardness ~400 MPa), with jagged edges that provide effective protection against predators. We describe here the structure of both ganoine and bony foundation and characterize the mechanical properties and fracture mechanisms. The bony foundation is characterized by two components: a mineralized matrix and parallel arrays of tubules, most of which contain collagen fibers. The spacing of the empty tubules is ~60 μm; the spacing of those filled with collagen fibers is ~7 μm. Using micromechanical testing of such scales in a variable-pressure scanning electron microscope, we identify interactions between propagating cracks and the microstructure, and show that the toughness of the scales increases with crack extension in a classical resistance-curve response from the activation of extrinsic toughening mechanisms. We demonstrate how mechanical damage evolves in these structures, and further identify that the reinforcement of the mineral by the network of collagen fibers is the principal toughening mechanism resisting such damage. Additionally, we define the anisotropy of the toughness of the scales and relate this to the collagen fiber orientation.

  4. Challenges of Engineering Grain Boundaries in Boron-Based Armor Ceramics

    NASA Astrophysics Data System (ADS)

    Coleman, Shawn P.; Hernandez-Rivera, Efrain; Behler, Kristopher D.; Synowczynski-Dunn, Jennifer; Tschopp, Mark A.

    2016-06-01

    Boron-based ceramics are appealing for lightweight applications in both vehicle and personnel protection, stemming from their combination of high hardness, high elastic modulus, and low density as compared to other ceramics and metal alloys. However, the performance of these ceramics and ceramic composites is lacking because of their inherent low fracture toughness and reduced strength under high-velocity threats. The objective of the present article is to briefly discuss both the challenges and the state of the art in experimental and computational approaches for engineering grain boundaries in boron-based armor ceramics, focusing mainly on boron carbide (B4C) and boron suboxide (B6O). The experimental challenges involve processing these ceramics at full density while trying to promote microstructure features such as intergranular films to improve toughness during shock. Many of the computational challenges for boron-based ceramics stem from their complex crystal structure which has hitherto complicated the exploration of grain boundaries and interfaces. However, bridging the gaps between experimental and computational studies at multiple scales to engineer grain boundaries in these boron-based ceramics may hold the key to maturing these material systems for lightweight defense applications.

  5. Environmental assessment of depleted uranium used in military armor-piercing rounds in terrestrial systems.

    PubMed

    Stanley, Jacob K; Coleman, Jessica G; Brasfield, Sandra M; Bednar, Anthony J; Ang, Choo Y

    2014-06-01

    Depleted uranium (DU) from the military testing and use of armor-piercing kinetic energy penetrators has been shown to accumulate in soils; however, little is known about the toxicity of DU geochemical species created through corrosion or weathering. The purpose of the present study was to assess the toxic effects and bioaccumulation potential of field-collected DU oxides to the model terrestrial invertebrates Eisenia fetida (earthworm) and Porcellio scaber (isopod). Earthworm studies were acute (72 h) dermal exposures or 28-d spiked soil exposures that used noncontaminated field-collected soils from the US Army's Yuma and Aberdeen Proving Grounds. Endpoints assessed in earthworm testing included bioaccumulation, growth, reproduction, behavior (soil avoidance), and cellular stress (neutral red uptake in coelomocytes). Isopod testing used spiked food, and endpoints assessed included bioaccumulation, survival, and feeding behavior. Concentration-dependent bioaccumulation of DU in earthworms was observed with a maximum bioaccumulation factor of 0.35; however, no significant reductions in survival or impacts to cellular stress were observed. Reproduction lowest-observed-effect concentrations (LOEC) of 158 mg/kg and 96 mg/kg were observed in Yuma Proving Ground and a Mississippi reference soil (Karnac Ferry), respectively. Earthworm avoidance of contaminated soils was not observed in 48-h soil avoidance studies; however, isopods were shown to avoid food spiked with 12.7% by weight DU oxides through digital tracking studies. PMID:24549573

  6. A performance measure based on principal component analysis for ceramic armor integrity

    NASA Astrophysics Data System (ADS)

    Rollins, D. K., Sr.; Stiehl, C. K.; Kotz, K.; Beverlin, L.; Brasche, L.

    2012-05-01

    Principal Component Analysis (PCA) has been applied to thru-transmission ultrasound data taken on ceramic armor. PCA will help find and accentuate differences within the tile, making it easier to find differences. First, the thru-transmission ultrasound data was analyzed. As the ultrasound transducer moves along the surface of the tile, the signal from the sound wave is measured as it reaches the receiver, giving a time signal at each tile location. The information from this time signal is dissected into ten equal segments, and the maximum peak is measured within each segment, or gate. This gives ten measurements at each tile location that correspond to tile depth An image can be made for each of the ten gate measurements. PCA was applied to this data for all of the tile samples, and a performance measure was developed from the loading information. A performance measure was developed and tested on six samples from each of the panels. When these performance measures are compared to the results of the ballistics tests, it can be seen that the performance measure correlates well to the penetration velocities found from the ballistics tests.

  7. Combat body armor and injuries to the head, face, and neck region: a systematic review.

    PubMed

    Tong, Darryl; Beirne, Ross

    2013-04-01

    There has been a reported increase in combat-related head, face, and neck (HFN) injuries among service personnel wearing combat body armor (CBA) that have deployed to Iraq and Afghanistan. Modern ceramic plate CBA has decreased the incidence of fatal-penetrating injuries to the torso but offers no protection to the limbs and face which remain exposed to gunshot wounds and fragments from explosive devices. The aim of this review was to systematically summarize the literature reporting on HFN injuries sustained by combat personnel wearing CBA and to highlight recommendations for increased protection to the facial region. Three major contributing factors were identified with this proportional increase in HFN injuries, namely the increased survivability of soldiers because of CBA, fragments injuries from explosive devices, and the lack of protection to the face and limbs. There appears to be no evidence to suggest that by virtue of wearing CBA the likelihood of sustaining an HFN injury increases as such, but a higher incidence of fragment injuries to the HFN region may be due to the more common use of improvised explosive devicess and other explosive devices. Further development of lightweight protection for the face is needed.

  8. Design of the PDX Tokamak wall armor and inner limiter system

    SciTech Connect

    Kugel, H.W.; Ulrickson, M.

    1981-08-01

    The inner wall protective plates for the PDX Tokamak are designed to absorb 8 MW of neutral deuterium beam power at maximum power densities of 3 kW/cm/sup 2/ for pulse lengths of 0.5 sec. Preliminary studies indicate that the design could survive several pulses of 1 sec 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 is 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 carbide coated 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.

  9. Environmental assessment of depleted uranium used in military armor-piercing rounds in terrestrial systems.

    PubMed

    Stanley, Jacob K; Coleman, Jessica G; Brasfield, Sandra M; Bednar, Anthony J; Ang, Choo Y

    2014-06-01

    Depleted uranium (DU) from the military testing and use of armor-piercing kinetic energy penetrators has been shown to accumulate in soils; however, little is known about the toxicity of DU geochemical species created through corrosion or weathering. The purpose of the present study was to assess the toxic effects and bioaccumulation potential of field-collected DU oxides to the model terrestrial invertebrates Eisenia fetida (earthworm) and Porcellio scaber (isopod). Earthworm studies were acute (72 h) dermal exposures or 28-d spiked soil exposures that used noncontaminated field-collected soils from the US Army's Yuma and Aberdeen Proving Grounds. Endpoints assessed in earthworm testing included bioaccumulation, growth, reproduction, behavior (soil avoidance), and cellular stress (neutral red uptake in coelomocytes). Isopod testing used spiked food, and endpoints assessed included bioaccumulation, survival, and feeding behavior. Concentration-dependent bioaccumulation of DU in earthworms was observed with a maximum bioaccumulation factor of 0.35; however, no significant reductions in survival or impacts to cellular stress were observed. Reproduction lowest-observed-effect concentrations (LOEC) of 158 mg/kg and 96 mg/kg were observed in Yuma Proving Ground and a Mississippi reference soil (Karnac Ferry), respectively. Earthworm avoidance of contaminated soils was not observed in 48-h soil avoidance studies; however, isopods were shown to avoid food spiked with 12.7% by weight DU oxides through digital tracking studies.

  10. Effect of armor and carrying load on body balance and leg muscle function.

    PubMed

    Park, Huiju; Branson, Donna; Kim, Seonyoung; Warren, Aric; Jacobson, Bert; Petrova, Adriana; Peksoz, Semra; Kamenidis, Panagiotis

    2014-01-01

    This study investigated the impact of weight and weight distribution of body armor and load carriage on static body balance and leg muscle function. A series of human performance tests were conducted with seven male, healthy, right-handed military students in seven garment conditions with varying weight and weight distributions. Static body balance was assessed by analyzing the trajectory of center of plantar pressure and symmetry of weight bearing in the feet. Leg muscle functions were assessed by analyzing the peak electromyography amplitude of four selected leg muscles during walking. Results of this study showed that uneven weight distribution of garment and load beyond an additional 9 kg impaired static body balance as evidenced by increased sway of center of plantar pressure and asymmetry of weight bearing in the feet. Added weight on non-dominant side of the body created greater impediment to static balance. Increased garment weight also elevated peak EMG amplitude in the rectus femoris to maintain body balance and in the medial gastrocnemius to increase propulsive force. Negative impacts on balance and leg muscle function with increased carrying loads, particularly with an uneven weight distribution, should be stressed to soldiers, designers, and sports enthusiasts.

  11. Oxidation and Volatilization from Tungsten Brush High Heat Flux Armor During High Temperature Steam Exposure

    SciTech Connect

    Smolik, Galen Richard; Pawelko, Robert James; Anderl, Robert Andrew; Petti, David Andrew

    2000-05-01

    Tungsten brush accommodates thermal stresses and high heat flux in fusion reactor components such as plasma facing surfaces or armor. However, inherently higher surface areas are introduced with the brush design. We have tested a specific design of tungsten brush in steam between 500 and 1100°C. Hydrogen generation and tungsten volatilization rates were determined to address fusion safety issues. The brush prepared from 3.2-mm diameter welding rods had a packing density of 85 percent. We found that both hydrogen generation and tungsten volatilization from brush, fixtured to represent a unit within a larger component, were less than projections based upon the total integrated surface area (TSA). Steam access and the escape of hydrogen and volatile oxide from void spaces within the brush are restricted compared to specimens with more direct diffusion pathways to the test environment. Hydrogen generation rates from restrained specimens based on normal surface area (NSA) remain about five times higher than rates based on total surface areas from specimens with direct steam access. Volatilization rates from restrained specimens based upon normal surface area (NSA) were only 50 percent higher than our historic cumulative maximum flux plot (CMFP) for tungsten. This study has shown that hydrogen generation and tungsten volatilization from brush do not scale according to predictions with previously determined rates, but in fact, with higher packing density could approach those from flat surfaces.

  12. Development of aluminum nitride: A new low-cost armor. Final report, August 1988-March 1992

    SciTech Connect

    Rafaniello, W.

    1992-12-01

    High performance and low cost are the two essential requirements necessary for advanced ceramics to be considered for incorporation into future armor systems. This work involved a comprehensive program, focused on aluminum nitride based ceramics, which examined the critical ceramic processing parameters and studied the impact these modifications had on ballistic performance. The accomplished objective was to demonstrate that low-cost fabrication methods could be utilized to produce high performance AlN based ceramics. Using a spray-dry, dry-press, pressureless sintering process, thick tiles were produced with ballistic performance equivalent to hot-pressed AlN materials. While penetration resistance against the long rod penetrator (LRP) was the ultimate measure of performance, several other ballistic tests were also performed. Ballistic limits were obtained for ceramic targets with a .30 caliber AP simulant and penetration tests were performed against .50 caliber APDS and SLAP rounds. These tests were used as screening tools to guide AIN powder and sintering aid optimization.

  13. Cyanobacterial Ecotypes in Different Optical Microenvironments of a 68°C Hot Spring Mat Community Revealed by 16S-23S rRNA Internal Transcribed Spacer Region Variation†

    PubMed Central

    Ferris, Mike J.; Kühl, Michael; Wieland, Andrea; Ward, David M.

    2003-01-01

    We examined the population of unicellular cyanobacteria (Synechococcus) in the upper 3-mm vertical interval of a 68°C region of a microbial mat in a hot spring effluent channel (Yellowstone National Park, Wyoming). Fluorescence microscopy and microsensor measurements of O2 and oxygenic photosynthesis demonstrated the existence of physiologically distinct Synechococcus populations at different depths along a light gradient quantified by scalar irradiance microprobes. Molecular methods were used to evaluate whether physiologically distinct populations could be correlated with genetically distinct populations over the vertical interval. We were unable to identify patterns in genetic variation in Synechococcus 16S rRNA sequences that correlate with different vertically distributed populations. However, patterns of variation at the internal transcribed spacer locus separating 16S and 23S rRNA genes suggested the existence of closely related but genetically distinct populations corresponding to different functional populations occurring at different depths. PMID:12732563

  14. Influence of the Internalization Pathway on the Efficacy of siRNA Delivery by Cationic Fluorescent Nanodiamonds in the Ewing Sarcoma Cell Model

    PubMed Central

    Alhaddad, Anna; Durieu, Catherine; Dantelle, Géraldine; Le Cam, Eric; Malvy, Claude; Treussart, François; Bertrand, Jean-Rémi

    2012-01-01

    Small interfering RNAs (siRNAs) are powerful tools commonly used for the specific inhibition of gene expression. However, vectorization is required to facilitate cell penetration and to prevent siRNA degradation by nucleases. We have shown that diamond nanocrystals coated with cationic polymer can be used to carry siRNAs into Ewing sarcoma cells, in which they remain traceable over long periods, due to their intrinsic stable fluorescence. We tested two cationic polymers, polyallylamine and polyethylenimine. The release of siRNA, accompanied by Ewing sarcoma EWS-Fli1 oncogene silencing, was observed only with polyethylenimine. We investigated cell penetration and found that the underlying mechanisms accounted for these differences in behavior. Using drugs selectively inhibiting particular pathways and a combination of fluorescence and electronic microscopy, we showed that siRNA gene silencing occurred only if the siRNA:cationic nanodiamond complex followed the macropinocytosis route. These results have potential implications for the design of efficient drug-delivery vectors. PMID:23284935

  15. Initial effects of light armored vehicle use on grassland vegetation at Fort Lewis, Washington.

    PubMed

    Foster, Jeffrey R; Ayers, Paul D; Lombardi-Przybylowicz, Angela M; Simmons, Katie

    2006-12-01

    Sustainable use of military training lands requires understanding and prediction of the effects of military vehicles on vegetation. We examined the initial impacts of an 8-wheeled, light armored vehicle (LAV) on grassland vegetation at Fort Lewis, Washington. The LAV drove replicate spiral paths at two starting velocities, 10.3 and 5.1 m s(-1). The disturbed width (width of ground impacted by the tires) increased as turning radius decreased, but was unaffected by vehicle velocity. An inverse-exponential model predicted disturbed width (r(2)=0.68) at all turning radii for both velocities combined. In low-velocity spirals, and for straight tracking (turning radius>40 m) and moderate turns (radius 20-40 m) in high-velocity spirals, all vegetation damage was imprint (plants flattened by wheels). During sharp (radius <20 m), high-velocity turns, most or all of the disturbed width was scraped free of surface vegetation and soil, which was piled to the outside of each tire track. Total plant cover (all species) was not affected by track curvature in low-velocity spirals, but decreased in the order straight tracking>moderate turns>sharp turns in high-velocity spirals. In low-velocity spirals, post-tracking cover of several plant growth forms (non-native species, perennial species, sod-forming grasses) was similar to pre-tracking cover, but in high-velocity spirals, post-tracking cover of these growth forms decreased in the order straight > or =moderate=sharp. Cover of native species and forbs decreased more in high- than in low-velocity spirals, but was unaffected by curvature. Pre- and post-tracking cover of annual species, bunchgrasses, and shrubs was < or =3%. The most severe vegetation damage caused by operation of wheeled LAVs on grasslands is associated with sharp, high-velocity turns.

  16. Optimizing a basal bark spray of dinotefuran to manage armored scales (Hemiptera: Diaspididae) in Christmas tree plantations.

    PubMed

    Cowles, Richard S

    2010-10-01

    The armored scales Fiorinia externa Ferris and Aspidiotus cryptomeriae Kuwana (Hemiptera: Diaspididae) are increasingly damaging to Christmas tree plantings in southern New England. The systemic insecticide dinotefuran was investigated for selectively suppressing armored scale populations relative to their natural enemies in cooperating growers' fields in 2008 and 2009. Banded soil application of dinotefuran resulted in poor control. However, a dinotefuran spray applied to the basal 25 cm of trunk resulted in its absorption through the bark, translocation to the foliage, and good efficacy. The basal bark spray did not significantly impact the activity of predators Chilocorus stigma (Say) or Cybocephalus nipponicus Enrody-Younga and in 2009 showed a dosage-dependent improvement in the percentage of scales parasitized by Encarsia citrina Craw. A field dosage-response factorial experiment revealed that a 0.25% (vol:vol) addition of a surfactant with dinotefuran did not enhance insecticidal effect. Probit-transformed scale population reduction relative to the untreated check was subjected to linear regression analysis; reduction of scale populations was proportional to the log of insecticide dosage, whereas basal bark spray efficacy declined in proportion to the cube of tree height. The regression equation can be used to optimize dosage relative to tree height. Excellent efficacy resulted from basal bark spray application dates of 28 April (prebud break) to mid-June, but earlier spray timing within that treatment window had fewer crawlers discoloring new growth with their short-lived feeding. A basal bark spray of dinotefuran is well suited for integration with natural enemies to manage armored scales in Christmas tree plantations.

  17. Gene expression as a circular process: cross-talk between transcription and mRNA degradation in eukaryotes; International University of Andalusia (UNIA) Baeza, Spain.

    PubMed

    Collart, Martine A; Reese, Joseph C

    2014-01-01

    Studies on the regulation of gene expression in eukaryotes in the past 20 years have consistently revealed increasing levels of complexity. Thirty years ago it seemed that we had understood the basic principles of gene regulation in eukaryotes. It was thought that regulation of transcription was the first and most important stage at which gene expression was regulated, and transcriptional regulation was considered to be very simple, with DNA-binding activators and repressors talking to the basic transcription machinery. This simple model was overthrown when it became clear that other stages of gene expression are also highly regulated. More recently, other dogmas have started to collapse. In particular, the idea that a linkage between the different steps in gene expression is restricted to processes ongoing in the same compartment has fallen out of favor. It is now evident that functional and physical linkage occurs in eukaryotes. We know that factors contributing to transcription in the nucleus can be found in the cytoplasm, and that RNA binding proteins that contribute to RNA decay in the cytoplasm are present in the nucleus. However, shuttling of such factors between nucleus and cytoplasm has traditionally been thought to serve a simple regulatory purpose, for instance, to avoid untimely activation of a transcription factor in the nucleus. Alternatively, it was thought to be necessary to recruit RNA binding proteins to the relevant RNAs. The notion that is now emerging is that factors thought to have evolved to specialize in regulating a single step of gene regulation in one cellular compartment may be contributing to the regulation of mRNAs at multiple steps along the lifecycle of an mRNA.

  18. An international study comparing conventional versus mRNA level testing (TargetPrint) for ER, PR, and HER2 status of breast cancer.

    PubMed

    Wesseling, Jelle; Tinterri, Corrado; Sapino, Anna; Zanconati, Fabrizio; Lutke-Holzik, Martijn; Nguyen, Bichlien; Deck, Kenneth B; Querzoli, Patrizia; Perin, Tiziana; Giardina, Carmela; Seitz, Gerhard; Guinebretière, Jean-Marc; Barone, Julie; Dekker, Laura; de Snoo, Femke; Stork-Sloots, Lisette; Roepman, Paul; Watanabe, Toru; Cusumano, Pino

    2016-09-01

    To compare results from messenger RNA (mRNA)-based TargetPrint testing with those from immunohistochemistry (IHC) and in situ hybridization (ISH) conducted according to local standard procedures at hospitals worldwide. Tumor samples were prospectively obtained from 806 patients at 22 hospitals. The mRNA level of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) was assessed by TargetPrint quantitative gene expression readouts. IHC/ISH assessments were performed according to local standards at the participating hospitals. TargetPrint readout showed a high concordance with IHC/ISH of 95 % (kappa 0.81) for ER, 81 % (kappa 0.56) for PR, and 94 % (kappa 0.76) for HER2. The positive/negative agreement between TargetPrint and IHC for ER, PR, and HER2 was 96 %/87 %, 84 %/74 %, and 74 %/98 %, respectively. The concordance rate in IHC/ISH results between hospitals varied: 88-100 % for ER (kappa 0.50-1.00); 50-100 % for PR (kappa 0.20-1.00); and 90-100 % for HER2 (kappa 0.59-1.00). mRNA readout of ER, PR, and HER2 status by TargetPrint was largely comparable to local IHC/ISH analysis. However, there was substantial discordance in IHC/ISH results between different hospitals. When results are discordant, the use of TargetPrint would improve the reliability of hormone receptor and HER2 results by prompting retesting in a reference laboratory. PMID:27377889

  19. RNA epigenetics

    PubMed Central

    Liu, Nian; Pan, Tao

    2014-01-01

    Summary Mammalian messenger and long non-coding RNA contain tens of thousands of post-transcriptional chemical modifications. Among these, the N6-methyl-adenosine (m6A) modification is the most abundant and can be removed by specific mammalian enzymes. M6A modification is recognized by families of RNA binding proteins that affect many aspects of mRNA function. mRNA/lncRNA modification represents another layer of epigenetic regulation of gene expression, analogous to DNA methylation and histone modification. PMID:24768686

  20. River bed armoring in a local scour under no-supply conditions; experimental investigation and numerical model validation

    NASA Astrophysics Data System (ADS)

    Török, Gergerly; Baranya, Sandor; Rüther, Nils

    2016-04-01

    The aim of this study is to present a novel method for numerical modeling of morphological changes. The essence of the method doesn't mean the development of a new sediment transport formula, but the combined application of the existing, conditionally validated sediment transport models. Many bedload transport formulas can be found in the literature, which were developed based on different field and laboratory measurements. Thus, the most reliability of the models usually can be expected only for the given morphological and hydrological conditions connected to the base measurements. However, commonly in the analysed cases the morphological and hydrological features are more variable both in time and in space. Therefore, the hypothesis of this study is that, complex hydromorphological processes can't be modeled by one sediment transport formula. The authors present a solution based on laboratory experiments. Spatio-temporal developments of bed armoring, local scouring and local sediment deposition under no supply condition was monitored and analysed. The sediment transport model of Wilcock and Crowe (2003) was expected to calculate properly the local scouring and bed armoring processes, while the motion and aggradation of the finer materials were supposed to estimate reliably by the van Rijn formula (1984). The main challenge of the combining method is to find an appropriate criterion to decide which transport formula is activated in the given space and in the given time step. The result of the investigation showed that the most reliable criteria is based on the d50 value. As soon as the d50 grain size goes below a certain value, van Rijn is activated, otherwise the Wilcock and Crowe formula calculates the sorting and armoring processes. The results show that the combining method clearly improve the reliability of the morphological calculation. The benefit of the Wilcock and Crowe model is that it estimates quite well the sediment transport in mixed or armored

  1. Strategic Research Institute--first international siRNA conference. Prospect for new therapeutics and commercial opportunities for pharma and biotech. 24-25 March 2003, LaJolla, CA, USA.

    PubMed

    Xu, Jing

    2003-05-01

    Small interfering RNAs (siRNAs), with their power to selectively silence genes, have gained much attention from biotech and pharmaceutical companies and investors. Key players in the field, from innovative biotech start-ups to big pharmaceutical companies, gathered at Strategic Research Institute's First International siRNA conference in the scenic Hilton La Jolla Torrey Pines. Topics addressed ranged from the latest technology advances and applications of RNA interference (RNAi) in drug discovery, to critical business issues such as intellectual property portfolio strategy and market prospects. While RNAi is indisputably accepted as a powerful tool in target validation and functional genomics, the concept of an siRNA drug is still viewed by big pharma companies as next-generation therapeutics. Yet challenges seem tractable. Several companies, such as Ribozyme Pharmaceuticals Inc, Alnylam Pharmaceuticals and Intradigm Corp, are working hard to prove that the bigger companies are being too conservative. The conference provided a clear vision of RNAi in drug discovery today, its potential and remaining challenges.

  2. Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

    SciTech Connect

    Walters , William; Hyde, Embriette R.; Berg-Lyons, Donna; Ackermann, Gail; Humphrey, Greg; Parada , Alma; Gilbert, Jack A.; Jansson, Janet K.; Caporaso, Greg; Fuhrman, Jed A.; Apprill, Amy; Knight, Rob

    2015-12-22

    Designing primers for PCR-based taxonomic surveys that amplify a broad range of phylotypes in varied community samples is a difficult challenge, and the comparability of datasets amplified with varied primers requires attention. Here we examine the performance of modified 16S rRNA gene and ITS primers for archaea/bacteria and fungi, respectively, with non-aquatic samples. We moved primer barcodes to the 5’-end, allowing for a range of different 3’ primer pairings, such as the 515f/926r primer pair, which amplifies variable regions 4-5 of the 16S rRNA gene. We additionally demonstrate that modifications to the 515f/806r (variable region 4) 16S primer pair, which improves detection of Thaumarchaeota and SAR11 in marine samples, do not degrade performance on taxa already amplified effectively by the original primer set. Alterations to the fungal ITS primers did result in differential but overall improved performance compared to the original primers. In both cases, the improved primers should be widely adopted for amplicon studies.

  3. Clothing adjustments for concealed soft body armor during moderate physical exertion.

    PubMed

    Ryan, Greg A; Bishop, Stacy H; Herron, Robert L; Katica, Charles P; Elbon, Bre'anna L; Bosak, Andrew M; Bishop, Phillip

    2015-01-01

    Previous research has studied the impact of Level II concealed soft body armor (SBA) on the augmentation of heat storage in a hot environment simulating a typical summer day in the southeastern United States (wet bulb globe temperature [WBGT] = 30°C) and noted a significant difference between macro- and micro-WBGTs. The purpose of this study was to characterize the microclimate (micro-WBGT) under a concealed Level II SBA during 60 min of moderately intense work at two separate macro-WBGTs (26°C and 30°C), and to establish WBGT corrections to allow prediction of heat strain in an individual wearing a concealed Level II SBA. A single trial was performed with nine volunteers (27 ± 4 years) outfitted with a simulated standard law enforcement uniform and a traditional concealed Level II SBA, in a moderately warm environment (WBGT = 26°C). Each participant performed cycles of 12 min of walking (1.25 L · min(-1)) and 3 min of arm curls (14.3 kg, 0.6 L · min(-1)) with a 5 min rest after every other cycle, for a total of 60 minutes. This trial was compared to an identical previously completed 60-min work bout at 30°C. A two-way repeated measures ANOVA with Post hoc Bonferroni and paired samples t-test analysis was conducted. A greater difference between macro- micro-WBGTs existed at 26°C compared to the 30°C macro-WBGT. Under these conditions, a moderate work in Level II SBA requires a WBGT correction of 8.9°C and 6.2°C at macro-WBGTs of 26°C and 30°C, respectively. A modified simple linear regression prediction model was established for mean Micro-WBGT for each macro-WBGTs after the plateau point at the 30 min mark. The derivation regressions at 26°C (R(2) = 0.99), and 30°C (R(2) = 0.99) indicate that micro-WBGT could be predicted for each 15 minutes time at both macro-WBGTs tested for individuals doing moderate intensity (300 Kcals · hr(-1)) work wearing concealed Level II SBA. PMID:25437276

  4. Analysis of heat conduction in a drum brake system of the wheeled armored personnel carriers

    NASA Astrophysics Data System (ADS)

    Puncioiu, A. M.; Truta, M.; Vedinas, I.; Marinescu, M.; Vinturis, V.

    2015-11-01

    This paper is an integrated study performed over the Braking System of the Wheeled Armored Personnel Carriers. It mainly aims to analyze the heat transfer process which is present in almost any industrial and natural process. The vehicle drum brake systems can generate extremely high temperatures under high but short duration braking loads or under relatively light but continuous braking. For the proper conduct of the special vehicles mission in rough terrain, we are talking about, on one hand, the importance of the possibility of immobilization and retaining position and, on the other hand, during the braking process, the importance movement stability and reversibility or reversibility, to an encounter with an obstacle. Heat transfer processes influence the performance of the braking system. In the braking phase, kinetic energy transforms into thermal energy resulting in intense heating and high temperature states of analyzed vehicle wheels. In the present work a finite element model for the temperature distribution in a brake drum is developed, by employing commercial finite element software, ANSYS. These structural and thermal FEA models will simulate entire braking event. The heat generated during braking causes distortion which modifies thermoelastic contact pressure distribution drum-shoe interface. In order to capture the effect of heat, a transient thermal analysis is performed in order to predict the temperature distribution transitional brake components. Drum brakes are checked both mechanical and thermal. These tests aim to establish their sustainability in terms of wear and the variation coefficient of friction between the friction surfaces with increasing temperature. Modeling using simulation programs led eventually to the establishment of actual thermal load of the mechanism of brake components. It was drawn the efficiency characteristic by plotting the coefficient of effectiveness relative to the coefficient of friction shoe-drum. Thus induced

  5. Sediment mobility and bed armoring in the St Clair River: insights from hydrodynamic modeling

    USGS Publications Warehouse

    Liu, Xiaofeng; Parker, Gary; Czuba, Jonathan A.; Oberg, Kevin; Mier, Jose M.; Best, James L.; Parsons, Daniel R.; Ashmore, Peter; Krishnappan, Bommanna G.; Garcia, Marcelo H.

    2012-01-01

    The lake levels in Lake Michigan-Huron have recently fallen to near historical lows, as has the elevation difference between Lake Michigan-Huron compared to Lake Erie. This decline in lake levels has the potential to cause detrimental impacts on the lake ecosystems, together with social and economic impacts on communities in the entire Great Lakes region. Results from past work suggest that morphological changes in the St Clair River, which is the only natural outlet for Lake Michigan-Huron, could be an appreciable factor in the recent trends of lake level decline. A key research question is whether bed erosion within the river has caused an increase in water conveyance, therefore, contributed to the falling lake level. In this paper, a numerical modeling approach with field data is used to investigate the possibility of sediment movement in the St Clair River and assess the likelihood of morphological change under the current flow regime. A two-dimensional numerical model was used to study flow structure, bed shear stress, and sediment mobility/armoring over a range of flow discharges. Boundary conditions for the numerical model were provided by detailed field measurements that included high-resolution bathymetry and three-dimensional flow velocities. The results indicate that, without considering other effects, under the current range of flow conditions, the shear stresses produced by the river flow are too low to transport most of the coarse bed sediment within the reach and are too low to cause substantial bed erosion or bed scour. However, the detailed maps of the bed show mobile bedforms in the upper St Clair River that are indicative of sediment transport. Relatively high shear stresses near a constriction at the upstream end of the river and at channel bends could cause local scour and deposition. Ship-induced propeller wake erosion also is a likely cause of sediment movement in the entire reach. Other factors that may promote sediment movement, such as ice

  6. Development of a duplex one-step RT-qPCR assay for the simultaneous detection of Apple scar skin viroid and plant RNA internal control.

    PubMed

    Khan, Subuhi; Mackay, John; Liefting, Lia; Ward, Lisa

    2015-09-01

    Apple scar skin viroid (ASSVd) is an important quarantine pathogen for international movement of pome germplasm as it can cause significant damage to pip fruit. A one-step real-time RT-PCR assay was developed for the rapid and sensitive detection of ASSVd. The assay was able to detect a wide range of ASSVd isolates and was highly specific compared to a published conventional RT-PCR. The detection limit of the new assay was estimated to be about 100 copies of the ASSVd target. The assay can be run as a duplex with the nad5 internal control primers and probe to simultaneously check the PCR competency of the samples therefore reducing the risk of false negatives. It is expected that this real-time RT-PCR assay will facilitate efficient testing for ASSVd by regulatory services, and will also have a wider use for the general detection of ASSVd in a range of pip fruit.

  7. Development of a duplex one-step RT-qPCR assay for the simultaneous detection of Apple scar skin viroid and plant RNA internal control.

    PubMed

    Khan, Subuhi; Mackay, John; Liefting, Lia; Ward, Lisa

    2015-09-01

    Apple scar skin viroid (ASSVd) is an important quarantine pathogen for international movement of pome germplasm as it can cause significant damage to pip fruit. A one-step real-time RT-PCR assay was developed for the rapid and sensitive detection of ASSVd. The assay was able to detect a wide range of ASSVd isolates and was highly specific compared to a published conventional RT-PCR. The detection limit of the new assay was estimated to be about 100 copies of the ASSVd target. The assay can be run as a duplex with the nad5 internal control primers and probe to simultaneously check the PCR competency of the samples therefore reducing the risk of false negatives. It is expected that this real-time RT-PCR assay will facilitate efficient testing for ASSVd by regulatory services, and will also have a wider use for the general detection of ASSVd in a range of pip fruit. PMID:25962536

  8. RNA-Based Vaccines in Cancer Immunotherapy.

    PubMed

    McNamara, Megan A; Nair, Smita K; Holl, Eda K

    2015-01-01

    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.

  9. RNA-Based Vaccines in Cancer Immunotherapy

    PubMed Central

    McNamara, Megan A.; Nair, Smita K.; Holl, Eda K.

    2015-01-01

    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. PMID:26665011

  10. A Distinct Group of Hepacivirus/Pestivirus-Like Internal Ribosomal Entry Sites in Members of Diverse Picornavirus Genera: Evidence for Modular Exchange of Functional Noncoding RNA Elements by Recombination▿ †

    PubMed Central

    Hellen, Christopher U. T.; de Breyne, Sylvain

    2007-01-01

    The 5′ untranslated regions (UTRs) of the RNA genomes of Flaviviridae of the Hepacivirus and Pestivirus genera contain internal ribosomal entry sites (IRESs) that are unrelated to the two principal classes of IRESs of Picornaviridae. The mechanism of translation initiation on hepacivirus/pestivirus (HP) IRESs, which involves factor-independent binding to ribosomal 40S subunits, also differs fundamentally from initiation on these picornavirus IRESs. Ribosomal binding to HP IRESs requires conserved sequences that form a pseudoknot and the adjacent IIId and IIIe domains; analogous elements do not occur in the two principal groups of picornavirus IRESs. Here, comparative sequence analysis was used to identify a subset of picornaviruses from multiple genera that contain 5′ UTR sequences with significant similarities to HP IRESs. They are avian encephalomyelitis virus, duck hepatitis virus 1, duck picornavirus, porcine teschovirus, porcine enterovirus 8, Seneca Valley virus, and simian picornavirus. Their 5′ UTRs are predicted to form several structures, in some of which the peripheral elements differ from the corresponding HP IRES elements but in which the core pseudoknot, domain IIId, and domain IIIe elements are all closely related. These findings suggest that HP-like IRESs have been exchanged between unrelated virus families by recombination and support the hypothesis that RNA viruses consist of modular coding and noncoding elements that can exchange and evolve independently. PMID:17392358

  11. Armored scale insect endosymbiont diversity at the species level: genealogical patterns of Uzinura diasipipdicola in the Chionaspis pinifoliae-Chionaspis heterophyllae species complex (Hemiptera: Coccoidea: Diaspididae).

    PubMed

    Andersen, J C; Gwiazdowski, R A; Gdanetz, K; Gruwell, M E

    2015-02-01

    Armored scale insects and their primary bacterial endosymbionts show nearly identical patterns of co-diversification when viewed at the family level, though the persistence of these patterns at the species level has not been explored in this group. Therefore we investigated genealogical patterns of co-diversification near the species level between the primary endosymbiont Uzinura diaspidicola and its hosts in the Chionaspis pinifoliae-Chionaspis heterophyllae species complex. To do this we generated DNA sequence data from three endosymbiont loci (rspB, GroEL, and 16S) and analyzed each locus independently using statistical parsimony network analyses and as a concatenated dataset using Bayesian phylogenetic reconstructions. We found that for two endosymbiont loci, 16S and GroEL, sequences from U. diaspidicola were broadly associated with host species designations, while for rspB this pattern was less clear as C. heterophyllae (species S1) shared haplotypes with several other Chionaspis species. We then compared the topological congruence of the phylogenetic reconstructions generated from a concatenated dataset of endosymbiont loci (including all three loci, above) to that from a concatenated dataset of armored scale hosts, using published data from two nuclear loci (28S and EF1α) and one mitochondrial locus (COI-COII) from the armored scale hosts. We calculated whether the two topologies were congruent using the Shimodaira-Hasegawa test. We found no significant differences (P = 0.4892) between the topologies suggesting that, at least at this level of resolution, co-diversification of U. diaspidicola with its armored scale hosts also occurs near the species level. This is the first such study of co-speciation at the species level between U. diaspidicola and a group of armored scale insects.

  12. Internalization of oligodeoxynucleotide antisense to type-1 plasminogen activator inhibitor mRNA in endothelial cells: a three-dimensional reconstruction by confocal microscopy.

    PubMed

    Wyroba, E; Pawlowska, Z; Kobylanska, A; Pluskota, E; Maszewska, M; Stec, W J; Cierniewski, C S

    1996-01-01

    A three-dimensional reconstruction analysis of localization of phosphodiester and phosphorothioate oligonucleotide antisense to type-1 plasminogen activator inhibitor (PAI-1) mRNA within endothelial cells is described. When EA.hy 926 cells were incubated with fluorescently labelled phosphodiester (PO-16) or phosphorothioate (PS-16) oligonucleotides at low, not cytotoxical concentrations, the relative brightness composition of the images of the particular samples was much higher for PS-16 than PO-16 and dependent upon the extracellular concentration and the incubation time. The 3-D reconstructions based on the series of optical sections of the samples, spaced every 1.5 microns, showed the punctuate accumulation of the oligonucleotides and a striking difference in a spatial distribution between PO-16 and PS-16 within the cytoplasm. Even after 24 h incubation of endothelial cells with 2.5 microM of PO-16 and PS-16 oligonucleotides, there was a predominant oligonucleotide localization within the cytoplasm and only traces of oligonucleotides could be seen in the cell nucleus and/or perinuclear organelles.

  13. RNA Research

    NASA Technical Reports Server (NTRS)

    1998-01-01

    It is generally believed that an RNA World existed at an early stage in the history of life. During this early period, RNA molecules are seen to be potentially involved in both catalysis and the storage of genetic information. It is widely believed that this RNA World was extensive and therefore a sophisticated nucleic acid replication machinery would presumably predate the translation machinery which would not be needed until later stages in the development of life. This view of an extended RNA World is not necessarily correct. From the point of view of exobiology, the difference in these two views mainly affects the significance of studies of the extent of catalysis possible by RNA- In either case, the origin of the translation machinery and the principles of RNA evolution remain central problems in exobiology. Translation presents several interrelated themes of inquiry for exobiology. First, it is essential, for understanding the very origin of life, how peptides and eventually proteins might have come to be made on the early Earth in a template directed manner. Second, it is necessary to understand how a machinery of similar complexity to that found in the ribosomes of modem organisms came to exist by the time of the last common ancestor (as detected by 16S RRNA sequence studies). Third, the RNAs that comprise the ribosome are themselves likely of very early origin and studies of their history may be very informative about the nature of the RNA World. Moreover, studies of these RNAs will contribute to a better understanding of the potential roles of RNA in early evolution.

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

    USGS Publications Warehouse

    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.

  15. A Residual Mass Ballistic Testing Method to Compare Armor Materials or Components (Residual Mass Ballistic Testing Method)

    SciTech Connect

    Benjamin Langhorst; Thomas M Lillo; Henry S Chu

    2014-05-01

    A statistics based ballistic test method is presented for use when comparing multiple groups of test articles of unknown relative ballistic perforation resistance. The method is intended to be more efficient than many traditional methods for research and development testing. To establish the validity of the method, it is employed in this study to compare test groups of known relative ballistic performance. Multiple groups of test articles were perforated using consistent projectiles and impact conditions. Test groups were made of rolled homogeneous armor (RHA) plates and differed in thickness. After perforation, each residual projectile was captured behind the target and its mass was measured. The residual masses measured for each test group were analyzed to provide ballistic performance rankings with associated confidence levels. When compared to traditional V50 methods, the residual mass (RM) method was found to require fewer test events and be more tolerant of variations in impact conditions.

  16. Ballistic-Failure Mechanisms in Gas Metal Arc Welds of Mil A46100 Armor-Grade Steel: A Computational Investigation

    NASA Astrophysics Data System (ADS)

    Grujicic, M.; Snipes, J. S.; Galgalikar, R.; Ramaswami, S.; Yavari, R.; Yen, C.-F.; Cheeseman, B. A.

    2014-09-01

    In our recent work, a multi-physics computational model for the conventional gas metal arc welding (GMAW) joining process was introduced. The model is of a modular type and comprises five modules, each designed to handle a specific aspect of the GMAW process, i.e.: (i) electro-dynamics of the welding-gun; (ii) radiation-/convection-controlled heat transfer from the electric-arc to the workpiece and mass transfer from the filler-metal consumable electrode to the weld; (iii) prediction of the temporal evolution and the spatial distribution of thermal and mechanical fields within the weld region during the GMAW joining process; (iv) the resulting temporal evolution and spatial distribution of the material microstructure throughout the weld region; and (v) spatial distribution of the as-welded material mechanical properties. In the present work, the GMAW process model has been upgraded with respect to its predictive capabilities regarding the spatial distribution of the mechanical properties controlling the ballistic-limit (i.e., penetration-resistance) of the weld. The model is upgraded through the introduction of the sixth module in the present work in recognition of the fact that in thick steel GMAW weldments, the overall ballistic performance of the armor may become controlled by the (often inferior) ballistic limits of its weld (fusion and heat-affected) zones. To demonstrate the utility of the upgraded GMAW process model, it is next applied to the case of butt-welding of a prototypical high-hardness armor-grade martensitic steel, MIL A46100. The model predictions concerning the spatial distribution of the material microstructure and ballistic-limit-controlling mechanical properties within the MIL A46100 butt-weld are found to be consistent with prior observations and general expectations.

  17. Predicting RNA-RNA Interactions Using RNAstructure.

    PubMed

    DiChiacchio, Laura; Mathews, David H

    2016-01-01

    RNA-RNA binding is a required step for many regulatory and catalytic processes in the cell. Identifying RNA-RNA hybridization sites is challenging because of the competition between intramolecular and intermolecular structure formation. A complete picture of RNA-RNA binding includes an understanding of single-stranded folding and binding site accessibility, and is strongly concentration-dependent. This chapter provides guidance for using RNAstructure to predict RNA-RNA binding sites and RNA-RNA structures, utilizing free energy minimization and partition function calculations. RNAstructure is freely available at http://rna.urmc.rochester.edu/RNAstructure.html . PMID:27665592

  18. Internal Transcribed Spacer 2 (nu ITS2 rRNA) Sequence-Structure Phylogenetics: Towards an Automated Reconstruction of the Green Algal Tree of Life

    PubMed Central

    Buchheim, Mark A.; Keller, Alexander; Koetschan, Christian; Förster, Frank; Merget, Benjamin; Wolf, Matthias

    2011-01-01

    Background Chloroplast-encoded genes (matK and rbcL) have been formally proposed for use in DNA barcoding efforts targeting embryophytes. Extending such a protocol to chlorophytan green algae, though, is fraught with problems including non homology (matK) and heterogeneity that prevents the creation of a universal PCR toolkit (rbcL). Some have advocated the use of the nuclear-encoded, internal transcribed spacer two (ITS2) as an alternative to the traditional chloroplast markers. However, the ITS2 is broadly perceived to be insufficiently conserved or to be confounded by introgression or biparental inheritance patterns, precluding its broad use in phylogenetic reconstruction or as a DNA barcode. A growing body of evidence has shown that simultaneous analysis of nucleotide data with secondary structure information can overcome at least some of the limitations of ITS2. The goal of this investigation was to assess the feasibility of an automated, sequence-structure approach for analysis of IT2 data from a large sampling of phylum Chlorophyta. Methodology/Principal Findings Sequences and secondary structures from 591 chlorophycean, 741 trebouxiophycean and 938 ulvophycean algae, all obtained from the ITS2 Database, were aligned using a sequence structure-specific scoring matrix. Phylogenetic relationships were reconstructed by Profile Neighbor-Joining coupled with a sequence structure-specific, general time reversible substitution model. Results from analyses of the ITS2 data were robust at multiple nodes and showed considerable congruence with results from published phylogenetic analyses. Conclusions/Significance Our observations on the power of automated, sequence-structure analyses of ITS2 to reconstruct phylum-level phylogenies of the green algae validate this approach to assessing diversity for large sets of chlorophytan taxa. Moreover, our results indicate that objections to the use of ITS2 for DNA barcoding should be weighed against the utility of an automated

  19. SCOR: a Structural Classification of RNA database.

    PubMed

    Klosterman, Peter S; Tamura, Makio; Holbrook, Stephen R; Brenner, Steven E

    2002-01-01

    The Structural Classification of RNA (SCOR) database provides a survey of the three-dimensional motifs contained in 259 NMR and X-ray RNA structures. In one classification, the structures are grouped according to function. The RNA motifs, including internal and external loops, are also organized in a hierarchical classification. The 259 database entries contain 223 internal and 203 external loops; 52 entries consist of fully complementary duplexes. A classification of the well-characterized tertiary interactions found in the larger RNA structures is also included along with examples. The SCOR database is accessible at http://scor.lbl.gov.

  20. Protective ability of the standard U.S. Military Personal Armor System, Ground Troops (PASGT) fragmentation vest against common small arms projectiles.

    PubMed

    Roberts, G K; Bullian, M E

    1993-08-01

    This study analyzes the ballistic protection provided by the standard U.S. Military Personal Armor System, Ground Troops fragmentation vest against threats from handgun and shotgun projectiles. Damage assessment was conducted using 10% ordnance gelatin, a tissue simulant which has been proven to have a close correlation with living tissue. The standard fragmentation vest was shown to provide protection from commonly encountered handgun bullets and shotgun pellets, but not from shotgun slugs or center-fire rifle bullets. PMID:8414082

  1. Armored CAR T-cells: utilizing cytokines and pro-inflammatory ligands to enhance CAR T-cell anti-tumour efficacy.

    PubMed

    Yeku, Oladapo O; Brentjens, Renier J

    2016-04-15

    Chimaeric antigen receptor (CAR) T-cells are T-cells that have been genetically modified to express an artificial construct consisting of a synthetic T-cell receptor (TCR) targeted to a predetermined antigen expressed on a tumour. Coupling the T-cell receptor to a CD3ζ signalling domain paved the way for first generation CAR T-cells that were efficacious against cluster of differentiation (CD)19-expressing B-cell malignancies. Optimization with additional signalling domains such as CD28 or 4-1BB in addition to CD3ζ provided T-cell activation signal 2 and further improved the efficacy and persistence of these second generation CAR T-cells. Third generation CAR T-cells which utilize two tandem costimulatory domains have also been reported. In this review, we discuss a different approach to optimization of CAR T-cells. Through additional genetic modifications, these resultant armored CAR T-cells are typically modified second generation CAR T-cells that have been further optimized to inducibly or constitutively secrete active cytokines or express ligands that further armor CAR T-cells to improve efficacy and persistence. The choice of the 'armor' agent is based on knowledge of the tumour microenvironment and the roles of other elements of the innate and adaptive immune system. Although there are several variants of armored CAR T-cells under investigation, here we focus on three unique approaches using interleukin-12 (IL-12), CD40L and 4-1BBL. These agents have been shown to further enhance CAR T-cell efficacy and persistence in the face of a hostile tumour microenvironment via different mechanisms.

  2. Monitoring lingering oil from the Exxon Valdez spill on Gulf of Alaska armored beaches and mussel beds sixteen years post-spill

    USGS Publications Warehouse

    Irvine, G.V.; Mann, D.H.; Short, J.W.

    2008-01-01

    Final Rept. ; Prepared in Cooperation With Alaska Univ., Fairbanks. Inst. of Arctic Biology. Sponsored By National Marine Fisheries Service, Juneau, Ak. AlaskaFisheries Science Center. ; Stranded Exxon Valdez Oil Has Persisted for 16 Years At Boulder-Armored Beach Sites Along National Park Coastlines Bordering the Gulf of Alaska. These Sites Are Up to 640 Km From the Spill Origin and Were Contaminated By Oil Mousse, a Viscous Water-in-Oil Emulsion. Although Surface Oil Has Continued to Decline, Subsurface Oiling Persists in Patches. Especially Striking Is the General Lack of Weathering of Stranded Oil on Armored Beaches Over the Last 16 Years. At Three of the Four Sites Where Oil Was Sampled in 2005, the Oil Was Compositionally Similar to 11-Day Old Exxon Valdez Oil, Even After 16 Years. The Formation of Mousse Allowed Less-Weathered Oil to Be Transported Long Distances. The Sequestration of the Oil Beneath a Boulder Armor, Coupled With the Stability of the Boulder Armoring (Investigated By Examining Movement of Marked Boulders), Had Contributed to the Lengthy Persistence of This Stranded Oil. Opportunistic Sampling of Several Previously Studied Oiled Mussel Beds Indicates Continued Contamination of At Least One of the Sites By Not Very Weathered Exxon Valdez Oil. Long-Term Persistence of Oil in These Habitats Should Cause Reconsideration of Response Activities After Spills, and May Influence the Environmental Sensitivity Indices Applied to These Habitats. 

  3. Analysis of recurring sinking events of armored tracked vehicles along dirt roads in the agricultural periphery of the Gaza Strip

    NASA Astrophysics Data System (ADS)

    Roskin, Joel

    2013-04-01

    The second (Al-Aqsa) intifada (Arab violent uprising) which erupted across Israel in 2000 eventually led the Israel Defense Forces to deploy armored tracked vehicles (ATVs) (tanks, armored personal carriers, and D-9 bulldozers) within Israel's agricultural periphery of the Gaza Strip, following daily attempts by Arab terrorists and guerillas to penetrate Israel. Combat movement of the ATVs was mainly concentrated to dirt roads, between agricultural fields, wherever possible. As a result of semi-arid Mediterranean (climate) winter rains, annually averaging 250 - 350 mm, it was reported that ATVs often sank in muddy terrain. This study investigated what caused ATVs to sink. The main data collected concerning the types of vehicles that sank related to: land-use characteristics, soil type, and daily rainfall. Interviews with commanders were also conducted for additional details. Between the fall and spring, surveys and weekly / bi-weekly field soil cone penetrometer tests were conducted at ten sites with different pedological and land-use characteristics. The loess soils, especially in agricultural fields, were generally found to be conducive to ATV traffic, even shortly after rainstorms of 10-30 mm. However, following several rainfall events exceeding 10 mm, ATVs and tanks regularly sank into local topographic depressions in the undulating landscape. These consisted of short segments of dirt roads where runoff and suspended sediment collected. After the early rains in late fall, tank ruts fossilize and become conduits of concentrated runoff and fine particles eroded by ATV activity during the summer months. Tank track ruts that formed in mud, compacted the soil, drastically altered drainage patterns by directing significant surface flow, and suspended sediment into these depressions, creating "tank-traps" whose trafficability ranged from "untrafficable" to "trafficable with constraints." This study shows that intense, routine, defensive military activity operated

  4. Biochemical responses in armored catfish (Pterygoplichthys anisitsi) after short-term exposure to diesel oil, pure biodiesel and biodiesel blends.

    PubMed

    Nogueira, Lílian; da Silva, Danilo Grünig Humberto; Oliveira, Thiago Yukio Kikuchi; da Rosa, Joel Maurício Correa; Felício, Andréia Arantes; de Almeida, Eduardo Alves

    2013-09-01

    Biodiesel fuel is gradually replacing petroleum-based diesel oil use. Despite the biodiesel being considered friendlier to the environment, little is known about its effects in aquatic organisms. In this work we evaluated whether biodiesel exposure can affect oxidative stress parameters and biotransformation enzymes in armored catfish (Pterygoplichthys anisitsi, Loricariidae), a South American endemic species. Thus, fish were exposed for 2 and 7d to 0.01mLL(-1) and 0.1mLL(-1) of pure diesel, pure biodiesel (B100) and blends of diesel with 5% (B5) and 20% (B20) biodiesel. Lipid peroxidation (malondialdehyde) levels and the activities of the enzymes glutathione S-transferase, superoxide dismutase, catalase and glutathione peroxidase were measured in liver and gills. Also, DNA damage (8-oxo-7, 8-dihydro-2'-deoxyguanosine) levels in gills and 7-ethoxyresorufin-O-deethylase activity in liver were assessed. Pure diesel, B5 and B20 blends changed most of the enzymes tested and in some cases, B5 and B20 induced a higher enzyme activity than pure diesel. Antioxidant system activation in P. anisitsi was effective to counteract reactive oxygen species effects, since DNA damage and lipid peroxidation levels were maintained at basal levels after all treatments. However, fish gills exposed to B20 and B100 presented increased lipid peroxidation. Despite biodiesel being more biodegradable fuel that emits less greenhouse gases, the increased lipid peroxidation showed that biofuel and its blends also represent hazards to aquatic biota.

  5. Titanosaur osteoderms from the Upper Cretaceous of Lo Hueco (Spain) and their implications on the armor of Laurasian titanosaurs.

    PubMed

    Vidal, Daniel; Ortega, Francisco; Sanz, José Luis

    2014-01-01

    Titanosaurs are the only sauropod dinosaurs known to bear a dermal armor. Their osteoderms are relatively rare finds, with few more than a hundred specimens recovered worldwide. Also, little is known about their intra-individual, intra-specific or inter-specific variability. The macrovertebrate site of Lo Hueco (Upper Cretaceous; Cuenca, Spain) has yielded several complete specimens of osteoderms, some associated with fairly articulated specimens. They are all variations of the morphotype known as bulb and root. The presence of only this morphotype in Europe, which is considered as the primitive condition among titanosaurs, seems to indicate that the known Upper Cretaceous Laurasian titanosaurs only bore these referred bulb and root osteoderms. An eliptic Fourier analysis on the outline of complete specimens from this morphotype reveals: i) that they truly are part of a morphological cline; and ii) the existence of a consistent correlation between the outline and the morphology of the bulb. Such variation along a cline is more consistent with intra-individual rather than inter-specific variation. The osteoderms associated with a single titanosaur individual from Lo Hueco reinforce this hypothesis. PMID:25118985

  6. Water-assisted self-healing and property recovery in a natural dermal armor of pangolin scales.

    PubMed

    Liu, Z Q; Jiao, D; Weng, Z Y; Zhang, Z F

    2016-03-01

    Self-healing capacity, of which the inspiration comes from biological systems, is significant for restoring the mechanical properties of materials by autonomically repairing damages. Clarifying the naturally occurring self-healing behaviors and mechanisms may provide valuable inspiration for designing synthetic self-healing materials. In this study, water-assisted self-healing behavior was revealed in a natural dermal armor of pangolin scales. The indentation damages which imitate the injury caused by predatory attack can be continuously mitigated through hydration. The healing kinetics was characterized according to the variations of indentation crater dimension and quantitatively described in terms of the viscoelastic behavior of biopolymer. The mechanical properties of original, damaged, and recovered scales in both dry and wet states were systematically evaluated by three-point bending and compared through statistical analysis. The hydration effects and mechanisms were explored by examining the dynamic mechanical properties and thermal behaviors. The promoted self-healing process can be attributed to the improved flexibility of macromolecules in the biopolymer. This study may stimulate useful self-healing strategies in bio-inspired design and aid in developing high-performance synthetic self-healing materials. PMID:26651064

  7. Dual targeting and enhanced cytotoxicity to HER2-overexpressing tumors by immunoapoptotin-armored mesenchymal stem cells.

    PubMed

    Cai, Yanhui; Xi, Yujing; Cao, Zhongyuan; Xiang, Geng; Ni, Qingrong; Zhang, Rui; Chang, Jing; Du, Xiao; Yang, Angang; Yan, Bo; Zhao, Jing

    2016-10-10

    Mesenchymal stem cells (MSCs) are promising vehicles for the delivery of anticancer agents in cancer therapy. However, the tumor targeting of loaded therapeutics is essential. Here, we explored a dual-targeting strategy to incorporate tumor-tropic MSC delivery with HER2-specific killing by the immunoapoptotin e23sFv-Fdt-tBid generated in our previous studies. The MSC engineering allowed simultaneous immunoapoptotin secretion and bioluminescence detection of the modified MSCs. Systemic administration of the immunoapoptotin-engineered MSCs was investigated in human HER2-reconstituted syngeneic mouse models of orthotopic and metastatic breast cancer, as well as in a xenograft nude mouse model of orthotopic gastric cancer. In vivo dual tumor targeting was confirmed by local accumulation of the bioluminescence-imaged MSCs and persistence of His-immunostained immunoapoptotins in tumor sites. The added tumor preference of MSC-secreted immunoapoptotins resulted in a significantly stronger antitumor effect compared with purified immunoapoptotins and Jurkat-delivered immunoapoptotins. This immunoapoptotin-armored MSC strategy provides a rationale for its use in extended malignancies by combining MSC mobility with redirected immunoapoptotins against a given tumor antigen. PMID:27473824

  8. Gas Metal Arc Welding Process Modeling and Prediction of Weld Microstructure in MIL A46100 Armor-Grade Martensitic Steel

    NASA Astrophysics Data System (ADS)

    Grujicic, M.; Arakere, A.; Ramaswami, S.; Snipes, J. S.; Yavari, R.; Yen, C.-F.; Cheeseman, B. A.; Montgomery, J. S.

    2013-06-01

    A conventional gas metal arc welding (GMAW) butt-joining process has been modeled using a two-way fully coupled, transient, thermal-mechanical finite-element procedure. To achieve two-way thermal-mechanical coupling, the work of plastic deformation resulting from potentially high thermal stresses is allowed to be dissipated in the form of heat, and the mechanical material model of the workpiece and the weld is made temperature dependent. Heat losses from the deposited filler-metal are accounted for by considering conduction to the adjoining workpieces as well as natural convection and radiation to the surroundings. The newly constructed GMAW process model is then applied, in conjunction with the basic material physical-metallurgy, to a prototypical high-hardness armor martensitic steel (MIL A46100). The main outcome of this procedure is the prediction of the spatial distribution of various crystalline phases within the weld and the heat-affected zone regions, as a function of the GMAW process parameters. The newly developed GMAW process model is validated by comparing its predictions with available open-literature experimental and computational data.

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

    SciTech Connect

    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.

  10. Water-assisted self-healing and property recovery in a natural dermal armor of pangolin scales.

    PubMed

    Liu, Z Q; Jiao, D; Weng, Z Y; Zhang, Z F

    2016-03-01

    Self-healing capacity, of which the inspiration comes from biological systems, is significant for restoring the mechanical properties of materials by autonomically repairing damages. Clarifying the naturally occurring self-healing behaviors and mechanisms may provide valuable inspiration for designing synthetic self-healing materials. In this study, water-assisted self-healing behavior was revealed in a natural dermal armor of pangolin scales. The indentation damages which imitate the injury caused by predatory attack can be continuously mitigated through hydration. The healing kinetics was characterized according to the variations of indentation crater dimension and quantitatively described in terms of the viscoelastic behavior of biopolymer. The mechanical properties of original, damaged, and recovered scales in both dry and wet states were systematically evaluated by three-point bending and compared through statistical analysis. The hydration effects and mechanisms were explored by examining the dynamic mechanical properties and thermal behaviors. The promoted self-healing process can be attributed to the improved flexibility of macromolecules in the biopolymer. This study may stimulate useful self-healing strategies in bio-inspired design and aid in developing high-performance synthetic self-healing materials.

  11. Titanosaur Osteoderms from the Upper Cretaceous of Lo Hueco (Spain) and Their Implications on the Armor of Laurasian Titanosaurs

    PubMed Central

    Vidal, Daniel; Ortega, Francisco; Sanz, José Luis

    2014-01-01

    Titanosaurs are the only sauropod dinosaurs known to bear a dermal armor. Their osteoderms are relatively rare finds, with few more than a hundred specimens recovered worldwide. Also, little is known about their intra-individual, intra-specific or inter-specific variability. The macrovertebrate site of Lo Hueco (Upper Cretaceous; Cuenca, Spain) has yielded several complete specimens of osteoderms, some associated with fairly articulated specimens. They are all variations of the morphotype known as bulb and root. The presence of only this morphotype in Europe, which is considered as the primitive condition among titanosaurs, seems to indicate that the known Upper Cretaceous Laurasian titanosaurs only bore these referred bulb and root osteoderms. An eliptic Fourier analysis on the outline of complete specimens from this morphotype reveals: i) that they truly are part of a morphological cline; and ii) the existence of a consistent correlation between the outline and the morphology of the bulb. Such variation along a cline is more consistent with intra-individual rather than inter-specific variation. The osteoderms associated with a single titanosaur individual from Lo Hueco reinforce this hypothesis. PMID:25118985

  12. Novel manufacturing processing route for forming high-density ceramic armor materials: Phase 2 -- SBIR. Final report, 1994

    SciTech Connect

    Raman, R.V.

    1999-04-01

    The feasibility of a combustion synthesis/Ceracon forging (CS/CF) fabrication process for low-cost high-quality ceramic armor is demonstrated. CS of titanium (Ti) and carbon (C) forming titanium carbide (TiC) was followed by a quasi-isostatic pressurization and densification to produce tiles with 95% + densities with sizes of up to 15 cm x 15 cm x 2.5 Cm. Several tiles were fabricated and delivered to the US Army Research Laboratory (ARL) for evaluation and testing. A cost model, which showed that approximately 60% in cost savings can be realized with the CS/CF method, was developed. Temperature measurements and one-dimensional (1-D) computations were used to develop thermal management practices to make crack-free tiles. X-ray diffraction (XRD) verified full conversion of reactants to products. A considerable variation in TiC grain size and microhardness was found between the surface ([minus]10 pm, high hardness) and the interior (up to 100 pm, low hardness) that depended on conditions during processing. Fractography showed transgranular fracture in the interior and intergranular fracture at the surface. Quasi-static compressive strength was found to be 1.79 GPa, while the flexural strength, determined from four-point bending tests, was 0.17 GPa.

  13. Voronoia4RNA--a database of atomic packing densities of RNA structures and their complexes.

    PubMed

    Ismer, Jochen; Rose, Alexander S; Tiemann, Johanna K S; Goede, Andrean; Rother, Kristian; Hildebrand, Peter W

    2013-01-01

    Voronoia4RNA (http://proteinformatics.charite.de/voronoia4rna/) is a structural database storing precalculated atomic volumes, atomic packing densities (PDs) and coordinates of internal cavities for currently 1869 RNAs and RNA-protein complexes. Atomic PDs are a measure for van der Waals interactions. Regions of low PD, containing water-sized internal cavities, refer to local structure flexibility or compressibility. RNA molecules build up the skeleton of large molecular machineries such as ribosomes or form smaller flexible structures such as riboswitches. The wealth of structural data on RNAs and their complexes allows setting up representative data sets and analysis of their structural features. We calculated atomic PDs from atomic volumes determined by the Voronoi cell method and internal cavities analytically by Delaunay triangulation. Reference internal PD values were derived from a non-redundant sub-data set of buried atoms. Comparison of internal PD values shows that RNA is more tightly packed than proteins. Finally, the relation between structure size, resolution and internal PD of the Voronoia4RNA entries is discussed. RNA, protein structures and their complexes can be visualized by the Jmol-based viewer Provi. Variations in PD are depicted by a color code. Internal cavities are represented by their molecular boundaries or schematically as balls.

  14. Single-Cell DNA barcoding using sequences from the small subunit rRNA and internal transcribed spacer region identifies new species of Trichonympha and Trichomitopsis from the hindgut of the termite Zootermopsis angusticollis.

    PubMed

    Tai, Vera; James, Erick R; Perlman, Steve J; Keeling, Patrick J

    2013-01-01

    To aid in their digestion of wood, lower termites are known to harbour a diverse community of prokaryotes as well as parabasalid and oxymonad protist symbionts. One of the best-studied lower termite gut communities is that of Zootermopsis angusticollis which has been known for almost 100 years to possess 3 species of Trichonympha (T. campanula, T. collaris, and T. sphaerica), 1 species of Trichomitopsis (T. termopsidis), as well as smaller flagellates. We have re-assessed this community by sequencing the small subunit (SSU) rRNA gene and the internal transcribed spacer (ITS) region from a large number of single Trichonympha and Trichomitopsis cells for which morphology was also documented. Based on phylogenetic clustering and sequence divergence, we identify 3 new species: Trichonympha postcylindrica, Trichomitopsis minor, and Trichomitopsis parvus spp. nov. Once identified by sequencing, the morphology of the isolated cells for all 3 new species was re-examined and found to be distinct from the previously described species: Trichonympha postcylindrica can be morphologically distinguished from the other Trichonympha species by an extension on its posterior end, whereas Trichomitopsis minor and T. parvus are smaller than T. termopsidis but similar in size to each other and cannot be distinguished based on morphology using light microscopy. Given that Z. angusticollis has one of the best characterized hindgut communities, the near doubling of the number of the largest and most easily identifiable symbiont species suggests that the diversity of hindgut symbionts is substantially underestimated in other termites as well. Accurate descriptions of the diversity of these microbial communities are essential for understanding hindgut ecology and disentangling the interactions among the symbionts, and molecular barcoding should be a priority for these systems.

  15. RNA families in Epstein-Barr virus.

    PubMed

    Moss, Walter N; Lee, Nara; Pimienta, Genaro; Steitz, Joan A

    2014-01-01

    Epstein-Barr virus (EBV) is a tumorigenic human γ-herpesvirus, which produces several known structured RNAs with functional importance: two are implicated in latency maintenance and tumorigenic phenotypes, EBER1 and EBER2; a viral small nucleolar RNA (v-snoRNA1) that may generate a small regulatory RNA; and an internal ribosomal entry site in the EBNA1 mRNA. A recent bioinformatics and RNA-Seq study of EBV identified two novel EBV non-coding (nc)RNAs with evolutionary conservation in lymphocryptoviruses and likely functional importance. Both RNAs are transcribed from a repetitive region of the EBV genome (the W repeats) during a highly oncogenic type of viral latency. One novel ncRNA can form a massive (586 nt) hairpin, while the other RNA is generated from a short (81 nt) intron and is found in high abundance in EBV-infected cells.

  16. RNA families in Epstein–Barr virus

    PubMed Central

    Moss, Walter N; Lee, Nara; Pimienta, Genaro; Steitz, Joan A

    2014-01-01

    Epstein–Barr virus (EBV) is a tumorigenic human γ-herpesvirus, which produces several known structured RNAs with functional importance: two are implicated in latency maintenance and tumorigenic phenotypes, EBER1 and EBER2; a viral small nucleolar RNA (v-snoRNA1) that may generate a small regulatory RNA; and an internal ribosomal entry site in the EBNA1 mRNA. A recent bioinformatics and RNA-Seq study of EBV identified two novel EBV non-coding (nc)RNAs with evolutionary conservation in lymphocryptoviruses and likely functional importance. Both RNAs are transcribed from a repetitive region of the EBV genome (the W repeats) during a highly oncogenic type of viral latency. One novel ncRNA can form a massive (586 nt) hairpin, while the other RNA is generated from a short (81 nt) intron and is found in high abundance in EBV-infected cells. PMID:24441309

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

    PubMed

    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

    2014-07-01

    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.

  18. Helical Defects in MicroRNA Influence Protein Binding by TAR RNA Binding Protein

    PubMed Central

    Acevedo, Roderico; Orench-Rivera, Nichole; Quarles, Kaycee A.; Showalter, Scott A.

    2015-01-01

    Background MicroRNAs (miRNAs) are critical post-transcriptional regulators of gene expression. Their precursors have a globally A-form helical geometry, which prevents most proteins from identifying their nucleotide sequence. This suggests the hypothesis that local structural features (e.g., bulges, internal loops) play a central role in specific double-stranded RNA (dsRNA) selection from cellular RNA pools by dsRNA binding domain (dsRBD) containing proteins. Furthermore, the processing enzymes in the miRNA maturation pathway require tandem-dsRBD cofactor proteins for optimal function, suggesting that dsRBDs play a key role in the molecular mechanism for precise positioning of the RNA within these multi-protein complexes. Here, we focus on the tandem-dsRBDs of TRBP, which have been shown to bind dsRNA tightly. Methodology/Principal Findings We present a combination of dsRNA binding assays demonstrating that TRBP binds dsRNA in an RNA-length dependent manner. Moreover, circular dichroism data shows that the number of dsRBD moieties bound to RNA at saturation is different for a tandem-dsRBD construct than for constructs with only one dsRBD per polypeptide, revealing another reason for the selective pressure to maintain multiple domains within a polypeptide chain. Finally, we show that helical defects in precursor miRNA alter the apparent dsRNA size, demonstrating that imperfections in RNA structure influence the strength of TRBP binding. Conclusion/Significance We conclude that TRBP is responsible for recognizing structural imperfections in miRNA precursors, in the sense that TRBP is unable to bind imperfections efficiently and thus is positioned around them. We propose that once positioned around structural defects, TRBP assists Dicer and the rest of the RNA-induced silencing complex (RISC) in providing efficient and homogenous conversion of substrate precursor miRNA into mature miRNA downstream. PMID:25608000

  19. Combination of natural fiber Boehmeria nivea (ramie) with matrix epoxide for bullet proof vest body armor

    NASA Astrophysics Data System (ADS)

    Anggoro, Didi Dwi; Kristiana, Nunung

    2015-12-01

    Ballistic protection equipment, such as a bulletproof vest, is a soldier's most important means of preserving life and survivability in extreme combat conditions. The bulletproof vests are designed to protect the user's chest from injury without disturbing the ability to perform his duties. Aromatic polyamide or aramid fibers known under the trade name Kevlar, Trawon and so is synthetic fiber materials commonly used in the manufacture of bulletproof vests. This synthetic fibers have high tensile strength and ductility. Kevlar is expensive and imported material. In this study, will introduce local natural raw materials, ramie fiber (Boehmeria nivea) which is cheaper and environmentally friendly. It has enough tenacity and tensile strength as a bulletproof vest. This experiment uses two panels, there are Panel A as front surface of Panel B. Panel A is a combination of ramie and epoxide matrix, while panel B is only ramie. From several variations of experimental combinations between Panel A and Panel B, optimal combination obtained with 16 layers of panel A and 31-34 layers of panel B which is able to protect againts cal. 7.65 mm × 17 mm (.32 ACP) bullet fired through pistol .32 Pindad from a distance of 20 meters. Panel with a size of 20 cm × 20 cm has a total thickness between 12,922 to13,745 mm and a total weight between 506,26 to 520,926gram. Scanning electron microscopy (SEM) observations indicated that the porosity and surface area of the ramie fiber is smooth, fiber surfaces showed topography with micropores. SEM also showed well-arranged structure of fibers bonding. Energy Dispersive X-ray (EDX) analysis indicated 100 % carbon contents in ramie fiber. Test result indicates that panel from composite ramie-epoxide can reach the level 1of International Standard of NIJ - 010104. Compared to panel from polyester fiber, the panel from composite ramie-epoxide (0,50-0,52 kg) is lighter weight than panel polyester fiber (1,642 kg).

  20. Combination of natural fiber Boehmeria nivea (ramie) with matrix epoxide for bullet proof vest body armor

    SciTech Connect

    Anggoro, Didi Dwi Kristiana, Nunung

    2015-12-29

    Ballistic protection equipment, such as a bulletproof vest, is a soldier’s most important means of preserving life and survivability in extreme combat conditions. The bulletproof vests are designed to protect the user’s chest from injury without disturbing the ability to perform his duties. Aromatic polyamide or aramid fibers known under the trade name Kevlar, Trawon and so is synthetic fiber materials commonly used in the manufacture of bulletproof vests. This synthetic fibers have high tensile strength and ductility. Kevlar is expensive and imported material. In this study, will introduce local natural raw materials, ramie fiber (Boehmeria nivea) which is cheaper and environmentally friendly. It has enough tenacity and tensile strength as a bulletproof vest. This experiment uses two panels, there are Panel A as front surface of Panel B. Panel A is a combination of ramie and epoxide matrix, while panel B is only ramie. From several variations of experimental combinations between Panel A and Panel B, optimal combination obtained with 16 layers of panel A and 31-34 layers of panel B which is able to protect againts cal. 7.65 mm × 17 mm (.32 ACP) bullet fired through pistol .32 Pindad from a distance of 20 meters. Panel with a size of 20 cm × 20 cm has a total thickness between 12,922 to13,745 mm and a total weight between 506,26 to 520,926gram. Scanning electron microscopy (SEM) observations indicated that the porosity and surface area of the ramie fiber is smooth, fiber surfaces showed topography with micropores. SEM also showed well-arranged structure of fibers bonding. Energy Dispersive X-ray (EDX) analysis indicated 100 % carbon contents in ramie fiber. Test result indicates that panel from composite ramie-epoxide can reach the level 1of International Standard of NIJ - 010104. Compared to panel from polyester fiber, the panel from composite ramie-epoxide (0,50-0,52 kg) is lighter weight than panel polyester fiber (1,642 kg)

  1. Reticulocyte RNA-Dependent RNA Polymerase

    PubMed Central

    Downey, Kathleen M.; Byrnes, John J.; Jurmark, Bonnie S.; So, Antero G.

    1973-01-01

    A cytoplasmic, microsomal bound RNA-dependent RNA polymerase has been purified 2500-fold from rabbit reticulocyte lysates. The synthesis of RNA with the purified enzyme is absolutely dependent on the addition of an RNA template. The best template is hemoglobin messenger RNA, while bacteriophage RNA and poly(A,G) are less active, and DNA is completely inactive as a template. With poly(A,G) as a template, only UTP and CTP are incorporated into polynucleotide chains, indicating that the RNA polymerase is an RNA replicase and not a terminal transferase. With messenger RNA as a template, all four ribonucleoside triphosphates are required for maximal activity. The RNA-dependent RNA polymerase reaction is extremely sensitive to low concentrations of heme, rifamycin AF/013, and ribonuclease and resistant to actinomycin D and DNase. The discovery of RNA-directed RNA synthesis in reticulocytes offers an additional site for control of gene expression in mammalian cells and provides a possible mechanism for amplification of the expression of specific genes. PMID:4519633

  2. RNA as an Enzyme.

    ERIC Educational Resources Information Center

    Cech, Thomas R.

    1986-01-01

    Reviews current findings that explain RNA's function as an enzyme in addition to being an informational molecule. Highlights recent research efforts and notes changes in the information base on RNA activity. Includes models and diagrams of RNA activity. (ML)

  3. Who Watches the Watchmen: Roles of RNA Modifications in the RNA Interference Pathway

    PubMed Central

    Xhemalce, Blerta

    2016-01-01

    RNA levels are widely thought to be predictive of RNA function. However, the existence of more than a hundred chemically distinct modifications of RNA alone is a major indication that these moieties may impart distinct functions to subgroups of RNA molecules that share a primary sequence but display distinct RNA “epigenetic” marks. RNAs can be modified on many sites, including 5′ and 3′ ends, the sugar phosphate backbone, or internal bases, which collectively provide many opportunities for posttranscriptional regulation through a variety of mechanisms. Here, we will focus on how modifications on messenger and microRNAs may affect the process of RNA interference in mammalian cells. We believe that taking RNA modifications into account will not only advance our understanding of this crucial pathway in disease and cancer but will also open the path to exploiting the enzymes that “write” and “erase” them as targets for therapeutic drug development. PMID:27441695

  4. Who Watches the Watchmen: Roles of RNA Modifications in the RNA Interference Pathway.

    PubMed

    Shelton, Samantha B; Reinsborough, Calder; Xhemalce, Blerta

    2016-07-01

    RNA levels are widely thought to be predictive of RNA function. However, the existence of more than a hundred chemically distinct modifications of RNA alone is a major indication that these moieties may impart distinct functions to subgroups of RNA molecules that share a primary sequence but display distinct RNA "epigenetic" marks. RNAs can be modified on many sites, including 5' and 3' ends, the sugar phosphate backbone, or internal bases, which collectively provide many opportunities for posttranscriptional regulation through a variety of mechanisms. Here, we will focus on how modifications on messenger and microRNAs may affect the process of RNA interference in mammalian cells. We believe that taking RNA modifications into account will not only advance our understanding of this crucial pathway in disease and cancer but will also open the path to exploiting the enzymes that "write" and "erase" them as targets for therapeutic drug development.

  5. Discovery of South American suckermouth armored catfishes (Loricariidae, Pterygoplichthys spp.) in the Santa Fe River drainage, Suwannee River basin, USA

    USGS Publications Warehouse

    Nico, Leo G.; Butt, Peter L.; Johnston, Gerald R.; Jelks, Howard L.; Kail, Matthew; Walsh, Stephen J.

    2012-01-01

    We report on the occurrence of South American suckermouth armored catfishes (Loricariidae) in the Suwannee River basin, southeastern USA. Over the past few years (2009-2012), loricariid catfishes have been observed at various sites in the Santa Fe River drainage, a major tributary of the Suwannee in the state of Florida. Similar to other introduced populations of Pterygoplichthys, there is high likelihood of hybridization. To date, we have captured nine specimens (270-585 mm, standard length) in the Santa Fe River drainage. One specimen taken from Poe Spring best agrees with Pterygoplichthys gibbiceps (Kner, 1854) or may be a hybrid with either P. pardalis or P. disjunctivus. The other specimens were taken from several sites in the drainage and include seven that best agree with Pterygoplichthys disjunctivus (Weber, 1991); and one a possible P. disjunctivus x P. pardalis hybrid. We observed additional individuals, either these or similar appearing loricariids, in Hornsby and Poe springs and at various sites upstream and downstream of the long (> 4 km) subterranean portion of the Santa Fe River. These specimens represent the first confirmed records of Pterygoplichthys in the Suwannee River basin. The P. gibbiceps specimen represents the first documented record of an adult or near adult of this species in open waters of North America. Pterygoplichthys disjunctivus or its hybrids (perhaps hybrid swarms) are already abundant and widespread in other parts of peninsular Florida, but the Santa Fe River represents a northern extension of the catfish in the state. Pterygoplichthys are still relatively uncommon in the Santa Fe drainage and successful reproduction not yet documented. However, in May 2012 we captured five adult catfish (two mature or maturing males and three gravid females) from a single riverine swallet pool. One male was stationed at a nest burrow (no eggs present). To survive the occasional harsh Florida winters, these South American catfish apparently use

  6. The Selenocysteine tRNA Gene in Leishmania major Is Transcribed by both RNA Polymerase II and RNA Polymerase III

    PubMed Central

    Padilla-Mejía, Norma E.; Florencio-Martínez, Luis E.; Moreno-Campos, Rodrigo; Vizuet-de-Rueda, Juan C.; Cevallos, Ana M.; Hernández-Rivas, Rosaura; Manning-Cela, Rebeca

    2014-01-01

    Eukaryotic tRNAs, transcribed by RNA polymerase III (Pol III), contain boxes A and B as internal promoter elements. One exception is the selenocysteine (Sec) tRNA (tRNA-Sec), whose transcription is directed by an internal box B and three extragenic sequences in vertebrates. Here we report on the transcriptional analysis of the tRNA-Sec gene in the protozoan parasite Leishmania major. This organism has unusual mechanisms of gene expression, including Pol II polycistronic transcription and maturation of mRNAs by trans splicing, a process that attaches a 39-nucleotide miniexon to the 5′ end of all the mRNAs. In L. major, tRNA-Sec is encoded by a single gene inserted into a Pol II polycistronic unit, in contrast to most tRNAs, which are clustered at the boundaries of polycistronic units. 5′ rapid amplification of cDNA ends and reverse transcription-PCR experiments showed that some tRNA-Sec transcripts contain the miniexon at the 5′ end and a poly(A) tail at the 3′ end, indicating that the tRNA-Sec gene is polycistronically transcribed by Pol II and processed by trans splicing and polyadenylation, as was recently reported for the tRNA-Sec genes in the related parasite Trypanosoma brucei. However, nuclear run-on assays with RNA polymerase inhibitors and with cells that were previously UV irradiated showed that the tRNA-Sec gene in L. major is also transcribed by Pol III. Thus, our results indicate that RNA polymerase specificity in Leishmania is not absolute in vivo, as has recently been found in other eukaryotes. PMID:25548151

  7. N6-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions

    PubMed Central

    Liu, Nian; Dai, Qing; Zheng, Guanqun; He, Chuan; Parisien, Marc; Pan, Tao

    2015-01-01

    RNA-binding proteins control many aspects of cellular biology through binding single-stranded RNA binding motifs (RBM)1-3. However, RBMs can be buried within their local RNA structures4-7, thus inhibiting RNA-protein interactions. N6-methyladenosine (m6A), the most abundant and dynamic internal modification in eukaryotic messenger RNA8-19, can be selectively recognized by the YTHDF2 protein to affect the stability of cytoplasmic mRNAs15, but how m6A achieves wide-ranging physiological significance needs further exploration. Here we show that m6A controls the RNA-structure-dependent accessibility of RBMs to affect RNA-protein interactions for biological regulation; we term this mechanism “m6A-switch”. We found that m6A alters the local structure in mRNA and long non-coding RNA (lncRNA) to facilitate binding of heterogeneous nuclear ribonucleoprotein C (hnRNP C), an abundant nuclear RNA-binding protein responsible for pre-mRNA processing20-24. Combining PAR-CLIP and m6A/MeRIP approaches enabled us to identify 39,060 m6A-switches among hnRNP C binding sites; and global m6A reduction decreased hnRNP C binding at 2,798 high confidence m6A-switches. We determined that these m6A-switch-regulated hnRNP C binding activities affect the abundance as well as alternative splicing of target mRNAs, demonstrating the regulatory role of m6A-switches on gene expression and RNA maturation. Our results illustrate how RNA-binding proteins gain regulated access to their RBMs through m6A-dependent RNA structural remodeling, and provide a new direction for investigating RNA-modification-coded cellular biology. PMID:25719671

  8. T7-RNA Polymerase

    NASA Technical Reports Server (NTRS)

    1997-01-01

    T7-RNA Polymerase grown on STS-81. Structure-Function Relationships of RNA Polymerase: DNA-dependent RNA polymerase is the key enzyme responsible for the biosynthesis of RNA, a process known as transcription. Principal Investigator's include Dr. Dan Carter, Dr. B.C. Wang, and Dr. John Rose of New Century Pharmaceuticals.

  9. Lightweight armor system

    DOEpatents

    Chu, Henry S; Langhorst, Benjamin R; Bakas, Michael P; Thinnes, Gary L

    2013-02-26

    The disclosure provides a shock absorbing layer comprised of one or more shock absorbing cells, where a shock absorbing cell is comprised of a cell interior volume containing a plurality of hydrogel particles and a free volume, and where the cell interior volume is surrounded by a containing layer. The containing layer has a permeability such that the hydrogel particles when swollen remain at least partially within the cell interior volume when subjected to a design shock pressure wave, allowing for force relaxation through hydrogel compression response. Additionally, the permeability allows for the flow of exuded free water, further dissipating wave energy. In an embodiment, a plurality of shock absorbing cells is combined with a penetration resistant material to mitigate the transmitted shock wave generated by an elastic precursor wave in the penetration resistant material.

  10. Armored Geomembrane Cover Engineering

    PubMed Central

    Foye, Kevin

    2011-01-01

    Geomembranes are an important component of modern engineered barriers to prevent the infiltration of stormwater and runoff into contaminated soil and rock as well as waste containment facilities—a function generally described as a geomembrane cover. This paper presents a case history involving a novel implementation of a geomembrane cover system. Due to this novelty, the design engineers needed to assemble from disparate sources the design criteria for the engineering of the cover. This paper discusses the design methodologies assembled by the engineering team. This information will aid engineers designing similar cover systems as well as environmental and public health professionals selecting site improvements that involve infiltration barriers. PMID:21776229

  11. Crystal structure of Mil (Mth680): internal duplication and similarity between the Imp4/Brix domain and the anticodon-binding domain of class IIa aminoacyl-tRNA synthetases

    PubMed Central

    Ng, Chyan Leong; Waterman, David; Koonin, Eugene V; Antson, Alfred A; Ortiz-Lombardía, Miguel

    2005-01-01

    Proteins of the Imp4/Brix superfamily are involved in ribosomal RNA processing, an essential function in all cells. We report the first structure of an Imp4/Brix superfamily protein, the Mil (for Methanothermobacter thermautotrophicus Imp4-like) protein (gene product Mth680), from the archaeon M. thermautotrophicus. The amino- and carboxy-terminal halves of Mil show significant structural similarity to one another, suggesting an origin by means of an ancestral duplication. Both halves show the same fold as the anticodon-binding domain of class IIa aminoacyl-tRNA synthetases, with greater conservation seen in the N-terminal half. This structural similarity, together with the charge distribution in Mil, suggests that Imp4/Brix superfamily proteins could bind single-stranded segments of RNA along a concave surface formed by the N-terminal half of their β-sheet and a central α-helix. The crystal structure of Mil is incompatible with the presence, in the Imp4/Brix domain, of a helix–turn–helix motif that was proposed to comprise the RNA-binding moiety of the Imp4/Brix proteins. PMID:15654320

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

    PubMed

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

    2013-10-01

    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.

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

    PubMed Central

    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

  14. Analysis RNA-seq and Noncoding RNA.

    PubMed

    Arrigoni, Alberto; Ranzani, Valeria; Rossetti, Grazisa; Panzeri, Ilaria; Abrignani, Sergio; Bonnal, Raoul J P; Pagani, Massimiliano

    2016-01-01

    RNA-Seq is an approach to transcriptome profiling that uses deep-sequencing technologies to detect and accurately quantify RNA molecules originating from a genome at a given moment in time. In recent years, the advent of RNA-Seq has facilitated genome-wide expression profiling, including the identification of novel and rare transcripts like noncoding RNAs and novel alternative splicing isoforms.Here, we describe the analytical steps required for the identification and characterization of noncoding RNAs starting from RNA-Seq raw samples, with a particular emphasis on long noncoding RNAs (lncRNAs). PMID:27659980

  15. The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs.

    PubMed

    Parlea, Lorena G; Sweeney, Blake A; Hosseini-Asanjan, Maryam; Zirbel, Craig L; Leontis, Neocles B

    2016-07-01

    RNA 3D motifs occupy places in structured RNA molecules that correspond to the hairpin, internal and multi-helix junction "loops" of their secondary structure representations. As many as 40% of the nucleotides of an RNA molecule can belong to these structural elements, which are distinct from the regular double helical regions formed by contiguous AU, GC, and GU Watson-Crick basepairs. With the large number of atomic- or near atomic-resolution 3D structures appearing in a steady stream in the PDB/NDB structure databases, the automated identification, extraction, comparison, clustering and visualization of these structural elements presents an opportunity to enhance RNA science. Three broad applications are: (1) identification of modular, autonomous structural units for RNA nanotechnology, nanobiology and synthetic biology applications; (2) bioinformatic analysis to improve RNA 3D structure prediction from sequence; and (3) creation of searchable databases for exploring the binding specificities, structural flexibility, and dynamics of these RNA elements. In this contribution, we review methods developed for computational extraction of hairpin and internal loop motifs from a non-redundant set of high-quality RNA 3D structures. We provide a statistical summary of the extracted hairpin and internal loop motifs in the most recent version of the RNA 3D Motif Atlas. We also explore the reliability and accuracy of the extraction process by examining its performance in clustering recurrent motifs from homologous ribosomal RNA (rRNA) structures. We conclude with a summary of remaining challenges, especially with regard to extraction of multi-helix junction motifs. PMID:27125735

  16. Biochemical properties of full-length hepatitis C virus RNA-dependent RNA polymerase expressed in insect cells.

    PubMed

    Choi, Han-Byul; Kim, Yeon-Gu; Oh, Jong-Won

    2003-12-31

    The hepatitis C virus (HCV) RNA-dependent RNA polymerase, NS5B protein, is the key viral enzyme responsible for replication of the HCV viral RNA genome. Although several full-length and truncated forms of the HCV NS5B proteins have been expressed previously in insect cells, contamination of host terminal transferase (TNTase) has hampered analysis of the RNA synthesis initiation mechanism using natural HCV RNA templates. We have expressed the HCV NS5B protein in insect cells using a recombinant baculovirus and purified it to near homogeneity without contaminated TNTase. The highly purified recombinant HCV NS5B was capable of copying 9.6-kb full-length HCV RNA template, and mini-HCV RNA carrying both 5'- and 3'-untranslated regions (UTRs) of the HCV genome. In the absence of a primer, and other cellular and viral factors, the NS5B could elongate over HCV RNA templates, but the synthesized products were primarily in the double stranded form, indicating that no cyclic replication occurred with NS5B alone. RNA synthesis using RNA templates representing the 3'-end region of HCV minus-strand RNA and the X-RNA at the 3'-end of HCV RNA genome was also initiated de novo. No formation of dimer-size self-primed RNA products resulting from extension of the 3'-end hydroxyl group was observed. Despite the internal de novo initiation from the X-RNA, the NS5B could not initiate RNA synthesis from the internal region of oligouridylic acid (U)(20), suggesting that HCV RNA polymerase initiates RNA synthesis from the selected region in the 3'-UTR of HCV genome.

  17. Stranded Whole Transcriptome RNA-Seq for All RNA Types

    PubMed Central

    Yan, Pearlly X.; Fang, Fang; Buechlein, Aaron; Ford, James B.; Tang, Haixu; Huang, Tim H.; Burow, Matthew E.; Liu, Yunlong; Rusch, Douglas B.

    2015-01-01

    Stranded whole transcriptome RNA-Seq described in this unit captures quantitative expression data for all types of RNA including, but not limited to miRNA (microRNA), piRNA (Piwi-interacting RNA), snoRNA (small nucleolar RNA), lincRNA (large non-coding intergenic RNA), SRP RNA (signal recognition particle RNA), tRNA (transfer RNA), mtRNA (mitochondrial RNA) and mRNA (messenger RNA). The size and nature of these types of RNA are irrelevant to the approach described here. Barcoded libraries for multiplexing on the Illumina platform are generated with this approach but it can be applied to other platforms with a few modifications. PMID:25599667

  18. Stranded Whole Transcriptome RNA-Seq for All RNA Types.

    PubMed

    Miller, David F B; Yan, Pearlly X; Fang, Fang; Buechlein, Aaron; Ford, James B; Tang, Haixu; Huang, Tim H; Burow, Matthew E; Liu, Yunlong; Rusch, Douglas B; Nephew, Kenneth P

    2015-01-20

    Stranded whole transcriptome RNA-Seq described in this unit captures quantitative expression data for all types of RNA including, but not limited to, miRNA (microRNA), piRNA (Piwi-interacting RNA), snoRNA (small nucleolar RNA), lincRNA (large non-coding intergenic RNA), SRP RNA (signal recognition particle RNA), tRNA (transfer RNA), mtRNA (mitochondrial RNA), and mRNA (messenger RNA). The size and nature of these types of RNA are irrelevant to the approach described here. Barcoded libraries for multiplexing on the Illumina platform are generated with this approach but it can be applied to other platforms with a few modifications.

  19. Mechanism of RNA recombination in carmo- and tombusviruses: evidence for template switching by the RNA-dependent RNA polymerase in vitro.

    PubMed

    Cheng, Chi-Ping; Nagy, Peter D

    2003-11-01

    RNA recombination occurs frequently during replication of tombusviruses and carmoviruses, which are related small plus-sense RNA viruses of plants. The most common recombinants generated by these viruses are either defective interfering (DI) RNAs or chimeric satellite RNAs, which are thought to be generated by template switching of the viral RNA-dependent RNA polymerase (RdRp) during the viral replication process. To test if RNA recombination is mediated by the viral RdRp, we used either a purified recombinant RdRp of Turnip crinkle carmovirus or a partially purified RdRp preparation of Cucumber necrosis tombusvirus. We demonstrated that these RdRp preparations generated RNA recombinants in vitro. The RdRp-driven template switching events occurred between either identical templates or two different RNA templates. The template containing a replication enhancer recombined more efficiently than templates containing artificial sequences. We also observed that AU-rich sequences promote recombination more efficiently than GC-rich sequences. Cloning and sequencing of the generated recombinants revealed that the junction sites were located frequently at the ends of the templates (end-to-end template switching). We also found several recombinants that were generated by template switching involving internal positions in the RNA templates. In contrast, RNA ligation-based RNA recombination was not detected in vitro. Demonstration of the ability of carmo- and tombusvirus RdRps to switch RNA templates in vitro supports the copy-choice models of RNA recombination and DI RNA formation for these viruses.

  20. The initiator tRNA acceptance assay as a short-term test for carcinogens. 2. Results with ten compounds selected by the International Programme on Chemical Safety for the evaluation of short-term tests for carcinogens.

    PubMed

    Hradec, J; Spiegelhalder, B; Preussmann, R

    1988-05-01

    Eight carcinogenic and two non-carcinogenic compounds that are difficult to detect by short-term tests (acrylonitrile, benzene, benzoin, caprolactam, diethylhexylphtalate, diethylstilbestrol, hexamethylphosphoramide, phenobarbital, safrole and o-toluidine) were tested independently in Prague and in Heidelberg by the newly developed initiator tRNA acceptance assay. Seven out of eight tested carcinogens gave a positive response in this assay, only safrole showed a false negativity in both laboratories. Both non-carcinogenic compounds, benzoin and caprolactam, exhibited no activity. An absolute qualitative agreement was found with all compounds tested between the results of both laboratories. With the exception only of phenobarbital (intermediate activity in Prague and low in Heidelberg) the quantitative results obtained in both laboratories were comparable. The initiator tRNA acceptance assay thus appears to be a reliable short-term test for carcinogenicity with good reproducibility.

  1. RNA-Catalyzed RNA Ligation on an External RNA Template

    NASA Technical Reports Server (NTRS)

    McGinness, Kathleen E.; Joyce, Gerald F.

    2002-01-01

    Variants of the hc ligase ribozyme, which catalyzes ligation of the 3' end of an RNA substrate to the 5' end of the ribozyme, were utilized to evolve a ribozyme that catalyzes ligation reactions on an external RNA template. The evolved ribozyme catalyzes the joining of an oligonucleotide 3'-hydroxyl to the 5'-triphosphate of an RNA hairpin molecule. The ribozyme can also utilize various substrate sequences, demonstrating a largely sequence-independent mechanism for substrate recognition. The ribozyme also carries out the ligation of two oligonucleotides that are bound at adjacent positions on a complementary template. Finally, it catalyzes addition of mononucleoside '5-triphosphates onto the '3 end of an oligonucleotide primer in a template-dependent manner. The development of ribozymes that catalyze polymerase-type reactions contributes to the notion that an RNA world could have existed during the early history of life on Earth.

  2. Closing the Circle: Replicating RNA with RNA

    PubMed Central

    Cheng, Leslie K.L.; Unrau, Peter J.

    2010-01-01

    How life emerged on this planet is one of the most important and fundamental questions of science. Although nearly all details concerning our origins have been lost in the depths of time, there is compelling evidence to suggest that the earliest life might have exploited the catalytic and self-recognition properties of RNA to survive. If an RNA based replicating system could be constructed in the laboratory, it would be much easier to understand the challenges associated with the very earliest steps in evolution and provide important insight into the establishment of the complex metabolic systems that now dominate this planet. Recent progress into the selection and characterization of ribozymes that promote nucleotide synthesis and RNA polymerization are discussed and outstanding problems in the field of RNA-mediated RNA replication are summarized. PMID:20554706

  3. siRNA Delivery to the Glomerular Mesangium Using Polycationic Cyclodextrin Nanoparticles Containing siRNA

    PubMed Central

    Gale, Aaron; Wu, Peiwen; Ma, Rong; Davis, Mark E.

    2015-01-01

    There is an urgent need for new therapies that can halt or reverse the course of chronic kidney disease with minimal side-effect burden on the patient. Small interfering RNA (siRNA) nanoparticles are new therapeutic entities in clinical development that could be useful for chronic kidney disease treatment because they combine the tissue-specific targeting properties of nanoparticles with the gene-specific silencing effects of siRNA. Recent reports have emerged demonstrating that the kidney, specifically the glomerulus, is a readily accessible site for nanoparticle targeting. Here, we explore the hypothesis that intravenously administered polycationic cyclodextrin nanoparticles containing siRNA (siRNA/CDP-NPs) can be used for delivery of siRNA to the glomerular mesangium. We demonstrate that siRNA/CDP-NPs localize to the glomerular mesangium with limited deposition in other areas of the kidney after intravenous injection. Additionally, we report that both mouse and human mesangial cells rapidly internalize siRNA/CDP-NPs in vitro and that nanoparticle uptake can be enhanced by attaching the targeting ligands mannose or transferrin to the nanoparticle surface. Lastly, we show knockdown of mesangial enhanced green fluorescent protein expression in a reporter mouse strain following iv treatment with siRNA/CDP-NPs. Altogether, these data demonstrate the feasibility of mesangial targeting using intravenously administered siRNA/CDP-NPs. PMID:25734248

  4. Designing Efficient Double RNA trans-Splicing Molecules for Targeted RNA Repair.

    PubMed

    Hüttner, Clemens; Murauer, Eva M; Hainzl, Stefan; Kocher, Thomas; Neumayer, Anna; Reichelt, Julia; Bauer, Johann W; Koller, Ulrich

    2016-09-22

    RNA trans-splicing is a promising tool for mRNA modification in a diversity of genetic disorders. In particular, the substitution of internal exons of a gene by combining 3' and 5' RNA trans-splicing seems to be an elegant way to modify especially large pre-mRNAs. Here we discuss a robust method for designing double RNA trans-splicing molecules (dRTM). We demonstrate how the technique can be implemented in an endogenous setting, using COL7A1, the gene encoding type VII collagen, as a target. An RTM screening system was developed with the aim of testing the replacement of two internal COL7A1 exons, harbouring a homozygous mutation, with the wild-type version. The most efficient RTMs from a pool of randomly generated variants were selected via our fluorescence-based screening system and adapted for use in an in vitro disease model system. Transduction of type VII collagen-deficient keratinocytes with the selected dRTM led to accurate replacement of two internal COL7A1 exons resulting in a restored wild-type RNA sequence. This is the first study demonstrating specific exon replacement by double RNA trans-splicing within an endogenous transcript in cultured cells, corroborating the utility of this technology for mRNA repair in a variety of genetic disorders.

  5. Designing Efficient Double RNA trans-Splicing Molecules for Targeted RNA Repair

    PubMed Central

    Hüttner, Clemens; Murauer, Eva M.; Hainzl, Stefan; Kocher, Thomas; Neumayer, Anna; Reichelt, Julia; Bauer, Johann W.; Koller, Ulrich

    2016-01-01

    RNA trans-splicing is a promising tool for mRNA modification in a diversity of genetic disorders. In particular, the substitution of internal exons of a gene by combining 3′ and 5′ RNA trans-splicing seems to be an elegant way to modify especially large pre-mRNAs. Here we discuss a robust method for designing double RNA trans-splicing molecules (dRTM). We demonstrate how the technique can be implemented in an endogenous setting, using COL7A1, the gene encoding type VII collagen, as a target. An RTM screening system was developed with the aim of testing the replacement of two internal COL7A1 exons, harbouring a homozygous mutation, with the wild-type version. The most efficient RTMs from a pool of randomly generated variants were selected via our fluorescence-based screening system and adapted for use in an in vitro disease model system. Transduction of type VII collagen-deficient keratinocytes with the selected dRTM led to accurate replacement of two internal COL7A1 exons resulting in a restored wild-type RNA sequence. This is the first study demonstrating specific exon replacement by double RNA trans-splicing within an endogenous transcript in cultured cells, corroborating the utility of this technology for mRNA repair in a variety of genetic disorders. PMID:27669223

  6. Designing Efficient Double RNA trans-Splicing Molecules for Targeted RNA Repair.

    PubMed

    Hüttner, Clemens; Murauer, Eva M; Hainzl, Stefan; Kocher, Thomas; Neumayer, Anna; Reichelt, Julia; Bauer, Johann W; Koller, Ulrich

    2016-01-01

    RNA trans-splicing is a promising tool for mRNA modification in a diversity of genetic disorders. In particular, the substitution of internal exons of a gene by combining 3' and 5' RNA trans-splicing seems to be an elegant way to modify especially large pre-mRNAs. Here we discuss a robust method for designing double RNA trans-splicing molecules (dRTM). We demonstrate how the technique can be implemented in an endogenous setting, using COL7A1, the gene encoding type VII collagen, as a target. An RTM screening system was developed with the aim of testing the replacement of two internal COL7A1 exons, harbouring a homozygous mutation, with the wild-type version. The most efficient RTMs from a pool of randomly generated variants were selected via our fluorescence-based screening system and adapted for use in an in vitro disease model system. Transduction of type VII collagen-deficient keratinocytes with the selected dRTM led to accurate replacement of two internal COL7A1 exons resulting in a restored wild-type RNA sequence. This is the first study demonstrating specific exon replacement by double RNA trans-splicing within an endogenous transcript in cultured cells, corroborating the utility of this technology for mRNA repair in a variety of genetic disorders. PMID:27669223

  7. RNA self-assembly and RNA nanotechnology.

    PubMed

    Grabow, Wade W; Jaeger, Luc

    2014-06-17

    CONSPECTUS: Nanotechnology's central goal involves the direct control of matter at the molecular nanometer scale to build nanofactories, nanomachines, and other devices for potential applications including electronics, alternative fuels, and medicine. In this regard, the nascent use of nucleic acids as a material to coordinate the precise arrangements of specific molecules marked an important milestone in the relatively recent history of nanotechnology. While DNA served as the pioneer building material in nucleic acid nanotechnology, RNA continues to emerge as viable alternative material with its own distinct advantages for nanoconstruction. Several complementary assembly strategies have been used to build a diverse set of RNA nanostructures having unique structural attributes and the ability to self-assemble in a highly programmable and controlled manner. Of the different strategies, the architectonics approach uniquely endeavors to understand integrated structural RNA architectures through the arrangement of their characteristic structural building blocks. Viewed through this lens, it becomes apparent that nature routinely uses thermodynamically stable, recurrent modular motifs from natural RNA molecules to generate unique and more complex programmable structures. With the design principles found in natural structures, a number of synthetic RNAs have been constructed. The synthetic nanostructures constructed to date have provided, in addition to affording essential insights into RNA design, important platforms to characterize and validate the structural self-folding and assembly properties of RNA modules or building blocks. Furthermore, RNA nanoparticles have shown great promise for applications in nanomedicine and RNA-based therapeutics. Nevertheless, the synthetic RNA architectures achieved thus far consist largely of static, rigid particles that are still far from matching the structural and functional complexity of natural responsive structural elements such

  8. RNA Signal Amplifier Circuit with Integrated Fluorescence Output

    PubMed Central

    2015-01-01

    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. PMID:25354355

  9. RNA signal amplifier circuit with integrated fluorescence output.

    PubMed

    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.

  10. Combinatorics of RNA-RNA interaction.

    PubMed

    Li, Thomas J X; Reidys, Christian M

    2012-02-01

    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 their generating function, singularity analysis as well as explicit recurrence relations. In particular, our results imply simple asymptotic formulas for the number of joint structures.

  11. International Reports.

    ERIC Educational Resources Information Center

    Valauskas, Edward J.; Crosby, John, IV; Haycock, Ken; Oh, Mary

    1999-01-01

    Includes the following international reports: International Federation of Library Associations and Institutions; Special Libraries Association; and Trends and Issues in Library and Information Services in Canada, 1998. (AEF)

  12. Cytoplasmic Z-RNA

    SciTech Connect

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

    1987-09-01

    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.

  13. Raman crystallography of RNA.

    PubMed

    Gong, Bo; Chen, Jui-Hui; Yajima, Rieko; Chen, Yuanyuan; Chase, Elaine; Chadalavada, Durga M; Golden, Barbara L; Carey, Paul R; Bevilacqua, Philip C

    2009-10-01

    Raman crystallography is the application of Raman spectroscopy to single crystals. This technique has been applied to a variety of protein molecules where it has provided unique information about biopolymer folding, substrate binding, and catalysis. Here, we describe the application of Raman crystallography to functional RNA molecules. RNA represents unique opportunities and challenges for Raman crystallography. One issue that confounds studies of RNA is its tendency to adopt multiple non-functional folds. Raman crystallography has the advantage that it isolates a single state of the RNA within the crystal and can evaluate its fold, metal ion binding properties (ligand identity, stoichiometry, and affinity), proton binding properties (identity, stoichiometry, and affinity), and catalytic potential. In particular, base-specific stretches can be identified and then associated with the binding of metal ions and protons. Because measurements are carried out in the hanging drop at ambient, rather than cryo, conditions and because RNA crystals tend to be approximately 70% solvent, RNA dynamics and conformational changes become experimentally accessible. This review focuses on experimental setup and procedures, acquisition and interpretation of Raman data, and determination of physicochemical properties of the RNA. Raman crystallographic and solution biochemical experiments on the HDV RNA enzyme are summarized and found to be in excellent agreement. Remarkably, characterization of the crystalline state has proven to help rather than hinder functional characterization of functional RNA, most likely because the tendency of RNA to fold heterogeneously is limited in a crystalline environment. Future applications of Raman crystallography to RNA are briefly discussed.

  14. Secondary structure of the HIV-2 leader RNA comprising the tRNA-primer binding site.

    PubMed Central

    Berkhout, B; Schoneveld, I

    1993-01-01

    The initiation of reverse transcription of a retroviral RNA genome occurs by a tRNA primer bound near the 5' end of the genomic RNA at a position called the primer-binding site (PBS). To understand the molecular basis for this RNA-RNA interaction, the secondary structure of the leader RNA of the human immunodeficiency virus type 2 (HIV-2) RNA was analyzed. In vitro synthesized HIV-2 RNA was probed with various structure-specific enzymes and chemicals. A computer program was then used to predict the secondary structure consistent with these data. In addition, the nucleotide sequences of different HIV-2 isolates were used to screen for the occurrence of covariation among putative base pairs. The primary sequences have diverged rapidly in some HIV-2 isolates, however, some strikingly conserved secondary structure elements were identified. Most nucleotides in the leader region are involved in base pairing. An exception is the PBS sequence, of which 15 out of 18 nucleotides are exposed in an internal loop. These findings suggest that the overall structure of the HIV-2 genome has evolved to facilitate an optimal interaction with its tRNA primer. Images PMID:8464701

  15. An RNA Topoisomerase

    NASA Astrophysics Data System (ADS)

    Wang, Hui; di Gate, Russell J.; Seeman, Nadrian C.

    1996-09-01

    A synthetic strand of RNA has been designed so that it can adopt two different topological states (a circle and a trefoil knot) when ligated into a cyclic molecule. The RNA knot and circle have been characterized by their behavior in gel electrophoresis and sedimentation experiments. This system allows one to assay for the existence of an RNA topoisomerase, because the two RNA molecules can be interconverted only by a strand passage event. We find that the interconversion of these two species can be catalyzed by Escherichia coli DNA topoisomerase III, indicating that this enzyme can act as an RNA topoisomerase. The conversion of circles to knots is accompanied by a small amount of RNA catenane generation. These findings suggest that strand passage must be considered a potential component of the folding and modification of RNA structures.

  16. mRNA imprinting

    PubMed Central

    2011-01-01

    Following its synthesis in the nucleus, mRNA undergoes various stages that are critical for the proper synthesis, localization and possibly functionality of its encoded protein. Recently, we have shown that two RNA polymerase II (Pol II) subunits, Rpb4p and Rpb7p, associate with the nascent transcript co-transcriptionally. This “mRNA imprinting” lasts throughout the mRNA lifetime and is required for proper regulation of all major stages that the mRNA undergoes. Other possible cases of co-transcriptional imprinting are discussed. Since mRNAs can be transported from the synthesizing cell to other cells, we propose that mRNA imprinting can also affect the phenotype of the recipient cells. This can be viewed as “mRNA-based epigenetics.” PMID:21686103

  17. An expanding universe of mRNA modifications

    PubMed Central

    Jaffrey, Samie R.

    2015-01-01

    The fate of mRNA can be regulated by internal base modifications, with the currently known modified bases being N6-methyladenosine, 5-methylcytosine, and inosine. Three new studies show that yeast and human mRNA also contain pseudouridine residues and that pseudouridylation is induced in various stress states, hinting at a new pathway for post-transcriptional control of mRNA. PMID:25372308

  18. Coupling mRNA Synthesis and Decay

    PubMed Central

    Braun, Katherine A.

    2014-01-01

    What has been will be again, what has been done will be done again; there is nothing new under the sun.—Ecclesiastes 1:9 (New International Version) Posttranscriptional regulation of gene expression has an important role in defining the phenotypic characteristics of an organism. Well-defined steps in mRNA metabolism that occur in the nucleus—capping, splicing, and polyadenylation—are mechanistically linked to the process of transcription. Recent evidence suggests another link between RNA polymerase II (Pol II) and a posttranscriptional process that occurs in the cytoplasm—mRNA decay. This conclusion appears to represent a conundrum. How could mRNA synthesis in the nucleus and mRNA decay in the cytoplasm be mechanistically linked? After a brief overview of mRNA processing, we will review the recent evidence for transcription-coupled mRNA decay and the possible involvement of Snf1, the Saccharomyces cerevisiae ortholog of AMP-activated protein kinase, in this process. PMID:25154419

  19. Use of DNA, RNA, and Chimeric Templates by a Viral RNA-Dependent RNA Polymerase: Evolutionary Implications for the Transition from the RNA to the DNA World

    PubMed Central

    Siegel, Robert W.; Bellon, Laurent; Beigelman, Leonid; Kao, C. Cheng

    1999-01-01

    All polynucleotide polymerases have a similar structure and mechanism of catalysis, consistent with their evolution from one progenitor polymerase. Viral RNA-dependent RNA polymerases (RdRp) are expected to have properties comparable to those from this progenitor and therefore may offer insight into the commonalities of all classes of polymerases. We examined RNA synthesis by the brome mosaic virus RdRp on DNA, RNA, and hybrid templates and found that precise initiation of RNA synthesis can take place from all of these templates. Furthermore, initiation can take place from either internal or penultimate initiation sites. Using a template competition assay, we found that the BMV RdRp interacts with DNA only three- to fourfold less well than it interacts with RNA. Moreover, a DNA molecule with a ribonucleotide at position −11 relative to the initiation nucleotide was able to interact with RdRp at levels comparable to that observed with RNA. These results suggest that relatively few conditions were needed for an ancestral RdRp to replicate DNA genomes. PMID:10400735

  20. RIP: RNA Immunoprecipitation.

    PubMed

    Gagliardi, Miriam; Matarazzo, Maria R

    2016-01-01

    The relevance of RNA-protein interactions in modulating mRNA and noncoding RNA function is increasingly appreciated and several methods have been recently developed to map them. The RNA immunoprecipitation (RIP) is a powerful method to study the physical association between individual proteins and RNA molecules in vivo. The basic principles of RIP are very similar to those of chromatin immunoprecipitation (ChIP), a largely used tool in the epigenetic field, but with some important caveats. The approach is based on the use of a specific antibody raised against the protein of interest to pull down the RNA-binding protein (RBP) and target-RNA complexes. Any RNA that is associated with this protein complex will also be isolated and can be further analyzed by polymerase chain reaction-based methods, hybridization, or sequencing.Several variants of this technique exist and can be divided into two main classes: native and cross-linked RNA immunoprecipitation. The native RIP allows to reveal the identity of RNAs directly bound by the protein and their abundance in the immunoprecipitated sample, while cross-linked RIP leads to precisely map the direct and indirect binding site of the RBP of interest to the RNA molecule.In this chapter both the protocols applied to mammalian cells are described taking into account the caveats and considerations required for designing, performing, and interpreting the results of these experiments. PMID:27659976

  1. RNA Viruses Infecting Pest Insects

    Technology Transfer Automated Retrieval System (TEKTRAN)

    RNA viruses are viruses whose genetic material is ribonucleic acid (RNA). RNA viruses may be double or single-stranded based on the type of RNA they contain. Single-stranded RNA viruses can be further grouped into negative sense or positive-sense viruses according to the polarity of their RNA. Fur...

  2. Cellulolytic potential of a novel strain of Paenibacillus sp. isolated from the armored catfish Parotocinclus maculicauda gut

    PubMed Central

    de Castro, André L. M.; Vollú, Renata E.; Peixoto, Raquel S.; Grigorevski-Lima, André L.; Coelho, Rosalie R. R.; Bon, Elba P. S.; Rosado, Alexandre S.; Seldin, Lucy

    2011-01-01

    A cellulolytic bacterial strain, designated P118, isolated from the gut of the tropical fish Parotocinclus maculicauda was identified as belonging to the genus Paenibacillus based on phenotypic and chemotaxonomic characteristics and the 16S rRNA gene sequence. The novel strain was Gram-positive, spore-forming and rod-shaped. Catalase but not oxidase was produced. Carboxymethylcellulose was hydrolyzed but starch or gelatin was not. Acetoin production was negative whereas nitrate reduction and urease production were positive. Many carbohydrates served as carbon sources for growth. MK-7 was the predominant isoprenoid quinone. Anteiso-C15:0 (38.73%) and C16:0 (20.85%) were the dominant cellular fatty acids. Strain P118 was closely related to Paenibacillus amylolyticus NRRL NRS-290, P. pabuli HSCC 492, P. tundrae Ab10b, P. xylanexedens B22a, and P. tylopili MK2 with 98.3–98.8% 16S rRNA gene sequence similarity. The results presented here suggest that strain P118 represents a novel species of the genus Paenibacillus and it is a potential strain for further studies concerning its role in the production of industrially important products from cellulosic biomass. PMID:24031795

  3. Helix Capping in RNA Structure

    PubMed Central

    Lee, Jung C.; Gutell, Robin R.

    2014-01-01

    Helices are an essential element in defining the three-dimensional architecture of structured RNAs. While internal basepairs in a canonical helix stack on both sides, the ends of the helix stack on only one side and are exposed to the loop side, thus susceptible to fraying unless they are protected. While coaxial stacking has long been known to stabilize helix ends by directly stacking two canonical helices coaxially, based on analysis of helix-loop junctions in RNA crystal structures, herein we describe helix capping, topological stacking of a helix end with a basepair or an unpaired nucleotide from the loop side, which in turn protects helix ends. Beyond the topological protection of helix ends against fraying, helix capping should confer greater stability onto the resulting composite helices. Our analysis also reveals that this general motif is associated with the formation of tertiary structure interactions. Greater knowledge about the dynamics at the helix-junctions in the secondary structure should enhance the prediction of RNA secondary structure with a richer set of energetic rules and help better understand the folding of a secondary structure into its three-dimensional structure. These together suggest that helix capping likely play a fundamental role in driving RNA folding. PMID:24691270

  4. pRNA

    PubMed Central

    Wehner, Stefanie; Dörrich, Anja K; Ciba, Philipp; Wilde, Annegret; Marz, Manja

    2014-01-01

    Promoter-associated RNAs (pRNAs) are a family of ~90–100 nt-long divergent RNAs overlapping the promoter of the rRNA (rDNA) operon. pRNA transcripts interact with TIP5, a component of the chromatin remodeling complex NoRC, which recruits enzymes for heterochromatin formation and mediates silencing of rRNA genes. Here we present a comprehensive analysis of pRNA homologs, including different versions per species, as result of in silico studies in available metazoan genome assemblies. Comparative sequence analysis and secondary structure prediction ended up in two possible secondary structures, which let us assume a possible dual function of pRNAs for regulation of rRNA operons. Furthermore, we validated parts of our computational predictions experimentally by RT-PCR and sequencing. A representative seed alignment of the pRNA family, annotated with possible secondary structures was released to the Rfam database. PMID:24440945

  5. Strategies in RNA crystallography.

    PubMed

    Reyes, Francis E; Garst, Andrew D; Batey, Robert T

    2009-01-01

    A number of RNAs ranging from small helices to large megadalton ribonucleoprotein complexes have been solved to atomic resolution using X-ray crystallography. As with proteins, RNA crystallography involves a number of screening trials in which the concentration of macromolecule, precipitant, salt, and temperature are varied, an approach known as searching "condition space." In contrast to proteins, the nature of base pairing in nucleic acids creates predictable secondary structure that facilitates the rational design of RNA variants, allowing "sequence space" to be screened in parallel. This chapter reviews RNA-specific techniques and considerations for RNA crystallography and presents a complete workflow used by our laboratory for solving RNA structures starting with initial library construction, methods to investigate and improve RNA crystal quality, and finally phase determination and structure solution. PMID:20946787

  6. RNA Sequencing in Schizophrenia

    PubMed Central

    Li, Xin; Teng, Shaolei

    2015-01-01

    Schizophrenia (SCZ) is a serious psychiatric disorder that affects 1% of general population and places a heavy burden worldwide. The underlying genetic mechanism of SCZ remains unknown, but studies indicate that the disease is associated with a global gene expression disturbance across many genes. Next-generation sequencing, particularly of RNA sequencing (RNA-Seq), provides a powerful genome-scale technology to investigate the pathological processes of SCZ. RNA-Seq has been used to analyze the gene expressions and identify the novel splice isoforms and rare transcripts associated with SCZ. This paper provides an overview on the genetics of SCZ, the advantages of RNA-Seq for transcriptome analysis, the accomplishments of RNA-Seq in SCZ cohorts, and the applications of induced pluripotent stem cells and RNA-Seq in SCZ research. PMID:27053919

  7. Multifunctional RNA Nanoparticles

    PubMed Central

    2015-01-01

    Our recent advancements in RNA nanotechnology introduced novel nanoscaffolds (nanorings); however, the potential of their use for biomedical applications was never fully revealed. As presented here, besides functionalization with multiple different short interfering RNAs for combinatorial RNA interference (e.g., against multiple HIV-1 genes), nanorings also allow simultaneous embedment of assorted RNA aptamers, fluorescent dyes, proteins, as well as recently developed RNA–DNA hybrids aimed to conditionally activate multiple split functionalities inside cells. PMID:25267559

  8. RNA-modifying enzymes.

    PubMed

    Ferré-D'Amaré, Adrian R

    2003-02-01

    A bewildering number of post-transcriptional modifications are introduced into cellular RNAs by enzymes that are often conserved among archaea, bacteria and eukaryotes. The modifications range from those with well-understood functions, such as tRNA aminoacylation, to widespread but more mysterious ones, such as pseudouridylation. Recent structure determinations have included two types of RNA nucleobase modifying enzyme: pseudouridine synthases and tRNA guanine transglycosylases.

  9. RNA in evolution.

    PubMed

    Lehman, Niles

    2010-01-01

    RNA has played a variety of roles in the evolutionary history of life on the Earth. While this molecule was once considered a poor cousin of the more influential polymers in the cell, namely DNA and proteins, a string of important discoveries over the last 50 years has revealed that RNA may in fact be the cornerstone of biological function. In particular, the finding that RNA can be catalytic, and thus possess both a genotype and a phenotype, has forced us to consider the possibility that life's origins began with RNA, and that the subsequent diversification of life is aptly described as a string of innovations by RNA to adapt to a changing environment. Some of these adaptations include riboswitches, ribonucleoproteins (RNPs), RNA editing, and RNA interference (RNAi). Although many of these functions may seem at first glance to be recent evolutionary developments, it may be the case that all of their catalytic activities trace their roots back to a primordial 'RNA World' some four billion years ago, and that RNA's diversity has a continuous thread that pervades life from its very origins. PMID:21935885

  10. ALKBH5 Is a Mammalian RNA Demethylase that Impacts RNA Metabolism and Mouse Fertility

    PubMed Central

    Zheng, Guanqun; Dahl, John Arne; Niu, Yamei; Fedorcsak, Peter; Huang, Chun-Min; Li, Charles J.; Vågbø, Cathrine B.; Shi, Yue; Wang, Wen-Ling; Song, Shu-Hui; Lu, Zhike; Bosmans, Ralph P.G.; Dai, Qing; Hao, Ya-Juan; Yang, Xin; Zhao, Wen-Ming; Tong, Wei-Min; Wang, Xiu-Jie; Bogdan, Florian; Furu, Kari; Fu, Ye; Jia, Guifang; Zhao, Xu; Liu, Jun; Krokan, Hans E.; Klungland, Arne; Yang, Yun-Gui; He, Chuan

    2013-01-01

    SUMMARY N6-methyladenosine (m6A) is the most prevalent internal modification of messenger RNA (mRNA) in higher eukaryotes. Here we report ALKBH5 as another mammalian demethylase that oxidatively reverses m6A in mRNA in vitro and in vivo. This demethylation activity of ALKBH5 significantly affects mRNA export and RNA metabolism as well as the assembly of mRNA processing factors in nuclear speckles. Alkbh5-deficient male mice have increased m6A in mRNA and are characterized by impaired fertility resulting from apoptosis that affects meiotic metaphase-stage spermatocytes. In accordance with this defect, we have identified in mouse testes 1,551 differentially expressed genes that cover broad functional categories and include spermatogenesis-related mRNAs involved in the p53 functional interaction network. The discovery of this RNA demethylase strongly suggests that the reversible m6A modification has fundamental and broad functions in mammalian cells. PMID:23177736

  11. Use of PCR Targeting of Internal Transcribed Spacer Regions and Single-Stranded Conformation Polymorphism Analysis of Sequence Variation in Different Regions of rRNA Genes in Fungi for Rapid Diagnosis of Mycotic Keratitis†

    PubMed Central

    Kumar, Manish; Shukla, P. K.

    2005-01-01

    The increased incidence of fungal infections in the recent past has been attributed to the increase in the number of human immunodeficiency virus-positive and AIDS patients. Early diagnosis of mycoses in patients is crucial for prompt antifungal therapy. Immunological methods of diagnosis have not been found to be satisfactory, and recent research has been diverted to the use of PCR for the sensitive and early diagnosis at the molecular level. In the present study we targeted different regions of the rRNA gene to diagnose cases of mycotic keratitis and identify the causal agents. Six fungus-specific primers (primers ITS1, ITS2, ITS3, ITS4, invSR1R, and LR12R) were used, and the amplified products were analyzed by single-stranded conformation polymorphism (SSCP) analysis. Dendrograms of these SSCP patterns, prepared on the basis of Jaccard's coefficient, indicated that the PCR products obtained with primer pair ITS1 and ITS2 were the best for the identification of fungi. The results were confirmed by sequencing of the PCR products, and the approach was successfully tested experimentally for the detection of mycotic keratitis caused by Aspergillus fumigatus and was used for the diagnosis of fungal corneal ulcers in patients. PMID:15695661

  12. Development of the Symbolic Manipulator Laboratory modeling package for the kinematic design and optimization of the Future Armor Rearm System robot

    SciTech Connect

    March-Leuba, S.; Jansen, J.F.; Kress, R.L.; Babcock, S.M. ); Dubey, R.V. . Dept. of Mechanical and Aerospace Engineering)

    1992-08-01

    A new program package, Symbolic Manipulator Laboratory (SML), for the automatic generation of both kinematic and static manipulator models in symbolic form is presented. Critical design parameters may be identified and optimized using symbolic models as shown in the sample application presented for the Future Armor Rearm System (FARS) arm. The computer-aided development of the symbolic models yields equations with reduced numerical complexity. Important considerations have been placed on the closed form solutions simplification and on the user friendly operation. The main emphasis of this research is the development of a methodology which is implemented in a computer program capable of generating symbolic kinematic and static forces models of manipulators. The fact that the models are obtained trigonometrically reduced is among the most significant results of this work and the most difficult to implement. Mathematica, a commercial program that allows symbolic manipulation, is used to implement the program package. SML is written such that the user can change any of the subroutines or create new ones easily. To assist the user, an on-line help has been written to make of SML a user friendly package. Some sample applications are presented. The design and optimization of the 5-degrees-of-freedom (DOF) FARS manipulator using SML is discussed. Finally, the kinematic and static models of two different 7-DOF manipulators are calculated symbolically.

  13. Development of the Symbolic Manipulator Laboratory modeling package for the kinematic design and optimization of the Future Armor Rearm System robot. Ammunition Logistics Program

    SciTech Connect

    March-Leuba, S.; Jansen, J.F.; Kress, R.L.; Babcock, S.M.; Dubey, R.V.

    1992-08-01

    A new program package, Symbolic Manipulator Laboratory (SML), for the automatic generation of both kinematic and static manipulator models in symbolic form is presented. Critical design parameters may be identified and optimized using symbolic models as shown in the sample application presented for the Future Armor Rearm System (FARS) arm. The computer-aided development of the symbolic models yields equations with reduced numerical complexity. Important considerations have been placed on the closed form solutions simplification and on the user friendly operation. The main emphasis of this research is the development of a methodology which is implemented in a computer program capable of generating symbolic kinematic and static forces models of manipulators. The fact that the models are obtained trigonometrically reduced is among the most significant results of this work and the most difficult to implement. Mathematica, a commercial program that allows symbolic manipulation, is used to implement the program package. SML is written such that the user can change any of the subroutines or create new ones easily. To assist the user, an on-line help has been written to make of SML a user friendly package. Some sample applications are presented. The design and optimization of the 5-degrees-of-freedom (DOF) FARS manipulator using SML is discussed. Finally, the kinematic and static models of two different 7-DOF manipulators are calculated symbolically.

  14. Transcriptome-wide dynamics of RNA pseudouridylation.

    PubMed

    Karijolich, John; Yi, Chengqi; Yu, Yi-Tao

    2015-10-01

    Pseudouridylation is the most abundant internal post-transcriptional modification of stable RNAs, with fundamental roles in the biogenesis and function of spliceosomal small nuclear RNAs (snRNAs) and ribosomal RNAs (rRNAs). Recently, the first transcriptome-wide maps of RNA pseudouridylation were published, greatly expanding the catalogue of known pseudouridylated RNAs. These data have further implicated RNA pseudouridylation in the cellular stress response and, moreover, have established that mRNAs are also targets of pseudouridine synthases, potentially representing a novel mechanism for expanding the complexity of the cellular proteome.

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

    PubMed

    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.

  16. Site-specific labeling of RNA.

    PubMed

    Nilsen, Timothy W

    2013-03-01

    In this protocol, RNAs containing a specific internally labeled phosphate are generated. The entire transcript of interest is synthesized using in vitro transcription. It is then digested with RNase H in the presence of a complementary chimeric oligonucleotide of the sequence 5'-NNNddddNNNNNNN-3', where N is a 2'-O-methyl (2' OMe) ribonucleotide and d is a de-oxy-nu-cle-o-tide. RNase H specifically cleaves the RNA in the oligonucleotide-RNA hybrid at the phosphodiester bond opposite the 5'-most deoxynucleotide, creating 3'-hydroxyl and 5'-phosphate termini. After dephosphorylation of the 5' end of the 3' fragment with phosphatase, this terminus is labeled to high specific activity with [γ-(32)P]ATP. The fragments of the original RNA are then resealed with T4 DNA ligase in the presence of a splint (or bridge) oligonucleotide. These labeled RNAs can be used in subsequent procedures to probe RNA-protein or RNA-RNA interactions.

  17. RNA secondary structure prediction using soft computing.

    PubMed

    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. PMID:23702539

  18. Ocular Delivery of pRNA Nanoparticles: Distribution and Clearance After Subconjunctival Injection

    PubMed Central

    Feng, Liang; Liu, Hongshan; Liu, Chia-Yang; LaSance, Kathleen; Haque, Farzin; Shu, Dan; Guo, Peixuan

    2014-01-01

    Purpose RNA nanoparticles derived from the three-way junction (3WJ) of the pRNA of bacteriophage phi29 DNA packaging motor were previously found to be thermodynamically stable. As the nanoparticles could have potential in ocular drug delivery, the objectives in the present study were to investigate the distribution of pRNA nanoparticles after subconjunctival injection and examine the feasibility to deliver the nanoparticles to the cells of cornea and retina. Methods Alexa647-labeled pRNA nanoparticles (pRNA-3WJ and pRNA-X) and double-stranded RNA (dsRNA) were administered via subconjunctival injection in mice. Alexa647 dye was a control. Topical administration was performed for comparison. Ocular clearance of pRNA nanoparticles and dsRNA after the injection was assessed using whole-body fluorescence imaging of the eyes. The numbers of cells in the ocular tissues with nanoparticle cell internalization were determined in fluorescence microscopy of dissected eye tissues. Results After subconjunctival injection, pRNA nanoparticles and dsRNA were observed to distribute into the eyes and cleared through the lymph. pRNA-3WJ, pRNA-X, and dsRNA were found in the cells of the conjunctiva, cornea, and sclera, but only pRNA-X was in the cells of the retina. Topical administration was not effective in delivering the nanoparticles to the eye. Conclusions The pRNA nanoparticles were delivered to the cells in the eye via subconjunctival injection, and cell internalization was achieved in the cornea with pRNA-3WJ and pRNA-X and in the retina with pRNA-X. Only the X-shape pRNA-X could enter the retina. PMID:24297069

  19. RNA based evolutionary optimization.

    PubMed

    Schuster, P

    1993-12-01

    The notion of an RNA world has been introduced for a prebiotic scenario that is dominated by RNA molecules and their properties, in particular their capabilities to act as templates for reproduction and as catalysts for several cleavage and ligation reactions of polynucleotides and polypeptides. This notion is used here also for simple experimental assays which are well suited to study evolution in the test tube. In molecular evolution experiments fitness is determined in essence by the molecular structures of RNA molecules. Evidence is presented for adaptation to environment in cell-free media. RNA based molecular evolution experiments have led to interesting spin-offs in biotechnology, commonly called 'applied molecular evolution', which make use of Darwinian trial-and-error strategies in order to synthesize new pharmacological compounds and other advanced materials on a biological basis. Error-propagation in RNA replication leads to formation of mutant spectra called 'quasispecies'. An increase in the error rate broadens the mutant spectrum. There exists a sharply defined threshold beyond which heredity breaks down and evolutionary adaptation becomes impossible. Almost all RNA viruses studied so far operate at conditions close to this error threshold. Quasispecies and error thresholds are important for an understanding of RNA virus evolution, and they may help to develop novel antiviral strategies. Evolution of RNA molecules can be studied and interpreted by considering secondary structures. The notion of sequence space introduces a distance between pairs of RNA sequences which is tantamount to counting the minimal number of point mutations required to convert the sequences into each other. The mean sensitivity of RNA secondary structures to mutation depends strongly on the base pairing alphabet: structures from sequences which contain only one base pair (GC or AU are much less stable against mutation than those derived from the natural (AUGC) sequences

  20. Ab initio RNA folding

    NASA Astrophysics Data System (ADS)

    Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela

    2015-06-01

    RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, the experimental determination of RNA structures through x-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, the need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties, when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding.

  1. Structure Prediction of RNA Loops with a Probabilistic Approach

    PubMed Central

    Li, Jun; Zhang, Jian; Wang, Jun; Li, Wenfei; Wang, Wei

    2016-01-01

    The knowledge of the tertiary structure of RNA loops is important for understanding their functions. In this work we develop an efficient approach named RNApps, specifically designed for predicting the tertiary structure of RNA loops, including hairpin loops, internal loops, and multi-way junction loops. It includes a probabilistic coarse-grained RNA model, an all-atom statistical energy function, a sequential Monte Carlo growth algorithm, and a simulated annealing procedure. The approach is tested with a dataset including nine RNA loops, a 23S ribosomal RNA, and a large dataset containing 876 RNAs. The performance is evaluated and compared with a homology modeling based predictor and an ab initio predictor. It is found that RNApps has comparable performance with the former one and outdoes the latter in terms of structure predictions. The approach holds great promise for accurate and efficient RNA tertiary structure prediction. PMID:27494763

  2. Functional RNA delivery targeted to dendritic cells by synthetic nanoparticles.

    PubMed

    McCullough, Kenneth C; Bassi, Isabelle; Démoulins, Thomas; Thomann-Harwood, Lisa J; Ruggli, Nicolas

    2012-09-01

    Dendritic cells (DCs) are essential to many aspects of immune defense development and regulation. They provide important targets for prophylactic and therapeutic delivery. While protein delivery has had considerable success, RNA delivery is still expanding. Delivering RNA molecules for RNAi has shown particular success and there are reports on successful delivery of mRNA. Central, therein, is the application of cationic entities. Following endocytosis of the delivery vehicle for the RNA, cationic entities should promote vesicular membrane perturbation, facilitating cytosolic release. The present review explains the diversity of DC function in immune response development and control. Promotion of delivered RNA cytosolic release is discussed, relating to immunoprophylactic and therapeutic potential, and DC endocytic machinery is reviewed, showing how DC endocytic pathways influence the handling of internalized material. The potential advantages for application of replicating RNA are presented and discussed, in consideration of their value and development in the near future.

  3. CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains.

    PubMed

    Wright, Patrick R; Georg, Jens; Mann, Martin; Sorescu, Dragos A; Richter, Andreas S; Lott, Steffen; Kleinkauf, Robert; Hess, Wolfgang R; Backofen, Rolf

    2014-07-01

    CopraRNA (Comparative prediction algorithm for small RNA targets) is the most recent asset to the Freiburg RNA Tools webserver. It incorporates and extends the functionality of the existing tool IntaRNA (Interacting RNAs) in order to predict targets, interaction domains and consequently the regulatory networks of bacterial small RNA molecules. The CopraRNA prediction results are accompanied by extensive postprocessing methods such as functional enrichment analysis and visualization of interacting regions. Here, we introduce the functionality of the CopraRNA and IntaRNA webservers and give detailed explanations on their postprocessing functionalities. Both tools are freely accessible at http://rna.informatik.uni-freiburg.de. PMID:24838564

  4. CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains

    PubMed Central

    Wright, Patrick R.; Georg, Jens; Mann, Martin; Sorescu, Dragos A.; Richter, Andreas S.; Lott, Steffen; Kleinkauf, Robert; Hess, Wolfgang R.; Backofen, Rolf

    2014-01-01

    CopraRNA (Comparative prediction algorithm for small RNA targets) is the most recent asset to the Freiburg RNA Tools webserver. It incorporates and extends the functionality of the existing tool IntaRNA (Interacting RNAs) in order to predict targets, interaction domains and consequently the regulatory networks of bacterial small RNA molecules. The CopraRNA prediction results are accompanied by extensive postprocessing methods such as functional enrichment analysis and visualization of interacting regions. Here, we introduce the functionality of the CopraRNA and IntaRNA webservers and give detailed explanations on their postprocessing functionalities. Both tools are freely accessible at http://rna.informatik.uni-freiburg.de. PMID:24838564

  5. Methods of forming aluminum oxynitride-comprising bodies, including methods of forming a sheet of transparent armor

    DOEpatents

    Chu, Henry Shiu-Hung [Idaho Falls, ID; Lillo, Thomas Martin [Idaho Falls, ID

    2008-12-02

    The invention includes methods of forming an aluminum oxynitride-comprising body. For example, a mixture is formed which comprises A:B:C in a respective molar ratio in the range of 9:3.6-6.2:0.1-1.1, where "A" is Al.sub.2O.sub.3, "B" is AlN, and "C" is a total of one or more of B.sub.2O.sub.3, SiO.sub.2, Si--Al--O--N, and TiO.sub.2. The mixture is sintered at a temperature of at least 1,600.degree. C. at a pressure of no greater than 500 psia effective to form an aluminum oxynitride-comprising body which is at least internally transparent and has at least 99% maximum theoretical density.

  6. RNA epigenetic modification: N6-methyladenosine.

    PubMed

    Xiao, Zhang; Guifang, Jia

    2016-04-01

    N(6)-methyladenosine (m(6)A) is one of the most prevalent internal modifications in eukaryotic messenger RNA. The dynamic and reversible modification is installed by methyltransferase complex charactered three subunits: METTL3 (Methyltransferase-like protein 3), METTL14 (Methyltransferase-like protein 14) and WTAP (Wilms tumor 1-associating protein), and erased by two independent demethylases, FTO (Fat mass and obesity associated protein) and ALKBH5 (AlkB homolog 5), in an α-ketoglutarate (α-KG)- and Fe(II)-dependent manner. m(6)A plays funtions in controlling RNA metabolism through the recognition by m(6)A reader proteins, the YTH domain family proteins and HNRNPA2B1 (Heterogeneous nuclear ribonucleoproteins A2B1) . In this review, we summarized distributive features and vital roles of m(6)A and its associated proteins in RNA metabolisms and biological significance, which will help us better understand this new exciting emerging epitranscriptome research field. PMID:27103452

  7. Cuboplexes: Topologically Active siRNA Delivery.

    PubMed

    Kim, Hojun; Leal, Cecilia

    2015-10-27

    RNAi technology is currently experiencing a revival due to remarkable improvements in efficacy and viability through oligonucleotide chemical manipulations and/or via their packaging into nanoscale carriers. At present, there is no FDA-approved system for siRNA technology in humans. The design of the next generation of siRNA carriers requires a deep understanding of how a nanoparticle's physicochemical properties truly impart biological stability and efficiency. For example, we now know that nanoparticles need to be sterically stabilized in order to meet adequate biodistribution profiles. At present, targeting, uptake, and, in particular, endosomal escape are among the most critical challenges impairing RNAi technologies. The disruption of endosomes encompasses membrane transformations (for example, pore formation) that cost significant elastic energy. Nanoparticle size and shape have been identified as relevant parameters impacting tissue accumulation and cellular uptake. In this paper, we demonstrate that the internal structure of lipid-based particles offers a different handle to promote endosomal membrane topological disruptions that enhance siRNA delivery. Specifically, we designed sterically stabilized lipid-based particles that differ from traditional liposomal systems by displaying highly ordered bicontinuous cubic internal structures that can be loaded with large amounts of siRNA. This system differs from traditional siRNA-containing liposomes (lipoplexes) as the particle-endosomal membrane interactions are controlled by elasticity energetics and not by electrostatics. The resulting "PEGylated cuboplex" has the ability to deliver siRNA and specifically knockdown genes with efficiencies that surpass those achieved by traditional lipoplex systems. PMID:26390340

  8. lncRNA/MicroRNA interactions in the vasculature

    PubMed Central

    Ballantyne, MD; McDonald, RA

    2016-01-01

    MicroRNA (miRNA) have gained widespread attention for their role in diverse vascular processes including angiogenesis, apoptosis, proliferation, and migration. Despite great understanding of miRNA expression and function, knowledge of long noncoding RNA (lncRNA) molecular mechanisms still remains limited. The influence of miRNA on lncRNA function, and the converse, is now beginning to emerge. lncRNA may regulate miRNA function by acting as endogenous sponges to regulate gene expression and miRNA have been shown to bind and regulate lncRNA stability. A detailed understanding of the molecular and cellular effects of lncRNA‐miRNA‐mediated interactions in vascular pathophysiology could pave the way for new diagnostic markers and therapeutic approaches, but first there is a requirement for a more detailed understanding of the impact of such regulatory networks. PMID:26910520

  9. Generation of siRNA Nanosheets for Efficient RNA Interference

    NASA Astrophysics Data System (ADS)

    Kim, Hyejin; Lee, Jae Sung; Lee, Jong Bum

    2016-04-01

    After the discovery of small interference RNA (siRNA), nanostructured siRNA delivery systems have been introduced to achieve an efficient regulation of the target gene expression. Here we report a new siRNA-generating two dimensional nanostructure in a formation of nanosized sheet. Inspired by tunable mechanical and functional properties of the previously reported RNA membrane, siRNA nanosized sheets (siRNA-NS) with multiple Dicer cleavage sites were prepared. The siRNA-NS has two dimensional structure, providing a large surface area for Dicer to cleave the siRNA-NS for the generation of functional siRNAs. Furthermore, downregulation of the cellular target gene expression was achieved by delivery of siRNA-NS without chemical modification of RNA strands or conjugation to other substances.

  10. Generation of siRNA Nanosheets for Efficient RNA Interference

    PubMed Central

    Kim, Hyejin; Lee, Jae Sung; Lee, Jong Bum

    2016-01-01

    After the discovery of small interference RNA (siRNA), nanostructured siRNA delivery systems have been introduced to achieve an efficient regulation of the target gene expression. Here we report a new siRNA-generating two dimensional nanostructure in a formation of nanosized sheet. Inspired by tunable mechanical and functional properties of the previously reported RNA membrane, siRNA nanosized sheets (siRNA-NS) with multiple Dicer cleavage sites were prepared. The siRNA-NS has two dimensional structure, providing a large surface area for Dicer to cleave the siRNA-NS for the generation of functional siRNAs. Furthermore, downregulation of the cellular target gene expression was achieved by delivery of siRNA-NS without chemical modification of RNA strands or conjugation to other substances. PMID:27120975

  11. Generation of siRNA Nanosheets for Efficient RNA Interference.

    PubMed

    Kim, Hyejin; Lee, Jae Sung; Lee, Jong Bum

    2016-01-01

    After the discovery of small interference RNA (siRNA), nanostructured siRNA delivery systems have been introduced to achieve an efficient regulation of the target gene expression. Here we report a new siRNA-generating two dimensional nanostructure in a formation of nanosized sheet. Inspired by tunable mechanical and functional properties of the previously reported RNA membrane, siRNA nanosized sheets (siRNA-NS) with multiple Dicer cleavage sites were prepared. The siRNA-NS has two dimensional structure, providing a large surface area for Dicer to cleave the siRNA-NS for the generation of functional siRNAs. Furthermore, downregulation of the cellular target gene expression was achieved by delivery of siRNA-NS without chemical modification of RNA strands or conjugation to other substances. PMID:27120975

  12. Cooperative Interaction Within RNA Virus Mutant Spectra.

    PubMed

    Shirogane, Yuta; Watanabe, Shumpei; Yanagi, Yusuke

    2016-01-01

    RNA viruses usually consist of mutant spectra because of high error rates of viral RNA polymerases. Growth competition occurs among different viral variants, and the fittest clones predominate under given conditions. Individual variants, however, may not be entirely independent of each other, and internal interactions within mutant spectra can occur. Examples of cooperative and interfering interactions that exert enhancing and suppressing effects on replication of the wild-type virus, respectively, have been described, but their underlying mechanisms have not been well defined. It was recently found that the cooperation between wild-type and variant measles virus genomes produces a new phenotype through the heterooligomer formation of a viral protein. This observation provides a molecular mechanism underlying cooperative interactions within mutant spectra. Careful attention to individual sequences, in addition to consensus sequences, may disclose further examples of internal interactions within mutant spectra. PMID:26162566

  13. RNA Ligation and the Origin of tRNA

    NASA Astrophysics Data System (ADS)

    Nagaswamy, Uma; Fox, George E.

    2003-04-01

    A straightforward origin of transfer RNA, (tRNA), is difficult to envision because of the apparently complex idiosyncratic interaction between the D-loop and T-loop. Recently, multiple examples of the T-loop structural motif have been identified in ribosomal RNA. These examples show that the long-range interactions between the T-loop and D-loops seen in tRNA are not an essential part of the motif but rather are facilitated by it. Thus, the core T-loop structure could already have existed in a small RNA prior to the emergence of the tRNA. The tRNA might then have arisen by expansion of an RNA that carried the motif. With this idea in mind, Di Giulio's earlier hypothesis that tRNA evolved by a simple duplication or ligation of a minihelix RNA was re-examined. It is shown that an essentially modern tRNA structure can in fact be generated by the ligation of two 38-nucleotide RNA minihelices of appropriate sequence. Although rare, such sequences occur with sufficient frequency, (1 in 3 × 107), that they could be found in a standard in vitro RNA selection experiment. The results demonstrate that a series of RNA duplications, as previously proposed, can in principal account for the origin of tRNA. More generally, the results point out that RNA ligation can be a powerful driving force for increased complexity in the RNA World.

  14. Shapes of Interacting RNA Complexes

    PubMed Central

    Fu, Benjamin M.M.

    2014-01-01

    Abstract Shapes of interacting RNA complexes are studied using a filtration via their topological genus. A shape of an RNA complex is obtained by (iteratively) collapsing stacks and eliminating hairpin loops. This shape projection preserves the topological core of the RNA complex, and for fixed topological genus there are only finitely many such shapes. Our main result is a new bijection that relates the shapes of RNA complexes with shapes of RNA structures. This allows for computing the shape polynomial of RNA complexes via the shape polynomial of RNA structures. We furthermore present a linear time uniform sampling algorithm for shapes of RNA complexes of fixed topological genus. PMID:25075750

  15. International Perspectives.

    ERIC Educational Resources Information Center

    Allen, Kenn; Habermann, Ulla; Chowdhury, Omar Faruque; Guerra, Iraida Manzanilla

    1998-01-01

    Includes "Introduction to International Perspectives" (Allen); "Volunteerism in the Welfare State: The Case of Denmark" (Habermann); "Grassroots Organizing in Bangladesh" (Chowdhury); and "Volunteerism in Latin America" (Guerra). (SK)

  16. RNA splicing and genes

    SciTech Connect

    Sharp, P.A.

    1988-11-25

    The splicing of long transcripts RNA (copied from DNA in the cell nucleus) into smaller specific mRNA is an important event in the regulation of gene expression in eukaryotic cells. The splicing reaction occurs as a late step in the nuclear pathway for synthesis of mRNAs. This pathway commences with initiation of transcription by RNA polymerase II and probably involves an integrated series of steps each dependent on previous events. Splicing of precursors to mRNAs involves the formation of a spliceosome complex containing 5' and 3' splice sites. This complex contains the evolutionary highly conserved small nuclear RNAs (snRNAs) Us, U4, U5, and U6. The most abundant snRNA, U1, is required to form the spliceosome and may be a part of the spliceosome. Analogues of these snRNAs have been identified in yeast. Assembly of the spliceosome probably involves the binding of a multi-snRNA complex containing U4, U5, and U6 snRNAs. Several observations suggest that the association of snRNAs in such complexes is quite dynamic. It is argued that the snRANs in the spliceosome form a catalytic RNA structure that is responsible for the cleavage and ligation steps during splicing.

  17. Optimization of Gas Metal Arc Welding (GMAW) Process for Maximum Ballistic Limit in MIL A46100 Steel Welded All-Metal Armor

    NASA Astrophysics Data System (ADS)

    Grujicic, M.; Ramaswami, S.; Snipes, J. S.; Yavari, R.; Yen, C.-F.; Cheeseman, B. A.

    2015-01-01

    Our recently developed multi-physics computational model for the conventional gas metal arc welding (GMAW) joining process has been upgraded with respect to its predictive capabilities regarding the process optimization for the attainment of maximum ballistic limit within the weld. The original model consists of six modules, each dedicated to handling a specific aspect of the GMAW process, i.e., (a) electro-dynamics of the welding gun; (b) radiation-/convection-controlled heat transfer from the electric arc to the workpiece and mass transfer from the filler metal consumable electrode to the weld; (c) prediction of the temporal evolution and the spatial distribution of thermal and mechanical fields within the weld region during the GMAW joining process; (d) the resulting temporal evolution and spatial distribution of the material microstructure throughout the weld region; (e) spatial distribution of the as-welded material mechanical properties; and (f) spatial distribution of the material ballistic limit. In the present work, the model is upgraded through the introduction of the seventh module in recognition of the fact that identification of the optimum GMAW process parameters relative to the attainment of the maximum ballistic limit within the weld region entails the use of advanced optimization and statistical sensitivity analysis methods and tools. The upgraded GMAW process model is next applied to the case of butt welding of MIL A46100 (a prototypical high-hardness armor-grade martensitic steel) workpieces using filler metal electrodes made of the same material. The predictions of the upgraded GMAW process model pertaining to the spatial distribution of the material microstructure and ballistic limit-controlling mechanical properties within the MIL A46100 butt weld are found to be consistent with general expectations and prior observations.

  18. Levelized cost-benefit analysis of proposed diagnostics for the Ammunition Transfer Arm of the US Army`s Future Armored Resupply Vehicle

    SciTech Connect

    Wilkinson, V.K.; Young, J.M.

    1995-07-01

    The US Army`s Project Manager, Advanced Field Artillery System/Future Armored Resupply Vehicle (PM-AFAS/FARV) is sponsoring the development of technologies that can be applied to the resupply vehicle for the Advanced Field Artillery System. The Engineering Technology Division of the Oak Ridge National Laboratory has proposed adding diagnostics/prognostics systems to four components of the Ammunition Transfer Arm of this vehicle, and a cost-benefit analysis was performed on the diagnostics/prognostics to show the potential savings that may be gained by incorporating these systems onto the vehicle. Possible savings could be in the form of reduced downtime, less unexpected or unnecessary maintenance, fewer regular maintenance checks. and/or tower collateral damage or loss. The diagnostics/prognostics systems are used to (1) help determine component problems, (2) determine the condition of the components, and (3) estimate the remaining life of the monitored components. The four components on the arm that are targeted for diagnostics/prognostics are (1) the electromechanical brakes, (2) the linear actuators, (3) the wheel/roller bearings, and (4) the conveyor drive system. These would be monitored using electrical signature analysis, vibration analysis, or a combination of both. Annual failure rates for the four components were obtained along with specifications for vehicle costs, crews, number of missions, etc. Accident scenarios based on component failures were postulated, and event trees for these scenarios were constructed to estimate the annual loss of the resupply vehicle, crew, arm. or mission aborts. A levelized cost-benefit analysis was then performed to examine the costs of such failures, both with and without some level of failure reduction due to the diagnostics/prognostics systems. Any savings resulting from using diagnostics/prognostics were calculated.

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

    PubMed

    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.

  20. Ligand-responsive RNA mechanical switches.

    PubMed

    Boerneke, Mark A; Hermann, Thomas

    2015-01-01

    Ligand-responsive RNA mechanical switches represent a new class of simple switching modules that adopt well-defined ligand-free and bound conformational states, distinguishing them from metabolite-sensing riboswitches. Initially discovered in the internal ribosome entry site (IRES) of hepatitis C virus (HCV), these RNA switch motifs were found in the genome of diverse other viruses. Although large variations are seen in sequence and local secondary structure of the switches, their function in viral translation initiation that requires selective ligand recognition is conserved. We recently determined the crystal structure of an RNA switch from Seneca Valley virus (SVV) which is able to functionally replace the switch of HCV. The switches from both viruses recognize identical cognate ligands despite their sequence dissimilarity. Here, we describe the discovery of 7 new switches in addition to the previously established 5 examples. We highlight structural and functional features unique to this class of ligand-responsive RNA mechanical switches and discuss implications for therapeutic development and the construction of RNA nanostructures. PMID:26158858

  1. Non-canonical translation in RNA viruses

    PubMed Central

    Brierley, Ian

    2012-01-01

    Viral protein synthesis is completely dependent upon the translational machinery of the host cell. However, many RNA virus transcripts have marked structural differences from cellular mRNAs that preclude canonical translation initiation, such as the absence of a 5′ cap structure or the presence of highly structured 5′UTRs containing replication and/or packaging signals. Furthermore, whilst the great majority of cellular mRNAs are apparently monocistronic, RNA viruses must often express multiple proteins from their mRNAs. In addition, RNA viruses have very compact genomes and are under intense selective pressure to optimize usage of the available sequence space. Together, these features have driven the evolution of a plethora of non-canonical translational mechanisms in RNA viruses that help them to meet these challenges. Here, we review the mechanisms utilized by RNA viruses of eukaryotes, focusing on internal ribosome entry, leaky scanning, non-AUG initiation, ribosome shunting, reinitiation, ribosomal frameshifting and stop-codon readthrough. The review will highlight recently discovered examples of unusual translational strategies, besides revisiting some classical cases. PMID:22535777

  2. International Curriculums.

    ERIC Educational Resources Information Center

    Neal, Larry L.

    This workshop presentation on international curriculums in the field of parks, recreation, leisure, cultural services, and travel/tourism comments that the literature is replete with articles addressing what the field is about, but not about curriculum issues, models, and structure. It reports an international survey of 12 college educators…

  3. An all RNA hypercycle network

    NASA Astrophysics Data System (ADS)

    Vaidya, Nilesh; Lehman, Niles

    The RNA world hypothesis suggests RNA-based catalysis and information storage as the first step in the evolution of life on the Earth. The central process of the RNA world was the replica-tion of RNA, which may have involved the joining of oligonucleotides, perhaps by recombination rather than organization along a linear template. To assist this build-up of information, a hy-percycle may have played a significant role by allowing cooperation between autocatalytic units in a cyclic linkage in such a way that there is a mutual survival and regulated growth of all the units involved (1). Compared to non-coupled self-replicating units, which can only sustain a limited amount of genetic information, the hypercycle allows the maintenance of large amounts of information through cooperation among otherwise competitive units. However, hypercycles have never been empirically demonstrated in the absence of cell-like compartmentalization. In the current work, hypercyclic behavior is demonstrated in the autocatalytic assembly of Azoar-cus group I ribozyme (2). Three different constructs of the Azoarcus ribozyme with different internal guide sequences (IGS) -GUG (canonical), GAG, and GCG -are capable of a min-imal amount of self-assembly when broken into two fragments. Here, self-assembly depends on a mismatch with non-complementary sequences, CGU, CAU and CUU, respectively, to be recognized by IGS via autocatalysis. Yet when all three constructs are present in the same reaction vessel, concomitant assembly of all three is enhanced through an interdependent hy-percyclic reaction network. Analysis of these reactions indicates that each system is capable of guiding its own reproduction weakly, along with providing enhanced catalytic support for the reproduction of one other construct system through matched IGS-tag interactions. Also, when co-incubated with non-interacting (i.e., selfish) yet efficient self-assembly systems, the hypercyclic assembly outcompetes the selfish self

  4. Polyion complex stability and gene silencing efficiency with a siRNA-grafted polymer delivery system.

    PubMed

    Takemoto, Hiroyasu; Ishii, Atsushi; Miyata, Kanjiro; Nakanishi, Masataka; Oba, Makoto; Ishii, Takehiko; Yamasaki, Yuichi; Nishiyama, Nobuhiro; Kataoka, Kazunori

    2010-11-01

    An siRNA-grafted polymer through disulfide linkage was prepared to improve the physicochemical properties and transfection efficacies of the polyion complexes (PICs) as a nanocarrier of siRNA. The siRNA-grafted polymer formed stable PICs due to its larger numbers and higher density of anionic charges compared with monomeric siRNA, leading to effective internalization by cultured cells. Following the endosomal escape of the PIC, the disulfide linkage of the siRNA-grafted polymer allowed efficient siRNA release from the PIC under intracellular reductive conditions. Consequently, the PIC from the siRNA-grafted polymer showed a potent gene silencing effect without cytotoxicity or immunogenicity, demonstrating a promising feature of the siRNA-grafted polymer to construct the PIC-based nanocarrier for in vivo siRNA delivery.

  5. Simultaneous RNA-DNA FISH.

    PubMed

    Lai, Lan-Tian; Meng, Zhenyu; Shao, Fangwei; Zhang, Li-Feng

    2016-01-01

    A highly useful tool for studying lncRNAs is simultaneous RNA-DNA FISH, which reveals the localization and quantitative information of RNA and DNA in cellular contexts. However, a simple combination of RNA FISH and DNA FISH often generates disappointing results because the fragile RNA signals are often damaged by the harsh conditions used in DNA FISH for denaturing the DNA. Here, we describe a robust and simple RNA-DNA FISH protocol, in which amino-labeled nucleic acid probes are used for RNA FISH. The method is suitable to detect single-RNA molecules simultaneously with DNA.

  6. [Progress of RNA interference mechanism].

    PubMed

    Yan, Fei; Cheng, Zhuo-Min

    2005-01-01

    RNA interference (RNAi) is a phenomenon that the double-stranded RNA (dsRNA) intermediates the degradation of complementary mRNA found in many organisms. This is a specifically mechanism involved in kinds of proteins to complete the interference function. Structure of siRNA affects which strand will be assembled into RISC. Another role of siRNA is directing RITS complex to bind with homologue chromosome, and then induces heterochromatinization. Although systemic silence induced by dsRNA is observed in Caenorhabditis elegans and plants, this progress is probably transmembrane protein-dependent, and mostly, the systemic silencing is controlled by multi-factors.

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

    PubMed Central

    Schneider, Britta; Grote, Michael; John, Matthias; Haas, Alexander; Bramlage, Birgit; lckenstein, Ludger M; Jahn-Hofmann, Kerstin; Bauss, Frieder; Cheng, Weijun; Croasdale, Rebecca; Daub, Karin; Dill, Simone; Hoffmann, Eike; Lau, Wilma; Burtscher, Helmut; Ludtke, James L; Metz, Silke; Mundigl, Olaf; Neal, Zane C; Scheuer, Werner; Stracke, Jan; Herweijer, Hans; Brinkmann, Ulrjch

    2012-01-01

    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. PMID:23344238

  8. Systemic Delivery of Anti-miRNA for Suppression of Triple Negative Breast Cancer Utilizing RNA Nanotechnology.

    PubMed

    Shu, Dan; Li, Hui; Shu, Yi; Xiong, Gaofeng; Carson, William E; Haque, Farzin; Xu, Ren; Guo, Peixuan

    2015-10-27

    MicroRNAs play important roles in regulating the gene expression and life cycle of cancer cells. In particular, miR-21, an oncogenic miRNA is a major player involved in tumor initiation, progression, invasion and metastasis in several cancers, including triple negative breast cancer (TNBC). However, delivery of therapeutic miRNA or anti-miRNA specifically into cancer cells in vivo without collateral damage to healthy cells remains challenging. We report here the application of RNA nanotechnology for specific and efficient delivery of anti-miR-21 to block the growth of TNBC in orthotopic mouse models. The 15 nm therapeutic RNA nanoparticles contains the 58-nucleotide (nt) phi29 pRNA-3WJ as a core, a 8-nt sequence complementary to the seed region of miR-21, and a 39-nt epidermal growth factor receptor (EGFR) targeting aptamer for internalizing RNA nanoparticles into cancer cells via receptor mediated endocytosis. The RNase resistant and thermodynamically stable RNA nanoparticles remained intact after systemic injection into mice and strongly bound to tumors with little or no accumulation in healthy organs 8 h postinjection, and subsequently repressed tumor growth at low doses. The observed specific cancer targeting and tumor regression is a result of several key attributes of RNA nanoparticles: anionic charge which disallows nonspecific passage across negatively charged cell membrane; "active" targeting using RNA aptamers which increases the homing of RNA nanoparticles to cancer cells; nanoscale size and shape which avoids rapid renal clearance and engulfment by lung macrophages and liver Kupffer cells; favorable biodistribution profiles with little accumulation in healthy organs, which minimizes nonspecific side effects; and favorable pharmacokinetic profiles with extended in vivo half-life. The results demonstrate the clinical potentials of RNA nanotechnology based platform to deliver miRNA based therapeutics for cancer treatment.

  9. Systemic Delivery of Anti-miRNA for Suppression of Triple Negative Breast Cancer Utilizing RNA Nanotechnology

    PubMed Central

    2015-01-01

    MicroRNAs play important roles in regulating the gene expression and life cycle of cancer cells. In particular, miR-21, an oncogenic miRNA is a major player involved in tumor initiation, progression, invasion and metastasis in several cancers, including triple negative breast cancer (TNBC). However, delivery of therapeutic miRNA or anti-miRNA specifically into cancer cells in vivo without collateral damage to healthy cells remains challenging. We report here the application of RNA nanotechnology for specific and efficient delivery of anti-miR-21 to block the growth of TNBC in orthotopic mouse models. The 15 nm therapeutic RNA nanoparticles contains the 58-nucleotide (nt) phi29 pRNA-3WJ as a core, a 8-nt sequence complementary to the seed region of miR-21, and a 39-nt epidermal growth factor receptor (EGFR) targeting aptamer for internalizing RNA nanoparticles into cancer cells via receptor mediated endocytosis. The RNase resistant and thermodynamically stable RNA nanoparticles remained intact after systemic injection into mice and strongly bound to tumors with little or no accumulation in healthy organs 8 h postinjection, and subsequently repressed tumor growth at low doses. The observed specific cancer targeting and tumor regression is a result of several key attributes of RNA nanoparticles: anionic charge which disallows nonspecific passage across negatively charged cell membrane; “active” targeting using RNA aptamers which increases the homing of RNA nanoparticles to cancer cells; nanoscale size and shape which avoids rapid renal clearance and engulfment by lung macrophages and liver Kupffer cells; favorable biodistribution profiles with little accumulation in healthy organs, which minimizes nonspecific side effects; and favorable pharmacokinetic profiles with extended in vivo half-life. The results demonstrate the clinical potentials of RNA nanotechnology based platform to deliver miRNA based therapeutics for cancer treatment. PMID:26387848

  10. Porous silicon microparticles for delivery of siRNA therapeutics.

    PubMed

    Shen, Jianliang; Wu, Xiaoyan; Lee, Yeonju; Wolfram, Joy; Yang, Zhizhou; Mao, Zong-Wan; Ferrari, Mauro; Shen, Haifa

    2015-01-15

    Small interfering RNA (siRNA) can be used to suppress gene expression, thereby providing a new avenue for the treatment of various diseases. However, the successful implementation of siRNA therapy requires the use of delivery platforms that can overcome the major challenges of siRNA delivery, such as enzymatic degradation, low intracellular uptake and lysosomal entrapment. Here, a protocol for the preparation and use of a biocompatible and effective siRNA delivery system is presented. This platform consists of polyethylenimine (PEI) and arginine (Arg)-grafted porous silicon microparticles, which can be loaded with siRNA by performing a simple mixing step. The silicon particles are gradually degraded over time, thereby triggering the formation of Arg-PEI/siRNA nanoparticles. This delivery vehicle provides a means for protecting and internalizing siRNA, without causing cytotoxicity. The major steps of polycation functionalization, particle characterization, and siRNA loading are outlined in detail. In addition, the procedures for determining particle uptake, cytotoxicity, and transfection efficacy are also described.

  11. Nucleotide sequence of a human tRNA gene heterocluster

    SciTech Connect

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

    1986-05-01

    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'-/sup 32/P)-labeled bovine liver leucine tRNA and total tRNA as hybridization probes. An 8-kb Hind III fragment of one of these ..gamma..-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.

  12. Pyrite footprinting of RNA

    SciTech Connect

    Schlatterer, Joerg C.; Wieder, Matthew S.; Jones, Christopher D.; Pollack, Lois; Brenowitz, Michael

    2012-08-24

    Highlights: Black-Right-Pointing-Pointer RNA structure is mapped by pyrite mediated {sup {center_dot}}OH footprinting. Black-Right-Pointing-Pointer Repetitive experiments can be done in a powdered pyrite filled cartridge. Black-Right-Pointing-Pointer High {sup {center_dot}}OH reactivity of nucleotides imply dynamic role in Diels-Alderase catalysis. -- Abstract: In RNA, function follows form. Mapping the surface of RNA molecules with chemical and enzymatic probes has revealed invaluable information about structure and folding. Hydroxyl radicals ({sup {center_dot}}OH) map the surface of nucleic acids by cutting the backbone where it is accessible to solvent. Recent studies showed that a microfluidic chip containing pyrite (FeS{sub 2}) can produce sufficient {sup {center_dot}}OH to footprint DNA. The 49-nt Diels-Alder RNA enzyme catalyzes the C-C bond formation between a diene and a dienophile. A crystal structure, molecular dynamics simulation and atomic mutagenesis studies suggest that nucleotides of an asymmetric bulge participate in the dynamic architecture of the ribozyme's active center. Of note is that residue U42 directly interacts with the product in the crystallized RNA/product complex. Here, we use powdered pyrite held in a commercially available cartridge to footprint the Diels-Alderase ribozyme with single nucleotide resolution. Residues C39 to U42 are more reactive to {sup {center_dot}}OH than predicted by the solvent accessibility calculated from the crystal structure suggesting that this loop is dynamic in solution. The loop's flexibility may contribute to substrate recruitment and product release. Our implementation of pyrite-mediated {sup {center_dot}}OH footprinting is a readily accessible approach to gleaning information about the architecture of small RNA molecules.

  13. The ribosomal RNA transcription unit of Entamoeba invadens: accumulation of unprocessed pre-rRNA and a long non coding RNA during encystation.

    PubMed

    Ojha, Sandeep; Singh, Nishant; Bhattacharya, Alok; Bhattacharya, Sudha

    2013-01-01

    The ribosomal RNA genes in Entamoeba spp. are located on extrachromosomal circular molecules. Unlike model organisms where rRNA transcription stops during growth stress, Entamoeba histolytica continues transcription; but unprocessed pre-rRNA accumulates during stress, along with a novel class of circular transcripts from the 5'-external transcribed spacer (ETS). To determine the fate of rRNA transcription during stage conversion between trophozoite to cyst we analyzed Entamoeba invadens, a model system for differentiation studies in Entamoeba. We characterized the complete rDNA transcription unit by mapping the ends of pre-rRNA and mature rRNAs. The 3' end of mature 28S rRNA was located 321 nt downstream of the end predicted by sequence homology with E. histolytica. The major processing sites were mapped in external and internal transcribed spacers. The promoter located within 146 nt upstream of 5' ETS was used to transcribe the pre-rRNA. On the other hand, a second promoter located at the 3' end of 28S rDNA was used to transcribe almost the entire intergenic spacer into a long non coding (nc) RNA (>10 kb). Interestingly we found that the levels of pre-rRNA and long ncRNA, measured by northern hybridization, decreased initially in cells shifted to encystation medium, after which they began to increase and reached high levels by 72 h when mature cysts were formed. Unlike E. histolytica, no circular transcripts were found in E. invadens. E. histolytica and E. invadens express fundamentally different ncRNAs from the rDNA locus, which may reflect their adaptation to different hosts (human and reptiles, respectively). This is the first description of rDNA organization and transcription in E. invadens, and provides the framework for further studies on regulation of rRNA synthesis during cyst formation.

  14. RNA editing of microRNA prevents RNA-induced silencing complex recognition of target mRNA

    PubMed Central

    Cui, Yalei; Huang, Tianzhi; Zhang, Xiaobo

    2015-01-01

    MicroRNAs (miRNAs) integrate with Argonaut (Ago) to create the RNA-induced silencing complex, and regulate gene expression by silencing target mRNAs. RNA editing of miRNA may affect miRNA processing, assembly of the Ago complex and target mRNA binding. However, the function of edited miRNA, assembled within the Ago complex, has not been extensively investigated. In this study, sequence analysis of the Ago complex of Marsupenaeus japonicus shrimp infected with white spot syndrome virus (WSSV) revealed that host ADAR (adenosine deaminase acting on RNA) catalysed A-to-I RNA editing of a viral miRNA (WSSV-miR-N12) at the +16 site. This editing of the non-seed sequence did not affect association of the edited miRNA with the Ago protein, but inhibited interaction between the miRNA and its target gene (wsv399). The WSSV early gene wsv399 inhibited WSSV infection. As a result, the RNA editing of miRNA caused virus latency. Our results highlight a novel example of miRNA editing in the miRNA-induced silencing complex. PMID:26674414

  15. RNA editing of microRNA prevents RNA-induced silencing complex recognition of target mRNA.

    PubMed

    Cui, Yalei; Huang, Tianzhi; Zhang, Xiaobo

    2015-12-01

    MicroRNAs (miRNAs) integrate with Argonaut (Ago) to create the RNA-induced silencing complex, and regulate gene expression by silencing target mRNAs. RNA editing of miRNA may affect miRNA processing, assembly of the Ago complex and target mRNA binding. However, the function of edited miRNA, assembled within the Ago complex, has not been extensively investigated. In this study, sequence analysis of the Ago complex of Marsupenaeus japonicus shrimp infected with white spot syndrome virus (WSSV) revealed that host ADAR (adenosine deaminase acting on RNA) catalysed A-to-I RNA editing of a viral miRNA (WSSV-miR-N12) at the +16 site. This editing of the non-seed sequence did not affect association of the edited miRNA with the Ago protein, but inhibited interaction between the miRNA and its target gene (wsv399). The WSSV early gene wsv399 inhibited WSSV infection. As a result, the RNA editing of miRNA caused virus latency. Our results highlight a novel example of miRNA editing in the miRNA-induced silencing complex.

  16. microRNA Therapeutics

    PubMed Central

    Broderick, JA; Zamore, PD

    2011-01-01

    MicroRNAs (miRNAs) provide new therapeutic targets for many diseases, while their myriad roles in development and cellular processes make them fascinating to study. We still do not fully understand the molecular mechanisms by which miRNAs regulate gene expression nor do we know the complete repertoire of mRNAs each miRNA regulates. However, recent progress in the development of effective strategies to block miRNAs suggests that anti-miRNA drugs may soon be used in the clinic. PMID:21525952

  17. International Health

    MedlinePlus

    ... create refugee populations with immediate and long-term health problems. Some of the major diseases currently affecting ... also an international problem which can affect people's health. Many countries and health organizations are working together ...

  18. International Reports.

    ERIC Educational Resources Information Center

    Valauskas, Edward J.; Stowe, Jennifer L.; Haycock, Ken; Dodd, Frances

    1998-01-01

    Presents three reports: International Federation of Library Associations and Institutions; Special Libraries Association; and Canadian library trends, focusing on information technology and access to information and rights and examining provincial libraries and library education. (PEN)

  19. International Geology

    ERIC Educational Resources Information Center

    Hoover, Linn

    1977-01-01

    Briefly discusses recent international programs in various areas of geology, including land-use problems, coping with geological hazards, and conserving the environment while searching for energy and mineral resources. (MLH)

  20. RNA-binding region of Macrobrachium rosenbergii nodavirus capsid protein.

    PubMed

    Goh, Zee Hong; Mohd, Nur Azmina Syakirin; Tan, Soon Guan; Bhassu, Subha; Tan, Wen Siang

    2014-09-01

    White tail disease (WTD) kills prawn larvae and causes drastic losses to the freshwater prawn (Macrobrachium rosenbergii) industry. The main causative agent of WTD is Macrobrachium rosenbergii nodavirus (MrNV). The N-terminal end of the MrNV capsid protein is very rich in positively charged amino acids and is postulated to interact with RNA molecules. N-terminal and internal deletion mutagenesis revealed that the RNA-binding region is located at positions 20-29, where 80 % of amino acids are positively charged. Substitution of all these positively charged residues with alanine abolished the RNA binding. Mutants without the RNA-binding region still assembled into virus-like particles, suggesting that this region is not a part of the capsid assembly domain. This paper is, to the best of our knowledge, the first to report the specific RNA-binding region of MrNV capsid protein. PMID:24878641

  1. RNA-binding region of Macrobrachium rosenbergii nodavirus capsid protein.

    PubMed

    Goh, Zee Hong; Mohd, Nur Azmina Syakirin; Tan, Soon Guan; Bhassu, Subha; Tan, Wen Siang

    2014-09-01

    White tail disease (WTD) kills prawn larvae and causes drastic losses to the freshwater prawn (Macrobrachium rosenbergii) industry. The main causative agent of WTD is Macrobrachium rosenbergii nodavirus (MrNV). The N-terminal end of the MrNV capsid protein is very rich in positively charged amino acids and is postulated to interact with RNA molecules. N-terminal and internal deletion mutagenesis revealed that the RNA-binding region is located at positions 20-29, where 80 % of amino acids are positively charged. Substitution of all these positively charged residues with alanine abolished the RNA binding. Mutants without the RNA-binding region still assembled into virus-like particles, suggesting that this region is not a part of the capsid assembly domain. This paper is, to the best of our knowledge, the first to report the specific RNA-binding region of MrNV capsid protein.

  2. RNA Polymerases of Maize: Nuclear RNA Polymerases*

    PubMed Central

    Strain, Gustave C.; Mullinix, Kathleen P.; Bogorad, Lawrence

    1971-01-01

    Two DNA-dependent RNA polymerases of nuclear origin have been purified from leaves of Zea mays. The two enzymes can be separated on DEAE-cellulose columns. Enzymes I and II are eluted with 0.08 and 0.20 M (NH4)2SO4, respectively. Both enzymes prefer maize nuclear DNA as a template; they are also more active in the presence of Mg++ than Mn++ and are inhibited by (NH4)2-SO4 or KCl. Neither enzyme is inhibited by rifamycin SV. Enzyme II is strongly inhibited by α-amanitin, whereas enzyme I is not significantly affected. Their ability to use native and denatured DNA as templates varies according to the extent and method of purification of the polymerase. Furthermore, enzyme II can be resolved by DEAE-chromatography or glycerol-gradient centrifugation into two components, one of which prefers native DNA, while the other prefers denatured DNA. PMID:5288239

  3. The 5′ RNA Terminus of Spleen Necrosis Virus Stimulates Translation of Nonviral mRNA

    PubMed Central

    Roberts, Tiffiney M.; Boris-Lawrie, Kathleen

    2000-01-01

    The RU5 region at the 5′ RNA terminus of spleen necrosis virus (SNV) has been shown to facilitate expression of human immunodeficiency virus type 1 (HIV) unspliced RNA independently of the Rev-responsive element (RRE) and Rev. The SNV sequences act as a distinct posttranscriptional control element to stimulate gag RNA nuclear export and association with polyribosomes. Here we sought to determine whether RU5 functions to neutralize the cis-acting inhibitory sequences (INSs) in HIV RNA that confer RRE/Rev dependence or functions as an independent stimulatory sequence. Experiments with HIV gag reporter plasmids that contain inactivated INS-1 indicated that neutralization of INSs does not account for RU5 function. Results with luciferase reporter gene (luc) plasmids further indicated that RU5 stimulates expression of a nonretroviral RNA that lacks INSs. Northern blot and RT-PCR analyses indicated that RU5 does not increase the steady-state levels or nuclear export of the luc transcript but rather that the U5 region facilitates efficient polyribosomal association of the mRNA. RU5 does not function as an internal ribosome entry site in bicistronic reporter plasmids, and it requires the 5′-proximal position for efficient function. Our results indicate that RU5 contains stimulatory sequences that function in a 5′-proximal position to enhance initiation of translation of a nonretroviral reporter gene RNA. We speculate that RU5 evolved to overcome the translation-inhibitory effect of the highly structured encapsidation signal and other replication motifs in the 5′ untranslated region of the retroviral RNA. PMID:10933721

  4. [Ribosomal RNA Evolution

    NASA Technical Reports Server (NTRS)

    1997-01-01

    It is generally believed that an RNA World existed at an early stage in the history of life. During this early period, RNA molecules are seen to be potentially involved in both catalysis and the storage of genetic information. Translation presents several interrelated themes of inquiry for exobiology. First, it is essential, for understanding the very origin of life, how peptides and eventually proteins might have come to be made on the early Earth in a template directed manner. Second, it is necessary to understand how a machinery of similar complexity to that found in the ribosomes of modern organisms came to exist by the time of the last common ancestor (as detected by 16S rRNA sequence studies). Third, the ribosomal RNAs themselves likely had a very early origin and studies of their history may be very informative about the nature of the RNA World. Moreover, studies of these RNAs will contribute to a better understanding of the potential roles of RNA in early evolution.During the past year we have ave conducted a comparative study of four completely sequenced bacterial genoames. We have focused initially on conservation of gene order. The second component of the project continues to build on the model system for studying the validity of variant 5S rRNA sequences in the vicinity of the modern Vibrio proteolyticus 5S rRNA that we established earlier. This system has made it possible to conduct a detailed and extensive analysis of a local portion of the sequence space. These core methods have been used to construct numerous mutants during the last several years. Although it has been a secondary focus, this work has continued over the last year such that we now have in excess of 125 V. proteolyticus derived constructs which have been made and characterized. We have also continued high resolution NMR work on RNA oligomers originally initiated by G. Kenneth Smith who was funded by a NASA Graduate Student Researcher's Fellowship Award until May of 1996. Mr. Smith

  5. A Boost for the Emerging Field of RNA Nanotechnology

    PubMed Central

    2011-01-01

    This Nano Focus article highlights recent advances in RNA nanotechnology as presented at the First International Conference of RNA Nanotechnology and Therapeutics, which took place in Cleveland, OH, USA (October 23–25, 2010) (http://www.eng.uc.edu/nanomedicine/RNA2010/), chaired by Peixuan Guo and co-chaired by David Rueda and Scott Tenenbaum. The conference was the first of its kind to bring together more than 30 invited speakers in the frontier of RNA nanotechnology from France, Sweden, South Korea, China, and throughout the United States to discuss RNA nanotechnology and its applications. It provided a platform for researchers from academia, government, and the pharmaceutical industry to share existing knowledge, vision, technology, and challenges in the field and promoted collaborations among researchers interested in advancing this emerging scientific discipline. The meeting covered a range of topics, including biophysical and single-molecule approaches for characterization of RNA nanostructures; structure studies on RNA nanoparticles by chemical or biochemical approaches, computation, prediction, and modeling of RNA nanoparticle structures; methods for the assembly of RNA nanoparticles; chemistry for RNA synthesis, conjugation, and labeling; and application of RNA nanoparticles in therapeutics. A special invited talk on the well-established principles of DNA nanotechnology was arranged to provide models for RNA nanotechnology. An Administrator from National Institutes of Health (NIH) National Cancer Institute (NCI) Alliance for Nanotechnology in Cancer discussed the current nanocancer research directions and future funding opportunities at NCI. As indicated by the feedback received from the invited speakers and the meeting participants, this meeting was extremely successful, exciting, and informative, covering many groundbreaking findings, pioneering ideas, and novel discoveries. PMID:21604810

  6. Molecular Beacon-Based MicroRNA Imaging During Neurogenesis.

    PubMed

    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.

  7. RNA antisense purification (RAP) for mapping RNA interactions with chromatin.

    PubMed

    Engreitz, Jesse; Lander, Eric S; Guttman, Mitchell

    2015-01-01

    RNA-centric biochemical purification is a general approach for studying the functions and mechanisms of noncoding RNAs. Here, we describe the experimental procedures for RNA antisense purification (RAP), a method for selective purification of endogenous RNA complexes from cell extracts that enables mapping of RNA interactions with chromatin. In RAP, the user cross-links cells to fix endogenous RNA complexes and purifies these complexes through hybrid capture with biotinylated antisense oligos. DNA loci that interact with the target RNA are identified using high-throughput DNA sequencing.

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

    PubMed

    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.

  9. Differential regulation of plastid mRNA stability. Progress report

    SciTech Connect

    Stern, D.B.

    1993-09-01

    Our goal is to identify cis-acting sequences and transacting factors that function in plastid mRNA maturation, stabilization, and/or decay through an in vitro and in vivo analysis of mRNA:protein interactions. Our previous results emphasized the study of 3{prime}end inverted repeat sequences (IRs) that serve both as mRNA processing elements and stability determinants, and associate with plastid proteins that potentially play enzymatic, structural and/or regulatory roles. We seek to define, by single base and internal deletion mutagenesis, the sequence and structural requirements for protein binding to the 3{prime} IRs of petD and psbA mRNAs; to purify RNA-binding proteins that demonstrate gene- or sequence-specific binding, or that are implicated in RNA stabilization or decay; and to investigate the native form of mRNA in the plastid, by attempting to purify ribonucleoprotein (RNP) particles from organelles. Our view of mRNA decay is that it is regulated by three interactive components: RNA structure, ribonucleases and RNA-binding proteins. We have used mutagenesis to study the role of RNA structure in regulating RNA decay rates, and to identify protein binding and endonuclease recognition sites. We have identified at least three endonuclease activities; one that cleaves psbA RNA; and two whose cleavage patterns with petD 3{prime} IR-RNA has been studied (endoC1 and endoC2). Additionally, we have continued to analyze the properties of the major RNA processing exoribonuclease. We have concentrated our efforts on three RNA-binding proteins. A 100 kd protein with properties suggestive of a mammalian RNP component has been purified. A protein of 55 kd that may also be an endonuclease has been partially purified. We have studied the interaction of a 29 kd protein with the petD stem/loop, and its role in RNA processing. Recently, we have used a novel gel shift/SDS-PAGE technique to identify new RNA-binding proteins.

  10. Shaping tRNA

    ERIC Educational Resources Information Center

    Priano, Christine

    2013-01-01

    This model-building activity provides a quick, visual, hands-on tool that allows students to examine more carefully the cloverleaf structure of a typical tRNA molecule. When used as a supplement to lessons that involve gene expression, this exercise reinforces several concepts in molecular genetics, including nucleotide base-pairing rules, the…

  11. RNA extraction from cereal vegetative tissue.

    PubMed

    Pattemore, Julie A

    2014-01-01

    Ribonucleic acid (RNA) extraction is the necessary first step in many protocols, primarily to investigate genes and gene expression. RNA comes in a variety of forms: total RNA, ribosomal RNA, messenger RNA (mRNA), and small interfering RNA (siRNA) to name a few. In some instances, total RNA is all that is required; however most applications will require the enrichment for some particular form of RNA. In plants, including cereals, total RNA is a mixture of many types of RNA and enrichment is generally required. In this protocol, the TRIzol(®) method of RNA extraction from cereal leaf material is described, as it is a relatively simple technique.

  12. Messenger RNA (mRNA) nanoparticle tumour vaccination

    NASA Astrophysics Data System (ADS)

    Phua, Kyle K. L.; Nair, Smita K.; Leong, Kam W.

    2014-06-01

    Use of mRNA-based vaccines for tumour immunotherapy has gained increasing attention in recent years. A growing number of studies applying nanomedicine concepts to mRNA tumour vaccination show that the mRNA delivered in nanoparticle format can generate a more robust immune response. Advances in the past decade have deepened our understanding of gene delivery barriers, mRNA's biological stability and immunological properties, and support the notion for engineering innovations tailored towards a more efficient mRNA nanoparticle vaccine delivery system. In this review we will first examine the suitability of mRNA for engineering manipulations, followed by discussion of a model framework that highlights the barriers to a robust anti-tumour immunity mediated by mRNA encapsulated in nanoparticles. Finally, by consolidating existing literature on mRNA nanoparticle tumour vaccination within the context of this framework, we aim to identify bottlenecks that can be addressed by future nanoengineering research.

  13. RNA-catalysed synthesis of complementary-strand RNA

    NASA Astrophysics Data System (ADS)

    Doudna, Jennifer A.; Szostak, Jack W.

    1989-06-01

    The Tetrahymena ribozyme can splice together multiple oligonucleotides aligned on a template strand to yield a fully complementary product strand. This reaction demonstrates the feasibility of RNA-catalysed RNA replications.

  14. A Grammatical Approach to RNA-RNA Interaction Prediction

    NASA Astrophysics Data System (ADS)

    Kato, Yuki; Akutsu, Tatsuya; Seki, Hiroyuki

    2007-11-01

    Much attention has been paid to two interacting RNA molecules involved in post-transcriptional control of gene expression. Although there have been a few studies on RNA-RNA interaction prediction based on dynamic programming algorithm, no grammar-based approach has been proposed. The purpose of this paper is to provide a new modeling for RNA-RNA interaction based on multiple context-free grammar (MCFG). We present a polynomial time parsing algorithm for finding the most likely derivation tree for the stochastic version of MCFG, which is applicable to RNA joint secondary structure prediction including kissing hairpin loops. Also, elementary tests on RNA-RNA interaction prediction have shown that the proposed method is comparable to Alkan et al.'s method.

  15. Assessment of groundwater, soil-gas, and soil contamination at the Vietnam Armor Training Facility, Fort Gordon, Georgia, 2009-2011

    USGS Publications Warehouse

    Guimaraes, Wladmir B.; Falls, W. Fred; Caldwell, Andral W.; Ratliff, W. Hagan; Wellborn, John B.; Landmeyer, James E.

    2012-01-01

    The U.S. Geological Survey, in cooperation with the U.S. Department of the Army Environmental and Natural Resources Management Office of the U.S. Army Signal Center and Fort Gordon, Georgia, assessed the groundwater, soil gas, and soil for contaminants at the Vietnam Armor Training Facility (VATF) at Fort Gordon, from October 2009 to September 2011. The assessment included the detection of organic compounds in the groundwater and soil gas, and inorganic compounds in the soil. In addition, organic contaminant assessment included organic compounds classified as explosives and chemical agents in selected areas. The assessment was conducted to provide environmental contamination data to the U.S. Army at Fort Gordon pursuant to requirements of the Resource Conservation and Recovery Act Part B Hazardous Waste Permit process. This report is a revision of "Assessment of soil-gas, surface-water, and soil contamination at the Vietnam Armor Training Facility, Fort Gordon, Georgia, 2009-2010," Open-File Report 2011-1200, and supersedes that report to include results of additional samples collected in July 2011. Four passive samplers were deployed in groundwater wells at the VATF in Fort Gordon. Total petroleum hydrocarbons and benzene and octane were detected above the method detection level at all four wells. The only other volatile organic compounds detected above their method detection level were undecane and pentadecane, which were detected in two of the four wells. Soil-gas samplers were deployed at 72 locations in a grid pattern across the VATF on June 3, 2010, and then later retrieved on June 9, 2010. Total petroleum hydrocarbons were detected in 71 of the 72 samplers (one sampler was destroyed in the field and not analyzed) at levels above the method detection level, and the combined mass of benzene, toluene, ethylbenzene, and total xylene (BTEX) was detected above the detection level in 31 of the 71 samplers that were analyzed. Other volatile organic compounds

  16. Assessment of groundwater, soil-gas, and soil contamination at the Vietnam Armor Training Facility, Fort Gordon, Georgia, 2009-2011

    USGS Publications Warehouse

    Guimaraes, Wladmir B.; Falls, W. Fred; Caldwell, Andral W.; Ratliff, W. Hagan; Wellborn, John B.; Landmeyer, James E.

    2012-01-01

    The U.S. Geological Survey, in cooperation with the U.S. Department of the Army Environmental and Natural Resources Management Office of the U.S. Army Signal Center and Fort Gordon, Georgia, assessed the groundwater, soil gas, and soil for contaminants at the Vietnam Armor Training Facility (VATF) at Fort Gordon, from October 2009 to September 2011. The assessment included the detection of organic compounds in the groundwater and soil gas, and inorganic compounds in the soil. In addition, organic contaminant assessment included organic compounds classified as explosives and chemical agents in selected areas. The assessment was conducted to provide environmental contamination data to the U.S. Army at Fort Gordon pursuant to requirements of the Resource Conservation and Recovery Act Part B Hazardous Waste Permit process. This report is a revision of "Assessment of soil-gas, surface-water, and soil contamination at the Vietnam Armor Training Facility, Fort Gordon, Georgia, 2009-2010," Open-File Report 2011-1200, and supersedes that report to include results of additional samples collected in July 2011. Four passive samplers were deployed in groundwater wells at the VATF in Fort Gordon. Total petroleum hydrocarbons and benzene and octane were detected above the method detection level at all four wells. The only other volatile organic compounds detected above their method detection level were undecane and pentadecane, which were detected in two of the four wells. Soil-gas samplers were deployed at 72 locations in a grid pattern across the VATF on June 3, 2010, and then later retrieved on June 9, 2010. Total petroleum hydrocarbons were detected in 71 of the 72 samplers (one sampler was destroyed in the field and not analyzed) at levels above the method detection level, and the combined mass of benzene, toluene, ethylbenzene, and total xylene (BTEX) was detected above the detection level in 31 of the 71 samplers that were analyzed. Other volatile organic compounds

  17. Mammalian synthetic circuits with RNA binding proteins delivered by RNA

    PubMed Central

    Wroblewska, Liliana; Kitada, Tasuku; Endo, Kei; Siciliano, Velia; Stillo, Breanna; Saito, Hirohide; Weiss, Ron

    2015-01-01

    Synthetic regulatory circuits encoded on RNA rather than DNA could provide a means to control cell behavior while avoiding potentially harmful genomic integration in therapeutic applications. We create post-transcriptional circuits using RNA-binding proteins, which can be wired in a plug-and-play fashion to create networks of higher complexity. We show that the circuits function in mammalian cells when encoded on modified mRNA or self-replicating RNA. PMID:26237515

  18. Internal shim

    DOEpatents

    Barth, Clyde H.; Blizinski, Theodore W.

    2003-05-13

    An internal shim used to accurately measure spaces in conjunction with a standard small probe has a shim top and a chassis. The internal shim is adjustably fixed within the space to be measured using grippers that emerge from the chassis and which are controlled by an arm pivotably attached to the shim top. A standard small probe passes through the shim along guides on the chassis and measures the distance between the exterior of the chassis and the boundary. By summing the measurements on each side of the chassis and the width of the chassis, the dimension of the space can be determined to within 0.001 inches.

  19. LigandRNA: computational predictor of RNA-ligand interactions.

    PubMed

    Philips, Anna; Milanowska, Kaja; Lach, Grzegorz; Bujnicki, Janusz M

    2013-12-01

    RNA molecules have recently become attractive as potential drug targets due to the increased awareness of their importance in key biological processes. The increase of the number of experimentally determined RNA 3D structures enabled structure-based searches for small molecules that can specifically bind to defined sites in RNA molecules, thereby blocking or otherwise modulating their function. However, as of yet, computational methods for structure-based docking of small molecule ligands to RNA molecules are not as well established as analogous methods for protein-ligand docking. This motivated us to create LigandRNA, a scoring function for the prediction of RNA-small molecule interactions. Our method employs a grid-based algorithm and a knowledge-based potential derived from ligand-binding sites in the experimentally solved RNA-ligand complexes. As an input, LigandRNA takes an RNA receptor file and a file with ligand poses. As an output, it returns a ranking of the poses according to their score. The predictive power of LigandRNA favorably compares to five other publicly available methods. We found that the combination of LigandRNA and Dock6 into a "meta-predictor" leads to further improvement in the identification of near-native ligand poses. The LigandRNA program is available free of charge as a web server at http://ligandrna.genesilico.pl.

  20. RNA-RNA interaction prediction using genetic algorithm

    PubMed Central

    2014-01-01

    Background RNA-RNA interaction plays an important role in the regulation of gene expression and cell development. In this process, an RNA molecule prohibits the translation of another RNA molecule by establishing stable interactions with it. In the RNA-RNA interaction prediction problem, two RNA sequences are given as inputs and the goal is to find the optimal secondary structure of two RNAs and between them. Some different algorithms have been proposed to predict RNA-RNA interaction structure. However, most of them suffer from high computational time. Results In this paper, we introduce a novel genetic algorithm called GRNAs to predict the RNA-RNA interaction. The proposed algorithm is performed on some standard datasets with appropriate accuracy and lower time complexity in comparison to the other state-of-the-art algorithms. In the proposed algorithm, each individual is a secondary structure of two interacting RNAs. The minimum free energy is considered as a fitness function for each individual. In each generation, the algorithm is converged to find the optimal secondary structure (minimum free energy structure) of two interacting RNAs by using crossover and mutation operations. Conclusions This algorithm is properly employed for joint secondary structure prediction. The results achieved on a set of known interacting RNA pairs are compared with the other related algorithms and the effectiveness and validity of the proposed algorithm have been demonstrated. It has been shown that time complexity of the algorithm in each iteration is as efficient as the other approaches. PMID:25114714

  1. RNA binding specificity of Ebola virus transcription factor VP30.

    PubMed

    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. PMID:27315567

  2. lncRNA-RNA Interactions across the Human Transcriptome.

    PubMed

    Szcześniak, Michał Wojciech; Makałowska, Izabela

    2016-01-01

    Long non-coding RNAs (lncRNAs) represent a numerous class of non-protein coding transcripts longer than 200 nucleotides. There is possibility that a fraction of lncRNAs are not functional and represent mere transcriptional noise but a growing body of evidence shows they are engaged in a plethora of molecular functions and contribute considerably to the observed diversification of eukaryotic transcriptomes and proteomes. Still, however, only ca. 1% of lncRNAs have well established functions and much remains to be done towards decipherment of their biological roles. One of the least studied aspects of lncRNAs biology is their engagement in gene expression regulation through RNA-RNA interactions. By hybridizing with mate RNA molecules, lncRNAs could potentially participate in modulation of pre-mRNA splicing, RNA editing, mRNA stability control, translation activation, or abrogation of miRNA-induced repression. Here, we implemented a similarity-search based method for transcriptome-wide identification of RNA-RNA interactions, which enabled us to find 18,871,097 lncRNA-RNA base-pairings in human. Further analyses showed that the interactions could be involved in processing, stability control and functions of 57,303 transcripts. An extensive use of RNA-Seq data provided support for approximately one third of the interactions, at least in terms of the two RNA components being co-expressed. The results suggest that lncRNA-RNA interactions are broadly used to regulate and diversify the human transcriptome.

  3. lncRNA-RNA Interactions across the Human Transcriptome

    PubMed Central

    Szcześniak, Michał Wojciech; Makałowska, Izabela

    2016-01-01

    Long non-coding RNAs (lncRNAs) represent a numerous class of non-protein coding transcripts longer than 200 nucleotides. There is possibility that a fraction of lncRNAs are not functional and represent mere transcriptional noise but a growing body of evidence shows they are engaged in a plethora of molecular functions and contribute considerably to the observed diversification of eukaryotic transcriptomes and proteomes. Still, however, only ca. 1% of lncRNAs have well established functions and much remains to be done towards decipherment of their biological roles. One of the least studied aspects of lncRNAs biology is their engagement in gene expression regulation through RNA-RNA interactions. By hybridizing with mate RNA molecules, lncRNAs could potentially participate in modulation of pre-mRNA splicing, RNA editing, mRNA stability control, translation activation, or abrogation of miRNA-induced repression. Here, we implemented a similarity-search based method for transcriptome-wide identification of RNA-RNA interactions, which enabled us to find 18,871,097 lncRNA-RNA base-pairings in human. Further analyses showed that the interactions could be involved in processing, stability control and functions of 57,303 transcripts. An extensive use of RNA-Seq data provided support for approximately one third of the interactions, at least in terms of the two RNA components being co-expressed. The results suggest that lncRNA-RNA interactions are broadly used to regulate and diversify the human transcriptome. PMID:26930590

  4. International Reports.

    ERIC Educational Resources Information Center

    Anderson, Nancy D.; And Others

    1994-01-01

    Three reports discuss the International Federation of Library Associations and Institutions; the Frankfurt Book Fair, focusing on electronics; and Canadian library trends, including resource sharing, technology projects, information policy, censorship, services for persons with disabilities, construction projects, and library education and…

  5. International Marketplace.

    ERIC Educational Resources Information Center

    Wells, Donald A.; And Others

    1985-01-01

    This issue begins with a conceptual introduction to economic specialization, exports and imports, and the importance of international trade. Four instructional units follow this introduction, beginning with a preschool and kindergarten unit called "Traders and Travelers," which involves young students in five activities that illustrate our…

  6. rrnDB: documenting the number of rRNA and tRNA genes in bacteria and archaea.

    PubMed

    Lee, Zarraz May-Ping; Bussema, Carl; Schmidt, Thomas M

    2009-01-01

    A dramatic exception to the general pattern of single-copy genes in bacterial and archaeal genomes is the presence of 1-15 copies of each ribosomal RNA encoding gene. The original version of the Ribosomal RNA Database (rrnDB) cataloged estimates of the number of 16S rRNA-encoding genes; the database now includes the number of genes encoding each of the rRNAs (5S, 16S and 23S), an internally transcribed spacer region, and the number of tRNA genes. The rrnDB has been used largely by microbiologists to predict the relative rate at which microbial populations respond to favorable growth conditions, and to interpret 16S rRNA-based surveys of microbial communities. To expand the functionality of the rrnDB (http://ribosome.mmg.msu.edu/rrndb/index.php), the search engine has been redesigned to allow database searches based on 16S rRNA gene copy number, specific organisms or taxonomic subsets of organisms. The revamped database also computes average gene copy numbers for any collection of entries selected. Curation tools now permit rapid updates, resulting in an expansion of the database to include data for 785 bacterial and 69 archaeal strains. The rrnDB continues to serve as the authoritative, curated source that documents the phylogenetic distribution of rRNA and tRNA genes in microbial genomes.

  7. Responsible Body Armor Possession Act

    THOMAS, 113th Congress

    Rep. Honda, Michael M. [D-CA-17

    2014-07-31

    09/26/2014 Referred to the Subcommittee on Crime, Terrorism, Homeland Security, and Investigations. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

  8. Passive Cooling of Body Armor

    NASA Astrophysics Data System (ADS)

    Holtz, Ronald; Matic, Peter; Mott, David

    2013-03-01

    Warfighter performance can be adversely affected by heat load and weight of equipment. Current tactical vest designs are good insulators and lack ventilation, thus do not provide effective management of metabolic heat generated. NRL has undertaken a systematic study of tactical vest thermal management, leading to physics-based strategies that provide improved cooling without undesirable consequences such as added weight, added electrical power requirements, or compromised protection. The approach is based on evaporative cooling of sweat produced by the wearer of the vest, in an air flow provided by ambient wind or ambulatory motion of the wearer. Using an approach including thermodynamic analysis, computational fluid dynamics modeling, air flow measurements of model ventilated vest architectures, and studies of the influence of fabric aerodynamic drag characteristics, materials and geometry were identified that optimize passive cooling of tactical vests. Specific architectural features of the vest design allow for optimal ventilation patterns, and selection of fabrics for vest construction optimize evaporation rates while reducing air flow resistance. Cooling rates consistent with the theoretical and modeling predictions were verified experimentally for 3D mockups.

  9. A miRNA-tRNA mix-up: tRNA origin of proposed miRNA.

    PubMed

    Schopman, Nick C T; Heynen, Stephan; Haasnoot, Joost; Berkhout, Ben

    2010-01-01

    The rapid release of new data from DNA genome sequencing projects has led to a variety of misannotations in public databases. Our results suggest that next generation sequencing approaches are particularly prone to such misannotations. Two related miRNA candidates did recently enter the miRBase database, miR-1274b and miR-1274a, but they share identical 18-nucleotide stretches with tRNA (Lys3) and tRNA (Lys5) , respectively. The possibility that the small RNA fragments that led to the description of these two miRNAs originated from the two tRNAs was examined. The ratio of the miR-1274b:miR-1274a fragments does closely resemble the known tRNA lys3:lys5 ratio in the cell. Furthermore, the proposed miRNA hairpins have a very low prediction score and the proposed miRNA genes are in fact endogenous retroviral elements. We searched for other miRNA-mimics in the human genome and found more examples of tRNA-miRNA mimicry. We propose that the corresponding miRNAs should be validated in more detail, as the small RNA fragments that led to their description are likely derived from tRNA processing. PMID:20818168

  10. Amplification of RNA by an RNA polymerase ribozyme.

    PubMed

    Horning, David P; Joyce, Gerald F

    2016-08-30

    In all extant life, genetic information is stored in nucleic acids that are replicated by polymerase proteins. In the hypothesized RNA world, before the evolution of genetically encoded proteins, ancestral organisms contained RNA genes that were replicated by an RNA polymerase ribozyme. In an effort toward reconstructing RNA-based life in the laboratory, in vitro evolution was used to improve dramatically the activity and generality of an RNA polymerase ribozyme by selecting variants that can synthesize functional RNA molecules from an RNA template. The improved polymerase ribozyme is able to synthesize a variety of complex structured RNAs, including aptamers, ribozymes, and, in low yield, even tRNA. Furthermore, the polymerase can replicate nucleic acids, amplifying short RNA templates by more than 10,000-fold in an RNA-catalyzed form of the PCR. Thus, the two prerequisites of Darwinian life-the replication of genetic information and its conversion into functional molecules-can now be accomplished with RNA in the complete absence of proteins. PMID:27528667

  11. RNA-SSPT: RNA Secondary Structure Prediction Tools.

    PubMed

    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. PMID:24250115

  12. Current Progress of RNA Aptamer-Based Therapeutics

    PubMed Central

    Zhou, Jiehua; Bobbin, Maggie L.; Burnett, John C.; Rossi, John J.

    2012-01-01

    Aptamers are single-stranded nucleic acids that specifically recognize and bind tightly to their cognate targets due to their stable three-dimensional structure. Nucleic acid aptamers have been developed for various applications, including diagnostics, molecular imaging, biomarker discovery, target validation, therapeutics, and drug delivery. Due to their high specificity and binding affinity, aptamers directly block or interrupt the functions of target proteins making them promising therapeutic agents for the treatment of human maladies. Additionally, aptamers that bind to cell surface proteins are well suited for the targeted delivery of other therapeutics, such as conjugated small interfering RNAs (siRNA) that induce RNA interference (RNAi). Thus, aptamer-siRNA chimeras may offer dual-functions, in which the aptamer inhibits a receptor function, while the siRNA internalizes into the cell to target a specific mRNA. This review focuses on the current progress and therapeutic potential of RNA aptamers, including the use of cell-internalizing aptamers as cell-type specific delivery vehicles for targeted RNAi. In particular, we discuss emerging aptamer-based therapeutics that provide unique clinical opportunities for the treatment various cancers and neurological diseases. PMID:23130020

  13. Human polypyrimidine tract-binding protein interacts with mitochondrial tRNA(Thr) in the cytosol.

    PubMed

    Marnef, Aline; Jády, Beáta E; Kiss, Tamás

    2016-02-18

    Human polypyrimidine tract-binding protein PTB is a multifunctional RNA-binding protein with four RNA recognition motifs (RRM1 to RRM4). PTB is a nucleocytoplasmic shuttle protein that functions as a key regulator of alternative pre-mRNA splicing in the nucleoplasm and promotes internal ribosome entry site-mediated translation initiation of viral and cellular mRNAs in the cytoplasm. Here, we demonstrate that PTB and its paralogs, nPTB and ROD1, specifically interact with mitochondrial (mt) tRNA(Thr) both in human and mouse cells. In vivo and in vitro RNA-binding experiments demonstrate that PTB forms a direct interaction with the T-loop and the D-stem-loop of mt tRNA(Thr) using its N-terminal RRM1 and RRM2 motifs. RNA sequencing and cell fractionation experiments show that PTB associates with correctly processed and internally modified, mature mt tRNA(Thr) in the cytoplasm outside of mitochondria. Consistent with this, PTB activity is not required for mt tRNA(Thr) biogenesis or for correct mitochondrial protein synthesis. PTB association with mt tRNA(Thr) is largely increased upon induction of apoptosis, arguing for a potential role of the mt tRNA(Thr)/PTB complex in apoptosis. Our results lend strong support to the recently emerging conception that human mt tRNAs can participate in novel cytoplasmic processes independent from mitochondrial protein synthesis. PMID:26657638

  14. Teaching International Law: Concepts in International Relations

    ERIC Educational Resources Information Center

    Starbird, Caroline; Pettit, Jenny; Singleton, Laurel

    2004-01-01

    This book is designed to introduce students to public international law. Topics covered include international public organizations, such as the United Nations and World Trade Organization, international courts, international human rights law, international trade law, and international environmental law. The goal of each study is to examine how…

  15. Assessment of groundwater, soil-gas, and soil contamination at the Vietnam Armor Training Facility, Fort Gordon, Georgia, 2009-2010

    USGS Publications Warehouse

    Guimaraes, Wladmir B.; Falls, W. Fred; Caldwell, Andral W.; Ratliff, W. Hagan; Wellborn, John B.; Landmeyer, James E.

    2011-01-01

    The U.S. Geological Survey, in cooperation with the U.S. Department of the Army Environmental and Natural Resources Management Office of the U.S. Army Signal Center and Fort Gordon, Georgia, assessed the groundwater, soil gas, and soil for contaminants at the Vietnam Armor Training Facility (VATF) at Fort Gordon, from October 2009 to September 2010. The assessment included the detection of organic compounds in the groundwater and soil gas, and inorganic compounds in the soil. In addition, organic contaminant assessment included organic compounds classified as explosives and chemical agents in selected areas. The assessment was conducted to provide environmental contamination data to the U.S. Army at Fort Gordon pursuant to requirements of the Resource Conservation and Recovery Act Part B Hazardous Waste Permit process. Four passive samplers were deployed in groundwater wells at the VATF in Fort Gordon. Total petroleum hydrocarbons were detected above the method detection level at all four wells. The only other volatile organic compounds detected above their method detection level were undecane and pentadecane, which were detected in two of the four wells sampled. Soil-gas samplers were deployed at 72 locations in a grid pattern across the VATF. Total petroleum hydrocarbons were detected in 71 of the 72 samplers (one sampler was destroyed in the field and not analyzed) at levels above the method detection level, and the combined mass of benzene, toluene, ethylbenzene, and total xylene was detected above the detection level in 31 of the 71 samplers that were analyzed. Other volatile organic compounds detected above their respective method detection levels were naphthalene, 2-methyl-naphthalene, tridecane, 1,2,4-trimethylbenzene, and perchloroethene. Subsequent to the soil-gas survey, four areas determined to have elevated contaminant mass were selected and sampled for explosives and chemical agents. No detections of explosives or chemical agents above their

  16. Healthcare international.

    PubMed

    Hensley, S; Jaklevic, M C; Rauber, C; Weissenstein, E; Moore, J D; Shinkman, R; Pallarito, K; Katzman, C N; Hallam, K; Morrissey, J

    1998-11-01

    How people are treated when they need medical care depends on where in the world they are. In deciding which tools of the medical trade are used to treat disease and when they're used, location is paramount. A country's social policy, healthcare payment systems and cultural factors bear heavily on the utilization of medical technology. The cover story kicks off the magazine's third international healthcare section. PMID:10186352

  17. Rotary International.

    PubMed

    Young, Janis

    2008-01-01

    Rotary International is the oldest United States service organization and one of the largest volunteer groups in the world. There are hundreds of educational, health, and humanitarian activities, almost all of which are conducted locally in order to ensure that Rotary clubs meet the needs of the communities they serve. Club membership requires regular active participation and offers Rotarians multiple opportunities for involvement. PMID:18551844

  18. International cooperation.

    PubMed

    1999-04-01

    As the most densely populated country in the world, China actively conducts international exchanges and cooperation. It takes every opportunity to publicize its family planning policies and practices during international forums. Moreover, the country's State Family Planning Commission has been collaborating with the United Nations Population Fund in implementing health and family planning programs. This program covers public awareness campaigns, technical services, sex education for the youth, and social marketing. For years, China has also been cooperating with WHO in the area of family planning and reproductive health, and has established partnership with the Japanese Organization for International Cooperation in Family Planning. In addition, the State Family Planning Commission has worked with the Public Media Center of the US as well as with the Rockefeller Foundation and Ford Foundation in introducing "contraceptive methods by informed choice" and "male participation in family planning" in the rural areas of the country. China has also worked closely with many other developing countries on population issues. In October 1998, China collaborated with the Partners in Population and Development for a reporting mission that was attended by journalists from 11 countries.

  19. The tmRNA website

    DOE PAGES

    Hudson, Corey M.; Williams, Kelly P.

    2014-11-05

    We report that the transfer-messenger RNA (tmRNA) and its partner protein SmpB act together in resolving problems arising when translating bacterial ribosomes reach the end of mRNA with no stop codon. Their genes have been found in nearly all bacterial genomes and in some organelles. The tmRNA Website serves tmRNA sequences, alignments and feature annotations, and has recently moved to http: //bioinformatics.sandia.gov/tmrna/. New features include software used to find the sequences, an update raising the number of unique tmRNA sequences from 492 to 1716, and a database of SmpB sequences which are served along with the tmRNA sequence from themore » same organism.« less

  20. The tmRNA website

    SciTech Connect

    Hudson, Corey M.; Williams, Kelly P.

    2014-11-05

    We report that the transfer-messenger RNA (tmRNA) and its partner protein SmpB act together in resolving problems arising when translating bacterial ribosomes reach the end of mRNA with no stop codon. Their genes have been found in nearly all bacterial genomes and in some organelles. The tmRNA Website serves tmRNA sequences, alignments and feature annotations, and has recently moved to http: //bioinformatics.sandia.gov/tmrna/. New features include software used to find the sequences, an update raising the number of unique tmRNA sequences from 492 to 1716, and a database of SmpB sequences which are served along with the tmRNA sequence from the same organism.

  1. Flavivirus RNA synthesis in vitro.

    PubMed

    Padmanabhan, Radhakrishnan; Takhampunya, Ratree; Teramoto, Tadahisa; Choi, Kyung H

    2015-12-01

    Establishment of in vitro systems to study mechanisms of RNA synthesis for positive strand RNA viruses have been very useful in the past and have shed light on the composition of protein and RNA components, optimum conditions, the nature of the products formed, cis-acting RNA elements and trans-acting protein factors required for efficient synthesis. In this review, we summarize our current understanding regarding the requirements for flavivirus RNA synthesis in vitro. We describe details of reaction conditions, the specificity of template used by either the multi-component membrane-bound viral replicase complex or by purified, recombinant RNA-dependent RNA polymerase. We also discuss future perspectives to extend the boundaries of our knowledge. PMID:26272247

  2. The tmRNA website.

    PubMed

    Hudson, Corey M; Williams, Kelly P

    2015-01-01

    The transfer-messenger RNA (tmRNA) and its partner protein SmpB act together in resolving problems arising when translating bacterial ribosomes reach the end of mRNA with no stop codon. Their genes have been found in nearly all bacterial genomes and in some organelles. The tmRNA Website serves tmRNA sequences, alignments and feature annotations, and has recently moved to http://bioinformatics.sandia.gov/tmrna/. New features include software used to find the sequences, an update raising the number of unique tmRNA sequences from 492 to 1716, and a database of SmpB sequences which are served along with the tmRNA sequence from the same organism.

  3. [Internal migration].

    PubMed

    Borisovna, L

    1991-06-01

    Very few studies have been conducted that truly permit explanation of internal migration and it repercussions on social and economic structure. It is clear however that a profound knowledge of the determinants and consequences of internal migration will be required as a basis for economic policy decisions that advance the goal of improving the level of living of the population. the basic supposition of most studies of the relationship of population and development is that socioeconomic development conditions demographic dynamics. The process of development in Mexico, which can be characterized by great heterogeneity, consequently produces great regional disparities. At the national level various studies have estimated the volume of internal migration in Mexico, but they have usually been limited to interstate migration because the main source of data, the census, is classified by states. But given the great heterogeneity within states in all the elements related to internal migration, it is clear that studies of internal migration within states are also needed. Such studies are almost nonexistent because of their technical difficulty. National level studies show that interstate migration increased significantly between 1940-80. The proportion of Mexicans living outside their states of birth increased by 558% in those years, compared to the 342% increase in the total Mexican population. Although Puebla has a high rate of increase, migration has kept it below Mexico's national growth rate. Migration between Puebla and other states and within Puebla has led to an increasing unevenness of spatial distribution. Between 1970-80, 57 of Puebla's municipios had growth rates above the state average of 2.8%/year, 6 had growth rates equal to the average, and 129 had growth rates that were below the average but not negative. 25 states with negative growth rates that were considered strongly expulsive. In 1980, 51.7% of the population was concentrated in the 57 municipios

  4. Computational biology of RNA interactions.

    PubMed

    Dieterich, Christoph; Stadler, Peter F

    2013-01-01

    The biodiversity of the RNA world has been underestimated for decades. RNA molecules are key building blocks, sensors, and regulators of modern cells. The biological function of RNA molecules cannot be separated from their ability to bind to and interact with a wide space of chemical species, including small molecules, nucleic acids, and proteins. Computational chemists, physicists, and biologists have developed a rich tool set for modeling and predicting RNA interactions. These interactions are to some extent determined by the binding conformation of the RNA molecule. RNA binding conformations are approximated with often acceptable accuracy by sequence and secondary structure motifs. Secondary structure ensembles of a given RNA molecule can be efficiently computed in many relevant situations by employing a standard energy model for base pair interactions and dynamic programming techniques. The case of bi-molecular RNA-RNA interactions can be seen as an extension of this approach. However, unbiased transcriptome-wide scans for local RNA-RNA interactions are computationally challenging yet become efficient if the binding motif/mode is known and other external information can be used to confine the search space. Computational methods are less developed for proteins and small molecules, which bind to RNA with very high specificity. Binding descriptors of proteins are usually determined by in vitro high-throughput assays (e.g., microarrays or sequencing). Intriguingly, recent experimental advances, which are mostly based on light-induced cross-linking of binding partners, render in vivo binding patterns accessible yet require new computational methods for careful data interpretation. The grand challenge is to model the in vivo situation where a complex interplay of RNA binders competes for the same target RNA molecule. Evidently, bioinformaticians are just catching up with the impressive pace of these developments.

  5. RNA Thermodynamic Structural Entropy

    PubMed Central

    Garcia-Martin, Juan Antonio; Clote, Peter

    2015-01-01

    Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs). However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE) element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner’99 and Turner’04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http

  6. RNA Thermodynamic Structural Entropy.

    PubMed

    Garcia-Martin, Juan Antonio; Clote, Peter

    2015-01-01

    Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs). However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE) element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner'99 and Turner'04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http

  7. Identifying microRNA/mRNA dysregulations in ovarian cancer

    PubMed Central

    2012-01-01

    Background 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). Methods 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. Results 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

  8. U-Th-Pb systematics of zircon inclusions in rock-forming minerals: A study of armoring against isotopic loss using the Sherman Granite of Colorado-Wyoming, USA

    USGS Publications Warehouse

    Aleinikoff, J.N.

    1983-01-01

    Zircon inclusions were separated from the five major rock-forming minerals of the Sherman Granite of southern Wyoming, in order to evaluate the degree of discordance as a possible function of host minerals. U-Th-Pb isotopic ratios were determined for two size fractions of zircon inclusions from each mineral, plus five size fractions from the bulk rock. Isotopic data from the inclusions have more than double the spread of data on a discordia obtained from the bulk sample, thereby yielding better-resolved concordia intercepts. However, isotopic ratios and morphologic characteristics indicate that the Pb/U systematics are complicated by inherited radiogenic lead. Although the data array cannot unequivocally be explained by the armoring process, the proposed methodology has succeeded in identifying groups of zircon with different isotopic characteristics. As such, this technique can be used to decipher complex geologic/isotopic histories and may be a useful addition to routine zircon geochronology. ?? 1983 Springer-Verlag.

  9. The organization and contribution of helicases to RNA splicing.

    PubMed

    De, Inessa; Schmitzová, Jana; Pena, Vladimir

    2016-01-01

    Splicing is an essential step of gene expression. It occurs in two consecutive chemical reactions catalyzed by a large protein-RNA complex named the spliceosome. Assembled on the pre-mRNA substrate from five small nuclear proteins, the spliceosome acts as a protein-controlled ribozyme to catalyze the two reactions and finally dissociates into its components, which are re-used for a new round of splicing. Upon following this cyclic pathway, the spliceosome undergoes numerous intermediate stages that differ in composition as well as in their internal RNA-RNA and RNA-protein contacts. The driving forces and control mechanisms of these remodeling processes are provided by specific molecular motors called RNA helicases. While eight spliceosomal helicases are present in all organisms, higher eukaryotes contain five additional ones potentially required to drive a more intricate splicing pathway and link it to an RNA metabolism of increasing complexity. Spliceosomal helicases exhibit a notable structural diversity in their accessory domains and overall architecture, in accordance with the diversity of their task-specific functions. This review summarizes structure-function knowledge about all spliceosomal helicases, including the latter five, which traditionally are treated separately from the conserved ones. The implications of the structural characteristics of helicases for their functions, as well as for their structural communication within the multi-subunits environment of the spliceosome, are pointed out. PMID:26874649

  10. Intracellular processing of immunostimulatory CpG-siRNA: Toll-like receptor 9 facilitates siRNA dicing and endosomal escape

    PubMed Central

    Nechaev, Sergey; Gao, Chan; Moreira, Dayson; Swiderski, Piotr; Jozwiak, Agnieszka; Kowolik, Claudia M.; Zhou, Jiehua; Armstrong, Brian; Raubitschek, Andrew; Rossi, John J.; Kortylewski, Marcin

    2013-01-01

    Dicer-substrate siRNAs equipped with CpG oligodeoxyribonucleotides overcome the major hurdle in cell-specific siRNA delivery. The CpG-siRNA molecules are actively internalized by TLR9+ cells, without the need for transfection reagents, leading to RNA interference both in vitro and in vivo. Here, we elucidate the molecular mechanisms of CpG-siRNA processing in target cells. We show that shortly after uptake into early endosomes (EE), CpG and siRNA parts of the conjugate are uncoupled in the presence of Dicer endonuclease. Diced siRNA molecules are translocated from endosomes to endoplasmic reticulum, where they can interact with the RNA interference machinery. We previously observed that even though TLR9 is not involved in CpG-siRNA uptake, it is indispensable for induction of gene silencing. To explain the role of TLR9 in intracellular processing of CpG-siRNA, we used primary macrophages derived from wild-type and Tlr9-deficient mice. Macrophages lacking TLR9 showed extended endosomal colocalization of CpG and siRNA parts of the conjugate. However, Tlr9 ablation did not interfere with the interaction of CpG-siRNA with Dicer as shown by in situ proximity ligation assay. Using CpG-siRNA labeled with pH-sensitive dye, we finally identified that lack of TLR9 in macrophages resulted in significant retention of the siRNA in endosomes. Thus, TLR9 facilitates the critical step following CpG-siRNA uncoupling, which is cytoplasmic release of the diced siRNA. These findings suggest that the class of immunostimulatory siRNAs may benefit from activation of certain endosomal immune receptors, such as TLR9, in augmented gene silencing and therapeutic efficacy. PMID:23777886

  11. ALFALFA MOSAIC VIRUS COAT PROTEIN BRIDGES RNA AND RNA-DEPENDENT RNA POLYMERASE IN VITRO

    PubMed Central

    Reichert, Vienna L.; Choi, Mehee; Petrillo, Jessica E.; Gehrke, Lee

    2007-01-01

    Alfalfa mosaic virus (AMV) RNA replication requires the viral coat protein (CP). AMV CP is an integral component of the viral replicase; moreover, it binds to the viral RNA 3' termini and induces the formation of multiple new base pairs that organize the RNA conformation. The results described here suggest that AMV coat protein binding defines template selection by organizing the 3'-terminal RNA conformation and by positioning the RNA-dependent RNA polymerase (RdRp) at the initiation site for minus strand synthesis. RNA-protein interactions were analyzed by using a modified northwestern blotting protocol that included both viral coat protein and labeled RNA in the probe solution (“far-northwestern blotting”). We observed that labeled RNA alone bound the replicase proteins poorly; however, complex formation was enhanced significantly in the presence of AMV CP. The RNA-replicase bridging function of the AMV CP may represent a mechanism for accurate de novo initiation in the absence of canonical 3' transfer RNA signals. PMID:17400272

  12. RNA:RNA interaction can enhance RNA localization in Drosophila oocytes.

    PubMed

    Hartswood, Eve; Brodie, Jim; Vendra, Georgia; Davis, Ilan; Finnegan, David J

    2012-04-01

    RNA localization is a key mechanism for targeting proteins to particular subcellular domains. Sequences necessary and sufficient for localization have been identified, but little is known about factors that affect its kinetics. Transcripts of gurken and the I factor, a non-LTR retrotransposon, colocalize at the nucleus in the dorso-antero corner of the Drosophila oocyte directed by localization signals, the GLS and ILS. I factor RNA localizes faster than gurken after injection into oocytes, due to a difference in the intrinsic localization ability of the GLS and ILS. The kinetics of localization of RNA containing the ILS are enhanced by the presence of a stem-loop, the A loop. This acts as an RNA:RNA interaction element in vivo and in vitro, and stimulates localization of RNA containing other localization signals. RNA:RNA interaction may be a general mechanism for modulating RNA localization and could allow an mRNA that lacks a localization signal to hitchhike on another RNA that has one.

  13. On RNA-RNA interaction structures of fixed topological genus.

    PubMed

    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.

  14. RNA Binding Proteins in the miRNA Pathway

    PubMed Central

    Connerty, Patrick; Ahadi, Alireza; Hutvagner, Gyorgy

    2015-01-01

    microRNAs (miRNAs) are short ~22 nucleotides (nt) ribonucleic acids which post-transcriptionally regulate gene expression. miRNAs are key regulators of all cellular processes, and the correct expression of miRNAs in an organism is crucial for proper development and cellular function. As a result, the miRNA biogenesis pathway is highly regulated. In this review, we outline the basic steps of miRNA biogenesis and miRNA mediated gene regulation focusing on the role of RNA binding proteins (RBPs). We also describe multiple mechanisms that regulate the canonical miRNA pathway, which depends on a wide range of RBPs. Moreover, we hypothesise that the interaction between miRNA regulation and RBPs is potentially more widespread based on the analysis of available high-throughput datasets. PMID:26712751

  15. Light-Triggered RNA Annealing by an RNA Chaperone.

    PubMed

    Panja, Subrata; Paul, Rakesh; Greenberg, Marc M; Woodson, Sarah A

    2015-06-15

    Non-coding antisense RNAs regulate bacterial genes in response to nutrition or environmental stress, and can be engineered for artificial gene control. The RNA chaperone Hfq accelerates antisense pairing between non-coding RNAs and their mRNA targets, by a mechanism still unknown. We used a photocaged guanosine derivative in an RNA oligonucleotide to temporally control Hfq catalyzed annealing. Using a fluorescent molecular beacon as a reporter, we observed RNA duplex formation within 15 s following irradiation (3 s) of photocaged RNA complexed with Hfq. The results showed that the Hfq chaperone directly stabilizes the initiation of RNA base pairs, and suggests a strategy for light-activated control of gene expression by non-coding RNAs.

  16. RNA Binding Proteins in the miRNA Pathway.

    PubMed

    Connerty, Patrick; Ahadi, Alireza; Hutvagner, Gyorgy

    2016-01-01

    microRNAs (miRNAs) are short ~22 nucleotides (nt) ribonucleic acids which post-transcriptionally regulate gene expression. miRNAs are key regulators of all cellular processes, and the correct expression of miRNAs in an organism is crucial for proper development and cellular function. As a result, the miRNA biogenesis pathway is highly regulated. In this review, we outline the basic steps of miRNA biogenesis and miRNA mediated gene regulation focusing on the role of RNA binding proteins (RBPs). We also describe multiple mechanisms that regulate the canonical miRNA pathway, which depends on a wide range of RBPs. Moreover, we hypothesise that the interaction between miRNA regulation and RBPs is potentially more widespread based on the analysis of available high-throughput datasets. PMID:26712751

  17. RNA Accessibility in cubic time

    PubMed Central

    2011-01-01

    Background The accessibility of RNA binding motifs controls the efficacy of many biological processes. Examples are the binding of miRNA, siRNA or bacterial sRNA to their respective targets. Similarly, the accessibility of the Shine-Dalgarno sequence is essential for translation to start in prokaryotes. Furthermore, many classes of RNA binding proteins require the binding site to be single-stranded. Results We introduce a way to compute the accessibility of all intervals within an RNA sequence in (n3) time. This improves on previous implementations where only intervals of one defined length were computed in the same time. While the algorithm is in the same efficiency class as sampling approaches, the results, especially if the probabilities get small, are much more exact. Conclusions Our algorithm significantly speeds up methods for the prediction of RNA-RNA interactions and other applications that require the accessibility of RNA molecules. The algorithm is already available in the program RNAplfold of the ViennaRNA package. PMID:21388531

  18. Multimodality Imaging of RNA Interference

    PubMed Central

    Nayak, Tapas R.; Krasteva, Lazura K.; Cai, Weibo

    2013-01-01

    The discovery of small interfering RNAs (siRNAs) and their potential to knock down virtually any gene of interest has ushered in a new era of RNA interference (RNAi). Clinical use of RNAi faces severe limitations due to inefficiency delivery of siRNA or short hairpin RNA (shRNA). Many molecular imaging techniques have been adopted in RNAi-related research for evaluation of siRNA/shRNA delivery, biodistribution, pharmacokinetics, and the therapeutic effect. In this review article, we summarize the current status of in vivo imaging of RNAi. The molecular imaging techniques that have been employed include bioluminescence/fluorescence imaging, magnetic resonance imaging/spectroscopy, positron emission tomography, single-photon emission computed tomography, and various combinations of these techniques. Further development of non-invasive imaging strategies for RNAi, not only focusing on the delivery of siRNA/shRNA but also the therapeutic efficacy, is critical for future clinical translation. Rigorous validation will be needed to confirm that biodistribution of the carrier is correlated with that of siRNA/shRNA, since imaging only detects the label (e.g. radioisotopes) but not the gene or carrier themselves. It is also essential to develop multimodality imaging approaches for realizing the full potential of therapeutic RNAi, as no single imaging modality may be sufficient to simultaneously monitor both the gene delivery and silencing effect of RNAi. PMID:23745567

  19. mRNA transcript therapy.

    PubMed

    Weissman, Drew

    2015-02-01

    mRNA is the central molecule of all forms of life. It is generally accepted that current life on Earth descended from an RNA world. mRNA, after its first therapeutic description in 1992, has recently come into increased focus as a method to deliver genetic information. The recent solution to the two main difficulties in using mRNA as a therapeutic, immune stimulation and potency, has provided the basis for a wide range of applications. While mRNA-based cancer immunotherapies have been in clinical trials for a few years, novel approaches; including, in vivo delivery of mRNA to replace or supplement proteins, mRNA-based generation of pluripotent stem cells, or genome engineering using mRNA-encoded meganucleases are beginning to be realized. This review presents the current state of mRNA drug technologies and potential applications, as well as discussing the challenges and prospects in mRNA development and drug discovery. PMID:25359562

  20. Quantification of miRNA-mRNA interactions.

    PubMed

    Muniategui, Ander; Nogales-Cadenas, Rubén; Vázquez, Miguél; Aranguren, Xabier L; Agirre, Xabier; Luttun, Aernout; Prosper, Felipe; Pascual-Montano, Alberto; Rubio, Angel

    2012-01-01

    miRNAs are small RNA molecules (' 22nt) that interact with their corresponding target mRNAs inhibiting the translation of the mRNA into proteins and cleaving the target mRNA. This second effect diminishes the overall expression of the target mRNA. Several miRNA-mRNA relationship databases have been deployed, most of them based on sequence complementarities. However, the number of false positives in these databases is large and they do not overlap completely. Recently, it has been proposed to combine expression measurement from both miRNA and mRNA and sequence based predictions to achieve more accurate relationships. In our work, we use LASSO regression with non-positive constraints to integrate both sources of information. LASSO enforces the sparseness of the solution and the non-positive constraints restrict the search of miRNA targets to those with down-regulation effects on the mRNA expression. We named this method TaLasso (miRNA-Target LASSO).We used TaLasso on two public datasets that have paired expression levels of human miRNAs and mRNAs. The top ranked interactions recovered by TaLasso are especially enriched (more than using any other algorithm) in experimentally validated targets. The functions of the genes with mRNA transcripts in the top-ranked interactions are meaningful. This is not the case using other algorithms.TaLasso is available as Matlab or R code. There is also a web-based tool for human miRNAs at http://talasso.cnb.csic.es/.