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Sample records for armored rna internal

  1. Preparation of His-Tagged Armored RNA Phage Particles as a Control for Real-Time Reverse Transcription-PCR Detection of Severe Acute Respiratory Syndrome Coronavirus

    PubMed Central

    Cheng, Yangjian; Niu, Jianjun; Zhang, Yongyou; Huang, Jianwei; Li, Qingge

    2006-01-01

    Armored RNA has been increasingly used as both an external and internal positive control in nucleic acid-based assays for RNA virus. In order to facilitate armored RNA purification, a His6 tag was introduced into the loop region of the MS2 coat protein, which allows the exposure of multiple His tags on the surface during armored RNA assembly. The His-tagged armored RNA particles were purified to homogeneity and verified to be free of DNA contamination in a single run of affinity chromatography. A fragment of severe acute respiratory syndrome coronavirus (SARS-CoV) genome targeted for SARS-CoV detection was chosen for an external positive control preparation. A plant-specific gene sequence was chosen for a universal noncompetitive internal positive control preparation. Both controls were purified by Co2+ affinity chromatography and were included in a real-time reverse transcription-PCR assay for SARS-CoV. The noncompetitive internal positive control can be added to clinical samples before RNA extraction and enables the identification of potential inhibitive effects without interfering with target amplification. The external control could be used for the quantification of viral loads in clinical samples. PMID:17021082

  2. External Quality Assessment for the Detection of Measles Virus by Reverse Transcription-PCR Using Armored RNA

    PubMed Central

    Jia, Tingting; Zhang, Lei; Wang, Guojing; Zhang, Rui; Zhang, Kuo; Lin, Guigao; Xie, Jiehong; Wang, Lunan; Li, Jinming

    2015-01-01

    In recent years, nucleic acid tests for detection of measles virus RNA have been widely applied in laboratories belonging to the measles surveillance system of China. An external quality assessment program was established by the National Center for Clinical Laboratories to evaluate the performance of nucleic acid tests for measles virus. The external quality assessment panel, which consisted of 10 specimens, was prepared using armored RNAs, complex of noninfectious MS2 bacteriophage coat proteins encapsulated RNA of measles virus, as measles virus surrogate controls. Conserved sequences amplified from a circulating measles virus strain or from a vaccine strain were encapsulated into these armored RNAs. Forty-one participating laboratories from 15 provinces, municipalities, or autonomous regions that currently conduct molecular detection of measles virus enrolled in the external quality assessment program, including 40 measles surveillance system laboratories and one diagnostic reagent manufacturer. Forty laboratories used commercial reverse transcription-quantitative PCR kits, with only one laboratory applying a conventional PCR method developed in-house. The results indicated that most of the participants (38/41, 92.7%) were able to accurately detect the panel with 100% sensitivity and 100% specificity. Although a wide range of commercially available kits for nucleic acid extraction and reverse transcription polymerase chain reaction were used by the participants, only two false-negative results and one false-positive result were generated; these were generated by three separate laboratories. Both false-negative results were obtained with tests performed on specimens with the lowest concentration (1.2 × 104 genomic equivalents/mL). In addition, all 18 participants from Beijing achieved 100% sensitivity and 100% specificity. Overall, we conclude that the majority of the laboratories evaluated have reliable diagnostic capacities for the detection of measles virus

  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. 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...

  9. 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

  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. Use of an internal positive control in a multiplex reverse transcription-PCR to detect West Nile virus RNA in mosquito pools.

    PubMed

    Eisler, Diane L; McNabb, Alan; Jorgensen, Danielle R; Isaac-Renton, Judith L

    2004-02-01

    We report on the use of West Nile virus Armored RNA as an internal positive control (IPC) for the extraction and reverse transcription-PCR (RT-PCR) of RNA extracted from field-collected mosquitoes and on a multiplex real-time Taqman RT-PCR to simultaneously detect the 3' noncoding region of West Nile virus and the West Nile virus NS5-2 region comprising the IPC. Mosquito pools from the province of British Columbia, Canada (n = 635), were tested in duplicate and found to be negative for West Nile virus and positive for the IPC. Known West Nile virus-positive supernatants from mosquito pools from the provinces of Alberta and Manitoba were tested in duplicate and found to be positive for both regions of the West Nile virus genome. The mean cycle threshold (Ct) value for the IPC in batch extraction controls +/- 2 standard deviations was found to be 36.43 +/- 1.78 cycles. IPCs of 98.4% (624) of West Nile virus-negative pools fell within this range, indicating the reproducibility of RNA extraction and RT-PCR for pools varying in mosquito genus and number. A comparison of mosquito pool genera revealed no significant genus effect on the Ct value of the IPC. The incorporation of West Nile virus Armored RNA as an IPC allows monitoring of RNA extraction and RT-PCR and detection of false-negative results due to failures in these processes or to PCR inhibition, respectively. PMID:14766868

  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. 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

  18. RNAcentral: an international database of ncRNA sequences

    PubMed Central

    2015-01-01

    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. PMID:25352543

  19. RNAcentral: an international database of ncRNA sequences.

    PubMed

    2015-01-01

    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. PMID:25352543

  20. RNAcentral: an international database of ncRNA sequences

    DOE PAGESBeta

    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. RNAcentral: A vision for an international database of RNA sequences.

    PubMed

    Bateman, Alex; Agrawal, Shipra; Birney, Ewan; Bruford, Elspeth A; Bujnicki, Janusz M; Cochrane, Guy; Cole, James R; Dinger, Marcel E; Enright, Anton J; Gardner, Paul P; Gautheret, Daniel; Griffiths-Jones, Sam; Harrow, Jen; Herrero, Javier; Holmes, Ian H; Huang, Hsien-Da; Kelly, Krystyna A; Kersey, Paul; Kozomara, Ana; Lowe, Todd M; Marz, Manja; Moxon, Simon; Pruitt, Kim D; Samuelsson, Tore; Stadler, Peter F; Vilella, Albert J; Vogel, Jan-Hinnerk; Williams, Kelly P; Wright, Mathew W; Zwieb, Christian

    2011-11-01

    During the last decade there has been a great increase in the number of noncoding RNA genes identified, including new classes such as microRNAs and piRNAs. There is also a large growth in the amount of experimental characterization of these RNA components. Despite this growth in information, it is still difficult for researchers to access RNA data, because key data resources for noncoding RNAs have not yet been created. The most pressing omission is the lack of a comprehensive RNA sequence database, much like UniProt, which provides a comprehensive set of protein knowledge. In this article we propose the creation of a new open public resource that we term RNAcentral, which will contain a comprehensive collection of RNA sequences and fill an important gap in the provision of biomedical databases. We envision RNA researchers from all over the world joining a federated RNAcentral network, contributing specialized knowledge and databases. RNAcentral would centralize key data that are currently held across a variety of databases, allowing researchers instant access to a single, unified resource. This resource would facilitate the next generation of RNA research and help drive further discoveries, including those that improve food production and human and animal health. We encourage additional RNA database resources and research groups to join this effort. We aim to obtain international network funding to further this endeavor. PMID:21940779

  4. RNAcentral: A vision for an international database of RNA sequences

    PubMed Central

    Bateman, Alex; Agrawal, Shipra; Birney, Ewan; Bruford, Elspeth A.; Bujnicki, Janusz M.; Cochrane, Guy; Cole, James R.; Dinger, Marcel E.; Enright, Anton J.; Gardner, Paul P.; Gautheret, Daniel; Griffiths-Jones, Sam; Harrow, Jen; Herrero, Javier; Holmes, Ian H.; Huang, Hsien-Da; Kelly, Krystyna A.; Kersey, Paul; Kozomara, Ana; Lowe, Todd M.; Marz, Manja; Moxon, Simon; Pruitt, Kim D.; Samuelsson, Tore; Stadler, Peter F.; Vilella, Albert J.; Vogel, Jan-Hinnerk; Williams, Kelly P.; Wright, Mathew W.; Zwieb, Christian

    2011-01-01

    During the last decade there has been a great increase in the number of noncoding RNA genes identified, including new classes such as microRNAs and piRNAs. There is also a large growth in the amount of experimental characterization of these RNA components. Despite this growth in information, it is still difficult for researchers to access RNA data, because key data resources for noncoding RNAs have not yet been created. The most pressing omission is the lack of a comprehensive RNA sequence database, much like UniProt, which provides a comprehensive set of protein knowledge. In this article we propose the creation of a new open public resource that we term RNAcentral, which will contain a comprehensive collection of RNA sequences and fill an important gap in the provision of biomedical databases. We envision RNA researchers from all over the world joining a federated RNAcentral network, contributing specialized knowledge and databases. RNAcentral would centralize key data that are currently held across a variety of databases, allowing researchers instant access to a single, unified resource. This resource would facilitate the next generation of RNA research and help drive further discoveries, including those that improve food production and human and animal health. We encourage additional RNA database resources and research groups to join this effort. We aim to obtain international network funding to further this endeavor. PMID:21940779

  5. 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

  6. 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

  7. Consecutive GA Pairs Stabilize Medium Size RNA Internal Loops†

    PubMed Central

    Chen, Gang; Turner, Douglas H.

    2014-01-01

    Internal loops in RNA are important for folding and function. Consecutive non-canonical pairs can form in internal loops having at least two nucleotides on each side. Thermodynamic and structural insights for such internal loops should improve approximations for their stabilities and predictions of secondary and three-dimensional structures. Most natural internal loops are purine rich. A series of oligoribonucleotides that form purine rich internal loops of 5 – 10 nucleotides, including kink-turn loops, were studied by UV melting, exchangeable proton and phosphorus NMR. Three consecutive GA pairs with the motif of 5′YGGA¯3′RAAG or GGA¯R3′AAGY5′ (i.e. 5′GGA¯3′3′AAG5′ closed on at least one side with a CG, UA, or UG pair with Y representing C or U and R representing A or G) stabilize internal loops having six to ten nucleotides. Certain motifs with two consecutive GA pairs are also stabilizing. In internal loops with three or more nucleotides on each side, the motif 5′UG¯3′GA has stability similar to 5′CG¯3′GA. A revised model for predicting stabilities of internal loops with 6 – 10 nucleotides is derived by multiple linear regression. Loops with 2 × 3 nucleotides are predicted well by a previous thermodynamic model. PMID:16548530

  8. 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.

  9. Alternative ferritin mRNA translation via internal initiation

    PubMed Central

    Daba, Alina; Koromilas, Antonis E.; Pantopoulos, Kostas

    2012-01-01

    Ferritin stores and detoxifies an excess of intracellular iron, and thereby plays an important role in the metabolism of this metal. As unshielded iron promotes oxidative stress, ferritin is crucial in maintaining cellular redox balance and may also modulate cell growth, survival, and apoptosis. The expression of ferritin is controlled by transcriptional and post-transcriptional mechanisms. In light of the well-established transcriptional induction of ferritin by inflammatory signals, we examined how ferritin mRNA translation responds to stress conditions. We first used HT1080 fibrosarcoma cells engineered for coumermycin-inducible expression of PKR, a stress kinase that inhibits protein synthesis in virus-infected cells by phosphorylating eIF2α. In this setting, iron triggered partial ferritin mRNA translation despite a PKR-induced global shutdown in protein synthesis. Moreover, iron-mediated ferritin synthesis was evident in cells infected with an attenuated strain of poliovirus; when eIF4GI was cleaved, eIF2α was phosphorylated, and host protein synthesis was inhibited. Under global inhibition of protein synthesis or specific inhibition of ferritin mRNA translation in cells overexpressing PKR or IRP1, respectively, we demonstrate association of ferritin mRNA with heavy polysomes. Further experiments revealed that the 5′ untranslated region (5′ UTR) of ferritin mRNA contains a bona fide internal ribosomal entry site (IRES). Our data are consistent with the existence of an alternative, noncanonical mechanism for ferritin mRNA translation, which may primarily operate under stress conditions to protect cells from oxidative stress. PMID:22271759

  10. RNA-Binding Proteins Impacting on Internal Initiation of Translation

    PubMed Central

    Martínez-Salas, Encarnación; Lozano, Gloria; Fernandez-Chamorro, Javier; Francisco-Velilla, Rosario; Galan, Alfonso; Diaz, Rosa

    2013-01-01

    RNA-binding proteins (RBPs) are pivotal regulators of all the steps of gene expression. RBPs govern gene regulation at the post-transcriptional level by virtue of their capacity to assemble ribonucleoprotein complexes on certain RNA structural elements, both in normal cells and in response to various environmental stresses. A rapid cellular response to stress conditions is triggered at the step of translation initiation. Two basic mechanisms govern translation initiation in eukaryotic mRNAs, the cap-dependent initiation mechanism that operates in most mRNAs, and the internal ribosome entry site (IRES)-dependent mechanism activated under conditions that compromise the general translation pathway. IRES elements are cis-acting RNA sequences that recruit the translation machinery using a cap-independent mechanism often assisted by a subset of translation initiation factors and various RBPs. IRES-dependent initiation appears to use different strategies to recruit the translation machinery depending on the RNA organization of the region and the network of RBPs interacting with the element. In this review we discuss recent advances in understanding the implications of RBPs on IRES-dependent translation initiation. PMID:24189219

  11. Nanotechnology for armor: hype, facts, and future

    NASA Astrophysics Data System (ADS)

    Maher, Mick

    2012-06-01

    Over the past two decades, nanotechnology has offered the promise of revolutionary performance improvements over existing armor materials. During that time there was substantial effort and resources put into developing the material technology and supporting theories, with only limited emphasis placed on understanding the ballistic event, mechanisms that drive armor performance, and the dependent nature of the threat. As a result, this large investment in nanotechnology for armor has not produced improved performance on the ballistics testing range, and armor nanotechnologies have never been fielded. No matter what the platform, armor systems have several functions that they have to perform in order to function properly. In order to defeat a threat, armor systems are designed to: deform/deflect the threat; dissipate energy; and prevent residual debris penetration. To date there is no definitive answer as to what material properties drive the system behavior of these functions at high rates in response to a specific threat, making the adaptation of nanotechnology that much harder. However, these functions are now being considered with respect to the material system and armor mechanism being utilized, and nanotechnology is beginning to be shown as an effective means of improving performance. When looking at the materials being used today, there are examples of nanotechnology making inroads into today's latest systems. Nano-particles are being used to manipulate grain boundaries in both metals and ceramics to tailor performance. Composite materials are utilizing nanotechnology to enhance basic material properties and enhance the system level behaviors to high rate events. While the anticipated revolution never occurred, nanotechnology is beginning to be utilized as an enabler in the latest armor performance improvements.

  12. 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.

  13. 77 FR 39259 - Agency Information Collection Activities; Proposed Collection; Comments Requested: Body Armor in...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-02

    ... Information Collection Activities; Proposed Collection; Comments Requested: Body Armor in Correctional...: Body Armor in Correctional Institutions Survey. The collections include the forms Body Armor Administrative Agency-Level Survey and Body Armor Individual-level Correctional Officer Survey. (3) Agency...

  14. Fast Flexible Modeling of RNA Structure Using Internal Coordinates

    PubMed Central

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

    2015-01-01

    Modeling the structure and dynamics of large macromolecules remains a critical challenge. Molecular dynamics (MD) simulations are expensive because they model every atom independently, and are difficult to combine with experimentally derived knowledge. Assembly of molecules using fragments from libraries relies on the database of known structures and thus may not work for novel motifs. Coarse-grained modeling methods have yielded good results on large molecules but can suffer from difficulties in creating more detailed full atomic realizations. There is therefore a need for molecular modeling algorithms that remain chemically accurate and economical for large molecules, do not rely on fragment libraries, and can incorporate experimental information. RNABuilder works in the internal coordinate space of dihedral angles and thus has time requirements proportional to the number of moving parts rather than the number of atoms. It provides accurate physics-based response to applied forces, but also allows user-specified forces for incorporating experimental information. A particular strength of RNABuilder is that all Leontis-Westhof basepairs can be specified as primitives by the user to be satisfied during model construction. We apply RNABuilder to predict the structure of an RNA molecule with 160 bases from its secondary structure, as well as experimental information. Our model matches the known structure to 10.2 Angstroms RMSD and has low computational expense. PMID:21778523

  15. Roughness of stable, armored gravel beds

    NASA Astrophysics Data System (ADS)

    Gomez, Basil

    1993-11-01

    The grain roughness of stable armored beds that formed in a laboratory flume under a range of steady flow conditions on rounded, flat and angular gravel is analyzed. Gravel roughness geometry is determined from bed surface profiles and vertical photographs. These techniques have been employed in field situations. Thus the methodology is potentially applicable to the analysis of grain roughness in natural gravel bed channels. The description of representative roughness geometry is also analogous to that used to characterize artificial roughness arrays. Armor roughness increases with increasing flow. Armored surfaces composed of angular gravel are roughest, and surfaces formed of flat gravel offer least resistance to the flow. Stable armored beds may exhibit a tendency to maximize the ratio of the shear due to drag on representative roughness elements to total shear. Roughness concentration is strongly correlated with the energy slope, and there is a linear increase in equivalent roughness height with increasing roughness concentration. The friction factor for an armored surface varies in a linear manner with representative roughness geometry. The equation defining this relation is probably similar to that used to characterize variations in the friction factor with artificial roughness geometry at low roughness concentrations. However, to reconcile the relations for artificial and natural roughness completely, it may be necessary to explicitly consider the contribution to flow resistance made by roughness shape, background roughness, and blocking in shallow flows.

  16. 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.

  17. 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

  18. Armored instrumentation cable for geothermal well logging

    SciTech Connect

    Dennis, B.R.; Johnson, J.; Todd, B.

    1981-01-01

    Multiconductor armored well-logging cable is used extensively by the oil and natural gas industry to lower various instruments used to measure the geological and geophysical parameters into deep wellbores. Advanced technology in oil-well drilling makes it possible to achieve borehole depths of 9 km (30,000 ft). The higher temperatures in these deeper boreholes demand advancements in the design and manufacturing of wireline cable and in the electrical insulating and armoring materials used as integral components. If geothermal energy is proved an abundant economic resource, drilling temperatures approaching and exceeding 300/sup 0/C will become commonplace. The adaptation of teflons as electrical insulating material permitted use of armored cable in geothermal wellbores where temperatures are slightly in excess of 200/sup 0/C, and where the concentrations of corrosive minerals and gases are high. Teflon materials presently used in wireline cables, however, are not capable of continuous operation at the anticipated higher temperatures.

  19. 75 FR 25208 - Announcement of Body Armor Research Needs Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-07

    ... National Institute of Standards and Technology Announcement of Body Armor Research Needs Meeting AGENCY...-day High Strength Fiber and Body Armor Research Needs Meeting. The Meeting will provide a forum to... Body Armor Research Needs Meeting will be held June 15, 2010. The workshop will be held from 9 a.m....

  20. Resonance and streaming of armored microbubbles

    NASA Astrophysics Data System (ADS)

    Spelman, Tamsin; Bertin, Nicolas; Stephen, Olivier; Marmottant, Philippe; Lauga, Eric

    2015-11-01

    A new experimental technique involves building a hollow capsule which partially encompasses a microbubble, creating an ``armored microbubble'' with long lifespan. Under acoustic actuation, such bubble produces net streaming flows. In order to theoretically model the induced flow, we first extend classical models of free bubbles to describe the streaming flow around a spherical body for any known axisymmetric shape oscillation. A potential flow model is then employed to determine the resonance modes of the armored microbubble. We finally use a more detailed viscous model to calculate the surface shape oscillations at the experimental driving frequency, and from this we predict the generated streaming flows.

  1. RNA-protein crosslinking to AMP residues at internal positions in RNA with a new photocrosslinking ATP analog.

    PubMed

    Costas, C; Yuriev, E; Meyer, K L; Guion, T S; Hanna, M M

    2000-05-01

    A new photocrosslinking purine analog was synthesized and evaluated as a transcription substrate for Escherichia coli RNA polymerase. This analog, 8-[(4-azidophenacyl)thio]adenosine 5'-triphosphate (8-APAS-ATP) contains an aryl azide photocrosslinking group that is attached to the ATP base via a sulfur-linked arm on the 8 position of the purine ring. This position is not involved in the normal Watson-Crick base pairing needed for specific hybridization. Although 8-APAS-ATP could not replace ATP as a substrate for transcription initiation, once stable elongation complexes were formed, 8-APAS-AMP could be site-specifically incorporated into the RNA, and this transcript could be further elongated, placing the photoreactive analog at internal positions in the RNA. Irradiation of transcription elongation complexes in which the RNA contained the analog exclusively at the 3' end of an RNA 22mer, or a 23mer with the analog 1 nt from the 3' end, produced RNA crosslinks to the RNA polymerase subunits that form the RNA 3' end binding site (beta, beta'). Both 8-APAS-AMP and the related 8-azido-AMP were subjected to conformational modeling as nucleoside monophosphates and in DNA-RNA hybrids. Surprisingly, the lowest energy conformation for 8-APAS-AMP was found to be syn, while that of 8-azido-AMP was anti, suggesting that the conformational properties and transcription substrate properties of 8-azido-ATP should be re-evaluated. Although the azide and linker together are larger in 8-APAS-ATP than in 8-N(3)-ATP, the flexibility of the linker itself allows this analog to adopt several different energetically favorable conformations, making it a good substrate for the RNA polymerase. PMID:10756182

  2. 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.

  3. 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.

  4. EMBEDDED FIBER OPTIC SENSORS FOR INTEGRAL ARMOR

    EPA Science Inventory

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

  5. Complete Genome Sequence of the WHO International Standard for HIV-2 RNA Determined by Deep Sequencing

    PubMed Central

    Ham, Claire; Morris, Clare

    2016-01-01

    The World Health Organization (WHO) International Standard for HIV-2 RNA nucleic acid assays was characterized by complete genome deep sequencing. The entire coding sequence and flanking long terminal repeats (LTRs), including minority species, were assigned subtype A. This information will aid design, development, and evaluation of HIV-2 RNA amplification assays. PMID:26847885

  6. 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

  7. 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

  8. Constrained ceramic-filled polymer armor

    DOEpatents

    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.

  9. 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.

  10. Preliminary design of Viking Armored Gun System

    SciTech Connect

    Gogolewski, R.P.; Cunningham, B.J.

    1990-10-24

    We have completed the preliminary design of our third lightweight armored fighting vehicle -- the Viking Armored Gun System (AGS). The AGS vehicle features a two-man crew, the Ares 75mm Universal Turret System, and the John Deere 4026R Rotary Engine. In the spirit of our earlier AFV designs, our primary concern is to provide the AGS with sufficient firepower and survivability while utilizing off-the-shelf'' sub-systems and components in order to reduce developmental time and acquisition cost. We still envision that prototypic vehicles could be built within a thirty (30) month developmental/demonstration program. We still believe that vehicles of this class should be built and tested soon to assess their full tactical, operational, and strategic utilities.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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 stands ready for a practice drive in an M-113 armored personnel carrier during 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 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.

  16. 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.

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

    NASA Technical Reports Server (NTRS)

    2002-01-01

    KENNEDY SPACE CENTER, FLA. -- Expedition 6 Commander Ken Bowersox stands ready for a practice drive in an M-113 armored personnel carrier during 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 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.

  18. 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.

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

    NASA Technical Reports Server (NTRS)

    2002-01-01

    KENNEDY SPACE CENTER, FLA. -- During emergency egress training at the pad, Expedition 6 crew member Donald Pettit stands inside an M-113 armored personnel carrier before his practice drive. The training is part of Terminal Countdown Demonstration Test activities in preparation for launch. The TCDT also 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.

  20. 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 stands ready for a practice drive in an M-113 armored personnel carrier during 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 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.

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

    PubMed Central

    Banfield, Bruce W.; Mouland, Andrew J.; McCormick, Craig

    2014-01-01

    In recent years, important linkages have been made between RNA granules and human disease processes. On June 8-10 of this year, we hosted a new symposium, dubbed the 1st International Symposium on Stress-Associated RNA Granules in Human Disease and Viral Infection. This symposium brought together experts from diverse research disciplines ranging from cancer and neuroscience to infectious disease. This report summarizes speaker presentations and highlights current challenges in the field. PMID:25256393

  2. 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

  3. Armor Procedural Skills: Learning and Retention. Technical Report 621.

    ERIC Educational Resources Information Center

    Knerr, C. Mazie; And Others

    Research investigated learning and retention of eight armor tasks selected to represent tasks varying in length, complexity, and extent of practice in operational units. Performance data were collected from soldiers in operational units and from soldiers attending One Station Unit Training (OSUT) in Armor Military Occupational Specialty (19E).…

  4. COST-EFFECTIVE MANUFACTURING OF DAMAGE-TOLERANT INTEGRAL ARMOR

    EPA Science Inventory

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

  5. 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.

  6. 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

  7. 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

  8. 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

  9. 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...

  10. Defining the RNA internal loops preferred by benzimidazole derivatives via 2D combinatorial screening and computational analysis.

    PubMed

    Velagapudi, Sai Pradeep; Seedhouse, Steven J; French, Jonathan; Disney, Matthew D

    2011-07-01

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

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

    PubMed Central

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

    2011-01-01

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

  12. 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…

  13. Negligible heat strain in armored vehicle officers wearing personal body armor

    PubMed Central

    2011-01-01

    Objectives This study evaluated the heat strain experienced by armored vehicle officers (AVOs) wearing personal body armor (PBA) in a sub-tropical climate. Methods Twelve male AVOs, aged 35-58 years, undertook an eight hour shift while wearing PBA. Heart rate and core temperature were monitored continuously. Urine specific gravity (USG) was measured before and after, and with any urination during the shift. Results Heart rate indicated an intermittent and low-intensity nature of the work. USG revealed six AVOs were dehydrated from pre through post shift, and two others became dehydrated. Core temperature averaged 37.4 ± 0.3°C, with maximum's of 37.7 ± 0.2°C. Conclusions Despite increased age, body mass, and poor hydration practices, and Wet-Bulb Globe Temperatures in excess of 30°C; the intermittent nature and low intensity of the work prevented excessive heat strain from developing. PMID:21801453

  14. Quantifying Ballistic Armor Performance: A Minimally Invasive Approach

    NASA Astrophysics Data System (ADS)

    Holmes, Gale; Kim, Jaehyun; Blair, William; McDonough, Walter; Snyder, Chad

    2006-03-01

    Theoretical and non-dimensional analyses suggest a critical link between the performance of ballistic resistant armor and the fundamental mechanical properties of the polymeric materials that comprise them. Therefore, a test methodology that quantifies these properties without compromising an armored vest that is exposed to the industry standard V-50 ballistic performance test is needed. Currently, there is considerable speculation about the impact that competing degradation mechanisms (e.g., mechanical, humidity, ultraviolet) may have on ballistic resistant armor. We report on the use of a new test methodology that quantifies the mechanical properties of ballistic fibers and how each proposed degradation mechanism may impact a vest's ballistic performance.

  15. Armor systems including coated core materials

    SciTech Connect

    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.

  16. Armor systems including coated core materials

    SciTech Connect

    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.

  17. 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. PMID:19886461

  18. 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.

  19. 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.

  20. 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

  1. 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

  2. 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

  3. 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.

  4. Nondestructive characterization of UHMWPE armor materials

    SciTech Connect

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

    2012-05-17

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

  5. 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.

  6. 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.

  7. Probing a 2-Aminobenzimidazole Library for Binding to RNA Internal Loops via Two-Dimensional Combinatorial Screening

    PubMed Central

    Velegapudi, Sai Pradeep; Pushechnikov, Alexei; Labuda, Lucas P.; French, Jonathan M.; Disney, Matthew D.

    2012-01-01

    There are many potential RNA drug targets in bacterial, viral, and the human transcriptomes. However, there are few small molecules that modulate RNA function. This is due, in part, to a lack of fundamental understanding about RNA-ligand interactions including the types of small molecules that bind to RNA structural elements and the RNA structural elements that bind to small molecules. In an effort to better understand RNA-ligand interactions, we diversified the 2-aminobenzimidazole core (2AB) and probed the resulting library for binding to a library of RNA internal loops. We chose the 2AB core for these studies because it is a privileged scaffold for binding RNA based on previous reports. These studies identified that N-methyl pyrrolidine, imidazole, and propylamine diversity elements at the R1 position increase binding to internal loops; variability at the R2 position is well tolerated. The preferred RNA loop space was also determined for five ligands using a statistical approach and identified trends that lead to selective recognition. PMID:22958065

  8. Probing a 2-aminobenzimidazole library for binding to RNA internal loops via two-dimensional combinatorial screening.

    PubMed

    Velagapudi, Sai Pradeep; Pushechnikov, Alexei; Labuda, Lucas P; French, Jonathan M; Disney, Matthew D

    2012-11-16

    There are many potential RNA drug targets in bacterial, viral, and human transcriptomes. However, there are few small molecules that modulate RNA function. This is due, in part, to a lack of fundamental understanding about RNA-ligand interactions including the types of small molecules that bind to RNA structural elements and the RNA structural elements that bind to small molecules. In an effort to better understand RNA-ligand interactions, we diversified the 2-aminobenzimidazole core (2AB) and probed the resulting library for binding to a library of RNA internal loops. We chose the 2AB core for these studies because it is a privileged scaffold for binding RNA based on previous reports. These studies identified that N-methyl pyrrolidine, imidazole, and propylamine diversity elements at the R1 position increase binding to internal loops; variability at the R2 position is well tolerated. The preferred RNA loop space was also determined for five ligands using a statistical approach and identified trends that lead to selective recognition. PMID:22958065

  9. 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. PMID:25329264

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  11. 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

  12. Contemporary body armor: technical data, injuries, and limits.

    PubMed

    Prat, N; Rongieras, F; Sarron, J-C; Miras, A; Voiglio, E

    2012-04-01

    The introduction of firearms in the fifteenth century led to the continuous development of bulletproof personal protection. Due to recent industrial progress and the emergence of a new generation of ballistic fibers in the 1960s, the ability of individual ballistic protections to stop projectiles greatly increased. While protective equipment is able to stop increasingly powerful missiles, deformation during the impact can cause potentially lethal nonpenetrating injuries that are grouped under the generic term of behind armor blunt trauma, and the scope and consequences of these are still unclear. This review first summarizes current technical data for modern bulletproof vests, the materials used in them, and the stopping mechanisms they employ. Then it describes recent research into the specific ballistic injury patterns of soldiers wearing body armor, focusing on behind-armor blunt trauma. PMID:26815825

  13. 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...

  14. 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...

  15. 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...

  16. 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...

  17. 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...

  18. 46 CFR 111.05-7 - Armored and metallic sheathed cable.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 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 2013-10-01 2013-10-01 false Armored and metallic sheathed cable. 111.05-7...

  19. 46 CFR 111.05-7 - Armored and metallic sheathed cable.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 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 2012-10-01 2012-10-01 false Armored and metallic sheathed cable. 111.05-7...

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

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 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 2011-10-01 2011-10-01 false Armored and metallic sheathed cable. 111.05-7...

  1. 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.

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

    SciTech Connect

    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.

  3. 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

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

    PubMed Central

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

    2014-01-01

    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

  5. Identification of novel non-canonical RNA-binding sites in Gemin5 involved in internal initiation of translation

    PubMed Central

    Fernandez-Chamorro, Javier; Piñeiro, David; Gordon, James M. B.; Ramajo, Jorge; Francisco-Velilla, Rosario; Macias, Maria J.; Martinez-Salas, Encarnación

    2014-01-01

    Ribonucleic acid (RNA)-binding proteins are key players of gene expression control. We have shown that Gemin5 interacts with internal ribosome entry site (IRES) elements and modulates initiation of translation. However, little is known about the RNA-binding sites of this protein. Here we show that the C-terminal region of Gemin5 bears two non-canonical bipartite RNA-binding sites, encompassing amino acids 1297–1412 (RBS1) and 1383–1508 (RBS2). While RBS1 exhibits greater affinity for RNA than RBS2, it does not affect IRES-dependent translation in G5-depleted cells. In solution, the RBS1 three-dimensional structure behaves as an ensemble of flexible conformations rather than having a defined tertiary structure. However, expression of the polypeptide G51383–1508, bearing the low RNA-binding affinity RBS2, repressed IRES-dependent translation. A comparison of the RNA-binding capacity and translation control properties of constructs expressed in mammalian cells to that of the Gemin5 proteolysis products observed in infected cells reveals that non-repressive products accumulated during infection while the repressor polypeptide is not stable. Taken together, our results define the low affinity RNA-binding site as the minimal element of the protein being able to repress internal initiation of translation. PMID:24598255

  6. Armor of cermet with metal therein increasing with depth

    DOEpatents

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

    1973-07-01

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

  7. 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.

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

    DOE PAGESBeta

    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

  9. 76 FR 69764 - Stab-Resistant Body Armor Standard Workshop

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-09

    ...The National Institute of Justice (NIJ) and the National Institute of Standards and Technology (NIST) are jointly hosting a workshop focused on the NIJ Stab-resistant Body Armor Standard, and the discussion is directed toward manufacturers, certification bodies, and test laboratories. This workshop is being held specifically to discuss with interested parties recent progress made toward the......

  10. 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.

  11. 75 FR 25884 - NIJ Body Armor Compliance Testing Program Workshop

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-10

    ...The National Institute of Justice (NIJ) is hosting a Body Armor Compliance Testing Program Workshop for manufacturers and test laboratories on Tuesday, May 18, 2010, from 8 a.m. to 3 p.m. NIJ is hosting this workshop specifically to update manufacturers and test laboratories with regard to the Compliance Testing Program, status of testing, administrative clarifications, and the follow-up......

  12. 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.

  13. Hardness and damage associated with pointed indentations in armor ceramics

    NASA Astrophysics Data System (ADS)

    Swab, Jeffrey J.

    It is empirically known that an armor ceramic should be as hard as or harder than the projectile it intends to defeat. Quasi-static indentation testing is one of the most widely utilized techniques for determining the hardness of armor ceramics. Hardness measurements can also be used to generate other property values (fracture toughness, elastic properties and even the yield strength) that may be relevant to ballistic performance. While the indentation methodologies are simple and straightforward the resultant hardness values for ceramic materials can be influenced by the indenter geometry, indentation load, loading rate, specimen surface finish and ceramic microstructure. This presentation will summarize the results of a study to determine the hardness of a variety of armor-grade ceramics (Al2O3, B 4C, SiC, and WC) with different indenter geometries (Vickers and Knoop) over a range of indentation loads (0.98N to 98N) and discuss the implications for armor ceramics. The resulting data strongly indicates that the best means of determining the hardness of armor ceramics is the use of 19.6N Knoop indentations. While the hardness data and the subsequent analysis clearly support the use of the Knoop methodology to determine the hardness, it does not take into account the response of the ceramic to the indentation process. One response that is continually overlooked is the role of damage and cracking. A detailed understanding of the damage and cracking that occurs during indentation may provide valuable insights to the ballistic performance of the armor ceramics during the earliest stages of impact. To explore this material response a detailed examination of the topography of the indents and the damage and cracking that develops underneath both Knoop and Vickers indentations in a WC and SiC armor ceramic was conducted. The analysis shows that while the same types of cracks are produced in both materials the magnitude of these cracks as well as the type of damage that is

  14. 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

  15. RNA–protein crosslinking to AMP residues at internal positions in RNA with a new photocrosslinking ATP analog

    PubMed Central

    Costas, Celina; Yuriev, Elizabeth; Meyer, Karen L.; Guion, Tina S.; Hanna, Michelle M.

    2000-01-01

    A new photocrosslinking purine analog was synthesized and evaluated as a transcription substrate for Escherichia coli RNA polymerase. This analog, 8-[(4-azidophenacyl)thio]adenosine 5′-triphosphate (8-APAS-ATP) contains an aryl azide photocrosslinking group that is attached to the ATP base via a sulfur-linked arm on the 8 position of the purine ring. This position is not involved in the normal Watson–Crick base pairing needed for specific hybridization. Although 8-APAS-ATP could not replace ATP as a substrate for transcription initiation, once stable elongation complexes were formed, 8-APAS-AMP could be site-specifically incorporated into the RNA, and this transcript could be further elongated, placing the photoreactive analog at internal positions in the RNA. Irradiation of transcription elongation complexes in which the RNA contained the analog exclusively at the 3′ end of an RNA 22mer, or a 23mer with the analog 1 nt from the 3′ end, produced RNA crosslinks to the RNA polymerase subunits that form the RNA 3′ end binding site (β,β′). Both 8-APAS-AMP and the related 8-azido-AMP were subjected to conformational modeling as nucleoside monophosphates and in DNA–RNA hybrids. Surprisingly, the lowest energy conformation for 8-APAS-AMP was found to be syn, while that of 8-azido-AMP was anti, suggesting that the conformational properties and transcription substrate properties of 8-azido-ATP should be re-evaluated. Although the azide and linker together are larger in 8-APAS-ATP than in 8-N3-ATP, the flexibility of the linker itself allows this analog to adopt several different energetically favorable conformations, making it a good substrate for the RNA polymerase. PMID:10756182

  16. 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

  17. Transcription of the Xenopus laevis selenocysteine tRNA(Ser)Sec gene: a system that combines an internal B box and upstream elements also found in U6 snRNA genes.

    PubMed Central

    Carbon, P; Krol, A

    1991-01-01

    The transcription mode of the Xenopus tRNA(Ser)Sec gene by RNA polymerase III was deciphered by injection of mutant templates into Xenopus oocyte nuclei. tRNA(Ser)Sec represents the paradigm of a new class of RNA polymerase III genes combining tRNA and U snRNA gene regulatory elements. Its promoter is tripartite, constituted by two upstream elements, a PSE and a TATA motif that are interchangeable with those of U6 snRNA genes and an internal box B as in other tRNAs. The B box enables the transcription level dependent on the upstream promoter to be increased. Data obtained indicate that U1 snRNA (Pol II) and tRNA(Ser)Sec (Pol III) genes share at least one transcription factor, implying that the border between transcription systems is less tight than expected. Images PMID:2001675

  18. Internal translation initiation from HIV-1 transcripts is conferred by a common RNA structure

    PubMed Central

    Plank, Terra-Dawn M; Whitehurst, James T; Cencic, Regina; Pelletier, Jerry; Kieft, Jeffrey S

    2014-01-01

    Alternative splicing of the human immunodeficiency virus 1 (HIV-1) RNA transcripts produces mRNAs encoding nine different viral proteins. The leader of each contains a common non-coding exon at the 5' end. Previous studies showed that the leaders from the common exon-containing transcripts gag, nef, vif, vpr and vpu can direct protein synthesis through internal ribosome entry sites (IRESs) with varying efficiencies. Here we explored whether the common exon acts as an IRES element in the context of all the 5' leaders or if each harbors a distinct IRES. We also explored the relationship between the IRESs and initiation codon selection. We find that the common exon adopts a similar conformation in every leader we explored and that the sequence and structure is required for IRES activity. We also find that each leader uses a scanning mechanism for start codon identification. Together, our data point to a model in which the common exon on HIV-1 transcripts acts as the ribosome landing pad, recruiting preinitiation complexes upstream of the initiation codon, followed by scanning to each transcript's initiator AUG. PMID:26779399

  19. Internal translation initiation from HIV-1 transcripts is conferred by a common RNA structure.

    PubMed

    Plank, Terra-Dawn M; Whitehurst, James T; Cencic, Regina; Pelletier, Jerry; Kieft, Jeffrey S

    2014-01-01

    Alternative splicing of the human immunodeficiency virus 1 (HIV-1) RNA transcripts produces mRNAs encoding nine different viral proteins. The leader of each contains a common non-coding exon at the 5' end. Previous studies showed that the leaders from the common exon-containing transcripts gag, nef, vif, vpr and vpu can direct protein synthesis through internal ribosome entry sites (IRESs) with varying efficiencies. Here we explored whether the common exon acts as an IRES element in the context of all the 5' leaders or if each harbors a distinct IRES. We also explored the relationship between the IRESs and initiation codon selection. We find that the common exon adopts a similar conformation in every leader we explored and that the sequence and structure is required for IRES activity. We also find that each leader uses a scanning mechanism for start codon identification. Together, our data point to a model in which the common exon on HIV-1 transcripts acts as the ribosome landing pad, recruiting preinitiation complexes upstream of the initiation codon, followed by scanning to each transcript's initiator AUG. PMID:26779399

  20. 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

  1. Molecular phylogeny of pneumocystis based on 5.8S rRNA gene and the internal transcribed spacers of rRNA gene sequences.

    PubMed

    Li, ZiHui; Feng, XianMin; Lu, SiQi; Zhang, Fan; Wang, FengYun; Huang, Song

    2008-05-01

    To clarify the phylogenetic relationships and species status of Pneumocystis, the 5.8S rRNA gene and the internal transcribed spacers (ITS, 1 and 2) of Pneumocystis rRNA derived from rat, gerbil and human were amplified, cloned and sequenced. The genetic distance matrix of six Pneumocystis species compared with other fungi like Taphrina and Saccharomyces indicated that the Pneumocystis genus contained multiple species including Pneumocystis from gerbil. The phylogenetic tree also showed that Pneumocystis from human and monkey formed one group and four rodent Pneumocystis formed another group. Among the four members, Pneumocystis wakefieldiae was most closely related to Pneumocystis murina and Pneumocystis carinii, and was least related to gerbil Pneumocystis. PMID:18785590

  2. A comparative study of RNA and DNA as internal gene expression controls early in the developmental cycle of Chlamydia pneumoniae.

    PubMed

    Engström, Patrik; Bailey, Leslie; Onskog, Thomas; Bergström, Sven; Johansson, Jörgen

    2010-03-01

    Many microbial pathogens invade and proliferate within host cells and the molecular mechanism underlying this behavior is currently being revealed for several bacterial species. Testing clinically relevant antibacterial compounds and elucidating their effects on gene expression requires adequate controls, especially when studying genetically intractable organisms such as Chlamydia spp., for which various gene fusions cannot be constructed. Until now, relative mRNA levels in Chlamydia have been measured using different internal gene expression controls, including 16S rRNA, mRNAs, and DNA. Here, we compared the advantages and disadvantages of various internal expression controls during the early phase of Chlamydia pneumoniae development. The relative abundance of target mRNAs varied using the different internal control RNAs. This was partly due to variation in the transcript stability of the RNA species. Also, seven out of nine of the analyzed RNAs increased fivefold or more between 2 and 14 h postinfection, while the amount of DNA and number of cells remained essentially unaltered. Our results suggest that RNA should not be used as a gene expression control during the early phase of Chlamydia development, and that intrinsic bacterial DNA is preferable for that purpose because it is stable, abundant, and its relative amount is generally correlated with bacterial numbers. PMID:20002746

  3. Modeling of Bullet Penetration in Explosively Welded Composite Armor Plate

    NASA Astrophysics Data System (ADS)

    Joshi, Vasant S.; Carney, Theodore C.

    2006-07-01

    Normal impact of high-speed armor piercing bullet on titanium-steel composite has been investigated using smooth particle hydrodynamics (SPH) code. The objective is to understand the effects of impact during the ballistic testing of explosively welded armor plates. These plates have significant microstructural differences within the weld region, heat-affected zone and the base metal. The variances result in substantial ductility, hardness and strength differences, important criteria in determining the failure mode, specifically whether it occurs at the joint or within the virgin base metal. Several configurations of composite plates with different material combinations were modeled. The results were used to modify the heat treatment process of explosively welded plates, making them more likely to survive impact.

  4. Modeling of bullet penetration in explosively welded composite armor plate

    NASA Astrophysics Data System (ADS)

    Joshi, Vasant; Carney, Theodore

    2005-07-01

    Normal impact of high-speed armor piercing bullet on titanium-steel composite has been investigated using smooth particle hydrodynamics (SPH) code. The objective is to understand the effects of multiple hits during the ballistic testing of explosively welded armor plates. These plates have significant micro-structural differences within the weld region, heat-affected zone and the base metal. The variances result in substantial ductility, hardness and strength differences, important criteria in determining the failure mode, specifically whether it occurs at the joint or within the virgin base metal. Several configurations of composite plates with different material combination had to be modeled. The results were used to modify the heat treatment process of explosively welded plates, making them more likely to survive multiple hits.

  5. Armoring a droplet: Soft jamming of a dense granular interface

    NASA Astrophysics Data System (ADS)

    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.

  6. 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

  7. 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

  8. 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. PMID:23470547

  9. 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.

  10. Modeling of Bullet Penetration in Explosively Welded Composite Armor Plate

    SciTech Connect

    Joshi, Vasant S.; Carney, Theodore C.

    2006-07-28

    Normal impact of high-speed armor piercing bullet on titanium-steel composite has been investigated using smooth particle hydrodynamics (SPH) code. The objective is to understand the effects of impact during the ballistic testing of explosively welded armor plates. These plates have significant microstructural differences within the weld region, heat-affected zone and the base metal. The variances result in substantial ductility, hardness and strength differences, important criteria in determining the failure mode, specifically whether it occurs at the joint or within the virgin base metal. Several configurations of composite plates with different material combinations were modeled. The results were used to modify the heat treatment process of explosively welded plates, making them more likely to survive impact.

  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. Lightweight armor system and process for producing the same

    DOEpatents

    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.

  13. High Frequency Ultrasound of Armor-Grade Alumina Ceramics

    NASA Astrophysics Data System (ADS)

    Bottiglieri, S.; Haber, R. A.

    2009-03-01

    Different lots of high density, commercial, armor-grade alumina (Al2O3) 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.

  14. 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.

  15. 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.

  16. 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.

  17. Role of Polypyrimidine Tract Binding Protein in Mediating Internal Initiation of Translation of Interferon Regulatory Factor 2 RNA

    PubMed Central

    Dhar, Debojyoti; Venkataramana, Musturi; Ponnuswamy, Anand; Das, Saumitra

    2009-01-01

    Background Earlier we have reported translational control of interferon regulatory factor 2 (IRF2) by internal initiation (Dhar et al, Nucleic Acids Res, 2007). The results implied possible role of IRF2 in controlling the intricate balance of cellular gene expression under stress conditions in general. Here we have investigated the secondary structure of the Internal Ribosome Entry Site of IRF2 RNA and demonstrated the role of PTB protein in ribosome assembly to facilitate internal initiation. Methodology/Principal Findings We have probed the putative secondary structure of the IRF2 5′UTR RNA using various enzymatic and chemical modification agents to constrain the secondary structure predicted from RNA folding algorithm Mfold. The IRES activity was found to be influenced by the interaction of trans-acting factor, polypyrimidine tract binding protein (PTB). Deletion of 25 nts from the 3′terminus of the 5′untranslated region resulted in reduced binding with PTB protein and also showed significant decrease in IRES activity compared to the wild type. We have also demonstrated putative contact points of PTB on the IRF2–5′UTR using primer extension inhibition assay. Majority of the PTB toe-prints were found to be restricted to the 3′end of the IRES. Additionally, Circular Dichroism (CD) spectra analysis suggested change in the conformation of the RNA upon PTB binding. Further, binding studies using S10 extract from HeLa cells, partially silenced for PTB gene expression, resulted in reduced binding by other trans-acting factors. Finally, we have demonstrated that addition of recombinant PTB enhances ribosome assembly on IRF2 IRES suggesting possible role of PTB in mediating internal initiation of translation of IRF2 RNA. Conclusion/Significance It appears that PTB binding to multiple sites within IRF2 5′UTR leads to a conformational change in the RNA that facilitate binding of other trans-acting factors to mediate internal initiation of translation. PMID

  18. 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

  19. 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.

  20. 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. PMID:21988728

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

    PubMed Central

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

    2011-01-01

    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 are disclosed of a model DM1 triplet repeating construct, 5′r(UUGGGC(CUG)3GUCC)2, refined to 2.20 Å and 1.52 Å resolution. Here, differences in orientation of the 5′ dangling UU end between the two structures induce changes in the backbone groove width, which reveals that non-canonical 1×1 nucleotide UU internal loops can display an ensemble of pairing conformations. In the 2.20 Å structure, CUGa, the 5′UU forms one hydrogen-bonded pairs with a 5′UU of a neighboring helix in the unit cell to form a pseudo-infinite 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-bonded pair. In the 1.52 Å structure, CUGb, the 5′ UU dangling end is tucked into the major groove of the duplex. While the canonical paired bases show no change in base pairing, in CUGb the terminal 1×1 nucleotide UU internal loops form now two hydrogen-bonded pairs. Thus, the shift in major groove induced by the 5′UU dangling end alters non-canonical 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. PMID:21988728

  2. 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

  3. 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

  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. A CA(+) pair adjacent to a sheared GA or AA pair stabilizes size-symmetric RNA internal loops.

    PubMed

    Chen, Gang; Kennedy, Scott D; Turner, Douglas H

    2009-06-23

    RNA internal loops are often important sites for folding and function. Residues in internal loops can have pKa values shifted close to neutral pH because of the local structural environment. A series of RNA internal loops were studied at different pH by UV absorbance versus temperature melting experiments and imino proton nuclear magnetic resonance (NMR). A stabilizing CA pair forms at pH 7 in the CG/AA and CA/AA nearest neighbors when the CA pair is the first noncanonical pair (loop-terminal pair) in 3 x 3 nucleotide and larger size-symmetric internal loops. These CG/AA and CA/AA nearest neighbors, with CA adjacent to a closing Watson-Crick pair, are further stabilized when the pH is lowered from 7 to 5.5. The results are consistent with a significantly larger fraction (from approximately 20% at pH 7 to approximately 90% at pH 5.5) of adenines being protonated at the N1 position to form stabilizing wobble CA+ pairs adjacent to a sheared GA or AA pair. The noncanonical pair adjacent to the GA pair in CG/AA can either stabilize or destabilize the loop, consistent with the sequence-dependent thermodynamics of GA pairs. No significant pH-dependent stabilization is found for most of the other nearest neighbor combinations involving CA pairs (e.g., CA/AG and AG/CA), which is consistent with the formation of various nonwobble pairs observed in different local sequence contexts in crystal and NMR structures. A revised free-energy model, including stabilization by wobble CA+ pairs, is derived for predicting stabilities of medium-size RNA internal loops. PMID:19485416

  6. Outstanding Lobelia dortmanna in iron armor.

    PubMed

    Sand-Jensen, Kaj; Møller, Claus Lindskov; Raun, Ane Løvendahl

    2008-10-01

    Lobelia dortmanna leads a group of small, highly-valued rosette species that grow on coarse, nutrient-poor soils in temperate soft-water lakes. They acquire most CO(2) for photosynthesis by root uptake and efficient gas transport in large air channels to the leaves. Lobelia is the only species that releases virtually all photosynthetic oxygen from the roots and generates profound day-night changes in oxygen and CO(2) in the sediment pore-water. While oxygen release from roots stimulates decomposition and supports VA-mycorrhiza fungi, the ready gas exchange presents a risk of insufficient oxygen supply to the distal root meristems as sediments accumulate organic matter from lake pollution. So the plant with the greatest oxygen release from roots is also the most sensitive to oxygen depletion in sediments and it dies or losses anchorage by shortening the roots from 10 to 2 cm at even modest contents (2.4%) of degradable organic matter. Coatings of oxidized iron on roots in organically enriched sediments reduce radial oxygen loss and, thereby, increase internal concentrations and supply of oxygen to root tips. Oxidized iron is also a redox buffer which may prevent the ingress of sulfides and other reduced toxic solutes during nights. Controlled experiments are under way to test if iron enrichment can help survival of rosette species threatened by lake pollution or whether removal of organic surface sediments is required. PMID:19704529

  7. Enhanced stab resistance of armor composites with functionalized silica nanoparticles

    NASA Astrophysics Data System (ADS)

    Mahfuz, Hassan; Clements, Floria; Rangari, Vijaya; Dhanak, Vinod; Beamson, Graham

    2009-03-01

    Traditionally shear thickening fluid (STF) reinforced with Kevlar has been used to develop flexible armor. At the core of the STF-Kevlar composites is a mixture of polyethylene glycol (PEG) and silica particles. This mixture is often known as STF and is consisted of approximately 45 wt % PEG and 55 wt % silica. During rheological tests, STF shows instantaneous spike in viscosity above a critical shear rate. Fabrication of STF-Kevlar composites requires preparation of STF, dilution with ethanol, and then impregnation with Kevlar. In the current approach, nanoscale silica particles were dispersed directly into a mixture of PEG and ethanol through a sonic cavitation process. Two types of silica nanoparticles were used in the investigation: 30 nm crystalline silica and 7 nm amorphous silica. The admixture was then reinforced with Kevlar fabric to produce flexible armor composites. In the next step, silica particles are functionalized with a silane coupling agent to enhance bonding between silica and PEG. The performance of the resulting armor composites improved significantly. As evidenced by National Institute of Justice spike tests, the energy required for zero-layer penetration (i.e., no penetration) jumped twofold: from 12 to 25 J cm2/g. The source of this improvement has been traced to the formation of siloxane (Si-O-Si) bonds between silica and PEG and superior coating of Kevlar filaments with particles. Fourier transform infrared, x-ray photoemission spectroscopy, and scanning electron microscopy studies were performed to examine chemical bonds, elemental composition, and particle dispersion responsible for such improvement. In summary, our experiments have demonstrated that functionalization of silica particles followed by direct dispersion into PEG resulted in superior Kevlar composites having much higher spike resistance.

  8. 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....

  9. 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....

  10. 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....

  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, 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....

  13. 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

    ... of Justice Programs Stab Resistance of Personal Body Armor (2000) Standard Special Technical... Institute of Justice (NIJ) is in the process of revising its Stab Resistance of Personal Body Armor (2000... bodies and (2) test laboratories with experience in programs for similar types of personal...

  14. 76 FR 27355 - 2011 National Institute of Justice Body Armor Workshop

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-11

    ...The National Institute of Justice invites manufacturers of ballistic-resistant body armor, ballistic laboratory testing facilities and other interested parties to the 2011 NIJ Body Armor Workshop. This year's workshop will have topics of interest for management and technical personnel from the manufacturing and laboratory communities. The workshop will be held at the Baltimore Convention......

  15. Development, Field Test, and Refinement of Performance Training Programs in Armor Advanced Individual Training. Final Report.

    ERIC Educational Resources Information Center

    Young, Douglas L.; Taylor, John E.

    Performance-oriented instruction was developed, field tested, and refined in two Advanced Individual Training (AIT) programs--Armor Reconnaissance Specialist (MOS 11D) and Armor Crewman (MOS 11E). Tasks for both MOS (Military Occupational Specialty) were inventoried and the inventories were reduced by eliminating those tasks which are not required…

  16. 30 CFR 75.700 - Grounding metallic sheaths, armors, and conduits enclosing power conductors.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Grounding metallic sheaths, armors, and conduits enclosing power conductors. 75.700 Section 75.700 Mineral Resources MINE SAFETY AND HEALTH... Grounding § 75.700 Grounding metallic sheaths, armors, and conduits enclosing power conductors. All...

  17. 30 CFR 75.700 - Grounding metallic sheaths, armors, and conduits enclosing power conductors.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Grounding metallic sheaths, armors, and conduits enclosing power conductors. 75.700 Section 75.700 Mineral Resources MINE SAFETY AND HEALTH... Grounding § 75.700 Grounding metallic sheaths, armors, and conduits enclosing power conductors. All...

  18. 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.

  19. Field Emissions from Organic Nanorods Armored with Metal Nanoparticles

    NASA Astrophysics Data System (ADS)

    Suzuki, Toshiya; Ishikawa, Kenji; Takeda, Keigo; Kondo, Hiroki; Sekine, Makoto; Hori, Masaru

    2013-12-01

    We report the fabrication of organic nanorods with a diameter of approximately 10 nm and a height of 106.8 nm (a high aspect ratio of 10.5) armored by Pt nanoparticles. Our results demonstrate that Pt particles deposited by metalorganic supercritical chemical fluid deposition (MOCFD) covering the entire deposition area play important roles in not only etch resistance, especially in protecting the sidewalls, but also the formation of electroconductive Pt/C composites, which were found to have field emission properties.

  20. 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

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

    NASA Astrophysics Data System (ADS)

    Pérez-Benitez, J. A.; Padovese, L. R.

    2012-04-01

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

  2. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

    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.

  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. ARMOR Dual-Polarimetric Radar Observations of Tornadic Debris Signatures

    NASA Technical Reports Server (NTRS)

    Petersen, W. A,; Carey, L. D.; Knupp, K. R.; Schultz, C.; Johnson, E.

    2008-01-01

    During the Super-Tuesday tornado outbreak of 5-6 February 2008, two EF-4 tornadoes occurred in Northern Alabama within 75 km range of the University of Alabama in Huntsville (UAH) Advanced Radar for Meteorological and Operational Research (ARMOR, C-band dual-polarimetric). This study will present an analysis of ARMOR radar-indicated dual-polarimetric tornadic debris signatures. The debris signatures were associated with spatially-confined large decreases in the copolar correlation coefficient (rho(hv)hv) that were embedded within broader mesocyclone "hook" signatures. These debris signatures were most obviously manifest during the F-3 to F-4 intensity stages of the tornado(s) and extended to altitudes of approximately 3 km. The rho(hv) signatures of the tornadic debris were the most easily distinguished relative to other polarimetric and radial velocity parameters (e.g., associated with large hail and/or the incipient mesocyclone). Based on our analysis, and consistent with the small number of studies found in the literature, we conclude that dual-polarimetric radar data offer at least the possibility for enhancing specificity and confidence in the process of issuing tornado warnings based only on radar detection of threatening circulation features.

  6. 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.

  7. Two-Dimensional Combinatorial Screening (2DCS) of a Bacterial rRNA A-site-like Motif Library: Defining Privileged Asymmetric Internal Loops that Bind Aminoglycosides

    PubMed Central

    Tran, Tuan; Disney, Matthew D.

    2010-01-01

    RNAs have diverse structures that are important for biological function. These structures include bulges and internal loops that can form tertiary contacts or serve as ligand binding sites. The most commonly exploited RNA drug target for small molecule intervention is the bacterial ribosome, more specifically the ribosomal RNA aminoacyl-tRNA site (rRNA A-site) which is a major target for the aminoglycoside class of antibiotics. The bacterial A-site is composed of a 1×1 nucleotide all-U internal loop and a 2×1 nucleotide all-A internal loop separated by a single GC base pair. Therefore, we probed the molecular recognition of a small library of four aminoglycosides for binding a 16384-member bacterial rRNA A-site-like internal loop library using Two-Dimensional Combinatorial Screening (2DCS). 2DCS is a microarray-based method that probes RNA and chemical spaces simultaneously. These studies sought to determine if aminoglycosides select their therapeutic target if given a choice of binding all possible internal loops derived from an A-site-like library. Results show that the bacterial rRNA A-site was not selected by any aminoglycoside. Analyses of selected sequences using the RNA Privileged Space Predictor (RNA-PSP) program show that each aminoglycoside preferentially binds different types of internal loops. For three of the aminoglycosides, 6″-azido-kanamycin A, 5-O-(2-azidoethyl) neamine, and 6″-azido-tobramycin, the selected internal loops bind with ~10-fold higher affinity than the bacterial rRNA A-site. The internal loops selected to bind 5″-azido-neomycin B bind with similar affinity as the therapeutic target. Selected internal loops that are unique for each aminoglycoside have dissociation constants ranging from 25 to 270 nM and are specific for the aminoglycoside they were selected to bind compared to the other arrayed aminoglycosides. These studies further establish a database of RNA motifs that are recognized by small molecules that could be used to

  8. 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

  9. 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

  10. Structural Determinant of Human La Protein Critical for Internal Initiation of Translation of Hepatitis C Virus RNA ▿ †

    PubMed Central

    Mondal, Tanmoy; Ray, Upasana; Manna, Asit Kumar; Gupta, Romi; Roy, Siddhartha; Das, Saumitra

    2008-01-01

    Human La protein has been implicated in facilitating internal ribosome entry site (IRES)-mediated translation of hepatitis C virus (HCV). Earlier, we demonstrated that the RNA recognition motif (RRM) encompassing residues 112 to 184 of La protein [La (112-184)] interacts with the HCV IRES near the initiator AUG codon. A synthetic peptide, LaR2C (24-mer), derived from La RRM (112-184), retains RNA binding ability, competes with La protein binding to the HCV IRES, and inhibits translation. The peptide interferes with the assembly of 48S complexes, resulting in the accumulation of preinitiation complexes that are incompetent for the 60S ribosomal subunit joining. Here, nuclear magnetic resonance spectroscopy of the HCV IRES-bound peptide complex revealed putative contact points, mutations that showed reduced RNA binding and translation inhibitory activity. The residues responsible for RNA recognition were found to form a turn in the RRM (112-184) structure. A 7-mer peptide comprising this turn showed significant translation inhibitory activity. The bound structure of the peptide inferred from transferred nuclear Overhauser effect experiments suggests that it is a β turn. This conformation is significantly different from that observed in the free RRM (112-184) NMR structure, suggesting paths toward a better-stabilized mimetic peptide. Interestingly, addition of hexa-arginine tag enabled the peptide to enter Huh7 cells and showed inhibition of HCV IRES function. More importantly, the peptide significantly inhibited replication of the HCV monocistronic replicon. Elucidation of the structural determinant of the peptide provides a basis for developing small peptidomimetic structures as potent anti-HCV therapeutics. PMID:18829760

  11. 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.

  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 John Herrington is at the wheel of an M-113 armored personnel carrier during emergency egress training at the pad. He is accompanied by (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, 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 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.

  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 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.

  15. 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.

  16. 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.

  17. 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 gets ready to drive 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.

  18. 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 John Herrington stands inside an M-113 armored personnel carrier that he is about to drive as 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 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.

  19. 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.

  20. 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 stands inside an M-113 armored personnel carrier he is about to drive, 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 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.

  1. Polythioether Particles Armored with Modifiable Graphene Oxide Nanosheets.

    PubMed

    Rodier, Bradley J; Mosher, Eric P; Burton, Spencer T; Matthews, Rachael; Pentzer, Emily

    2016-06-01

    Facile and scalable fabrication methods are attractive to prepare materials for diverse applications. Herein, a method is presented to prepare cross-linked polymeric nanoparticles with graphene oxide (GO) nanosheets covalently attached to the surface. Alkene-modified GO serves as a surfactant in a miniemulsion polymerization, and the alkene functionalities of GO exposed to the oil-phase are incorporated into the polymer particle through thiol-ene reactions, leaving the unreacted alkene functional groups of the other face of GO available for further functionalization. The surface of GO-armored polymer particles is then modified with a small molecule fluorophore or carboxylic acid functional groups that bind to Fe2 O3 and TiO2 nanoparticles. This methodology provides a facile route to preparing complex hybrid composite materials. PMID:27076068

  2. 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.

  3. 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.

  4. Thermal contact conductance measurements on Doublet III armor tile graphite

    SciTech Connect

    Doll, D.W.; Reis, E.

    1983-12-01

    Several tests were performed on the Doublet III wall armor tiles to determine the cool-down rate and to evaluate improvements made by changing the conditions at the interface between the graphite tile and the stainless steel backing plate. Thermal diffusivity tests were performed in vacuum on both TiC coated and bare graphite tiles with and without 0.13 mm (.005'') thick silver foil at the interface. The results of the armor tile cool-down tests showed improvement when a 0.13 mm (0.005'') silver foil is used at the interface. At 2.1 x 10/sup 5/ Pa (30 psi) contact pressure, the e-folding cool-down times for a TiC coated tile, bare graphite and bare graphite with a 0.06 mm (0.0035'') silver shim were 10 min., 5.0 min., and 4.1 min., respectively. Tests using high contact pressures showed that the cool-down rates converged to approx. 4.0 min. At this limit, the conduction path along the backing plate to the two cooling tubes controls the heat flow, and no further improvement could be expected. Thermal diffusivity measurements confirmed the results of the cool-down test showing that by introducing a silver foil at the interface, the contact conductance between Poco AXF-5Q graphite and 316 stainless steel could be improved by a factor of three to eight. The tests showed an increasing improvement over a range of temperatures from 25/sup 0/C to 400/sup 0/C. The data provides a technical basis for further applications of graphite tiles to cooled backing plates.

  5. 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

  6. A computational analysis of the ballistic performance of light-weight hybrid composite armors

    NASA Astrophysics Data System (ADS)

    Grujicic, M.; Pandurangan, B.; Koudela, K. L.; Cheeseman, B. A.

    2006-11-01

    The ability of hybrid light-weight fiber-reinforced polymer-matrix composite laminate armor to withstand the impact of a fragment simulating projectile (FSP) is investigated using a non-linear dynamics transient computational analysis. The hybrid armor is constructed using various combinations and stacking sequences of a high-strength/high-stiffness carbon fiber-reinforced epoxy (CFRE) and a high-ductility/high-toughness Kevlar fiber-reinforced epoxy (KFRE) composite laminates of different thicknesses. The results obtained indicate that at a fixed thickness of the armor both the stacking sequence and the number of CFRE/KFRE laminates substantially affect the ballistic performance of the armor. Specifically, it is found that the armor consisting of one layer of KFRE and one layer of CFRE, with KFRE laminate constituting the outer surface of the armor, possesses the maximum resistance towards the projectile-induced damage and failure. The results obtained are rationalized using an analysis of the elastic wave reflection and transmission behavior at the inter-laminate and laminate/air interfaces.

  7. Characterization of the pre-mRNA binding site for yeast ribosomal protein L32: the importance of a purine-rich internal loop.

    PubMed

    Li, H; Dalal, S; Kohler, J; Vilardell, J; White, S A

    1995-07-21

    The structure of the RNA binding target for Saccharomyces cerevisiae ribosomal protein L32 was examined using chemical and enzymatic probes as well as thermodynamic methods. In vivo, the production of yeast RPL32 is regulated by a feedback mechanism whereby RPL32 binds to the 5' end of its transcript and inhibits splicing. The binding site of ribosomal protein L32 on the L32 RNA transcript can be reduced to fewer than 30 nucleotides which compromise a stem-internal loop-stem structural motif. The internal loop is closed by a potential G-U pair, is asymmetric and contains mostly purines. The existence of the two helical regions was confirmed by chemical and enzymatic probing. The reactivity of the loop region suggests a structure intermediate between that of single and double-stranded RNA. Base stacking continues into the loop, but two loop bases are extremely reactive to chemical agents. The interaction between the model RNA and the protein is specific and has a dissociation constant of approximately 10 nM. Several of the loop bases are critical for protein binding, as demonstrated by mutational data and chemical protection and modification interference studies. The internal loop destabilizes the RNA, and allows the RNA to melt in an all-or-none fashion. PMID:7616567

  8. The UAH/NSSTC Advanced Radar for Meteorological and Operational Research (ARMOR)

    NASA Technical Reports Server (NTRS)

    Petersen, Walter A.; Knupp, Kevin; Carey, Lawrence D.; Phillips, Dustin; Deierling, Wiebke; Gatlin, Patrick

    2009-01-01

    The past four years have seen a marked enhancement in meteorological-radar infrastructure and radar-research capability at the University of Alabama-Huntsville (UAH) and National Space Science and Technology Center (NSSTC; a collaborative center supported by UAH, NASA-MSFC and USRA). This enhancement is due in part to the development of the ARMOR C-band dual-polarimetric radar facility (amongst other mobile radar facilities also discussed in this conference). The ARMOR radar, located at Huntsville International Airport, originated as a unique collaboration between university, government and broadcast meteorologists (the very first of its kind relative to concurrent operational, research and broadcast applications of dual-polarimetry). Contributions from each of these entities resulted in the upgrade of a surplus National Weather Service WSR-74C radar to a research-grade C-band polarimetric radar. The initial upgrade of the radar took place in late 2004 with WHNT-TV purchase and installation of a SIGMET (now Vaisala) Antenna Mounted Receiver (AMR), RVP8/RCP8 radar processor/antenna controller, new radome, and a new dual-polarimetric antenna feed. The AMR enabled simultaneous transmit and receive (STSR) capability and hence collection of dual-polarimetric moments. During the initial part of the AMR upgrade the original WSR74C antenna reflector and 250 kW magnetron-transmitter were used. In early 2005, a new 350 kW magnetron transmitter was purchased from Baron Services and installed. In October of 2006 a new high performance parabolic antenna and dual-pol feed (Seavey) were installed together with a new Orbit pedestal. ARMOR Radar control and data delivery are facilitated through the use of T-1 lines that run from the airport to both NSSTC and WHNT-TV in Huntsville. Under current operating protocols radar scanning and product development are completed at NSSTC, though meteorologists at WHNT-TV can also control the radar if desired. In its default scanning

  9. 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.

  10. Nondestructive ultrasonic characterization of armor grade silicon carbide

    NASA Astrophysics Data System (ADS)

    Portune, Andrew Richard

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

  11. Secondary RNA structure and nucleotide specificity contribute to internal initiation mediated by the human tau 5′ leader

    PubMed Central

    Veo, Bethany L.; Krushel, Leslie A.

    2012-01-01

    Mechanisms by which eukaryotic internal ribosomal entry sites (IRESs) initiate translation have not been well described. Viral IRESs utilize a combination of secondary/tertiary structure concomitant with sequence specific elements to initiate translation. Eukaryotic IRESs are proposed to utilize the same components, although it appears that short sequence specific elements are more common. In this report we perform an extensive analysis of the IRES in the human tau mRNA. We demonstrate that the tau IRES exhibits characteristics similar to viral IRESs. It contains two main structural domains that exhibit secondary interactions, which are essential for internal initiation. Moreover, the tau IRES is extremely sensitive to small nucleotide substitutions. Our data also indicates that the 40S ribosome is recruited to the middle of the IRES, but whether it scans to the initiation codon in a linear fashion is questioned. Overall, these results identify structural and sequence elements critical for tau IRES activity and consequently, provide a novel target to regulate tau protein expression in disease states including Alzheimer disease and other tauopathies. PMID:22995835

  12. 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. PMID:25180641

  13. 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

  14. RNA amplification by nucleic acid sequence-based amplification with an internal standard enables reliable detection of Chlamydia trachomatis in cervical scrapings and urine samples.

    PubMed Central

    Morré, S A; Sillekens, P; Jacobs, M V; van Aarle, P; de Blok, S; van Gemen, B; Walboomers, J M; Meijer, C J; van den Brule, A J

    1996-01-01

    In the present study, the suitability of RNA amplification by nucleic acid sequence-based amplification (NASBA) for the detection of Chlamydia trachomatis infection was investigated. When comparing different primer sets for their sensitivities in NASBA, use of both the plasmid and omp1 targets resulted in a detection limit of 1 inclusion-forming unit (IFU), while the 16S rRNA appeared to be the most sensitive RNA target for amplification (10(-3) IFU). In contrast, for DNA amplification by PCR, the plasmid target was optimal (10(-2) IFU), which is 10 times less sensitive than rRNA NASBA. To exclude false negativity in NASBA detection because of inhibition of amplification and/or inefficient sample preparation, an internal standard was developed. The internal control was added prior to sample preparation. This 16S rRNA NASBA with an internal control was compared with a plasmid DNA PCR by using a group of C. trachomatis-negative (n = 41) and -positive (n = 37) cervical scrapings, as determined by enzyme immunoassay (EIA). In addition, urine samples from the EIA-positive women were tested (n = 17). Both NASBA and PCR assays were able to detect C. trachomatis in all EIA-positive cervical scrapings, the corresponding urine samples, and two samples from the EIA-negative group. The internal NASBA standard was found clearly in all EIA-negative samples. In conclusion, these results indicate that detection of C. trachomatis by RNA amplification by NASBA with an internal standard is a suitable and highly sensitive detection method, with potential use in the diagnosis of urogenital C. trachomatis infections with cervical scrapings as well as urine specimens. PMID:8940456

  15. 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.

  16. 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

  17. 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

  18. 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.

  19. 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

  20. Rapid identification of Helicoverpa armigera and Helicoverpa zea (Lepidoptera: Noctuidae) using ribosomal RNA internal transcribed spacer 1.

    PubMed

    Perera, Omaththage P; Allen, Kerry C; Jain, Devendra; Purcell, Matthew; Little, Nathan S; Luttrell, Randall G

    2015-01-01

    Rapid identification of invasive species is crucial for deploying management strategies to prevent establishment. Recent Helicoverpa armigera (Hübner) invasions and subsequent establishment in South America has increased the risk of this species invading North America. Morphological similarities make differentiation of H. armigera from the native Helicoverpa zea (Boddie) difficult. Characteristics of adult male genitalia and nucleotide sequence differences in mitochondrial DNA are two of the currently available methods to differentiate these two species. However, current methods are likely too slow to be employed as rapid detection methods. In this study, conserved differences in the internal transcribed spacer 1 (ITS1) of the ribosomal RNA genes were used to develop species-specific oligonucleotide primers that amplified ITS1 fragments of 147 and 334 bp from H. armigera and H. zea, respectively. An amplicon (83 bp) from a conserved region of 18S ribosomal RNA subunit served as a positive control. Melting temperature differences in ITS1 amplicons yielded species-specific dissociation curves that could be used in high resolution melt analysis to differentiate the two Helicoverpa species. In addition, a rapid and inexpensive procedure for obtaining amplifiable genomic DNA from a small amount of tissue was identified. Under optimal conditions, the process was able to detect DNA from one H. armigera leg in a pool of 25 legs. The high resolution melt analysis combined with rapid DNA extraction could be used as an inexpensive method to genetically differentiate large numbers of H. armigera and H. zea using readily available reagents. PMID:26516166

  1. Rapid Identification of Helicoverpa armigera and Helicoverpa zea (Lepidoptera: Noctuidae) Using Ribosomal RNA Internal Transcribed Spacer 1

    PubMed Central

    Perera, Omaththage P.; Allen, Kerry C.; Jain, Devendra; Purcell, Matthew; Little, Nathan S.; Luttrell, Randall G.

    2015-01-01

    Rapid identification of invasive species is crucial for deploying management strategies to prevent establishment. Recent Helicoverpa armigera (Hübner) invasions and subsequent establishment in South America has increased the risk of this species invading North America. Morphological similarities make differentiation of H. armigera from the native Helicoverpa zea (Boddie) difficult. Characteristics of adult male genitalia and nucleotide sequence differences in mitochondrial DNA are two of the currently available methods to differentiate these two species. However, current methods are likely too slow to be employed as rapid detection methods. In this study, conserved differences in the internal transcribed spacer 1 (ITS1) of the ribosomal RNA genes were used to develop species-specific oligonucleotide primers that amplified ITS1 fragments of 147 and 334 bp from H. armigera and H. zea, respectively. An amplicon (83 bp) from a conserved region of 18S ribosomal RNA subunit served as a positive control. Melting temperature differences in ITS1 amplicons yielded species-specific dissociation curves that could be used in high resolution melt analysis to differentiate the two Helicoverpa species. In addition, a rapid and inexpensive procedure for obtaining amplifiable genomic DNA from a small amount of tissue was identified. Under optimal conditions, the process was able to detect DNA from one H. armigera leg in a pool of 25 legs. The high resolution melt analysis combined with rapid DNA extraction could be used as an inexpensive method to genetically differentiate large numbers of H. armigera and H. zea using readily available reagents. PMID:26516166

  2. DNA polymorphism in morels: complete sequences of the internal transcribed spacer of genes coding for rRNA in Morchella esculenta (yellow morel) and Morchella conica (black morel).

    PubMed Central

    Wipf, D; Munch, J C; Botton, B; Buscot, F

    1996-01-01

    The internal transcribed spacer (ITS) of the gene coding for rRNA was sequenced in both directions with the gene walking technique in a black morel (Morchella conica) and a yellow morel (M. esculenta) to elucidate the ITS length discrepancy between the two species groups (750-bp ITS in black morels and 1,150-bp ITS in yellow morels. PMID:8795250

  3. 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.

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

    NASA Astrophysics Data System (ADS)

    Grujicic, M.; Pandurangan, B.; Arakere, A.; Yen, C.-F.; Cheeseman, B. A.

    2013-01-01

    A critical assessment is carried out of the microstructural changes in respect of the associated reductions in material mechanical properties and of the attendant ballistic-impact failure mechanisms in prototypical friction stir welding (FSW) joints found in armor structures made of high-performance aluminum alloys (including solution-strengthened and age-hardenable aluminum alloy grades). It is argued that due to the large width of FSW joints found in thick aluminum-armor weldments, the overall ballistic performance of the armor is controlled by the ballistic limits of its weld zones (e.g., heat-affected zone, the thermomechanically affected zone, the nugget, etc.). Thus, in order to assess the overall ballistic survivability of an armor weldment, one must predict/identify welding-induced changes in the material microstructure and properties, and the operative failure mechanisms in different regions of the weld. Toward this end, a procedure is proposed in the present study which combines the results of the FSW process modeling, basic physical-metallurgy principles concerning microstructure/property relations, and the fracture mechanics concepts related to the key blast/ballistic-impact failure modes. The utility of this procedure is demonstrated using the case of a solid-solution strengthened and cold-worked aluminum alloy armor FSW-weld test structure.

  5. 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

  6. 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...

  7. 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.

  8. 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.

  9. 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.

  10. The 5' leader of the mRNA encoding the mouse neurotrophin receptor TrkB contains two internal ribosomal entry sites that are differentially regulated.

    PubMed

    Timmerman, Stephanie L; Pfingsten, Jennifer S; Kieft, Jeffrey S; Krushel, Les A

    2008-01-01

    A single internal ribosomal entry site (IRES) in conjunction with IRES transactivating factors (ITAFs) is sufficient to recruit the translational machinery to a eukaryotic mRNA independent of the cap structure. However, we demonstrate that the mouse TrkB mRNA contains two independent IRESes. The mouse TrkB mRNA consists of one of two 5' leaders (1428 nt and 448 nt), both of which include the common 3' exon (Ex2, 344 nt). Dicistronic RNA transfections and in vitro translation of monocistronic RNA demonstrated that both full-length 5' leaders, as well as Ex2, exhibit IRES activity indicating the IRES is located within Ex2. Additional analysis of the upstream sequences demonstrated that the first 260 nt of exon 1 (Ex1a) also contains an IRES. Dicistronic RNA transfections into SH-SY5Y cells showed the Ex1a IRES is constitutively active. However, the Ex2 IRES is only active in response to retinoic acid induced neural differentiation, a state which correlates with the synthesis of the ITAF polypyrimidine tract binding protein (PTB1). Correspondingly, addition or knock-down of PTB1 altered Ex2, but not Ex1a IRES activity in vitro and ex vivo, respectively. These results demonstrate that the two functionally independent IRESes within the mouse TrkB 5' leader are differentially regulated, in part by PTB1. PMID:18779873

  11. 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.

  12. Microstructure-property relationship in silicon carbide armor ceramics

    NASA Astrophysics Data System (ADS)

    Demirbas, Memduh Volkan

    Defects are one of the factors that show a negative effect on the ballistic performance. Uniform microstructures with a low percentage of well distributed porosity could possibly demonstrate high ballistic strength; therefore, it is of interest to estimate the parameters that define the spatial arrangement of defects. This aspect of microstructures was investigated in a variety of silicon carbide ceramics ranging from off-density sintered samples to high density hot-pressed armor grade samples. The spatial distribution of defects was examined by various techniques including nearest neighbor distance distributions, tessellation analysis, and pair correlation functions. Random distributions were observed for most of the samples with some degree of clustering. Hardness was selected as a mechanical property to correlate with microstructural findings. Hardness contour maps were constructed by indenting samples with a statistically significant number of indents per load to see the variation in terms of location. The large number of indents allowed for Weibull analysis to be used to examine the spread in the data and to test spatial variability. A high degree of correlation was obtained between microstructural parameters and hardness/Weibull modulus values. Smaller defect sizes and homogenous distribution of defects were shown to provide higher hardness values. A sintered SiC tile was examined using ultrasound to determine high and low amplitude regions in C-scan image maps. Serial sectioning was performed on diced samples from these two regions. Although no significant difference was observed in terms of density and average defect size, statistical tests showed that the difference in the largest defect size detected in low amplitude and high amplitude regions was significant. Clusters of defects were also identified in the samples from the low amplitude regions. The signal loss that was observed in C-scans maps could partially be attributed to these results. A

  13. Analysis of inclusion distributions in silicon carbide armor ceramics

    NASA Astrophysics Data System (ADS)

    Bakas, Michael Paul

    It was determined that intrinsic microstructural defects (i.e. inclusions) are the preferential fragmentation path (initiation or propagation) for ballistically impacted SiC, and may contribute to variation in ballistic performance. Quasi-static and ballistic samples of SiC were studied and inclusions caused by common SiC sintering aids and/or impurities were identified. Ballistic rubble surfaces showed large inclusions of 10-400 micron size, while examination of polished cross-sections of the fragments showed only inclusions under 5 microns in size. The fact that large inclusions were found preferentially on rubble surfaces demonstrates a link between severe microstructural defects and the fragmentation of SiC armor. Rubble of both a "good" and "bad" performing SiC target were examined. Inclusion size data was gathered and fit to a distribution function. A difference was observed between the targets. The "good" target had twice the density of inclusions on its rubble in the size range less than 30 microns. No significant difference between distributions was observed for inclusion sizes greater than 40 microns. The "good" target fractured into an overall smaller fragment size distribution than the "bad" target, consistent with fragmentation at higher stresses. Literature suggests that the distribution of defects activated under dynamic conditions will be determined by the maximum stress reached locally in the target. On the basis of the defect distributions on its rubble, the "good" target appears to have withstood higher stresses. The fragment size distribution and inclusion size distribution on fragment surfaces both indicate higher stresses in the "good" target. Why the "good" target withstood a greater stress than the "bad" target remains a subject for conjecture. It is speculated that the position of severe "anomalous" defects may be influencing the target's performance, but this currently cannot be demonstrated conclusively. Certainly, this research shows

  14. An Internal Ribosome Entry Site Directs Translation of the 3′-Gene from Pelargonium Flower Break Virus Genomic RNA: Implications for Infectivity

    PubMed Central

    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. PMID:21818349

  15. Xenopus transcription factor IIIA binds primarily at junctions between double helical stems and internal loops in oocyte 5S RNA.

    PubMed Central

    Christiansen, J; Brown, R S; Sproat, B S; Garrett, R A

    1987-01-01

    RNases and chemical probes were used to study the accessibility of each nucleotide of 5S RNA in the native and reconstituted 7S particle from Xenopus laevis oocytes. RNase or chemically treated 5S RNA from intact 7S particles was isolated and analysed using an oligodeoxynucleotide primer and reverse transcriptase. The results were superimposed on a cylindrical projection of an RNA double helix and the protection effects were shown to cluster at two regions on the molecular surface. A three-dimensional model is proposed for the 7S particle in which protein-RNA contacts occur mainly in the major groove of 5S RNA. Images Fig. 1. Fig. 2. PMID:3582366

  16. 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...

  17. 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...

  18. 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...

  19. 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...

  20. 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...

  1. Establishment of the armored scale, Rhizaspidiotus donacis, a biological control agent of Arundo donax

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The armored scale biological control agent, Rhizaspidiotus donacis (Leonardi) (Hemiptera; Diaspididae) has established populations on the invasive weed, Arundo donax L. (Poaceae; Arundinoideae) in Del Rio (Val Verde, Co.) and in field plots at the USDA-APHIS-PPQ-Moore Airbase, Edinburg (Hidalgo Co.)...

  2. 27 CFR 478.92 - How must licensed manufacturers and licensed importers identify firearms, armor piercing...

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 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 2011-04-01 2010-04-01 true How must licensed manufacturers and licensed importers identify firearms, armor piercing ammunition, and large capacity...

  3. 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...

  4. 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...

  5. 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...

  6. 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...

  7. 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...

  8. 76 FR 35024 - National Institute of Justice Stab-Resistant Body Armor Standard Workshop

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-15

    ...The National Institute of Justice (NIJ) and the National Institute of Standards and Technology (NIST) are jointly hosting workshop focused on the NIJ Stab-Resistant Body Armor Standard. It is anticipated that the discussion at the workshop will be directed primarily toward manufacturers, certification bodies, and test laboratories. NIJ and NIST are hosting this workshop specifically to discuss......

  9. 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.

  10. 30 CFR 77.700 - Grounding metallic sheaths, armors, and conduits enclosing power conductors.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Grounding metallic sheaths, armors, and conduits enclosing power conductors. 77.700 Section 77.700 Mineral Resources MINE SAFETY AND HEALTH... AND SURFACE WORK AREAS OF UNDERGROUND COAL MINES Grounding § 77.700 Grounding metallic sheaths,...

  11. 30 CFR 77.700 - Grounding metallic sheaths, armors, and conduits enclosing power conductors.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Grounding metallic sheaths, armors, and conduits enclosing power conductors. 77.700 Section 77.700 Mineral Resources MINE SAFETY AND HEALTH... AND SURFACE WORK AREAS OF UNDERGROUND COAL MINES Grounding § 77.700 Grounding metallic sheaths,...

  12. 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...

  13. 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...

  14. 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...

  15. 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...

  16. 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...

  17. 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

  18. A Computational Investigation of the Multi-Hit Ballistic-Protection Performance of Laminated Transparent-armor Systems

    NASA Astrophysics Data System (ADS)

    Grujicic, Mica; Pandurangan, B.; Coutris, N.

    2012-06-01

    Multi-hit ballistic-protection performance of a prototypical laminated glass/polycarbonate transparent armor is investigated using a series of transient nonlinear dynamics analyses of armor impact with a sequence of four M2AP full metal jacket (FMJ) armor-piercing bullets. All calculations were carried out using ABAQUS/Explicit commercial finite element program (ABAQUS Version 6.7, User Documentation, Dessault Systems, 2007), and the computational results obtained were compared to their experimental counterparts obtained by Dolan (Ballistic Transparent-armor Testing Using a Multi-hit Rifle Pattern, Bachelors, Thesis, Kettering University, December 2007). The comparison revealed that (a) The proposed computational procedure can reasonably well account for the observed multi-hit ballistic-protection performance of the laminated transparent armor; (b) The role of prior bullet hits in reducing armor's ballistic-protection performance is clearly revealed; (c) The role of polycarbonate lamina in preventing glass fragments from entering the vehicle interior is clearly demonstrated; and (d) Experimentally observed inability of the transparent armor to defeat 0.50-caliber Fragment Simulating Projectiles (FSPs) is confirmed.

  19. Molecular Recognition of 6′-N-5-Hexynoate Kanamyin A and RNA 1×1 Internal Loops Containing CA Mismatches

    PubMed Central

    Tran, Tuan; Disney, Matthew D.

    2011-01-01

    In our previous study to identify the RNA internal loops that bind an aminoglycoside derivative, we determined that 6′-N-5-hexynoate kanamycin A prefers to bind 1×1 nucleotide internal loops containing C•A mismatches. In this present study, the molecular recognition between a variety of RNAs that are mutated around the C•A loop and the ligand was investigated. Studies show that both loop nucleotides and loop closing pairs affect binding affinity. Most interestingly, it was shown that there is a correlation between the thermodynamic stability of the C•A internal loops and ligand affinity. Specifically, C•A loops that had relatively high or low stability bound the ligand most weakly whereas loops with intermediate stability bound the ligand most tightly. In contrast, there is no correlation between the likelihood that a loop forms a C-A+ pair at lower pH and ligand affinity. It was also found that a 1×1 nucleotide C•A loop that bound to the ligand with the highest affinity is identical to the consensus site in RNAs that are edited by adenosine deaminases acting on RNA type 2 (ADAR2). These studies provide a detailed investigation of factors affecting small molecule recognition of internal loops containing C•A mismatches, which are present in a variety of RNAs that cause disease. PMID:21207945

  20. 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

  1. 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

  2. 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

  3. Internal translation initiation and eIF4F/ATP-independent scanning of mRNA by eukaryotic ribosomal particles

    PubMed Central

    Agalarov, Sultan Ch.; Sakharov, Pavel A.; Fattakhova, Dina Kh.; Sogorin, Evgeny A.; Spirin, Alexander S.

    2014-01-01

    The recombinant mRNAs with 5′-untranslated region, called omega leader, of tobacco mosaic virus RNA are known to be well translated in eukaryotic cell-free systems, even if deprived of cap structure. Using the method of primer extension inhibition (toe-printing), the ribosomal particles were shown to initiate translation at uncapped omega leader when its 5′-end was blocked by a stable RNA-DNA double helix, thus providing evidence for internal initiation. The scanning of the leader sequence and the formation of ribosomal 48S initiation complexes at the initiation AUG codon occurred in the absence of ATP-dependent initiation factor eIF4F, as well as without ATP. The latter results implied the ability of ribosomal initiation complexes for ATP-independent, diffusional wandering (also called bi-directional movement) along the leader sequence during scanning. PMID:24657959

  4. A gene-specific effect of an internal deletion in the Bdp1 subunit of the RNA polymerase III transcription initiation factor TFIIIB.

    PubMed

    Ishiguro, Akira; Kassavetis, George A

    2003-07-31

    The Saccharomyces cerevisiae RPR1 gene encodes the RNA subunit of its RNase P, which processes RNA polymerase (pol) III primary transcripts. RPR1, which is transcribed by pol III, has been isolated as a multicopy suppressor of a specific small internal deletion (amino acids 253-269) in the Bdp1 subunit of transcription factor TFIIIB, the core pol III transcription factor. The selective effect of this Bdp1 deletion on RPR1 transcription has been analyzed in vitro. It is shown that TFIIIC-dependent assembly of TFIIIB on the RPR1 promoter is specifically sensitive to this Bdp1 deletion, leading to gene-specifically defective single-round and multiple-round transcription. PMID:12885403

  5. 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

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. Simulation Tools for Ultrasonic Inspections of Multi-Layer Armor Panels

    NASA Astrophysics Data System (ADS)

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

    2011-06-01

    Some armor panels are fabricated from several layers of material including ceramics, graphite and/or glass composites, and rubber. This multi-layer makeup can complicate UT inspection, since many possible sound paths (including intra-layer reverberations) can contribute to observed UT signals. At last year's QNDE conference we reported on baseline property measurements (density, sound speed, attenuation, etc.) for the constituent layers of one prototype panel, and we discussed how that information was used to design an ultrasonic inspection to look for disbonding at interfaces. We now report on progress to develop better simulation tools for armor panel inspections. In particular we consider normal-incidence pulse/echo inspections and use a paraxial beam model to predict time-domain signals for unflawed panels and those containing large delaminations. The model uses the frequency-dependent baseline property data as inputs, and treats beam spread and focusing effects. We describe the modeling approach and present comparisons of model predictions to the experimental data gathered last year during inspections of five-layer armor panels.

  16. Validation of an internally controlled one-step real-time multiplex RT-PCR assay for the detection and quantitation of dengue virus RNA in plasma.

    PubMed

    Hue, Kien Duong Thi; Tuan, Trung Vu; Thi, Hanh Tien Nguyen; Bich, Chau Tran Nguyen; Anh, Huy Huynh Le; Wills, Bridget A; Simmons, Cameron P

    2011-11-01

    Dengue is mosquito-borne virus infection that annually causes ~50 million clinically apparent cases worldwide. An internally controlled one-step real-time multiplex RT-PCR assay was developed for detection and quantitation of DENV RNA in plasma sample by using specific primers and fluorogenic TaqMan probes. All primers and probes targeted sequences near the 3' end of the NS5 gene. The method comprised two multiplex assays and was validated for sensitivity, specificity, linearity, reproducibility and precision. An internal control template was spiked into each clinical specimen to provide quality assurance for each experimental step. The assay allowed for detection of between 0.5 and 3 infectious particles per mL, is rapid and has been operationally characterized in 287 Vietnamese dengue patients from two therapeutic intervention trials at the Hospital for Tropical Diseases, Ho Chi Minh City, Viet Nam. PMID:21843553

  17. 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

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

    PubMed

    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, Mg(2+)-induced switch between two alternative conformations: from 'open', elongated morphologies at 0-2 mM Mg(2+) concentration to a 'closed', comma-shaped conformation at 4-6 mM Mg(2+). 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 Mg(2+) 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

  19. [Internal initiation of translation in eukaryotes. Chemical probing of the encephalomyocarditis virus RNA IRES-element in the 48S preinitiation complex].

    PubMed

    Boroviagin, A V; Ezrokhi, M V; Shatskiĭ, I N

    1995-01-01

    Using in vitro T7 polymerase system, the transcript containing the IRES-element (nts 315-833), and the initial part of the coding sequence of encephalomyocarditis virus (EMCV) RNA (nts 834-1155) was prepared. Its complex with the 40S ribosomal subunit (48S preinitiation complex) was then isolated by sucrose gradient sedimentation from ascites carcinoma Krebs2 cell extracts after preincubation with the transcript. The complex was treated with dimethylsulphate (DMS), a common reagent for chemical probing of A and C residues in single-stranded RNA regions. The modified nucleotides were identified by primer extension inhibition analysis in reverse transcription reaction. The pattern of modification of the 48S complex was compared with that for the corresponding free mRNP. Multiple protection of A residues against DMS modification was found in the domains of the IRES-element proximal to the initiation AUG codon (nt 834-836). The mechanism of internal translational initiation of EMCV RNA and other picornaviral RNAs is discussed. PMID:8552069

  20. Genotyping of a miso and soy sauce fermentation yeast, Zygosaccharomyces rouxii, based on sequence analysis of the partial 26S ribosomal RNA gene and two internal transcribed spacers.

    PubMed

    Suezawa, Yasuhiko; Suzuki, Motofumi; Mori, Haruhiko

    2008-09-01

    We analyzed sequences of the D1D2 domain of the 26S ribosomal RNA gene (26S rDNA sequence), the internal transcribed spacer 1, the 5.8S ribosomal RNA gene, and the internal transcribed spacer 2 (the ITS sequence) from 46 strains of miso and soy sauce fermentation yeast, Zygosaccharomyces rouxii and a closely related species, Z. mellis, for typing. Based on the 26S rDNA sequence analysis, the Z. rouxii strains were of two types, and the extent of sequence divergence between them was 2.6%. Based on the ITS sequence analysis, they were divided into seven types (I-VII). Between the type strain (type I) and type VI, in particular, a 12% difference was detected. The occurrence of these nine genotypes with a divergence of more than 1% in these two sequences suggests that Z. rouxii is a species complex including novel species and hybrids. Z. mellis strains were of two types (type alpha and type beta) based on the ITS sequence. Z. rouxii could clearly be distinguished from Z. mellis by 26S rDNA and ITS sequence analyses, but not by the 16% NaCl tolerance, when used as the sole key characteristic for differentiation between the two species. PMID:18776675

  1. 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

  2. An RNA molecular switch: Intrinsic flexibility of 23S rRNA Helices 40 and 68 5’-UAA/5’-GAN internal loops studied by molecular dynamics methods

    PubMed Central

    Réblová, Kamila; Střelcová, Zora; Kulhánek, Petr; Beššeová, Ivana; Mathews, David H.; Nostrand, Keith Van; Yildirim, Ilyas; Turner, Douglas H.; Šponer, Jiří

    2010-01-01

    Functional RNA molecules such as ribosomal RNAs frequently contain highly conserved internal loops with a 5’-UAA/5’-GAN (UAA/GAN) consensus sequence. The UAA/GAN internal loops adopt distinctive structure inconsistent with secondary structure predictions. The structure has a narrow major groove and forms a trans Hoogsteen/Sugar edge (tHS) A/G base pair followed by an unpaired stacked adenine, a trans Watson-Crick/Hoogsteen (tWH) U/A base pair and finally by a bulged nucleotide (N). The structure is further stabilized by a three-adenine stack and base-phosphate interaction. In the ribosome, the UAA/GAN internal loops are involved in extensive tertiary contacts, mainly as donors of A-minor interactions. Further, this sequence can adopt an alternative 2D/3D pattern stabilized by a four-adenine stack involved in a smaller number of tertiary interactions. The solution structure of an isolated UAA/GAA internal loop shows substantially rearranged base pairing with three consecutive non-Watson-Crick base pairs. Its A/U base pair adopts an incomplete cis Watson-Crick/Sugar edge (cWS) A/U conformation instead of the expected Watson-Crick arrangement. We performed 3.1 µs of explicit solvent molecular dynamics (MD) simulations of the X-ray and NMR UAA/GAN structures, supplemented by MM-PBSA free energy calculations, locally enhanced sampling (LES) runs, targeted MD (TMD) and nudged elastic band (NEB) analysis. We compared parm99 and parmbsc0 force fields and net-neutralizing Na+ vs. excess salt KCl ion environments. Both force fields provide a similar description of the simulated structures, with the parmbsc0 leading to modest narrowing of the major groove. The excess salt simulations also cause a similar effect. While the NMR structure is entirely stable in simulations, the simulated X-ray structure shows considerable widening of the major groove, loss of base-phosphate interaction and other instabilities. The alternative X-ray geometry even undergoes conformational

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

    PubMed Central

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

    1998-01-01

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

  4. A single base deletion in the Tfm androgen receptor gene creates a short-lived messenger RNA that directs internal translation initiation.

    PubMed Central

    Gaspar, M L; Meo, T; Bourgarel, P; Guenet, J L; Tosi, M

    1991-01-01

    Testosterone-resistant male mice hemizygous for the X-chromosome-linked mutant gene Tfm express detectable but severely reduced levels of androgen receptor mRNA, amounting to about 10% of the level found in normal male littermates. No structural abnormality could be identified in the coding region of the messenger by a series of RNase-protection assays. However, cell-free translation of RNAs transcribed in vitro from enzymatically amplified overlapping segments of exon 1 revealed a truncated receptor protein and helped to localize the site of premature termination. Sequence analysis of the relevant DNA segment disclosed that deletion of a single nucleotide in the hexacytidine stretch at position 1107-1112 alters the reading frame of the messenger and introduces 41 missense amino acids before a premature termination codon at position 1235-1237. Separately initiated carboxyl-terminal polypeptides are synthesized in vitro, starting probably at the in-frame AUG codon 1507-1509, which lies in a favorable context for translation initiation, and at the non-AUG codon 1144-1146. Transcriptional impairments of the Tfm gene were ruled out by a quantitative analysis of enzymatically amplified nuclear RNA precursors. No other change could be identified by sequencing the complete coding region of Tfm cDNA. The finding of the unsuspected termination codon and the evidence of internally initiated carboxyl-terminal polypeptides reconcile previous conclusions and account for all known phenotypic properties of the mutation. Images PMID:1924321

  5. 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

  6. The Impacts of Armoring Our Deltas: Mapping and Modeling Large-Scale Deltaplain Aggradation

    NASA Astrophysics Data System (ADS)

    Overeem, I.; Higgins, S.; Syvitski, J. P.; Kettner, A. J.; Brakenridge, R.

    2014-12-01

    Humans have hardened land-water boundaries in almost every delta they live on. Engineering includes stabilizing and embanking channels to protect from river floods, building dikes around islands and emerging bars to reclaim land, and putting up sea walls to protect from waves and storm surges. These measures aim to reduce the exchange of water and sediment between the distributary delta channel network and the adjacent deltaplain. To first order, armoring of deltas results in net elevation loss of the floodplain, due to subsidence, compaction and reduced aggradation. Here, we ask what are the mechanisms of aggradation in 'armored' deltas? How do aggradation patterns compare to more natural depositional patterns? We analyze 2-week period aggregates of MODIS satellite data from 2000 onwards to map inundation patterns due to irrigation, river floods and storm surges for selected deltas. Using a MODIS band-ratio, we assess relative concentrations of suspended sediment in stagnant water on the floodplains. In addition, we use a simple approach to route sediment through the delta distributary network based on the relative channel geometries. A depositional process model then calculates cross-channel sediment flux as an exponential decay function, and determines sediment deposition over inundated areas. Stacked inundation maps show vast areas of deltaplains have flooded between 2000-2014, despite armoring channels with dikes, and coastlines with seawalls. Flooding is caused by overtopping of levees and more rarely by breaching and in those latter cases the flooded areas are often locally constrained. In Asian deltas, rice paddy irrigation with floodwater can be mapped even in the more distal floodplain. Our model predicts that inundated areas still receive significant amounts of fresh sediment, but that the pattern is more variable than in natural systems. Sparse in-situ observations of floodplain aggradation rates and storm surge deposits corroborate high, but localized

  7. 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.

  8. 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.

  9. Experimental and Numerical Investigations on the Ballistic Performance of Polymer Matrix Composites Used in Armor Design

    NASA Astrophysics Data System (ADS)

    Colakoglu, M.; Soykasap, O.; Özek, T.

    2007-01-01

    Ballistic properties of two different polymer matrix composites used for military and non-military purposes are investigated in this study. Backside deformation and penetration speed are determined experimentally and numerically for Kevlar 29/Polivnyl Butyral and Polyethylene fiber composites because designing armors for only penetration is not enough for protection. After experimental ballistic tests, a model is constructed using finite element program, Abaqus. The backside deformation and penetration speed are determined numerically. It is found that the experimental and numeric results are in agreement and Polyethylene fiber composite has much better ballistic limit, the backside deformation, and penetration speed than those of Kevlar 29/Polivnyl Butyral composite if areal densities are considered.

  10. 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.

  11. The weight optimization of an armored crashworthy crewseat through the use of advanced composites and design

    NASA Technical Reports Server (NTRS)

    Lindsay, Howard A.; Motoyama, Stephen M.; Smith, Kent F.

    1990-01-01

    The development of composite-related technology applicable to armored crashworthy helicopter crewseats is discussed. The main objective was to achieve a significant weight reduction relative to the first-generation seats exemplified by the UH-60A and the AH-64A designs. This weight reduction was achieved while maintaining full compliance with the most recent version of the military crashworthy crewseat specification, MIL-S-58095A. The technology developed during this effort is intended to apply to the next generation of Army helicopters, such as LHX.

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

    PubMed

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

    2015-01-01

    A number of biological armors, such as turtle shells, consist of a strong exoskeleton covered with a thin keratin coating. The mechanical role upon impact of this keratin coating has surprisingly not been investigated thus far. Low-velocity impact tests on the turtle shell reveal a unique toughening phenomenon attributed to the thin covering keratin layer, the presence of which noticeably improves the fracture energy and shell integrity. Synthetic substrate/coating analogues were subsequently prepared and exhibit an impact behavior similar to the biological ones. The results of the present study may improve our understanding, and even future designs, of impact-tolerant structures. PMID:25599251

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. An Investigation into Hot Deformation Characteristics and Processing Maps of High-Strength Armor Steel

    NASA Astrophysics Data System (ADS)

    Bobbili, Ravindranadh; Madhu, V.

    2015-12-01

    The isothermal hot compression tests of high-strength armor steel over wide ranges of strain rates (0.01-10 /s) and deformation temperatures (950-1100 °C) are carried out using Gleeble thermo-simulation machine. The true stress-strain data obtained from the experiments are employed to establish the constitutive equations based on the strain-compensated Arrhenius model. With strain-compensated Arrhenius model, good agreement between the experimental and predicted values is achieved, which represents the highest accuracy in comparison with the other models. The hot deformation activation energy is estimated to be 512 kJ/mol. By employing dynamic material model, the processing maps of high-strength armor steel at various strains are established. A maximum efficiency of about 45% of power dissipation is obtained at high temperature and low strain rate. Due to the high power dissipation efficiency and excellent processing ability in dynamic recrystallization zone for metal material, the optimum processing conditions are selected such that the temperature range is between 1050 and 1100°C and the strain rate range is between 0.01 and 0.1/s. Transmission electron microscopy observations show that the dislocation density is directly associated with the value of processing efficiency.

  18. Morphometric structural diversity of a natural armor assembly investigated by 2D continuum strain analysis.

    PubMed

    Varshney, Swati; Song, Juha; Li, Yaning; Boyce, Mary C; Ortiz, Christine

    2015-12-01

    Many armored fish scale assemblies use geometric heterogeneity of subunits as a design parameter to provide tailored biomechanical flexibility while maintaining protection from external penetrative threats. This study analyzes the spatially varying shape of individual ganoid scales as a structural element in a biological system, the exoskeleton of the armored fish Polypterus senegalus (bichir). X-ray microcomputed tomography is used to generate digital 3D reconstructions of the mineralized scales. Landmark-based geometric morphometrics is used to measure the geometric variation among scales and to define a set of geometric parameters to describe shape variation. A formalism using continuum mechanical strain analysis is developed to quantify the spatial geometry change of the scales and illustrate the mechanisms of shape morphing between scales. Five scale geometry variants are defined (average, anterior, tail, ventral, and pectoral fin) and their functional implications are discussed in terms of the interscale mobility mechanisms that enable flexibility within the exoskeleton. The results suggest that shape variation in materials design, inspired by structural biological materials, can allow for tunable behavior in flexible composites made of segmented scale assemblies to achieve enhanced user mobility, custom fit, and flexibility around joints for a variety of protective applications. PMID:26481418

  19. 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

  20. United States Marine Corps light armored vehicle ride and shock mobility test

    SciTech Connect

    Casterlow, D.; Salami, M.R.

    1995-06-01

    Mobility on the battlefield has been a major concern since the beginning of modern warfare. How do you transport troops more efficiently, in the least amount of time, from place to place on the battlefield? In the early days of World War I, came the invention of the tank and different types of armored vehicles. These vehicles were very slow and moved over a limited variety of terrain. Today, with faster, more powerful armored vehicles, extended testing is being done to determine their ability to move over various types of terrain encountered on the modern battlefield. Along with this testing, studies are performed which take into account the effect of the ride on soldiers. It has been proven that a sustained rough ride, of over 6 watts of vertical absorbed power, will affect a soldier`s ability to fight, once he reaches the battle. As a result, different vehicles go through testing in various off-road terrain to determine which one can handle the roughest terrain, at the fastest speed, while transporting troops, without imposing large amounts of human vibration on the soldiers. This is done through ride and shock mobility tests.

  1. Development of a Laboratory Scale Test Facility (LSTF) to investigate Armor solutions against buried explosive threats

    NASA Astrophysics Data System (ADS)

    Garcia, Felipe; Sinibaldi, Jose

    2009-11-01

    This LSTF will address the effects of High Velocity Sand Blast Impact; massive overpressures, impulsive effects, kinetic energy and momentum, from developing the type of flat sand- loading profile required for code validation purposes. The background of this study is to generate a planar shock-wave profile and a flat-loading profile from high velocity sand and air blast onto intended flat-plate targets, to properly characterize the codes under development; to do this we propose to use a flyer plate, which is explosively driven, so, we end with a design in which a slanted flyer plate, with an explosive layer underneath it, is set-up and detonated from one end, as the detonation wave runs through the explosive layer, it pushes the flyer plate. If all the geometry is carefully designed and the flyer plate/explosive layers are precisely positioned, in theory we should be able to produce a flat flyer plate that travels on the order of 1 to 2 km/s towards a layer of sand, therefore generating a shock wave within the sand that will eventually accelerate the sand with a flat top-hat profile towards the intended target, thus achieving a flat sand loading profile onto the target. Success in this domain will allow ease of testing of advanced armor concepts against simulate buried explosive threats, thus providing validation for numerical codes that will be used to perform optimization of novel armor designs at low costs.

  2. Differentiation of Phylogenetically Related Slowly Growing Mycobacteria Based on 16S-23S rRNA Gene Internal Transcribed Spacer Sequences

    PubMed Central

    Roth, Andreas; Fischer, Marga; Hamid, Mohamed E.; Michalke, Sabine; Ludwig, Wolfgang; Mauch, Harald

    1998-01-01

    Interspecific polymorphisms of the 16S rRNA gene (rDNA) are widely used for species identification of mycobacteria. 16S rDNA sequences, however, do not vary greatly within a species, and they are either indistinguishable in some species, for example, in Mycobacterium kansasii and M. gastri, or highly similar, for example, in M. malmoense and M. szulgai. We determined 16S-23S rDNA internal transcribed spacer (ITS) sequences of 60 strains in the genus Mycobacterium representing 13 species (M. avium, M. conspicuum, M. gastri, M. genavense, M. kansasii, M. malmoense, M. marinum, M. shimoidei, M. simiae, M. szulgai, M. triplex, M. ulcerans, and M. xenopi). An alignment of these sequences together with additional sequences available in the EMBL database (for M. intracellulare, M. phlei, M. smegmatis, and M. tuberculosis) was established according to primary- and secondary-structure similarities. Comparative sequence analysis applying different treeing methods grouped the strains into species-specific clusters with low sequence divergence between strains belonging to the same species (0 to 2%). The ITS-based tree topology only partially correlated to that based on 16S rDNA, but the main branching orders were preserved, notably, the division of fast-growing from slowly growing mycobacteria, separate branching for M. simiae, M. genavense, and M. triplex, and distinct branches for M. xenopi and M. shimoidei. Comparisons of M. gastri with M. kansasii and M. malmoense with M. szulgai revealed ITS sequence similarities of 93 and 88%, respectively. M. marinum and M. ulcerans possessed identical ITS sequences. Our results show that ITS sequencing represents a supplement to 16S rRNA gene sequences for the differentiation of closely related species. Slowly growing mycobacteria show a high sequence variation in the ITS; this variation has the potential to be used for the development of probes as a rapid approach to mycobacterial identification. PMID:9431937

  3. Complete Genome Sequences of Dengue Virus Type 1 to 4 Strains Used for the Development of CBER/FDA RNA Reference Reagents and WHO International Standard Candidates for Nucleic Acid Testing

    PubMed Central

    Añez, Germán; Heisey, Daniel A.; Volkova, Evgeniya

    2016-01-01

    Dengue virus (DENV), a member of the Flaviviridae family, is the most common and clinically significant arbovirus in the world and is endemic in more than 100 countries. Here, we report the complete sequences of four DENV serotypes used in the development of the CBER/FDA RNA reference reagents and WHO International Standard candidates for nucleic acid testing. PMID:26868382

  4. Effect of PTA Hardfaced Interlayer Thickness on Ballistic Performance of Shielded Metal Arc Welded Armor Steel Welds

    NASA Astrophysics Data System (ADS)

    Balakrishnan, M.; Balasubramanian, V.; Madhusudhan Reddy, G.

    2013-03-01

    Ballistic performance of armor steel welds is very poor due to the usage of low strength and low hardness austenitic stainless steel fillers, which are traditionally used to avoid hydrogen induced cracking. In the present investigation, an attempt has been made to study the effect of plasma transferred arc hardfaced interlayer thickness on ballistic performance of shielded metal arc welded armor steel weldments. The usefulness of austenitic stainless steel buttering layer on the armor grade quenched and tempered steel base metal was also considered in this study. Joints were fabricated using three different thickness (4, 5.5, and 7 mm) hardfaced middle layer by plasma transferred arc hardfacing process between the top and bottom layers of austenitic stainless steel using shielded metal arc welding process. Sandwiched joint, in addition with the buttering layer served the dual purpose of weld integrity and ballistic immunity due to the high hardness of hardfacing alloy and the energy absorbing capacity of soft backing weld deposits. This paper will provide some insight into the usefulness of austenitic stainless steel buttering layer on the weld integrity and plasma transferred arc hardfacing layer on ballistic performance enhancement of armor steel welds.

  5. 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 ...

  6. Skeletal histology of the dermal armor of Placodontia: the occurrence of ‘postcranial fibro-cartilaginous bone’ and its developmental implications

    PubMed Central

    Scheyer, Torsten M

    2007-01-01

    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

  7. RNA topology

    PubMed Central

    2013-01-01

    A new variety on non-coding RNA has been discovered by several groups: circular RNA (circRNA). This discovery raises intriguing questions about the possibility of the existence of knotted RNA molecules and the existence of a new class of enzymes changing RNA topology, RNA topoisomerases. PMID:23603781

  8. Secondary structure analyses of the nuclear rRNA internal transcribed spacers and assessment of its phylogenetic utility across the Brassicaceae (mustards).

    PubMed

    Edger, Patrick P; Tang, Michelle; Bird, Kevin A; Mayfield, Dustin R; Conant, Gavin; Mummenhoff, Klaus; Koch, Marcus A; Pires, J Chris

    2014-01-01

    The internal transcribed spacers of the nuclear ribosomal RNA gene cluster, termed ITS1 and ITS2, are the most frequently used nuclear markers for phylogenetic analyses across many eukaryotic groups including most plant families. The reasons for the popularity of these markers include: 1.) Ease of amplification due to high copy number of the gene clusters, 2.) Available cost-effective methods and highly conserved primers, 3.) Rapidly evolving markers (i.e. variable between closely related species), and 4.) The assumption (and/or treatment) that these sequences are non-functional, neutrally evolving phylogenetic markers. Here, our analyses of ITS1 and ITS2 for 50 species suggest that both sequences are instead under selective constraints to preserve proper secondary structure, likely to maintain complete self-splicing functions, and thus are not neutrally-evolving phylogenetic markers. Our results indicate the majority of sequence sites are co-evolving with other positions to form proper secondary structure, which has implications for phylogenetic inference. We also found that the lowest energy state and total number of possible alternate secondary structures are highly significantly different between ITS regions and random sequences with an identical overall length and Guanine-Cytosine (GC) content. Lastly, we review recent evidence highlighting some additional problematic issues with using these regions as the sole markers for phylogenetic studies, and thus strongly recommend additional markers and cost-effective approaches for future studies to estimate phylogenetic relationships. PMID:24984034

  9. Conservation of sequence in the internal transcribed spacers and 5.8S ribosomal RNA among geographically separated isolates of parasitic scuticociliates (Ciliophora, Orchitophryidae).

    PubMed

    Goggin, C L; Murphy, N E

    2000-02-24

    Nucleotide sequence from the internal transcribed spacers (ITS1 and ITS2) and the 5.8S gene from the ribosomal RNA gene cluster of isolates of the scuticociliate Orchitophrya stellarum from 4 asteroid hosts were compared. Surprisingly, these data (495 bp) were identical for O. stellarum isolated from the testes of Asterias amurensis from Japan; Pisaster ochraceus from British Columbia, Canada; Asterias rubens from The Netherlands; and Asterias vulgaris from Prince Edward Island, Canada. These sequence data were compared to those from 3 scuticociliates which parasitise crustaceans: Mesanophrys pugettensis, M. chesapeakensis and Anophryoides haemophila. No difference was found in this region between the nucleotide sequence of M. pugettensis and M. chesapeakensis. The sequence of Mesanophrys spp. differed by 9.2% in the ITS1 and 4.7% in the ITS2 from that of O. stellarum. The sequence from the ITS1 (135 bp) and ITS2 (233 bp) of A. haemophila differed by 42.6 and 20.5% respectively from those of O. stellarum. Therefore, nucleotide sequence of the ITS regions in these scuticociliates is highly conserved. PMID:10785865

  10. Analysis of the 5.8S rRNA gene and the internal transcribed spacers in Naegleria spp. and in N. fowleri.

    PubMed

    Pélandakis, M; Serre, S; Pernin, P

    2000-01-01

    Internal transcribed spacers (ITS) and the 5.8S ribosomal gene of 21 Naegleria fowleri strains and eight other species including Naegleria gruberi were sequenced. The results showed that this region can help differentiate between and within species. The phylogeny of Naegleria spp. deduced from the ITS and the 5.8S gene produced four major lineages, fowleri-lovaniensis, galeacystis-italica-clarki-gruberi-australiensis, andersoni-jamiesoni, and pussardi, that fit perfectly with those inferred from the 18S rRNA gene analysis. The N. gruberi isolate, NG260, was closely related to Naegleria pussardi. The other N. gruberi isolates branched together with Naegleria australiensis in another lineage. The ITS and 5.8S results for N. fowleri were congruent with those previously deduced by RAPD analysis. The phylogenetic analysis inferred from ITS and RAPD data revealed two major groups. The French Cattenom and Chooz and South Pacific strains constituted the first group. The second group encompassed the strains corresponding to the Euro-American and Widespread RAPD variants and shared the same substitution in the 5.8S gene. In addition, it was possible to define species specific primers in ITS regions to rapidly identify N. fowleri. PMID:10750838

  11. 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.

  12. 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

  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. Evaluation of bonds in armor plate and other materials using infrared nondestructive testing techniques.

    PubMed

    Vogel, P E

    1968-09-01

    Reported here are the results of using an ir technique in evaluating the bond in hot-roll bonded armor plate, a coating bond, and the bonds in the three-layer construction of a small missile motor. When a specimen is exposed to heat, the heat flows into it at a rate that can be determined. If the flow is interrupted by a void, the inclusion of a material of different conductivity, or any similar thermal barrier, a difference in surface temperature will result that can be defined with an ir radiometer or thermograph. Lack of bond, while not presenting a gross void, is shown here to be a sufficient impediment to be distinguishable. PMID:20068876

  16. 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

  17. 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

  18. 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. PMID:25666734

  19. From Genus to Phylum: Large-Subunit and Internal Transcribed Spacer rRNA Operon Regions Show Similar Classification Accuracies Influenced by Database Composition

    PubMed Central

    Liu, Kuan-Liang; Kuske, Cheryl R.

    2014-01-01

    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. PMID:24242255

  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. RNA genetics

    SciTech Connect

    Domingo, E. ); Holland, J.J. . Dept. of Biology); Ahlquist, P. . Dept. of Plant Pathology)

    1988-01-01

    This book contains the proceedings on RNA genetics: Retroviruses, Viroids, and RNA recombination, Volume 2. Topics covered include: Replication of retrovirus genomes, Hepatitis B virus replication, and Evolution of RNA viruses.

  2. 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.

  3. Development of a Meso-Scale Material Model for Ballistic Fabric and Its Use in Flexible-Armor Protection Systems

    NASA Astrophysics Data System (ADS)

    Grujicic, M.; Bell, W. C.; Arakere, G.; He, T.; Xie, X.; Cheeseman, B. A.

    2010-02-01

    A meso-scale ballistic material model for a prototypical plain-woven single-ply flexible armor is developed and implemented in a material user subroutine for the use in commercial explicit finite element programs. The main intent of the model is to attain computational efficiency when calculating the mechanical response of the multi-ply fabric-based flexible-armor material during its impact with various projectiles without significantly sacrificing the key physical aspects of the fabric microstructure, architecture, and behavior. To validate the new model, a comparative finite element method analysis is carried out in which: (a) the plain-woven single-ply fabric is modeled using conventional shell elements and weaving is done in an explicit manner by snaking the yarns through the fabric and (b) the fabric is treated as a planar continuum surface composed of conventional shell elements to which the new meso-scale unit-cell based material model is assigned. The results obtained show that the material model provides a reasonably good description for the fabric deformation and fracture behavior under different combinations of fixed and free boundary conditions. Finally, the model is used in an investigation of the ability of a multi-ply soft-body armor vest to protect the wearer from impact by a 9-mm round nose projectile. The effects of inter-ply friction, projectile/yarn friction, and the far-field boundary conditions are revealed and the results explained using simple wave mechanics principles, high-deformation rate material behavior, and the role of various energy-absorbing mechanisms in the fabric-based armor systems.

  4. 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

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

    PubMed

    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. PMID:25629660

  6. Comparing the comfort and potential military performance restriction of neck collars from the body armor of six different countries.

    PubMed

    Breeze, John; Watson, Celia H; Horsfall, Ian; Clasper, Jon

    2011-11-01

    The aim of this trial was to undertake an assessment of ballistic neck collars to assess comfort and potential military performance restriction. Neck collars from six different countries were procured with 71 U.K. servicemen assessing two randomly allocated collars to rate one against the other. 58% of participants had worn UK neck collars previously on exercise, but only 6% had used them on operational tours. Body armor with shorter and thinner collars was rated the most comfortable, despite lying close to the neck. It was easier to aim a rifle wearing collars with overlapping segments, especially when in the prone position. Although higher and more rigid collars fared worse overall, this could potentially be offset by the higher levels of ballistic protection they provide. There is a need to evaluate other methods of protecting the neck such as nape protectors and ballistic scarves in combination with the use of backpacks and biometric data collection. Currently, there exists no agreed method of performing ergonomic (or human factor) assessments of the varying components of military body armor systems. Published standards for the minimum military performance requirements of the various components of body armor, including neck collars, need to be established. PMID:22165655

  7. 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

  8. Dynamic failure mechanisms in armor grade ceramics (the effect of lateral confinement and membrane restraint)

    NASA Astrophysics Data System (ADS)

    Sarva, Sai Sushilkumar

    Light weight ceramics such as SiC and Al2O3, have been used in impact related applications such as integrated armor for more than a decade and are an excellent prospect for the next-generation multi-functional armor systems. It is known that ceramics fail under a wide variety of failure modes ranging from brittle to ductile depending on the deformation conditions, such as the strain rate and the state of stress. The dynamic properties are dependent on the underlying failure mechanisms. The underpinning mechanisms of compression failure and their effect on the mechanical properties have been examined over a range of deformation rates from quasi-static to ballistic strain rates. Under moderate confining pressures [˜350 MPa] and at moderate deformation rates [strain-rates up to a few thousand per second], occurring during quasi-static and Hopkinson bar experiments, brittle failure involves initiation of micro-cracks at dominant micro-flaws and pre-existing micro-cracks and their subsequent interactive growth leading to axial splitting, faulting or a mixture of brittle-ductile failure. Experimental results relating to SiC have been compared to a wing-crack array model, developed by Nemat-Nasser and Deng, which describes the influence of microstructure on the dynamic behavior of materials. Under extreme conditions of stress, attained during shock impact, ceramics pulverize into fine powder. Classical crack-growth models seem inadequate for representing the actual failure initiation and evolution. Experiments have also been conducted to study the ballistic performance and failure of ceramic tiles. It has been observed that the defeat capability can be vastly improved by restraining the impact-face of ceramic tiles with a membrane of suitable tensile strength. The comparative effect of restraint by materials such as E-glass/epoxy pre-preg, carbon-fiber/epoxy pre-preg and Ti-3%Al-2.5%V alloy has been studied. Tungsten heavy alloy was used as the projectile material. The

  9. RNA genetics

    SciTech Connect

    Domingo, E.; Holland, J.J.; Ahlquist, P.

    1988-01-01

    These three volumes comprise reference on RNA genomes. The replication, mutation, recombination-assortment, and extreme evolutionary variability of RNA viruses and related RNA replicons is emphasized. The replication mechanisms of positive, negative, and double-stranded RNA viruses of animals and plants are featured.

  10. 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.

  11. 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

  12. 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

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. An armored-cable-based fiber Bragg grating sensor array for perimeter fence intrusion detection

    NASA Astrophysics Data System (ADS)

    Hao, Jianzhong; Dong, Bo; Varghese, Paulose; Phua, Jiliang; Foo, Siang Fook

    2011-11-01

    In this paper, an armored-cable-based optical fiber Bragg grating (FBG) sensor array, for perimeter fence intrusion detection, is demonstrated and some of the field trial results are reported. The field trial was conducted at a critical local installation in Singapore in December 2010. The sensor array was put through a series of both simulated and live intrusion scenarios to test the stability and suitability of operation in the local environmental conditions and to determine its capabilities in detecting and reporting these intrusions accurately to the control station. Such a sensor array can provide perimeter intrusion detection with fine granularity and preset pin-pointing accuracy. The various types of intrusions included aided or unaided climbs, tampering and cutting of the fence, etc. The unique sensor packaging structure provides high sensitivity, crush resistance and protection against rodents. It is also capable of resolving nuisance events such as rain, birds sitting on the fence or seismic vibrations. These sensors are extremely sensitive with a response time of a few seconds. They can be customized for a desired spatial resolution and pre-determined sensitivity. Furthermore, it is easy to cascade a series of such sensors to monitor and detect intrusion events over a long stretch of fence line. Such sensors can be applied to real-time intrusion detection for perimeter security, pipeline security and communications link security.

  18. An armored-cable-based fiber Bragg grating sensor array for perimeter fence intrusion detection

    NASA Astrophysics Data System (ADS)

    Hao, Jianzhong; Dong, Bo; Varghese, Paulose; Phua, Jiliang; Foo, Siang Fook

    2012-01-01

    In this paper, an armored-cable-based optical fiber Bragg grating (FBG) sensor array, for perimeter fence intrusion detection, is demonstrated and some of the field trial results are reported. The field trial was conducted at a critical local installation in Singapore in December 2010. The sensor array was put through a series of both simulated and live intrusion scenarios to test the stability and suitability of operation in the local environmental conditions and to determine its capabilities in detecting and reporting these intrusions accurately to the control station. Such a sensor array can provide perimeter intrusion detection with fine granularity and preset pin-pointing accuracy. The various types of intrusions included aided or unaided climbs, tampering and cutting of the fence, etc. The unique sensor packaging structure provides high sensitivity, crush resistance and protection against rodents. It is also capable of resolving nuisance events such as rain, birds sitting on the fence or seismic vibrations. These sensors are extremely sensitive with a response time of a few seconds. They can be customized for a desired spatial resolution and pre-determined sensitivity. Furthermore, it is easy to cascade a series of such sensors to monitor and detect intrusion events over a long stretch of fence line. Such sensors can be applied to real-time intrusion detection for perimeter security, pipeline security and communications link security.

  19. 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.

  20. 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.

    2016-03-01

    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.

  1. 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

  2. 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

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

    PubMed

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

    2015-05-01

    Dermal plates from armored catfish are bony structures that cover their body. In this paper we characterized structural, chemical, and nanomechanical properties of the dermal plates from the Amazonian fish Pterygoplichthys pardalis. Analysis of the morphology of the plates using scanning electron microscopy (SEM) revealed that the dermal plates have a sandwich-like structure composed of an inner porous matrix surrounded by two external dense layers. This is different from the plywood-like laminated structure of elasmoid fish scales but similar to the structure of osteoderms found in the dermal armour of some reptiles and mammals. Chemical analysis performed using Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC) and X-ray diffraction (XRD) results revealed similarities between the composition of P. pardalis plates and the elasmoid fish scales of Arapaima gigas. Reduced moduli of P. pardalis plates measured using nanoindentation were also consistent with reported values for A. gigas scales, but further revealed that the dermal plate is an anisotropic and heterogeneous material, similar to many other fish scales and osteoderms. It is postulated that the sandwich-like structure of the dermal plates provides a lightweight and tough protective layer. PMID:25732181

  4. Persisting effects of armored military maneuvers on some soils of the Mojave Desert

    USGS Publications Warehouse

    Prose, D.V.

    1985-01-01

    Soil compaction and substrate modification produced during large-scale armored military maneuvers in the early 1940s were examined in 1981 at seven sites in California's eastern Mojave Desert Recording penetrometer measurements show that tracks left by a single pass of an M3 "medium" tank have average soil resistance values that are 50% greater than those of the surrounding untracked soil in the upper 20 cm At one site, measurements made along short segments of track that have been visually eliminated by erosion and deposition processes show a 73% increase in penetrometer resistance over adjacent, undisturbed soils Dirt roadways at three former base camp locations could not be penetrated below 5-10 cm because of extreme compaction Soil bulk density was not as sensitive an indicator of soil compaction as was penetrometer resistance Density values in the upper 10 cm of soil are not significantly different between tank tracks and undisturbed soils at most sites, and roadways at two base camps show an average increase in bulk density of only 12% over adjacent soils. Trench excavations across tank tracks show that physical modifications of the substrate can extend vertically beneath a track to a depth of 25 cm and outward from a track's edge to 50 cm These soil disturbances are probably major factors that encourage accelerated soil erosion throughout the manuever area and also retard or prevent the return of vegetation to pre-disturbance conditions ?? 1985 Springer-Verlag New York Inc.

  5. 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.

  6. Modeling the Importance of Baseflow and Sediment Supply on Armor Development: Contrasting Intermittent Dryland and Perennially-Flowing Gravel-Bedded Rivers

    NASA Astrophysics Data System (ADS)

    Goodwin, K.; Johnson, J. P.; Viparelli, E.

    2014-12-01

    Most gravel-bedded rivers with perennial base flow are often armored, defined as having a bed surface grain size distribution that is coarser than the subsurface. In contrast, ephemerally flowing rivers, which are commonly flash flood-dominated, are typically unarmored. Although both types of channels have high peak discharges during floods, a key difference between these hydrological settings is in flow intermittency and how much flow occurs during moderate and low flow periods. High sediment supply and elevated shear stresses during floods have been identified as processes that may reduce or prevent armor development, but the preferential transport of smaller grain sizes during lower flows may also strongly affect armor development. We use numerical modeling to explore the relative importance of these armor-related processes. Calculations are based on a previous model called the Spawning Gravel Refresher, which includes mixed grain size sediment transport, morphodynamic feedbacks with channel slope, variable discharge hydrographs, and interactions with the subsurface grain sizes as the bed surface aggrades and erodes. Model runs are calibrated to natural rivers with varying degrees of bed surface armoring and flood hydrograph shape. These natural rivers include: i) the Nahal Yatir, an ephemerally flowing unarmored river in the Negev Desert, Israel, and ii) Trinity River, California, a larger perennially flowing, armored mountain river with annual snowmelt floods. We present a thorough exploration of model parameters, including base flow duration and magnitude, flood hydrograph shape and sand supply, combined with data from natural rivers. This produces quantitative bounds on how armor development varies in a wide range of parameter spaces unobtainable in the field alone.

  7. 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

  8. Moving RNA moves RNA forward.

    PubMed

    Peng, Lina; Li, Yujiao; Zhang, Lan; Yu, Wenqiang

    2013-10-01

    Cell communication affects all aspects of cell structure and behavior, such as cell proliferation, differentiation, division, and coordination of various physiological functions. The moving RNA in plants and mammalian cells indicates that nucleic acid could be one of the various types of messengers for cell communication. The microvesicle is a critical pathway that mediates RNA moving and keeps moving RNA stable in body fluids. When moving miRNA enters the target cell, it functions by altering the gene expression profile and significantly inhibiting mRNA translation in recipient cells. Thus, moving RNA may act as a long-range modulator during development, organogenesis, and tumor metastasis. PMID:24008386

  9. 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

  10. 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. PMID:16549228

  11. 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

  12. 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

  13. Quantitative Model of microRNA-mRNA interaction

    NASA Astrophysics Data System (ADS)

    Noorbakhsh, Javad; Lang, Alex; Mehta, Pankaj

    2012-02-01

    MicroRNAs are short RNA sequences that regulate gene expression and protein translation by binding to mRNA. Experimental data reveals the existence of a threshold linear output of protein based on the expression level of microRNA. To understand this behavior, we propose a mathematical model of the chemical kinetics of the interaction between mRNA and microRNA. Using this model we have been able to quantify the threshold linear behavior. Furthermore, we have studied the effect of internal noise, showing the existence of an intermediary regime where the expression level of mRNA and microRNA has the same order of magnitude. In this crossover regime the mRNA translation becomes sensitive to small changes in the level of microRNA, resulting in large fluctuations in protein levels. Our work shows that chemical kinetics parameters can be quantified by studying protein fluctuations. In the future, studying protein levels and their fluctuations can provide a powerful tool to study the competing endogenous RNA hypothesis (ceRNA), in which mRNA crosstalk occurs due to competition over a limited pool of microRNAs.

  14. Surface water-groundwater interaction and chemistry in a mineral-armored hydrothermal outflow channel, Yellowstone National Park, USA

    NASA Astrophysics Data System (ADS)

    Vitale, M. V.; Gardner, P.; Hinman, N. W.

    2008-11-01

    Small quantities of groundwater interact with hydrothermal surface water to drive in-stream geochemical processes in a silica-armored hot-spring outflow channel in Yellowstone National Park, USA. The objective of this study was to characterize the hydrology and geochemistry of this unique system in order to (1) learn more about the Yellowstone Plateau’s subsurface water mixing between meteoric and hydrothermal waters and (2) learn more about the chemical and physical processes that lead to accumulation of streambed cements, i.e., streambed armor. A combination of hydrological, geochemical, mineralogical, microscopic, and petrographic techniques were used to identify groundwater and surface-water exchange. Interaction could be identified in winter because of differences in surface water and groundwater composition but interaction at other times of the year cannot be ruled out. Dissolved constituents originating from groundwater (e.g., Fe(II) and Mg) were traced downstream until oxidation and/or subsequent precipitation with silica removed them, particularly where high affinity substrates like cyanobacterial surfaces were present. Because the stream lies in a relatively flat drainage basin and is fed mainly by a seasonally relatively stable hot spring, this system allowed study of the chemical processes along a stream without the obscuring effects of sedimentation.

  15. 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

  16. 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

  17. 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.

  18. RNA helicases

    PubMed Central

    Ranji, Arnaz

    2010-01-01

    RNA helicases serve multiple roles at the virus-host interface. In some situations, RNA helicases are essential host factors to promote viral replication; however, in other cases they serve as a cellular sensor to trigger the antiviral state in response to viral infection. All family members share the conserved ATP-dependent catalytic core linked to different substrate recognition and protein-protein interaction domains. These flanking domains can be shuffled between different helicases to achieve functional diversity. This review summarizes recent studies, This review summarizes recent studies of RNA helicases in virus biology. First, RNA helicases are catalysts of progressive RNA-protein rearrangements that begin at gene transcription and culminate in release of infectious virus. Second, RNA helicases can act as a scaffold for alternative protein-protein interactions that can defeat the antiviral state. The mounting fundamental understanding of RNA helicases is being used to develop selective and efficacious drugs against human and animal pathogens. The analysis of RNA helicases in virus model systems continues to provide insights into virology, cell biology and immunology and has provided fresh perspective to continue unraveling the complexity of virus-host interactions. PMID:21173576

  19. RNA. Introduction.

    PubMed

    Bao, Marie Z; Kruger, Robert P; Rivas, Fabiola; Smith, Orla; Szewczak, Lara

    2009-02-20

    Two scientists walk into a bar. After a pint and an exchange of pleasantries, one says to the other, "Where do you come from? Scientifically, I mean." The queried scientist responds, "Out of the RNA world." "Don't we all," the asker responds chuckling. Fifteen years ago, the joke would have been made with a nod to the notion that life arose from an RNA-based precursor, the so-called "RNA world." Yet had this conversation happened last week, the scientists would also be grinning in appreciation of the extent to which contemporary cellular biology is steeped in all things RNA. Ours is truly an RNA world.In this year's special review issue, the Cell editorial team has brought together articles focused on RNA in the modern world, providing perspectives on classical and emerging areas of inquiry. We extend our thanks to the many distinguished experts who contributed their time and effort as authors and reviewers to make the issue informative, thought-provoking, and timely. We hope that this collection of articles, written as we stand on the verge of a new wave of RNA biology, edifies and inspires by revealing the inner workings of these versatile molecules and by highlighting the next key questions that need to be addressed as we strive to understand the full functional scope of RNA in cells. PMID:19263588

  20. Armoring CRAds with p21/Waf-1 shRNAs: the next generation of oncolytic adenoviruses

    PubMed Central

    Höti, N; Chowdhury, WH; Mustafa, S; Ribas, J; Castanares, M; Johnson, T; Liu, M; Lupold, SE; Rodriguez, R

    2011-01-01

    Conditionally replicating adenoviruses (CRAds) represent a promising modality for the treatment of neoplastic diseases, including Prostate Cancer. Selectively replicating viruses can be generated by placing a tissue or cancer-specific promoter upstream of one or more of the viral genes required for replication (for example, E1A, E1B). We have previously reported multiple cellular processes that can attenuate viral replication, which in turn compromises viral oncolysis and tumor kill. In this study, we investigated the importance of the cyclin-dependent kinase inhibitor p21/Waf-1, on viral replication and tumor growth. To our knowledge, this is the first report describing the importance of p21/Waf-1shRNA on the induction of an androgen responsive element (ARE) based promoter driving the E1A gene. As a proof of concept, the study emphasizes the use of RNA interference technology to overcome promoter weaknesses for tissue-specific oncolytic viruses, as well as the cellular inhibitor pathways on viral life cycle. Using RNA interference against p21/Waf-1, we were able to show an increase in viral replication and viral oncolysis of prostate cancer cells. Similarly, CRAd viruses that carry p21/Waf-1 shRNA (Ad5-RV004.21) were able to prevent tumor outgrowth that resulted in a marked increase in the mean survival time of tumor-bearing mice compared with CRAd without p21/Waf-1 shRNA (Ad5-RV004). In studies combining Ad5-RV004.21 with Adriamycin, a suprar-additive effect was observed only in CRAds that harbor shRNA against p21/Waf-1. Taken together, these findings of enhanced viral replication in prostate cancer cells by using RNA interference against the cdk inhibitor p21/Waf-1 have significant implications in the development of prostate-specific CRAd therapies. PMID:20448671

  1. The effect of the armored scale, Rhizaspidiotus donacis (Hemiptera: Diaspididae), on shoot growth of the invasive plant Arundo donax (Poaceae: Arundinoideae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this study, the effect of feeding by the armored scale, Rhizaspidiotus donacis (Leonardi, 1920) (Hemiptera: Diaspididae) on the growth of the plant Arundo donax L. (Poaceae) was evaluated under field conditions in its native range. This study was designed to evaluate the impact of R. donacis, a c...

  2. 75 FR 55313 - Record of Decision (ROD) for Conversion of the 3rd Armored Cavalry Regiment (3rd ACR) to a...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-10

    ... Department of the Army Record of Decision (ROD) for Conversion of the 3rd Armored Cavalry Regiment (3rd ACR...: Notice of Availability (NOA). SUMMARY: The Department of the Army announces a ROD for conversion of the... conversion, the 3rd ACR will provide the Army with a force structure that has the flexibility to...

  3. Impact of Internal RNA on Aggregation and Electrokinetics of Viruses: Comparison between MS2 Phage and Corresponding Virus-Like Particles ▿

    PubMed Central

    Dika, C.; Duval, J. F. L.; Ly-Chatain, H. M.; Merlin, C.; Gantzer, C.

    2011-01-01

    We compare for the first time the electrokinetic and aggregation properties of MS2 phage (pH 2.5 to 7, 1 to 100 mM NaNO3 electrolyte concentration) with those of the corresponding virus-like particles (VLPs), which lack entirely the inner viral RNA component. In line with our previous work (J. Langlet, F. Gaboriaud, C. Gantzer, and J. F. L. Duval, Biophys. J. 94:3293-3312, 2008), it is found that modifying the content of RNA within the virus leads to very distinct electrohydrodynamic and aggregation profiles for MS2 and MS2 VLPs. Under the given pH and concentration conditions, MS2 VLPs exhibit electrophoretic mobility larger in magnitude than that of MS2, and both have similar isoelectric point (IEP) values (∼4). The electrokinetic results reflect a greater permeability of MS2 VLPs to electroosmotic flow, developed within/around these soft particles during their migration under the action of the applied electrical field. Results also support the presence of some remaining negatively charged component within the VLPs. In addition, MS2 phage systematically forms aggregates at pH values below the IEP, regardless of the magnitude of the solution ionic strength, whereas MS2 VLPs aggregate under the strict condition where the pH is relatively equal to the IEP at sufficiently low salt concentrations (<10 mM). It is argued that the stability of VLPs against aggregation and the differences between electrokinetics of MS2 and corresponding VLPs conform to recently developed formalisms for the stability and electrohydrodynamics of soft multilayered particles. The differences between the surface properties of these two kinds of particles reported here suggest that VLPs may not be appropriate for predicting the behavior of pathogenic viruses in aqueous media. PMID:21622784

  4. 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

  5. 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

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

    PubMed

    Fujimoto, Rodrigo Y; Neves, Mikaelle S; Santos, Rudã F B; Souza, Natalino C; Do Couto, Márcia V S; Lopes, Josiane N S; Diniz, Daniel G; Eiras, Jorge C

    2013-09-01

    A total of 281 specimens of freshwater armored ornamental fish species (Leporacanthicus galaxias,Lasiancistrus saetiger, Cochliodon sp., Hypostomus sp., Pseudacanthicus spinosus, Ancistrus sp. and Rineloricaria cf. lanceolata) were captured at the hydrological basin of Guamá River, Pará, Brazil. The infection by Trypanosoma spp. was inspected. The morphological and morphometric characterization of the parasites and the hematological parameters were determined. Leporacanthicus galaxias and Pseudacanthicus spinosus presented 100% infection prevalence, and the other species showed a variable prevalence of infection. The parasites showed clearly different morphotypes and dimensions, and probably belong to different species. The hematological response to the infection varied with the host. Cochliodon sp. showed no differences between infected and not infected fish. In other species several modifications on some hematological parameters were found, but apparently without causing disease. It is emphasized the possibility of introduction of the parasites in new environments due to the artificial movements of these ornamental fish. PMID:23903566

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. Identification of cultured isolates of clinically important yeast species using fluorescent fragment length analysis of the amplified internally transcribed rRNA spacer 2 region

    PubMed Central

    De Baere, Thierry; Claeys, Geert; Swinne, Danielle; Massonet, Caroline; Verschraegen, Gerda; Muylaert, An; Vaneechoutte, Mario

    2002-01-01

    Background The number of patients with yeast infection has increased during the last years. Also the variety of species of clinical importance has increased. Correct species identification is often important for efficient therapy, but is currently mostly based on phenotypic features and is sometimes time-consuming and depends largely on the expertise of technicians. Therefore, we evaluated the feasibility of PCR-based amplification of the internally transcribed spacer region 2 (ITS2), followed by fragment size analysis on the ABI Prism 310 for the identification of clinically important yeasts. Results A rapid DNA-extraction method, based on simple boiling-freezing was introduced. Of the 26 species tested, 22 could be identified unambiguously by scoring the length of the ITS2-region. No distinction could be made between the species Trichosporon asteroides and T. inkin or between T. mucoides and T. ovoides. The two varieties of Cryptococcus neoformans (var. neoformans and var. gattii) could be differentiated from each other due to a one bp length difference of the ITS2 fragment. The three Cryptococcus laurentii isolates were split into two groups according to their ITS2-fragment lengths, in correspondence with the phylogenetic groups described previously. Since the obtained fragment lengths compare well to those described previously and could be exchanged between two laboratories, an internationally usable library of ITS2 fragment lengths can be constructed. Conclusions The existing ITS2 size based library enables identification of most of the clinically important yeast species within 6 hours starting from a single colony and can be easily updated when new species are described. Data can be exchanged between laboratories. PMID:12139769

  12. 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

  13. Traumatic brain injury risk while parachuting: comparison of the personnel armor system for ground troops helmet and the advanced combat helmet.

    PubMed

    Ivins, Brian J; Crowley, John S; Johnson, Jeffrey; Warden, Deborah L; Schwab, Karen A

    2008-12-01

    Military paratroopers are inherently at risk for a variety of injuries when they jump, including traumatic brain injuries (TBIs). U.S. Army paratroopers rely on their ballistic helmets for protection against TBIs when jumping. Currently, two different helmets are available to Army paratroopers, that is, the personnel armor system for ground troops helmet and the advanced combat helmet. This study compared the incidence of self-reported, jump-related TBIs in a small sample of paratroopers (N = 585) using each type of helmet. Data were obtained from surveys of soldiers at Fort Bragg, North Carolina. The overall relative risk of sustaining a TBI while jumping was 2.3 times (95% confidence interval, 1.3-4.3) higher for personnel armor system for ground troops helmet users. Most of the increase in risk was accounted for by the most-minor TBIs (American Academy of Neurology grade 1 or 2 concussion). PMID:19149333

  14. Effect of Hardness on the Ballistic Impact Behavior of High-Strength Steels Against 7.62-mm Armor Piercing Projectiles

    NASA Astrophysics Data System (ADS)

    Demir, Teyfik; Übeyli, Mustafa; Yıldırım, R. O.

    2009-03-01

    Ballistic performance of engineering materials should be known in selection of the most suitable armor material to protect civilian or military system with the lowest possible weight against various threats. In this study, the ballistic impact characterization of high-strength steels, namely AISI 4340 and DIN 100Cr6, was investigated using 7.62-mm armor piercing (AP) projectiles by considering four hardness levels and five areal densities. The main aim was to examine the effect of hardness and areal density on the ballistic behavior of these steels. Hence, four different heat-treatment schedules were applied to these steels to get different mechanical properties. After ballistic testing, macro and micro examinations of the specimens were carried out to clarify their failure mechanisms. According to the results, the AISI 4340 steel having a hardness of ~50 HRC showed the best ballistic performance among the investigated materials.

  15. Psychological factors that limit the endurance capabilities of armor crews operating in a simulated NBC environment. Technical report, July 1985-May 1986

    SciTech Connect

    Tharion, W.J.; Rauch, T.M.; Munro, I.; Lussier, A.R.; Banderet, L.E.

    1986-05-01

    Factors which limit the performance capabilities of sustained armor operations in simulated conventional- and chemical-warfare environments were studied. In the simulated chemical-warfare environment, extreme symptom and mood changes resulted in medical casualties, combat ineffectiveness, and early termination of all testing. Significant personality differences existed between casualties and survivors. The majority of casualties voluntarily terminated operational duties because of intense symptoms associated with wearing the chemical protective mask and clothing system. These symptoms were manifestations of respiratory and thermal stress.

  16. 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

  17. 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. 

  18. Formation of lobate debris aprons on Mars: Assessment of regional ice sheet collapse and debris-cover armoring

    NASA Astrophysics Data System (ADS)

    Fastook, James L.; Head, James W.; Marchant, David R.

    2014-01-01

    Lobate debris aprons (LDA) are lobate-shaped aprons surrounding scarps and isolated massifs that are concentrated in the vicinity of the northern Dichotomy Boundary on Mars. LDAs have been interpreted as (1) ice-cemented talus aprons undergoing viscous flow, (2) local debris-covered alpine-like glaciers, or (3) remnants of the collapse of a regional retreating ice sheet. We investigate the plausibility that LDAs are remnants of a more extensive regional ice sheet by modeling this process. We find that as a regional ice sheet collapses, the surface drops below cliff and massif bedrock margins, exposing bedrock and regolith, and initiating debris deposition on the surface of a cold-based glacier. Reduced sublimation due to debris-cover armoring of the proto-LDA surface produces a surface slope and consequent ice flow that carries the armoring debris away from the rock outcrops. As collapse and ice retreat continue the debris train eventually reaches the substrate surface at the front of the glacier, leaving the entire LDA armored by debris cover. Using a simplified ice flow model we are able to characterize the temperature and sublimation rate that would be necessary to produce LDAs with a wide range of specified lateral extents and thicknesses. We then apply this method to a database of documented LDA parameters (height, lateral extent) from the Dichotomy Boundary region, and assess the implications for predicted climate conditions during their formation and the range of formation times implied by the model. We find that for the population examined here, typical temperatures are in the range of -85 to -40 °C and typical sublimation rates lie in the range of 6-14 mm/a. Lobate debris apron formation times (from the point of bedrock exposure to complete debris cover) cluster near 400-500 ka. These results show that LDA length and thickness characteristics are consistent with climate conditions and a formation scenario typical of the collapse of a regional retreating

  19. 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

  20. Diagnosis of histoplasmosis by detection of the internal transcribed spacer region of fungal rRNA gene from a paraffin-embedded skin sample from a dog in Japan.

    PubMed

    Ueda, Yachiyo; Sano, Ayako; Tamura, Miki; Inomata, Tomo; Kamei, Katsuhiko; Yokoyama, Koji; Kishi, Fukuko; Ito, Junko; Mikami, Yuzuru; Miyaji, Makoto; Nishimura, Kazuko

    2003-07-17

    The lesions of histoplasmosis in dogs in Japan differ from those in dogs in North America. Affected dogs in Japan have had multiple granulomatous or ulcerated foci in skin or gingiva and have not had pulmonary or gastrointestinal lesions. The present report introduces a polymerase chain reaction (PCR) diagnosis of canine histoplasmosis and the characteristic of disease in Japan. The surgically removed skin ulcerate samples from a 5-years-old female Shiba-inu native to Japan without traveling out of the country were evaluated. Tissue samples had many yeast-like organisms in the macrophages. DNA was extracted from paraffin-embedded tissue samples. A nested PCR technique was applied. The detected sequence of the internal transcribed spacer of ribosomal RNA gene had 99.7% in homology with Ajellomyces capsulatus (the teleomorph of Histoplasma capsulatum). Clinical manifestations, historical background of equine epizootic lymphangitis in Japan, and a human autochthonous case of histoplasmosis farciminosi indicated that this dog might have been infected with H. capsulatum var. farciminosum as a heteroecism. PMID:12814889

  1. Multiphysics Modeling and Simulations of Mil A46100 Armor-Grade Martensitic Steel Gas Metal Arc Welding Process

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

    A multiphysics computational model has been developed for the conventional Gas Metal Arc Welding (GMAW) joining process and used to analyze butt-welding of MIL A46100, a prototypical high-hardness armor martensitic steel. The model consists of five distinct modules, each covering a specific aspect of the GMAW process, i.e., (a) dynamics of welding-gun behavior; (b) heat transfer from the electric arc and mass transfer from the electrode to the weld; (c) development of thermal and mechanical fields during the GMAW process; (d) the associated evolution and spatial distribution of the material microstructure throughout the weld region; and (e) the final spatial distribution of the as-welded material properties. To make the newly developed GMAW process model applicable to MIL A46100, the basic physical-metallurgy concepts and principles for this material have to be investigated and properly accounted for/modeled. The newly developed GMAW process model enables establishment of the relationship between the GMAW process parameters (e.g., open circuit voltage, welding current, electrode diameter, electrode-tip/weld distance, filler-metal feed speed, and gun travel speed), workpiece material chemistry, and the spatial distribution of as-welded material microstructure and properties. The predictions of the present GMAW model pertaining to the spatial distribution of the material microstructure and properties within the MIL A46100 weld region are found to be consistent with general expectations and prior observations.

  2. 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.

  3. 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

  4. 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.

  5. 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. PMID:23726006

  6. 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

  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. 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. PMID:23161674

  9. Yeast eIF4B binds to the head of the 40S ribosomal subunit and promotes mRNA recruitment through its N-terminal and internal repeat domains.

    PubMed

    Walker, Sarah E; Zhou, Fujun; Mitchell, Sarah F; Larson, Victoria S; Valasek, Leos; Hinnebusch, Alan G; Lorsch, Jon R

    2013-02-01

    Eukaryotic translation initiation factor (eIF)4B stimulates recruitment of mRNA to the 43S ribosomal pre-initiation complex (PIC). Yeast eIF4B (yeIF4B), shown previously to bind single-stranded (ss) RNA, consists of an N-terminal domain (NTD), predicted to be unstructured in solution; an RNA-recognition motif (RRM); an unusual domain comprised of seven imperfect repeats of 26 amino acids; and a C-terminal domain. Although the mechanism of yeIF4B action has remained obscure, most models have suggested central roles for its RRM and ssRNA-binding activity. We have dissected the functions of yeIF4B's domains and show that the RRM and its ssRNA-binding activity are dispensable in vitro and in vivo. Instead, our data indicate that the 7-repeats and NTD are the most critical domains, which mediate binding of yeIF4B to the head of the 40S ribosomal subunit via interaction with Rps20. This interaction induces structural changes in the ribosome's mRNA entry channel that could facilitate mRNA loading. We also show that yeIF4B strongly promotes productive interaction of eIF4A with the 43S•mRNA PIC in a manner required for efficient mRNA recruitment. PMID:23236192

  10. Non-Baseline Damage Detection from Changes in Strain Energy Mode Shapes Experiments on Armored Vehicle Launched Bridge

    NASA Astrophysics Data System (ADS)

    Sazonov, E. S.; Klinkhachorn, P.; GangaRao, H. V. S.; Halabe, U. B.

    2003-03-01

    There are several existing methods for damage detection based on identifying changes in strain energy mode shapes. Most of these methods require knowing strain energy mode shapes for a structure without damage in order to establish a baseline for damage detection. Usually, the mode shapes from the structure under test should be compared to the baseline mode shapes to identify and locate damage. However, these methods of damage detection are not very suitable for application on structures where baseline mode shapes cannot be readily obtained, for example, structures with preexisting damage. Conventional methods, like building a finite element model of a structure to be used as a baseline might be an expensive and time-consuming task that can be impossible for complex structures. A new (non-baseline) method for the extraction of localized changes (damage peaks) from strain energy mode shapes based on Fourier analysis of the strain energy mode shapes has been developed and analytically proved for the cases of a pinned-pinned and a free-free beam. The new method looks for characteristic changes in the power spectrum of the strain energy mode shapes in order to locate and identify damage. The analytical results have been confirmed both by the finite element model and impact testing experiments on a free-free aluminum beam, including single and multiple damage scenarios. This paper presents results of testing the non-baseline method on a complex structure — Armored Vehicle Launched Bridge, which consists of loosely coupled hinged beams with variable cross-section. The results of testing confirm applicability of the non-baseline method to damage detection in complex structures and highlight certain particularities of its use.

  11. STS-92 crew get training on driving the M-113 armored vehicle

    NASA Technical Reports Server (NTRS)

    2000-01-01

    As part of emergency egress training during Terminal Countdown Demonstration Test (TCDT) activities, members of the STS-92 crew get instructions about the M-113 they are seated in at Launch Pad 39A. Seen on the left are Pilot Pam Melroy and Mission Specialists Leroy Chaio and Koichi Wakata of Japan In the middle, giving the instructions, is Capt. George Hoggard, trainer with the KSC Fire Department. At right are Commander Brian Duffy (leaning back) and Mission Specialist Michael Lopez-Alegria. The other crew members (not seen) are Mission Specialists Jeff Wisoff and Bill McArthur. The tracked vehicle could be used by the crew in the event of an emergency at the pad during which the crew must make a quick exit from the area. The TCDT also provides simulated countdown exercises and opportunities to inspect the mission payloads in the orbiter's payload bay. STS-92 is scheduled to launch Oct. 5 at 9:30 p.m. EDT on the fifth flight to the International Space Station. It will carry two elements of the Space Station, the Integrated Truss Structure Z1 and the third Pressurized Mating Adapter. The mission is also the 100th flight in the Shuttle program.

  12. 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. PMID:24803509

  13. 6.6kV XLPE submarine cable with optical fiber sensors to detect anchor damage and defacement of wire armor

    SciTech Connect

    Tayama, Hirohumi; Fukuda, Osamu; Yamamoto, Kenichi; Inoue, Yosimasa; Koike, Yohji

    1995-10-01

    The Kansai Electric Power Co., Inc. and Fujikura Ltd. have developed a 6.6kV XLPE submarine cable with optical fiber sensors to detect anchor damage and defacement of wire armor. The cable was installed between Kata and Tomogashima island in Wakayama prefecture, Japan. The ability to detect cable damage was confirmed by compression test, curved tensile test using CIGRE-recommended method, and loop tests. Also, in this power cable, the distributed optical fiber sensor was built-in to measure cable temperature. This report shows the results of these tests and the outline of the cable installation.

  14. 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).

  15. 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)

  16. 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)

  17. 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

  18. 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

  19. N(6)-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions.

    PubMed

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

    2015-02-26

    RNA-binding proteins control many aspects of cellular biology through binding single-stranded RNA binding motifs (RBMs). However, RBMs can be buried within their local RNA structures, thus inhibiting RNA-protein interactions. N(6)-methyladenosine (m(6)A), the most abundant and dynamic internal modification in eukaryotic messenger RNA, can be selectively recognized by the YTHDF2 protein to affect the stability of cytoplasmic mRNAs, but how m(6)A achieves its wide-ranging physiological role needs further exploration. Here we show in human cells that m(6)A controls the RNA-structure-dependent accessibility of RBMs to affect RNA-protein interactions for biological regulation; we term this mechanism 'the m(6)A-switch'. We found that m(6)A alters the local structure in mRNA and long non-coding RNA (lncRNA) to facilitate binding of heterogeneous nuclear ribonucleoprotein C (HNRNPC), an abundant nuclear RNA-binding protein responsible for pre-mRNA processing. Combining photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) and anti-m(6)A immunoprecipitation (MeRIP) approaches enabled us to identify 39,060 m(6)A-switches among HNRNPC-binding sites; and global m(6)A reduction decreased HNRNPC binding at 2,798 high-confidence m(6)A-switches. We determined that these m(6)A-switch-regulated HNRNPC-binding activities affect the abundance as well as alternative splicing of target mRNAs, demonstrating the regulatory role of m(6)A-switches on gene expression and RNA maturation. Our results illustrate how RNA-binding proteins gain regulated access to their RBMs through m(6)A-dependent RNA structural remodelling, and provide a new direction for investigating RNA-modification-coded cellular biology. PMID:25719671

  20. 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.

  1. 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

  2. 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.

  3. Analyzing MiRNA-LncRNA Interactions.

    PubMed

    Paraskevopoulou, Maria D; Hatzigeorgiou, Artemis G

    2016-01-01

    Long noncoding RNAs (lncRNAs) are noncoding transcripts usually longer than 200 nts that have recently emerged as one of the largest and significantly diverse RNA families. The biological role and functions of lncRNAs are still mostly uncharacterized. Their target-mimetic, sponge/decoy function on microRNAs was recently uncovered. miRNAs are a class of noncoding RNA species (~22 nts) that play a central role in posttranscriptional regulation of protein coding genes by mRNA cleavage, direct translational repression and/or mRNA destabilization. LncRNAs can act as miRNA sponges, reducing their regulatory effect on mRNAs. This function introduces an extra layer of complexity in the miRNA-target interaction network. This chapter focuses on the study of miRNA-lncRNA interactions with either in silico or experimentally supported analyses. The proposed methodologies can be appropriately adapted in order to become the backbone of advanced multistep functional miRNA analyses. PMID:26721498

  4. 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

  5. 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

  6. RNA quaternary structure and global symmetry.

    PubMed

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

    2015-04-01

    Many proteins associate into symmetric multisubunit complexes. Structural analyses suggested that, by contrast, virtually all RNAs with complex 3D structures function as asymmetric monomers. Recent crystal structures revealed that several biological RNAs exhibit global symmetry at the level of their tertiary and quaternary structures. Here we survey known examples of global RNA symmetry, including the true quaternary symmetry of the bacteriophage ϕ29 prohead RNA (pRNA) and the internal pseudosymmetry of the single-chain flavin mononucleotide (FMN), glycine, and cyclic di-AMP (c-di-AMP) riboswitches. For these RNAs, global symmetry stabilizes the RNA fold, coordinates ligand-RNA interactions, and facilitates association with symmetric binding partners. PMID:25778613

  7. RNA quaternary structure and global symmetry

    PubMed Central

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

    2015-01-01

    Many proteins associate into symmetric multisubunit complexes. Structural analyses suggested that, in contrast, virtually all RNAs with complex three-dimensional structures function as asymmetric monomers. Recent crystal structures revealed that several biological RNAs exhibit global symmetry at the level of their tertiary and quaternary structures. Here, we survey known examples of global RNA symmetry, including the true quaternary symmetry of the bacteriophage ϕ29 prohead RNA (pRNA), and the internal pseudosymmetry of the single-chain flavin mononucleotide (FMN), glycine, and cyclic diadenosine monophosphate (c-di-AMP) riboswitches. For these RNAs, global symmetry stabilizes the RNA fold, coordinates ligand-RNA interactions, and facilitates association with symmetric binding partners. PMID:25778613

  8. Mitochondrial Transcription Factor A (TFAM) Binds to RNA Containing 4-Way Junctions and Mitochondrial tRNA

    PubMed Central

    Brown, Timothy A.; Tkachuk, Ariana N.; Clayton, David A.

    2015-01-01

    Mitochondrial DNA (mtDNA) is maintained within nucleoprotein complexes known as nucleoids. These structures are highly condensed by the DNA packaging protein, mitochondrial Transcription Factor A (TFAM). Nucleoids also include RNA, RNA:DNA hybrids, and are associated with proteins involved with RNA processing and mitochondrial ribosome biogenesis. Here we characterize the ability of TFAM to bind various RNA containing substrates in order to determine their role in TFAM distribution and function within the nucleoid. We find that TFAM binds to RNA-containing 4-way junctions but does not bind appreciably to RNA hairpins, internal loops, or linear RNA:DNA hybrids. Therefore the RNA within nucleoids largely excludes TFAM, and its distribution is not grossly altered with removal of RNA. Within the cell, TFAM binds to mitochondrial tRNAs, consistent with our RNA 4-way junction data. Kinetic binding assays and RNase-insensitive TFAM distribution indicate that DNA remains the preferred substrate within the nucleoid. However, TFAM binds to tRNA with nanomolar affinity and these complexes are not rare. TFAM-immunoprecipitated tRNAs have processed ends, suggesting that binding is not specific to RNA precursors. The amount of each immunoprecipitated tRNA is not well correlated with tRNA celluar abundance, indicating unequal TFAM binding preferences. TFAM-mt-tRNA interaction suggests potentially new functions for this protein. PMID:26545237

  9. 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

  10. Replication of Tobamovirus RNA.

    PubMed

    Ishibashi, Kazuhiro; Ishikawa, Masayuki

    2016-08-01

    Tobacco mosaic virus and other tobamoviruses have served as models for studying the mechanisms of viral RNA replication. In tobamoviruses, genomic RNA replication occurs via several steps: (a) synthesis of viral replication proteins by translation of the genomic RNA; (b) translation-coupled binding of the replication proteins to a 5'-terminal region of the genomic RNA; (c) recruitment of the genomic RNA by replication proteins onto membranes and formation of a complex with host proteins TOM1 and ARL8; (d) synthesis of complementary (negative-strand) RNA in the complex; and (e) synthesis of progeny genomic RNA. This article reviews current knowledge on tobamovirus RNA replication, particularly regarding how the genomic RNA is specifically selected as a replication template and how the replication proteins are activated. We also focus on the roles of the replication proteins in evading or suppressing host defense systems. PMID:27296148

  11. 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.

  12. 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

  13. Roles for RNA in Telomerase Nucleotide and Repeat Addition Processivity

    PubMed Central

    Lai, Cary K.; Miller, Michael C.; Collins, Kathleen

    2010-01-01

    Summary Telomerase is a ribonucleoprotein reverse transcriptase with two subunits critical for catalytic activity, the protein telomerase reverse transcriptase (TERT) and telomerase RNA. In this study, we establish additional roles of the telomerase RNA subunit by demonstrating that RNA motifs stimulate the processivity of nucleotide and repeat addition. These functions are both functionally and physically separable from the roles of other RNA motifs in establishing a properly defined template. Binding of Tetrahymena telomerase RNA stem IV to TERT enhances nucleotide addition processivity, while a cooperation of the RNA pseudoknot and stem IV promotes repeat addition processivity. The low processivity of DNA synthesis by telomerase ribonucleoproteins lacking the pseudoknot and/or stem IV can be rescued by addition of the deleted region in trans. These findings demonstrate RNA elements with roles in telomerase elongation processivity that are distinct from RNA elements that specify the internal template. PMID:12820978

  14. Fast Prediction of RNA-RNA Interaction

    NASA Astrophysics Data System (ADS)

    Salari, Raheleh; Backofen, Rolf; Sahinalp, S. Cenk

    Regulatory antisense RNAs are a class of ncRNAs that regulate gene expression by prohibiting the translation of an mRNA by establishing stable interactions with a target sequence. There is great demand for efficient computational methods to predict the specific interaction between an ncRNA and its target mRNA(s). There are a number of algorithms in the literature which can predict a variety of such interactions - unfortunately at a very high computational cost. Although some existing target prediction approaches are much faster, they are specialized for interactions with a single binding site.

  15. Characterization of a Novel 5′ Subgenomic RNA3a Derived from RNA3 of Brome Mosaic Bromovirus▿

    PubMed Central

    Wierzchoslawski, Rafal; Urbanowicz, Anna; Dzianott, Aleksandra; Figlerowicz, Marek; Bujarski, Jozef J.

    2006-01-01

    The synthesis of 3′ subgenomic RNA4 (sgRNA4) by initiation from an internal sg promoter in the RNA3 segment was first described for Brome mosaic bromovirus (BMV), a model tripartite positive-sense RNA virus (W. A. Miller, T. W. Dreher, and T. C. Hall, Nature 313:68-70, 1985). In this work, we describe a novel 5′ sgRNA of BMV (sgRNA3a) that we propose arises by premature internal termination and that encapsidates in BMV virions. Cloning and sequencing revealed that, unlike any other BMV RNA segment, sgRNA3a carries a 3′ oligo(A) tail, in which respect it resembles cellular mRNAs. Indeed, both the accumulation of sgRNA3a in polysomes and the synthesis of movement protein 3a in in vitro systems suggest active functions of sgRNA3a during protein synthesis. Moreover, when copied in the BMV replicase in vitro reaction, the minus-strand RNA3 template generated the sgRNA3a product, likely by premature termination at the minus-strand oligo(U) tract. Deletion of the oligo(A) tract in BMV RNA3 inhibited synthesis of sgRNA3a during infection. We propose a model in which the synthesis of RNA3 is terminated prematurely near the sg promoter. The discovery of 5′ sgRNA3a sheds new light on strategies viruses can use to separate replication from the translation functions of their genomic RNAs. PMID:17005659

  16. 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. PMID:21541694

  17. 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.

  18. 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

  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. 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...

  1. 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

  2. Hepatitis C virus RNA: molecular switches mediated by long-range RNA–RNA interactions?

    PubMed Central

    Shetty, Sumangala; Stefanovic, Snezana; Mihailescu, Mihaela Rita

    2013-01-01

    Multiple conserved structural cis-acting regulatory elements have been recognized both in the coding and untranslated regions (UTRs) of the hepatitis C virus (HCV) genome. For example, the cis-element 5BSL3.2 in the HCV-coding region has been predicted to use both its apical and internal loops to interact with the X RNA in the 3′-UTR, with the IIId domain in the 5′-UTR and with the Alt sequence in the coding region. Additionally, the X RNA region uses a palindromic sequence that overlaps the sequence required for the interaction with 5BSL3.2, to dimerize with another HCV genome. The ability of the 5BSL3.2 and X RNA regions to engage in multi-interactions suggests the existence of one or more molecular RNA switches which may regulate different steps of the HCV life cycle. In this study, we used biophysical methods to characterize the essential interactions of these HCV cis-elements at the molecular level. Our results indicate that X RNA interacts with 5BSL3.2 and another X RNA molecule by adopting two different conformations and that 5BSL3.2 engages simultaneously in kissing interactions using its apical and internal loops. Based on these results, we propose a mode of action for possible molecular switches involving the HCV RNA. PMID:23275555

  3. 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

  4. 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

  5. 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

  6. Induced tRNA Import into Human Mitochondria: Implication of a Host Aminoacyl-tRNA-Synthetase

    PubMed Central

    Gowher, Ali; Smirnov, Alexandre; Tarassov, Ivan; Entelis, Nina

    2013-01-01

    In human cell, a subset of small non-coding RNAs is imported into mitochondria from the cytosol. Analysis of the tRNA import pathway allowing targeting of the yeast tRNALysCUU into human mitochondria demonstrates a similarity between the RNA import mechanisms in yeast and human cells. We show that the cytosolic precursor of human mitochondrial lysyl-tRNA synthetase (preKARS2) interacts with the yeast tRNALysCUU and small artificial RNAs which contain the structural elements determining the tRNA mitochondrial import, and facilitates their internalization by isolated human mitochondria. The tRNA import efficiency increased upon addition of the glycolytic enzyme enolase, previously found to be an actor of the yeast RNA import machinery. Finally, the role of preKARS2 in the RNA mitochondrial import has been directly demonstrated in vivo, in cultured human cells transfected with the yeast tRNA and artificial importable RNA molecules, in combination with preKARS2 overexpression or downregulation by RNA interference. These findings suggest that the requirement of protein factors for the RNA mitochondrial targeting might be a conserved feature of the RNA import pathway in different organisms. PMID:23799079

  7. Inhibition of RNA polymerase III transcription by BRCA1.

    PubMed

    Veras, Ingrid; Rosen, Eliot M; Schramm, Laura

    2009-04-01

    RNA polymerase III (RNA pol III) transcribes structural RNAs involved in RNA processing (U6 snRNA) and translation (tRNA), thereby regulating the growth rate of cells. Proper initiation by RNA pol III requires the transcription factor TFIIIB. Gene-external U6 snRNA transcription requires TFIIIB consisting of Bdp1, TBP, and Brf2. Transcription from the gene-internal tRNA promoter requires TFIIIB composed of Bdp1, TBP, and Brf1. TFIIIB is a target of tumor suppressors, including PTEN, ARF, p53, and RB, and RB-related pocket proteins. Breast cancer susceptibility gene 1 (BRCA1) tumor suppressor plays a role in DNA repair, cell cycle regulation, apoptosis, genome integrity, and ubiquitination. BRCA1 has a conserved amino-terminal RING domain, an activation domain 1 (AD1), and an acidic carboxyl-terminal domain (BRCA1 C-terminal region). In Saccharomyces cerevisiae, TFIIB interacts with the BRCA1 C-terminal region domain of Fcp1p, an RNA polymerase II phosphatase. The TFIIIB subunits Brf1 and Brf2 are structurally similar to TFIIB. Hence, we hypothesize that RNA pol III may be regulated by BRCA1 via the TFIIB family members Brf1 and Brf2. Here we report that: (1) BRCA1 inhibits both VAI (tRNA) and U6 snRNA RNA pol III transcription; (2) the AD1 of BRCA1 is responsible for inhibition of U6 snRNA transcription, whereas the RING domain and AD1 of BRCA1 are required for VAI transcription inhibition; and (3) overexpression of Brf1 and Brf2 alleviates inhibition of U6 snRNA and VAI transcription by BRCA1. Taken together, these data suggest that BRCA1 is a general repressor of RNA pol III transcription. PMID:19361418

  8. 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

  9. Overview of the Capstone depleted uranium study of aerosols from impact with armored vehicles: test setup and aerosol generation, characterization, and application in assessing dose and risk.

    PubMed

    Parkhurst, Mary Ann; Guilmette, Raymond A

    2009-03-01

    The Capstone Depleted Uranium (DU) Aerosol Characterization and Risk Assessment Study was conducted to generate data about DU aerosols generated during the perforation of armored combat vehicles with large-caliber DU penetrators, and to apply the data in assessments of human health risks to personnel exposed to these aerosols, primarily through inhalation, during the 1991 Gulf War or in future military operations. The Capstone study consisted of two components: 1) generating, sampling, and characterizing DU aerosols by firing at and perforating combat vehicles, and 2) applying the source-term quantities and characteristics of the aerosols to the evaluation of doses and risks. This paper reviews the background of the study including the bases for the study, previous reviews of DU particles and health assessments from DU used by the U.S. military, the objectives of the study components, the participants and oversight teams, and the types of exposures it was intended to evaluate. It then discusses exposure scenarios used in the dose and risk assessment and provides an overview of how the field tests and dose and risk assessments were conducted. PMID:19204481

  10. Effect of Capping Front Layer Materials on the Penetration Resistance of Q&T Steel Welded Joints Against 7.62-mm Armor-Piercing Projectile

    NASA Astrophysics Data System (ADS)

    Balakrishnan, M.; Balasubramanian, V.; Madhusudhan Reddy, G.; Parameswaran, P.

    2013-09-01

    In the present investigation, an attempt has been made to study the effect of capping front layers on the ballistic performance of shielded metal arc-welded armor steel joints which were fabricated with a chromium carbide-rich hardfaced middle layer on the buttered/beveled edge. Two different capping front layer materials were chosen for achieving better ballistic performance, namely, low hydrogen ferritic (LHF) and austenitic stainless steel (SS) fillers. On the other hand, the bottom layers are welded with SS filler for both joints. The consequent sandwiched joint served the dual purpose of weld integrity and penetration resistance of the bullet. It is observed that the penetration resistance is due to the high hardness of the hardfacing layer on the one hand and the energy-absorbing capacity of the soft backing SS weld deposits on the other hand. The complementary effect of layers successfully provided resistance to the projectile penetration. On a comparative analysis, the joint fabricated using the LHF filler capping front layer offered superior ballistic performance with respect to depth of penetration. This is mainly due to the presence of acicular ferrite along the bainitic structure in the LHF capping front layer, which caused a shallow hardness gradient along the weld center line.

  11. 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.

  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. Benchmarking of the state-of-the-art in nondestructive testing/evaluation for applicability in the Composite Armored Vehicle (CAV) Advanced Technology Demonstrator (ATD) program, phase 1

    NASA Astrophysics Data System (ADS)

    Carriveau, Gary W.

    1993-11-01

    This technology assessment report is the result of compilation, review, and assessment of information and data concerning the development and use of NDE/T as applied to advanced composites that may be used in the CAV (Composite Armored Vehicle) ATD (Advanced Technology Demonstrator) Program. This information has been gained from both published literature and as well as work in progress. It includes the results of a detailed bibliographic search using all the data bases held within the Defense Technical Information Center, supplemented wherever possible by other data bases. In addition, direct contacts and academic, industrial, and government research and development centers and applications laboratories were made. Discussions and recommendations contained in this report focus on the current state-of-the-art of composite NDE/T technologies and their capabilities and limitations for both the classical post process and real-time in-process inspection techniques. Furthermore, this effort includes an assessment of future developments and research trends including a projected time line.

  14. Updates on quick identification of acetic acid bacteria with a focus on the 16S-23S rRNA gene internal transcribed spacer and the analysis of cell proteins by MALDI-TOF mass spectrometry.

    PubMed

    Trček, Janja; Barja, François

    2015-03-01

    Acetic acid bacteria have attracted much attention over the past few years, due mainly to their metabolic traits that are of interest to the biotechnology industry. In addition, it turns out that their ecological habitats are almost unlimited since they have been found as symbionts in different insects and also as emerging opportunistic human pathogens. Very surprising is the finding that they colonize niches considered anaerobic, disproving the generalized statement that they are strict aerobes. Since they have taken on different biological roles in our environment, more and more people are charged with the task of identifying them. However, this turns out to be not always easy, especially if we are using phenotypic approaches for identification. A substantial step forward in making the identification of acetic acid bacteria easier was made possible using molecular biological methods, which have been extensively tested since 2000. However, some molecular methods require expensive machines and experienced staff, and moreover the level of their discrimination varies. All these factors must be considered when selecting the most appropriate approach for identifying acetic acid bacteria. With this objective in mind, this review article discusses the benefits and drawbacks of molecular biological methods for identification of acetic acid bacteria, with a focus on the 16S-23S rRNA gene ITS regions and the recently described alternative method for identification of acetic acid bacteria, MALDI-TOF MS. PMID:25589227

  15. 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

  16. Architecture of a yeast U6 RNA gene promoter.

    PubMed Central

    Eschenlauer, J B; Kaiser, M W; Gerlach, V L; Brow, D A

    1993-01-01

    The promoters of vertebrate and yeast U6 small nuclear RNA genes are structurally dissimilar, although both are recognized by RNA polymerase III. Vertebrate U6 RNA genes have exclusively upstream promoters, while the U6 RNA gene from the yeast Saccharomyces cerevisiae (SNR6) has internal and downstream promoter elements that match the tRNA gene intragenic A- and B-block elements, respectively. Substitution of the SNR6 A or B block greatly diminished U6 RNA accumulation in vivo, and a subcellular extract competent for RNA polymerase III transcription generated nearly identical DNase I protection patterns over the SNR6 downstream B block and a tRNA gene intragenic B block. We conclude that the SNR6 promoter is functionally similar to tRNA gene promoters, although the effects of extragenic deletion mutations suggest that the downstream location of the SNR6 B block imposes unique positional constraints on its function. Both vertebrate and yeast U6 RNA genes have an upstream TATA box element not normally found in tRNA genes. Substitution of the SNR6 TATA box altered the site of transcription initiation in vivo, while substitution of sequences further upstream had no effect on SNR6 transcription. We present a model for the SNR6 transcription complex that explains these results in terms of their effects on the binding of transcription initiation factor TFIIIB. Images PMID:8474459

  17. 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

  18. RNA based evolutionary optimization

    NASA Astrophysics Data System (ADS)

    Schuster, Peter

    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

  19. RNA Structural Elements of Hepatitis C Virus Controlling Viral RNA Translation and the Implications for Viral Pathogenesis

    PubMed Central

    Piñeiro, David; Martinez-Salas, Encarnación

    2012-01-01

    Hepatitis C virus (HCV) genome multiplication requires the concerted action of the viral RNA, host factors and viral proteins. Recent studies have provided information about the requirement of specific viral RNA motifs that play an active role in the viral life cycle. RNA regulatory motifs controlling translation and replication of the viral RNA are mostly found at the 5' and 3' untranslated regions (UTRs). In particular, viral protein synthesis is under the control of the internal ribosome entry site (IRES) element, a complex RNA structure located at the 5'UTR that recruits the ribosomal subunits to the initiator codon. Accordingly, interfering with this RNA structural motif causes the abrogation of the viral cycle. In addition, RNA translation initiation is modulated by cellular factors, including miRNAs and RNA-binding proteins. Interestingly, a RNA structural motif located at the 3'end controls viral replication and establishes long-range RNA-RNA interactions with the 5'UTR, generating functional bridges between both ends on the viral genome. In this article, we review recent advances on virus-host interaction and translation control modulating viral gene expression in infected cells. PMID:23202462

  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. Ab initio RNA folding.

    PubMed

    Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela

    2015-06-17

    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. PMID:25993396

  2. 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

  3. 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

  4. tRNA-mRNA mimicry drives translation initiation from a viral IRES.

    PubMed

    Costantino, David A; Pfingsten, Jennifer S; Rambo, Robert P; Kieft, Jeffrey S

    2008-01-01

    Internal ribosome entry site (IRES) RNAs initiate protein synthesis in eukaryotic cells by a noncanonical cap-independent mechanism. IRESes are critical for many pathogenic viruses, but efforts to understand their function are complicated by the diversity of IRES sequences as well as by limited high-resolution structural information. The intergenic region (IGR) IRESes of the Dicistroviridae viruses are powerful model systems to begin to understand IRES function. Here we present the crystal structure of a Dicistroviridae IGR IRES domain that interacts with the ribosome's decoding groove. We find that this RNA domain precisely mimics the transfer RNA anticodon-messenger RNA codon interaction, and its modeled orientation on the ribosome helps explain translocation without peptide bond formation. When combined with a previous structure, this work completes the first high-resolution description of an IRES RNA and provides insight into how RNAs can manipulate complex biological machines. PMID:18157151

  5. 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

  6. Structure Prediction of RNA Loops with a Probabilistic Approach.

    PubMed

    Li, Jun; Zhang, Jian; Wang, Jun; Li, Wenfei; Wang, Wei

    2016-08-01

    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

  7. 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.

  8. Viral IRES RNA structures and ribosome interactions.

    PubMed

    Kieft, Jeffrey S

    2008-06-01

    In eukaryotes, protein synthesis initiates primarily by a mechanism that requires a modified nucleotide 'cap' on the mRNA and also proteins that recruit and position the ribosome. Many pathogenic viruses use an alternative, cap-independent mechanism that substitutes RNA structure for the cap and many proteins. The RNAs driving this process are called internal ribosome-entry sites (IRESs) and some are able to bind the ribosome directly using a specific 3D RNA structure. Recent structures of IRES RNAs and IRES-ribosome complexes are revealing the structural basis of viral IRES' 'hijacking' of the protein-making machinery. It now seems that there are fundamental differences in the 3D structures used by different IRESs, although there are some common features in how they interact with ribosomes. PMID:18468443

  9. Viral IRES RNA structures and ribosome interactions

    PubMed Central

    Kieft, Jeffrey S.

    2009-01-01

    In eukaryotes, protein synthesis initiates primarily by a mechanism that requires a modified nucleotide ‘cap’ on the mRNA and also proteins that recruit and position the ribosome. Many pathogenic viruses use an alternative, cap-independent mechanism that substitutes RNA structure for the cap and many proteins. The RNAs driving this process are called internal ribosome-entry sites (IRESs) and some are able to bind the ribosome directly using a specific 3D RNA structure. Recent structures of IRES RNAs and IRES–ribosome complexes are revealing the structural basis of viral IRES’ ‘hijacking’ of the protein-making machinery. It now seems that there are fundamental differences in the 3D structures used by different IRESs, although there are some common features in how they interact with ribosomes. PMID:18468443

  10. 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

  11. 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

  12. 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.

  13. 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

  14. 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

  15. 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.

  16. 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.

  17. 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

  18. Intrinsic noise in post-transcriptional gene regulation by small non-coding RNA.

    PubMed

    Jia, Ya; Liu, Wangheng; Li, Anbang; Yang, Lijian; Zhan, Xuan

    2009-07-01

    Small non-coding RNA (sRNA) plays very important role in the post transcriptional regulation in various organisms. In complex regulatory networks, highly significant relative fluctuations in RNAs copy numbers can not be neglected due to very small copy number of individual RNA molecules. Here we consider two simple regulation schemes, where one is single target gene regulated by a sRNA and the other is two target mRNAs (mRNA(R) and mRNA(T)) regulated by one sRNA. The Fano factor (a measure of the relative size of the internal fluctuations) formulae of RNA molecules in the post transcriptional regulation are theoretically derived by using of the Langevin theory. For single target gene regulated by a sRNA, it is shown that the intrinsic noise of both mRNA and sRNA approaches the bare Poissonian limit in the regimen of both target RNA silencing and surviving. However, the strong anti-correlation between the fluctuations of two components result in a large intrinsic fluctuations in the level of RNA molecules in the regimen of crossover. For two target mRNAs regulated by one sRNA, in the regimen of crossover, it is found that, with the increasing of transcription rate of target mRNA(T), the maximal intrinsic fluctuation of RNA molecules is shifted from sRNA to target mRNA(R), and then to target mRNA(T). The intrinsic noise intensity of target mRNA(R) is determined by both the transcriptional rate of itself and that of sRNA, and independent of the transcriptional rate of the other target mRNA(T). PMID:19403234

  19. Specific ligation to double-stranded RNA for analysis of cellular RNA::RNA interactions.

    PubMed

    Faridani, Omid R; McInerney, Gerald M; Gradin, Katarina; Good, Liam

    2008-09-01

    Double-stranded RNA (dsRNA) is formed in cells as intra- and intermolecular RNA interactions and is involved in a range of biological processes including RNA metabolism, RNA interference and translation control mediated by natural antisense RNA and microRNA. Despite this breadth of activities, few molecular tools are available to analyse dsRNA as native hybrids. We describe a two-step ligation method for enzymatic joining of dsRNA adaptors to any dsRNA molecule in its duplex form without a need for prior sequence or termini information. The method is specific for dsRNA and can ligate various adaptors to label, map or amplify dsRNA sequences. When combined with reverse transcription-polymerase chain reaction, the method is sensitive and can detect low nanomolar concentrations of dsRNA in total RNA. As examples, we mapped dsRNA/single-stranded RNA junctions within Escherichia coli hok mRNA and the human immunodeficiency virus TAR element using RNA from bacteria and mammalian cells. PMID:18628292

  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. 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

  3. Biology Today: Respect for RNA.

    ERIC Educational Resources Information Center

    Flannery, Maura C., Ed.

    1991-01-01

    The high points of the story of RNA are presented. The functions of RNA within the cell, how these functions are carried out, and how they evolved are described. The topics of splicing, self-splicing, RNA editing, transcription and translation, and antisense RNA are discussed. (KR)

  4. Topology of RNA-RNA interaction structures.

    PubMed

    Andersen, Jørgen E; Huang, Fenix W D; Penner, Robert C; Reidys, Christian M

    2012-07-01

    The topological filtration of interacting RNA complexes is studied, and the role is analyzed of certain diagrams called irreducible shadows, which form suitable building blocks for more general structures. We prove that, for two interacting RNAs, called interaction structures, there exist for fixed genus only finitely many irreducible shadows. This implies that, for fixed genus, there are only finitely many classes of interaction structures. In particular, the simplest case of genus zero already provides the formalism for certain types of structures that occur in nature and are not covered by other filtrations. This case of genus zero interaction structures is already of practical interest, is studied here in detail, and is found to be expressed by a multiple context-free grammar that extends the usual one for RNA secondary structures. We show that, in O(n(6)) time and O(n(4)) space complexity, this grammar for genus zero interaction structures provides not only minimum free energy solutions but also the complete partition function and base pairing probabilities. PMID:22731621

  5. Complete sequence and gene organization of the Nosema spodopterae rRNA gene.

    PubMed

    Tsai, Shu-Jen; Huang, Wei-Fone; Wang, Chung-Hsiung

    2005-01-01

    By sequencing the entire ribosomal RNA (rRNA) gene of Nosema spodopterae, we show here that its gene organization follows a pattern similar to the Nosema type species, Nosema bombycis, i.e. 5'-large subunit rRNA (2,497 bp)-internal transcribed spacer (185 bp)-small subunit rRNA (1,232 bp)-intergenic spacer (277 bp)-5S rRNA (114 bp)-3'. Gene sequences and the secondary structures of large subunit rRNA, small subunit rRNA, and 5S rRNA are compared with the known corresponding sequences and structures of closely related microsporidia. The results suggest that the Nosema genus may be heterogeneous and that the rRNA gene organization may be a useful characteristic for determining which species are closely related to the type species. PMID:15702980

  6. 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

  7. Alignments of RNA structures.

    PubMed

    Blin, Guillaume; Denise, Alain; Dulucq, Serge; Herrbach, Claire; Touzet, Hélène

    2010-01-01

    We describe a theoretical unifying framework to express the comparison of RNA structures, which we call alignment hierarchy. This framework relies on the definition of common supersequences for arc-annotated sequences and encompasses the main existing models for RNA structure comparison based on trees and arc-annotated sequences with a variety of edit operations. It also gives rise to edit models that have not been studied yet. We provide a thorough analysis of the alignment hierarchy, including a new polynomial-time algorithm and an NP-completeness proof. The polynomial-time algorithm involves biologically relevant edit operations such as pairing or unpairing nucleotides. It has been implemented in a software, called gardenia, which is available at the Web server http://bioinfo.lifl.fr/RNA/gardenia. PMID:20431150

  8. 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.

  9. 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

    2015-01-01

    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. PMID:25651103

  10. 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.

  11. Editor meets silencer: crosstalk between RNA editing and RNA interference

    PubMed Central

    Nishikura, Kazuko

    2010-01-01

    The most prevalent type of RNA editing is mediated by ADAR (adenosine deaminase acting on RNA) enzymes, which convert adenosines to inosines (a process known as A→I RNA editing) in double-stranded (ds)RNA substrates. A→I RNA editing was long thought to affect only selected transcripts by altering the proteins they encode. However, genome-wide screening has revealed numerous editing sites within inverted Alu repeats in introns and untranslated regions. Also, recent evidence indicates that A→I RNA editing crosstalks with RNA-interference pathways, which, like A→I RNA editing, involve dsRNAs. A→I RNA editing therefore seems to have additional functions, including the regulation of retrotransposons and gene silencing, which adds a new urgency to the challenges of fully understanding ADAR functions. PMID:17139332

  12. Genome-scale identification of miRNA-mRNA and miRNA-lncRNA interactions in domestic animals.

    PubMed

    Li, A; Zhang, J; Zhou, Z; Wang, L; Sun, X; Liu, Y

    2015-12-01

    Domestic animals show considerable genetic diversity. Previous studies suggested that animal phenotypes were affected by miRNA-mRNA interplay, but these studies focused mainly on the analysis of one or several miRNA-mRNA interactions. However, in this study, we investigated miRNA-mRNA and miRNA-lncRNA interactions on a genomic scale using miranda and targetscan algorithms. There has been strong directional artificial selection practiced during the domestication of animals. Thus, we investigated SNPs that were located in miRNAs and miRNA binding sites and found that several SNPs located in 3'-UTRs of mRNAs had the potential to affect miRNA-mRNA interactions. In addition, a database, named miRBond, was developed to provide visualization, analysis and downloading of the resulting datasets. Our results open the way to further experimental verification of miRNA-mRNA and miRNA-lncRNA interactions as well as the influence of SNPs upon such interplay. PMID:26360131

  13. 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

  14. 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)

  15. 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. PMID:24200639

  16. [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

  17. Endoribonucleases--enzymes gaining spotlight in mRNA metabolism.

    PubMed

    Li, Wai Ming; Barnes, Tavish; Lee, Chow H

    2010-02-01

    The efficient turnover of messenger RNA represents an important mechanism that allows the cell to control gene expression. Until recently, the mechanism of mRNA decay was mainly attributed to exonucleases, comprising enzymes that degrade RNAs from the ends of the molecules. This article summarizes the endoribonucleases, comprising enzymes that cleave RNA molecules internally, which were identified in more recent years in eukaryotic mRNA metabolism. Endoribonucleases have received little attention in the past, based on the difficulty in their identification and a lack of understanding of their physiological significance. This review aims to compare the similarities and differences among this group of enzymes, as well as their known cellular functions. Despite the many differences in protein structure, and thus difficulties in identifying them based on amino acid sequence, most endoribonucleases possess essential cellular functions and have been shown to play an important role in mRNA turnover. PMID:19968858

  18. 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

  19. RNA recombination in a coronavirus: recombination between viral genomic RNA and transfected RNA fragments.

    PubMed Central

    Liao, C L; Lai, M M

    1992-01-01

    Mouse hepatitis virus (MHV), a coronavirus, has been shown to undergo a high frequency of RNA recombination both in tissue culture and in animal infection. So far, RNA recombination has been demonstrated only between genomic RNAs of two coinfecting viruses. To understand the mechanism of RNA recombination and to further explore the potential of RNA recombination, we studied whether recombination could occur between a replicating MHV RNA and transfected RNA fragments. We first used RNA fragments which represented the 5' end of genomic-sense sequences of MHV RNA for transfection. By using polymerase chain reaction amplification with two specific primers, we were able to detect recombinant RNAs which incorporated the transfected fragment into the 5' end of the viral RNA in the infected cells. Surprisingly, even the anti-genomic-sense RNA fragments complementary to the 5' end of MHV genomic RNA could also recombine with the MHV genomic RNAs. This observation suggests that RNA recombination can occur during both positive- and negative-strand RNA synthesis. Furthermore, the recombinant RNAs could be detected in the virion released from the infected cells even after several passages of virus in tissue culture cells, indicating that these recombinant RNAs represented functional virion RNAs. The crossover sites of these recombinants were detected throughout the transfected RNA fragments. However, when an RNA fragment with a nine-nucleotide (CUUUAUAAA) deletion immediately downstream of a pentanucleotide (UCUAA) repeat sequence in the leader RNA was transfected into MHV-infected cells, most of the recombinants between this RNA and the MHV genome contained crossover sites near this pentanucleotide repeat sequence. In contrast, when exogenous RNAs with the intact nine-nucleotide sequence were used in similar experiments, the crossover sites of recombinants in viral genomic RNA could be detected at more-downstream sites. This study demonstrated that recombination can occur

  20. 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

  1. A boost for the emerging field of RNA nanotechnology.

    PubMed

    Shukla, Girish C; Haque, Farzin; Tor, Yitzhak; Wilhelmsson, L Marcus; Toulmé, Jean-Jacques; Isambert, Hervé; Guo, Peixuan; Rossi, John J; Tenenbaum, Scott A; Shapiro, Bruce A

    2011-05-24

    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

  2. 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. PMID:26530921

  3. 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…

  4. Mapping RNA-RNA interactome and RNA structure in vivo by MARIO.

    PubMed

    Nguyen, Tri C; Cao, Xiaoyi; Yu, Pengfei; Xiao, Shu; Lu, Jia; Biase, Fernando H; Sridhar, Bharat; Huang, Norman; Zhang, Kang; Zhong, Sheng

    2016-01-01

    The pervasive transcription of our genome presents a possibility of revealing new genomic functions by investigating RNA interactions. Current methods for mapping RNA-RNA interactions have to rely on an 'anchor' protein or RNA and often require molecular perturbations. Here we present the MARIO (Mapping RNA interactome in vivo) technology to massively reveal RNA-RNA interactions from unperturbed cells. We mapped tens of thousands of endogenous RNA-RNA interactions from mouse embryonic stem cells and brain. We validated seven interactions by RNA antisense purification and one interaction using single-molecule RNA-FISH. The experimentally derived RNA interactome is a scale-free network, which is not expected from currently perceived promiscuity in RNA-RNA interactions. Base pairing is observed at the interacting regions between long RNAs, including transposon transcripts, suggesting a class of regulatory sequences acting in trans. In addition, MARIO data reveal thousands of intra-molecule interactions, providing in vivo data on high-order RNA structures. PMID:27338251

  5. The RNA interference revolution.

    PubMed

    Lenz, G

    2005-12-01

    The discovery of double-stranded RNA-mediated gene silencing has rapidly led to its use as a method of choice for blocking a gene, and has turned it into one of the most discussed topics in cell biology. Although still in its infancy, the field of RNA interference has already produced a vast array of results, mainly in Caenorhabditis elegans, but recently also in mammalian systems. Micro-RNAs are short hairpins of RNA capable of blocking translation, which are transcribed from genomic DNA and are implicated in several aspects from development to cell signaling. The present review discusses the main methods used for gene silencing in cell culture and animal models, including the selection of target sequences, delivery methods and strategies for a successful silencing. Expected developments are briefly discussed, ranging from reverse genetics to therapeutics. Thus, the development of the new paradigm of RNA-mediated gene silencing has produced two important advances: knowledge of a basic cellular mechanism present in the majority of eukaryotic cells and access to a potent and specific new method for gene silencing. PMID:16302089

  6. 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…

  7. RNA in the Loop

    PubMed Central

    Kung, Johnny T.Y.; Lee, Jeannie T.

    2013-01-01

    Long noncoding RNAs (lncRNAs) have been implicated in a variety of biological roles, particularly as cis or trans gene expression regulators. Reporting recently in Nature, Lai et al. (2013) show that a class of gene-activating lncRNAs combines two gene regulation paradigms: enhancer-directed chromosomal looping and RNA-mediated protein effector recruitment. PMID:23537627

  8. Divergent RNA transcription

    PubMed Central

    Naughton, Catherine; Corless, Samuel; Gilbert, Nick

    2013-01-01

    New approaches using biotinylated-psoralen as a probe for investigating DNA structure have revealed new insights into the relationship between DNA supercoiling, transcription and chromatin compaction. We explore a hypothesis that divergent RNA transcription generates negative supercoiling at promoters facilitating initiation complex formation and subsequent promoter clearance. PMID:23863199

  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. 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.

  11. 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

  12. Electrophilic activity-based RNA probes reveal a self-alkylating RNA for RNA labeling

    PubMed Central

    McDonald, Richard I.; Guilinger, John P.; Mukherji, Shankar; Curtis, Edward A.; Lee, Won I.; Liu, David R.

    2014-01-01

    Probes that form covalent bonds with RNA molecules based on their chemical reactivity would advance our ability to study the transcriptome. We developed a set of electrophilic activity-based RNA probes designed to react with unusually nucleophilic RNAs. We used these probes to identify reactive genome-encoded RNAs, resulting in the discovery of a 42-nt catalytic RNA from an archaebacterium that reacts with a 2,3-disubstituted epoxide at N7 of a specific guanosine. Detailed characterization of the catalytic RNA revealed the structural requirements for reactivity. We developed this catalytic RNA into a general tool to selectively conjugate a small molecule to an RNA of interest. This strategy enabled up to 500-fold enrichment of target RNA from total mammalian RNA or from cell lysate. We demonstrated the utility of this approach by selectively capturing proteins in yeast cell lysate that bind to the ASH1 mRNA. PMID:25306441

  13. 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

  14. Protein-RNA networks revealed through covalent RNA marks.

    PubMed

    Lapointe, Christopher P; Wilinski, Daniel; Saunders, Harriet A J; Wickens, Marvin

    2015-12-01

    Protein-RNA networks are ubiquitous and central in biological control. We present an approach termed RNA Tagging that enables the user to identify protein-RNA interactions in vivo by analyzing purified cellular RNA, without protein purification or cross-linking. An RNA-binding protein of interest is fused to an enzyme that adds uridines to the end of RNA. RNA targets bound by the chimeric protein in vivo are covalently marked with uridines and subsequently identified from extracted RNA via high-throughput sequencing. We used this approach to identify hundreds of RNAs bound by a Saccharomyces cerevisiae PUF protein, Puf3p. The results showed that although RNA-binding proteins productively bind specific RNAs to control their function, they also 'sample' RNAs without exerting a regulatory effect. We used the method to uncover hundreds of new and likely regulated targets for a protein without canonical RNA-binding domains, Bfr1p. RNA Tagging is well suited to detect and analyze protein-RNA networks in vivo. PMID:26524240

  15. 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

  16. Protein-RNA networks revealed through covalent RNA marks

    PubMed Central

    Lapointe, Christopher P.; Wilinski, Daniel; Saunders, Harriet A. J.; Wickens, Marvin

    2015-01-01

    Protein-RNA networks are ubiquitous and central in biological control. We present an approach, termed “RNA Tagging,” that identifies protein-RNA interactions in vivo by analyzing purified cellular RNA, without protein purification or crosslinking. An RNA-binding protein of interest is fused to an enzyme that adds uridines to the end of RNA. RNA targets bound by the chimeric protein in vivo are covalently marked with uridines and subsequently identified from extracted RNA using high-throughput sequencing. We used this approach to identify hundreds of RNAs bound by a Saccharomyces cerevisiae PUF protein, Puf3p. The method revealed that while RNA-binding proteins productively bind specific RNAs to control their function, they also “sample” RNAs without exerting a regulatory effect. We exploited the method to uncover hundreds of new and likely regulated targets for a protein without canonical RNA-binding domains, Bfr1p. The RNA Tagging approach is well-suited to detect and analyze protein-RNA networks in vivo. PMID:26524240

  17. RNA Interference in Ticks

    PubMed Central

    Kocan, Katherine M.; Blouin, Edmour; de la Fuente, José

    2011-01-01

    Ticks are obligate hematophagous ectoparasites of wild and domestic animals and humans, and are considered to be second worldwide to mosquitoes as vectors of human diseases1 and the most important vectors affecting cattle industry worldwide2. Ticks are classified in the subclass Acari, order Parasitiformes, suborder Ixodida and are distributed worldwide from Arctic to tropical regions3. Despite efforts to control tick infestations, these ectoparasites remain a serious problem for human and animal health4,5. RNA interference (RNAi)6 is a nucleic acid-based reverse genetic approach that involves disruption of gene expression in order to determine gene function or its effect on a metabolic pathway. Small interfering RNAs (siRNAs) are the effector molecules of the RNAi pathway that is initiated by double-stranded RNA (dsRNA) and results in a potent sequence-specific degradation of cytoplasmic mRNAs containing the same sequence as the dsRNA trigger7-9. Post-transcriptional gene silencing mechanisms initiated by dsRNA have been discovered in all eukaryotes studied thus far, and RNAi has been rapidly developed in a variety of organisms as a tool for functional genomics studies and other applications10. RNAi has become the most widely used gene-silencing technique in ticks and other organisms where alternative approaches for genetic manipulation are not available or are unreliable5,11. The genetic characterization of ticks has been limited until the recent application of RNAi12,13. In the short time that RNAi has been available, it has proved to be a valuable tool for studying tick gene function, the characterization of the tick-pathogen interface and the screening and characterization of tick protective antigens14. Herein, a method for RNAi through injection of dsRNA into unfed ticks is described. It is likely that the knowledge gained from this experimental approach will contribute markedly to the understanding of basic biological systems and the development of vaccines

  18. 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)

  19. 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 ...

  20. Effect of cucurbitacins on mRNA coding for laccase in Botrytis cinerea.

    PubMed

    Gonen, L; Viterbo, A; Cantone, F; Staples, R C; Mayer, A M

    1996-05-01

    The effect of cucurbitacin and of Ecballium extract on the formation of mRNA coding for laccase was examined in cultures of Botrytis cinerea grown with inducers of laccase formation, in the presence or absence of the inhibitory compounds. RNA was isolated from the cultures and probed with specific DNA probes for laccase. As an internal control, the RNA was probed for Botrytis beta-tubulin mRNA. From an analysis of the results it is clear that cucurbitacin I and Ecballium extract specifically repress the amount of mRNA coding for laccase. This could account for the previously observed repression of laccase formation by cucurbitacins. PMID:8688171

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

    Theis, Corinna; Höner Zu Siederdissen, Christian; Hofacker, Ivo L; Gorodkin, Jan

    2013-12-01

    Recent progress in predicting RNA structure is moving towards filling the 'gap' in 2D RNA structure prediction where, for example, predicted internal loops often form non-canonical base pairs. This is increasingly recognized with the steady increase of known RNA 3D modules. There is a general interest in matching structural modules known from one molecule to other molecules for which the 3D structure is not known yet. We have created a pipeline, metaRNAmodules, which completely automates extracting putative modules from the FR3D database and mapping of such modules to Rfam alignments to obtain comparative evidence. Subsequently, the modules, initially represented by a graph, are turned into models for the RMDetect program, which allows to test their discriminative power using real and randomized Rfam alignments. An initial extraction of 22 495 3D modules in all PDB files results in 977 internal loop and 17 hairpin modules with clear discriminatory power. Many of these modules describe only minor variants of each other. Indeed, mapping of the modules onto Rfam families results in 35 unique locations in 11 different families. The metaRNAmodules pipeline source for the internal loop modules is available at http://rth.dk/resources/mrm. PMID:24005040

  5. 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.

  6. 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:

  7. 'RNA walk' a novel approach to study RNA-RNA interactions between a small RNA and its target.

    PubMed

    Lustig, Yaniv; Wachtel, Chaim; Safro, Mark; Liu, Li; Michaeli, Shulamit

    2010-01-01

    In this study we describe a novel method to investigate the RNA-RNA interactions between a small RNA and its target that we termed 'RNA walk'. The method is based on UV-induced AMT cross-linking in vivo followed by affinity selection of the hybrid molecules and mapping the intermolecular adducts by RT-PCR or real-time PCR. Domains carrying the cross-linked adducts fail to efficiently amplify by PCR compared with non-cross-linked domains. This method was calibrated and used to study the interaction between a special tRNA-like molecule (sRNA-85) that is part of the trypanosome signal recognition particle (SRP) complex and the ribosome. Four contact sites between sRNA-85 and rRNA were identified by 'RNA walk' and were further fine-mapped by primer extension. Two of the contact sites are expected; one contact site mimics the interaction of the mammalian Alu domain of SRP with the ribosome and the other contact sites include a canonical tRNA interaction. The two other cross-linked sites could not be predicted. We propose that 'RNA walk, is a generic method to map target RNA small RNAs interactions in vivo. PMID:19854950

  8. Structural and mechanistic characterization of 6S RNA from the hyperthermophilic bacterium Aquifex aeolicus.

    PubMed

    Köhler, Karen; Duchardt-Ferner, Elke; Lechner, Marcus; Damm, Katrin; Hoch, Philipp G; Salas, Margarita; Hartmann, Roland K

    2015-10-01

    Bacterial 6S RNAs competitively inhibit binding of RNA polymerase (RNAP) holoenzymes to DNA promoters, thereby globally regulating transcription. RNAP uses 6S RNA itself as a template to synthesize short transcripts, termed pRNAs (product RNAs). Longer pRNAs (approx. ≥ 10 nt) rearrange the 6S RNA structure and thereby disrupt the 6S RNA:RNAP complex, which enables the enzyme to resume transcription at DNA promoters. We studied 6S RNA of the hyperthermophilic bacterium Aquifex aeolicus, representing the thermodynamically most stable 6S RNA known so far. Applying structure probing and NMR, we show that the RNA adopts the canonical rod-shaped 6S RNA architecture with little structure formation in the central bulge (CB) even at moderate temperatures (≤37 °C). 6S RNA:pRNA complex formation triggers an internal structure rearrangement of 6S RNA, i.e. formation of a so-called central bulge collapse (CBC) helix. The persistence of several characteristic NMR imino proton resonances upon pRNA annealing demonstrates that defined helical segments on both sides of the CB are retained in the pRNA-bound state, thus representing a basic framework of the RNA's architecture. RNA-seq analyses revealed pRNA synthesis from 6S RNA in A. aeolicus, identifying 9 to ∼17-mers as the major length species. A. aeolicus 6S RNA can also serve as a template for in vitro pRNA synthesis by RNAP from the mesophile Bacillus subtilis. Binding of a synthetic pRNA to A. aeolicus 6S RNA blocks formation of 6S RNA:RNAP complexes. Our findings indicate that A. aeolicus 6S RNA function in its hyperthermophilic host is mechanistically identical to that of other bacterial 6S RNAs. The use of artificial pRNA variants, designed to disrupt helix P2 from the 3'-CB instead of the 5'-CB but preventing formation of the CBC helix, indicated that the mechanism of pRNA-induced RNAP release has been evolutionarily optimized for transcriptional pRNA initiation in the 5'-CB. PMID:25771336

  9. 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

  10. 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

  11. Genetic relatedness of orbiviruses by RNA-RNA blot hybridization

    SciTech Connect

    Bodkin, D.K.

    1985-01-01

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

  12. Current preclinical small interfering RNA (siRNA)-based conjugate systems for RNA therapeutics.

    PubMed

    Lee, Soo Hyeon; Kang, Yoon Young; Jang, Hyo-Eun; Mok, Hyejung

    2016-09-01

    Recent promising clinical results of RNA therapeutics have drawn big attention of academia and industries to RNA therapeutics and their carrier systems. To improve their feasibility in clinics, systemic evaluations of currently available carrier systems under clinical trials and preclinical studies are needed. In this review, we focus on recent noticeable preclinical studies and clinical results regarding siRNA-based conjugates for clinical translations. Advantages and drawbacks of siRNA-based conjugates are discussed, compared to particle-based delivery systems. Then, representative siRNA-based conjugates with aptamers, peptides, carbohydrates, lipids, polymers, and nanostructured materials are introduced. To improve feasibility of siRNA conjugates in preclinical studies, several considerations for the rational design of siRNA conjugates in terms of cleavability, immune responses, multivalent conjugations, and mechanism of action are also presented. Lastly, we discuss lessons from previous preclinical and clinical studies related to siRNA conjugates and perspectives of their clinical applications. PMID:26514375

  13. The Impact of mRNA Structure on Guide RNA Targeting in Kinetoplastid RNA Editing

    PubMed Central

    Reifur, Larissa; Yu, Laura E.; Cruz-Reyes, Jorge; vanHartesvelt, Michelle; Koslowsky, Donna J.

    2010-01-01

    Mitochondrial mRNA editing in Trypanosoma brucei requires the specific interaction of a guide RNA with its cognate mRNA. Hundreds of gRNAs are involved in the editing process, each needing to target their specific editing domain within the target message. We hypothesized that the structure surrounding the mRNA target may be a limiting factor and involved in the regulation process. In this study, we selected four mRNAs with distinct target structures and investigated how sequence and structure affected efficient gRNA targeting. Two of the mRNAs, including the ATPase subunit 6 and ND7-550 (5′ end of NADH dehydrogenase subunit 7) that have open, accessible anchor binding sites show very efficient gRNA targeting. Electrophoretic mobility shift assays indicate that the cognate gRNA for ND7-550 had 10-fold higher affinity for its mRNA than the A6 pair. Surface plasmon resonance studies indicate that the difference in affinity was due to a four-fold faster association rate. As expected, mRNAs with considerable structure surrounding the anchor binding sites were less accessible and had very low affinity for their cognate gRNAs. In vitro editing assays indicate that efficient pairing is crucial for gRNA directed cleavage. However, only the A6 substrate showed gRNA-directed cleavage at the correct editing site. This suggests that different gRNA/mRNA pairs may require different “sets” of accessory factors for efficient editing. By characterizing a number of different gRNA/mRNA interactions, we may be able to define a “bank” of RNA editing substrates with different putative chaperone and other co-factor requirements. This will allow the more efficient identification and characterization of transcript specific RNA editing accessory proteins. PMID:20808932

  14. 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

  15. 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

  16. 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

  17. Semiautomated improvement of RNA alignments

    PubMed Central

    Andersen, Ebbe S.; Lind-Thomsen, Allan; Knudsen, Bjarne; Kristensen, Susie E.; Havgaard, Jakob H.; Torarinsson, Elfar; Larsen, Niels; Zwieb, Christian; Sestoft, Peter; Kjems, Jørgen; Gorodkin, Jan

    2007-01-01

    We have developed a semiautomated RNA sequence editor (SARSE) that integrates tools for analyzing RNA alignments. The editor highlights different properties of the alignment by color, and its integrated analysis tools prevent the introduction of errors when doing alignment editing. SARSE readily connects to external tools to provide a flexible semiautomatic editing environment. A new method, Pcluster, is introduced for dividing the sequences of an RNA alignment into subgroups with secondary structure differences. Pcluster was used to evaluate 574 seed alignments obtained from the Rfam database and we identified 71 alignments with significant prediction of inconsistent base pairs and 102 alignments with significant prediction of novel base pairs. Four RNA families were used to illustrate how SARSE can be used to manually or automatically correct the inconsistent base pairs detected by Pcluster: the mir-399 RNA, vertebrate telomase RNA (vert-TR), bacterial transfer-messenger RNA (tmRNA), and the signal recognition particle (SRP) RNA. The general use of the method is illustrated by the ability to accommodate pseudoknots and handle even large and divergent RNA families. The open architecture of the SARSE editor makes it a flexible tool to improve all RNA alignments with relatively little human intervention. Online documentation and software are available at http://sarse.ku.dk. PMID:17804647

  18. Bacteriophage T5 transfer RNA

    SciTech Connect

    Hunt, C.; Desai, S.M.; Vaughan, J.; Weiss, S.B.

    1980-04-10

    Previous studies from this laboratory have provided a high resolution map for 16 tRNA genes located on the continuous heavy DNA strand of bacteriophage T5 DNA. All of the T5 tRNA genes were located in three clusters within the DNA C segment, except for tRNA/sup Arg/, which mapped on the left end of the DNA D segment. In this report, we present evidence for the presence of eight additional T5 tRNA species, five of which are located in two new loci within the DNA C segment. We also describe a two-dimensional gel electrophoresis system for the separation and isolation of T5 tRNA species from crude infected RNA preparations. The gel electrophoresis system separates tRNA isoacceptors specific for different amino acids; evidence is presented that the isoacceptors for isoleucine, histidine, and serine are coded by different T5 genes.

  19. 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

  20. The tmRNA website

    DOE PAGESBeta

    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