Novel essential residues of Hda for interaction with DnaA in the regulatory inactivation of DnaA: unique roles for Hda AAA Box VI and VII motifs.

PubMed

Nakamura, Kenta; Katayama, Tsutomu

2010-04-01

Escherichia coli ATP-DnaA initiates chromosomal replication. For preventing extra-initiations, a complex of ADP-Hda and the DNA-loaded replicase clamp promotes DnaA-ATP hydrolysis, yielding inactive ADP-DnaA. However, the Hda-DnaA interaction mode remains unclear except that the Hda Box VII Arg finger (Arg-153) and DnaA sensor II Arg-334 within each AAA(+) domain are crucial for the DnaA-ATP hydrolysis. Here, we demonstrate that direct and functional interaction of ADP-Hda with DnaA requires the Hda residues Ser-152, Phe-118 and Asn-122 as well as Hda Arg-153 and DnaA Arg-334. Structural analyses suggest intermolecular interactions between Hda Ser-152 and DnaA Arg-334 and between Hda Phe-118 and the DnaA Walker B motif region, in addition to an intramolecular interaction between Hda Asn-122 and Arg-153. These interactions likely sustain a specific association of ADP-Hda and DnaA, promoting DnaA-ATP hydrolysis. Consistently, ATP-DnaA and ADP-DnaA interact with the ADP-Hda-DNA-clamp complex with similar affinities. Hda Phe-118 and Asn-122 are contained in the Box VI region, and their hydrophobic and electrostatic features are basically conserved in the corresponding residues of other AAA(+) proteins, suggesting a conserved role for Box VI. These findings indicate novel interaction mechanisms for Hda-DnaA as well as a potentially fundamental mechanism in AAA(+) protein interactions.

RNA polymerase gate loop guides the nontemplate DNA strand in transcription complexes.

PubMed

NandyMazumdar, Monali; Nedialkov, Yuri; Svetlov, Dmitri; Sevostyanova, Anastasia; Belogurov, Georgiy A; Artsimovitch, Irina

2016-12-27

Upon RNA polymerase (RNAP) binding to a promoter, the σ factor initiates DNA strand separation and captures the melted nontemplate DNA, whereas the core enzyme establishes interactions with the duplex DNA in front of the active site that stabilize initiation complexes and persist throughout elongation. Among many core RNAP elements that participate in these interactions, the β' clamp domain plays the most prominent role. In this work, we investigate the role of the β gate loop, a conserved and essential structural element that lies across the DNA channel from the clamp, in transcription regulation. The gate loop was proposed to control DNA loading during initiation and to interact with NusG-like proteins to lock RNAP in a closed, processive state during elongation. We show that the removal of the gate loop has large effects on promoter complexes, trapping an unstable intermediate in which the RNAP contacts with the nontemplate strand discriminator region and the downstream duplex DNA are not yet fully established. We find that although RNAP lacking the gate loop displays moderate defects in pausing, transcript cleavage, and termination, it is fully responsive to the transcription elongation factor NusG. Together with the structural data, our results support a model in which the gate loop, acting in concert with initiation or elongation factors, guides the nontemplate DNA in transcription complexes, thereby modulating their regulatory properties.

Combination Space Station Handrail Clamp and Pointing Device

NASA Technical Reports Server (NTRS)

Hughes, Stephen J. (Inventor)

1999-01-01

A device for attaching an experiment carrier to a space station handrail is provided. The device has two major components, a clamping mechanism for attachment to a space station handrail, and a pointing carrier on which an experiment package can be mounted and oriented. The handrail clamp uses an overcenter mechanism and the carrier mechanism uses an adjustable preload ball and socket for carrier positioning. The handrail clamp uses a stack of disk springs to provide a spring loaded button. This configuration provides consistent clamping force over a range of possible handrail thicknesses. Three load points are incorporated in the clamping mechanism thereby spreading the clamping load onto three separate points on the handrail. A four bar linkage is used to provide for a single actuation lever for all three load points. For additional safety, a secondary lock consisting of a capture plate and push lock keeps the clamp attached to the handrail in the event of main clamp failure. For the carrier positioning mechanism, a ball in a spring loaded socket uses friction to provide locking torque; however. the ball and socket are torque limited so that the ball ran slip under kick loads (125 pounds or greater). A lead screw attached to disk spring stacks is used to provide an adjustable spring force on the socket. A locking knob is attached to the lead screw to allow for hand manipulation of the lead screw.

Fabrication and characterization of a piezoelectric energy harvester with clamped-clamped beams

NASA Astrophysics Data System (ADS)

Cui, Yan; Yu, Menglin; Gao, Shiqiao; Kong, Xiangxin; Gu, Wang; Zhang, Ran; Liu, Bowen

2018-05-01

This work presents a piezoelectric energy harvester with clamped-clamped beams, and it is fabricated with MEMS process. When excited by sinusoidal vibration, the energy harvester has a sharp jumping down phenomenon and the measured frequency responses of the clamped-clamped beams structure show a larger bandwidth which is about 56Hz, more efficient than that with cantilever beams. When the exciting acceleration ac is 12m/s2, the energy harvester achieves to a maximum open-circuit voltage of 94mV on one beam. The load voltage is proportional to the load resistance, and it increased with the increase of load resistance. Connected four beams in series, the output power reaches the maximum value of 730 nW and the optimal load is 15KΩ to one beam.

Electrostatic Interactions at the Dimer Interface Stabilize the E. coli β Sliding Clamp.

PubMed

Purohit, Anirban; England, Jennifer K; Douma, Lauren G; Tondnevis, Farzaneh; Bloom, Linda B; Levitus, Marcia

2017-08-22

Sliding clamps are ring-shaped oligomeric proteins that encircle DNA and associate with DNA polymerases for processive DNA replication. The dimeric Escherichia coli β-clamp is closed in solution but must adopt an open conformation to be assembled onto DNA by a clamp loader. To determine what factors contribute to the stability of the dimer interfaces in the closed conformation and how clamp dynamics contribute to formation of the open conformation, we identified conditions that destabilized the dimer and measured the effects of these conditions on clamp dynamics. We characterized the role of electrostatic interactions in stabilizing the β-clamp interface. Increasing salt concentration results in decreased dimer stability and faster subunit dissociation kinetics. The equilibrium dissociation constant of the dimeric clamp varies with salt concentration as predicted by simple charge-screening models, indicating that charged amino acids contribute to the remarkable stability of the interface at physiological salt concentrations. Mutation of a charged residue at the interface (Arg-103) weakens the interface significantly, whereas effects are negligible when a hydrophilic (Ser-109) or a hydrophobic (Ile-305) amino acid is mutated instead. It has been suggested that clamp opening by the clamp loader takes advantage of spontaneous opening-closing fluctuations at the clamp's interface, but our time-resolved fluorescence and fluorescence correlation experiments rule out conformational fluctuations that lead to a significant fraction of open states. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Plasma Chamber Restraints in Ignitor and Relevant Disruption Analysis

NASA Astrophysics Data System (ADS)

Gasparotto, M.; Cucchiaro, A.; Capriccioli, A.; Celentano, G.; Rita, C.; Roccella, M.; Macco, B.; Micheli, I.; Ferrari, G.; Orlandi, S.; Coppi, B.

2000-10-01

The plasmas chamber (PC) of Ignitor is made of 12 D-shaped toroidal sectors of Inconel 625 welded together by automatic remote equipment. The thickness of the inboard wall is 17 mm while the middle and outboard walls are 26 mm thick. The PC is supported through the ports by the C-Clamp structure of the toroidal magnet. The main function of the PC supports is to resist the vertical and radial electromagnetic loads and to allow for free movement under thermal loads while providing electrical insulation from the C-Clamps and cryostat. The largest estimated loads are due to a Vertical Displacement Event (VDE) disruption that is followed by a thermal quench and then by the current quench. The vertical supports involve a connection of each radial port to the C-Clamp structure by a link system that withstands the calculated loads. The radial supports resist, with high stiffness, the centripetal and centrifugal forces. The end flange of each radial port is connected to the C-Clamp structure by a clamping sleeve device. The clamping sleeves are hydraulically operated to provide locking during discharge. The clamping sleeves of the radial support system have been validated by an appropriate series of tests.

Synthetic polymers as substrates for a DNA-sliding clamp protein.

PubMed

van Dongen, S F M; Clerx, J; van den Boomen, O I; Pervaiz, M; Trakselis, M A; Ritschel, T; Schoonen, L; Schoenmakers, D C; Nolte, R J M

2018-04-26

The clamp protein (gp45) of the DNA polymerase III of the bacteriophage T4 is known to bind to DNA and stay attached to it in order to facilitate the process of DNA copying by the polymerase. As part of a project aimed at developing new biomimetic data-encoding systems we have investigated the binding of gp45 to synthetic polymers, that is, rigid, helical polyisocyanopeptides. Molecular modelling studies suggest that the clamp protein may interact with the latter polymers. Experiments aimed at verifying these interactions are presented and discussed. © 2018 The Authors Biopolymers Published by Wiley Periodicals, Inc.

Gas loading apparatus for the Paris-Edinburgh press

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bocian, A.; Kamenev, K. V.; Bull, C. L.

2010-09-15

We describe the design and operation of an apparatus for loading gases into the sample volume of the Paris-Edinburgh press at room temperature and high pressure. The system can be used for studies of samples loaded as pure or mixed gases as well as for loading gases as pressure-transmitting media in neutron-scattering experiments. The apparatus consists of a high-pressure vessel and an anvil holder with a clamp mechanism. The vessel, designed to operate at gas pressures of up to 150 MPa, is used for applying the load onto the anvils located inside the clamp. This initial load is sufficient formore » sealing the pressurized gas inside the sample containing gasket. The clamp containing the anvils and the sample is then transferred into the Paris-Edinburgh press by which further load can be applied to the sample. The clamp has apertures for scattered neutron beams and remains in the press for the duration of the experiment. The performance of the gas loading system is illustrated with the results of neutron-diffraction experiments on compressed nitrogen.« less

PCNA function in the activation and strand direction of MutLα endonuclease in mismatch repair

PubMed Central

Pluciennik, Anna; Dzantiev, Leonid; Iyer, Ravi R.; Constantin, Nicoleta; Kadyrov, Farid A.; Modrich, Paul

2010-01-01

MutLα (MLH1–PMS2) is a latent endonuclease that is activated in a mismatch-, MutSα-, proliferating cell nuclear antigen (PCNA)-, replication factor C (RFC)-, and ATP-dependent manner, with nuclease action directed to the heteroduplex strand that contains a preexisting break. RFC depletion experiments and use of linear DNAs indicate that RFC function in endonuclease activation is limited to PCNA loading. Whereas nicked circular heteroduplex DNA is a good substrate for PCNA loading and for endonuclease activation on the incised strand, covalently closed, relaxed circular DNA is a poor substrate for both reactions. However, covalently closed supercoiled or bubble-containing relaxed heteroduplexes, which do support PCNA loading, also support MutLα activation, but in this case cleavage strand bias is largely abolished. Based on these findings we suggest that PCNA has two roles in MutLα function: The clamp is required for endonuclease activation, an effect that apparently involves interaction of the two proteins, and by virtue of its loading orientation, PCNA determines the strand direction of MutLα incision. These results also provide a potential mechanism for activation of mismatch repair on nonreplicating DNA, an effect that may have implications for the somatic phase of triplet repeat expansion. PMID:20713735

Transcription initiation complex structures elucidate DNA opening.

PubMed

Plaschka, C; Hantsche, M; Dienemann, C; Burzinski, C; Plitzko, J; Cramer, P

2016-05-19

Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening. Here we report cryo-electron microscopy (cryo-EM) structures of yeast initiation complexes containing closed and open DNA at resolutions of 8.8 Å and 3.6 Å, respectively. DNA is positioned and retained over the Pol II cleft by a network of interactions between the TATA-box-binding protein TBP and transcription factors TFIIA, TFIIB, TFIIE, and TFIIF. DNA opening occurs around the tip of the Pol II clamp and the TFIIE 'extended winged helix' domain, and can occur in the absence of TFIIH. Loading of the DNA template strand into the active centre may be facilitated by movements of obstructing protein elements triggered by allosteric binding of the TFIIE 'E-ribbon' domain. The results suggest a unified model for transcription initiation with a key event, the trapping of open promoter DNA by extended protein-protein and protein-DNA contacts.

Hda, a novel DnaA-related protein, regulates the replication cycle in Escherichia coli

PubMed Central

Kato, Jun-ichi; Katayama, Tsutomu

2001-01-01

The bacterial DnaA protein binds to the chromosomal origin of replication to trigger a series of initiation reactions, which leads to the loading of DNA polymerase III. In Escherichia coli, once this polymerase initiates DNA synthesis, ATP bound to DnaA is efficiently hydrolyzed to yield the ADP-bound inactivated form. This negative regulation of DnaA, which occurs through interaction with the β-subunit sliding clamp configuration of the polymerase, functions in the temporal blocking of re-initiation. Here we show that the novel DnaA-related protein, Hda, from E.coli is essential for this regulatory inactivation of DnaA in vitro and in vivo. Our results indicate that the hda gene is required to prevent over-initiation of chromosomal replication and for cell viability. Hda belongs to the chaperone-like ATPase family, AAA+, as do DnaA and certain eukaryotic proteins essential for the initiation of DNA replication. We propose that the once-per-cell-cycle rule of replication depends on the timely interaction of AAA+ proteins that comprise the apparatus regulating the activity of the initiator of replication. PMID:11483528

Hda, a novel DnaA-related protein, regulates the replication cycle in Escherichia coli.

PubMed

Kato , J; Katayama, T

2001-08-01

The bacterial DnaA protein binds to the chromosomal origin of replication to trigger a series of initiation reactions, which leads to the loading of DNA polymerase III. In Escherichia coli, once this polymerase initiates DNA synthesis, ATP bound to DnaA is efficiently hydrolyzed to yield the ADP-bound inactivated form. This negative regulation of DnaA, which occurs through interaction with the beta-subunit sliding clamp configuration of the polymerase, functions in the temporal blocking of re-initiation. Here we show that the novel DnaA-related protein, Hda, from E.coli is essential for this regulatory inactivation of DnaA in vitro and in vivo. Our results indicate that the hda gene is required to prevent over-initiation of chromosomal replication and for cell viability. Hda belongs to the chaperone-like ATPase family, AAA(+), as do DnaA and certain eukaryotic proteins essential for the initiation of DNA replication. We propose that the once-per-cell-cycle rule of replication depends on the timely interaction of AAA(+) proteins that comprise the apparatus regulating the activity of the initiator of replication.

Large-deflection theory for end compression of long rectangular plates rigidly clamped along two edges

NASA Technical Reports Server (NTRS)

Levy, Samuel; Krupen, Philip

1943-01-01

The von Karman equations for flat plates are solved beyond the buckling load up to edge strains equal to eight time the buckling strain, for the extreme case of rigid clamping along the edges parallel to the load. Deflections, bending stresses, and membrane stresses are given as a function of end compressive load. The theoretical values of effective width are compared with the values derived for simple support along the edges parallel to the load. The increases in effective width due to rigid clamping drops from about 20 percent near the buckling strain to about 8 percent at an edge strain equal to eight times the buckling strain. Experimental values of effective width in the elastic range reported in NACA Technical Note No. 684 are between the theoretical curves for the extremes of simple support and rigid clamping.

Cryo-EM structure of a helicase loading intermediate containing ORC–Cdc6–Cdt1–MCM2-7 bound to DNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, Jingchuan; Evrin, Cecile; Samel, Stefan A.

2013-07-14

In eukaryotes, the Cdt1-bound replicative helicase core MCM2-7 is loaded onto DNA by the ORC–Cdc6 ATPase to form a prereplicative complex (pre-RC) with an MCM2-7 double hexamer encircling DNA. Using purified components in the presence of ATP-γS, we have captured in vitro an intermediate in pre-RC assembly that contains a complex between the ORC–Cdc6 and Cdt1–MCM2-7 heteroheptamers called the OCCM. Cryo-EM studies of this 14-subunit complex reveal that the two separate heptameric complexes are engaged extensively, with the ORC–Cdc6 N-terminal AAA+ domains latching onto the C-terminal AAA+ motor domains of the MCM2-7 hexamer. The conformation of ORC–Cdc6 undergoes a concertedmore » change into a right-handed spiral with helical symmetry that is identical to that of the DNA double helix. The resulting ORC–Cdc6 helicase loader shows a notable structural similarity to the replication factor C clamp loader, suggesting a conserved mechanism of action.« less

Thermodynamic basis for engineering high-affinity, high-specificity binding-induced DNA clamp nanoswitches.

PubMed

Idili, Andrea; Plaxco, Kevin W; Vallée-Bélisle, Alexis; Ricci, Francesco

2013-12-23

Naturally occurring chemoreceptors almost invariably employ structure-switching mechanisms, an observation that has inspired the use of biomolecular switches in a wide range of artificial technologies in the areas of diagnostics, imaging, and synthetic biology. In one mechanism for generating such behavior, clamp-based switching, binding occurs via the clamplike embrace of two recognition elements onto a single target molecule. In addition to coupling recognition with a large conformational change, this mechanism offers a second advantage: it improves both affinity and specificity simultaneously. To explore the physics of such switches we have dissected here the thermodynamics of a clamp-switch that recognizes a target DNA sequence through both Watson-Crick base pairing and triplex-forming Hoogsteen interactions. When compared to the equivalent linear DNA probe (which relies solely on Watson-Crick interactions), the extra Hoogsteen interactions in the DNA clamp-switch increase the probe's affinity for its target by ∼0.29 ± 0.02 kcal/mol/base. The Hoogsteen interactions of the clamp-switch likewise provide an additional specificity check that increases the discrimination efficiency toward a single-base mismatch by 1.2 ± 0.2 kcal/mol. This, in turn, leads to a 10-fold improvement in the width of the "specificity window" of this probe relative to that of the equivalent linear probe. Given these attributes, clamp-switches should be of utility not only for sensing applications but also, in the specific field of DNA nanotechnology, for applications calling for a better control over the building of nanostructures and nanomachines.

Dynamic analysis of clamp band joint system subjected to axial vibration

NASA Astrophysics Data System (ADS)

Qin, Z. Y.; Yan, S. Z.; Chu, F. L.

2010-10-01

Clamp band joints are commonly used for connecting circular components together in industry. Some of the systems jointed by clamp band are subjected to dynamic load. However, very little research on the dynamic characteristics for this kind of joint can be found in the literature. In this paper, a dynamic model for clamp band joint system is developed. Contact and frictional slip between the components are accommodated in this model. Nonlinear finite element analysis is conducted to identify the model parameters. Then static experiments are carried out on a scaled model of the clamp band joint to validate the joint model. Finally, the model is adopted to study the dynamic characteristics of the clamp band joint system subjected to axial harmonic excitation and the effects of the wedge angle of the clamp band joint and the preload on the response. The model proposed in this paper can represent the nonlinearity of the clamp band joint and be used conveniently to investigate the effects of the structural and loading parameters on the dynamic characteristics of this type of joint system.

Hda-mediated inactivation of the DnaA protein and dnaA gene autoregulation act in concert to ensure homeostatic maintenance of the Escherichia coli chromosome

PubMed Central

Riber, Leise; Olsson, Jan A.; Jensen, Rasmus B.; Skovgaard, Ole; Dasgupta, Santanu; Marinus, Martin G.; Løbner-Olesen, Anders

2006-01-01

Initiation of DNA replication in Eschericia coli requires the ATP-bound form of the DnaA protein. The conversion of DnaA–ATP to DnaA–ADP is facilitated by a complex of DnaA, Hda (homologous to DnaA), and DNA-loaded β-clamp proteins in a process termed RIDA (regulatory inactivation of DnaA). Hda-deficient cells initiate replication at each origin mainly once per cell cycle, and the rare reinitiation events never coincide with the end of the origin sequestration period. Therefore, RIDA is not the predominant mechanism to prevent immediate reinitiation from oriC. The cellular level of Hda correlated directly with dnaA gene expression such that Hda deficiency led to reduced dnaA gene expression, and overproduction of Hda led to DnaA overproduction. Hda-deficient cells were very sensitive to variations in the cellular level of DnaA, and DnaA overproduction led to uncontrolled initiation of replication from oriC, causing severe growth retardation or cell death. Based on these observations, we propose that both RIDA and dnaA gene autoregulation are required as homeostatic mechanisms to ensure that initiation of replication occurs at the same time relative to cell mass in each cell cycle. PMID:16882985

Hda-mediated inactivation of the DnaA protein and dnaA gene autoregulation act in concert to ensure homeostatic maintenance of the Escherichia coli chromosome.

PubMed

Riber, Leise; Olsson, Jan A; Jensen, Rasmus B; Skovgaard, Ole; Dasgupta, Santanu; Marinus, Martin G; Løbner-Olesen, Anders

2006-08-01

Initiation of DNA replication in Eschericia coli requires the ATP-bound form of the DnaA protein. The conversion of DnaA-ATP to DnaA-ADP is facilitated by a complex of DnaA, Hda (homologous to DnaA), and DNA-loaded beta-clamp proteins in a process termed RIDA (regulatory inactivation of DnaA). Hda-deficient cells initiate replication at each origin mainly once per cell cycle, and the rare reinitiation events never coincide with the end of the origin sequestration period. Therefore, RIDA is not the predominant mechanism to prevent immediate reinitiation from oriC. The cellular level of Hda correlated directly with dnaA gene expression such that Hda deficiency led to reduced dnaA gene expression, and overproduction of Hda led to DnaA overproduction. Hda-deficient cells were very sensitive to variations in the cellular level of DnaA, and DnaA overproduction led to uncontrolled initiation of replication from oriC, causing severe growth retardation or cell death. Based on these observations, we propose that both RIDA and dnaA gene autoregulation are required as homeostatic mechanisms to ensure that initiation of replication occurs at the same time relative to cell mass in each cell cycle.

Mutant DnaAs of Escherichia coli that are refractory to negative control

PubMed Central

Chodavarapu, Sundari; Felczak, Magdalena M.; Simmons, Lyle A.; Murillo, Alec; Kaguni, Jon M.

2013-01-01

DnaA is the initiator of DNA replication in bacteria. A mutant DnaA named DnaAcos is unusual because it is refractory to negative regulation. We developed a genetic method to isolate other mutant DnaAs that circumvent regulation to extend our understanding of mechanisms that control replication initiation. Like DnaAcos, one mutant bearing a tyrosine substitution for histidine 202 (H202Y) withstands the regulation exerted by datA, hda and dnaN (β clamp), and both DnaAcos and H202Y resist inhibition by the Hda-β clamp complex in vitro. Other mutant DnaAs carrying G79D, E244K, V303M or E445K substitutions are either only partially sensitive or refractory to inhibition by the Hda-β clamp complex in vitro but are responsive to hda expression in vivo. All mutant DnaAs remain able to interact directly with Hda. Of interest, both DnaAcos and DnaAE244K bind more avidly to Hda. These mutants, by sequestrating Hda, may limit its availability to regulate other DnaA molecules, which remain active to induce extra rounds of DNA replication. Other evidence suggests that a mutant bearing a V292M substitution hyperinitiates by escaping the effect of an unknown regulatory factor. Together, our results provide new insight into the mechanisms that regulate replication initiation in Escherichia coli. PMID:23990329

Mutant DnaAs of Escherichia coli that are refractory to negative control.

PubMed

Chodavarapu, Sundari; Felczak, Magdalena M; Simmons, Lyle A; Murillo, Alec; Kaguni, Jon M

2013-12-01

DnaA is the initiator of DNA replication in bacteria. A mutant DnaA named DnaAcos is unusual because it is refractory to negative regulation. We developed a genetic method to isolate other mutant DnaAs that circumvent regulation to extend our understanding of mechanisms that control replication initiation. Like DnaAcos, one mutant bearing a tyrosine substitution for histidine 202 (H202Y) withstands the regulation exerted by datA, hda and dnaN (β clamp), and both DnaAcos and H202Y resist inhibition by the Hda-β clamp complex in vitro. Other mutant DnaAs carrying G79D, E244K, V303M or E445K substitutions are either only partially sensitive or refractory to inhibition by the Hda-β clamp complex in vitro but are responsive to hda expression in vivo. All mutant DnaAs remain able to interact directly with Hda. Of interest, both DnaAcos and DnaAE244K bind more avidly to Hda. These mutants, by sequestrating Hda, may limit its availability to regulate other DnaA molecules, which remain active to induce extra rounds of DNA replication. Other evidence suggests that a mutant bearing a V292M substitution hyperinitiates by escaping the effect of an unknown regulatory factor. Together, our results provide new insight into the mechanisms that regulate replication initiation in Escherichia coli.

MACHINING ELIMINATION THROUGH APPLICATION OF THREAD FORMING FASTENERS IN NET SHAPED CAST HOLES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cleaver, Ryan J; Cleaver, Todd H; Talbott, Richard

The ultimate objective of this work was to eliminate approximately 30% of the machining performed in typical automotive engine and transmission plants by using thread forming fasteners in as-cast holes of aluminum and magnesium cast components. The primary issues at the source of engineers reluctance to implementing thread forming fasteners in lightweight castings are: * Little proof of consistency of clamp load vs. input torque in either aluminum or magnesium castings. * No known data to understand the effect on consistency of clamp load as casting dies wear. The clamp load consistency concern is founded in the fact that amore » portion of the input torque used to create clamp load is also used to create threads. The torque used for thread forming may not be consistent due to variations in casting material, hole size and shape due to tooling wear and process variation (thermal and mechanical). There is little data available to understand the magnitude of this concern or to form the basis of potential solutions if the range of clamp load variation is very high (> +/- 30%). The range of variation that can be expected in as-cast hole size and shape over the full life cycle of a high pressure die casting die was established in previous work completed by Pacific Northwest National Laboratory, (PNNL). This established range of variation was captured in a set of 12 cast bosses by designing core pins at the size and draft angles identified in the sited previous work. The cast bosses were cut into nuts that could be used in the Ford Fastener Laboratory test-cell to measure clamp load when a thread forming fastener was driven into a cast nut. There were two sets of experiments run. First, a series of cast aluminum nuts were made reflecting the range of shape and size variations to be expected over the life cycle of a die casting die. Taptite thread forming fasteners, (a widely used thread forming fastener suitable for aluminum applications), were driven into the various cored, as-cast nuts at a constant input torque and resulting clamp loads were recorded continuously. The clamp load data was used to determine the range of clamp loads to be expected. The bolts were driven to failure. The clamp load corresponding to the target input of 18.5 Nm was recorded for each fastener. In a like fashion, a second set of experiments were run with cast magnesium nuts and ALtracs thread forming fasteners, (a widely used thread forming fastener suitable for magnesium applications). Again all clamp loads were recorded and analyzed similarly to the Taptites in aluminum cast nuts. Results from previous work performed on the same test cell for a Battelle project using standard M8 bolts into standard M8 nuts were included as a comparator for a standard bolt and nut application. The results for the thread forming fasteners in aluminum cast holes were well within industry expectations of +/- 30% for out of the box and robustness range testing. The results for the dry and lubed extreme conditions were only slightly higher than industry expectations at +/- 35.6%. However, when compared to the actual Battelle results (+/- 40%) for a standard bolt and nut the tread forming fasteners performed slightly better. The results for the thread forming fasteners in magnesium cast holes were all well within industry expectations of +/- 30% for all three conditions. The robustness range (.05mm larger and smaller holes than the expected wear pattern of a die casting die at full life cycle) results also fell within the industry expectations for standard threaded fasteners. These results were very encouraging. It was concluded that this work showed that clamp load variation with thread forming fasteners is consistent with industry expectations for standard steel bolts and nuts at +/- 30%. There does not appear to be any significant increase in clamp load variation due to the application of thread forming fasteners in as-cast holes of aluminum or magnesium over the effective life of a die casting mold. The fully implemented potential benefit of thread forming fasteners in as-cast holes of aluminum and magnesium is estimated to be 6 trillion Btu per year for North America. Economic benefit is estimated to be nearly $800 million per year. Environmental benefits and quality improvements will also result from full implementation of this technology.« less

Structural insight into recruitment of translesion DNA polymerase Dpo4 to sliding clamp PCNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xing, G.; Kirouac, K.; Shin, Y.J.

2009-09-16

DNA polymerases are co-ordinated by sliding clamps (PCNA/{beta}-clamp) in translesion synthesis. It is unclear how these enzymes assemble on PCNA with geometric and functional compatibility. We report the crystal structure of a full-length Y-family polymerase, Dpo4, in complex with heterodimeric PCNA1-PCNA2 at 2.05 {angstrom} resolution. Dpo4 exhibits an extended conformation that differs from the Dpo4 structures in apo- or DNA-bound form. Two hinges have been identified in Dpo4, which render the multidomain polymerase flexible conformations and orientations relative to PCNA. Dpo4 binds specifically to PCNA1 on the conserved ligand binding site. The C-terminal peptide of Dpo4 becomes structured with amore » 3{sub 10} helix and dominates the specific binding. The Y-family polymerase also contacts PCNA1 with its finger, thumb and little finger domains, which are conformation-dependent protein-protein interactions that diversify the binding mode of Dpo4 on PCNA. The structure reveals a molecular model in which substrate/partner binding-coupled multiple conformations of a Y-family polymerase facilitate its recruitment and co-ordination on the sliding clamp. The conformational flexibility would turn the error-prone Y-family polymerase off when more efficient high-fidelity DNA polymerases work on undamaged DNA and turn it onto DNA templates to perform translesion synthesis when replication forks are stalled by DNA lesions.« less

Pitfalls during biomechanical testing - Evaluation of different fixation methods for measuring tendons endurance properties.

PubMed

Hangody, Gy; Pánics, G; Szebényi, G; Kiss, R; Hangody, L; Pap, K

2016-03-01

The goal of the study was to find a proper technique to fix tendon grafts into an INSTRON loading machine. From 8 human cadavers, 40 grafts were collected. We removed the bone-patella tendon-bone grafts, the semitendinosus and gracilis tendons, the quadriceps tendon-bone grafts, the Achilles tendons, and the peroneus longus tendons from each lower extremity. We tested the tendon grafts with five different types of fixation devices: surgical thread (Premicron 3), general mounting clamp, wire mesh, cement fixation, and a modified clamp for an INSTRON loading machine. The mean failure load in case of surgical thread fixation was (381N ± 26N). The results with the general clamp were (527N ± 45N). The wire meshes were more promising (750N ± 21N), but did not reach the outcomes we desired. Easy slippages of the ends of the tendons from the cement encasements were observed (253N ± 18N). We then began to use Shi's clamp that could produce 977N ± 416N peak force. We combined Shi's clamp with freezing of the graft and the rupture of the tendon itself demonstrated an average force of 2198 N ± 773N. We determined that our modified frozen clamp fixed the specimens against high tensile forces.

Screening of E. coli β-clamp Inhibitors Revealed that Few Inhibit Helicobacter pylori More Effectively: Structural and Functional Characterization.

PubMed

Pandey, Preeti; Verma, Vijay; Dhar, Suman Kumar; Gourinath, Samudrala

2018-01-11

The characteristic of interaction with various enzymes and processivity-promoting nature during DNA replication makes β-clamp an important drug target. Helicobacter pylori ( H. pylori ) have several unique features in DNA replication machinery that makes it different from other microorganisms. To find out whether difference in DNA replication proteins behavior accounts for any difference in drug response when compared to E. coli , in the present study, we have tested E. coli β-clamp inhibitor molecules against H. pylori β-clamp. Various approaches were used to test the binding of inhibitors to H. pylori β-clamp including docking, surface competition assay, complex structure determination, as well as antimicrobial assay. Out of five shortlisted inhibitor molecules on the basis of docking score, three molecules, 5-chloroisatin, carprofen, and 3,4-difluorobenzamide were co-crystallized with H. pylori β-clamp and the structures show that they bind at the protein-protein interaction site as expected. In vivo studies showed only two molecules, 5-chloroisatin, and 3,4-difluorobenzamide inhibited the growth of the pylori with MIC values in micro molar range, which is better than the inhibitory effect of the same drugs on E. coli . Therefore, the evaluation of such drugs against H. pylori may explore the possibility to use to generate species-specific pharmacophore for development of new drugs against H. pylori .

Specific amino acid residues in the beta sliding clamp establish a DNA polymerase usage hierarchy in Escherichia coli.

PubMed

Sutton, Mark D; Duzen, Jill M

2006-03-07

Escherichia coli dnaN159 strains encode a mutant form of the beta sliding clamp (beta159), causing them to display altered DNA polymerase (pol) usage. In order to better understand mechanisms of pol selection/switching in E. coli, we have further characterized pol usage in the dnaN159 strain. The dnaN159 allele contains two amino acid substitutions: G66E (glycine-66 to glutamic acid) and G174A (glycine-174 to alanine). Our results indicated that the G174A substitution impaired interaction of the beta clamp with the alpha catalytic subunit of pol III. In light of this finding, we designed two additional dnaN alleles. One of these dnaN alleles contained a G174A substitution (beta-G174A), while the other contained D173A, G174A and H175A substitutions (beta-173-175). Examination of strains bearing these different dnaN alleles indicated that each conferred a distinct UV sensitive phenotype that was dependent upon a unique combination of Delta polB (pol II), Delta dinB (pol IV) and/or Delta umuDC (pol V) alleles. Taken together, these findings indicate that mutations in the beta clamp differentially affect the functions of these three pols, and suggest that pol II, pol IV and pol V are capable of influencing each others' abilities to gain access to the replication fork. These findings are discussed in terms of a model whereby amino acid residues in the vicinity of those mutated in beta159 (G66 and G174) help to define a DNA polymerase usage hierarchy in E. coli following UV irradiation.

Numerical Study of Effects of Fluid-Structure Interaction on Dynamic Responses of Composite Plates

DTIC Science & Technology

2009-09-01

FORCE LOAD AND CLAMPED BOUNDARY.................73 APPENDIX F: ADDITIONAL FIGURES FOR COMPOSITE DE NSITY EFFECTS WITH CONCE NTRATED FORCE LOAD AND...Structure Strain and Kine tic Energy Comparison for Elastic Modulus Variations with Concentrated Force and Clamped Boundary .........................31...48 Figure 49. Experiment Strain Gage La yout on Underside of Composite Plate

The β2 clamp in the Mycobacterium tuberculosis DNA polymerase III αβ2ε replicase promotes polymerization and reduces exonuclease activity

PubMed Central

Gu, Shoujin; Li, Wenjuan; Zhang, Hongtai; Fleming, Joy; Yang, Weiqiang; Wang, Shihua; Wei, Wenjing; Zhou, Jie; Zhu, Guofeng; Deng, Jiaoyu; Hou, Jian; Zhou, Ying; Lin, Shiqiang; Zhang, Xian-En; Bi, Lijun

2016-01-01

DNA polymerase III (DNA pol III) is a multi-subunit replication machine responsible for the accurate and rapid replication of bacterial genomes, however, how it functions in Mycobacterium tuberculosis (Mtb) requires further investigation. We have reconstituted the leading-strand replication process of the Mtb DNA pol III holoenzyme in vitro, and investigated the physical and functional relationships between its key components. We verify the presence of an αβ2ε polymerase-clamp-exonuclease replicase complex by biochemical methods and protein-protein interaction assays in vitro and in vivo and confirm that, in addition to the polymerase activity of its α subunit, Mtb DNA pol III has two potential proofreading subunits; the α and ε subunits. During DNA replication, the presence of the β2 clamp strongly promotes the polymerization of the αβ2ε replicase and reduces its exonuclease activity. Our work provides a foundation for further research on the mechanism by which the replication machinery switches between replication and proofreading and provides an experimental platform for the selection of antimicrobials targeting DNA replication in Mtb. PMID:26822057

Reversible fastener clamp load monitor with continuous visual or remote readout

NASA Astrophysics Data System (ADS)

Hodge, Malcolm H.; Kausel, Theodore C., Jr.; Begley, Matthew R.

1998-03-01

SIMS has developed a simple means for detecting and monitoring both absolute and relative clamp load, or bolt tension, in fastener systems. More than twenty-five percent of automotive failures are known to be due to undetected loss of fastener clamp load. While the equivalent aerospace maintenance statistics are not known, the average automobile has 3,500 fasteners while a Boeing 747 has closer to one million. It is therefore anticipated that the new SensaBolt clamp load tracking system could find wide applications in the aerospace arena. We describe a visually-evident and retrofitted clamp load monitoring design which is based on the differential joint substrate compression at, and immediately adjacent to, the fastener location. This intrinsically-accurate indicator does not necessarily require alteration in either the bolt or nut geometries, thereby facilitating product introduction and retrofit in aging aircraft applications. In addition, SensaBolt's sole reliance on substrate compression renders it more accurate then torque wrench or turn-of-nut techniques. Readout may be accomplished by any of three principal methods: for those applications with ease of access to the sensor, loss of tension can be determined by direct visual inspection. Application of a standard wrench can then be made to restore the fastener's proper tightness, per the SensaBolt indicators. In those instances where line-of-sight is unimpeded and more formal inspection is desired, the SensaBolt may be interrogated by a laser scanner bar code reader. Finally, SensaBolt may be addressed by the SIMS fiber optic harness for those instances where full-time remote interrogation is desired.

Linear ultrasonic motor for absolute gravimeter.

PubMed

Jian, Yue; Yao, Zhiyuan; Silberschmidt, Vadim V

2017-05-01

Thanks to their compactness and suitability for vacuum applications, linear ultrasonic motors are considered as substitutes for classical electromagnetic motors as driving elements in absolute gravimeters. Still, their application is prevented by relatively low power output. To overcome this limitation and provide better stability, a V-type linear ultrasonic motor with a new clamping method is proposed for a gravimeter. In this paper, a mechanical model of stators with flexible clamping components is suggested, according to a design criterion for clamps of linear ultrasonic motors. After that, an effect of tangential and normal rigidity of the clamping components on mechanical output is studied. It is followed by discussion of a new clamping method with sufficient tangential rigidity and a capability to facilitate pre-load. Additionally, a prototype of the motor with the proposed clamping method was fabricated and the performance tests in vertical direction were implemented. Experimental results show that the suggested motor has structural stability and high dynamic performance, such as no-load speed of 1.4m/s and maximal thrust of 43N, meeting the requirements for absolute gravimeters. Copyright © 2017 Elsevier B.V. All rights reserved.

Pipe support

DOEpatents

Pollono, Louis P.

1979-01-01

A pipe support for high temperature, thin-walled piping runs such as those used in nuclear systems. A section of the pipe to be supported is encircled by a tubular inner member comprised of two walls with an annular space therebetween. Compacted load-bearing thermal insulation is encapsulated within the annular space, and the inner member is clamped to the pipe by a constant clamping force split-ring clamp. The clamp may be connected to pipe hangers which provide desired support for the pipe.

Vise holds specimens for microscope

NASA Technical Reports Server (NTRS)

Greule, W. N.

1980-01-01

Convenient, miniature, spring-loaded clamp holds specimens for scanning electron microscope. Clamp is made out of nesting sections of studded angle-aluminum. Specimens are easier to mount and dismount with vise than with conductive adhesive or paint.

Development of a peptide nucleic acid polymerase chain reaction clamping assay for semiquantitative evaluation of genetically modified organism content in food.

PubMed

Peano, C; Lesignoli, F; Gulli, M; Corradini, R; Samson, M C; Marchelli, R; Marmiroli, N

2005-09-15

In the present study a peptide nucleic acid (PNA)-mediated polymerase chain reaction (PCR) clamping method was developed and applied to the detection of genetically modified organisms (GMO), to test PCR products for band identity and to obtain a semiquantitative evaluation of GMO content. The minimal concentration of PNA necessary to block the PCR was determined by comparing PCRs containing a constant amount of DNA in the presence of increasing concentration of target-specific PNA. The lowest PNA concentration at which specific inhibition took place, by the inhibition of primer extension and/or steric hindrance, was the most efficient condition. Optimization of PCR clamping by PNA was observed by testing five different PNAs with a minimum of 13 bp to a maximum of 15 bp, designed on the target sequence of Roundup Ready soybean. The results obtained on the DNA extracted from Roundup Ready soybean standard flour were verified also on DNA extracted from standard flours of maize GA21, Bt176, Bt11, and MON810. A correlation between the PNA concentration necessary for inducing PCR clamping and the percentage of the GMO target sequence in the sample was found.

High throughput ion-channel pharmacology: planar-array-based voltage clamp.

PubMed

Kiss, Laszlo; Bennett, Paul B; Uebele, Victor N; Koblan, Kenneth S; Kane, Stefanie A; Neagle, Brad; Schroeder, Kirk

2003-02-01

Technological advances often drive major breakthroughs in biology. Examples include PCR, automated DNA sequencing, confocal/single photon microscopy, AFM, and voltage/patch-clamp methods. The patch-clamp method, first described nearly 30 years ago, was a major technical achievement that permitted voltage-clamp analysis (membrane potential control) of ion channels in most cells and revealed a role for channels in unimagined areas. Because of the high information content, voltage clamp is the best way to study ion-channel function; however, throughput is too low for drug screening. Here we describe a novel breakthrough planar-array-based HT patch-clamp technology developed by Essen Instruments capable of voltage-clamping thousands of cells per day. This technology provides greater than two orders of magnitude increase in throughput compared with the traditional voltage-clamp techniques. We have applied this method to study the hERG K(+) channel and to determine the pharmacological profile of QT prolonging drugs.

Biomechanical evaluation of a new fixation device for the thoracic spine.

PubMed

Hongo, Michio; Ilharreborde, Brice; Gay, Ralph E; Zhao, Chunfeng; Zhao, Kristin D; Berglund, Lawrence J; Zobitz, Mark; An, Kai-Nan

2009-08-01

The technology used in surgery for spinal deformity has progressed rapidly in recent years. Commonly used fixation techniques may include monofilament wires, sublaminar wires and cables, and pedicle screws. Unfortunately, neurological complications can occur with all of these, compromising the patients' health and quality of life. Recently, an alternative fixation technique using a metal clamp and polyester belt was developed to replace hooks and sublaminar wiring in scoliosis surgery. The goal of this study was to compare the pull-out strength of this new construct with sublaminar wiring, laminar hooks and pedicle screws. Forty thoracic vertebrae from five fresh frozen human thoracic spines (T5-12) were divided into five groups (8 per group), such that BMD values, pedicle diameter, and vertebral levels were equally distributed. They were then potted in polymethylmethacrylate and anchored with metal screws and polyethylene bands. One of five fixation methods was applied to the right side of the vertebra in each group: Pedicle screw, sublaminar belt with clamp, figure-8 belt with clamp, sublaminar wire, or laminar hook. Pull-out strength was then assessed using a custom jig in a servohydraulic tester. The mean failure load of the pedicle screw group was significantly larger than that of the figure-8 clamp (P = 0.001), sublaminar belt (0.0172), and sublaminar wire groups (P = 0.04) with no significant difference in pull-out strength between the latter three constructs. The most common mode of failure was the fracture of the pedicle. BMD was significantly correlated with failure load only in the figure-8 clamp and pedicle screw constructs. Only the pedicle screw had a statistically significant higher failure load than the sublaminar clamp. The sublaminar method of applying the belt and clamp device was superior to the figure-8 method. The sublaminar belt and clamp construct compared favorably to the traditional methods of sublaminar wires and laminar hooks, and should be considered as an alternative fixation device in the thoracic spine.

Biomechanical evaluation of a new fixation device for the thoracic spine

PubMed Central

Hongo, Michio; Ilharreborde, Brice; Zhao, Chunfeng; Zhao, Kristin D.; Berglund, Lawrence J.; Zobitz, Mark; An, Kai-Nan

2009-01-01

The technology used in surgery for spinal deformity has progressed rapidly in recent years. Commonly used fixation techniques may include monofilament wires, sublaminar wires and cables, and pedicle screws. Unfortunately, neurological complications can occur with all of these, compromising the patients’ health and quality of life. Recently, an alternative fixation technique using a metal clamp and polyester belt was developed to replace hooks and sublaminar wiring in scoliosis surgery. The goal of this study was to compare the pull-out strength of this new construct with sublaminar wiring, laminar hooks and pedicle screws. Forty thoracic vertebrae from five fresh frozen human thoracic spines (T5–12) were divided into five groups (8 per group), such that BMD values, pedicle diameter, and vertebral levels were equally distributed. They were then potted in polymethylmethacrylate and anchored with metal screws and polyethylene bands. One of five fixation methods was applied to the right side of the vertebra in each group: Pedicle screw, sublaminar belt with clamp, figure-8 belt with clamp, sublaminar wire, or laminar hook. Pull-out strength was then assessed using a custom jig in a servohydraulic tester. The mean failure load of the pedicle screw group was significantly larger than that of the figure-8 clamp (P = 0.001), sublaminar belt (0.0172), and sublaminar wire groups (P = 0.04) with no significant difference in pull-out strength between the latter three constructs. The most common mode of failure was the fracture of the pedicle. BMD was significantly correlated with failure load only in the figure-8 clamp and pedicle screw constructs. Only the pedicle screw had a statistically significant higher failure load than the sublaminar clamp. The sublaminar method of applying the belt and clamp device was superior to the figure-8 method. The sublaminar belt and clamp construct compared favorably to the traditional methods of sublaminar wires and laminar hooks, and should be considered as an alternative fixation device in the thoracic spine. PMID:19404687

Ultrasonic measurement and monitoring of loads in bolts used in structural joints

NASA Astrophysics Data System (ADS)

Koshti, Ajay M.

2015-04-01

The paper is an overview of work by the author in measuring and monitoring loads in bolts using an ultrasonic extensometer. A number of cases of bolted joints are covered. These include, a clamped joint with clearance fit between the bolt and hole, a clamped joint with bolt in an interference fit with the hole, a flanged joint which allows the flange and bolt to bend; and a shear joint in a clevis and tang configuration. These applications were initially developed for measuring and monitoring preload in National Aeronautics and Space Administration (NASA) Space Shuttle Orbiter critical joints but are also applicable for monitoring loads in other critical bolted joints of structures such as transportation bridges and other aerospace structures. The papers cited here explain how to set-up a model to estimate the ultrasonic load factor and accuracy for the ultrasonic preload application in a clamped joint with clearance fit. The ultrasonic preload application for clamped joint with bolt in an interference fit can also be used to measure diametrical interference between the bolt shank and hole, as well as interference pressure on the bolt shank. Results of simulation and experimental data are given to demonstrate use of ultrasonic measurements in a shear joint. A bolt in a flanged joint experiences both tensile and bending loads. This application involves measurement of bending and tensile preload in a bolt. The ultrasonic beam bends due to bending load on the bolt. Results of a numerical technique to compute the trace of ultrasonic ray are presented.

Modes of Overinitiation, dnaA Gene Expression, and Inhibition of Cell Division in a Novel Cold-Sensitive hda Mutant of Escherichia coli▿

PubMed Central

Fujimitsu, Kazuyuki; Su'etsugu, Masayuki; Yamaguchi, Yoko; Mazda, Kensaku; Fu, Nisi; Kawakami, Hironori; Katayama, Tsutomu

2008-01-01

The chromosomal replication cycle is strictly coordinated with cell cycle progression in Escherichia coli. ATP-DnaA initiates replication, leading to loading of the DNA polymerase III holoenzyme. The DNA-loaded form of the β clamp subunit of the polymerase binds the Hda protein, which promotes ATP-DnaA hydrolysis, yielding inactive ADP-DnaA. This regulation is required to repress overinitiation. In this study, we have isolated a novel cold-sensitive hda mutant, the hda-185 mutant. The hda-185 mutant caused overinitiation of chromosomal replication at 25°C, which most likely led to blockage of replication fork progress. Consistently, the inhibition of colony formation at 25°C was suppressed by disruption of the diaA gene, an initiation stimulator. Disruption of the seqA gene, an initiation inhibitor, showed synthetic lethality with hda-185 even at 42°C. The cellular ATP-DnaA level was increased in an hda-185-dependent manner. The cellular concentrations of DnaA protein and dnaA mRNA were comparable at 25°C to those in a wild-type hda strain. We also found that multiple copies of the ribonucleotide reductase genes (nrdAB or nrdEF) or dnaB gene repressed overinitiation. The cellular levels of dATP and dCTP were elevated in cells bearing multiple copies of nrdAB. The catalytic site within NrdA was required for multicopy suppression, suggesting the importance of an active form of NrdA or elevated levels of deoxyribonucleotides in inhibition of overinitiation in the hda-185 cells. Cell division in the hda-185 mutant was inhibited at 25°C in a LexA regulon-independent manner, suggesting that overinitiation in the hda-185 mutant induced a unique division inhibition pathway. PMID:18502852

Modes of overinitiation, dnaA gene expression, and inhibition of cell division in a novel cold-sensitive hda mutant of Escherichia coli.

PubMed

Fujimitsu, Kazuyuki; Su'etsugu, Masayuki; Yamaguchi, Yoko; Mazda, Kensaku; Fu, Nisi; Kawakami, Hironori; Katayama, Tsutomu

2008-08-01

The chromosomal replication cycle is strictly coordinated with cell cycle progression in Escherichia coli. ATP-DnaA initiates replication, leading to loading of the DNA polymerase III holoenzyme. The DNA-loaded form of the beta clamp subunit of the polymerase binds the Hda protein, which promotes ATP-DnaA hydrolysis, yielding inactive ADP-DnaA. This regulation is required to repress overinitiation. In this study, we have isolated a novel cold-sensitive hda mutant, the hda-185 mutant. The hda-185 mutant caused overinitiation of chromosomal replication at 25 degrees C, which most likely led to blockage of replication fork progress. Consistently, the inhibition of colony formation at 25 degrees C was suppressed by disruption of the diaA gene, an initiation stimulator. Disruption of the seqA gene, an initiation inhibitor, showed synthetic lethality with hda-185 even at 42 degrees C. The cellular ATP-DnaA level was increased in an hda-185-dependent manner. The cellular concentrations of DnaA protein and dnaA mRNA were comparable at 25 degrees C to those in a wild-type hda strain. We also found that multiple copies of the ribonucleotide reductase genes (nrdAB or nrdEF) or dnaB gene repressed overinitiation. The cellular levels of dATP and dCTP were elevated in cells bearing multiple copies of nrdAB. The catalytic site within NrdA was required for multicopy suppression, suggesting the importance of an active form of NrdA or elevated levels of deoxyribonucleotides in inhibition of overinitiation in the hda-185 cells. Cell division in the hda-185 mutant was inhibited at 25 degrees C in a LexA regulon-independent manner, suggesting that overinitiation in the hda-185 mutant induced a unique division inhibition pathway.

Postbuckling and vibration of end-supported elastica pipes conveying fluid and columns under follower loads

NASA Astrophysics Data System (ADS)

Plaut, R. H.

2006-01-01

Fluid-conveying pipes with supported ends buckle when the fluid velocity reaches a critical value. For higher velocities, the postbuckled equilibrium shape can be directly related to that for a column under a follower end load. However, the corresponding vibration frequencies are different due to the Coriolis force associated with the fluid flow. Clamped-clamped, pinned-pinned, and clamped-pinned pipes are considered first. Axial sliding is permitted at the downstream end. The pipe is modeled as an inextensible elastica. The equilibrium shape may have large displacements, and small motions about that shape are analyzed. The behavior is conservative in the prebuckling range and nonconservative in the postbuckling range (during which the Coriolis force does work and the motions decay). Next, related columns are studied, first with a concentrated follower load at the axially sliding end, and then with a distributed follower load. In all cases, a shooting method is used to solve the nonlinear boundary-value problem for the equilibrium configuration, and to solve the linear boundary-value problem for the first four vibration frequencies. The results for the three different types of loading are compared.

Double arch mirror study. Part 1: Preliminary engineering report

NASA Technical Reports Server (NTRS)

Vukobratovich, D.; Hillman, D.

1983-01-01

In the proposed design, the NASA AMES 20-in double arch mirror is supported by three clamp and flexure assemblies. The mirror clamp consists of a T-shaped Invar-36 member that goes into a similarly shaped socket in the back of the mirror. The mirror socket is made oversize and contacts the clamp only along the conical surface. The clamp is preloaded by a spring washer and pulls the mirror into contact with the flexure. The clamp is then inserted into the mirror socket through a cutout, is rotated 90 deg, and is then pinned in place. Loading conditions considered in socket design are discussed as well as stress in the socket and clamp. Flexure geometry and stress are examined as well as the effects of flexure error and of mirror cell error.

Laser beam guard clamps

DOEpatents

Dickson, Richard K.

2010-09-07

A quick insert and release laser beam guard panel clamping apparatus having a base plate mountable on an optical table, a first jaw affixed to the base plate, and a spring-loaded second jaw slidably carried by the base plate to exert a clamping force. The first and second jaws each having a face acutely angled relative to the other face to form a V-shaped, open channel mouth, which enables wedge-action jaw separation by and subsequent clamping of a laser beam guard panel inserted through the open channel mouth. Preferably, the clamping apparatus also includes a support structure having an open slot aperture which is positioned over and parallel with the open channel mouth.

Dynamic Uniaxial Tensile Loading of Vector Polymers

DTIC Science & Technology

2011-11-01

to apply the loading velocity to the strip at x = 0 after impact by a steel slug projectile. The flange has two sets of grooves. One set, denoted as...travels down the barrel . The strip is clamped to the outside of the barrel at x = L. A Photron SA1 high-speed video camera with a framing rate of...nominal stress. Equation 1 is expressed in terms of particle displacement to obtain the wave equation Flange Gun Barrel Rubber Strip Clamp x = 0

Sliding Clamp of DNA Polymerase III as a Drug Target for TB Therapy: Comprehensive Conformational and Binding Analysis from Molecular Dynamic Simulations.

PubMed

Machaba, Kgothatso E; Cele, Favorite N; Mhlongo, Ndumiso N; Soliman, Mahmoud E S

2016-12-01

Tuberculosis, caused by Mycobacterium tuberculosis, is one of the most common causes of death in the world. Mycobacterium tuberculosis -sliding clamp is a protein essential for many important DNA transactions including replication and DNA repair proteins, thus, a potential drug target for tuberculosis. Further investigation is needed in understanding DNA polymerase sliding clamp structure, especially from a computational perspective. In this study, we employ a wide-range of comparative molecular dynamic analyses on two systems: Mycobacterium tuberculosis - sliding clamp enzyme in its apo and bound form. The results reported in this study shows apo conformation to be less stable, as compared to bound conformation with an average radius of gyration of 25.812 and 25.459 Å, respectively. This was further supported by root mean square fluctuation, where an apo enzyme showed a higher degree of flexibility. However, the presence of the ligand lowers radius of gyration and root mean square fluctuation and also leads to an existence of negative correlated motions. Principal component analysis further justifies the same findings, whereby the apo enzyme exhibits a higher fluctuation compared to the bound complex. In addition, a stable 3 10 helix located at the binding site appears to be unstable in the presence of the ligand. Hence, it is possible that the binding of the ligand may have caused a rearrangement of the structure, leading to a change in the unwinding of 3 10 helix. Findings reported in this study further enhance the understanding of Mycobacterium tuberculosis -DnaN and also give a lead to the development of potent tuberculosis drugs.

The dark side of the ring: role of the DNA sliding surface of PCNA.

PubMed

De March, Matteo; De Biasio, Alfredo

2017-12-01

The proliferating cell nuclear antigen (PCNA) sliding clamp lies at the heart of the accurate duplication of eukaryotic genomes. While the outer surface of the PCNA ring interacts with polymerases and other factors, the role of the inner wall facing the DNA is elusive. Recent evidence shows that conserved basic residues in the PCNA central channel create a specific surface that recognizes the DNA backbone and enables the clamp to slide by rotationally tracking the DNA helix. The sliding surface can be modulated (i) through lysine acetylation, which triggers PCNA degradation during nucleotide excision repair (NER) and stimulates repair by homologous recombination (HR) or (ii) through binding of the protein factor p15 PAF , which turns off DNA lesion bypass. Thus, the inner surface of PCNA is unexpectedly highly regulated to control resistance to DNA damage. From a structural viewpoint, we reflect on these findings that open a new perspective on PCNA function and offer opportunities to develop tools to manipulate the DNA damage response in cancer treatment.

Steel bridge in interaction with modern slab track fastening systems under various vertical load levels

NASA Astrophysics Data System (ADS)

Stančík, Vojtěch; Ryjáček, Pavel; Vokáč, Miroslav

2017-09-01

In modern slab tracks the continuously welded rail (CWR) is coupled through the fastening system with the substructure. The resulting restriction of expansion movement causes significant rail stress increments, which in the case of extreme loading may cause rail failures. These interaction phenomenon effects are naturally higher on a bridge due to different deformation capabilities of the bridge and the CWR. The presented contribution aims at investigating the state of the art European direct fastening system that is suitable for application on steel bridges. Analysis involves experimental determination of its nonlinear longitudinal interaction parameters under various vertical loads and numerical validation. During experimental procedures a two and a half meter long laboratory sample equipped with four nodes of the Vossloh DFF 300 was tested. There have been checked both DFF 300 modifications using the skl 15 tension clamps and the low resistance skl B15 tension clamps. The effects of clamping force lowering on the interaction parameters have also been investigated. Results are discussed in the paper.

Mechanics of wafer bonding: Effect of clamping

NASA Astrophysics Data System (ADS)

Turner, K. T.; Thouless, M. D.; Spearing, S. M.

2004-01-01

A mechanics-based model is developed to examine the effects of clamping during wafer bonding processes. The model provides closed-form expressions that relate the initial geometry and elastic properties of the wafers to the final shape of the bonded pair and the strain energy release rate at the interface for two different clamping configurations. The results demonstrate that the curvature of bonded pairs may be controlled through the use of specific clamping arrangements during the bonding process. Furthermore, it is demonstrated that the strain energy release rate depends on the clamping configuration and that using applied loads usually leads to an undesirable increase in the strain energy release rate. The results are discussed in detail and implications for process development and bonding tool design are highlighted.

External Coulomb-Friction Damping For Hydrostatic Bearings

NASA Technical Reports Server (NTRS)

Buckmann, Paul S.

1992-01-01

External friction device damps vibrations of shaft and hydrostatic ring bearing in which it turns. Does not rely on wear-prone facing surfaces. Hydrostatic bearing ring clamped in radially flexing support by side plates clamped against radial surfaces by spring-loaded bolts. Plates provide friction against radial motions of shaft.

The logic of DNA replication in double-stranded DNA viruses: insights from global analysis of viral genomes

PubMed Central

Kazlauskas, Darius; Krupovic, Mart; Venclovas, Česlovas

2016-01-01

Abstract Genomic DNA replication is a complex process that involves multiple proteins. Cellular DNA replication systems are broadly classified into only two types, bacterial and archaeo-eukaryotic. In contrast, double-stranded (ds) DNA viruses feature a much broader diversity of DNA replication machineries. Viruses differ greatly in both completeness and composition of their sets of DNA replication proteins. In this study, we explored whether there are common patterns underlying this extreme diversity. We identified and analyzed all major functional groups of DNA replication proteins in all available proteomes of dsDNA viruses. Our results show that some proteins are common to viruses infecting all domains of life and likely represent components of the ancestral core set. These include B-family polymerases, SF3 helicases, archaeo-eukaryotic primases, clamps and clamp loaders of the archaeo-eukaryotic type, RNase H and ATP-dependent DNA ligases. We also discovered a clear correlation between genome size and self-sufficiency of viral DNA replication, the unanticipated dominance of replicative helicases and pervasive functional associations among certain groups of DNA replication proteins. Altogether, our results provide a comprehensive view on the diversity and evolution of replication systems in the DNA virome and uncover fundamental principles underlying the orchestration of viral DNA replication. PMID:27112572

Mispair-specific Recruitment of the Mlh1-Pms1 Complex Identifies Repair Substrates of the Saccharomyces cerevisiae Msh2-Msh3 Complex*

PubMed Central

Srivatsan, Anjana; Bowen, Nikki; Kolodner, Richard D.

2014-01-01

DNA mismatch repair is initiated by either the Msh2-Msh6 or the Msh2-Msh3 mispair recognition heterodimer. Here we optimized the expression and purification of Saccharomyces cerevisiae Msh2-Msh3 and performed a comparative study of Msh2-Msh3 and Msh2-Msh6 for mispair binding, sliding clamp formation, and Mlh1-Pms1 recruitment. Msh2-Msh3 formed sliding clamps and recruited Mlh1-Pms1 on +1, +2, +3, and +4 insertion/deletions and CC, AA, and possibly GG mispairs, whereas Msh2-Msh6 formed mispair-dependent sliding clamps and recruited Mlh1-Pms1 on 7 of the 8 possible base:base mispairs, the +1 insertion/deletion mispair, and to a low level on the +2 but not the +3 or +4 insertion/deletion mispairs and not on the CC mispair. The mispair specificity of sliding clamp formation and Mlh1-Pms1 recruitment but not mispair binding alone correlated best with genetic data on the mispair specificity of Msh2-Msh3- and Msh2-Msh6-dependent mismatch repair in vivo. Analysis of an Msh2-Msh6/Msh3 chimeric protein and mutant Msh2-Msh3 complexes showed that the nucleotide binding domain and communicating regions but not the mispair binding domain of Msh2-Msh3 are responsible for the extremely rapid dissociation of Msh2-Msh3 sliding clamps from DNA relative to that seen for Msh2-Msh6, and that amino acid residues predicted to stabilize Msh2-Msh3 interactions with bent, strand-separated mispair-containing DNA are more critical for the recognition of small +1 insertion/deletions than larger +4 insertion/deletions. PMID:24550389

Mispair-specific recruitment of the Mlh1-Pms1 complex identifies repair substrates of the Saccharomyces cerevisiae Msh2-Msh3 complex.

PubMed

Srivatsan, Anjana; Bowen, Nikki; Kolodner, Richard D

2014-03-28

DNA mismatch repair is initiated by either the Msh2-Msh6 or the Msh2-Msh3 mispair recognition heterodimer. Here we optimized the expression and purification of Saccharomyces cerevisiae Msh2-Msh3 and performed a comparative study of Msh2-Msh3 and Msh2-Msh6 for mispair binding, sliding clamp formation, and Mlh1-Pms1 recruitment. Msh2-Msh3 formed sliding clamps and recruited Mlh1-Pms1 on +1, +2, +3, and +4 insertion/deletions and CC, AA, and possibly GG mispairs, whereas Msh2-Msh6 formed mispair-dependent sliding clamps and recruited Mlh1-Pms1 on 7 of the 8 possible base:base mispairs, the +1 insertion/deletion mispair, and to a low level on the +2 but not the +3 or +4 insertion/deletion mispairs and not on the CC mispair. The mispair specificity of sliding clamp formation and Mlh1-Pms1 recruitment but not mispair binding alone correlated best with genetic data on the mispair specificity of Msh2-Msh3- and Msh2-Msh6-dependent mismatch repair in vivo. Analysis of an Msh2-Msh6/Msh3 chimeric protein and mutant Msh2-Msh3 complexes showed that the nucleotide binding domain and communicating regions but not the mispair binding domain of Msh2-Msh3 are responsible for the extremely rapid dissociation of Msh2-Msh3 sliding clamps from DNA relative to that seen for Msh2-Msh6, and that amino acid residues predicted to stabilize Msh2-Msh3 interactions with bent, strand-separated mispair-containing DNA are more critical for the recognition of small +1 insertion/deletions than larger +4 insertion/deletions.

Functional Dissection of the DNA Interface of the Nucleotidyltransferase Domain of Chlorella Virus DNA Ligase*

PubMed Central

Samai, Poulami; Shuman, Stewart

2011-01-01

Chlorella virus DNA ligase (ChVLig) has pluripotent biological activity and an intrinsic nick-sensing function. ChVLig consists of three structural modules that envelop nicked DNA as a C-shaped protein clamp: a nucleotidyltransferase (NTase) domain and an OB domain (these two are common to all DNA ligases) as well as a distinctive β-hairpin latch module. The NTase domain, which performs the chemical steps of ligation, binds the major groove flanking the nick and the minor groove on the 3′-OH side of the nick. Here we performed a structure-guided mutational analysis of the NTase domain, surveying the effects of 35 mutations in 19 residues on ChVLig activity in vivo and in vitro, including biochemical tests of the composite nick sealing reaction and of the three component steps of the ligation pathway (ligase adenylylation, DNA adenylylation, and phosphodiester synthesis). The results highlight (i) key contacts by Thr-84 and Lys-173 to the template DNA strand phosphates at the outer margins of the DNA ligase footprint; (ii) essential contacts of Ser-41, Arg-42, Met-83, and Phe-75 with the 3′-OH strand at the nick; (iii) Arg-176 phosphate contacts at the nick and with ATP during ligase adenylylation; (iv) the role of Phe-44 in forming the protein clamp around the nicked DNA substrate; and (v) the importance of adenine-binding residue Phe-98 in all three steps of ligation. Kinetic analysis of single-turnover nick sealing by ChVLig-AMP underscored the importance of Phe-75-mediated distortion of the nick 3′-OH nucleoside in the catalysis of DNA 5′-adenylylation (step 2) and phosphodiester synthesis (step 3). Induced fit of the nicked DNA into a distorted conformation when bound within the ligase clamp may account for the nick-sensing capacity of ChVLig. PMID:21335605

Functional dissection of the DNA interface of the nucleotidyltransferase domain of chlorella virus DNA ligase.

PubMed

Samai, Poulami; Shuman, Stewart

2011-04-15

Chlorella virus DNA ligase (ChVLig) has pluripotent biological activity and an intrinsic nick-sensing function. ChVLig consists of three structural modules that envelop nicked DNA as a C-shaped protein clamp: a nucleotidyltransferase (NTase) domain and an OB domain (these two are common to all DNA ligases) as well as a distinctive β-hairpin latch module. The NTase domain, which performs the chemical steps of ligation, binds the major groove flanking the nick and the minor groove on the 3'-OH side of the nick. Here we performed a structure-guided mutational analysis of the NTase domain, surveying the effects of 35 mutations in 19 residues on ChVLig activity in vivo and in vitro, including biochemical tests of the composite nick sealing reaction and of the three component steps of the ligation pathway (ligase adenylylation, DNA adenylylation, and phosphodiester synthesis). The results highlight (i) key contacts by Thr-84 and Lys-173 to the template DNA strand phosphates at the outer margins of the DNA ligase footprint; (ii) essential contacts of Ser-41, Arg-42, Met-83, and Phe-75 with the 3'-OH strand at the nick; (iii) Arg-176 phosphate contacts at the nick and with ATP during ligase adenylylation; (iv) the role of Phe-44 in forming the protein clamp around the nicked DNA substrate; and (v) the importance of adenine-binding residue Phe-98 in all three steps of ligation. Kinetic analysis of single-turnover nick sealing by ChVLig-AMP underscored the importance of Phe-75-mediated distortion of the nick 3'-OH nucleoside in the catalysis of DNA 5'-adenylylation (step 2) and phosphodiester synthesis (step 3). Induced fit of the nicked DNA into a distorted conformation when bound within the ligase clamp may account for the nick-sensing capacity of ChVLig.

Tribologic analyses of a self-mated aluminium contact used for overhead transmission lines

NASA Astrophysics Data System (ADS)

Steier, V. Franco

2017-05-01

The lifetime of aluminium components is often limited to their poor wear resistance. One example for such aluminium applications are overhead transmission lines. The sore points of these lines are the segments where the aluminium conductors are fixed to the line supports. The fixation is commonly realized via aluminium suspension clamps. Here, a superposition of different loads like traction and bending stresses, clamping forces and different types of wear occurs. To investigate the wear behaviour in these peculiar points, tribologic model tests were carried out. Within the tests, overhead conductor wires and aluminium plates, extracted from suspension clamps were reciprocally slid against aluminium plates (cylinder-on-plate test). The COF and a wear related parameter were recorded constantly. Subsequently, the loaded surfaces were analysed using confocal laser and electron scanning microscopy as well as energy dispersive X-ray spectroscopy. The investigation detected the formation of an oxidized tribologic layer between both components. The tribolayer, which mayor part adhered on the suspension clamps, was mostly formed from material removed from the conductor wires.

Characterization of active hair-bundle motility by a mechanical-load clamp

NASA Astrophysics Data System (ADS)

Salvi, Joshua D.; Maoiléidigh, Dáibhid Ó.; Fabella, Brian A.; Tobin, Mélanie; Hudspeth, A. J.

2015-12-01

Active hair-bundle motility endows hair cells with several traits that augment auditory stimuli. The activity of a hair bundle might be controlled by adjusting its mechanical properties. Indeed, the mechanical properties of bundles vary between different organisms and along the tonotopic axis of a single auditory organ. Motivated by these biological differences and a dynamical model of hair-bundle motility, we explore how adjusting the mass, drag, stiffness, and offset force applied to a bundle control its dynamics and response to external perturbations. Utilizing a mechanical-load clamp, we systematically mapped the two-dimensional state diagram of a hair bundle. The clamp system used a real-time processor to tightly control each of the virtual mechanical elements. Increasing the stiffness of a hair bundle advances its operating point from a spontaneously oscillating regime into a quiescent regime. As predicted by a dynamical model of hair-bundle mechanics, this boundary constitutes a Hopf bifurcation.

The logic of DNA replication in double-stranded DNA viruses: insights from global analysis of viral genomes.

PubMed

Kazlauskas, Darius; Krupovic, Mart; Venclovas, Česlovas

2016-06-02

Genomic DNA replication is a complex process that involves multiple proteins. Cellular DNA replication systems are broadly classified into only two types, bacterial and archaeo-eukaryotic. In contrast, double-stranded (ds) DNA viruses feature a much broader diversity of DNA replication machineries. Viruses differ greatly in both completeness and composition of their sets of DNA replication proteins. In this study, we explored whether there are common patterns underlying this extreme diversity. We identified and analyzed all major functional groups of DNA replication proteins in all available proteomes of dsDNA viruses. Our results show that some proteins are common to viruses infecting all domains of life and likely represent components of the ancestral core set. These include B-family polymerases, SF3 helicases, archaeo-eukaryotic primases, clamps and clamp loaders of the archaeo-eukaryotic type, RNase H and ATP-dependent DNA ligases. We also discovered a clear correlation between genome size and self-sufficiency of viral DNA replication, the unanticipated dominance of replicative helicases and pervasive functional associations among certain groups of DNA replication proteins. Altogether, our results provide a comprehensive view on the diversity and evolution of replication systems in the DNA virome and uncover fundamental principles underlying the orchestration of viral DNA replication. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Postbuckling analysis of shear deformable composite flat panels taking into account geometrical imperfections

NASA Technical Reports Server (NTRS)

Librescu, L.; Stein, M.

1990-01-01

The effects of initial geometrical imperfections on the postbuckling response of flat laminated composite panels to uniaxial and biaxial compressive loading are investigated analytically. The derivation of the mathematical model on the basis of first-order transverse shear deformation theory is outlined, and numerical results for perfect and imperfect, single-layer and three-layer square plates with free-free, clamped-clamped, or free-clamped edges are presented in graphs and briefly characterized. The present approach is shown to be more accurate than analyses based on the classical Kirchhoff plate model.

The role of the DNA sliding clamp in Okazaki fragment maturation in archaea and eukaryotes.

PubMed

Beattie, Thomas R; Bell, Stephen D

2011-01-01

Efficient processing of Okazaki fragments generated during discontinuous lagging-strand DNA replication is critical for the maintenance of genome integrity. In eukaryotes, a number of enzymes co-ordinate to ensure the removal of initiating primers from the 5'-end of each fragment and the generation of a covalently linked daughter strand. Studies in eukaryotic systems have revealed that the co-ordination of DNA polymerase δ and FEN-1 (Flap Endonuclease 1) is sufficient to remove the majority of primers. Other pathways such as that involving Dna2 also operate under certain conditions, although, notably, Dna2 is not universally conserved between eukaryotes and archaea, unlike the other core factors. In addition to the catalytic components, the DNA sliding clamp, PCNA (proliferating-cell nuclear antigen), plays a pivotal role in binding and co-ordinating these enzymes at sites of lagging-strand replication. Structural studies in eukaryotic and archaeal systems have revealed that PCNA-binding proteins can adopt different conformations when binding PCNA. This conformational malleability may be key to the co-ordination of these enzymes' activities.

Evidence for Roles of the Escherichia coli Hda Protein Beyond RIDA

PubMed Central

Baxter, Jamie C.; Sutton, Mark D.

2012-01-01

The ATP-bound form of the Escherichia coli DnaA protein binds ‘DnaA boxes’ present in the origin of replication (oriC) and operator sites of several genes, including dnaA, to coordinate their transcription with initiation of replication. The Hda protein, together with the β sliding clamp, stimulates the ATPase activity of DnaA via a process termed Regulatory Inactivation of DnaA (RIDA), to regulate the activity of DnaA in DNA replication. Here, we used the mutant dnaN159 strain, which expresses the β159 clamp protein, to gain insight into how the actions of Hda are coordinated with replication. Elevated expression of Hda impeded growth of the dnaN159 strain in a Pol II- and Pol IV-dependent manner, suggesting a role for Hda managing the actions of these Pols. In a wild type strain, elevated levels of Hda conferred sensitivity to nitrofurazone, and suppressed the frequency of −1 frameshift mutations characteristic of Pol IV, while loss of hda conferred cold sensitivity. Using the dnaN159 strain, we identified 24 novel hda alleles, four of which supported E. coli viability despite their RIDA defect. Taken together, these findings suggest that although one or more Hda functions are essential for cell viability, RIDA may be dispensable. PMID:22716942

Design and experimental research of a novel inchworm type piezo-driven rotary actuator with the changeable clamping radius.

PubMed

Zhao, Hongwei; Fu, Lu; Ren, Luquan; Huang, Hu; Fan, Zunqiang; Li, Jianping; Qu, Han

2013-01-01

In this paper, a novel piezo-driven rotary actuator with the changeable clamping radius is developed based on the inchworm principle. This actuator mainly utilizes three piezoelectric actuators, a flexible gripper, a clamping block, and a rotor to achieve large stroke rotation with high resolution. The design process of the flexible gripper consisting of the driving unit and the clamping unit is described. Lever-type mechanisms were used to amplify the micro clamping displacements. The amplifying factor and parasitic displacement of the lever-type mechanism in the clamping unit was analyzed theoretically and experimentally. In order to investigate the rotation characteristics of the actuator, a series of experiments was carried out. Experimental results indicate that the actuator can rotate at a speed of 77,488 μrad/s with a driving frequency of 167 Hz. The rotation resolution and maximum load torque of the actuator are 0.25 μrad and 37 N mm, respectively. The gripper is movable along the z direction based on an elevating platform, and the clamping radius can change from 10.6 mm to 25 mm. Experimental results confirm that the actuator can achieve different rotation speeds by changing the clamping radius.

SCBUCKLE user's manual: Buckling analysis program for simple supported and clamped panels

NASA Technical Reports Server (NTRS)

Cruz, Juan R.

1993-01-01

The program SCBUCKLE calculates the buckling loads and mode shapes of cylindrically curved, rectangular panels. The panel is assumed to have no imperfections. SCBUCKLE is capable of analyzing specially orthotropic symmetric panels (i.e., A(sub 16) = A(sub 26) = 0.0, D(sub 16) = D(sub 26) = 0.0, B(sub ij) = 0.0). The analysis includes first-order transverse shear theory and is capable of modeling sandwich panels. The analysis supports two types of boundary conditions: either simply supported or clamped on all four edges. The panel can be subjected to linearly varying normal loads N(sub x) and N(sub y) in addition to a constant shear load N(sub xy). The applied loads can be divided into two parts: a preload component; and a variable (eigenvalue-dependent) component. The analysis is based on the modified Donnell's equations for shallow shells. The governing equations are solved by Galerkin's method.

Evidence for roles of the Escherichia coli Hda protein beyond regulatory inactivation of DnaA.

PubMed

Baxter, Jamie C; Sutton, Mark D

2012-08-01

The ATP-bound form of the Escherichia coli DnaA protein binds 'DnaA boxes' present in the origin of replication (oriC) and operator sites of several genes, including dnaA, to co-ordinate their transcription with initiation of replication. The Hda protein, together with the β sliding clamp, stimulates the ATPase activity of DnaA via a process termed regulatory inactivation of DnaA (RIDA), to regulate the activity of DnaA in DNA replication. Here, we used the mutant dnaN159 strain, which expresses the β159 clamp protein, to gain insight into how the actions of Hda are co-ordinated with replication. Elevated expression of Hda impeded growth of the dnaN159 strain in a Pol II- and Pol IV-dependent manner, suggesting a role for Hda managing the actions of these Pols. In a wild-type strain, elevated levels of Hda conferred sensitivity to nitrofurazone, and suppressed the frequency of -1 frameshift mutations characteristic of Pol IV, while loss of hda conferred cold sensitivity. Using the dnaN159 strain, we identified 24 novel hda alleles, four of which supported E. coli viability despite their RIDA defect. Taken together, these findings suggest that although one or more Hda functions are essential for cell viability, RIDA may be dispensable. © 2012 Blackwell Publishing Ltd.

Single-molecule visualization of fast polymerase turnover in the bacterial replisome

PubMed Central

Lewis, Jacob S; Spenkelink, Lisanne M; Jergic, Slobodan; Wood, Elizabeth A; Monachino, Enrico; Horan, Nicholas P; Duderstadt, Karl E; Cox, Michael M; Robinson, Andrew; Dixon, Nicholas E; van Oijen, Antoine M

2017-01-01

The Escherichia coli DNA replication machinery has been used as a road map to uncover design rules that enable DNA duplication with high efficiency and fidelity. Although the enzymatic activities of the replicative DNA Pol III are well understood, its dynamics within the replisome are not. Here, we test the accepted view that the Pol III holoenzyme remains stably associated within the replisome. We use in vitro single-molecule assays with fluorescently labeled polymerases to demonstrate that the Pol III* complex (holoenzyme lacking the β2 sliding clamp), is rapidly exchanged during processive DNA replication. Nevertheless, the replisome is highly resistant to dilution in the absence of Pol III* in solution. We further show similar exchange in live cells containing labeled clamp loader and polymerase. These observations suggest a concentration-dependent exchange mechanism providing a balance between stability and plasticity, facilitating replacement of replisomal components dependent on their availability in the environment. DOI: http://dx.doi.org/10.7554/eLife.23932.001 PMID:28432790

Modulation of the Pyrococcus abyssi NucS Endonuclease Activity by Replication Clamp at Functional and Structural Levels*

PubMed Central

Creze, Christophe; Ligabue, Alessio; Laurent, Sébastien; Lestini, Roxane; Laptenok, Sergey P.; Khun, Joelle; Vos, Marten H.; Czjzek, Mirjam; Myllykallio, Hannu; Flament, Didier

2012-01-01

Pyrococcus abyssi NucS is the founding member of a new family of structure-specific DNA endonucleases that interact with the replication clamp proliferating cell nuclear antigen (PCNA). Using a combination of small angle x-ray scattering and surface plasmon resonance analyses, we demonstrate the formation of a stable complex in solution, in which one molecule of the PabNucS homodimer binds to the outside surface of the PabPCNA homotrimer. Using fluorescent labels, PCNA is shown to increase the binding affinity of NucS toward single-strand/double-strand junctions on 5′ and 3′ flaps, as well as to modulate the cleavage specificity on the branched DNA structures. Our results indicate that the presence of a single major contact between the PabNucS and PabPCNA proteins, together with the complex-induced DNA bending, facilitate conformational flexibility required for specific cleavage at the single-strand/double-strand DNA junction. PMID:22431731

Modulation of the Pyrococcus abyssi NucS endonuclease activity by replication clamp at functional and structural levels.

PubMed

Creze, Christophe; Ligabue, Alessio; Laurent, Sébastien; Lestini, Roxane; Laptenok, Sergey P; Khun, Joelle; Vos, Marten H; Czjzek, Mirjam; Myllykallio, Hannu; Flament, Didier

2012-05-04

Pyrococcus abyssi NucS is the founding member of a new family of structure-specific DNA endonucleases that interact with the replication clamp proliferating cell nuclear antigen (PCNA). Using a combination of small angle x-ray scattering and surface plasmon resonance analyses, we demonstrate the formation of a stable complex in solution, in which one molecule of the PabNucS homodimer binds to the outside surface of the PabPCNA homotrimer. Using fluorescent labels, PCNA is shown to increase the binding affinity of NucS toward single-strand/double-strand junctions on 5' and 3' flaps, as well as to modulate the cleavage specificity on the branched DNA structures. Our results indicate that the presence of a single major contact between the PabNucS and PabPCNA proteins, together with the complex-induced DNA bending, facilitate conformational flexibility required for specific cleavage at the single-strand/double-strand DNA junction.

[13C]Glucose Breath Testing Provides a Noninvasive Measure of Insulin Resistance: Calibration Analyses Against Clamp Studies

PubMed Central

Hussain, Maysa; Jangorbhani, Morteza; Schuette, Sally; Considine, Robert V.; Chisholm, Robin L.

2014-01-01

Abstract Background: Exhaled 13CO2 following ingestion of [13C]glucose with a standard oral glucose tolerance load correlates with blood glucose values but is determined by tissue glucose uptake. Therefore exhaled 13CO2 may also be a surrogate measure of the whole-body glucose disposal rate (GDR) measured by the gold standard hyperinsulinemic euglycemic clamp. Subjects and Methods: Subjects from across the glycemia range were studied on 2 consecutive days under fasting conditions. On Day 1, a 75-g oral glucose load spiked with [13C]glucose was administered. On Day 2, a hyperinsulinemic euglycemic clamp was performed. Correlations between breath parameters and clamp-derived GDR were evaluated, and calibration analyses were performed to evaluate the precision of breath parameter predictions of clamp measures. Results: Correlations of breath parameters with GDR and GDR per kilogram of fat-free mass (GDRffm) ranged from 0.54 to 0.61 and 0.54 to 0.66, respectively (all P<0.001). In calibration analyses the root mean square error for breath parameters predicting GDR and GDRffm ranged from 2.32 to 2.46 and from 3.23 to 3.51, respectively. Cross-validation prediction error (CVPE) estimates were 2.35–2.51 (GDR) and 3.29–3.57 (GDRffm). Prediction precision of breath enrichment at 180 min predicting GDR (CVPE=2.35) was superior to that for inverse insulin (2.68) and the Matsuda Index (2.51) but inferior to that for the log of homeostasis model assessment (2.21) and Quantitative Insulin Sensitivity Check Index (2.29) (all P<10−5). Similar patterns were seen for predictions of GDRffm. Conclusions: 13CO2 appearance in exhaled breath following a standard oral glucose load with added [13C]glucose provides a valid surrogate index of clamp-derived measures of whole-body insulin resistance, with good accuracy and precision. This noninvasive breath test-based approach can provide a useful measure of whole-body insulin resistance in physiologic and epidemiologic studies. PMID:24116833

Apparatus for unloading nuclear fuel pellets from a sintering boat

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bucher, G.D.; Raymond, T.E.

1987-02-10

An apparatus is described for unloading nuclear fuel pellets from a loaded sintering boat having an open top, comprising: (a) means for receiving the boat in an upright position with the pellets contained therein, the boat receiving means including a platform for supporting the loaded boat in the upright position, the boat supporting platform having first and second portions; (b) means for clamping the boat including a pair of plates disposed at lateral sides of the boat and being movable in a first direction relative to one another for applying clamping forces to the boat on the platform and inmore » a second direction relative to one another for releasing the clamping forces from the boat. The pair of plates have inner surfaces facing toward one another, the first and second platform portions of the boat supporting platform being mounted to the plates on the respective facing surfaces thereof and disposed in a common plane. One of the plates and one of the platform portions mounted thereto are disposed in a stationary position and the other of the plates and the other of the platform portions mounted thereto are movable relative thereto in the first and second directions for applying and releasing clamping forces to and from the boat while the boat is supported in the upright position by the platform portions; (c) means for transferring the clamped boat from the upright position to an inverted position and then back to the upright position; and (d) means of receiving the pellets from the clamped boat as the boat is being transferred from the upright position to the inverted position.« less

Finite element modelling to assess the effect of surface mounted piezoelectric patch size on vibration response of a hybrid beam

NASA Astrophysics Data System (ADS)

Rahman, N.; Alam, M. N.

2018-02-01

Vibration response analysis of a hybrid beam with surface mounted patch piezoelectric layer is presented in this work. A one dimensional finite element (1D-FE) model based on efficient layerwise (zigzag) theory is used for the analysis. The beam element has eight mechanical and a variable number of electrical degrees of freedom. The beams are also modelled in 2D-FE (ABAQUS) using a plane stress piezoelectric quadrilateral element for piezo layers and a plane stress quadrilateral element for the elastic layers of hybrid beams. Results are presented to assess the effect of size of piezoelectric patch layer on the free and forced vibration responses of thin and moderately thick beams under clamped-free and clamped-clamped configurations. The beams are subjected to unit step loading and harmonic loading to obtain the forced vibration responses. The vibration control using in phase actuation potential on piezoelectric patches is also studied. The 1D-FE results are compared with the 2D-FE results.

Resonant-type Smooth Impact Drive Mechanism (SIDM) actuator using a bolt-clamped Langevin transducer.

PubMed

Nishimura, Takuma; Hosaka, Hiroshi; Morita, Takeshi

2012-01-01

The Smooth Impact Drive Mechanism (SIDM) is a linear piezoelectric actuator that has seen practically applied to camera lens modules. Although previous SIDM actuators are easily miniaturized and enable accurate positioning, these actuators cannot actuate at high speed and cannot provide powerful driving because they are driven at an off-resonant frequency using a soft-type PZT. In the present study, we propose a resonant-type SIDM using a bolt-clamped Langevin transducer (BLT) with a hard-type PZT. The resonant-type SIDM overcomes the above-mentioned problems and high-power operation becomes possible with a very simple structure. As a result, we confirmed the operation of resonant-type SIDM by designing a bolt-clamped Langevin transducer. The properties of no-load maximum speed was 0.28m/s at driving voltages of 80V(p-p) for 44.9kHz and 48V(p-p) for 22.45kHz with a pre-load of 3.1N. Copyright © 2011 Elsevier B.V. All rights reserved.

Lightweight In-Plane Actuated Deformable Mirrors for Space Telescopes

DTIC Science & Technology

2006-09-01

dimensional beam-string and axisymmetric plate-membrane. The beam-string (a clamped beam simultaneously under an axial load ) is an important...Tensile load versus radius. . . . . . . . . . . . . . . . . . . . . . 175 7.4. Actuation voltage functions. . . . . . . . . . . . . . . . . . . . 179...membrane Asymptotic finite element Flint and De- noyer [45] 2003 In-plane Circular membrane Numerical least squares fit Actuators modelled as line loads

Application of Fracture Mechanics to Specify the Proof Load Factor for Clamp Band Systems of Launch Vehicles

NASA Astrophysics Data System (ADS)

Singaravelu, J.; Sundaresan, S.; Nageswara Rao, B.

2013-04-01

This article presents a methodology for evaluation of the proof load factor (PLF) for clamp band system (CBS) made of M250 Maraging steel following fracture mechanics principles.CBS is most widely used as a structural element and as a separation system. Using Taguchi's design of experiments and the response surface method (RSM) the compact tension specimens were tested to establish an empirical relation for the failure load ( P max) in terms of the ultimate strength, width, thickness, and initial crack length. The test results of P max closely matched with the developed RSM empirical relation. Crack growth rates of the maraging steel in different environments were examined. Fracture strength (σf) of center surface cracks and through-crack tension specimens are evaluated utilizing the fracture toughness ( K IC). Stress induced in merman band at flight loading conditions is evaluated to estimate the higher load factor and PLF. Statistical safety factor and reliability assessments were made for the specified flaw sizes useful in the development of fracture control plan for CBS of launch vehicles.

Ready to Use Tissue Construct for Military Bone & Cartilage Trauma

DTIC Science & Technology

2014-10-01

during nail introduction and reaming. In the present study, we examined the load - bearing capacity and optimal internal fixation of a bone/poly-ε...segmental defect, (a) axial loading via ball bearing , (b) torsional loading via square clamp allowing axial displacement, (c) three-point bending of tibia...knee joints by simulating loads seen during ambulation and knee range of motion. Our central hypothesis is that an anatomically and

The role of peel stresses in cyclic debonding

NASA Technical Reports Server (NTRS)

Everett, R. A., Jr.

1982-01-01

When an adhesively bonded joint is undergoing cyclic loading, one of the possible damage modes that occurs is called cyclic debonding - progressive separation of the adherends by failure of the adhesive bond under cyclic loading. In most practical structures, both peel and shear stresses exist in the adhesive bonding during cyclic loading. The results of an experimental and analytical study to determine the role of peel stresses on cyclic debonding in a mixed mode specimen are presented. Experimentally, this was done by controlling the forces that create the peel stresses by applying a clamping force to oppose the peel stresses. Cracked lap shear joints were chosen for this study. A finite element analysis was developed to assess the effect of the clamping force on the strain energy release rates due to shear and peel stresses. The results imply that the peel stress is the principal stress causing cyclic debonding.

Aeroelastic deformation of a perforated strip

NASA Astrophysics Data System (ADS)

Guttag, M.; Karimi, H. H.; Falcón, C.; Reis, P. M.

2018-01-01

We perform a combined experimental and numerical investigation into the static deformation of perforated elastic strips under uniform aerodynamic loading at high-Reynolds-number conditions. The static shape of the porous strips, clamped either horizontally or vertically, is quantified as they are deformed by wind loading, induced by a horizontal flow. The experimental profiles are compared to numerical simulations using a reduced model that takes into account the normal drag force on the deformed surface. For both configurations (vertical and horizontal clamping), we compute the drag coefficient of the strip, by fitting the experimental data to the model, and find that it decreases as a function of porosity. Surprisingly, we find that, for every value of porosity, the drag coefficients for the horizontal configuration are larger than those of the vertical configuration. For all data in both configurations, with the exception of the continuous strip clamped vertically, a linear relation is found between the porosity and drag. Making use of this linearity, we can rescale the drag coefficient in a way that it becomes constant as a function of the Cauchy number, which relates the force due to fluid loading on the elastic strip to its bending rigidity, independently of the material properties and porosity of the strip and the flow speed. Our findings on flexible strips are contrasted to previous work on rigid perforated plates. These results highlight some open questions regarding the usage of reduced models to describe the deformation of flexible structures subjected to aerodynamic loading.

The clp1 gene of the mushroom Coprinus cinereus is essential for A-regulated sexual development.

PubMed Central

Inada, K; Morimoto, Y; Arima, T; Murata, Y; Kamada, T

2001-01-01

Sexual development in the mushroom Coprinus cinereus is under the control of the A and B mating-type loci, both of which must be different for a compatible, dikaryotic mycelium to form between two parents. The A genes, encoding proteins with homeodomain motifs, regulate conjugate division of the two nuclei from each mating partner and promote the formation of clamp connections. The latter are hyphal configurations required for the maintenance of the nuclear status in the dikaryotic phase of basidiomycetes. The B genes encode pheromones and pheromone receptors. They regulate the cellular fusions that complete clamp connections during growth, as well as the nuclear migration required for dikaryosis. The AmutBmut strain (326) of C. cinereus, in which both A- and B-regulated pathways are constitutively activated by mutations, produces, without mating, dikaryon-like, fertile hyphae with clamp connections. In this study we isolated and characterized clampless1-1 (clp1-1), a mutation that blocks clamp formation, an essential step in A-regulated sexual development, in the AmutBmut background. A genomic DNA fragment that rescues the clp1-1 mutation was identified by transformations. Sequencing of the genomic DNA, together with RACE experiments, identified an ORF interrupted by one intron, encoding a novel protein of 365 amino acids. The clp1-1 mutant allele carries a deletion of four nucleotides, which is predicted to cause elimination of codon 128 and frameshifts thereafter. The clp1 transcript was normally detected only in the presence of the A protein heterodimer formed when homokaryons with compatible A genes were mated. Forced expression of clp1 by promoter replacements induced clamp development without the need for a compatible A gene combination. These results indicate that expression of clp1 is necessary and sufficient for induction of the A-regulated pathway that leads to clamp development. PMID:11139497

Silicon controlled rectifier polyphase bridge inverter commutated with gate-turn-off thyristor

NASA Technical Reports Server (NTRS)

Edwards, Dean B. (Inventor); Rippel, Wally E. (Inventor)

1986-01-01

A polyphase SCR inverter (10) having N switching poles, each comprised of two SCR switches (1A, 1B; 2A, 2B . . . NA, NB) and two diodes (D1B; D1B; D2A, D2B . . . DNA, DNB) in series opposition with saturable reactors (L1A, L1B; L2A, L2B . . . LNA, LNB) connecting the junctions between the SCR switches and diodes to an output terminal (1, 2 . . . 3) is commutated with only one GTO thyristor (16) connected between the common negative terminal of a dc source and a tap of a series inductor (14) connected to the positive terminal of the dc source. A clamp winding (22) and diode (24) are provided, as is a snubber (18) which may have its capacitance (c) sized for maximum load current divided into a plurality of capacitors (C.sub.1, C.sub.2 . . . C.sub.N), each in series with an SCR switch S.sub.1, S.sub.2 . . . S.sub.N). The total capacitance may be selected by activating selected switches as a function of load current. A resistor 28 and SCR switch 26 shunt reverse current when the load acts as a generator, such as a motor while braking.

Internal core tightener

DOEpatents

Brynsvold, Glen V.; Snyder, Jr., Harold J.

1976-06-22

An internal core tightener which is a linear actuated (vertical actuation motion) expanding device utilizing a minimum of moving parts to perform the lateral tightening function. The key features are: (1) large contact areas to transmit loads during reactor operation; (2) actuation cam surfaces loaded only during clamping and unclamping operation; (3) separation of the parts and internal operation involved in the holding function from those involved in the actuation function; and (4) preloaded pads with compliant travel at each face of the hexagonal assembly at the two clamping planes to accommodate thermal expansion and irradiation induced swelling. The latter feature enables use of a "fixed" outer core boundary, and thus eliminates the uncertainty in gross core dimensions, and potential for rapid core reactivity changes as a result of core dimensional change.

An automated two-dimensional optical force clamp for single molecule studies.

PubMed Central

Lang, Matthew J; Asbury, Charles L; Shaevitz, Joshua W; Block, Steven M

2002-01-01

We constructed a next-generation optical trapping instrument to study the motility of single motor proteins, such as kinesin moving along a microtubule. The instrument can be operated as a two-dimensional force clamp, applying loads of fixed magnitude and direction to motor-coated microscopic beads moving in vitro. Flexibility and automation in experimental design are achieved by computer control of both the trap position, via acousto-optic deflectors, and the sample position, using a three-dimensional piezo stage. Each measurement is preceded by an initialization sequence, which includes adjustment of bead height relative to the coverslip using a variant of optical force microscopy (to +/-4 nm), a two-dimensional raster scan to calibrate position detector response, and adjustment of bead lateral position relative to the microtubule substrate (to +/-3 nm). During motor-driven movement, both the trap and stage are moved dynamically to apply constant force while keeping the trapped bead within the calibrated range of the detector. We present details of force clamp operation and preliminary data showing kinesin motor movement subject to diagonal and forward loads. PMID:12080136

Device for measuring hole elongation in a bolted joint

NASA Technical Reports Server (NTRS)

Wichorek, Gregory R. (Inventor)

1987-01-01

A device to determine the operable failure mode of mechanically fastened lightweight composite joints by measuring the hole elongation of a bolted joint is disclosed. The double-lap joint test apparatus comprises a stud, a test specimen having a hole, two load transfer plates, and linear displacement measuring instruments. The test specimen is sandwiched between the two load transfer plates and clamped together with the stud. Spacer washers are placed between the test specimen and each load transfer plate to provide a known, controllable area for the determination of clamping forces around the hole of the specimen attributable to bolt torque. The spacer washers also provide a gap for the mounting of reference angles on each side of the test specimen. Under tensile loading, elongation of the hole of the test specimen causes the stud to move away from the reference angles. This displacement is measured by the voltage output of two linear displacement measuring instruments that are attached to the stud and remain in contact with the reference angles throughout the tensile loading. The present invention obviates previous problems in obtaining specimen deformation measurements by monitoring the reference angles to the test specimen and the linear displacement measuring instruments to the stud.

Inertial piezoelectric linear motor driven by a single-phase harmonic wave with automatic clamping mechanism

NASA Astrophysics Data System (ADS)

He, Liangguo; Chu, Yuheng; Hao, Sai; Zhao, Xiaoyong; Dong, Yuge; Wang, Yong

2018-05-01

A novel, single-phase, harmonic-driven, inertial piezoelectric linear motor using an automatic clamping mechanism was designed, fabricated, and tested to reduce the sliding friction and simplify the drive mechanism and power supply control of the inertial motor. A piezoelectric bimorph and a flexible hinge were connected in series to form the automatic clamping mechanism. The automatic clamping mechanism was used as the driving and clamping elements. A dynamic simulation by Simulink was performed to prove the feasibility of the motor. The finite element method software COMSOL was used to design the structure of the motor. An experimental setup was built to validate the working principle and evaluate the performance of the motor. The prototype motor outputted a no-load velocity of 3.178 mm/s at a voltage of 220 Vp-p and a maximum traction force of 4.25 N under a preload force of 8 N. The minimum resolution of 1.14 μm was achieved at a driving frequency of 74 Hz, a driving voltage of 50 Vp-p, and a preload force of 0 N.

BOLD Response to Semantic and Syntactic Processing during Hypoglycemia Is Load-Dependent

ERIC Educational Resources Information Center

Schafer, Robin J.; Page, Kathleen A.; Arora, Jagriti; Sherwin, Robert; Constable, R. Todd

2012-01-01

This study investigates how syntactic and semantic load factors impact sentence comprehension and BOLD signal under moderate hypoglycemia. A dual session, whole brain fMRI study was conducted on 16 healthy participants using the glucose clamp technique. In one session, they experienced insulin-induced hypoglycemia (plasma glucose at [image…

Comparison of Nonlinear Random Response Using Equivalent Linearization and Numerical Simulation

NASA Technical Reports Server (NTRS)

Rizzi, Stephen A.; Muravyov, Alexander A.

2000-01-01

A recently developed finite-element-based equivalent linearization approach for the analysis of random vibrations of geometrically nonlinear multiple degree-of-freedom structures is validated. The validation is based on comparisons with results from a finite element based numerical simulation analysis using a numerical integration technique in physical coordinates. In particular, results for the case of a clamped-clamped beam are considered for an extensive load range to establish the limits of validity of the equivalent linearization approach.

A complete dc characterization of a constant-frequency, clamped-mode, series-resonant converter

NASA Technical Reports Server (NTRS)

Tsai, Fu-Sheng; Lee, Fred C.

1988-01-01

The dc behavior of a clamped-mode series-resonant converter is characterized systematically. Given a circuit operating condition, the converter's mode of operation is determined and various circuit parameters are calculated, such as average inductor current (load current), rms inductor current, peak capacitor voltage, rms switch currents, average diode currents, switch turn-on currents, and switch turn-off currents. Regions of operation are defined, and various circuit characteristics are derived to facilitate the converter design.

Photovoltaic module mounting system

DOEpatents

Miros, Robert H. J.; Mittan, Margaret Birmingham; Seery, Martin N; Holland, Rodney H

2012-09-18

A solar array mounting system having unique installation, load distribution, and grounding features, and which is adaptable for mounting solar panels having no external frame. The solar array mounting system includes flexible, pedestal-style feet and structural links connected in a grid formation on the mounting surface. The photovoltaic modules are secured in place via the use of attachment clamps that grip the edge of the typically glass substrate. The panel mounting clamps are then held in place by tilt brackets and/or mid-link brackets that provide fixation for the clamps and align the solar panels at a tilt to the horizontal mounting surface. The tilt brackets are held in place atop the flexible feet and connected link members thus creating a complete mounting structure.

Photovoltaic module mounting system

DOEpatents

Miros, Robert H. J. [Fairfax, CA; Mittan, Margaret Birmingham [Oakland, CA; Seery, Martin N [San Rafael, CA; Holland, Rodney H [Novato, CA

2012-04-17

A solar array mounting system having unique installation, load distribution, and grounding features, and which is adaptable for mounting solar panels having no external frame. The solar array mounting system includes flexible, pedestal-style feet and structural links connected in a grid formation on the mounting surface. The photovoltaic modules are secured in place via the use of attachment clamps that grip the edge of the typically glass substrate. The panel mounting clamps are then held in place by tilt brackets and/or mid-link brackets that provide fixation for the clamps and align the solar panels at a tilt to the horizontal mounting surface. The tilt brackets are held in place atop the flexible feet and connected link members thus creating a complete mounting structure.

The Crystal Structure of PF-8, the DNA Polymerase Accessory Subunit from Kaposi's Sarcoma-Associated Herpesvirus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baltz, Jennifer L.; Filman, David J.; Ciustea, Mihai

2009-12-01

Kaposi's sarcoma-associated herpesvirus is an emerging pathogen whose mechanism of replication is poorly understood. PF-8, the presumed processivity factor of Kaposi's sarcoma-associated herpesvirus DNA polymerase, acts in combination with the catalytic subunit, Pol-8, to synthesize viral DNA. We have solved the crystal structure of residues 1 to 304 of PF-8 at a resolution of 2.8 {angstrom}. This structure reveals that each monomer of PF-8 shares a fold common to processivity factors. Like human cytomegalovirus UL44, PF-8 forms a head-to-head dimer in the form of a C clamp, with its concave face containing a number of basic residues that are predictedmore » to be important for DNA binding. However, there are several differences with related proteins, especially in loops that extend from each monomer into the center of the C clamp and in the loops that connect the two subdomains of each protein, which may be important for determining PF-8's mode of binding to DNA and to Pol-8. Using the crystal structures of PF-8, the herpes simplex virus catalytic subunit, and RB69 bacteriophage DNA polymerase in complex with DNA and initial experiments testing the effects of inhibition of PF-8-stimulated DNA synthesis by peptides derived from Pol-8, we suggest a model for how PF-8 might form a ternary complex with Pol-8 and DNA. The structure and the model suggest interesting similarities and differences in how PF-8 functions relative to structurally similar proteins.« less

A Genetic Selection for dinB Mutants Reveals an Interaction between DNA Polymerase IV and the Replicative Polymerase That Is Required for Translesion Synthesis.

PubMed

Scotland, Michelle K; Heltzel, Justin M H; Kath, James E; Choi, Jung-Suk; Berdis, Anthony J; Loparo, Joseph J; Sutton, Mark D

2015-09-01

Translesion DNA synthesis (TLS) by specialized DNA polymerases (Pols) is a conserved mechanism for tolerating replication blocking DNA lesions. The actions of TLS Pols are managed in part by ring-shaped sliding clamp proteins. In addition to catalyzing TLS, altered expression of TLS Pols impedes cellular growth. The goal of this study was to define the relationship between the physiological function of Escherichia coli Pol IV in TLS and its ability to impede growth when overproduced. To this end, 13 novel Pol IV mutants were identified that failed to impede growth. Subsequent analysis of these mutants suggest that overproduced levels of Pol IV inhibit E. coli growth by gaining inappropriate access to the replication fork via a Pol III-Pol IV switch that is mechanistically similar to that used under physiological conditions to coordinate Pol IV-catalyzed TLS with Pol III-catalyzed replication. Detailed analysis of one mutant, Pol IV-T120P, and two previously described Pol IV mutants impaired for interaction with either the rim (Pol IVR) or the cleft (Pol IVC) of the β sliding clamp revealed novel insights into the mechanism of the Pol III-Pol IV switch. Specifically, Pol IV-T120P retained complete catalytic activity in vitro but, like Pol IVR and Pol IVC, failed to support Pol IV TLS function in vivo. Notably, the T120P mutation abrogated a biochemical interaction of Pol IV with Pol III that was required for Pol III-Pol IV switching. Taken together, these results support a model in which Pol III-Pol IV switching involves interaction of Pol IV with Pol III, as well as the β clamp rim and cleft. Moreover, they provide strong support for the view that Pol III-Pol IV switching represents a vitally important mechanism for regulating TLS in vivo by managing access of Pol IV to the DNA.

Stress-Strain Properties of SIFCON in Uniaxial Compression and Tension

DTIC Science & Technology

1988-08-01

direction act as contacting beams whereas fibers aligned parallel to the loading direction act as individual columns . The combination of fiber-to-fiber...applicable to the study of SIFCON. These include such topics as the influence of strain rate on composite behavior, cyclic loading response, fiber-to-matrix...the specimen are shown in Figure 17. The grips consisted of self-clamping steel plates and a universal joint connection to the loading machine which

Mechanical testing of a steel-reinforced epoxy resin bar and clamp for external skeletal fixation of long-bone fractures in cats.

PubMed

Leitch, B J; Worth, A J

2018-05-01

To provide veterinarians with confidence when using a commercially available epoxy resin in external skeletal fixators (ESF), testing was conducted to determine exothermia during curing of the epoxy resin compared to polymethylmethacrylate (PMMA), the hardness of the epoxy resin as a bar over 16 weeks, and the strength of the epoxy resin bar compared with metal clamps in similarly constructed Type 1a ESF constructs simulating the repair of feline long bone fractures. Exothermia of the epoxy resin during curing was tested against PMMA with surface temperatures recorded over the first 15 minutes of curing, using four samples of each product. The hardness of 90 identical epoxy resin bars was tested by subjecting them to cyclic loads (1,000 cycles of 20.5 N, every 7 days) over a 16-week period and impact testing 10 bars every 2 weeks. Ten bars that were not subjected to cyclic loads were impact tested at 0 weeks and another 10 at 16 weeks. Strength of the epoxy resin product, as a bar and clamp composite, was tested against metal SK and Kirschner-Ehmer (KE) clamps and bars in Type 1a, tied-in intramedullary pin, ESF constructs with either 90° or 75° pin placement, subjected to compressive and bending loads to 75 N. The maximum temperature during curing of the epoxy resin (min 39.8, max 43.0)°C was less than the PMMA (min 85.2, max 98.5)°C (p<0.001). There was no change in hardness of the epoxy resin bars over the 16 weeks of cyclic loading (p=0.58). There were no differences between the median strength of the epoxy resin, SK or KE ESF constructs in compression or bending when tested to 75 N (p>0.05). Stiffness of constructs with 75° pin placement was greater for SK than epoxy resin constructs in compression (p=0.046), and was greater for KE than epoxy resin constructs in bending (p=0.033). The epoxy resin tested was found to be less exothermic than PMMA; bars made from the epoxy resin showed durability over an expected fracture healing timeframe and had mechanical strength characteristics comparable to metal bar and clamp ESF constructs. The epoxy resin ESF construct tested in this study can be considered a suitable replacement for SK or KE ESF constructs in the treatment of feline long-bone fractures, in terms of mechanical strength.

The buckling response of symmetrically laminated composite plates having a trapezoidal planform area. M.S. Thesis Interim Report No. 98, Aug. 1990 - May 1994

NASA Technical Reports Server (NTRS)

Radloff, H. D., II; Hyer, M. W.; Nemeth, M. P.

1994-01-01

The focus of this work is the buckling response of symmetrically laminated composite plates having a planform area in the shape of an isosceles trapezoid. The loading is assumed to be inplane and applied perpendicular to the parallel ends of the plate. The tapered edges of the plate are assumed to have simply supported boundary conditions, while the parallel ends are assumed to have either simply supported or clamped boundary conditions. A semi-analytic closed-form solution based on energy principles and the Trefftz stability criterion is derived and solutions are obtained using the Rayleigh-Ritz method. Intrinsic in this solution is a simplified prebuckling analysis which approximates the inplane force resultant distributions by the forms Nx=P/W(x) and Ny=Nxy=0, where P is the applied load and W(x) is the plate width which, for the trapezoidal planform, varies linearly with the lengthwise coordinate x. The out-of-plane displacement is approximated by a double trigonometric series. This analysis is posed in terms of four nondimensional parameters representing orthotropic and anisotropic material properties, and two nondimensional parameters representing geometric properties. For comparison purposes, a number of specific plate geometry, ply orientation, and stacking sequence combinations are investigated using the general purpose finite element code ABAQUS. Comparison of buckling coefficients calculated using the semi-analytical model and the finite element model show agreement within 5 percent, in general, and within 15 percent for the worst cases. In order to verify both the finite element and semi-analytical analyses, buckling loads are measured for graphite/epoxy plates having a wide range of plate geometries and stacking sequences. Test fixtures, instrumentation system, and experimental technique are described. Experimental results for the buckling load, the buckled mode shape, and the prebuckling plate stiffness are presented and show good agreement with the analytical results regarding the buckling load and the prebuckling plate stiffness. However, the experimental results show that for some cases the analysis underpredicts the number of halfwaves in the buckled mode shape. In the context of the definitions of taper ratio and aspect ratio used in this study, it is concluded that the buckling load always increases as taper ratio increases for a given aspect ratio for plates having simply supported boundary conditions on the parallel ends. There are combinations of plate geometry and ply stackling sequences, however, that reverse this trend for plates having clamped boundary conditions on the parallel ends such that an increase in the taper ratio causes a decrease in the buckling load. The clamped boundary conditions on the parallel ends of the plate are shown to increase the buckling load compared to simply supported boundary conditions. Also, anisotropy (the D16 and D26 terms) is shown to decrease the buckling load and skew the buckled mode shape for both the simply supported and clamped boundary conditions.

Structure-function analysis of the OB and latch domains of chlorella virus DNA ligase.

PubMed

Samai, Poulami; Shuman, Stewart

2011-06-24

Chlorella virus DNA ligase (ChVLig) is a minimized eukaryal ATP-dependent DNA sealing enzyme with an intrinsic nick-sensing function. ChVLig consists of three structural domains, nucleotidyltransferase (NTase), OB-fold, and latch, that envelop the nicked DNA as a C-shaped protein clamp. The OB domain engages the DNA minor groove on the face of the duplex behind the nick, and it makes contacts to amino acids in the NTase domain surrounding the ligase active site. The latch module occupies the DNA major groove flanking the nick. Residues at the tip of the latch contact the NTase domain to close the ligase clamp. Here we performed a structure-guided mutational analysis of the OB and latch domains. Alanine scanning defined seven individual amino acids as essential in vivo (Lys-274, Arg-285, Phe-286, and Val-288 in the OB domain; Asn-214, Phe-215, and Tyr-217 in the latch), after which structure-activity relations were clarified by conservative substitutions. Biochemical tests of the composite nick sealing reaction and of each of the three chemical steps of the ligation pathway highlighted the importance of Arg-285 and Phe-286 in the catalysis of the DNA adenylylation and phosphodiester synthesis reactions. Phe-286 interacts with the nick 5'-phosphate nucleotide and the 3'-OH base pair and distorts the DNA helical conformation at the nick. Arg-285 is a key component of the OB-NTase interface, where it forms a salt bridge to the essential Asp-29 side chain, which is imputed to coordinate divalent metal catalysts during the nick sealing steps.

A-Mating-Type Gene Expression Can Drive Clamp Formation in the Bipolar Mushroom Pholiota microspora (Pholiota nameko) ▿

PubMed Central

Yi, Ruirong; Mukaiyama, Hiroyuki; Tachikawa, Takashi; Shimomura, Norihiro; Aimi, Tadanori

2010-01-01

In the bipolar basidiomycete Pholiota microspora, a pair of homeodomain protein genes located at the A-mating-type locus regulates mating compatibility. In the present study, we used a DNA-mediated transformation system in P. microspora to investigate the homeodomain proteins that control the clamp formation. When a single homeodomain protein gene (A3-hox1 or A3-hox2) from the A3 monokaryon strain was transformed into the A4 monokaryon strain, the transformants produced many pseudoclamps but very few clamps. When two homeodomain protein genes (A3-hox1 and A3-hox2) were transformed either separately or together into the A4 monokaryon, the ratio of clamps to the clamplike cells in the transformants was significantly increased to ca. 50%. We therefore concluded that the gene dosage of homeodomain protein genes is important for clamp formation. When the sip promoter was connected to the coding region of A3-hox1 and A3-hox2 and the fused fragments were introduced into NGW19-6 (A4), the transformants achieved more than 85% clamp formation and exhibited two nuclei per cell, similar to the dikaryon (NGW12-163 × NGW19-6). The results of real-time reverse transcription-PCR confirmed that sip promoter activity is greater than that of the native promoter of homeodomain protein genes in P. microspora. Thus, we concluded that nearly 100% clamp formation requires high expression levels of homeodomain protein genes and that altered expression of the A-mating-type genes alone is sufficient to drive true clamp formation. PMID:20453073

Pressure vessel bottle mount

NASA Technical Reports Server (NTRS)

Wingett, Paul (Inventor)

2001-01-01

A mounting assembly for mounting a composite pressure vessel to a vehicle includes a saddle having a curved surface extending between two pillars for receiving the vessel. The saddle also has flanged portions which can be bolted to the vehicle. Each of the pillars has hole in which is mounted the shaft portion of an attachment member. A resilient member is disposed between each of the shaft portions and the holes and loaded by a tightening nut. External to the holes, each of the attachment members has a head portion to which a steel band is attached. The steel band circumscribes the vessel and translates the load on the springs into a clamping force on the vessel. As the vessel expands and contracts, the resilient members expand and contract so that the clamping force applied by the band to the vessel remains constant.

Force Generation in Single Conventional Actomyosin Complexes under High Dynamic Load

PubMed Central

Takagi, Yasuharu; Homsher, Earl E.; Goldman, Yale E.; Shuman, Henry

2006-01-01

The mechanical load borne by a molecular motor affects its force, sliding distance, and its rate of energy transduction. The control of ATPase activity by the mechanical load on a muscle tunes its efficiency to the immediate task, increasing ATP hydrolysis as the power output increases at forces less than isometric (the Fenn effect) and suppressing ATP hydrolysis when the force is greater than isometric. In this work, we used a novel ‘isometric’ optical clamp to study the mechanics of myosin II molecules to detect the reaction steps that depend on the dynamic properties of the load. An actin filament suspended between two beads and held in separate optical traps is brought close to a surface that is sparsely coated with motor proteins on pedestals of silica beads. A feedback system increases the effective stiffness of the actin by clamping the force on one of the beads and moving the other bead electrooptically. Forces measured during actomyosin interactions are increased at higher effective stiffness. The results indicate that single myosin molecules transduce energy nearly as efficiently as whole muscle and that the mechanical control of the ATP hydrolysis rate is in part exerted by reversal of the force-generating actomyosin transition under high load without net utilization of ATP. PMID:16326899

High-Precision Coupling Mechanism Operable By Robots

NASA Technical Reports Server (NTRS)

Voellmer, George

1992-01-01

Coupling mechanism has features making it easily operable by hand and suitable for operation by robots: tolerates some initial misalignment, imposes precise final alignment, and protects itself against overtightening. Typically used to mount equipment module on structure. Mechanism includes kinematic mounts, which tolerate small initial misalignment and enforce precise final alignment as two assemblies brought together. Clamping force applied to kinematic mounts via two flexible plates. Bolt and nut tightened on flexible plates to impose spring clamping load. Repeatability of interface tested and found to be better than forty-millionths of inch.

Atomistic Simulations of Complex DNA DSBs and the Interactions with Ku70/80 Heterodimer

NASA Technical Reports Server (NTRS)

Hu, Shaowen; Cucinotta, Francis A.

2011-01-01

Compared to DNA with simple DSBs, the complex lesions can enhance the hydrogen bonds opening rate at the DNA terminus, and increase the mobility of the whole duplex. Binding of Ku drastically reduces the structural disruption and flexibility caused by the complex lesions. In all complex DSBs systems, the binding of DSB terminus with Ku70 is softened while the binding of the middle duplex with Ku80 is tightened. Binding of Ku promotes the rigidity of DNA duplexes, due to the clamp structure of the inner surface of the rings of Ku70/80.

Piezoresistive cantilever force-clamp system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Sung-Jin; Petzold, Bryan C.; Pruitt, Beth L.

2011-04-15

We present a microelectromechanical device-based tool, namely, a force-clamp system that sets or ''clamps'' the scaled force and can apply designed loading profiles (e.g., constant, sinusoidal) of a desired magnitude. The system implements a piezoresistive cantilever as a force sensor and the built-in capacitive sensor of a piezoelectric actuator as a displacement sensor, such that sample indentation depth can be directly calculated from the force and displacement signals. A programmable real-time controller operating at 100 kHz feedback calculates the driving voltage of the actuator. The system has two distinct modes: a force-clamp mode that controls the force applied to amore » sample and a displacement-clamp mode that controls the moving distance of the actuator. We demonstrate that the system has a large dynamic range (sub-nN up to tens of {mu}N force and nm up to tens of {mu}m displacement) in both air and water, and excellent dynamic response (fast response time, <2 ms and large bandwidth, 1 Hz up to 1 kHz). In addition, the system has been specifically designed to be integrated with other instruments such as a microscope with patch-clamp electronics. We demonstrate the capabilities of the system by using it to calibrate the stiffness and sensitivity of an electrostatic actuator and to measure the mechanics of a living, freely moving Caenorhabditis elegans nematode.« less

Interaction of the Sliding Clamp β-Subunit and Hda, a DnaA-Related Protein

PubMed Central

Kurz, Mareike; Dalrymple, Brian; Wijffels, Gene; Kongsuwan, Kritaya

2004-01-01

In Escherichia coli, interactions between the replication initiation protein DnaA, the β subunit of DNA polymerase III (the sliding clamp protein), and Hda, the recently identified DnaA-related protein, are required to convert the active ATP-bound form of DnaA to an inactive ADP-bound form through the accelerated hydrolysis of ATP. This rapid hydrolysis of ATP is proposed to be the main mechanism that blocks multiple initiations during cell cycle and acts as a molecular switch from initiation to replication. However, the biochemical mechanism for this crucial step in DNA synthesis has not been resolved. Using purified Hda and β proteins in a plate binding assay and Ni-nitrilotriacetic acid pulldown analysis, we show for the first time that Hda directly interacts with β in vitro. A new β-binding motif, a hexapeptide with the consensus sequence QL[SP]LPL, related to the previously identified β-binding pentapeptide motif (QL[SD]LF) was found in the amino terminus of the Hda protein. Mutants of Hda with amino acid changes in the hexapeptide motif are severely defective in their ability to bind β. A 10-amino-acid peptide containing the E. coli Hda β-binding motif was shown to compete with Hda for binding to β in an Hda-β interaction assay. These results establish that the interaction of Hda with β is mediated through the hexapeptide sequence. We propose that this interaction may be crucial to the events that lead to the inactivation of DnaA and the prevention of excess initiation of rounds of replication. PMID:15150238

Interaction of the sliding clamp beta-subunit and Hda, a DnaA-related protein.

PubMed

Kurz, Mareike; Dalrymple, Brian; Wijffels, Gene; Kongsuwan, Kritaya

2004-06-01

In Escherichia coli, interactions between the replication initiation protein DnaA, the beta subunit of DNA polymerase III (the sliding clamp protein), and Hda, the recently identified DnaA-related protein, are required to convert the active ATP-bound form of DnaA to an inactive ADP-bound form through the accelerated hydrolysis of ATP. This rapid hydrolysis of ATP is proposed to be the main mechanism that blocks multiple initiations during cell cycle and acts as a molecular switch from initiation to replication. However, the biochemical mechanism for this crucial step in DNA synthesis has not been resolved. Using purified Hda and beta proteins in a plate binding assay and Ni-nitrilotriacetic acid pulldown analysis, we show for the first time that Hda directly interacts with beta in vitro. A new beta-binding motif, a hexapeptide with the consensus sequence QL[SP]LPL, related to the previously identified beta-binding pentapeptide motif (QL[SD]LF) was found in the amino terminus of the Hda protein. Mutants of Hda with amino acid changes in the hexapeptide motif are severely defective in their ability to bind beta. A 10-amino-acid peptide containing the E. coli Hda beta-binding motif was shown to compete with Hda for binding to beta in an Hda-beta interaction assay. These results establish that the interaction of Hda with beta is mediated through the hexapeptide sequence. We propose that this interaction may be crucial to the events that lead to the inactivation of DnaA and the prevention of excess initiation of rounds of replication.

A small protein inhibits proliferating cell nuclear antigen by breaking the DNA clamp

DOE PAGES

Altieri, Amanda S.; Ladner, Jane E.; Li, Zhuo; ...

2016-05-03

Here, proliferating cell nuclear antigen (PCNA) forms a trimeric ring that encircles duplex DNA and acts as an anchor for a number of proteins involved in DNA metabolic processes. PCNA has two structurally similar domains (I and II) linked by a long loop (inter-domain connector loop, IDCL) on the outside of each monomer of the trimeric structure that makes up the DNA clamp. All proteins that bind to PCNA do so via a PCNA-interacting peptide (PIP) motif that binds near the IDCL. A small protein, called TIP, binds to PCNA and inhibits PCNA-dependent activities although it does not contain amore » canonical PIP motif. The X-ray crystal structure of TIP bound to PCNA reveals that TIP binds to the canonical PIP interaction site, but also extends beyond it through a helix that relocates the IDCL. TIP alters the relationship between domains I and II within the PCNA monomer such that the trimeric ring structure is broken, while the individual domains largely retain their native structure. Small angle X-ray scattering (SAXS) confirms the disruption of the PCNA trimer upon addition of the TIP protein in solution and together with the X-ray crystal data, provides a structural basis for the mechanism of PCNA inhibition by TIP.« less

Improved Design Formulae for Buckling of Orthotropic Plates under Combined Loading

NASA Technical Reports Server (NTRS)

Weaver, Paul M.; Nemeth, Michael P.

2008-01-01

Simple, accurate buckling interaction formulae are presented for long orthotropic plates with either simply supported or clamped longitudinal edges and under combined loading that are suitable for design studies. The loads include 1) combined uniaxial compression (or tension) and shear, 2) combined pure inplane bending and 3) shear and combined uniaxial compression (or tension) and pure inplane bending. The interaction formulae are the results of detailed regression analysis of buckling data obtained from a very accurate Rayleigh-Ritz method.

Effect of Complete Syndesmotic Disruption and Deltoid Injuries and Different Reduction Methods on Ankle Joint Contact Mechanics.

PubMed

LaMothe, Jeremy; Baxter, Josh R; Gilbert, Susannah; Murphy, Conor I; Karnovsky, Sydney C; Drakos, Mark C

2017-06-01

Syndesmotic injuries can be associated with poor patient outcomes and posttraumatic ankle arthritis, particularly in the case of malreduction. However, ankle joint contact mechanics following a syndesmotic injury and reduction remains poorly understood. The purpose of this study was to characterize the effects of a syndesmotic injury and reduction techniques on ankle joint contact mechanics in a biomechanical model. Ten cadaveric whole lower leg specimens with undisturbed proximal tibiofibular joints were prepared and tested in this study. Contact area, contact force, and peak contact pressure were measured in the ankle joint during simulated standing in the intact, injured, and 3 reduction conditions: screw fixation with a clamp, screw fixation without a clamp (thumb technique), and a suture-button construct. Differences in these ankle contact parameters were detected between conditions using repeated-measures analysis of variance. Syndesmotic disruption decreased tibial plafond contact area and force. Syndesmotic reduction did not restore ankle loading mechanics to values measured in the intact condition. Reduction with the thumb technique was able to restore significantly more joint contact area and force than the reduction clamp or suture-button construct. Syndesmotic disruption decreased joint contact area and force. Although the thumb technique performed significantly better than the reduction clamp and suture-button construct, syndesmotic reduction did not restore contact mechanics to intact levels. Decreased contact area and force with disruption imply that other structures are likely receiving more loads (eg, medial and lateral gutters), which may have clinical implications such as the development of posttraumatic arthritis.

Electro-optic deflectors deliver advantages over acousto-optical deflectors in a high resolution, ultra-fast force-clamp optical trap.

PubMed

Woody, Michael S; Capitanio, Marco; Ostap, E Michael; Goldman, Yale E

2018-04-30

We characterized experimental artifacts arising from the non-linear response of acousto-optical deflectors (AODs) in an ultra-fast force-clamp optical trap and have shown that using electro-optical deflectors (EODs) instead eliminates these artifacts. We give an example of the effects of these artifacts in our ultra-fast force clamp studies of the interaction of myosin with actin filaments. The experimental setup, based on the concept of Capitanio et al. [Nat. Methods 9, 1013-1019 (2012)] utilizes a bead-actin-bead dumbbell held in two force-clamped optical traps which apply a load to the dumbbell to move it at a constant velocity. When myosin binds to actin, the filament motion stops quickly as the total force from the optical traps is transferred to the actomyosin attachment. We found that in our setup, AODs were unsuitable for beam steering due to non-linear variations in beam intensity and deflection angle as a function of driving frequency, likely caused by low-amplitude standing acoustic waves in the deflectors. These aberrations caused instability in the force feedback loops leading to artifactual jumps in the trap position. We demonstrate that beam steering with EODs improves the performance of our instrument. Combining the superior beam-steering capability of the EODs, force acquisition via back-focal-plane interferometry, and dual high-speed FPGA-based feedback loops, we apply precise and constant loads to study the dynamics of interactions between actin and myosin. The same concept applies to studies of other biomolecular interactions.

Structure-Function Analysis of the OB and Latch Domains of Chlorella Virus DNA Ligase*

PubMed Central

Samai, Poulami; Shuman, Stewart

2011-01-01

Chlorella virus DNA ligase (ChVLig) is a minimized eukaryal ATP-dependent DNA sealing enzyme with an intrinsic nick-sensing function. ChVLig consists of three structural domains, nucleotidyltransferase (NTase), OB-fold, and latch, that envelop the nicked DNA as a C-shaped protein clamp. The OB domain engages the DNA minor groove on the face of the duplex behind the nick, and it makes contacts to amino acids in the NTase domain surrounding the ligase active site. The latch module occupies the DNA major groove flanking the nick. Residues at the tip of the latch contact the NTase domain to close the ligase clamp. Here we performed a structure-guided mutational analysis of the OB and latch domains. Alanine scanning defined seven individual amino acids as essential in vivo (Lys-274, Arg-285, Phe-286, and Val-288 in the OB domain; Asn-214, Phe-215, and Tyr-217 in the latch), after which structure-activity relations were clarified by conservative substitutions. Biochemical tests of the composite nick sealing reaction and of each of the three chemical steps of the ligation pathway highlighted the importance of Arg-285 and Phe-286 in the catalysis of the DNA adenylylation and phosphodiester synthesis reactions. Phe-286 interacts with the nick 5′-phosphate nucleotide and the 3′-OH base pair and distorts the DNA helical conformation at the nick. Arg-285 is a key component of the OB-NTase interface, where it forms a salt bridge to the essential Asp-29 side chain, which is imputed to coordinate divalent metal catalysts during the nick sealing steps. PMID:21527793

Structural Crashworthiness and Failure

DTIC Science & Technology

1993-04-16

body motion occurs. This rigid -plastic idealization for dynamically loaded structures is based upon the fact that the plastic deformation of a...in general, for any tensor variable x, i represents the convective derivative. It should be noted that the rigid body rotation is included in the...clamped, impulsively loaded, rigid - plastic beam.’ (a) First phase of motion with stationary transverse plastic hinges at A and E and stationary plastic

Analysis of Cantilever-Beam Bending Stress Relaxation Properties of Thin Wood Composites

Treesearch

John F. Hunt; Houjiang Zhang; Yan Huang

2015-01-01

An equivalent strain method was used to analyze and determine material relaxation properties for specimens from particleboard, high density fiberboard, and medium density fiberboard. Cantilever beams were clamped and then deflected to 11 m and held for either 2 h or 3 h, while the load to maintain that deflection was measured vs. time. Plots of load relaxation for each...

Temperature-Controlled Clamping and Releasing Mechanism

NASA Technical Reports Server (NTRS)

Rosing, David; Ford, Virginia

2005-01-01

A report describes the development of a mechanism that automatically clamps upon warming and releases upon cooling between temperature limits of approx. =180 K and approx. =293 K. The mechanism satisfied a need specific to a program that involved repeated excursions of a spectrometer between a room-temperature atmospheric environment and a cryogenic vacuum testing environment. The mechanism was also to be utilized in the intended application of the spectrometer, in which the spectrometer would be clamped for protection during launch of a spacecraft and released in the cold of outer space to allow it to assume its nominal configuration for scientific observations. The mechanism is passive in the sense that its operation does not depend on a control system and does not require any power other than that incidental to heating and cooling. The clamping and releasing action is effected by bolt-preloaded stacks of shape-memory-alloy (SMA) cylinders. In designing this mechanism, as in designing other, similar SMA mechanisms, it was necessary to account for the complex interplay among thermal expansion, elastic and inelastic deformation under load, and SMA thermomechanical properties.

Experimental transient and permanent deformation studies of steel-sphere-impacted or impulsively-loaded aluminum beams with clamped ends

NASA Technical Reports Server (NTRS)

Witmer, E. A.

1975-01-01

The sheet explosive loading technique (SELT) was employed to obtain elastic-plastic, large-deflection transient and/or permanent strain data on simple well-defined structural specimens and materials: initially-flat 6061-T651 aluminum beams with both ends ideally clamped via integral construction. The SELT loading technique was chosen since it is both convenient and provides forcing function information of small uncertainty. These data will be useful for evaluating pertinent structural response prediction methods. A second objective was to obtain high-quality transient-strain data for a well-defined structural/material model subjected to impact by a rigid body of known mass, impact velocity, and geometry; large-deflection, elastic-plastic transient response conditions are of primary interest. The beam with both ends clamped and a steel sphere as the impacting body were chosen. The steel sphere was launched vertically by explosive propulsion to achieve various desired impact velocities. The sphere/beam impact tests resulted in producing a wide range of structural responses and permanent deformations, including rupture of the beam from excessive structural response in two cases. The transient and permanent strain data as well as the permanent deflection data obtained are of high quality and should be useful for checking and evaluating methods for predicting the responses of simple 2-d structures to fragment (sphere) impact. Transient strain data very close to the point of impact were not obtained over as long a time as desirable because the gage(s) in that region became detached during the transient response.

A 3 kbar hydrogen-compatible gas loader for Paris-Edinburgh presses

NASA Astrophysics Data System (ADS)

Klotz, S.; Philippe, J.; Bull, C. L.; Loveday, J. S.; Nelmes, R. J.

2013-03-01

We present a device which allows compressed gases to be loaded into large volume opposed anvils used for high pressure neutron scattering in the multi-10 GPa range. The gases are initially loaded into clamps which can then be inserted into VX-Paris-Edinburgh load frames. The system is compatible with all inert gases as well as hydrogen and permits loading pressures of up to 3 kbar for which most gases have densities close to that of the liquid at ambient pressure. The device should have applications for the study of simple molecular solids as well as for loading gases as pressure-transmitting media.

Structure-Based Virtual Ligand Screening on the XRCC4/DNA Ligase IV Interface

NASA Astrophysics Data System (ADS)

Menchon, Grégory; Bombarde, Oriane; Trivedi, Mansi; Négrel, Aurélie; Inard, Cyril; Giudetti, Brigitte; Baltas, Michel; Milon, Alain; Modesti, Mauro; Czaplicki, Georges; Calsou, Patrick

2016-03-01

The association of DNA Ligase IV (Lig4) with XRCC4 is essential for repair of DNA double-strand breaks (DSBs) by Non-homologous end-joining (NHEJ) in humans. DSBs cytotoxicity is largely exploited in anticancer therapy. Thus, NHEJ is an attractive target for strategies aimed at increasing the sensitivity of tumors to clastogenic anticancer treatments. However the high affinity of the XRCC4/Lig4 interaction and the extended protein-protein interface make drug screening on this target particularly challenging. Here, we conducted a pioneering study aimed at interfering with XRCC4/Lig4 assembly. By Molecular Dynamics simulation using the crystal structure of the complex, we first delineated the Lig4 clamp domain as a limited suitable target. Then, we performed in silico screening of ~95,000 filtered molecules on this Lig4 subdomain. Hits were evaluated by Differential Scanning Fluorimetry, Saturation Transfer Difference - NMR spectroscopy and interaction assays with purified recombinant proteins. In this way we identified the first molecule able to prevent Lig4 binding to XRCC4 in vitro. This compound has a unique tripartite interaction with the Lig4 clamp domain that suggests a starting chemotype for rational design of analogous molecules with improved affinity.

29 CFR Appendix V to Part 1918 - Basic Elements of a First Aid Training Program (Non-mandatory)

Code of Federal Regulations, 2010 CFR

2010-07-01

...) Repairs .62(h)(4) Safe Working Load .62(h)(1) Shortened .62(h)(6) Chutes .63(a), (b), (c), (d) Clamps...) Certification .11 Coaming Rollers .52(e) Falls .52(c) Heel Blocks .52(d) Preventers .52(a), .54(d) Safe Working...)). Shackles: Safe Working Loads .62(i)(1) Used Aloft .62(i)(2) Other Decks .34 Slippery Conditions .91(b...

From the elastica compass to the elastica catapult: an essay on the mechanics of soft robot arm

PubMed Central

Armanini, C.; Dal Corso, F.; Misseroni, D.

2017-01-01

An elastic rod is clamped at one end and has a dead load attached to the other (free) end. The rod is then slowly rotated using the clamp. When the load is smaller than the buckling value, the rod describes a continuous set of quasi-static forms and its end traces a (smooth, convex and simple) closed curve, which would be a circle if the rod were rigid. The closed curve is analytically determined through the integration of the Euler’s elastica, so that for sufficiently small loads the mechanical system behaves as an ‘elastica compass’. For loads higher than that of buckling, the elastica reaches a configuration from which a snap-back instability occurs, realizing a sort of ‘elastica catapult’. The whole quasi-static evolution leading to the critical configuration for snapping is calculated through the elastica and the subsequent dynamic motion simulated using two numerical procedures, one ad hoc developed and another based on a finite-element scheme. The theoretical results are then validated on a specially designed and built apparatus. An obvious application of the present model would be in the development of soft robotic limbs, but the results are also of interest for the optimization analysis in pole vaulting. PMID:28293144

From the elastica compass to the elastica catapult: an essay on the mechanics of soft robot arm.

PubMed

Armanini, C; Dal Corso, F; Misseroni, D; Bigoni, D

2017-02-01

An elastic rod is clamped at one end and has a dead load attached to the other (free) end. The rod is then slowly rotated using the clamp. When the load is smaller than the buckling value, the rod describes a continuous set of quasi-static forms and its end traces a (smooth, convex and simple) closed curve, which would be a circle if the rod were rigid. The closed curve is analytically determined through the integration of the Euler's elastica, so that for sufficiently small loads the mechanical system behaves as an 'elastica compass'. For loads higher than that of buckling, the elastica reaches a configuration from which a snap-back instability occurs, realizing a sort of 'elastica catapult'. The whole quasi-static evolution leading to the critical configuration for snapping is calculated through the elastica and the subsequent dynamic motion simulated using two numerical procedures, one ad hoc developed and another based on a finite-element scheme. The theoretical results are then validated on a specially designed and built apparatus. An obvious application of the present model would be in the development of soft robotic limbs, but the results are also of interest for the optimization analysis in pole vaulting.

Spatial buckling analysis of current-carrying nanowires in the presence of a longitudinal magnetic field accounting for both surface and nonlocal effects

NASA Astrophysics Data System (ADS)

Foroutan, Shahin; Haghshenas, Amin; Hashemian, Mohammad; Eftekhari, S. Ali; Toghraie, Davood

2018-03-01

In this paper, three-dimensional buckling behavior of nanowires was investigated based on Eringen's Nonlocal Elasticity Theory. The electric current-carrying nanowires were affected by a longitudinal magnetic field based upon the Lorentz force. The nanowires (NWs) were modeled based on Timoshenko beam theory and the Gurtin-Murdoch's surface elasticity theory. Generalized Differential Quadrature (GDQ) method was used to solve the governing equations of the NWs. Two sets of boundary conditions namely simple-simple and clamped-clamped were applied and the obtained results were discussed. Results demonstrated the effect of electric current, magnetic field, small-scale parameter, slenderness ratio, and nanowires diameter on the critical compressive buckling load of nanowires. As a key result, increasing the small-scale parameter decreased the critical load. By the same token, increasing the electric current, magnetic field, and slenderness ratio resulted in a decrease in the critical load. As the slenderness ratio increased, the effect of nonlocal theory decreased. In contrast, by expanding the NWs diameter, the nonlocal effect increased. Moreover, in the present article, the critical values of the magnetic field of strength and slenderness ratio were revealed, and the roles of the magnetic field, slenderness ratio, and NWs diameter on higher buckling loads were discussed.

Structure-guided Mutational Analysis of the OB, HhH, and BRCT Domains of Escherichia coli DNA Ligase*S⃞

PubMed Central

Wang, Li Kai; Nair, Pravin A.; Shuman, Stewart

2008-01-01

NAD+-dependent DNA ligases (LigAs) are ubiquitous in bacteria and essential for growth. LigA enzymes have a modular structure in which a central catalytic core composed of nucleotidyltransferase and oligonucleotide-binding (OB) domains is linked via a tetracysteine zinc finger to distal helix-hairpin-helix (HhH) and BRCT (BRCA1-like C-terminal) domains. The OB and HhH domains contribute prominently to the protein clamp formed by LigA around nicked duplex DNA. Here we conducted a structure-function analysis of the OB and HhH domains of Escherichia coli LigA by alanine scanning and conservative substitutions, entailing 43 mutations at 22 amino acids. We thereby identified essential functional groups in the OB domain that engage the DNA phosphodiester backbone flanking the nick (Arg333); penetrate the minor grove and distort the nick (Val383 and Ile384); or stabilize the OB fold (Arg379). The essential constituents of the HhH domain include: four glycines (Gly455, Gly489, Gly521, Gly553), which bind the phosphate backbone across the minor groove at the outer margins of the LigA-DNA interface; Arg487, which penetrates the minor groove at the outer margin on the 3 ®-OH side of the nick; and Arg446, which promotes protein clamp formation via contacts to the nucleotidyltransferase domain. We find that the BRCT domain is required in its entirety for effective nick sealing and AMP-dependent supercoil relaxation. PMID:18515356

Structure-guided mutational analysis of the OB, HhH, and BRCT domains of Escherichia coli DNA ligase.

PubMed

Wang, Li Kai; Nair, Pravin A; Shuman, Stewart

2008-08-22

NAD(+)-dependent DNA ligases (LigAs) are ubiquitous in bacteria and essential for growth. LigA enzymes have a modular structure in which a central catalytic core composed of nucleotidyltransferase and oligonucleotide-binding (OB) domains is linked via a tetracysteine zinc finger to distal helix-hairpin-helix (HhH) and BRCT (BRCA1-like C-terminal) domains. The OB and HhH domains contribute prominently to the protein clamp formed by LigA around nicked duplex DNA. Here we conducted a structure-function analysis of the OB and HhH domains of Escherichia coli LigA by alanine scanning and conservative substitutions, entailing 43 mutations at 22 amino acids. We thereby identified essential functional groups in the OB domain that engage the DNA phosphodiester backbone flanking the nick (Arg(333)); penetrate the minor grove and distort the nick (Val(383) and Ile(384)); or stabilize the OB fold (Arg(379)). The essential constituents of the HhH domain include: four glycines (Gly(455), Gly(489), Gly(521), Gly(553)), which bind the phosphate backbone across the minor groove at the outer margins of the LigA-DNA interface; Arg(487), which penetrates the minor groove at the outer margin on the 3 (R)-OH side of the nick; and Arg(446), which promotes protein clamp formation via contacts to the nucleotidyltransferase domain. We find that the BRCT domain is required in its entirety for effective nick sealing and AMP-dependent supercoil relaxation.

Artificial limb connection

NASA Technical Reports Server (NTRS)

Owens, L. J.

1974-01-01

Connection simplifies and eases donning and removing artificial limb; eliminates harnesses and clamps; and reduces skin pressures by allowing bone to carry all tensile and part of compressive loads between prosthesis and stump. Because connection is modular, it is easily modified to suit individual needs.

Structure and Biochemical Activities of Escherichia coli MgsA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Page, Asher N.; George, Nicholas P.; Marceau, Aimee H.

2012-02-27

Bacterial 'maintenance of genome stability protein A' (MgsA) and related eukaryotic enzymes play important roles in cellular responses to stalled DNA replication processes. Sequence information identifies MgsA enzymes as members of the clamp loader clade of AAA{sup +} proteins, but structural information defining the family has been limited. Here, the x-ray crystal structure of Escherichia coli MgsA is described, revealing a homotetrameric arrangement for the protein that distinguishes it from other clamp loader clade AAA{sup +} proteins. Each MgsA protomer is composed of three elements as follows: ATP-binding and helical lid domains (conserved among AAA{sup +} proteins) and a tetramerizationmore » domain. Although the tetramerization domains bury the greatest amount of surface area in the MgsA oligomer, each of the domains participates in oligomerization to form a highly intertwined quaternary structure. Phosphate is bound at each AAA{sup +} ATP-binding site, but the active sites do not appear to be in a catalytically competent conformation due to displacement of Arg finger residues. E. coli MgsA is also shown to form a complex with the single-stranded DNA-binding protein through co-purification and biochemical studies. MgsA DNA-dependent ATPase activity is inhibited by single-stranded DNA-binding protein. Together, these structural and biochemical observations provide insights into the mechanisms of MgsA family AAA{sup +} proteins.« less

Structure and Biochemical Activities of Escherichia coli MgsA*♦

PubMed Central

Page, Asher N.; George, Nicholas P.; Marceau, Aimee H.; Cox, Michael M.; Keck, James L.

2011-01-01

Bacterial “maintenance of genome stability protein A” (MgsA) and related eukaryotic enzymes play important roles in cellular responses to stalled DNA replication processes. Sequence information identifies MgsA enzymes as members of the clamp loader clade of AAA+ proteins, but structural information defining the family has been limited. Here, the x-ray crystal structure of Escherichia coli MgsA is described, revealing a homotetrameric arrangement for the protein that distinguishes it from other clamp loader clade AAA+ proteins. Each MgsA protomer is composed of three elements as follows: ATP-binding and helical lid domains (conserved among AAA+ proteins) and a tetramerization domain. Although the tetramerization domains bury the greatest amount of surface area in the MgsA oligomer, each of the domains participates in oligomerization to form a highly intertwined quaternary structure. Phosphate is bound at each AAA+ ATP-binding site, but the active sites do not appear to be in a catalytically competent conformation due to displacement of Arg finger residues. E. coli MgsA is also shown to form a complex with the single-stranded DNA-binding protein through co-purification and biochemical studies. MgsA DNA-dependent ATPase activity is inhibited by single-stranded DNA-binding protein. Together, these structural and biochemical observations provide insights into the mechanisms of MgsA family AAA+ proteins. PMID:21297161

Discrimination of Single Base Pair Differences Among Individual DNA Molecules Using a Nanopore

NASA Technical Reports Server (NTRS)

Vercoutere, Wenonah; DeGuzman, Veronica

2003-01-01

The protein toxin alpha-hemolysin form nanometer scale channels across lipid membranes. Our lab uses a single channel in an artificial lipid bilayer in a patch clamp device to capture and examine individual DNA molecules. This nanopore detector used with a support vector machine (SVM) can analyze DNA hairpin molecules on the millisecond time scale. We distinguish duplex stem length, base pair mismatches, loop length, and single base pair differences. The residual current fluxes also reveal structural molecular dynamics elements. DNA end-fraying (terminal base pair dissociation) can be observed as near full blockades, or spikes, in current. This technique can be used to investigate other biological processes dependent on DNA end-fraying, such as the processing of HIV DNA by HIV integrase.

Experimental and Numerical Analysis of Axially Compressed Circular Cylindrical Fiber-Reinforced Panels with Various Boundary Conditions.

DTIC Science & Technology

1981-10-01

Numerical predictions used in the compari- sons were obtained from the energy -based, finite-difference computer proqram CLAPP. Test specimens were clamped...edges V LONGITUDINAL STIFFENERS 45 I. Introduction 45 2. Stiffener Strain Energy 46 3. Stiffener Energy in Matrix Form 47 4. Displacement Continuity 49...that theoretical bifurcation loads predicted by the energy method represent upper bounds to the classical bifurcation loads associated with the test

Inflatable Launch and Recovery System

DTIC Science & Technology

2014-07-31

clamping fixture connects the ramp structure to the vessel. A snubber element dampens vibrations and transient tow loads. Unclassified Unclassified...integrated dynamic snubber element to dampen out vibrations and transient tow loads. The main air fill line from the handling system to the inflatable ramp...of the vessel A with standard container cam locks 12a (two of which are shown in phantom in FIG. 1). The system 10 can connect to a vessel power

Development of Torsional and Linear Piezoelectrically Driven Motors

NASA Technical Reports Server (NTRS)

Duong, Khanh; Newton, David; Garcia, Ephrahim

1996-01-01

The development of rotary and linear inchworm-motors using piezoelectric actuators is presented. The motors' design has the advantage of a macro and micro stepper motor with high load and speed. The torsional design is capable of fast angular positioning with micro level accuracy. Additionally, the rotary motor, as designed, can be used as a clutch/brake mechanism. Constructed prototype motors of both types along with their characteristics are presented. The torsional motor consists of a torsional section that provides angular displacement and torque, and two alternating clamping sections which provide the holding force. The motor relies on the principal piezoelectric coupling coefficient (d33) with no torsional elements, increasing its torque capability. The linear motor consists of a longitudinal vibrator that provides displacement and load, and two alternating clamping sections which provide the holding force. This design eliminates bending moment, tension and shear applied to the actuator elements, increase its load capability and life. Innovative flexure designs have been introduced for both motor types. Critical issues that affect the design and performance of the motors are explored and discussed. Experiments are performed demonstrating the motor prototypes based on the aforementioned design considerations.

Piezoresistive cantilever force-clamp system

PubMed Central

Park, Sung-Jin; Petzold, Bryan C.; Goodman, Miriam B.; Pruitt, Beth L.

2011-01-01

We present a microelectromechanical device-based tool, namely, a force-clamp system that sets or “clamps” the scaled force and can apply designed loading profiles (e.g., constant, sinusoidal) of a desired magnitude. The system implements a piezoresistive cantilever as a force sensor and the built-in capacitive sensor of a piezoelectric actuator as a displacement sensor, such that sample indentation depth can be directly calculated from the force and displacement signals. A programmable real-time controller operating at 100 kHz feedback calculates the driving voltage of the actuator. The system has two distinct modes: a force-clamp mode that controls the force applied to a sample and a displacement-clamp mode that controls the moving distance of the actuator. We demonstrate that the system has a large dynamic range (sub-nN up to tens of μN force and nm up to tens of μm displacement) in both air and water, and excellent dynamic response (fast response time, <2 ms and large bandwidth, 1 Hz up to 1 kHz). In addition, the system has been specifically designed to be integrated with other instruments such as a microscope with patch-clamp electronics. We demonstrate the capabilities of the system by using it to calibrate the stiffness and sensitivity of an electrostatic actuator and to measure the mechanics of a living, freely moving Caenorhabditis elegans nematode. PMID:21529009

Nanopore Logic Operation with DNA to RNA Transcription in a Droplet System.

PubMed

Ohara, Masayuki; Takinoue, Masahiro; Kawano, Ryuji

2017-07-21

This paper describes an AND logic operation with amplification and transcription from DNA to RNA, using T7 RNA polymerase. All four operations, (0 0) to (1 1), with an enzyme reaction can be performed simultaneously, using four-droplet devices that are directly connected to a patch-clamp amplifier. The output RNA molecule is detected using a biological nanopore with single-molecule translocation. Channel current recordings can be obtained using the enzyme solution. The integration of DNA logic gates into electrochemical devices is necessary to obtain output information in a human-recognizable form. Our method will be useful for rapid and confined DNA computing applications, including the development of programmable diagnostic devices.

Satisloh centering technology developments past to present

NASA Astrophysics Data System (ADS)

Leitz, Ernst Michael; Moos, Steffen

2015-10-01

The centering of an optical lens is the grinding of its edge profile or contour in relationship to its optical axis. This is required to ensure that the lens vertex and radial centers are accurately positioned within an optical system. Centering influences the imaging performance and contrast of an optical system. Historically, lens centering has been a purely manual process. Along its 62 years of assembling centering machines, Satisloh introduced several technological milestones to improve the accuracy and quality of this process. During this time more than 2.500 centering machines were assembled. The development went from bell clamping and diamond grinding to Laser alignment, exchange chuckor -spindle systems, to multi axis CNC machines with integrated metrology and automatic loading systems. With the new centering machine C300, several improvements for the clamping and grinding process were introduced. These improvements include a user friendly software to support the operator, a coolant manifold and "force grinding" technology to ensure excellent grinding quality and process stability. They also include an air bearing directly driven centering spindle to provide a large working range of lenses made of all optical materials and diameters from below 10 mm to 300 mm. The clamping force can be programmed between 7 N and 1200 N to safely center lenses made of delicate materials. The smaller C50 centering machine for lenses below 50 mm diameter is available with an optional CNC loading system for automated production.

Characterization of human translesion DNA synthesis across a UV-induced DNA lesion

PubMed Central

Hedglin, Mark; Pandey, Binod; Benkovic, Stephen J

2016-01-01

Translesion DNA synthesis (TLS) during S-phase uses specialized TLS DNA polymerases to replicate a DNA lesion, allowing stringent DNA synthesis to resume beyond the offending damage. Human TLS involves the conjugation of ubiquitin to PCNA clamps encircling damaged DNA and the role of this post-translational modification is under scrutiny. A widely-accepted model purports that ubiquitinated PCNA recruits TLS polymerases such as pol η to sites of DNA damage where they may also displace a blocked replicative polymerase. We provide extensive quantitative evidence that the binding of pol η to PCNA and the ensuing TLS are both independent of PCNA ubiquitination. Rather, the unique properties of pols η and δ are attuned to promote an efficient and passive exchange of polymerases during TLS on the lagging strand. DOI: http://dx.doi.org/10.7554/eLife.19788.001 PMID:27770570

The Impact Response of Carbon/Epoxy Laminates (Center Director's Discretionary Fund, Project No. 94-13)

NASA Technical Reports Server (NTRS)

Nettles, A. T.; Hodge, A. J.

1997-01-01

Low velocity dropweight impact tests were conducted on carbon/epoxy laminates under various boundary conditions. The composite plates were 8-ply (+45,0,-45,90)s laminates supported in a clamped-clamped/free-free configuration with varying amounts of in-plane load, N(sub x), applied. Specimens were impacted at energies of 3.4, 4.5, and 6 Joules (2.5, 3.3, and 4.4 ft-lb). The amount of damage induced into the specimen was evaluated using instrumented impact techniques, x-ray inspection, and cross-sectional photomicroscopy. Some static identation tests were performed to examine if the impact events utilized in this study were of a quasi-static nature and also to gain insight into the shape of the deflected surface at various impact load combinations. Load-displacement curves from these tests were compared to those of the impact tests, as was damage determined from x-ray inspection. The finite element technique was used to model the impact event and determine the stress field within the laminae. Results showed that for a given impact energy level, more damage was induced into the specimen as the external in-plane load, N(sub x), was increased. The majority of damage observed consisted of back face splitting of the matrix parallel to the fibers in that ply, associated with delaminations emanating from these splits. The analysis showed qualitatively the results of impact conditions on maximum load of impact, maximum transverse deflection, and first failure mode and location.

Autonomous generation and loading of DNA guides by bacterial Argonaute

PubMed Central

Chandradoss, Stanley D.; Zhu, Yifan; Timmers, Elizabeth M.; Zhang, Yong; Zhao, Hongtu; Lou, Jizhong; Wang, Yanli; Joo, Chirlmin; van der Oost, John

2018-01-01

Summary Several prokaryotic Argonaute proteins (pAgos) utilize small DNA guides to mediate host defense by targeting invading DNA complementary to the DNA guide. It is unknown how these DNA guides are being generated and loaded onto pAgo. Here we demonstrate that guide-free Argonaute from Thermus thermophilus (TtAgo) can degrade dsDNA, thereby generating small dsDNA fragments that subsequently are loaded onto TtAgo. Combining single-molecule fluorescence, molecular dynamic simulations and structural studies, we show that TtAgo loads dsDNA molecules with a preference towards a deoxyguanosine on the passenger strand at the position opposite to the 5’-end of the guide strand. This explains why in vivo TtAgo is preferentially loaded with guides with a 5’-end deoxycytidine. Our data demonstrate that TtAgo can independently generate and selectively load functional DNA guides. PMID:28262506

A new Sparassis species from Spain described using morphological and molecular data.

PubMed

Blanco-Dios, Jaime B; Wang, Zheng; Binder, Manfred; Hibbett, David S

2006-10-01

Sparassis miniensis, collected in Pinus pinaster forests in Galicia (northwest Iberian Peninsula) is described as a new species, based on morphological and molecular data. Sparassis miniensis is morphologically distinct from all other species in the genus Sparassis based on scattered flabellae, which are strongly laciniated, azonate, and arise from an orange to rose-purplish base. The sporadic presence of clamp connections is restricted to subhymenial hyphae. Molecular data from LSU-rDNA, ITS and partial gene coding RNA polymerase subunit II (rpb2) suggest a close relationship between the new species S. miniensis and S. brevipes, another European species producing large fruiting bodies but with entire flabellae and no clamp connections.

Serrated kiln sticks and top load substantially reduce warp in southern pine studs dried at 240°F

Treesearch

Peter Koch

1974-01-01

Sharply toothed aluminum kiln sticks pressed into 2 by 4's cut from veneer cores, with a clamping force of 50 to 200 pounds per stick-pair per stud, significantly reduced warp from that observed in matched studs stacked on smooth sticks with a top load of 10 pounds per stick-pair per stud. When dried in 24 hours to an average MC of 8.1 percent (standard deviation...

Serrated kiln sticks and top load substantially reduce warp in southern pine studs dried at 240°F

Treesearch

P. Koch

1974-01-01

Sharply toothed luminum kiln sticks pressed into 2 by 4's cut from veneer cores, willi a clamping force of 50 to 200 pounds per stick-pair per stud, significantly reduced warp from that observed in matched studs stacked on smooth sticks with a top load of 10 pounds per stick-pair per stud. When dried in 24 hours to an average MC of 8.1 percent (standard deviation...

Tubing cutter for tight spaces

NASA Technical Reports Server (NTRS)

Girala, A. S.

1980-01-01

Cutter requires few short swings of handle to rotate its cutting edge full 360 around tube. It will cut tubing installed in confined space that prevents free movement of conventional cutter. Cutter is snapped onto tube and held in place by spring-loaded clamp. Screw ratchet advances cutting wheel.

Roles of the checkpoint sensor clamp Rad9-Rad1-Hus1 (911)-complex and the clamp loaders Rad17-RFC and Ctf18-RFC in Schizosaccharomyces pombe telomere maintenance.

PubMed

Khair, Lyne; Chang, Ya-Ting; Subramanian, Lakxmi; Russell, Paul; Nakamura, Toru M

2010-06-01

While telomeres must provide mechanisms to prevent DNA repair and DNA damage checkpoint factors from fusing chromosome ends and causing permanent cell cycle arrest, these factors associate with functional telomeres and play critical roles in the maintenance of telomeres. Previous studies have established that Tel1 (ATM) and Rad3 (ATR) kinases play redundant but essential roles for telomere maintenance in fission yeast. In addition, the Rad9-Rad1-Hus1 (911) and Rad17-RFC complexes work downstream of Rad3 (ATR) in fission yeast telomere maintenance. Here, we investigated how 911, Rad17-RFC and another RFC-like complex Ctf18-RFC contribute to telomere maintenance in fission yeast cells lacking Tel1 and carrying a novel hypomorphic allele of rad3 (DBD-rad3), generated by the fusion between the DNA binding domain (DBD) of the fission yeast telomere capping protein Pot1 and Rad3. Our investigations have uncovered a surprising redundancy for Rad9 and Hus1 in allowing Rad1 to contribute to telomere maintenance in DBD-rad3 tel1 cells. In addition, we found that Rad17-RFC and Ctf18-RFC carry out redundant telomere maintenance functions in DBD-rad3 tel1 cells. Since checkpoint sensor proteins are highly conserved, genetic redundancies uncovered here may be relevant to telomere maintenance and detection of DNA damage in other eukaryotes.

Roles of the Checkpoint Sensor Clamp Rad9-Rad1-Hus1 (911)-Complex and the Clamp Loaders Rad17-RFC and Ctf18-RFC in Schizosaccharomyces pombe Telomere Maintenance

PubMed Central

Khair, Lyne; Chang, Ya-Ting; Subramanian, Lakxmi; Russell, Paul; Nakamura, Toru M.

2011-01-01

While telomeres must provide mechanisms to prevent DNA repair and DNA damage checkpoint factors from fusing chromosome ends and causing permanent cell cycle arrest, these factors associate with functional telomeres and play critical roles in the maintenance of telomeres. Previous studies have established that Tel1 (ATM) and Rad3 (ATR) kinases play redundant but essential roles for telomere maintenance in fission yeast. In addition, the Rad9-Rad1-Hus1 (911) and Rad17-RFC complexes work downstream of Rad3 (ATR) in fission yeast telomere maintenance. Here, we investigated how 911, Rad17-RFC and another RFC-like complex Ctf18-RFC contribute to telomere maintenance in fission yeast cells lacking Tel1 and carrying a novel hypomorphic allele of rad3 (DBD-rad3), generated by the fusion between the DNA binding domain (DBD) of the fission yeast telomere capping protein Pot1 and Rad3. Our investigations have uncovered a surprising redundancy for Rad9 and Hus1 in allowing Rad1 to contribute to telomere maintenance in DBD-rad3 tel1Δ cells. In addition, we found that Rad17-RFC and Ctf18-RFC carry out redundant telomere maintenance functions in DBD-rad3 tel1Δ cells. Since checkpoint sensor proteins are highly conserved, genetic redundancies uncovered here may be relevant to telomere maintenance and detection of DNA damage in other eukaryotes. PMID:20505337

Last stop on the road to repair: structure of E. coli DNA ligase bound to nicked DNA-adenylate.

PubMed

Nandakumar, Jayakrishnan; Nair, Pravin A; Shuman, Stewart

2007-04-27

NAD(+)-dependent DNA ligases (LigA) are ubiquitous in bacteria and essential for growth. Their distinctive substrate specificity and domain organization vis-a-vis human ATP-dependent ligases make them outstanding targets for anti-infective drug discovery. We report here the 2.3 A crystal structure of Escherichia coli LigA bound to an adenylylated nick, which captures LigA in a state poised for strand closure and reveals the basis for nick recognition. LigA envelopes the DNA within a protein clamp. Large protein domain movements and remodeling of the active site orchestrate progression through the three chemical steps of the ligation reaction. The structure inspires a strategy for inhibitor design.

Plug-in connector socket accepts coaxial cable end

NASA Technical Reports Server (NTRS)

Mitchell, D.; Van Loon, J.

1966-01-01

Connector which includes a spring-loaded contact to receive a protruding center conductor and an internal collet to clamp against a collar attached to a woven outer conductor, is used as a receptacle for the end of a coaxial cable. This plug-in connector socket is used successfully with remote manipulators.

Elastoviscoplastic snap-through behavior of shallow arches subjected to thermomechanical loads

NASA Technical Reports Server (NTRS)

Simitses, George J.; Song, Yuzhao; Sheinman, Izhak

1991-01-01

The problem of snap-through buckling of clamped shallow arches under thermomechanical loads is investigated. The analysis is based on nonlinear kinematic relations and nonlinear rate-dependent unified constitutive equations. A finite element approach is employed to predict the, in general, inelastic buckling behavior. The construction material is alloy B1900 + Hf, which is commonly utilized in high-temperature environments. The effect of several parameters is assessed. These parameters include the rise parameter and temperature. Comparison between elastic and elastoviscoplastic responses is also presented.

Experimental transient and permanent deformation studies of steel-sphere-impacted or explosively-impulsed aluminum panels

NASA Technical Reports Server (NTRS)

Witmer, E. A.; Merlis, F.; Rodal, J. J. A.; Stagliano, T. R.

1977-01-01

The sheet explosive loading technique (SELT) was employed to obtain elastic-plastic, large deflection 3-d transient and/or permanent strain data on simple well defined structural specimens and materials: initially-flat 6061-T651 aluminum panels with all four sides ideally clamped via integral construction. The SELT loading technique was chosen since it is both convenient and provides "forcing function information" of small uncertainty. These data will be useful for evaluating pertinent 3-d structural response prediction methods.

Epstein-Barr virus DNA load in chronic lymphocytic leukemia is an independent predictor of clinical course and survival

PubMed Central

Visco, Carlo; Falisi, Erika; Young, Ken H.; Pascarella, Michela; Perbellini, Omar; Carli, Giuseppe; Novella, Elisabetta; Rossi, Davide; Giaretta, Ilaria; Cavallini, Chiara; Scupoli, Maria Teresa; De Rossi, Anita; D'Amore, Emanuele Stefano Giovanni; Rassu, Mario; Gaidano, Gianluca; Pizzolo, Giovanni; Ambrosetti, Achille; Rodeghiero, Francesco

2015-01-01

The relation between Epstein-Barr virus (EBV) DNA load and clinical course of patients with chronic lymphocytic leukemia (CLL) is unknown. We assessed EBV DNA load by quantitative PCR at CLL presentation in mononuclear cells (MNC) of 220 prospective patients that were enrolled and followed-up in two major Institutions. In 20 patients EBV DNA load was also assessed on plasma samples. Forty-one age-matched healthy subjects were tested for EBV DNA load on MNC. Findings were validated in an independent retrospective cohort of 112 patients with CLL. EBV DNA load was detectable in 59%, and high (≥2000 copies/µg DNA) in 19% of patients, but it was negative in plasma samples. EBV DNA load was significantly higher in CLL patients than in healthy subjects (P < .0001). No relation was found between high EBV load and clinical stage or biological variables, except for 11q deletion (P = .004), CD38 expression (P = .003), and NOTCH1 mutations (P = .05). High EBV load led to a 3.14-fold increase in the hazard ratio of death and to a shorter overall survival (OS; P = .001). Poor OS was attributable, at least in part, to shorter time-to-first-treatment (P = .0008), with no higher risk of Richter's transformation or second cancer. Multivariate analysis selected high levels of EBV load as independent predictor of OS after controlling for confounding clinical and biological variables. EBV DNA load at presentation is an independent predictor of OS in patients with CLL. PMID:26087198

Spectrum fatigue testing of T-shaped tension clips

NASA Astrophysics Data System (ADS)

Palmberg, Bjoern; Wallstenius, Bengt

1992-12-01

An investigation of strain distributions during static loading and crack propagation and fatigue lives under spectrum loading of T-shaped tension clips was carried out. Three slightly different, with respect to geometry, T shaped tension clips made of aluminum alloy 7010-T73651 were studied. The type 1 and 4 test specimens were different only with respect to the web thickness of the clamping end. The type 1 and 2 test specimens were different with repect to milled flat circular countersink around the holes in the type 2 specimens and with respect to the radius between the web and foot. The spectrum fatigue loading consisted of a load sequence representative for the wing root, lower side, of a fighter aircraft. Tests were made at two different load levels for each specimen type. The strain measurements show that the countersink in the type 2 specimens increases the stresses in the fatigue critical region. This is also manifested in the spectrum fatigue life results, where type 2 specimens show the shortest fatigue lives. The strain measurements show that the torque used for the bolts in joining two test specimens or one test specimen and a dummy has a rather large impact on the strain in the fatigue region. The strains decrease with increasing torque. The spectrum fatigue loading resulted in approximately an equal number of flights to obtain a 10.0 mm crack for specimens of type 1 and 4. This suggests that the type 1 configuration is superior since the web thickness is smaller for this type as compared to the type 4 specimens. In other words, the type 4 specimens have an unnecessary oversize of the clamping end web thickness.

Polymorphism at the 5' end flanking region of the insulin gene is associated with reduced insulin secretion in healthy individuals.

PubMed

Cocozza, S; Riccardi, G; Monticelli, A; Capaldo, B; Genovese, S; Krogh, V; Celentano, E; Farinaro, E; Varrone, S; Avvedimento, V E

1988-12-01

Sixty-four unrelated healthy subjects were studied for the detection of a DNA polymorphism at the 5' end of the insulin gene. No significant difference between the groups was found in blood glucose values at fasting and after an oral glucose load. A significant association was found between fasting (P less than 0.05) and after load plasma C-peptide levels (P less than 0.01) and the presence of a 1.6 Kb insertion at the 5' end of the insulin gene. A gene dose-dependent effect was noted, class 3/3 individuals having the lowest after-load C-peptide concentration and class 1/3 an intermediate level (F for the linear trend: P = 0.007). This might suggest that insulin gene polymorphism affects insulin secretion in healthy individuals. In order to confirm this, a subgroup of six class 3/3 and eight class 1/1 individuals subsequently underwent a hyperglycaemic clamp. The tissue sensitivity to insulin was similar in the two groups but glucose-stimulated insulin secretion was markedly impaired in homozygotes for the class 3 allele. In this group, insulin secretion was, on average, only one-third of that in class 1/1 individuals (P less than 0.02). Similarly impaired in class 3/3 persons was the glucose + arginine-stimulated insulin secretion (P less than 0.05). We conclude that the polymorphism at the 5' end of the insulin gene is associated with variations in insulin secretion in healthy humans.

Effects of Active Site Mutations on Specificity of Nucleobase Binding in Human DNA Polymerase η.

PubMed

Ucisik, Melek N; Hammes-Schiffer, Sharon

2017-04-20

Human DNA polymerase η (Pol η) plays a vital role in protection against skin cancer caused by damage from ultraviolet light. This enzyme rescues stalled replication forks at cyclobutane thymine-thymine dimers (TTDs) by inserting nucleotides opposite these DNA lesions. Residue R61 is conserved in the Pol η enzymes across species, but the corresponding residue, as well as its neighbor S62, is different in other Y-family polymerases, Pol ι and Pol κ. Herein, R61 and S62 are mutated to their Pol ι and Pol κ counterparts. Relative binding free energies of dATP to mutant Pol η•DNA complexes with and without a TTD were calculated using thermodynamic integration. The binding free energies of dATP to the Pol η•DNA complex with and without a TTD are more similar for all of these mutants than for wild-type Pol η, suggesting that these mutations decrease the ability of this enzyme to distinguish between a TTD lesion and undamaged DNA. Molecular dynamics simulations of the mutant systems provide insights into the molecular level basis for the changes in relative binding free energies. The simulations identified differences in hydrogen-bonding, cation-π, and π-π interactions of the side chains with the dATP and the TTD or thymine-thymine (TT) motif. The simulations also revealed that R61 and Q38 act as a clamp to position the dATP and the TTD or TT and that the mutations impact the balance among the interactions related to this clamp. Overall, these calculations suggest that R61 and S62 play key roles in the specificity and effectiveness of Pol η for bypassing TTD lesions during DNA replication. Understanding the basis for this specificity is important for designing drugs aimed at cancer treatment.

Effects of Active Site Mutations on Specificity of Nucleobase Binding in Human DNA Polymerase η

PubMed Central

2016-01-01

Human DNA polymerase η (Pol η) plays a vital role in protection against skin cancer caused by damage from ultraviolet light. This enzyme rescues stalled replication forks at cyclobutane thymine–thymine dimers (TTDs) by inserting nucleotides opposite these DNA lesions. Residue R61 is conserved in the Pol η enzymes across species, but the corresponding residue, as well as its neighbor S62, is different in other Y-family polymerases, Pol ι and Pol κ. Herein, R61 and S62 are mutated to their Pol ι and Pol κ counterparts. Relative binding free energies of dATP to mutant Pol η•DNA complexes with and without a TTD were calculated using thermodynamic integration. The binding free energies of dATP to the Pol η•DNA complex with and without a TTD are more similar for all of these mutants than for wild-type Pol η, suggesting that these mutations decrease the ability of this enzyme to distinguish between a TTD lesion and undamaged DNA. Molecular dynamics simulations of the mutant systems provide insights into the molecular level basis for the changes in relative binding free energies. The simulations identified differences in hydrogen-bonding, cation−π, and π–π interactions of the side chains with the dATP and the TTD or thymine–thymine (TT) motif. The simulations also revealed that R61 and Q38 act as a clamp to position the dATP and the TTD or TT and that the mutations impact the balance among the interactions related to this clamp. Overall, these calculations suggest that R61 and S62 play key roles in the specificity and effectiveness of Pol η for bypassing TTD lesions during DNA replication. Understanding the basis for this specificity is important for designing drugs aimed at cancer treatment. PMID:28423907

Crystal structure of Thermoplasma acidophilum XerA recombinase shows large C-shape clamp conformation and cis-cleavage mode for nucleophilic tyrosine.

PubMed

Jo, Chang Hwa; Kim, Junsoo; Han, Ah-reum; Park, Sam Yong; Hwang, Kwang Yeon; Nam, Ki Hyun

2016-03-01

Site-specific Xer recombination plays a pivotal role in reshuffling genetic information. Here, we report the 2.5 Å crystal structure of XerA from the archaean Thermoplasma acidophilum. Crystallographic data reveal a uniquely open conformational state, resulting in a C-shaped clamp with an angle of ~ 48° and a distance of 57 Å between the core-binding and the catalytic domains. The catalytic nucleophile, Tyr264, is positioned in cis-cleavage mode by XerA's C-term tail that interacts with the CAT domain of a neighboring monomer without DNA substrate. Structural comparisons of tyrosine recombinases elucidate the dynamics of Xer recombinase. © 2016 Federation of European Biochemical Societies.

Whole exome sequencing for determination of tumor mutation load in liquid biopsy from advanced cancer patients.

PubMed

Koeppel, Florence; Blanchard, Steven; Jovelet, Cécile; Genin, Bérengère; Marcaillou, Charles; Martin, Emmanuel; Rouleau, Etienne; Solary, Eric; Soria, Jean-Charles; André, Fabrice; Lacroix, Ludovic

2017-01-01

Tumor mutation load (TML) has been proposed as a biomarker of patient response to immunotherapy in several studies. TML is usually determined by tumor biopsy DNA (tDNA) whole exome sequencing (WES), therefore TML evaluation is limited by informative biopsy availability. Circulating cell free DNA (cfDNA) provided by liquid biopsy is a surrogate specimen to biopsy for molecular profiling. Nevertheless performing WES on DNA from plasma is technically challenging and the ability to determine tumor mutation load from liquid biopsies remains to be demonstrated. In the current study, WES was performed on cfDNA from 32 metastatic patients of various cancer types included into MOSCATO 01 (NCT01566019) and/or MATCHR (NCT02517892) molecular triage trials. Results from targeted gene sequencing (TGS) and WES performed on cfDNA were compared to results from tumor tissue biopsy. In cfDNA samples, WES mutation detection sensitivity was 92% compared to targeted sequencing (TGS). When comparing cfDNA-WES to tDNA-WES, mutation detection sensitivity was 53%, consistent with previously published prospective study comparing cfDNA-TGS to tDNA-TGS. For samples in which presence of tumor DNA was confirmed in cfDNA, tumor mutation load from liquid biopsy was correlated with tumor biopsy. Taken together, this study demonstrated that liquid biopsy may be applied to determine tumor mutation load. Qualification of liquid biopsy for interpretation is a crucial point to use cfDNA for mutational load estimation.

Whole exome sequencing for determination of tumor mutation load in liquid biopsy from advanced cancer patients

PubMed Central

Blanchard, Steven; Jovelet, Cécile; Genin, Bérengère; Marcaillou, Charles; Martin, Emmanuel; Rouleau, Etienne; Solary, Eric; Soria, Jean-Charles; André, Fabrice; Lacroix, Ludovic

2017-01-01

Tumor mutation load (TML) has been proposed as a biomarker of patient response to immunotherapy in several studies. TML is usually determined by tumor biopsy DNA (tDNA) whole exome sequencing (WES), therefore TML evaluation is limited by informative biopsy availability. Circulating cell free DNA (cfDNA) provided by liquid biopsy is a surrogate specimen to biopsy for molecular profiling. Nevertheless performing WES on DNA from plasma is technically challenging and the ability to determine tumor mutation load from liquid biopsies remains to be demonstrated. In the current study, WES was performed on cfDNA from 32 metastatic patients of various cancer types included into MOSCATO 01 (NCT01566019) and/or MATCHR (NCT02517892) molecular triage trials. Results from targeted gene sequencing (TGS) and WES performed on cfDNA were compared to results from tumor tissue biopsy. In cfDNA samples, WES mutation detection sensitivity was 92% compared to targeted sequencing (TGS). When comparing cfDNA-WES to tDNA-WES, mutation detection sensitivity was 53%, consistent with previously published prospective study comparing cfDNA-TGS to tDNA-TGS. For samples in which presence of tumor DNA was confirmed in cfDNA, tumor mutation load from liquid biopsy was correlated with tumor biopsy. Taken together, this study demonstrated that liquid biopsy may be applied to determine tumor mutation load. Qualification of liquid biopsy for interpretation is a crucial point to use cfDNA for mutational load estimation. PMID:29161279

Enhancement of Buckling Load with the Use of Active Materials

NASA Technical Reports Server (NTRS)

Yuan, F. G.

2002-01-01

In this paper, active buckling control of a beam using piezoelectric materials is investigated. Under small deformation, mathematical models are developed to describe the behavior of the beams subjected to an axial compressive load with geometric imperfections and load eccentricities under piezoelectric force. Two types of supports, simply supported and clamped, of the beam with a partially bonded piezoelectric actuator are used to illustrate the concept. For the beam with load eccentricities and initial geometric imperfections, the load- carrying capacity can be significantly enhanced by counteracting moments from the piezoelectric actuator. For the single piezoelectric actuator, using static feedback closed-loop control, the first buckling load can be eliminated. In the case of initially straight beams, analytical solutions of the enhanced first critical buckling load due to the increase of bending stiffness by piezoelectric actuators are derived based on linearized buckling analysis.

MCM interference during licensing of DNA replication in Xenopus egg extracts-Possible Role of a C-terminal region of MCM3.

PubMed

Mimura, Satoru; Kubota, Yumiko; Takisawa, Haruhiko

2018-01-01

The minichromosome maintenance (MCM) complex, consisting of six subunits, Mcm2-7, is loaded onto replication origins through loading factors (origin recognition complex [ORC], Cdc6, and Cdt1) and forms an MCM double hexamer that licenses the initiation of DNA replication. Previous studies with Xenopus egg extracts showed that loading factors, especially Cdc6, dissociate from chromatin on MCM loading, but the molecular mechanism and physiological significance remain largely unknown. Using a cell-free system for MCM loading onto plasmid DNA in Xenopus egg extracts, we found that MCM loaded onto DNA prevents DNA binding of the loading factors ORC, Cdc6, and Cdt1. We further report that a peptide of the C-terminal region of MCM3 (MCM3-C), previously implicated in the initial association with ORC/Cdc6 in budding yeast, prevents ORC/Cdc6/Cdt1 binding to DNA in the absence of MCM loading. ATP-γ-S suppresses inhibitory activities of both the MCM loaded onto DNA and the MCM3-C peptide. Other soluble factors in the extract, but neither MCM nor Cdt1, are required for the activity. Conservation of the amino acid sequences of MCM3-C and its activity in vertebrates implies a novel negative autoregulatory mechanism that interferes with MCM loading in the vicinity of licensed origins to ensure proper origin licensing.

29 CFR 1910.254 - Arc welding and cutting.

Code of Federal Regulations, 2013 CFR

2013-07-01

... rated load with rated temperature rises where the temperature of the cooling air does not exceed 40 °C... work; magnetic work clamps shall be freed from adherent metal particles of spatter on contact surfaces... given to safety ground connections of portable machines. (4) Leaks. There shall be no leaks of cooling...

29 CFR 1910.254 - Arc welding and cutting.

Code of Federal Regulations, 2012 CFR

2012-07-01

... rated load with rated temperature rises where the temperature of the cooling air does not exceed 40 °C... work; magnetic work clamps shall be freed from adherent metal particles of spatter on contact surfaces... given to safety ground connections of portable machines. (4) Leaks. There shall be no leaks of cooling...

29 CFR 1910.254 - Arc welding and cutting.

Code of Federal Regulations, 2014 CFR

2014-07-01

... rated load with rated temperature rises where the temperature of the cooling air does not exceed 40 °C... work; magnetic work clamps shall be freed from adherent metal particles of spatter on contact surfaces... given to safety ground connections of portable machines. (4) Leaks. There shall be no leaks of cooling...

Mechanical and Thermal Analysis of Classical Functionally Graded Coated Beam

NASA Astrophysics Data System (ADS)

Toudehdehghan, Abdolreza; Mujibur Rahman, Md.; Tarlochan, Faris

2018-03-01

The governing equation of a classical rectangular coated beam made of two layers subjected to thermal and uniformly distributed mechanical loads are derived by using the principle of virtual displacements and based on Euler-Bernoulli deformation beam theory (EBT). The aim of this paper was to analyze the static behavior of clamped-clamped thin coated beam under thermo-mechanical load using MATLAB. Two models were considered for composite coated. The first model was consisting of ceramic layer as a coated and substrate which was metal (HC model). The second model was consisting of Functionally Graded Material (FGM) as a coated layer and metal substrate (FGC model). From the result it was apparent that the superiority of the FGC composite against conventional coated composite has been demonstrated. From the analysis, the stress level throughout the thickness at the interface of the coated beam for the FGC was reduced. Yet, the deflection in return was observed to increase. Therefore, this could cater to various new engineering applications where warrant the utilization of material that has properties that are well-beyond the capabilities of the conventional or yesteryears materials.

Classical and numerical approaches to determining V-section band clamp axial stiffness

NASA Astrophysics Data System (ADS)

Barrans, Simon M.; Khodabakhshi, Goodarz; Muller, Matthias

2015-01-01

V-band clamp joints are used in a wide range of applications to connect circular flanges, for ducts, pipes and the turbocharger housing. Previous studies and research on V-bands are either purely empirical or analytical with limited applicability on the variety of V-band design and working conditions. In this paper models of the V-band are developed based on the classical theory of solid mechanics and the finite element method to study the behaviour of theV-bands under axial loading conditions. The good agreement between results from the developed FEA and the classical model support the suitability of the latter to modelV-band joints with diameters greater than 110mm under axial loading. The results from both models suggest that the axial stiffness for thisV-band cross section reaches a peak value for V-bands with radius of approximately 150 mmacross a wide range of coefficients of friction. Also, it is shown that the coefficient of friction and the wedge angle have a significant effect on the axial stiffness of V-bands.

The acoustic power of a vibrating clamped circular plate revisited in the wide low frequency range using expansion into the radial polynomials.

PubMed

Rdzanek, Wojciech P

2016-06-01

This study deals with the classical problem of sound radiation of an excited clamped circular plate embedded into a flat rigid baffle. The system of the two coupled differential equations is solved, one for the excited and damped vibrations of the plate and the other one-the Helmholtz equation. An approach using the expansion into radial polynomials leads to results for the modal impedance coefficients useful for a comprehensive numerical analysis of sound radiation. The results obtained are accurate and efficient in a wide low frequency range and can easily be adopted for a simply supported circular plate. The fluid loading is included providing accurate results in resonance.

Unitaxial constant velocity microactuator

DOEpatents

McIntyre, Timothy J.

1994-01-01

A uniaxial drive system or microactuator capable of operating in an ultra-high vacuum environment. The mechanism includes a flexible coupling having a bore therethrough, and two clamp/pusher assemblies mounted in axial ends of the coupling. The clamp/pusher assemblies are energized by voltage-operated piezoelectrics therewithin to operatively engage the shaft and coupling causing the shaft to move along its rotational axis through the bore. The microactuator is capable of repeatably positioning to sub-manometer accuracy while affording a scan range in excess of 5 centimeters. Moreover, the microactuator generates smooth, constant velocity motion profiles while producing a drive thrust of greater than 10 pounds. The system is remotely controlled and piezoelectrically driven, hence minimal thermal loading, vibrational excitation, or outgassing is introduced to the operating environment.

Reactive oxygen-mediated damage to a human DNA replication and repair protein.

PubMed

Montaner, Beatriz; O'Donovan, Peter; Reelfs, Olivier; Perrett, Conal M; Zhang, Xiaohong; Xu, Yao-Zhong; Ren, Xiaolin; Macpherson, Peter; Frith, David; Karran, Peter

2007-11-01

Ultraviolet A (UVA) makes up more than 90% of incident terrestrial ultraviolet radiation. Unlike shorter wavelength UVB, which damages DNA directly, UVA is absorbed poorly by DNA and is therefore considered to be less hazardous. Organ transplant patients treated with the immunosuppressant azathioprine frequently develop skin cancer. Their DNA contains 6-thioguanine-a base analogue that generates DNA-damaging singlet oxygen ((1)O(2)) when exposed to UVA. Here, we show that this (1)O(2) damages proliferating cell nuclear antigen (PCNA), the homotrimeric DNA polymerase sliding clamp. It causes covalent oxidative crosslinking between the PCNA subunits through a histidine residue in the intersubunit domain. Crosslinking also occurs after treatment with higher-although still moderate-doses of UVA alone or with chemical oxidants. Chronic accumulation of oxidized proteins is linked to neurodegenerative disorders and ageing. Our findings identify oxidative damage to an important DNA replication and repair protein as a previously unrecognized hazard of acute oxidative stress.

Quantification of DNA-associated proteins inside eukaryotic cells using single-molecule localization microscopy

PubMed Central

Etheridge, Thomas J.; Boulineau, Rémi L.; Herbert, Alex; Watson, Adam T.; Daigaku, Yasukazu; Tucker, Jem; George, Sophie; Jönsson, Peter; Palayret, Matthieu; Lando, David; Laue, Ernest; Osborne, Mark A.; Klenerman, David; Lee, Steven F.; Carr, Antony M.

2014-01-01

Development of single-molecule localization microscopy techniques has allowed nanometre scale localization accuracy inside cells, permitting the resolution of ultra-fine cell structure and the elucidation of crucial molecular mechanisms. Application of these methodologies to understanding processes underlying DNA replication and repair has been limited to defined in vitro biochemical analysis and prokaryotic cells. In order to expand these techniques to eukaryotic systems, we have further developed a photo-activated localization microscopy-based method to directly visualize DNA-associated proteins in unfixed eukaryotic cells. We demonstrate that motion blurring of fluorescence due to protein diffusivity can be used to selectively image the DNA-bound population of proteins. We designed and tested a simple methodology and show that it can be used to detect changes in DNA binding of a replicative helicase subunit, Mcm4, and the replication sliding clamp, PCNA, between different stages of the cell cycle and between distinct genetic backgrounds. PMID:25106872

Glove box shield

DOEpatents

Brackenbush, L.W.; Hoenes, G.R.

A shield for a glove box housing radioactive material is comprised of spaced apart clamping members which maintain three overlapping flaps in place therebetween. There is a central flap and two side flaps, the side flaps overlapping at the interior edges thereof and the central flap extending past the intersection of the side flaps in order to insure that the shield is always closed when the user wthdraws his hand from the glove box. Lead loaded neoprene rubber is the preferred material for the three flaps, the extent of lead loading depending upon the radiation levels within the glove box.

Strain measurements in a rotary engine housing

NASA Technical Reports Server (NTRS)

Lee, C. M.; Bond, T. H.; Addy, H. E.; Chun, K. S.; Lu, C. Y.

1989-01-01

The development of structural design tools for Rotary Combustion Engines (RCE) using Finite Element Modeling (FEM) requires knowledge about the response of engine materials to various service conditions. This paper describes experimental work that studied housing deformation as a result of thermal, pressure and mechanical loads. The measurement of thermal loads, clamping pressure, and deformation was accomplished by use of high-temperature strain gauges, thermocouples, and a high speed data acquisition system. FEM models for heat transfer stress analysis of the rotor housing will be verified and refined based on these experimental results.

Family of columns isospectral to gravity-loaded columns with tip force: A discrete approach

NASA Astrophysics Data System (ADS)

Ramachandran, Nirmal; Ganguli, Ranjan

2018-06-01

A discrete model is introduced to analyze transverse vibration of straight, clamped-free (CF) columns of variable cross-sectional geometry under the influence of gravity and a constant axial force at the tip. The discrete model is used to determine critical combinations of loading parameters - a gravity parameter and a tip force parameter - that cause onset of dynamic instability in the CF column. A methodology, based on matrix-factorization, is described to transform the discrete model into a family of models corresponding to weightless and unloaded clamped-free (WUCF) columns, each with a transverse vibration spectrum isospectral to the original model. Characteristics of models in this isospectral family are dependent on three transformation parameters. A procedure is discussed to convert the isospectral discrete model description into geometric description of realistic columns i.e. from the discrete model, we construct isospectral WUCF columns with rectangular cross-sections varying in width and depth. As part of numerical studies to demonstrate efficacy of techniques presented, frequency parameters of a uniform column and three types of tapered CF columns under different combinations of loading parameters are obtained from the discrete model. Critical combinations of these parameters for a typical tapered column are derived. These results match with published results. Example CF columns, under arbitrarily-chosen combinations of loading parameters are considered and for each combination, isospectral WUCF columns are constructed. Role of transformation parameters in determining characteristics of isospectral columns is discussed and optimum values are deduced. Natural frequencies of these WUCF columns computed using Finite Element Method (FEM) match well with those of the given gravity-loaded CF column with tip force, hence confirming isospectrality.

Biochemical, histologic, and biomechanical characterization of native and decellularized flexor tendon specimens harvested from the pelvic limbs of orthopedically normal dogs.

PubMed

Balogh, Daniel G; Biskup, Jeffery J; O'Sullivan, M Gerard; Scott, Ruth M; Groschen, Donna; Evans, Richard B; Conzemius, Michael G

2016-04-01

To evaluate the biochemical and biomechanical properties of native and decellularized superficial digital flexor tendons (SDFTs) and deep digital flexor tendons (DDFTs) harvested from the pelvic limbs of orthopedically normal dogs. 22 commercially supplied tendon specimens (10 SDFT and 12 DDFT) harvested from the pelvic limbs of 13 canine cadavers. DNA, glycosaminoglycan, collagen, and protein content were measured to biochemically compare native and decellularized SDFT and DDFT specimens. Mechanical testing was performed on 4 groups consisting of native tendons (5 SDFTs and 6 DDFTs) and decellularized tendons (5 SDFTs and 6 DDFTs). All tendons were preconditioned, and tension was applied to failure at 0.5 mm/s. Failure mode was video recorded for each tendon. Load-deformation and stress-strain curves were generated; calculations were performed to determine the Young modulus and stiffness. Biochemical and biomechanical data were statistically compared by use of the Wilcoxon rank sum test. Decellularized SDFT and DDFT specimens had significantly less DNA content than did native tendons. No significant differences were identified between native and decellularized specimens with respect to glycosaminoglycan, collagen, or protein content. Biomechanical comparison yielded no significant intra- or intergroup differences. All DDFT constructs failed at the tendon-clamp interface, whereas nearly half (4/10) of the SDFT constructs failed at midsubstance. Decellularized commercial canine SDFT and DDFT specimens had similar biomechanical properties, compared with each other and with native tendons. The decellularization process significantly decreased DNA content while minimizing loss of extracellular matrix components. Decellularized canine flexor tendons may provide suitable, biocompatible graft scaffolds for bioengineering applications such as tendon or ligament repair.

Single-molecule analysis of DNA uncoiling by a type II topoisomerase

NASA Astrophysics Data System (ADS)

Strick, Terence R.; Croquette, Vincent; Bensimon, David

2000-04-01

Type II DNA topoisomerases are ubiquitous ATP-dependent enzymes capable of transporting a DNA through a transient double-strand break in a second DNA segment. This enables them to untangle DNA and relax the interwound supercoils (plectonemes) that arise in twisted DNA. In vivo, they are responsible for untangling replicated chromosomes and their absence at mitosis or meiosis ultimately causes cell death. Here we describe a micromanipulation experiment in which we follow in real time a single Drosophila melanogaster topoisomerase II acting on a linear DNA molecule which is mechanically stretched and supercoiled. By monitoring the DNA's extension in the presence of ATP, we directly observe the relaxation of two supercoils during a single catalytic turnover. By controlling the force pulling on the molecule, we determine the variation of the reaction rate with the applied stress. Finally, in the absence of ATP, we observe the clamping of a DNA crossover by a single topoisomerase on at least two different timescales (configurations). These results show that single molecule experiments are a powerful new tool for the study of topoisomerases.

Free vibration of thermally loaded panels including initial imperfections and post-buckling effects

NASA Technical Reports Server (NTRS)

Murphy, K. D.; Virgin, L. N.; Rizzi, S. A.

1994-01-01

A combined theoretical and experimental approach is developed to consider the small amplitude free vibration characteristics of fully clamped panels under the influence of uniform heating. Included in this study are the effects of higher modes, in-plane boundary elasticity, initial imperfections, and post-buckling. Comparisons between theory and experiment reveal excellent agreement.

Early hepatitis B viral DNA clearance predicts treatment response at week 96

PubMed Central

Fu, Xiao-Yu; Tan, De-Ming; Liu, Cui-Mei; Gu, Bin; Hu, Li-Hua; Peng, Zhong-Tian; Chen, Bin; Xie, Yuan-Lin; Gong, Huan-Yu; Hu, Xiao-Xuan; Yao, Lian-Hui; Xu, Xiao-Ping; Fu, Zheng-Yuan; He, Lang-Qiu; Li, Si-Hai; Long, Yun-Zhu; Li, De-Hui; Gu, Ji-Long; Peng, Shi-Fang

2017-01-01

AIM To investigate whether hepatitis viral DNA load at 24 wk of treatment predicts response at 96 wk in patients with chronic hepatitis B. METHODS A total of 172 hepatitis B envelope antigen (HBeAg)-positive chronic hepatitis B patients who received initial treatment at 16 tertiary hospitals in Hunan Province, China were enrolled in this study. All patients received conventional doses of lamivudine and adefovir dipivoxil, telbivudine, entecavir dispersible tablets, or entecavir tablets for 96 wk. Patients who used other antiviral drugs or antitumor and immune regulation therapy were excluded. Patients were stratified into three groups according to their viral DNA load at 24 wk: < 10 IU/mL (group 1), 10-103 IU/mL (group 2), and > 103 IU/mL (group 3). Correlations of 24-wk DNA load with HBeAg negative status and HBeAg seroconversion at 96 wk were analyzed. Receiver operating characteristic curve analysis was used to test the predictive value of the HBV DNA load at 24 wk for long-term response. RESULTS The rates of conversion to HBeAg negative status and HBeAg seroconversion rates were 53.7% and 51.9%, respectively, in group 1; 35.21% and 32.39% in group 2; and 6.38% and 6.38% in group 3. The receiver operating characteristic curves for the three subgroups revealed that the lowest DNA load (< 10 IU/mL) was better correlated with response at 96 wk than a higher DNA load (10-103 IU/mL). Nested PCR was used for amplifying and sequencing viral DNA in patients with a viral DNA load > 200 IU/mL at 96 wk; resistance mutations involving different loci were present in 26 patients, and three of these patients had a viral DNA load 10-103 IU/mL at 96 wk. CONCLUSION Hepatitis B viral DNA load at 24 wk of antiviral treatment in patients with chronic hepatitis B is a predictor of the viral load and response rate at 96 wk. PMID:28522916

Simple practical approach for sample loading prior to DNA extraction using a silica monolith in a microfluidic device.

PubMed

Shaw, Kirsty J; Joyce, Domino A; Docker, Peter T; Dyer, Charlotte E; Greenman, John; Greenway, Gillian M; Haswell, Stephen J

2009-12-07

A novel DNA loading methodology is presented for performing DNA extraction on a microfluidic system. DNA in a chaotropic salt solution was manually loaded onto a silica monolith orthogonal to the subsequent flow of wash and elution solutions. DNA was successfully extracted from buccal swabs using electro-osmotic pumping (EOP) coupled with in situ reagents contained within a 1.5% agarose gel matrix. The extracted DNA was of sufficient quantity and purity for polymerase chain reaction (PCR) amplification.

Cdc45-induced loading of human RPA onto single-stranded DNA

PubMed Central

Tessmer, Ingrid; Prus, Piotr; Schlott, Bernhard; Pospiech, Helmut

2017-01-01

Abstract Cell division cycle protein 45 (Cdc45) is an essential component of the eukaryotic replicative DNA helicase. We found that human Cdc45 forms a complex with the single-stranded DNA (ssDNA) binding protein RPA. Moreover, it actively loads RPA onto nascent ssDNA. Pull-down assays and surface plasmon resonance studies revealed that Cdc45-bound RPA complexed with ssDNA in the 8–10 nucleotide binding mode, but dissociated when RPA covered a 30-mer. Real-time analysis of RPA-ssDNA binding demonstrated that Cdc45 catalytically loaded RPA onto ssDNA. This placement reaction required physical contacts of Cdc45 with the RPA70A subdomain. Our results imply that Cdc45 controlled stabilization of the 8-nt RPA binding mode, the subsequent RPA transition into 30-mer mode and facilitated an ordered binding to ssDNA. We propose that a Cdc45-mediated loading guarantees a seamless deposition of RPA on newly emerging ssDNA at the nascent replication fork. PMID:28100698

Confinement-induced Molecular Templating and Controlled Ligation

NASA Astrophysics Data System (ADS)

Berard, Daniel; Shayegan, Marjan; Michaud, François; Henkin, Gil; Scott, Shane; Leith, Jason; Leslie, Sabrina; Leslie Lab Team

Loading and manipulating long DNA molecules within sub-50 nm cross-section nanostructures for genomic and biochemical analyses, while retaining their structural integrity, present key technological challenges to the biotechnology sector, such as device clogging and molecular breakage. We overcome these challenges by using Convex Lens-induced Confinement (CLiC) technology to gently load DNA into nanogrooves from above. Here, we demonstrate single-fluorophore visualization of custom DNA barcodes as well as efficient top-loading of DNA into sub-50 nm nanogrooves of variable topographies. We study confinement-enhanced self-ligation of polymers loaded in circular nanogrooves. Further, we use concentric, circular nanogrooves to eliminate confinement gradient-induced drift of stretched DNA.

Reliability at the lower limits of HIV-1 RNA quantification in clinical samples: a comparison of RT-PCR versus bDNA assays.

PubMed

Lubelchek, Ronald J; Max, Blake; Sandusky, Caroline J; Hota, Bala; Barker, David E

2009-06-23

To explore whether an assay change was responsible for an increasing proportion of patients with undetectable HIV viral loads at our urban HIV clinic, we selected highly stable patients, examining their viral loads before and after changing assays. We compared the proportion with detectable viremia during RT-PCR vs. bDNA periods. We selected patients with > or =1 viral loads assessed during both RT-PCR and bDNA periods. We included patients with stable CD4 counts, excluding patients with viral loads > or =1,000 copies/ml or any significant changes in therapy. Out of 4500 clinic patients, 419 patients (1588 viral loads) were included. 39% of viral loads were reported as detectable by RT-PCR vs. 5% reported as detectable by bDNA. The mean coefficient of variation was higher before vs. after assay change. We found an odds' ratio of 16.7 for having a viral load >75 copies/ml during the RT-PCR vs. bDNA periods. These data support previous reports, suggesting that bDNA may more reliably discriminate between viral suppression and low level viremia in stable patients on therapy. Low-level viremia, noted more with RT-PCR, may promote unneeded testing, while differences in viral load reliability may impact antiretroviral trial and quality assurance endpoints. Commonly used plasma separator tubes may differentially affect RT-PCR and bDNA results.

Indentation law for composite laminates

NASA Technical Reports Server (NTRS)

Yang, S. H.

1981-01-01

Static indentation tests are described for glass/epoxy and graphite/epoxy composite laminates with steel balls as the indentor. Beam specimens clamped at various spans were used for the tests. Loading, unloading, and reloading data were obtained and fitted into power laws. Results show that: (1) contact behavior is not appreciably affected by the span; (2) loading and reloading curves seem to follow the 1.5 power law; and (3) unloading curves are described quite well by a 2.5 power law. In addition, values were determined for the critical indentation, alpha sub cr which can be used to predict permanent indentations in unloading. Since alpha sub cr only depends on composite material properties, only the loading and an unloading curve are needed to establish the complete loading-unloading-reloading behavior.

Capturing Snapshots of APE1 Processing DNA Damage

PubMed Central

Freudenthal, Bret D.; Beard, William A.; Cuneo, Matthew J.; Dyrkheeva, Nadezhda S.; Wilson, Samuel H.

2015-01-01

DNA apurinic-apyrimidinic (AP) sites are prevalent non-coding threats to genomic stability and are processed by AP endonuclease 1 (APE1). APE1 incises the AP-site phosphodiester backbone, generating a DNA repair intermediate that is potentially cytotoxic. The molecular events of the incision reaction remain elusive due in part to limited structural information. We report multiple high-resolution human APE1:DNA structures that divulge novel features of the APE1 reaction, including the metal binding site, nucleophile, and arginine clamps that mediate product release. We also report APE1:DNA structures with a T:G mismatch 5′ to the AP-site, representing a clustered lesion occurring in methylated CpG dinucleotides. These reveal that APE1 molds the T:G mismatch into a unique Watson-Crick like geometry that distorts the active site reducing incision. These snapshots provide mechanistic clarity for APE1, while affording a rational framework to manipulate biological responses to DNA damage. PMID:26458045

Capturing snapshots of APE1 processing DNA damage

DOE PAGES

Freudenthal, Bret D.; Beard, William A.; Cuneo, Matthew J.; ...

2015-10-12

DNA apurinic-apyrimidinic (AP) sites are prevalent noncoding threats to genomic stability and are processed by AP endonuclease 1 (APE1). APE1 incises the AP-site phosphodiester backbone, generating a DNA-repair intermediate that is potentially cytotoxic. The molecular events of the incision reaction remain elusive, owing in part to limited structural information. Here we report multiple high-resolution human APE1-DNA structures that divulge new features of the APE1 reaction, including the metal-binding site, the nucleophile and the arginine clamps that mediate product release. We also report APE1-DNA structures with a T-G mismatch 5' to the AP site, representing a clustered lesion occurring in methylatedmore » CpG dinucleotides. Moreover, these structures reveal that APE1 molds the T-G mismatch into a unique Watson-Crick-like geometry that distorts the active site, thus reducing incision. Finally, these snapshots provide mechanistic clarity for APE1 while affording a rational framework to manipulate biological responses to DNA damage.« less

Specific interaction of mutant p53 with regions of matrix attachment region DNA elements (MARs) with a high potential for base-unpairing

PubMed Central

Will, Katrin; Warnecke, Gabriele; Wiesmüller, Lisa; Deppert, Wolfgang

1998-01-01

Mutant, but not wild-type p53 binds with high affinity to a variety of MAR-DNA elements (MARs), suggesting that MAR-binding of mutant p53 relates to the dominant-oncogenic activities proposed for mutant p53. MARs recognized by mutant p53 share AT richness and contain variations of an AATATATTT “DNA-unwinding motif,” which enhances the structural dynamics of chromatin and promotes regional DNA base-unpairing. Mutant p53 specifically interacted with MAR-derived oligonucleotides carrying such unwinding motifs, catalyzing DNA strand separation when this motif was located within a structurally labile sequence environment. Addition of GC-clamps to the respective MAR-oligonucleotides or introducing mutations into the unwinding motif strongly reduced DNA strand separation, but supported the formation of tight complexes between mutant p53 and such oligonucleotides. We conclude that the specific interaction of mutant p53 with regions of MAR-DNA with a high potential for base-unpairing provides the basis for the high-affinity binding of mutant p53 to MAR-DNA. PMID:9811860

Human papillomavirus types 16 and 18 DNA load in relation to coexistence of other types, particularly those in the same species.

PubMed

Xi, Long Fu; Edelstein, Zoe R; Meyers, Craig; Ho, Jesse; Cherne, Stephen L; Schiffman, Mark

2009-09-01

Infection with multiple human papillomavirus (HPV) types is common. However, it is unknown whether viral DNA load is related to the coexistence of other types. Study subjects were 802 and 303 women who were positive for HPV16 and HPV18, respectively, at enrollment into the Atypical Squamous Cells of Undetermined Significance and Low-Grade Squamous Intraepithelial Lesion Triage Study. HPV16 and HPV18 E7 copies per nanogram of cellular DNA in cervical swab samples were measured by real-time PCR in triplicate. Concurrent coinfection was common in this population of women with minor cervical lesions; multiple HPV types were detected in 573 (71.4%) of 802 HPV16-positive women and 227 (74.9%) of 303 HPV18-positive women. The adjusted odds ratio associating coinfection with per 1 log unit increase in HPV16 DNA load was 0.78 (95% confidence interval, 0.68-0.89); it was 0.64 (95% confidence interval, 0.52-0.79) for a similar analysis of HPV18 DNA load. Women with, compared with without, coinfection of A9 species types possessed a significantly lower HPV16 DNA load (P < 0.001), whereas women with, compared with without, coinfection of A7 species types possessed a significantly lower HPV18 DNA load (P = 0.001). A trend of decrease in HPV16 DNA load with increasing number of the coexisting non-HPV16 A9 species types was statistically significant (P(trend) = 0.001). Coinfection with other types was associated with lower HPV16 and HPV18 DNA load. The extent of reduction was correlated to phylogenetic distance of the coexisting types to HPV16 and HPV18, respectively.

Research on mechanical and sensoric set-up for high strain rate testing of high performance fibers

NASA Astrophysics Data System (ADS)

Unger, R.; Schegner, P.; Nocke, A.; Cherif, C.

2017-10-01

Within this research project, the tensile behavior of high performance fibers, such as carbon fibers, is investigated under high velocity loads. This contribution (paper) focuses on the clamp set-up of two testing machines. Based on a kinematic model, weight optimized clamps are designed and evaluated. By analyzing the complex dynamic behavior of conventional high velocity testing machines, it has been shown that the impact typically exhibits an elastic characteristic. This leads to barely predictable breaking speeds and will not work at higher speeds when acceleration force exceeds material specifications. Therefore, a plastic impact behavior has to be achieved, even at lower testing speeds. This type of impact behavior at lower speeds can be realized by means of some minor test set-up adaptions.

A Novel AS1411 Aptamer-Based Three-Way Junction Pocket DNA Nanostructure Loaded with Doxorubicin for Targeting Cancer Cells in Vitro and in Vivo.

PubMed

Taghdisi, Seyed Mohammad; Danesh, Noor Mohammad; Ramezani, Mohammad; Yazdian-Robati, Rezvan; Abnous, Khalil

2018-05-07

Active targeting of nanostructures containing chemotherapeutic agents can improve cancer treatment. Here, a three-way junction pocket DNA nanostructure was developed for efficient doxorubicin (Dox) delivery into cancer cells. The three-way junction pocket DNA nanostructure is composed of three strands of AS1411 aptamer as both a therapeutic aptamer and nucleolin target, the potential biomarker of prostate (PC-3 cells) and breast (4T1 cells) cancers. The properties of the Dox-loaded three-way junction pocket DNA nanostructure were characterized and verified to have several advantages, including high serum stability and a pH-responsive property. Cellular uptake studies showed that the Dox-loaded DNA nanostructure was preferably internalized into target cancer cells (PC-3 and 4T1 cells). MTT cell viability assay demonstrated that the Dox-loaded DNA nanostructure had significantly higher cytotoxicity for PC-3 and 4T1 cells compared to that of nontarget cells (CHO cells, Chinese hamster ovary cell). The in vivo antitumor effect showed that the Dox-loaded DNA nanostructure was more effective in prohibition of the tumor growth compared to free Dox. These findings showed that the Dox-loaded three-way junction pocket DNA nanostructure could significantly reduce the cytotoxic effects of Dox against nontarget cells.

An equivalent network representation of a clamped bimorph piezoelectric micromachined ultrasonic transducer with circular and annular electrodes using matrix manipulation techniques.

PubMed

Sammoura, Firas; Smyth, Katherine; Kim, Sang-Gook

2013-09-01

An electric circuit model for a clamped circular bimorph piezoelectric micromachined ultrasonic transducer (pMUT) was developed for the first time. The pMUT consisted of two piezoelectric layers sandwiched between three thin electrodes. The top and bottom electrodes were separated into central and annular electrodes by a small gap. While the middle electrode was grounded, the central and annular electrodes were biased with two independent voltage sources. The strain mismatch between the piezoelectric layers caused the plate to vibrate and transmit a pressure wave, whereas the received echo generated electric charges resulting from plate deformation. The clamped pMUT plate was separated into a circular and an annular plate, and the respective electromechanical transformation matrices were derived. The force and velocity vectors were properly selected using Hamilton's principle and the necessary boundary conditions were invoked. The electromechanical transformation matrix for the clamped circular pMUT was deduced using simple matrix manipulation techniques. The pMUT performance under three biasing schemes was elaborated: 1) central electrode only, 2) central and annular electrodes with voltages of the same magnitude and polarity, and 3) central and annular electrodes with voltages of the same magnitude and opposite polarity. The circuit parameters of the pMUT were extracted for each biasing scheme, including the transformer ratio, the clamped electric impedance, and the open-circuit mechanical impedance. Each pMUT scheme was characterized under different acoustic loadings using the theoretically developed model, which was verified with finite element modeling (FEM) simulation. The electrode size was optimized to maximize the electromechanical transformer ratio. As such, the developed model could provide more insight into the design, optimization, and characterization of pMUTs and allow for performance comparison with their cMUT counterparts.

Application of Locked Nucleic Acid (LNA) Primer and PCR Clamping by LNA Oligonucleotide to Enhance the Amplification of Internal Transcribed Spacer (ITS) Regions in Investigating the Community Structures of Plant-Associated Fungi.

PubMed

Ikenaga, Makoto; Tabuchi, Masakazu; Kawauchi, Tomohiro; Sakai, Masao

2016-09-29

The simultaneous extraction of host plant DNA severely limits investigations of the community structures of plant-associated fungi due to the similar homologies of sequences in primer-annealing positions between fungi and host plants. Although fungal-specific primers have been designed, plant DNA continues to be excessively amplified by PCR, resulting in the underestimation of community structures. In order to overcome this limitation, locked nucleic acid (LNA) primers and PCR clamping by LNA oligonucleotides have been applied to enhance the amplification of fungal internal transcribed spacer (ITS) regions. LNA primers were designed by converting DNA into LNA, which is specific to fungi, at the forward primer side. LNA oligonucleotides, the sequences of which are complementary to the host plants, were designed by overlapping a few bases with the annealing position of the reverse primer. Plant-specific DNA was then converted into LNA at the shifted position from the 3' end of the primer-binding position. PCR using the LNA technique enhanced the amplification of fungal ITS regions, whereas those of the host plants were more likely to be amplified without the LNA technique. A denaturing gradient gel electrophoresis (DGGE) analysis displayed patterns that reached an acceptable level for investigating the community structures of plant-associated fungi using the LNA technique. The sequences of the bands detected using the LNA technique were mostly affiliated with known isolates. However, some sequences showed low similarities, indicating the potential to identify novel fungi. Thus, the application of the LNA technique is considered effective for widening the scope of community analyses of plant-associated fungi.

Application of Locked Nucleic Acid (LNA) Primer and PCR Clamping by LNA Oligonucleotide to Enhance the Amplification of Internal Transcribed Spacer (ITS) Regions in Investigating the Community Structures of Plant–Associated Fungi

PubMed Central

Ikenaga, Makoto; Tabuchi, Masakazu; Kawauchi, Tomohiro; Sakai, Masao

2016-01-01

The simultaneous extraction of host plant DNA severely limits investigations of the community structures of plant–associated fungi due to the similar homologies of sequences in primer–annealing positions between fungi and host plants. Although fungal-specific primers have been designed, plant DNA continues to be excessively amplified by PCR, resulting in the underestimation of community structures. In order to overcome this limitation, locked nucleic acid (LNA) primers and PCR clamping by LNA oligonucleotides have been applied to enhance the amplification of fungal internal transcribed spacer (ITS) regions. LNA primers were designed by converting DNA into LNA, which is specific to fungi, at the forward primer side. LNA oligonucleotides, the sequences of which are complementary to the host plants, were designed by overlapping a few bases with the annealing position of the reverse primer. Plant-specific DNA was then converted into LNA at the shifted position from the 3′ end of the primer–binding position. PCR using the LNA technique enhanced the amplification of fungal ITS regions, whereas those of the host plants were more likely to be amplified without the LNA technique. A denaturing gradient gel electrophoresis (DGGE) analysis displayed patterns that reached an acceptable level for investigating the community structures of plant–associated fungi using the LNA technique. The sequences of the bands detected using the LNA technique were mostly affiliated with known isolates. However, some sequences showed low similarities, indicating the potential to identify novel fungi. Thus, the application of the LNA technique is considered effective for widening the scope of community analyses of plant–associated fungi. PMID:27600711

A Prospective Study on the Predictive Value of Plasma BK Virus-DNA Load for Hemorrhagic Cystitis in Pediatric Patients After Stem Cell Transplantation.

PubMed

Cesaro, Simone; Tridello, Gloria; Pillon, Marta; Calore, Elisabetta; Abate, Davide; Tumino, Manuela; Carucci, Nicolina; Varotto, Stefania; Cannata, Elisa; Pegoraro, Anna; Barzon, Luisa; Palù, Giorgio; Messina, Chiara

2015-06-01

In hematopoietic stem cell transplantation (HSCT), late hemorrhagic cystitis (HC) has been associated with BK virus (BKV) infection. We assessed the value of plasma BKV load in predicting HC. Plasma and urine BKV-DNA load were assessed prospectively in 107 pediatric patients. Twenty patients developed grade II and III HC, with 100-day cumulative incidence of 18.8%. At diagnosis of HC, the median load of BKV DNA was 2.3 × 10(3) copies/mL. A plasma BKV-DNA load of 10(3) copies/mL had a sensitivity of 100% and a specificity of 86% with a negative predictive value (NPV) of 100% and a positive predictive value (PPV) of 39% for HC. A urine BKV-DNA load of >10(7) copies/mL had a sensitivity of 86% and a specificity of 60% with a NPV of 98% and a PPV of 14% for HC. A BKV load of 10(3) copies/mL on plasma was significantly associated with HC in multivariate analysis (hazard ratio [HR], 6.1; P = .0006). Patients with HC had a significantly higher risk of mortality than patients who did not have HC (HR, 2.6; P = .018). The above values were used to monitor plasma BKV-DNA load, and they provided a better prediction of patients at risk of HC than urine BKV-DNA load. © The Author 2014. Published by Oxford University Press on behalf of the Pediatric Infectious Diseases Society. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Global changes in DNA methylation in Alzheimer's disease peripheral blood mononuclear cells.

PubMed

Di Francesco, Andrea; Arosio, Beatrice; Falconi, Anastasia; Micioni Di Bonaventura, Maria Vittoria; Karimi, Mohsen; Mari, Daniela; Casati, Martina; Maccarrone, Mauro; D'Addario, Claudio

2015-03-01

Changes in epigenetic marks may help explain the late onset of Alzheimer's disease (AD). In this study we measured genome-wide DNA methylation by luminometric methylation assay, a quantitative measurement of genome-wide DNA methylation, on DNA isolated from peripheral blood mononuclear cells of 37 subjects with late-onset AD (LOAD) and 44 healthy controls (CT). We found an increase in global DNA methylation in LOAD subjects compared to CT (p=0.0122), associated with worse cognitive performances (p=0.0002). DNA hypermethylation in LOAD group was paralleled by higher DNA methyltransferase 1 (DNMT1) gene expression and protein levels. When data were stratified on the basis of the APOE polymorphisms, higher DNA methylation levels were associated with the presence of APOE ε4 allele (p=0.0043) in the global population. Among the APOE ε3 carriers, a significant increase of DNA methylation was still observed in LOAD patients compared to healthy controls (p=0.05). Our data suggest global DNA methylation in peripheral samples as a useful marker for screening individuals at risk of developing AD. Copyright © 2014 Elsevier Inc. All rights reserved.

Cdc45-induced loading of human RPA onto single-stranded DNA.

PubMed

Szambowska, Anna; Tessmer, Ingrid; Prus, Piotr; Schlott, Bernhard; Pospiech, Helmut; Grosse, Frank

2017-04-07

Cell division cycle protein 45 (Cdc45) is an essential component of the eukaryotic replicative DNA helicase. We found that human Cdc45 forms a complex with the single-stranded DNA (ssDNA) binding protein RPA. Moreover, it actively loads RPA onto nascent ssDNA. Pull-down assays and surface plasmon resonance studies revealed that Cdc45-bound RPA complexed with ssDNA in the 8-10 nucleotide binding mode, but dissociated when RPA covered a 30-mer. Real-time analysis of RPA-ssDNA binding demonstrated that Cdc45 catalytically loaded RPA onto ssDNA. This placement reaction required physical contacts of Cdc45 with the RPA70A subdomain. Our results imply that Cdc45 controlled stabilization of the 8-nt RPA binding mode, the subsequent RPA transition into 30-mer mode and facilitated an ordered binding to ssDNA. We propose that a Cdc45-mediated loading guarantees a seamless deposition of RPA on newly emerging ssDNA at the nascent replication fork. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Reliability at the Lower Limits of HIV-1 RNA Quantification in Clinical Samples: A Comparison of RT-PCR versus bDNA Assays

PubMed Central

Lubelchek, Ronald J.; Max, Blake; Sandusky, Caroline J.; Hota, Bala; Barker, David E.

2009-01-01

Introduction To explore whether an assay change was responsible for an increasing proportion of patients with undetectable HIV viral loads at our urban HIV clinic, we selected highly stable patients, examining their viral loads before and after changing assays. We compared the proportion with detectable viremia during RT-PCR vs. bDNA periods. Methodology/Principal Findings We selected patients with ≥1 viral loads assessed during both RT-PCR and bDNA periods. We included patients with stable CD4 counts, excluding patients with viral loads ≥1,000 copies/ml or any significant changes in therapy. Out of 4500 clinic patients, 419 patients (1588 viral loads) were included. 39% of viral loads were reported as detectable by RT-PCR vs. 5% reported as detectable by bDNA. The mean coefficient of variation was higher before vs. after assay change. We found an odds' ratio of 16.7 for having a viral load >75 copies/ml during the RT-PCR vs. bDNA periods. Discussion These data support previous reports, suggesting that bDNA may more reliably discriminate between viral suppression and low level viremia in stable patients on therapy. Low-level viremia, noted more with RT-PCR, may promote unneeded testing, while differences in viral load reliability may impact antiretroviral trial and quality assurance endpoints. Commonly used plasma separator tubes may differentially affect RT-PCR and bDNA results. PMID:19547711

Use of bDNA testing in the immunologically nonresponding patient who has a low or undetectable viral load by RT-PCR testing.

PubMed

Grimes, Richard M; Lewis, Stanley T; Visnegarwala, Fehmida; Goodly, Joseph; Sutton, Richard; Rodriguez-Barradas, Maria

2003-01-01

Studies have shown that reverse transcription-polymerase chain reaction (RT-PCR) technology underquantifies viral loads in patients with non-B clades of HIV-1. Testing with bDNA technology gave higher viral loads in these subtypes. A study was conducted to determine whether virologically responding patients on HAART who were not immunologically responding would have higher viral loads using bDNA technology and whether these differences were due to non-B clades. Forty-eight patients receiving HAART for more than 6 months who were having inappropriate immunologic responses in spite of undetectable or very low viral loads determined by RT-PCR (<3000 copies by Roche Amplicor 1.0) were studied. These patients had bDNA viral loads performed. All patients who had bDNA viral loads equivalent to >3000 by RT-PCR had clade and genotypic studies performed. Fifteen patients had viral loads by bDNA that were equivalent to >3000 copies by RT-PCR. Four of these were found to have non-B clades (one D clade and three AG clade). The D clade patient had multidrug resistance; none of the AG clade patients had resistance. Of the remaining 11 patients, virus could not be recovered from 2 and 9 had a B clade. Six of these nine had genotypic resistance to HAART drugs. bDNA testing may be useful in the immunologically nonresponding patient.

Isolated and soft-switched power converter

DOEpatents

Peng, Fang Zheng; Adams, Donald Joe

2002-01-01

An isolated and soft-switched power converter is used for DC/DC and DC/DC/AC power conversion. The power converter includes two resonant tank circuits coupled back-to-back through an isolation transformer. Each resonant tank circuit includes a pair of resonant capacitors connected in series as a resonant leg, a pair of tank capacitors connected in series as a tank leg, and a pair of switching devices with anti-parallel clamping diodes coupled in series as resonant switches and clamping devices for the resonant leg. The power converter is well suited for DC/DC and DC/DC/AC power conversion applications in which high-voltage isolation, DC to DC voltage boost, bidirectional power flow, and a minimal number of conventional switching components are important design objectives. For example, the power converter is especially well suited to electric vehicle applications and load-side electric generation and storage systems, and other applications in which these objectives are important. The power converter may be used for many different applications, including electric vehicles, hybrid combustion/electric vehicles, fuel-cell powered vehicles with low-voltage starting, remote power sources utilizing low-voltage DC power sources, such as photovoltaics and others, electric power backup systems, and load-side electric storage and generation systems.

The dynamic natures of implant loading.

PubMed

Wang, Rui-Feng; Kang, Byungsik; Lang, Lisa A; Razzoog, Michael E

2009-06-01

A fundamental problem in fully understanding the dynamic nature of implant loading is the confusion that exists regarding the torque load delivered to the implant complex, the initial force transformation/stress/strain developed within the system during the implant complex assembly, and how the clamping forces at the interfaces and the preload stress impact the implant prior to any external loading. The purpose of this study was to create an accurately dimensioned finite element model with spiral threads and threaded bores included in the implant complex, positioned in a bone model, and to determine the magnitude and distribution of the force transformation/stress/strain patterns developed in the modeled implant system and bone and, thus, provide the foundational data for the study of the dynamic loading of dental implants prior to any external loading. An implant (Brånemark Mark III), abutment (CeraOne), abutment screw (Unigrip), and the bone surrounding the implant were modeled using HyperMesh software. The threaded interfaces between screw/implant and implant/bone were designed as a spiral thread helix assigned with specific coefficient of friction values. Assembly simulation using ABAQUS and LS-DYNA was accomplished by applying a 32-Ncm horizontal torque load on the abutment screw (Step 1), then decreasing the torque load to 0 Ncm to simulate the wrench removal (Step 2). The postscript data were collected and reviewed by HyperMesh. A regression analysis was used to depict the relationships between the torque load and the mechanical parameters. During the 32-Ncm tightening sequence, the abutment screw elongated 13.3 mum. The tightening torque generated a 554-N clamping force at the abutment/implant interface and a 522-N preload. The von Mises stress values were 248 MPa in the abutment at the abutment-implant interface, 765 MPa at the top of the screw shaft, 694 MPa at the bottom of the screw shaft, 1365 MPa in the top screw thread, and 21 MPa in the bone at the top of the implant-bone interface. This study also identified various characteristic isosurface stress patterns. The maximum stress magnitude to complete the von Mises stress joint pattern in the present model was 107 MPa during screw tightening, and was reduced to 104 MPa with removal of the wrench. Various specific stress patterns were identified within all elements of the implant complex during the assembly simulation. During the torque moment application, the abutment screw was elongated, and every 1.0-mum elongation of the screw was equivalent to a 47.9-N increase of the preload in the implant complex. The ideal index to determine the preload amount was the contact force at the interface between the screw threads and the threaded screw bore. The isosurface mode identified various characteristic stress patterns developed within the implant complex at the various interfaces during the assembly simulation. These patterns are the (1) spiral and ying-yang pattern of the XY stress, (2) spring, cap, clamping, and preload pattern of the ZZ stress, and (3) bone holding and joint pattern of the von Mises stress.

Measurement of Epstein-Barr virus DNA load using a novel quantification standard containing two EBV DNA targets and SYBR Green I dye.

PubMed

Lay, Meav-Lang J; Lucas, Robyn M; Ratnamohan, Mala; Taylor, Janette; Ponsonby, Anne-Louise; Dwyer, Dominic E

2010-09-22

Reactivation of Epstein-Barr virus (EBV) infection may cause serious, life-threatening complications in immunocompromised individuals. EBV DNA is often detected in EBV-associated disease states, with viral load believed to be a reflection of virus activity. Two separate real-time quantitative polymerase chain reaction (QPCR) assays using SYBR Green I dye and a single quantification standard containing two EBV genes, Epstein-Barr nuclear antigen-1 (EBNA-1) and BamHI fragment H rightward open reading frame-1 (BHRF-1), were developed to detect and measure absolute EBV DNA load in patients with various EBV-associated diseases. EBV DNA loads and viral capsid antigen (VCA) IgG antibody titres were also quantified on a population sample. EBV DNA was measurable in ethylenediaminetetraacetic acid (EDTA) whole blood, peripheral blood mononuclear cells (PBMCs), plasma and cerebrospinal fluid (CSF) samples. EBV DNA loads were detectable from 8.0 × 10(2) to 1.3 × 10(8) copies/ml in post-transplant lymphoproliferative disease (n = 5), 1.5 × 10(3) to 2.0 × 10(5) copies/ml in infectious mononucleosis (n = 7), 7.5 × 10(4) to 1.1 × 10(5) copies/ml in EBV-associated haemophagocytic syndrome (n = 1), 2.0 × 10(2) to 5.6 × 10(3) copies/ml in HIV-infected patients (n = 12), and 2.0 × 10(2) to 9.1 × 10(4) copies/ml in the population sample (n = 218). EBNA-1 and BHRF-1 DNA were detected in 11.0% and 21.6% of the population sample respectively. There was a modest correlation between VCA IgG antibody titre and BHRF-1 DNA load (rho = 0.13, p = 0.05) but not EBNA-1 DNA load (rho = 0.11, p = 0.11). Two sensitive and specific real-time PCR assays using SYBR Green I dye and a single quantification standard containing two EBV DNA targets, were developed for the detection and measurement of EBV DNA load in a variety of clinical samples. These assays have application in the investigation of EBV-related illnesses in immunocompromised individuals.

Toward Standardization of Epstein-Barr Virus DNA Load Monitoring: Unfractionated Whole Blood as Preferred Clinical Specimen

PubMed Central

Stevens, Servi J. C.; Pronk, Inge; Middeldorp, Jaap M.

2001-01-01

Epstein-Barr virus (EBV) DNA load monitoring in peripheral blood has been shown to be a useful tool for the diagnosis of aberrant EBV infections. In the present study we compared the relative diagnostic values of EBV DNA load monitoring in unfractionated whole blood and simultaneously obtained serum or plasma samples from Burkitt's lymphoma (BL) patients, transplant recipients, human immunodeficiency virus (HIV)-infected individuals, and infectious mononucleosis (IM) patients by a quantitative competitive PCR (Q-PCR). The EBV DNA load in BL patients was mainly situated in the cellular blood compartment (up to 4.5 × 106 copies/ml). EBV DNA loads in unfractionated whole blood and parallel serum samples showed no correlation. In transplant recipients, IM patients, and HIV-infected patients, the EBV burden in the circulation was almost exclusively restricted to the cellular blood compartment, because serum or plasma samples from these patients yielded negative results by Q-PCR, despite high viral loads in corresponding whole-blood samples. A 10-fold more sensitive but qualitative BamHI-W-repeat PCR occasionally revealed the presence of EBV at <2,000 copies of EBV DNA per ml of serum. Spiking of 100 copies of EBV DNA in samples with negative Q-PCR results excluded the presence of inhibitory factors in serum or plasma that influenced the Q-PCR result. Serum samples from all populations were often positive for β-globin DNA, indicating cell damage in vivo or during serum preparation. We conclude that serum is an undesirable clinical specimen for EBV DNA load monitoring because it omits the presence of cell-associated virus and uncontrolled cell lysis may give irreproducible results or overestimation of the DNA load. Unfractionated whole blood is strongly preferred since it combines all blood compartments that may harbor EBV and it best reflects the absolute viral burden in the patient's circulation. PMID:11283029

Glove box shield

DOEpatents

Brackenbush, Larry W.; Hoenes, Glenn R.

1981-01-01

According to the present invention, a shield for a glove box housing radioactive material is comprised of spaced apart clamping members which maintain three overlapping flaps in place therebetween. There is a central flap and two side flaps, the side flaps overlapping at the interior edges thereof and the central flap extending past the intersection of the side flaps in order to insure that the shield is always closed when the user withdraws his hand from the glove box. Lead loaded neoprene rubber is the preferred material for the three flaps, the extent of lead loading depending upon the radiation levels within the glove box.

Axisymmetric buckling of the circular graphene sheets with the nonlocal continuum plate model

NASA Astrophysics Data System (ADS)

Farajpour, A.; Mohammadi, M.; Shahidi, A. R.; Mahzoon, M.

2011-08-01

In this article, the buckling behavior of nanoscale circular plates under uniform radial compression is studied. Small-scale effect is taken into consideration. Using nonlocal elasticity theory the governing equations are derived for the circular single-layered graphene sheets (SLGS). Explicit expressions for the buckling loads are obtained for clamped and simply supported boundary conditions. It is shown that nonlocal effects play an important role in the buckling of circular nanoplates. The effects of the small scale on the buckling loads considering various parameters such as the radius of the plate and mode numbers are investigated.

High voltage dc--dc converter with dynamic voltage regulation and decoupling during load-generated arcs

DOEpatents

Shimer, D.W.; Lange, A.C.

1995-05-23

A high-power power supply produces a controllable, constant high voltage output under varying and arcing loads. The power supply includes a voltage regulator, an inductor, an inverter for producing a high frequency square wave current of alternating polarity, an improved inverter voltage clamping circuit, a step up transformer, an output rectifier for producing a dc voltage at the output of each module, and a current sensor for sensing output current. The power supply also provides dynamic response to varying loads by controlling the voltage regulator duty cycle and circuitry is provided for sensing incipient arc currents at the output of the power supply to simultaneously decouple the power supply circuitry from the arcing load. The power supply includes a plurality of discrete switching type dc--dc converter modules. 5 Figs.

High voltage dc-dc converter with dynamic voltage regulation and decoupling during load-generated arcs

DOEpatents

Shimer, Daniel W.; Lange, Arnold C.

1995-01-01

A high-power power supply produces a controllable, constant high voltage output under varying and arcing loads. The power supply includes a voltage regulator, an inductor, an inverter for producing a high frequency square wave current of alternating polarity, an improved inverter voltage clamping circuit, a step up transformer, an output rectifier for producing a dc voltage at the output of each module, and a current sensor for sensing output current. The power supply also provides dynamic response to varying loads by controlling the voltage regulator duty cycle and circuitry is provided for sensing incipient arc currents at the output of the power supply to simultaneously decouple the power supply circuitry from the arcing load. The power supply includes a plurality of discrete switching type dc--dc converter modules.

Base excision repair in Archaea: back to the future in DNA repair.

PubMed

Grasso, Stefano; Tell, Gianluca

2014-09-01

Together with Bacteria and Eukarya, Archaea represents one of the three domain of life. In contrast with the morphological difference existing between Archaea and Eukarya, these two domains are closely related. Phylogenetic analyses confirm this evolutionary relationship showing that most of the proteins involved in DNA transcription and replication are highly conserved. On the contrary, information is scanty about DNA repair pathways and their mechanisms. In the present review the most important proteins involved in base excision repair, namely glycosylases, AP lyases, AP endonucleases, polymerases, sliding clamps, flap endonucleases, and ligases, will be discussed and compared with bacterial and eukaryotic ones. Finally, possible applications and future perspectives derived from studies on Archaea and their repair pathways, will be taken into account. Copyright © 2014 Elsevier B.V. All rights reserved.

HBsAg level and hepatitis B viral load correlation with focus on pregnancy

PubMed Central

Belopolskaya, Maria; Avrutin, Viktor; Firsov, Sergey; Yakovlev, Alexey

2015-01-01

Background Viral load measurement is necessary to estimate mother-to-child transmission risk for women with chronic hepatitis B (CHB), however, it is expensive. The present study aimed to investigate the relationship between HBsAg and hepatitis B virus (HBV) DNA levels, and to determine potential applications of HBsAg level monitoring for estimating viral load. Methods 85 patients with CHB (31 pregnant women, 26 non-pregnant women, 28 men) were included in the study. HBV DNA level was measured by real-time PCR, and HBsAg level by chemiluminescent immunoassay method. Dependency between viral load and HBsAg level was determined by Spearman correlation coefficient ρ. Results The correlation between HBsAg and HBV DNA levels was significant for all patients [ρ=0.3762 (P<0.0005; n=85)]. In the group of pregnant women, a low (unmeasurable) HBV DNA level led to a decrease in the Spearman coefficient ρ. In almost all cases a low level of the HBsAg corresponded to a low HBV DNA level. Only 2 patients had a low level of HBsAg and a relatively high viral load. By contrast, a high HBsAg level was observed in patients both with high and low viral load. Conclusions Correlation between HBsAg and HBV DNA levels is significant. In most cases, a low level of HBsAg indicates a low HBV DNA level, whereas a high HBsAg level does not always correspond to a high viral load. The measurement of HBV DNA level is necessary for pregnant women with a high HBsAg level. PMID:26127004

Mechanics of hydrogenated amorphous carbon deposits from electron-beam-induced deposition of a paraffin precursor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ding, W.; Dikin, D.A.; Chen, X.

2005-07-01

Many experiments on the mechanics of nanostructures require the creation of rigid clamps at specific locations. In this work, electron-beam-induced deposition (EBID) has been used to deposit carbon films that are similar to those that have recently been used for clamping nanostructures. The film deposition rate was accelerated by placing a paraffin source of hydrocarbon near the area where the EBID deposits were made. High-resolution transmission electron microscopy, electron-energy-loss spectroscopy, Raman spectroscopy, secondary-ion-mass spectrometry, and nanoindentation were used to characterize the chemical composition and the mechanics of the carbonaceous deposits. The typical EBID deposit was found to be hydrogenated amorphousmore » carbon (a-C:H) having more sp{sup 2}- than sp{sup 3}-bonded carbon. Nanoindentation tests revealed a hardness of {approx}4 GPa and an elastic modulus of 30-60 GPa, depending on the accelerating voltage. This reflects a relatively soft film, which is built out of precursor molecular ions impacting the growing surface layer with low energies. The use of such deposits as clamps for tensile tests of poly(acrylonitrile)-based carbon nanofibers loaded between opposing atomic force microscope cantilevers is presented as an example application.« less

NUMERICAL SIMULATION OF NANOINDENTATION AND PATCH CLAMP EXPERIMENTS ON MECHANOSENSITIVE CHANNELS OF LARGE CONDUCTANCE IN ESCHERICHIA COLI

PubMed Central

Tang, Yuye; Chen, Xi; Yoo, Jejoong; Yethiraj, Arun; Cui, Qiang

2010-01-01

A hierarchical simulation framework that integrates information from all-atom simulations into a finite element model at the continuum level is established to study the mechanical response of a mechanosensitive channel of large conductance (MscL) in bacteria Escherichia Coli (E.coli) embedded in a vesicle formed by the dipalmitoylphosphatidycholine (DPPC) lipid bilayer. Sufficient structural details of the protein are built into the continuum model, with key parameters and material properties derived from molecular mechanics simulations. The multi-scale framework is used to analyze the gating of MscL when the lipid vesicle is subjective to nanoindentation and patch clamp experiments, and the detailed structural transitions of the protein are obtained explicitly as a function of external load; it is currently impossible to derive such information based solely on all-atom simulations. The gating pathways of E.coli-MscL qualitatively agree with results from previous patch clamp experiments. The gating mechanisms under complex indentation-induced deformation are also predicted. This versatile hierarchical multi-scale framework may be further extended to study the mechanical behaviors of cells and biomolecules, as well as to guide and stimulate biomechanics experiments. PMID:21874098

Mechanical testing and development of the helical field coil joint for the Advanced Toroidal Facility

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nelson, B.E.; Bryan, W.E.; Goranson, P.L.

1985-01-01

The helical field (HF) coil set for the Advanced Toroidal Facility (ATF) is an M = 12, l = 2, constant-ratio torsatron winding consisting of 2 coils, each with 14 turns of heavy copper conductor. The coils are divided into 24 identical segments to facilitate fabrication and minimize the assembly schedule. The segments are connected across through-bolted lap joints that must carry up to 124,000 A per turn for 5 s or 62,500 A steady-state. In addition, the joints must carry the high magnetic and thermal loads induced in the conductor and still fit within the basic 140- by 30-mmmore » copper envelope. Extensive testing and development were undertaken to verify and refine the basic joint design. Tests included assembly force and clamping force for various types of misalignment; joint resistance as a function of clamping force; clamp bolt relaxation due to thermal cycling; fatigue testing of full-size, multiturn joint prototypes; and low-cycle fatigue and tensile tests of annealed CDA102 copper. The required performance parameters and actual test results, as well as the final joint configuration, are presented. 2 refs., 9 figs., 4 tabs.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Freudenthal, Bret D.; Beard, William A.; Cuneo, Matthew J.

DNA apurinic-apyrimidinic (AP) sites are prevalent noncoding threats to genomic stability and are processed by AP endonuclease 1 (APE1). APE1 incises the AP-site phosphodiester backbone, generating a DNA-repair intermediate that is potentially cytotoxic. The molecular events of the incision reaction remain elusive, owing in part to limited structural information. Here we report multiple high-resolution human APE1-DNA structures that divulge new features of the APE1 reaction, including the metal-binding site, the nucleophile and the arginine clamps that mediate product release. We also report APE1-DNA structures with a T-G mismatch 5' to the AP site, representing a clustered lesion occurring in methylatedmore » CpG dinucleotides. Moreover, these structures reveal that APE1 molds the T-G mismatch into a unique Watson-Crick-like geometry that distorts the active site, thus reducing incision. Finally, these snapshots provide mechanistic clarity for APE1 while affording a rational framework to manipulate biological responses to DNA damage.« less

The force-dependent mechanism of DnaK-mediated mechanical folding

PubMed Central

Perales-Calvo, Judit; Giganti, David; Stirnemann, Guillaume; Garcia-Manyes, Sergi

2018-01-01

It is well established that chaperones modulate the protein folding free-energy landscape. However, the molecular determinants underlying chaperone-mediated mechanical folding remain largely elusive, primarily because the force-extended unfolded conformation fundamentally differs from that characterized in biochemistry experiments. We use single-molecule force-clamp spectroscopy, combined with molecular dynamics simulations, to study the effect that the Hsp70 system has on the mechanical folding of three mechanically stiff model proteins. Our results demonstrate that, when working independently, DnaJ (Hsp40) and DnaK (Hsp70) work as holdases, blocking refolding by binding to distinct substrate conformations. Whereas DnaK binds to molten globule–like forms, DnaJ recognizes a cryptic sequence in the extended state in an unanticipated force-dependent manner. By contrast, the synergetic coupling of the Hsp70 system exhibits a marked foldase behavior. Our results offer unprecedented molecular and kinetic insights into the mechanisms by which mechanical force finely regulates chaperone binding, directly affecting protein elasticity. PMID:29487911

Ligand Assisted Stabilization of Fluorescence Nanoparticles; an Insight on the Fluorescence Characteristics, Dispersion Stability and DNA Loading Efficiency of Nanoparticles.

PubMed

Rhouati, Amina; Hayat, Akhtar; Mishra, Rupesh K; Bueno, Diana; Shahid, Shakir Ahmad; Muñoz, Roberto; Marty, Jean Louis

2016-07-01

This work reports on the ligand assisted stabilization of Fluospheres® carboxylate modified nanoparticles (FCMNPs), and subsequently investigation on the DNA loading capacity and fluorescence response of the modified particles. The designed fluorescence bioconjugate was characterized with enhanced fluorescence characteristics, good stability and large surface area with high DNA loading efficiency. For comparison purpose, bovine serum albumin (BSA) and polyethylene glycol (PEG) with three different length strands were used as cross linkers to modify the particles, and their DNA loading capacity and fluorescence characteristics were investigated. By comparing the performance of the particles, we found that the most improved fluorescence characteristics, enhanced DNA loading and high dispersion stability were obtained, when employing PEG of long spacer arm length. The designed fluorescence bioconjugate was observed to maintain all its characteristics under varying pH over an extended period of time. These types of bioconjugates are in great demand for fluorescence imaging and in vivo fluorescence biomedical application, especially when most of the as synthesized fluorescence particles cannot withstand to varying in vivo physiological conditions with decreases in fluorescence response and DNA loading efficiency.

Dynamic properties of unbonded, multi-strand beams subjected to flexural loading

NASA Astrophysics Data System (ADS)

Asker, Haval K.; Rongong, Jem A.; Lord, Charles E.

2018-02-01

Beam-like structures, constructed from many long strands that are constrained rather than bonded together, can provide appreciable levels of structural damping through friction between individual strands. This paper describes experimental and numerical studies, carried out on square-section metal beams, which are aimed at improving understanding of the relationship between construction and performance. A beam is formed from a pack of square-section strands that is held together at various compression loads with pre-calibrated clamps. Flexural deformation of the assembled beam is simulated using standard finite element analysis employing simple Coulomb friction at the interfaces. The validity of the assumptions used in the models is confirmed by comparison with three point bend tests on a regular nine strand construction at several different clamp loads. Dynamic loss factors for this beam are obtained by conducting forced vibration tests, which show that the damping is insensitive to frequency. Subsequent numerical studies are used to investigate the effects of increasing the number of strands whilst maintaining the overall cross-section geometry of the beam. It is found that the system stiffness drops and loss factor increases when more strands are used for a maintained beam cross-section. Interestingly, the energy dissipated by each beam construction is almost the same. These results provide a vital and necessary insight into the physics for stranded structures and materials that are largely prevalent in mechanical (e.g. cables) and electrical (e.g. wires) elements.

Effect of lubricant on the reliability of dental implant abutment screw joint: An in vitro laboratory and three-dimension finite element analysis.

PubMed

Wu, Tingting; Fan, Hongyi; Ma, Ruiyang; Chen, Hongyu; Li, Zhi; Yu, Haiyang

2017-06-01

Biomechanical factors play a key role in the success of dental implants. Fracture and loosening of abutment screws are major issues. This study investigated the effect of lubricants on the stability of dental implant-abutment connection. As lubricants, graphite and vaseline were coated on the abutment screw surface, respectively, and a blank without lubricant served as the control. The total friction coefficient (μ tot ), clamping force, fatigue behavior and detorque of the joint combined with dynamic cyclic loading were measured under different lubricating conditions. Further, a three-dimensional finite element analysis was used to investigate stress distribution, in conjunction with experimental images. The results showed that the lubricant reduced μ tot , which in turn led to an increase in clamping force. Decrease in loading increased the fatigue life of the screw. However, use of lubricant at high load reduced the fatigue life. Ductile fracture at the first thread of the screw was the chief failure mode, which was due to maximum von Mises stress. Higher stress levels occurred in the lubricant groups. Lubricated screws resulted in lower detorque which made the joint easier to loosen. In conclusion, the lubricant cannot effectively improve the reliability of dental implant-abutment connection. Keeping the interfaces of implant-screw uncontaminated and strengthening the surface of the screw may be recommend for clinical operation and future design. Copyright © 2016 Elsevier B.V. All rights reserved.

Vibration Testing of Electrical Cables to Quantify Loads at Tie-Down Locations

NASA Technical Reports Server (NTRS)

Dutson, Joseph D.

2013-01-01

The standard method for defining static equivalent structural load factors for components is based on Mile s equation. Unless test data is available, 5% critical damping is assumed for all components when calculating loads. Application of this method to electrical cable tie-down hardware often results in high loads, which often exceed the capability of typical tie-down options such as cable ties and P-clamps. Random vibration testing of electrical cables was used to better understand the factors that influence component loads: natural frequency, damping, and mass participation. An initial round of vibration testing successfully identified variables of interest, checked out the test fixture and instrumentation, and provided justification for removing some conservatism in the standard method. Additional testing is planned that will include a larger range of cable sizes for the most significant contributors to load as variables to further refine loads at cable tie-down points. Completed testing has provided justification to reduce loads at cable tie-downs by 45% with additional refinement based on measured cable natural frequencies.

The influence of freezing on the tensile strength of tendon grafts : a biomechanical study.

PubMed

Arnout, Nele; Myncke, Jan; Vanlauwe, Johan; Labey, Luc; Lismont, Daniel; Bellemans, Johan

2013-08-01

We investigated the influence of freezing on the tensile strength of fresh frozen tendon grafts. The biomechanical characteristics of tendons that are less commonly used in knee surgery (tibialis anterior, tibialis posterior, peroneus longus and medial and lateral half of Achilles tendons) were compared to those of a semitendinosus and gracilis graft harvested from the same 10 multi-organ donors. All right side tendons constituted the study group and were frozen at -80 degrees C and thawed at room temperature 5 times. All left side tendons were frozen at -80 degrees C and thawed at room temperature once. There were 59 tendons in the control group and 56 in the study group. The looped grafts were clamped at one side using a custom-made freeze clamp and loaded until failure on an Instron 4505 testing machine. The average ultimate failure load was not significantly different between the control and the study group (p > 0.05). The failure load of the medial tendon Achilles was the lowest in both study and control group (p < 0.001). There was no significant difference in maximum stress, maximum displacement, maximum strain and stiffness between the control and study group (p > 0.05). From our study, we conclude that freezing tendons at -80 degrees C and thawing several times does not influence the maximum load, maximum stress, maximum displacement, maximum strain and stiffness. The medial half of the Achilles tendon is clearly the weakest tendon (p < 0.001). These findings show that tendon grafts can be frozen at -80 degrees C and thawed at room temperature several times without altering their biomechanical properties.

Loop-Mediated Isothermal Amplification for Laboratory Confirmation of Buruli Ulcer Disease—Towards a Point-of-Care Test

PubMed Central

Beissner, Marcus; Phillips, Richard Odame; Battke, Florian; Bauer, Malkin; Badziklou, Kossi; Sarfo, Fred Stephen; Maman, Issaka; Rhomberg, Agata; Piten, Ebekalisai; Frimpong, Michael; Huber, Kristina Lydia; Symank, Dominik; Jansson, Moritz; Wiedemann, Franz Xaver; Banla Kere, Abiba; Herbinger, Karl-Heinz; Löscher, Thomas; Bretzel, Gisela

2015-01-01

Background As the major burden of Buruli ulcer disease (BUD) occurs in remote rural areas, development of point-of-care (POC) tests is considered a research priority to bring diagnostic services closer to the patients. Loop-mediated isothermal amplification (LAMP), a simple, robust and cost-effective technology, has been selected as a promising POC test candidate. Three BUD-specific LAMP assays are available to date, but various technical challenges still hamper decentralized application. To overcome the requirement of cold-chains for transport and storage of reagents, the aim of this study was to establish a dry-reagent-based LAMP assay (DRB-LAMP) employing lyophilized reagents. Methodology/Principal Findings Following the design of an IS2404 based conventional LAMP (cLAMP) assay suitable to apply lyophilized reagents, a lyophylization protocol for the DRB-LAMP format was developed. Clinical performance of cLAMP was validated through testing of 140 clinical samples from 91 suspected BUD cases by routine assays, i.e. IS2404 dry-reagent-based (DRB) PCR, conventional IS2404 PCR (cPCR), IS2404 qPCR, compared to cLAMP. Whereas qPCR rendered an additional 10% of confirmed cases and samples respectively, case confirmation and positivity rates of DRB-PCR or cPCR (64.84% and 56.43%; 100% concordant results in both assays) and cLAMP (62.64% and 52.86%) were comparable and there was no significant difference between the sensitivity of the assays (DRB PCR and cPCR, 86.76%; cLAMP, 83.82%). Likewise, sensitivity of cLAMP (95.83%) and DRB-LAMP (91.67%) were comparable as determined on a set of 24 samples tested positive in all routine assays. Conclusions/Significance Both LAMP formats constitute equivalent alternatives to conventional PCR techniques. Provided the envisaged availability of field friendly DNA extraction formats, both assays are suitable for decentralized laboratory confirmation of BUD, whereby DRB-LAMP scores with the additional advantage of not requiring cold-chains. As validation of the assays was conducted in a third-level laboratory environment, field based evaluation trials are necessary to determine the clinical performance at peripheral health care level. PMID:26566026

Panel flutter optimization by gradient projection

NASA Technical Reports Server (NTRS)

Pierson, B. L.

1975-01-01

A gradient projection optimal control algorithm incorporating conjugate gradient directions of search is described and applied to several minimum weight panel design problems subject to a flutter speed constraint. New numerical solutions are obtained for both simply-supported and clamped homogeneous panels of infinite span for various levels of inplane loading and minimum thickness. The minimum thickness inequality constraint is enforced by a simple transformation of variables.

Use of vacuum tubes in test instrumentation for measuring characteristics of fast high-voltage semiconductor devices

NASA Technical Reports Server (NTRS)

Berning, D.

1981-01-01

Circuits are described that permit measurement of fast events occurring in power semiconductors. These circuits were developed for the dynamic characterization of transistors used in inductive-load switching applications. Fast voltage clamping using vacuum diodes is discussed, and reference is made to a unique circuit that was built for performing nondestructive, reverse-bias, second-breakdown tests on transistors.

Structural insights into the adaptation of proliferating cell nuclear antigen (PCNA) from Haloferax volcanii to a high-salt environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morgunova, Ekaterina, E-mail: ekaterina.morgunova@ki.se; Gray, Fiona C.; MacNeill, Stuart A.

2009-10-01

The crystal structure of PCNA from the halophilic archaeon H. volcanii reveals specific features of the charge distribution on the protein surface that reflect adaptation to a high-salt environment and suggests a different type of interaction with DNA in halophilic PCNAs. The sliding clamp proliferating cell nuclear antigen (PCNA) plays vital roles in many aspects of DNA replication and repair in eukaryotic cells and in archaea. Realising the full potential of archaea as a model for PCNA function requires a combination of biochemical and genetic approaches. In order to provide a platform for subsequent reverse genetic analysis, PCNA from themore » halophilic archaeon Haloferax volcanii was subjected to crystallographic analysis. The gene was cloned and expressed in Escherichia coli and the protein was purified by affinity chromatography and crystallized by the vapour-diffusion technique. The structure was determined by molecular replacement and refined at 3.5 Å resolution to a final R factor of 23.7% (R{sub free} = 25%). PCNA from H. volcanii was found to be homotrimeric and to resemble other homotrimeric PCNA clamps but with several differences that appear to be associated with adaptation of the protein to the high intracellular salt concentrations found in H. volcanii cells.« less

Epstein-Barr virus (EBV) load in cerebrospinal fluid and peripheral blood of patients with EBV-associated central nervous system diseases after allogeneic hematopoietic stem cell transplantation.

PubMed

Liu, Q-F; Ling, Y-W; Fan, Z-P; Jiang, Q-L; Sun, J; Wu, X-L; Zhao, J; Wei, Q; Zhang, Y; Yu, G-P; Wu, M-Q; Feng, R

2013-08-01

To evaluate the diagnostic and prognostic utility of monitoring the Epstein-Barr virus (EBV) load in the cerebrospinal fluid (CSF) and peripheral blood for the patients with EBV-associated central nervous system (CNS) diseases after allogeneic hematopoietic stem cell transplantation (allo-HSCT), 172 patients undergoing allo-HSCT were enrolled in the study. The EBV DNA levels of blood were monitored regularly in recipients of transplants for 3 years post transplantation. The EBV DNA levels of CSF were monitored in patients with EBV-associated CNS diseases before the treatment and at different points following the treatment. Post-transplant EBV-associated diseases developed in 27 patients, including 12 patients with EBV-associated CNS diseases. The 3-year cumulative incidences of EBV-associated diseases and EBV-associated CNS diseases were 19.5 ± 3.5% and 8.6 ± 2.4%, respectively. Patients with EBV-associated diseases showed higher loads of EBV DNA in their blood compared with patients with EBV DNA-emia. No difference was seen between the EBV DNA levels of blood in patients with CNS involvement and patients without CNS involvement. The EBV DNA loads of blood increased 3-14 days before the clinical manifestations of EBV-associated diseases emerged. The EBV DNA loads of CSF were higher than that of blood in patients with EBV-associated CNS diseases. In 12 patients with EBV-associated CNS diseases, EBV DNA levels were declining in both blood and CSF with the control of diseases, and the EBV DNA loads of CSF decreased faster than that of blood in 5 patients who responded to treatment, and the EBV DNA levels of CSF increased in 5 patients who were unresponsive to treatment. On multivariate analysis, the use of anti-thymocyte globulin and intensified conditioning regimens were independent risk factors for EBV-associated diseases and EBV-associated CNS diseases. EBV-associated CNS diseases are not rare after allo-HSCT. The EBV DNA loads of CSF could act as an important indicator, but the EBV DNA loads of blood could not, for the diagnosis, prognosis, and therapeutic evaluation of EBV-associated CNS diseases. © 2013 John Wiley & Sons A/S.

Biodegradable brain-penetrating DNA nanocomplexes and their use to treat malignant brain tumors

PubMed Central

Mastorakos, Panagiotis; Zhang, Clark; Song, Eric; Kim, Young Eun; Park, Hee Won; Berry, Sneha; Choi, Won Kyu; Hanes, Justin; Suk, Jung Soo

2018-01-01

The discovery of powerful genetic targets has spurred clinical development of gene therapy approaches to treat patients with malignant brain tumors. However, lack of success in the clinic has been attributed to the inability of conventional gene vectors to achieve gene transfer throughout highly disseminated primary brain tumors. Here, we demonstrate ex vivo that small nanocomplexes composed of DNA condensed by a blend of biodegradable polymer, poly(β-amino ester) (PBAE), with PBAE conjugated with 5 kDa polyethylene glycol (PEG) molecules (PBAE-PEG) rapidly penetrate healthy brain parenchyma and orthotopic brain tumor tissues in rats. Rapid diffusion of these DNA-loaded nanocomplexes observed in fresh tissues ex vivo demonstrated that they avoided adhesive trapping in the brain owing to their dense PEG coating, which was critical to achieving widespread transgene expression throughout orthotopic rat brain tumors in vivo following administration by convection enhanced delivery. Transgene expression with the PBAE/PBAE-PEG blended nanocomplexes (DNA-loaded brain-penetrating nanocomplexes, or DNA-BPN) was uniform throughout the tumor core compared to nanocomplexes composed of DNA with PBAE only (DNA-loaded conventional nanocomplexes, or DNA-CN), and transgene expression reached beyond the tumor edge, where infiltrative cancer cells are found, only for the DNA-BPN formulation. Finally, DNA-BPN loaded with anti-cancer plasmid DNA provided significantly enhanced survival compared to the same plasmid DNA loaded in DNA-CN in two aggressive orthotopic brain tumor models in rats. These findings underscore the importance of achieving widespread delivery of therapeutic nucleic acids within brain tumors and provide a promising new delivery platform for localized gene therapy in the brain. PMID:28694032

Probing Conformational Changes in Human DNA Topoisomerase IIα by Pulsed Alkylation Mass Spectrometry*

PubMed Central

Chen, Yu-tsung; Collins, Tammy R. L.; Guan, Ziqiang; Chen, Vincent B.; Hsieh, Tao-Shih

2012-01-01

Type II topoisomerases are essential enzymes for solving DNA topological problems by passing one segment of DNA duplex through a transient double-strand break in a second segment. The reaction requires the enzyme to precisely control DNA cleavage and gate opening coupled with ATP hydrolysis. Using pulsed alkylation mass spectrometry, we were able to monitor the solvent accessibilities around 13 cysteines distributed throughout human topoisomerase IIα by measuring the thiol reactivities with monobromobimane. Most of the measured reactivities are in accordance with the predicted ones based on a homology structural model generated from available crystal structures. However, these results reveal new information for both the residues not covered in the structural model and potential differences between the modeled and solution holoenzyme structures. Furthermore, on the basis of the reactivity changes of several cysteines located at the N-gate and DNA gate, we could monitor the movement of topoisomerase II in the presence of cofactors and detect differences in the DNA gate between two closed clamp enzyme conformations locked by either 5′-adenylyl β,γ-imidodiphosphate or the anticancer drug ICRF-193. PMID:22679013

Diagnostic values for the viral load in peripheral blood mononuclear cells of patients with chronic active Epstein-Barr virus disease.

PubMed

Ito, Yoshinori; Suzuki, Michio; Kawada, Jun-ichi; Kimura, Hiroshi

2016-04-01

Chronic active Epstein-Barr virus disease (CAEBV) is a distinct EBV-associated lymphoproliferative disease with a poor prognosis. Although the viral load in blood samples has been widely used for diagnosing CAEBV, well-defined viral load thresholds to guide clinicians are currently lacking. The aim of the present study was to determine standardized diagnostic values for EBV load in blood samples of CAEBV patients using the World Health Organization international standard for reporting. Levels of EBV DNA in 103 peripheral blood mononuclear cells (PBMCs) and 95 plasma/serum samples from 107 cases with CAEBV were quantified and expressed in international units. Receiver operating characteristic curves were analyzed to assess the most appropriate cut-off values for levels of EBV DNA to distinguish CAEBV from EBV-associated infectious mononucleosis (IM) and controls with past EBV infection. Levels of EBV DNA in PBMCs were significantly higher in the CAEBV group (median, 10(4.2) IU/μgDNA) compared to the IM (median, 10(2.1) IU/μgDNA) and control groups. An inconsistent qualitative result was seen in 13 of 86 CAEBV patients; in these, EBV-DNA was positive in PBMCs, but negative in plasma. Diagnostic cut-off values for viral load in PBMCs from CAEBV patients, as compared to those of healthy controls and IM patients, were 10(2.0) IU/μgDNA and 10(3.2) IU/μgDNA, respectively. For diagnostic purposes, the viral load of PBMCs was better than of plasma/serum. A diagnostic cut-off EBV load for CAEBV may be useful for the management of CAEBV patients. Copyright © 2015 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Electrochemical detection of DNA hybridization based on signal DNA probe modified with Au and apoferritin nanoparticles.

PubMed

Yu, Fengli; Li, Gang; Qu, Bin; Cao, Wei

2010-11-15

A novel and ultrasensitive electrochemical approach for sequence-specific DNA detection based on signal dual-amplification with Au NPs and marker-loaded apoferritin NPs was reported. Target DNA was sandwiched between capture DNA coupled to magnetic beads and signal DNA self-assembled on Au NPs which were incorporated with marker-loaded apoferritin NPs. Subsequent electrochemical stripping analysis of the electroactive markers released from apoferritin NPs in acidic buffers provided a means to quantify the concentration of target DNA. In this means, one target signal could be transformed into multiple redox signals of the markers since a single Au NP could be loaded with dozens of apoferritin NPs, and an apoferritin NP could be loaded with thousands of markers. Under the optimum conditions, the linear range was from 2.0 × 10(-16) to 1.0 × 10(-14)M and the detection limit was 5.1 × 10(-17)M by using the cadmium as a model marker. The proposed DNA biosensor not only exhibited excellent sensitivity but also had good reproducibility and selectivity against two-base mismatched DNA. Copyright © 2010 Elsevier B.V. All rights reserved.

Comparison between gradient-dependent hydraulic conductivities of roots using the root pressure probe: the role of pressure propagations and implications for the relative roles of parallel radial pathways.

PubMed

Bramley, Helen; Turner, Neil C; Turner, David W; Tyerman, Stephen D

2007-07-01

Hydrostatic pressure relaxations with the root pressure probe are commonly used for measuring the hydraulic conductivity (Lp(r)) of roots. We compared the Lp(r) of roots from species with different root hydraulic properties (Lupinus angustifolius L. 'Merrit', Lupinus luteus L. 'Wodjil', Triticum aestivum L. 'Kulin' and Zea mays L. 'Pacific DK 477') using pressure relaxations, a pressure clamp and osmotic gradients to induce water flow across the root. Only the pressure clamp measures water flow under steady-state conditions. Lp(r) determined by pressure relaxations was two- to threefold greater than Lp(r) from pressure clamps and was independent of the direction of water flow. Lp(r) (pressure clamp) was two- to fourfold higher than for Lp(r) (osmotic) for all species except Triticum aestivum where Lp(r) (pressure clamp) and Lp(r) (osmotic) were not significantly different. A novel technique was developed to measure the propagation of pressure through roots to investigate the cause of the differences in Lp(r). Root segments were connected between two pressure probes so that when root pressure (P(r)) was manipulated by one probe, the other probe recorded changes in P(r). Pressure relaxations did not induce the expected kinetics in pressure in the probe at the other end of the root when axial hydraulic conductance, and probe and root capacitances were accounted for. An electric circuit model of the root was constructed that included an additional capacitance in the root loaded by a series of resistances. This accounted for the double exponential kinetics for intact roots in pressure relaxation experiments as well as the reduced response observed with the double probe experiments. Although there were potential errors with all the techniques, we considered that the measurement of Lp(r) using the pressure clamp was the most unambiguous for small pressure changes, and provided that sufficient time was allowed for pressure propagation through the root. The differences in Lp(r) from different methods of measurement have implications for the models describing water transport through roots and the potential role of aquaporins.

Formation and oral administration of alginate microspheres loaded with pDNA coding for lymphocystis disease virus (LCDV) to Japanese flounder.

PubMed

Tian, Ji-Yuan; Sun, Xiu-Qin; Chen, Xi-Guang

2008-05-01

Oral delivery of plasmid DNA (pDNA) is a desirable approach for fish immunization in intensive culture. However, its effectiveness is limited because of possible degradation of pDNA in the fish's digestive system. In this report, alginate microspheres loaded with pDNA coding for fish lymphocystis disease virus (LCDV) and green fluorescent protein were prepared with a modified oil containing water (W/O) emulsification method. Yield, loading percent and encapsulation efficiency of alginate microspheres were 90.5%, 1.8% and 92.7%, respectively. The alginate microspheres had diameters of less than 10 microm, and their shape was spherical. As compared to sodium alginate, a remarkable increase of DNA-phosphodiester and DNA-phosphomonoester bonds was observed for alginate microspheres loaded with pDNA by Fourier transform infrared (FTIR) spectroscopic analysis. Agarose gel electrophoresis showed a little supercoiled pDNA was transformed to open circular and linear pDNA during encapsulation. The cumulative release of pDNA in alginate microspheres was or=0.3) for anti-LCDV antibody from week 3 to week 16 for fish orally vaccinated with alginate microspheres loaded with pDNA, in comparison with fish orally vaccinated with naked pDNA. Our results display that alginate microspheres obtained by W/O emulsification are promising carriers for oral delivery of pDNA. This encapsulation technique has the potential for DNA vaccine delivery applications due to its ease of operation, low cost and significant immune effect.

High-Frequency, High-Temperature Fretting Experiments

NASA Technical Reports Server (NTRS)

Matlik, J. F.; Farris, T. N.; Haake, F. K.; Swanson, G. R.; Duke, G. C.

2005-01-01

Fretting is a structural damage mechanism observed when two nominally clamped surfaces are subjected to an oscillatory loading. A critical location for fretting induced damage has been identified at the blade/disk and blade/damper interfaces of gas turbine engine turbomachinery and space propulsion components. The high-temperature, high-frequency loading environment seen by these components lead to severe stress gradients at the edge-of-contact. These contact stresses drive crack nucleation and propagation in fretting and are very sensitive to the geometry of the contacting bodies, the contact loads, materials, temperature, and contact surface tribology (friction). To diagnose the threat that small and relatively undetectable fretting cracks pose to damage tolerance and structural integrity of in-service components, the objective of this work is to develop a well-characterized experimental fretting rig capable of investigating fretting behavior of advanced aerospace alloys subjected to load and temperature conditions representative of such turbomachinery components.

Postbuckling behavior of axially compressed graphite-epoxy cylindrical panels with circular holes

NASA Technical Reports Server (NTRS)

Knight, N. F., Jr.; Starnes, J. H., Jr.

1984-01-01

The results of an experimental and analytical study of the effects of circular holes on the postbuckling behavior of graphite-epoxy cylindrical panels loaded in axial compression are presented. The STAGSC-1 general shell analysis computer code is used to determine the buckling and postbuckling response of the panels. The loaded, curved ends of the specimens were clamped by fixtures and the unloaded, straight edges were simply supported by knife-edge restraints. The panels are loaded by uniform end shortening to several times the end shortening at buckling. The unstable equilibrium path of the postbuckling response is obtained analytically by using a method based on controlling an equilibrium-path-arc-length parameter instead of the traditional load parameter. The effects of hole diameter, panel radius, and panel thickness on postbuckling response are considered in the study. Experimental results are compared with the analytical results and the failure characteristics of the graphite-epoxy panels are described.

Dynamic piezoresistive response of hybrid nanocomposites

NASA Astrophysics Data System (ADS)

Gbaguidi, Audrey; Anees, Muhammad; Namilae, Sirish; Kim, Daewon

2017-04-01

Hybrid nanocomposites with carbon nanotubes and graphitic platelets as fillers are known to exhibit remarkable electrical and mechanical properties with many potential strain and damage sensing applications. In this work, we fabricate hybrid nanocomposites with carbon nanotube sheet and coarse graphite platelets as fillers with epoxy matrix. We then examine the electromechanical behavior of these nanocomposites under dynamic loading. The electrical resistivity responses of the nanocomposites are measured in frequency range of 1 Hz to 50 Hz with different levels of induced strains. Axial cycling loading is applied using a uniaxial electrodynamic shaker, and transverse loading is applied on end-clamped specimen using modified speakers. In addition, a dynamic mechanical analysis of nanocomposite specimen is performed to characterize the thermal and dynamic behavior of the nanocomposite. Our results indicate that these hybrid nanocomposites exhibit a distinct piezoresistive response under a wide range of dynamic loading conditions, which can be beneficial for potential sensing applications.

E-beam high voltage switching power supply

DOEpatents

Shimer, D.W.; Lange, A.C.

1996-10-15

A high-power power supply produces a controllable, constant high voltage output under varying and arcing loads. The power supply includes a voltage regulator, an inductor, an inverter for producing a high frequency square wave current of alternating polarity, an improved inverter voltage clamping circuit, a step up transformer, an output rectifier for producing a dc voltage at the output of each module, and a current sensor for sensing output current. The power supply also provides dynamic response to varying loads by controlling the voltage regulator duty cycle and circuitry is provided for sensing incipient arc currents at the output of the power supply to simultaneously decouple the power supply circuitry from the arcing load. The power supply includes a plurality of discrete switching type dc--dc converter modules. 5 figs.

E-beam high voltage switching power supply

DOEpatents

Shimer, Daniel W.; Lange, Arnold C.

1996-01-01

A high-power power supply produces a controllable, constant high voltage put under varying and arcing loads. The power supply includes a voltage regulator, an inductor, an inverter for producing a high frequency square wave current of alternating polarity, an improved inverter voltage clamping circuit, a step up transformer, an output rectifier for producing a dc voltage at the output of each module, and a current sensor for sensing output current. The power supply also provides dynamic response to varying loads by controlling the voltage regulator duty cycle and circuitry is provided for sensing incipient arc currents at the output of the power supply to simultaneously decouple the power supply circuitry from the arcing load. The power supply includes a plurality of discrete switching type dc--dc converter modules.

The renoprotective effects of mannitol and udenafil in renal ischemia-reperfusion injury model.

PubMed

Özlülerden, Yusuf; Toktaş, Cihan; Aybek, Hülya; Küçükatay, Vural; Şen Türk, Nilay; Zumrutbas, Ali Ersin

2017-07-01

The aim of this study was to investigate and compare the effects of udenafil and mannitol in an experimental renal ischemia-reperfusion (I/R) injury model. A total of 64 female Wister Albino rats were used. Right nephrectomy was performed in all groups. In the control group; I/R injury was not performed. In the I/R group; left renal pedicle was clamped for 45 minutes and then underwent 60 minutes and 24 hours of reperfusion. In the mannitol group; 1 mL 20% mannitol was given intravenously 15 minutes before clamping. In the udenafil group; 10-mg/kg udenafil was given orally 1 hour before clamping. Creatinine (Cr), blood urea nitrogen (BUN), Cr clearance, malondialdehyde, neutrophil gelatinase associated lipocalin (NGAL), histological examination and DNA damage (Comet Assay method) levels were compared in tissue, serum and urine samples. Udenafil had a better protective effect than mannitol according to biochemical parameters (Cr, BUN, Cr clearance, and NGAL levels) and histopathological findings when compared with the I/R group. In the Comet sampling analysis no significant difference was detected. Udenafil has a better renoprotective effect than mannitol against I/R injury and this effect supports more functional improvements. Further clinical trials are needed to demonstrate those effects and clinical utility of udenafil for that purpose in humans.

[Identification of hepatitis B virus YMDD point mutation using peptide nucleic acid clamping PCR].

PubMed

Zhang, Yingying; He, Haitang; Yang, Jie; Hou, Jinlin

2013-06-01

To establish a peptide nucleic acid clamping PCR assay for detecting hepatitis B virus (HBV) drug resistance mutation. RtM204I (ATT) mutant, rtM204V (GTG) mutant and rtM204 (ATG) wild-type plasmids mixed at different ratios were detected for mutations by PNA clamping PCR assay and direct sequencing, and the sensitivity and specificity of the two methods were compared. Serum samples from 85 patients with chronic HBV infection were detected for drug resistance using the two methods. The sensitivity of PNA-PCR assay was 0.001% in a 10(5)-fold excess of wild-type HBV DNA with a detection limit of 10(1) copies. The sensitivity of direct sequencing was 10% with a detection limit of 10(4) copies. Mutants were detected in 73 of the 85 serum samples (85.9%), including YIDD in 40 samples, YVDD in 23 samples, and YIDD+YVDD in 10 samples. The agreement of PNA-PCR assay with direct sequencing was only 40% (34/85, YIDD in 21 samples, YVDD in 11 samples, and YIDD+YVDD in 2 samples). Neither of the two methods yielded positive results for the negative control samples, suggesting their good specificity. PNA-PCR assay appears to be a more sensitive and rapid assay for detection of HBV genotypic resistance.

HIV-1 tropism: a comparison between RNA and proviral DNA in routine clinical samples from Chilean patients

PubMed Central

2013-01-01

Background HIV in Chile has a notification rate of 0.01%. Coreceptor antagonists are a family of antiretroviral drugs that are used with the prior knowledge of patients HIV-1 tropism. Viral RNA-based tropism detection requires a plasma viral load ≥1000 copies/mL, while proviral DNA-based detection can be performed regardless of plasma viral load. This test is useful in patients with low or undetectable viral loads and would benefit with a proper therapy. The aim of this study was to determine the correlation between HIV RNA and proviral genotypic DNA tropism tests. Findings Forty three Chilean patients were examined using population-based V3 sequencing, and a geno2pheno false-positive rate (FPR) cutoff values of 5, 5.75, 10 and 20%. With cutoff 5.75% a concordance of 88.4% in tropism prediction was found after a simultaneous comparison between HIV tropism assessment by RNA and DNA. In total, five discrepancies (11.6%) were found, 3 patients were RNA-R5/DNA-X4 and two were RNA-X4/DNA-R5. Proviral DNA enabled the prediction of tropism in patients with a low or undetectable viral load. For cutoff 5 and 5.75% genotypic testing using proviral DNA showed a similar sensitivity for X4 as RNA. We found that the highest sensitivity for detecting the X4 strain occurred with proviral DNA and cutoff of 10 and 20%. Viral loads were higher among X4 strain carriers than among R5 strain carriers (p < 0.05). Conclusions A high degree of concordance was found between tropism testing with RNA and testing with proviral DNA. Our results suggest that proviral DNA-based genotypic tropism testing is a useful option for patients with low or undetectable viral load who require a different therapy. PMID:24165156

Effect of Temperature and Viscoelastic Creep on the Clamp-Up Load in Hybrid Composite/Metal Bolted Joints

DTIC Science & Technology

2009-08-17

aluminum bolted to aluminum specimens. 2. Similarly to the temperature effects on the response of the specimens tested, relative humidity swings have a...bolted to aluminum specimens show the highest susceptibility to relative humidity shifts. This response is believed to be related to their ability to...relaxation stage, little effects are detected from relative humidity fluctuations. 81 9. The data

Design and analysis of seals for extended service life

NASA Technical Reports Server (NTRS)

Bower, Mark V.

1992-01-01

Space Station Freedom is being developed for a service life of up to thirty years. As a consequence, the design requirements for the seals to be used are unprecedented. Full scale testing to assure the selected seals can satisfy the design requirements are not feasible. As an alternative, a sub-scale test program has been developed by MSFC to calibrate the analysis tools to be used to certify the proposed design. This research has been conducted in support of the MSFC Integrated Seal Test Program. The ultimate objective of this research is to correlate analysis and test results to qualify the analytical tools, which in turn, are to be used to qualify the flight hardware. This research is totally focused on O-rings that are compressed by perpendicular clamping forces. In this type of seal the O-ring is clamped between the sealing surfaces by loads perpendicular to the circular cross section.

Cytomegalovirus (CMV) DNA load predicts relapsing CMV infection after solid organ transplantation.

PubMed

Sia, I G; Wilson, J A; Groettum, C M; Espy, M J; Smith, T F; Paya, C V

2000-02-01

Cytomegalovirus (CMV) DNA load was analyzed as a marker for relapse of CMV infection in 24 solid organ transplant patients with CMV infection or disease who received a fixed 14-day course of intravenous ganciclovir. Viral load was measured in blood samples obtained before and at the completion of treatment. Eight (33%) of 24 patients developed relapsing CMV infection. Median pretreatment viral loads were higher in the relapsing group (80,150 copies/106 leukocytes) than in the nonrelapsing group (5500 copies/106 leukocytes; P=.007). The relapsing group also had persistent detectable viral DNA (median, 5810 copies/106 leukocytes) after treatment, whereas it was undetectable in the nonrelapsing group (P<. 0001). Primary CMV infection (seronegative recipients of seropositive organs, D+R-) was an independent marker for CMV relapse (P=.03), and these patients had higher pre- and posttreatment viral loads than did non-D+/R- patients (P<.0001 and P=.0014, respectively). CMV DNA load is a useful marker for individualizing antiviral treatment of CMV infection in solid organ transplant recipients.

Evaluation of Laboratory Scale Testing of Tunnels and Tunnel Intersections. Volume 1

DTIC Science & Technology

1991-11-01

Bakhtar, K. and DiBona , B. G., Dynamic Loading Experiments on Model Underground Structures," DNA-TR-85-387, prepared by Terra Tek, Inc. for Defense...34, TR 84-01, prepared by Terra Tek, Inc, for DNA Contract No. DNA 001-82-C-0253. DNA TR-85-387 Bakhtar, K. and DiBona , B. G., Dynamic Loading Experiments

Effects of poly(lactic-co-glycolic acid) on preparation and characteristics of plasmid DNA-loaded solid lipid nanoparticles.

PubMed

Zhu, L; Xie, S; Dong, Z; Wang, X; Wang, Y; Zhou, W

2011-09-01

Poly(lactic-co-glycolic acid) (PLGA) was used as a polymeric emulsifier to encapsulate plasmid DNA into hydrogenated castor oil (HCO)-solid lipid nanoparticles (SLN) by w/o/w double emulsion and solvent evaporation techniques. The effects of PLGA on the preparation, characteristics and transfection efficiency of DNA-loaded SLN were studied. The results showed that PLGA was essential to form the primary w/o emulsion and the stability of the emulsion was enhanced with the increase of PLGA content. DNA-loaded SLN were spherical with smooth surfaces. The SLN had a negative charge in weak acid and alkaline environment but acquired a positive charge in acidic pH and the cationisation capacity of the SLN increased with the increase of PLGA/HCO ratio. Agarose gel electrophoresis demonstrated that the majority of the DNA maintained its structural integrity after preparation and being extracted or released from DNA-loaded SLN. When PLGA/HCO ratio increased from 5 to 15%, the encapsulation efficiency, loading capacity and transfection efficiency of the nanoparticles increased significantly, whereas the changes of particle size and polydispersity index were insignificant. Cytotoxicity study in cell culture demonstrated that the SLN was not toxic.

Meticulous plasma isolation is essential to avoid false low-level viraemia in Roche Cobas HIV-1 viral load assays.

PubMed

Mortier, Virginie; Vancoillie, Leen; Dauwe, Kenny; Staelens, Delfien; Demecheleer, Els; Schauvliege, Marlies; Dinakis, Sylvie; Van Maerken, Tom; Dessilly, Géraldine; Ruelle, Jean; Verhofstede, Chris

2017-10-24

Pre-analytical sample processing is often overlooked as a potential cause of inaccurate assay results. Here we demonstrate how plasma, extracted from standard EDTA-containing blood collection tubes, may contain traces of blood cells consequently resulting in a false low-level HIV-1 viral load when using Roche Cobas HIV-1 assays. The presence of human DNA in Roche Cobas 4800 RNA extracts and in RNA extracts from the Abbott HIV-1 RealTime assay was assessed by quantifying the human albumin gene by means of quantitative PCR. RNA was extracted from plasma samples before and after an additional centrifugation and tested for viral load and DNA contamination. The relation between total DNA content and viral load was defined. Elevated concentrations of genomic DNA were detected in 28 out of 100 Cobas 4800 extracts and were significantly more frequent in samples processed outside of the AIDS Reference Laboratory. An association between genomic DNA presence and spurious low-level viraemia results was demonstrated. Supplementary centrifugation of plasma before RNA extraction eliminated the contamination and the false viraemia. Plasma isolated from standard EDTA-containing blood collection tubes may contain traces of HIV DNA leading to false viral load results above the clinical cutoff. Supplementary centrifugation of plasma before viral load analysis may eliminate the occurrence of this spurious low-level viraemia.

Clinical comparison of branched DNA and reverse transcriptase-PCR and nucleic acid sequence-based amplification assay for the quantitation of circulating recombinant form_BC HIV-1 RNA in plasma.

PubMed

Pan, Pinliang; Tao, Xiaoxia; Zhang, Qi; Xing, Wenge; Sun, Xianguang; Pei, Lijian; Jiang, Yan

2007-12-01

To investigate the correlation between three viral load assays for circulating recombinant form (CRF)_BC. Recent studies in HIV-1 molecular epidemiology, reveals that CRF_BC is the dominant subtype of HIV-1 virus in mainland China, representing over 45% of the HIV-1 infected population. The performances of nucleic acid sequence-based amplification (NASBA), branched DNA (bDNA) and reverse transcriptase polymerase chain reaction (RT-PCR) were compared for the HIV-1 viral load detection and quantitation of CRF_BC in China. Sixteen HIV-1 positive and three HIV-1 negative samples were collected. Sequencing of the positive samples in the gp41 region was conducted. The HIV-1 viral load values were determined using bDNA, RT-PCR and NASBA assays. Deming regression analysis with SPSS 12.0 (SPS Inc., Chicago, Illinois, USA) was performed for data analysis. Sequencing and phylogenetic analysis of env gene (gp41) region of the 16 HIV-1 positive clinical specimens from Guizhou Province in southwest China revealed the dominance of the subtype CRF_BC in that region. A good correlation of their viral load values was observed among three assays. Pearson's correlation between RT-PCR and bDNA is 0.969, Lg(VL)RT-PCR = 0.969 * Lg(VL)bDNA + 0.55; Pearson's correlation between RT-PCR and NASBA is 0.968, Lg(VL)RT-PCR = 0.968 * Lg(VL)NASBA + 0.937; Pearson's correlation between NASBA and bDNA is 0.980, Lg(VL)NASBA = 0.980 * Lg(VL)bDNA - 0.318. When testing with 3 different assays, RT-PCR, bDNA and NASBA, the group of 16 HIV-1 positive samples showed the viral load value was highest for RT-PCR, followed by bDNA then NASBA, which is consistent with the former results in subtype B. The three viral load assays are highly correlative for CRF_BC in China.

Cable load sensing device

DOEpatents

Beus, Michael J.; McCoy, William G.

1998-01-01

Apparatus for sensing the magnitude of a load on a cable as the cable is employed to support the load includes a beam structure clamped to the cable so that a length of the cable lies along the beam structure. A spacer associated with the beam structure forces a slight curvature in a portion of the length of cable under a cable "no-load" condition so that the portion of the length of cable is spaced from the beam structure to define a cable curved portion. A strain gauge circuit including strain gauges is secured to the beam structure by welding. As the cable is employed to support a load the load causes the cable curved portion to exert a force normal to the cable through the spacer and on the beam structure to deform the beam structure as the cable curved portion attempts to straighten under the load. As this deformation takes place, the resistance of the strain gauges is set to a value proportional to the magnitude of the normal strain on the beam structure during such deformation. The magnitude of the normal strain is manipulated in a control device to generate a value equal to the magnitude or weight of the load supported by the cable.

Is early cord clamping, delayed cord clamping or cord milking best?

PubMed

Vatansever, Binay; Demirel, Gamze; Ciler Eren, Elif; Erel, Ozcan; Neselioglu, Salim; Karavar, Hande Nur; Gundogdu, Semra; Ulfer, Gozde; Bahadir, Selcen; Tastekin, Ayhan

2018-04-01

To compare the antioxidant status of three cord clamping procedures (early clamping, delayed clamping and milking) by analyzing the thiol-disulfide balance. This randomized controlled study enrolled 189 term infants who were divided into three groups according to the cord clamping procedure: early clamping, delayed clamping and milking. Blood samples were collected from the umbilical arteries immediately after clamping, and the thiol/disulfide homeostasis was analyzed. The native and total thiol levels were significantly (p < .05) lower in the early cord clamping group compared with the other two groups. The disulfide/total thiol ratio was significantly (p = .026) lower in the delayed cord clamping and milking groups compared with the early clamping groups. Early cord clamping causes the production of more disulfide bonds and lower thiol levels, indicating that oxidation reactions are increased in the early cord clamping procedure compared with the delayed cord clamping and milking procedures. The oxidant capacity is greater with early cord clamping than with delayed clamping or cord milking. Delayed cord clamping or milking are beneficial in neonatal care, and we suggest that they be performed routinely in all deliveries.

Herpes simplex virus type 2 (HSV-2) genital shedding in HSV-2-/HIV-1-co-infected women receiving effective combination antiretroviral therapy.

PubMed

Péré, Héléne; Rascanu, Aida; LeGoff, Jérome; Matta, Mathieu; Bois, Frédéric; Lortholary, Olivier; Leroy, Valériane; Launay, Odile; Bélec, Laurent

2016-03-01

The dynamics of genital shedding of HSV-2 DNA was assessed in HIV-1-infected women taking combination antiretroviral therapy (cART). HIV-1 RNA, HIV-1 DNA and HSV DNA loads were measured during 12-18 months using frozen plasma, PBMC and cervicovaginal lavage samples from 22 HIV-1-infected women, including 17 women naive for antiretroviral therapy initiating cART and 5 women with virological failure switching to a new regimen. Nineteen (86%) women were HSV-2-seropositive. Among HSV-2-/HIV-1-co-infected women, HIV-1 RNA loads showed a rapid fall from baseline after one month of cART, in parallel in paired plasma and cervicovaginal secretions. In contrast, HIV-1 DNA loads did not show significant variations from baseline up to 18 months of treatment in both systemic and genital compartments. HSV DNA was detected at least once in 12 (63%) of 19 women during follow up: HSV-2 shedding in the genital compartment was observed in 11% of cervicovaginal samples at baseline and in 16% after initiating or switching cART. Cervicovaginal HIV-1 RNA loads were strongly associated with plasma HIV-1 RNA loads over time, but not with cervicovaginal HSV DNA loads. Reactivation of genital HSV-2 replication frequently occurred despite effective cART in HSV-2-/HIV-1-co-infected women. Genital HSV-2 replication under cART does not influence cervicovaginal HIV-1 RNA or DNA shedding. © The Author(s) 2015.

The 9-1-1 DNA Clamp Is Required for Immunoglobulin Gene Conversion▿

PubMed Central

Saberi, Alihossein; Nakahara, Makoto; Sale, Julian E.; Kikuchi, Koji; Arakawa, Hiroshi; Buerstedde, Jean-Marie; Yamamoto, Kenichi; Takeda, Shunichi; Sonoda, Eiichiro

2008-01-01

Chicken DT40 cells deficient in the 9-1-1 checkpoint clamp exhibit hypersensitivity to a variety of DNA-damaging agents. Although recent work suggests that, in addition to its role in checkpoint activation, this complex may play a role in homologous recombination and translesion synthesis, the cause of this hypersensitivity has not been studied thoroughly. The immunoglobulin locus of DT40 cells allows monitoring of homologous recombination and translesion synthesis initiated by activation-induced deaminase (AID)-dependent abasic sites. We show that both the RAD9−/− and RAD17−/− mutants exhibit substantially reduced immunoglobulin gene conversion. However, the level of nontemplated immunoglobulin point mutation increased in these mutants, a finding that is reminiscent of the phenotype resulting from the loss of RAD51 paralogs or Brca2. This suggests that the 9-1-1 complex does not play a central role in translesion synthesis in this context. Despite reduced immunoglobulin gene conversion, the RAD9−/− and RAD17−/− cells do not exhibit a prominent defect in double-strand break-induced gene conversion or a sensitivity to camptothecin. This suggests that the roles of Rad9 and Rad17 may be confined to a subset of homologous recombination reactions initiated by replication-stalling lesions rather than those associated with double-strand break repair. PMID:18662998

Development and Testing of a Friction-Based Post-Installable Sensor for Subsea Fiber-Optic Monitoring System

NASA Technical Reports Server (NTRS)

Bentley, Nicole L.; Brower, David V.; Le, Suy Q.; Seaman, Calvin H.; Tang, Henry H.

2017-01-01

This paper presents the design and development of a friction-based coupling device for a fiber-optic monitoring system that can be deployed on existing subsea structures. This paper provides a summary of the design concept, prototype development, prototype performance testing, and design refinements of the device. The results of the laboratory testing of the first prototype performed at the National Aeronautics and Space Administration (NASA) Johnson Space Center (JSC) are included in this paper. Limitations of the initial design were identified and future design improvements were proposed. These new features will enhance the coupling of the device and improve the monitoring system measurement capabilities. A major challenge of a post-installed instrumentation monitoring system is to ensure adequate coupling between the instruments and the structure of interest for reliable measurements. Friction-based coupling devices have the potential to overcome coupling limitations caused by marine growth and soil contamination on subsea structures, flowlines or risers. The work described in this paper investigates the design of a friction-based coupling device (friction clamp), which is applicable for pipelines and structures that are suspended in the water column and those that are resting on the seabed. The monitoring elements consist of fiber-optic sensors that are bonded to a metal clamshell with a high-friction coating. The friction clamp has a single hinge design to facilitate the operation of the clamp and dual rows of opposing fasteners to distribute the clamping force on the structure. The friction clamp can be installed by divers in shallow depths or by remotely operated vehicles in deep-water applications. NASA-JSC was involved in the selection and testing of the friction coating, and in the design and testing of the prototype clamp device. Four-inch diameter and eight-inch diameter sub-scale friction clamp prototypes were built and tested to evaluate the strain measuring capabilities of the design under different loading scenarios. The testing revealed some limitations of the initial design concept, and subsequent refinements were explored to improve the measurement performance of the system. This study was part of a collaboration between NASA-JSC and Astro Technology, Inc. within a study called Clear Gulf. The primary objective of the Clear Gulf study is to develop advanced instrumentation technologies that will improve operational safety and reduce the risk of hydrocarbon spillage. NASA provided unique insights, expansive test facilities, and technical expertise to advance these technologies that would benefit the environment, the public, and commercial industries.

Development and Testing of a Friction-Based Post-Installable Sensor for Subsea Fiber-Optic Monitoring Systems

NASA Technical Reports Server (NTRS)

Bentley, Nicole; Brower, David; Le, Suy Q.; Seaman, Calvin; Tang, Henry

2017-01-01

This paper presents the design and development of a friction-based coupling device for a fiber-optic monitoring system that can be deployed on existing subsea structures. This paper provides a summary of the design concept, prototype development, prototype performance testing, and design refinements of the device. The results of the laboratory testing of the first prototype performed at the National Aeronautics and Space Administration (NASA) Johnson Space Center (JSC) are included in this paper. Limitations of the initial design were identified and future design improvements were proposed. These new features will enhance the coupling of the device and improve the monitoring system measurement capabilities. A major challenge of a post-installed instrumentation monitoring system is to ensure adequate coupling between the instruments and the structure of interest for reliable measurements. Friction-based coupling devices have the potential to overcome coupling limitations caused by marine growth and soil contamination on subsea structures, flowlines or risers. The work described in this paper investigates the design of a friction-based coupling device (friction clamp), which is applicable for pipelines and structures that are suspended in the water column and those that are resting on the seabed. The monitoring elements consist of fiber-optic sensors that are bonded to a metal clamshell with a high-friction coating. The friction clamp has a single hinge design to facilitate the operation of the clamp and dual rows of opposing fasteners to distribute the clamping force on the structure. The friction clamp can be installed by divers in shallow depths or by remotely operated vehicles in deep-water applications. NASA-JSC was involved in the selection and testing of the friction coating, and in the design and testing of the prototype clamp device. Four-inch diameter and eight-inch diameter sub-scale friction clamp prototypes were built and tested to evaluate the strain measuring capabilities of the design under different loading scenarios. The testing revealed some limitations of the initial design concept, and subsequent refinements were explored to improve the measurement performance of the system. This study was part of a collaboration between NASA-JSC and Astro Technology, Inc. within a study called Clear Gulf. The primary objective of the Clear Gulf study is to develop advanced instrumentation technologies that will improve operational safety and reduce the risk of hydrocarbon spillage. NASA provided unique insights, expansive test facilities, and technical expertise to advance these technologies that would benefit the environment, the public, and commercial industries.

Evaluation of Mucorales DNA load in cerebrospinal fluid in a patient with possible cerebral mucormycosis treated with intravenous liposomal amphotericin B.

PubMed

Shigemura, Tomonari; Nakazawa, Yozo; Matsuda, Kazuyuki; Motobayashi, Mitsuo; Saito, Shoji; Koike, Kenichi

2014-12-01

We report the case of a 19-year-old male with possible cerebral mucormycosis following chemotherapy. We detected a Lichtheimia DNA load of 2.0×10(4) copies/ml in cerebrospinal fluid (CSF), although a CSF culture showed no growth. After treatment with intravenous liposomal amphotericin B, the Lichtheimia DNA load fell below the detection limit, and at the same time the patient's headache and imaging findings improved. The quantification of Mucorales DNA in CSF may be useful for evaluating cerebral mucormycosis. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Molecular Dissection of the Homotrimeric Sliding Clamp of T4 Phage: Two Domains of a Subunit Display Asymmetric Characteristics.

PubMed

Singh, Manika Indrajit; Jain, Vikas

2016-01-26

Sliding clamp proteins are circular dimers or trimers that encircle DNA and serve as processivity factors during DNA replication. Their presence in all the three domains of life and in bacteriophages clearly indicates their high level of significance. T4 gp45, besides functioning as the DNA polymerase processivity factor, also moonlights as the late promoter transcription determinant. Here we report a detailed biophysical analysis of gp45. The chemical denaturation of gp45 probed by circular dichroism spectroscopy, tryptophan fluorescence anisotropy, and blue-native polyacrylamide gel electrophoresis suggests that the protein follows a three-state denaturation profile and displays an intermediate molten globule-like state. The three-state transition was found to be the result of the sequential unfolding of the two domains, the N-terminal domain (NTD) and the C-terminal domain (CTD), of gp45. The experiments involving Trp fluorescence quenching by acrylamide demonstrate that the CTD undergoes substantial changes in conformation during formation of the intermediate state. Further biophysical dissection of the individual domain reveals contrasting properties of the two domains. The NTD unfolds at low urea concentrations and is also susceptible to protease cleavage, whereas the CTD resists urea-mediated denaturation and is not amenable to protease digestion even at higher urea concentrations. These experiments allow us to conclude that the two domains of gp45 differ in their dynamics. While the CTD shows stability and rigidity, we find that the NTD is unstable and flexible. We believe that the asymmetric characteristics of the two domains and the interface they form hold significance in gp45 structure and function.

A Simplified Method of Elastic-Stability Analysis for Thin Cylindrical Shells

NASA Technical Reports Server (NTRS)

Batdorf, S B

1947-01-01

This paper develops a new method for determining the buckling stresses of cylindrical shells under various loading conditions. In part I, the equation for the equilibrium of cylindrical shells introduced by Donnell in NACA report no. 479 to find the critical stresses of cylinders in torsion is applied to find critical stresses for cylinders with simply supported edges under other loading conditions. In part II, a modified form of Donnell's equation for the equilibrium of thin cylindrical shells is derived which is equivalent to Donnell's equation but has certain advantages in physical interpretation and in ease of solution, particularly in the case of shells having clamped edges. The question of implicit boundary conditions is also considered.

Chitosan microspheres as candidate plasmid vaccine carrier for oral immunisation of Japanese flounder (Paralichthys olivaceus).

PubMed

Tian, Jiyuan; Yu, Juan; Sun, Xiuqin

2008-12-15

Oral DNA-based immunotherapy is a new treatment option for fish immunisation in intensive culture. However, because of the existence of the nucleases and severe gastrointestinal conditions, DNA-based vaccines can be hydrolyzed or denatured. In our laboratory, a plasmid DNA (pDNA) containing major capsid protein (MCP) gene of lymphocystis disease virus (LCDV) was prepared, and then pDNA was encapsulated in chitosan microspheres through an emulsion-based methodology. The yield, loading percent and encapsulation efficiency of microspheres were 93.6%, 0.3% and 94.5%, respectively. Scanning electron microscopy (SEM) showed that pDNA-loaded microspheres yielded a spherical shape with smooth surfaces. The disproportion of super-coiled to open circle and linear pDNA suggested that high transfection efficiencies of pDNA in microspheres were retained. The cumulative release of pDNA showed that chitosan microspheres were resistant to degradation in simulated gastrointestinal tract environment. The release profile at PBS buffer (pH 7.4) displayed that pDNA-loaded chitosan microspheres had a release up to 42 days after intestinal imbibition. RT-PCR showed that RNA containing information of MCP gene existed in various tissues 10-90 days post-vaccination. SDS-PAGE and immunofluorescent images indicated that pDNA expressed MCP in tissues of fish 10-90 days after oral administration. In addition, indirect ELISA displayed that the immune responses of sera were positive (O.D.> or =0.3) from week 1 to week 16 for fish vaccinated with microspheres, in comparison with fish vaccinated with naked pDNA. Data obtained suggested that chitosan microspheres were promising carriers for oral pDNA vaccine. Because this encapsulation technique was easy to operate and immunisation efficacy of microspheres loaded with pDNA was significant, it had potential to be used in drug delivery applications.

Tethered particle analysis of supercoiled circular DNA using peptide nucleic acid handles.

PubMed

Norregaard, Kamilla; Andersson, Magnus; Nielsen, Peter Eigil; Brown, Stanley; Oddershede, Lene B

2014-09-01

This protocol describes how to monitor individual naturally supercoiled circular DNA plasmids bound via peptide nucleic acid (PNA) handles between a bead and a surface. The protocol was developed for single-molecule investigation of the dynamics of supercoiled DNA, and it allows the investigation of both the dynamics of the molecule itself and of its interactions with a regulatory protein. Two bis-PNA clamps designed to bind with extremely high affinity to predetermined homopurine sequence sites in supercoiled DNA are prepared: one conjugated with digoxigenin for attachment to an anti-digoxigenin-coated glass cover slide, and one conjugated with biotin for attachment to a submicron-sized streptavidin-coated polystyrene bead. Plasmids are constructed, purified and incubated with the PNA handles. The dynamics of the construct is analyzed by tracking the tethered bead using video microscopy: less supercoiling results in more movement, and more supercoiling results in less movement. In contrast to other single-molecule methodologies, the current methodology allows for studying DNA in its naturally supercoiled state with constant linking number and constant writhe. The protocol has potential for use in studying the influence of supercoils on the dynamics of DNA and its associated proteins, e.g., topoisomerase. The procedure takes ~4 weeks.

Hypomorphic PCNA mutation underlies a human DNA repair disorder

PubMed Central

Baple, Emma L.; Chambers, Helen; Cross, Harold E.; Fawcett, Heather; Nakazawa, Yuka; Chioza, Barry A.; Harlalka, Gaurav V.; Mansour, Sahar; Sreekantan-Nair, Ajith; Patton, Michael A.; Muggenthaler, Martina; Rich, Phillip; Wagner, Karin; Coblentz, Roselyn; Stein, Constance K.; Last, James I.; Taylor, A. Malcolm R.; Jackson, Andrew P.; Ogi, Tomoo; Lehmann, Alan R.; Green, Catherine M.; Crosby, Andrew H.

2014-01-01

Numerous human disorders, including Cockayne syndrome, UV-sensitive syndrome, xeroderma pigmentosum, and trichothiodystrophy, result from the mutation of genes encoding molecules important for nucleotide excision repair. Here, we describe a syndrome in which the cardinal clinical features include short stature, hearing loss, premature aging, telangiectasia, neurodegeneration, and photosensitivity, resulting from a homozygous missense (p.Ser228Ile) sequence alteration of the proliferating cell nuclear antigen (PCNA). PCNA is a highly conserved sliding clamp protein essential for DNA replication and repair. Due to this fundamental role, mutations in PCNA that profoundly impair protein function would be incompatible with life. Interestingly, while the p.Ser228Ile alteration appeared to have no effect on protein levels or DNA replication, patient cells exhibited marked abnormalities in response to UV irradiation, displaying substantial reductions in both UV survival and RNA synthesis recovery. The p.Ser228Ile change also profoundly altered PCNA’s interaction with Flap endonuclease 1 and DNA Ligase 1, DNA metabolism enzymes. Together, our findings detail a mutation of PCNA in humans associated with a neurodegenerative phenotype, displaying clinical and molecular features common to other DNA repair disorders, which we showed to be attributable to a hypomorphic amino acid alteration. PMID:24911150

Resonant micro and nanoelectromechanical systems: Actuation and biological sensing studies

NASA Astrophysics Data System (ADS)

Ilic, Bojan

This thesis explores various actuation mechanisms of resonant nanoelectro-mechanical systems (NEMS) with emphasis directed towards detection of biomolecules. Arrays of bulk and surface micromachined devices, made using conventional thin film fabrication methods, are used to explore the mass loading effects of selective molecular immobilization on the surface of the NEMS resonators. Experimentally measured shift in the first eigenfrequency is correlated to the amount of mass loading from the binding events and verified using theoretical constructs. Under ambient conditions where considerable damping occurs, immunospecific detection of single Escherichia coli O157:H7 cells is demonstrated by measuring the out of plane vibrational resonant mode using an optical deflection system with thermal noise as an excitation mechanism. Further sensitivity enhancement utilizing vacuum encapsulation in conjunction with piezoelectric actuation and tailoring of the cantilever dimensions is demonstrated by measuring mass loading of a nonpathogenic insect baculovirus, single Aminopropyltriethoxysilane (APTS), Hexamethyldisilazane (HMDS) and Octade-cyltrichlorosilane (OTS) monolayers. To highlight the lower detectable mass limit, surface machined NEMS oscillators with integrated circular Au contacts and sub-attogram mass detection sensitivity are used for selective immobilization of dinitrophenyl poly(ethylene glycol) undecanthiol based molecules. Experimental and theoretical elucidation of optical actuation of NEMS cantilevers at large distances from the clamped end is presented. These observations are considered within the theoretical framework of heat transfer and used to measure binding events of single double-stranded deoxyribonucleic acid (dsDNA) molecules to localized gold nanodots near the free end of a NEMS oscillator. Because this method allows direct coupling of energy into the device layer, several modes of in-plane vibrations are observed and employed in shaking off spherical latex particles. Finally, this thesis describes studies of dynamic detection of vibrational characteristics of suspended NEMS oscillators through direct coupling with a micromechanical probe. Changes in the dynamic amplitude and phase of the probe allow the measurement of the mechanical quality factor. Measured spectral response of the NEMS is in good agreement with optical characterization and modelling results.

An ultra-fast EOD-based force-clamp detects rapid biomechanical transitions

NASA Astrophysics Data System (ADS)

Woody, Michael S.; Capitanio, Marco; Ostap, E. Michael; Goldman, Yale E.

2017-08-01

We assembled an ultra-fast infrared optical trapping system to detect mechanical events that occur less than a millisecond after a ligand binds to its filamentous substrate, such as myosin undergoing its 5 - 10 nm working stroke after actin binding. The instrument is based on the concept of Capitanio et al.1, in which a polymer bead-actin-bead dumbbell is held in two force-clamped optical traps. A force applied by the traps causes the filament to move at a constant velocity as hydrodynamic drag balances the applied load. When the ligand binds, the filament motion stops within 100 μs as the total force from the optical traps is transferred to the attachment. Subsequent translations signal active motions, such as the magnitude and timing of the motor's working stroke. In our instrument, the beads defining the dumbbell are held in independent force clamps utilizing a field-programmable gate array (FPGA) to update the trap beam positions at 250 kHz. We found that in our setup, acousto-optical deflectors (AODs) steering the beams were unsuitable for this purpose due to a slightly non-linear response in the beam intensity and deflection angle vs. the AOD ultra-sound wavelength, likely caused by low-amplitude standing acoustic waves in the deflectors. These aberrations caused instability in the force feedback loops leading to artefactual 20 nm jumps in position. This type of AOD non-linearity has been reported to be absent in electro-optical deflectors (EODs)2. We demonstrate that replacement of the AODs with EODs improves the performance of our instrument. Combining the superior beam-steering capability of the EODs, force acquisition via back-plane interferometry, and the dual high-speed FPGA-based feedback loops, we smoothly and precisely apply constant loads to study the dynamics of interactions between biological molecules such as actin and myosin.

Data on DNA gel sample load, gel electrophoresis, PCR and cost analysis.

PubMed

Kuhn, Ramona; Böllmann, Jörg; Krahl, Kathrin; Bryant, Isaac Mbir; Martienssen, Marion

2018-02-01

The data presented in this article provide supporting information to the related research article "Comparison of ten different DNA extraction procedures with respect to their suitability for environmental samples" (Kuhn et al., 2017) [1]. In that article, we compared the suitability of ten selected DNA extraction methods based on DNA quality, purity, quantity and applicability to universal PCR. Here we provide the data on the specific DNA gel sample load, all unreported gel images of crude DNA and PCR results, and the complete cost analysis for all tested extraction procedures and in addition two commercial DNA extraction kits for soil and water.

Intracellular levels of hepatitis B virus DNA and pregenomic RNA in peripheral blood mononuclear cells of chronically infected patients.

PubMed

Lu, L; Zhang, H-Y; Yueng, Y-H; Cheung, K-F; Luk, J M; Wang, F-S; Lau, G K K

2009-02-01

It remains uncertain whether hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) and pregenomic RNA (pgRNA) can be detected in the serum or peripheral blood mononuclear cells (PBMC) of patients with chronic hepatitis B (CHB) infection. We examined HBV cccDNA and pgRNA in the serum and PBMC, and investigated the effect of lamivudine therapy on the viral loads in the PBMC of CHB patients. Paired serum and PBMC samples from 50 treatment-naïve CHB patients [25 hepatitis B e antigen (HBeAg) positive and 25 HBeAg negative] were quantified for total HBV DNA, cccDNA and pgRNA by real time polymerase chain reaction. HBV cccDNA and pgRNA were below the lower detection limit in all serum samples, and in 84% of PBMC. HBV DNA (r = 0.889, P < 0.001) and pgRNA (r = 0.696, P < 0.001) in PBMC correlated with the HBV DNA in serum. In the longitudinal study, 30 patients treated with lamivudine therapy for a median duration of 34 weeks (range 12-48 weeks) were examined. The median HBV DNA reduction in PBMC before and after treatment was 1.318 (range -0.471 to 3.846) log units, which was significantly lower than serum HBV DNA reduction [3.371 (range -0.883 to 9.454) log units, P < 0.05]. HBV cccDNA and pgRNA were undetectable in the serum of CHB patients. HBV viral loads in PBMC correlated with serum HBV DNA. Lamivudine therapy had less effect on the HBV viral loads in PBMC compared with the serum viral loads.

Detection of Human Cytomegalovirus DNA by Real-Time Quantitative PCR

PubMed Central

Nitsche, Andreas; Steuer, Nina; Schmidt, Christian Andreas; Landt, Olfert; Ellerbrok, Heinz; Pauli, Georg; Siegert, Wolfgang

2000-01-01

A real-time PCR assay was developed to quantify human cytomegalovirus (CMV) DNA. This assay was used to demonstrate a higher CMV DNA load in plasma of bone marrow transplant patients than in that of blood donors. The CMV load was higher in CMV antigen-positive patients than in antigen-negative patients. PMID:10878073

The renoprotective effects of mannitol and udenafil in renal ischemia-reperfusion injury model

PubMed Central

Toktaş, Cihan; Aybek, Hülya; Küçükatay, Vural; Şen Türk, Nilay; Zumrutbas, Ali Ersin

2017-01-01

Purpose The aim of this study was to investigate and compare the effects of udenafil and mannitol in an experimental renal ischemia-reperfusion (I/R) injury model. Materials and Methods A total of 64 female Wister Albino rats were used. Right nephrectomy was performed in all groups. In the control group; I/R injury was not performed. In the I/R group; left renal pedicle was clamped for 45 minutes and then underwent 60 minutes and 24 hours of reperfusion. In the mannitol group; 1 mL 20% mannitol was given intravenously 15 minutes before clamping. In the udenafil group; 10-mg/kg udenafil was given orally 1 hour before clamping. Creatinine (Cr), blood urea nitrogen (BUN), Cr clearance, malondialdehyde, neutrophil gelatinase associated lipocalin (NGAL), histological examination and DNA damage (Comet Assay method) levels were compared in tissue, serum and urine samples. Results Udenafil had a better protective effect than mannitol according to biochemical parameters (Cr, BUN, Cr clearance, and NGAL levels) and histopathological findings when compared with the I/R group. In the Comet sampling analysis no significant difference was detected. Conclusions Udenafil has a better renoprotective effect than mannitol against I/R injury and this effect supports more functional improvements. Further clinical trials are needed to demonstrate those effects and clinical utility of udenafil for that purpose in humans. PMID:28681040

Long-term shedding of infectious epstein-barr virus after infectious mononucleosis.

PubMed

Fafi-Kremer, Samira; Morand, Patrice; Brion, Jean-Paul; Pavese, Patricia; Baccard, Monique; Germi, Raphaele; Genoulaz, Odile; Nicod, Sandrine; Jolivet, Michel; Ruigrok, Rob W H; Stahl, Jean-Paul; Seigneurin, Jean-Marie

2005-03-15

Epstein-Barr virus (EBV) DNA loads in peripheral blood mononuclear cells (PBMCs), plasma, and saliva, as well as infectivity of the virus in saliva, were evaluated in 20 patients for 6 months after the onset of infectious mononucleosis (IM). All patients displayed sustained high EBV DNA loads in the saliva, associated with a persistent infectivity of saliva at day 180. EBV DNA load in PBMCs decreased significantly from day 0 to day 180 (in spite of a viral rebound between day 30 and day 90 in 90% of the patients), and EBV DNA rapidly disappeared from plasma. These data show that patients with IM remain highly infectious during convalescence.

DNA packaging and ejection forces in bacteriophage

PubMed Central

Kindt, James; Tzlil, Shelly; Ben-Shaul, Avinoam; Gelbart, William M.

2001-01-01

We calculate the forces required to package (or, equivalently, acting to eject) DNA into (from) a bacteriophage capsid, as a function of the loaded (ejected) length, under conditions for which the DNA is either self-repelling or self-attracting. Through computer simulation and analytical theory, we find the loading force to increase more than 10-fold (to tens of piconewtons) during the final third of the loading process; correspondingly, the internal pressure drops 10-fold to a few atmospheres (matching the osmotic pressure in the cell) upon ejection of just a small fraction of the phage genome. We also determine an evolution of the arrangement of packaged DNA from toroidal to spool-like structures. PMID:11707588

Triple bar, high efficiency mechanical sealer

DOEpatents

Pak, Donald J.; Hawkins, Samantha A.; Young, John E.

2013-03-19

A clamp with a bottom clamp bar that has a planar upper surface is provided. The clamp may also include a top clamp bar connected to the bottom clamp bar, and a pressure distribution bar between the top clamp bar and the bottom clamp bar. The pressure distribution bar may have a planar lower surface in facing relation to the upper surface of the bottom clamp bar. An object is capable of being disposed in a clamping region between the upper surface and the lower surface. The width of the planar lower surface may be less than the width of the upper surface within the clamping region. Also, the pressure distribution bar may be capable of being urged away from the top clamp bar and towards the bottom clamp bar.

A computer-based servo system for controlling isotonic contractions of muscle.

PubMed

Smith, J P; Barsotti, R J

1993-11-01

We have developed a computer-based servo system for controlling isotonic releases in muscle. This system is a composite of commercially available devices: an IBM personal computer, an analog-to-digital (A/D) board, an Akers AE801 force transducer, and a Cambridge Technology motor. The servo loop controlling the force clamp is generated by computer via the A/D board, using a program written in QuickBASIC 4.5. Results are shown that illustrate the ability of the system to clamp the force generated by either skinned cardiac trabeculae or single rabbit psoas fibers down to the resolution of the force transducer within 4 ms. This rate is independent of the level of activation of the tissue and the size of the load imposed during the release. The key to the effectiveness of the system consists of two algorithms that are described in detail. The first is used to calculate the error signal to hold force to the desired level. The second algorithm is used to calculate the appropriate gain of the servo for a particular fiber and the size of the desired load to be imposed. The results show that the described computer-based method for controlling isotonic releases in muscle represents a good compromise between simplicity and performance and is an alternative to the custom-built digital/analog servo devices currently being used in studies of muscle mechanics.

Evaluation of a nontoxic rigid polymer as connecting bar in external skeletal fixators.

PubMed

Störk, Christoph K; Canivet, Philippe; Baidak, Alexandre A; Balligand, Marc H

2003-01-01

To investigate the mechanical characteristics of a nontoxic, low-cost, rigid polymer (RP) and to compare the structural and mechanical properties of a full-frame external skeletal fixator (ESF) with either RP connecting bars, polymethylmethacrylate (PMMA) connecting bars, or stainless-steel (SS) clamps and connecting bars. In vitro mechanical evaluation. Mechanical properties were assessed using an in vitro bone fracture model with a bilateral uniplanar ESF (type II). Identical ESF were built with connecting bars using RP (n = 8), PMMA (n = 8), and SS connecting bars and clamps (System Meynard; n = 3). Nondestructive mechanical tests were performed in uniaxial compression (AC) and craniocaudal (CC) 4-point bending, as well as fatigue AC. Composite stiffness for each specimen and for each loading mode was calculated from 6 replicate measures using the slope of the load displacement curve at small displacements. RP, PMMA, and SS ESF constructs yielded mean +/- SD composite stiffness values of 227 +/- 15, 381 +/- 30, and 394 +/- 9 N/mm in AC and of 35 +/- 2, 24 +/- 2, and 15 +/- 0 N/mm in CC, respectively. Structural and mechanical properties of RP are satisfactorily rigid and fatigue resistant for its use as a connecting bar in ESF. RP connecting bars in an ESF are a reliable, versatile, nontoxic and inexpensive option for the veterinary surgeon. Copyright 2003 by The American College of Veterinary Surgeons

How and why multiple MCMs are loaded at origins of DNA replication.

PubMed

Das, Shankar P; Rhind, Nicholas

2016-07-01

Recent work suggests that DNA replication origins are regulated by the number of multiple mini-chromosome maintenance (MCM) complexes loaded. Origins are defined by the loading of MCM - the replicative helicase which initiates DNA replication and replication kinetics determined by origin's location and firing times. However, activation of MCM is heterogeneous; different origins firing at different times in different cells. Also, more MCMs are loaded in G1 than are used in S phase. These aspects of MCM biology are explained by the observation that multiple MCMs are loaded at origins. Having more MCMs at early origins makes them more likely to fire, effecting differences in origin efficiency that define replication timing. Nonetheless, multiple MCM loading raises new questions, such as how they are loaded, where these MCMs reside at origins, and how their presence affects replication timing. In this review, we address these questions and discuss future avenues of research. © 2016 WILEY Periodicals, Inc.

Two subunits of human ORC are dispensable for DNA replication and proliferation.

PubMed

Shibata, Etsuko; Kiran, Manjari; Shibata, Yoshiyuki; Singh, Samarendra; Kiran, Shashi; Dutta, Anindya

2016-12-01

The six-subunit Origin Recognition Complex (ORC) is believed to be an essential eukaryotic ATPase that binds to origins of replication as a ring-shaped heterohexamer to load MCM2-7 and initiate DNA replication. We have discovered that human cell lines in culture proliferate with intact chromosomal origins of replication after disruption of both alleles of ORC2 or of the ATPase subunit, ORC1 . The ORC1 or ORC2 -depleted cells replicate with decreased chromatin loading of MCM2-7 and become critically dependent on another ATPase, CDC6, for survival and DNA replication. Thus, either the ORC ring lacking a subunit, even its ATPase subunit, can load enough MCM2-7 in partnership with CDC6 to initiate DNA replication, or cells have an ORC-independent, CDC6-dependent mechanism to load MCM2-7 on origins of replication.

Post clamp

NASA Technical Reports Server (NTRS)

Ramsey, John K. (Inventor); Meyn, Erwin H. (Inventor)

1990-01-01

A pair of spaced collars are mounted at right angles on a clamp body by retaining rings which enable the collars to rotate with respect to the clamp body. Mounting posts extend through aligned holes in the collars and clamp body. Each collar can be clamped onto the inserted post while the clamp body remains free to rotate about the post and collar. The clamp body is selectively clamped onto each post.

Highly active antiretroviral therapy started during pregnancy or postpartum suppresses HIV-1 RNA, but not DNA, in breast milk.

PubMed

Shapiro, Roger L; Ndung'u, Thumbi; Lockman, Shahin; Smeaton, Laura M; Thior, Ibou; Wester, Carolyn; Stevens, Lisa; Sebetso, Gaseene; Gaseitsiwe, Simani; Peter, Trevor; Essex, Max

2005-09-01

The ability of highly active antiretroviral therapy (HAART) to reduce human immunodeficiency virus type 1 (HIV-1) RNA and DNA in breast milk has not been described. We compared breast-milk HIV-1 RNA and DNA loads of women in Botswana who received HAART (nevirapine, lamivudine, and zidovudine) and women who did not receive HAART. Women in the HAART group received treatment for a median of 98 days (range, 67-222 days) at the time of breast-milk sampling; 23 (88%) of 26 had whole breast-milk HIV-1 RNA loads <50 copies/mL, compared with 9 (36%) of 25 women who did not receive HAART (P=.0001). This finding remained significant in a multivariate logistic-regression model (P = .0006). The whole-milk HIV-1 DNA load was unaffected by HAART. Of women who received HAART, 13 (50%) of 26 had HIV-1 DNA loads <10 copies/10(6) cells, compared with 15 (65%) of 23 who did not receive HAART (P = .39). HAART suppressed cell-free HIV-1 RNA in breast milk and may therefore reduce mother-to-child transmission (MTCT) of HIV-1 via breast-feeding. However, HAART initiated during pregnancy or early after delivery had no apparent effect on cell-associated HIV-1 DNA loads in breast milk. Clinical trials to determine MTCT among breast-feeding women receiving HAART are needed.

Fatigue and creep to leak tests of proton exchange membranes using pressure-loaded blisters

NASA Astrophysics Data System (ADS)

Li, Yongqiang; Dillard, David A.; Case, Scott W.; Ellis, Michael W.; Lai, Yeh-Hung; Gittleman, Craig S.; Miller, Daniel P.

In this study, three commercially available proton exchange membranes (PEMs) are biaxially tested using pressure-loaded blisters to characterize their resistance to gas leakage under either static (creep) or cyclic fatigue loading. The pressurizing medium, air, is directly used for leak detection. These tests are believed to be more relevant to fuel cell applications than quasi-static uniaxial tensile-to-rupture tests because of the use of biaxial cyclic and sustained loading and the use of gas leakage as the failure criterion. They also have advantages over relative humidity cycling test, in which a bare PEM or catalyst coated membrane is clamped with gas diffusion media and flow field plates and subjected to cyclic changes in relative humidity, because of the flexibility in allowing controlled mechanical loading and accelerated testing. Nafion ® NRE-211 membranes are tested at three different temperatures and the time-temperature superposition principle is used to construct stress-lifetime master curve. Tested at 90 °C, 2%RH extruded Ion Power ® N111-IP membranes have a longer lifetime than Gore™-Select ® 57 and Nafion ® NRE-211 membranes.

Condensin promotes the juxtaposition of DNA flanking its loading site in Bacillus subtilis

PubMed Central

Wang, Xindan; Le, Tung B.K.; Lajoie, Bryan R.; Dekker, Job; Laub, Michael T.; Rudner, David Z.

2015-01-01

SMC condensin complexes play a central role in compacting and resolving replicated chromosomes in virtually all organisms, yet how they accomplish this remains elusive. In Bacillus subtilis, condensin is loaded at centromeric parS sites, where it encircles DNA and individualizes newly replicated origins. Using chromosome conformation capture and cytological assays, we show that condensin recruitment to origin-proximal parS sites is required for the juxtaposition of the two chromosome arms. Recruitment to ectopic parS sites promotes alignment of large tracks of DNA flanking these sites. Importantly, insertion of parS sites on opposing arms indicates that these “zip-up” interactions only occur between adjacent DNA segments. Collectively, our data suggest that condensin resolves replicated origins by promoting the juxtaposition of DNA flanking parS sites, drawing sister origins in on themselves and away from each other. These results are consistent with a model in which condensin encircles the DNA flanking its loading site and then slides down, tethering the two arms together. Lengthwise condensation via loop extrusion could provide a generalizable mechanism by which condensin complexes act dynamically to individualize origins in B. subtilis and, when loaded along eukaryotic chromosomes, resolve them during mitosis. PMID:26253537

Nonlinear analysis of thermally and electrically actuated functionally graded material microbeam.

PubMed

Li, Yingli; Meguid, S A; Fu, Yiming; Xu, Daolin

2014-02-08

In this paper, we provide a unified and self-consistent treatment of a functionally graded material (FGM) microbeam with varying thermal conductivity subjected to non-uniform or uniform temperature field. Specifically, it is our objective to determine the effect of the microscopic size of the beam, the electrostatic gap, the temperature field and material property on the pull-in voltage of the microbeam under different boundary conditions. The non-uniform temperature field is obtained by integrating the steady-state heat conduction equation. The governing equations account for the microbeam size by introducing an internal material length-scale parameter that is based on the modified couple stress theory. Furthermore, it takes into account Casimir and van der Waals forces, and the associated electrostatic force with the first-order fringing field effects. The resulting nonlinear differential equations were converted to a coupled system of algebraic equations using the differential quadrature method. The outcome of our work shows the dramatic effect and dependence of the pull-in voltage of the FGM microbeam upon the temperature field, its gradient for a given boundary condition. Specifically, both uniform and non-uniform thermal loading can actuate the FGM microbeam even without an applied voltage. Our work also reveals that the non-uniform temperature field is more effective than the uniform temperature field in actuating a FGM cantilever-type microbeam. For the clamped-clamped case, care must be taken to account for the effective use of thermal loading in the design of microbeams. It is also observed that uniform thermal loading will lead to a reduction in the pull-in voltage of a FGM microbeam for all the three boundary conditions considered.

Smoking and anal high-risk human papillomavirus DNA loads in HIV-positive men who have sex with men.

PubMed

Wieland, Ulrike; Hellmich, Martin; Wetendorf, Janna; Potthoff, Anja; Höfler, Daniela; Swoboda, Jochen; Fuchs, Wolfgang; Brockmeyer, Norbert; Pfister, Herbert; Kreuter, Alexander

2015-10-01

HIV-positive men who have sex with men (MSM) have an increased risk for anal human papillomavirus (HPV) infection, anal high-grade intraepithelial lesions (HSIL), and anal cancer. Smoking is associated with abnormal anal cytology and with an increased risk for anal cancer. We collected 3736 intraanal swabs from 803 HIV-positive MSM who participated in an anal cancer screening program between October 2003 and August 2014. HPV prevalence, anal cytology and HPV DNA load of high-risk (HR) HPV-types 16, 18, 31 and 33 of non-smokers and smokers were compared. HPV-typing was performed by alpha-HPV genus-specific PCR and hybridization with 38 type-specific probes using a multiplex genotyping assay. In samples positive for HPV16, 18, 31, or 33, HPV DNA loads were determined by type-specific real-time PCRs and expressed as HPV DNA copies per betaglobin gene copy. At baseline, HR-HPV DNA (80.5 vs. 89.0%, p=0.001), HPV16 DNA (41.6 vs. 52.3%, p=0.003), HPV18 DNA (15.5 vs. 26.0%, p<0.001), anal dysplasia (LSIL+HSIL; 51.5 vs. 58.4%, p=0.045) and HSIL (17.2 vs. 22.7%, p=0.048) were detected more frequently in smokers compared to non-smokers. Throughout the study period 32.7% of non-smokers and 39.9% of smokers developed HSIL (p=0.011), and three smokers developed anal cancer. Considering swabs from the entire study period (median HPV load value per patient per cytology grade), smokers with normal anal cytology had significantly higher HPV16 loads (median 0.29 vs. 0.87, n=201, p=0.007) and cumulative high-risk-HPV loads (median 0.53 vs. 1.08, n=297, p=0.004) than non-smokers. Since elevated HR-HPV DNA loads are associated with an increased risk for HPV-induced anogenital cancers, HPV-infected HIV-positive MSM should be counseled to refrain from smoking. Additionally, for smokers, shorter anal cancer screening intervals than for non-smokers may be appropriate. Copyright © 2015 Elsevier GmbH. All rights reserved.

Postbuckling behaviors of nanorods including the effects of nonlocal elasticity theory and surface stress

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thongyothee, Chawis, E-mail: chawist@hotmail.com; Chucheepsakul, Somchai

2013-12-28

This paper is concerned with postbuckling behaviors of nanorods subjected to an end concentrated load. One end of the nanorod is clamped while the other end is fixed to a support that can slide in the slot. The governing equation is developed from static equilibrium and geometrical conditions by using the exact curvature corresponding to the elastica theory. The nonlocal elasticity, the effect of surface stress, and their combined effects are taken into account in Euler–Bernoulli beam theory. Differential equations in this problem can be solved numerically by using the shooting-optimization technique for the postbuckling loads and the buckled configurations.more » The results show that nanorods with the nonlocal elasticity effect undergo increasingly large deformation while the effect of surface stress in combination with nonlocal elasticity decreases the deflection of nanorods under the same postbuckling load.« less

Fretting Fatigue of Single Crystal/Polycrystalline Nickel Subjected to Blade/Disk Contact Loading

NASA Astrophysics Data System (ADS)

Matlik, J. F.; Murthy, H.; Farris, T. N.

2002-01-01

Fretting fatigue describes the formation and growth of cracks at the edge-of-contact of nominally clamped components subjected to cyclic loading. Components that are known to be subject to fretting fatigue include riveted lap joints and blade/disk contacts in launch vehicle turbomachinery. Recent efforts have shown that conventional mechanics tools, both fatigue and fracture based, can be used to model fretting fatigue experiments leading to successful life predictions. In particular, experiments involving contact load configurations similar to those that occur in the blade/disk connection of gas turbine engines have been performed extensively. Predictions of fretting fatigue life have been compared favorably to experimental observations [1]. Recent efforts are aimed at performing experiments at higher temperatures as shown in the photograph below along with a sample fracture surface. The talk will describe the status of these experiments as will as model developments relevant to the single crystal material properties.

Investigating Delamination Migration in Composite Tape Laminates

NASA Technical Reports Server (NTRS)

Ratcliffe, James G.; DeCarvalho, Nelson V.

2014-01-01

A modification to a recently developed test specimen designed to investigate migration of a delamination between neighboring ply interfaces in tape laminates is presented. The specimen is a cross-ply laminated beam consisting of 40 plies with a polytetrafluoroethylene insert spanning part way along its length. The insert is located between a lower 0-degree ply (specimen length direction) and a stack of four 90-degree plies (specimen width direction). The modification involved a stacking sequence that promotes stable delamination growth prior to migration, and included a relocation of the insert from the specimen midplane to the interface between plies 14 and 15. Specimens were clamped at both ends onto a rigid baseplate and loaded on their upper surface via a piano hinge assembly, resulting in a predominantly flexural loading condition. Tests were conducted with the load-application point positioned at various locations along a specimen's span. This position affected the sequence of damage events during a test.

Bipolar square-wave current source for transient electromagnetic systems based on constant shutdown time

NASA Astrophysics Data System (ADS)

Wang, Shilong; Yin, Changchun; Lin, Jun; Yang, Yu; Hu, Xueyan

2016-03-01

Cooperative work of multiple magnetic transmitting sources is a new trend in the development of transient electromagnetic system. The key is the bipolar current waves shutdown, concurrently in the inductive load. In the past, it was difficult to use the constant clamping voltage technique to realize the synchronized shutdown of currents with different peak values. Based on clamping voltage technique, we introduce a new controlling method with constant shutdown time. We use the rising time to control shutdown time and use low voltage power source to control peak current. From the viewpoint of the circuit energy loss, by taking the high-voltage capacitor bypass resistance and the capacitor of the passive snubber circuit into account, we establish the relationship between the rising time and the shutdown time. Since the switch is not ideal, we propose a new method to test the shutdown time by the low voltage, the high voltage and the peak current. Experimental results show that adjustment of the current rising time can precisely control the value of the clamp voltage. When the rising time is fixed, the shutdown time is unchanged. The error for shutdown time deduced from the energy consumption is less than 6%. The new controlling method on current shutdown proposed in this paper can be used in the cooperative work of borehole and ground transmitting system.

Effect of a 2-h hyperglycemic-hyperinsulinemic glucose clamp to promote glucose storage on endurance exercise performance.

PubMed

Maclaren, D P M; Mohebbi, H; Nirmalan, M; Keegan, M A; Best, C T; Perera, D; Harvie, M N; Campbell, I T

2011-09-01

Carbohydrate stores within muscle are considered essential as a fuel for prolonged endurance exercise, and regimes for enhancing such stores have proved successful in aiding performance. This study explored the effects of a hyperglycaemic-hyperinsulinemic clamp performed 18 h previously on subsequent prolonged endurance performance in cycling. Seven male subjects, accustomed to prolonged endurance cycling, performed 90 min of cycling at ~65% VO(2max) followed by a 16-km time trial 18 h after a 2-h hyperglycemic-hyperinsulinemic clamp (HCC). Hyperglycemia (10 mM) with insulin infused at 300 mU/m(2)/min over a 2-h period resulted in a total glucose uptake of 275 g (assessed by the area under the curve) of which glucose storage accounted for about 73% (i.e. 198 g). Patterns of substrate oxidation during 90-min exercise at 65% VO(2max) were not altered by HCC. Blood glucose and plasma insulin concentrations were higher during exercise after HCC compared with control (p < 0.05) while plasma NEFA was similar. Exercise performance was improved by 49 s and power output was 10-11% higher during the time trial (p < 0.05) after HCC. These data suggest that carbohydrate loading 18 h previously by means of a 2-h HCC improves cycling performance by 3.3% without any change in pattern of substrate oxidation.

Static and free-vibrational response of semi-circular graphite-epoxy frames with thin-walled open sections

NASA Technical Reports Server (NTRS)

Collins, J. Scott; Johnson, Eric R.

1989-01-01

Experiments were conducted to measure the three-dimensional static and free vibrational response of two graphite-epoxy, thin-walled, open section frames. The frames are semi-circular with a radius of three feet, and one specimen has an I cross section and the other has a channel cross section. The flexibility influence coefficients were measured in static tests for loads applied at midspan with the ends of the specimens clamped. Natural frequencies and modes were determined from vibrational tests for free and clamped end conditions. The experimental data is used to evaluate a new finite element which was developed specifically for the analysis of curved, thin-walled structures. The formulation of the element is based on a Vlasov-type, thin-walled, curved beam theory. The predictions from the finite element program generally correlated well with the experimental data for the symmetric I-specimen. Discrepancies in some of the data were found to be due to flexibility in the clamped end conditions. With respect to the data for the channel specimen, the correlation was less satisfactory. The finite element analysis predicted the out-of-plane response of the channel specimen reasonably well, but large discrepancies occurred between the predicted in-plane response and the experimental data. The analysis predicted a much more compliant in-plane response than was observed in the experiments.

Bipolar square-wave current source for transient electromagnetic systems based on constant shutdown time.

PubMed

Wang, Shilong; Yin, Changchun; Lin, Jun; Yang, Yu; Hu, Xueyan

2016-03-01

Cooperative work of multiple magnetic transmitting sources is a new trend in the development of transient electromagnetic system. The key is the bipolar current waves shutdown, concurrently in the inductive load. In the past, it was difficult to use the constant clamping voltage technique to realize the synchronized shutdown of currents with different peak values. Based on clamping voltage technique, we introduce a new controlling method with constant shutdown time. We use the rising time to control shutdown time and use low voltage power source to control peak current. From the viewpoint of the circuit energy loss, by taking the high-voltage capacitor bypass resistance and the capacitor of the passive snubber circuit into account, we establish the relationship between the rising time and the shutdown time. Since the switch is not ideal, we propose a new method to test the shutdown time by the low voltage, the high voltage and the peak current. Experimental results show that adjustment of the current rising time can precisely control the value of the clamp voltage. When the rising time is fixed, the shutdown time is unchanged. The error for shutdown time deduced from the energy consumption is less than 6%. The new controlling method on current shutdown proposed in this paper can be used in the cooperative work of borehole and ground transmitting system.

Use of the Satinsky clamp for hilar clamping during robotic partial nephrectomy: indications, technique, and multi-center outcomes.

PubMed

Abdullah, Newaj; Rahbar, Haider; Barod, Ravi; Dalela, Deepansh; Larson, Jeff; Johnson, Michael; Mass, Alon; Zargar, Homayoun; Kaouk, Jihad; Allaf, Mohamad; Bhayani, Sam; Stifelman, Michael; Rogers, Craig

2017-03-01

A Satinsky clamp may be a backup option for hilar clamping during robotic partial nephrectomy (RPN) if there are challenges with application of bulldog clamps, but there are potential safety concerns. We evaluate outcomes of RPN using Satinsky vs. bulldog clamps, and provide tips for safe use of the Satinsky as a backup option. Using a multi-center database, we identified 1073 patients who underwent RPN between 2006 and 2013, and had information available about method of hilar clamping (bulldog clamp vs. Satinsky clamp). Patient baseline characteristics, tumor features, and perioperative outcomes were compared between the Satinsky and bulldog clamp groups. A Satinsky clamp was used for hilar clamping in 94 (8.8 %) RPN cases, and bulldog clamps were used in 979 (91.2 %) cases. The use of a Satinsky clamp was associated with greater operative time (198 vs. 175 min, p < 0.001), estimated blood loss (EBL, 200 vs. 100 ml, p < 0.001), warm ischemia time (WIT, 20 vs. 19 min, p = 0.036), transfusion rate (12.8 vs. 4.8 %, p = 0.001), and hospital stay (3 vs. 2 days, p < 0.001). Tumor characteristics and number of renal vessels were similar between groups. There were six intraoperative complications in the Satinsky clamp group, but none were directly related to the Satinsky clamp. On multivariable analysis, the use of the Satinsky clamp was not associated with increase in intraoperative or Clavien ≥3 postoperative complications, positive surgical margin rate or percentage change in estimated glomerular filtration rate. A Satinsky clamp can be a backup option for hilar clamping during challenging RPN cases, but requires careful technique, and was rarely necessary.

Effect of sterilization on stiffness and dimensional stability of rubber-dam clamps.

PubMed

Giebink, D L; Mathieu, G P; Hondrum, S O

1996-01-01

Simulated clinical conditions were used to test the effect of sterilization on rubber-dam clamp stiffness and dimension. Sixty Hygienic and Ivory W7 clamps were either steam or dry heat sterilized and compared to controls. Stiffness and dimensional change between Ivory clamp groups was significant (p<.0001); the sterilized clamps showed less change than the controls. Hygienic groups showed a significant different between the control and dry heat groups (p<.05); the sterilized clamps showed less change than the controls. The change in stiffness and interjaw width for all Ivory clamps compared to all Hygienic clamps was significant (p<.0001). The Hygienic clamps changes less than the Ivory clamps. The results indicate that steam and dry heat sterilization do not affect retention of rubber-dam clamps.

Human papillomavirus (HPV) types 16, 18, 31, 45 DNA loads and HPV-16 integration in persistent and transient infections in young women

PubMed Central

2010-01-01

Background HPV burden is a predictor for high-grade cervical intraepithelial neoplasia and cancer. The natural history of HPV load in young women being recently exposed to HPV is described in this paper. Methods A total of 636 female university students were followed for 2 years. Cervical specimens with HPV-16, -18, -31, or -45 DNA by consensus PCR were further evaluated with type-specific and β-globin real-time PCR assays. Proportional hazards regression was used to estimate hazard ratios (HR) of infection clearance. Generalized estimating equations assessed whether HPV loads was predictive of HPV infection at the subsequent visit. Results HPV loads were consistently higher among women <25 years old, and those who had multiple sex partners, multiple HPV type infections and smokers. HPV-16 integration was encountered only in one sample. Infection clearance was faster among women at lower tertiles of HPV-16 (HR = 2.8, 95%CI: 1.0-8.1), HPV-18 (HR = 3.5, 95%CI: 1.1-11.2) or combined (HR = 2.4, 95%CI: 1.8-6.2) DNA loads. The relationship between HPV-16 and HPV-18 DNA loads and infection clearance followed a clear dose-response pattern, after adjusting for age and number of sexual partners. GEE Odds Ratios for HPV persistence of the middle and upper tertiles relative to the lower tertile were 2.7 and 3.0 for HPV-16 and 3.8 and 39.1 for HPV-18, respectively. There was no association between HPV-31 or -45 DNA loads and persistence. Conclusions The association between HPV load and persistence is not uniform across high-risk genital genotypes. HPV-16 integration was only rarely demonstrated in young women. PMID:21070660

Excellent performances of energy harvester using cantilever driving double-clamped 0.7Pb(Mg{sub 1/3}Nb{sub 2/3})O{sub 3}-0.3PbTiO{sub 3} plates and symmetric middle-stops

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zeng, Zhou; Xu, Qing; University of Chinese Academy of Sciences, Beijing 100049

We present a high performance nonlinear piezoelectric energy harvester constituted by a cantilever with symmetrically middle-stops and double-clamped piezoelectric plates based on piezoelectric single crystal 0.7Pb(Mg{sub 1/3}Nb{sub 2/3})O{sub 3}-0.3PbTiO{sub 3}. Electrical properties of the device under different excitation frequencies, accelerations, and load resistances are studied systematically. Under a low acceleration of 3 m/s{sup 2} (0.3 g), a peak voltage of 26.2 V and a maximum normalized power of 25.6 mW/g{sup 2} were obtained across a matching impedance of 600 kΩ with favorable bandwidths. The low excitation acceleration and excellent performances indicate that the device can be a promising candidate for energy harvesting in low-power electronicsmore » and wireless sensors.« less

Roles of PCNA ubiquitination and TLS polymerases κ and η in the bypass of methyl methanesulfonate-induced DNA damage

PubMed Central

Wit, Niek; Buoninfante, Olimpia Alessandra; van den Berk, Paul C.M.; Jansen, Jacob G.; Hogenbirk, Marc A.; de Wind, Niels; Jacobs, Heinz

2015-01-01

Translesion synthesis (TLS) provides a highly conserved mechanism that enables DNA synthesis on a damaged template. TLS is performed by specialized DNA polymerases of which polymerase (Pol) κ is important for the cellular response to DNA damage induced by benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide (BPDE), ultraviolet (UV) light and the alkylating agent methyl methanesulfonate (MMS). As TLS polymerases are intrinsically error-prone, tight regulation of their activity is required. One level of control is provided by ubiquitination of the homotrimeric DNA clamp PCNA at lysine residue 164 (PCNA-Ub). We here show that Polκ can function independently of PCNA modification and that Polη can function as a backup during TLS of MMS-induced lesions. Compared to cell lines deficient for PCNA modification (PcnaK164R) or Polκ, double mutant cell lines display hypersensitivity to MMS but not to BPDE or UV-C. Double mutant cells also displayed delayed post-replicative TLS, accumulate higher levels of replication stress and delayed S-phase progression. Furthermore, we show that Polη and Polκ are redundant in the DNA damage bypass of MMS-induced DNA damage. Taken together, we provide evidence for PCNA-Ub-independent activation of Polκ and establish Polη as an important backup polymerase in the absence of Polκ in response to MMS-induced DNA damage. PMID:25505145

Experimental observations on the decay of environmental DNA from bighead and silver carps

USGS Publications Warehouse

Lance, Richard F.; Klymus, Katy E.; Richter, Cathy; Guan, Xin; Farrington, Heather L.; Carr, Matthew R.; Thompson, Nathan; Chapman, Duane C.; Baerwaldt, Kelly L.

2017-01-01

Interest in the field of environmental DNA (eDNA) is growing rapidly and eDNA surveys are becoming an important consideration for aquatic resource managers dealing with invasive species. However, in order for eDNA monitoring to mature as a research and management tool, there are several critical knowledge gaps that must be filled. One such gap is the fate of eDNA materials in the aquatic environment. Understanding the environmental factors that influence the decay of eDNA and how these factors impact detection probabilities over time and space could have significant implications for eDNA survey design and data interpretation. Here we experimentally explore decay of eDNA associated with bighead carp (Hypophthalmichthys nobilis) biological waste collected from an aquaculture filtration system and with sperm collected from captive silver carp (H. molitrix), and how decay may be influenced by differing levels of water turbulence, temperature, microbial load, and pH. We found that the decay patterns of eDNA associated with both H. nobilis biological waste and H. molitrix milt significantly fit monophasic exponential decay curves. Secondly, we observed that the highest temperature we tested resulted in a decay half-life as much as 5.5× more rapid than the lowest temperature we tested. When we suppressed microbial loads in eDNA samples, we observed that overall losses of eDNA were reduced by about 2.5×. When we amended eDNA samples with pond water the half-life of eDNA was reduced by about 2.25×, despite relatively little apparent increase in the overall microbial load. This pattern indicated that species constituency of the microbial community, in addition to microbial load, might play a critical role in eDNA degradation. A shift in pH from 6.5 to 8.0 in the samples resulted in a 1.6× reduction in eDNA halflife. Water turbulence in our study had no apparent effect on eDNA decay. When we combined different temperature, pH, and microbial load treatments to create a rapid decay condition and a slow decay condition, and tracked eDNA decay over 91 days, we observed a 5.0× greater loss of eDNA by Day 5 under rapid decay conditions than under slow decay conditions. At the end of the trials, the differences in eDNA loss between the rapid decay and baseline and slow decay conditions were 0.1× and 3.3×, respectively. Our results strongly demonstrate the potential for environmental factors to influence eDNA fate and, thus, the interpretation of eDNA survey results.

A Photosensitizer-Loaded DNA Origami Nanosystem for Photodynamic Therapy.

PubMed

Zhuang, Xiaoxi; Ma, Xiaowei; Xue, Xiangdong; Jiang, Qiao; Song, Linlin; Dai, Luru; Zhang, Chunqiu; Jin, Shubin; Yang, Keni; Ding, Baoquan; Wang, Paul C; Liang, Xing-Jie

2016-03-22

Photodynamic therapy (PDT) offers an alternative for cancer treatment by using ultraviolet or visible light in the presence of a photosensitizer and molecular oxygen, which can produce highly reactive oxygen species that ultimately leading to the ablation of tumor cells by multifactorial mechanisms. However, this technique is limited by the penetration depth of incident light, the hypoxic environment of solid tumors, and the vulnerability of photobleaching reduces the efficiency of many imaging agents. In this work, we reported a cellular level dual-functional imaging and PDT nanosystem BMEPC-loaded DNA origami for photodynamic therapy with high efficiency and stable photoreactive property. The carbazole derivative BMEPC is a one- and two-photon imaging agent and photosensitizer with large two-photon absorption cross section, which can be fully excited by near-infrared light, and is also capable of destroying targets under anaerobic condition by generating reactive intermediates of Type I photodynamic reactions. However, the application of BMEPC was restricted by its poor solubility in aqueous environment and its aggregation caused quenching. We observed BMEPC-loaded DNA origami effectively reduced the photobleaching of BMEPC within cells. Upon binding to DNA origami, the intramolecular rotation of BMEPC became proper restricted, which intensify fluorescence emission and radicals production when being excited. After the BMEPC-loaded DNA origami are taken up by tumor cells, upon irradiation, BMEPC could generate free radicals and be released due to DNA photocleavage as well as the following partially degradation. Apoptosis was then induced by the generation of free radicals. This functional nanosystem provides an insight into the design of photosensitizer-loaded DNA origami for effective intracellular imaging and photodynamic therapy.

High voltage load resistor array

DOEpatents

Lehmann, Monty Ray [Smithfield, VA

2005-01-18

A high voltage resistor comprising an array of a plurality of parallel electrically connected resistor elements each containing a resistive solution, attached at each end thereof to an end plate, and about the circumference of each of the end plates, a corona reduction ring. Each of the resistor elements comprises an insulating tube having an electrode inserted into each end thereof and held in position by one or more hose clamps about the outer periphery of the insulating tube. According to a preferred embodiment, the electrode is fabricated from stainless steel and has a mushroom shape at one end, that inserted into the tube, and a flat end for engagement with the end plates that provides connection of the resistor array and with a load.

Experimental studies on the tripping behavior of narrow T-stiffened flat plates subjected to hydrostatic pressure and underwater shock

NASA Technical Reports Server (NTRS)

Budweg, H. L.; Shin, Y. S.

1987-01-01

An experimental investigation was conducted to determine the static and dynamic responses of a specific stiffened flat plate design. The air-backed rectangular flat plates of 6061-T6 aluminum with an externally machined longitudinal narrow-flanged T-stiffener and clamped boundary conditions were subjected to static loading by water hydropump pressure and shock loading from an eight pound TNT charge detonated underwater. The dynamic test plate was instrumented to measure transient strains and free field pressure. The static test plate was instrumented to measure transient strains, plate deflection, and pressure. Emphasis was placed upon forcing static and dynamic stiffener tripping, obtaining relevant strain and pressure data, and studying the associated plate-stiffener behavior.

Piezoelectric film load cell robot collision detector

DOEpatents

Lembke, J.R.

1988-03-15

A piezoelectric load cell which can be utilized for detecting collisions and obstruction of a robot arm end effector includes a force sensing element of metallized polyvinylidene fluoride (PVDF) film. The piezoelectric film sensing element and a resilient support pad are clamped in compression between upper and lower plates. The lower plate has a central recess in its upper face for supporting the support pad and sensing element, while the upper plate has a corresponding central projection formed on its lower face for bearing on the sensing element and support pad. The upper and lower plates are dowelled together for concentric alignment and screwed together. The upper and lower plates are also adapted for mounting between the robot arm wrist and end effector. 3 figs.

Piezoelectric film load cell robot collision detector

DOEpatents

Lembke, John R.

1989-04-18

A piezoelectric load cell which can be utilized for detecting collisions and obstruction of a robot arm end effector includes a force sensing element of metallized polyvinylidene fluoride (PVDF) film. The piezoelectric film sensing element and a resilient support pad are clamped in compression between upper and lower plates. The lower plate has a central recess in its upper face for supporting the support pad and sensing element, while the upper plate has a corresponding central projection formed on its lower face for bearing on the sensing element and support pad. The upper and lower plates are dowelled together for concentric alignment and screwed together. The upper and lower plates are also adapted for mounting between the robot arm wrist and end effector.

Piezoelectric film load cell robot collision detector

DOEpatents

Lembke, J.R.

1989-04-18

A piezoelectric load cell which can be utilized for detecting collisions and obstruction of a robot arm end effector includes a force sensing element of metallized polyvinylidene fluoride (PVDF) film. The piezoelectric film sensing element and a resilient support pad are clamped in compression between upper and lower plates. The lower plate has a central recess in its upper face for supporting the support pad and sensing element, while the upper plate has a corresponding central projection formed on its lower face for bearing on the sensing element and support pad. The upper and lower plates are doweled together for concentric alignment and screwed together. The upper and lower plates are also adapted for mounting between the robot arm wrist and end effector. 3 figs.

The preliminary design of bearings for the control system of a high-temperature lithium-cooled nuclear reactor

NASA Technical Reports Server (NTRS)

Yacobucci, H. G.; Waldron, W. D.; Walowit, J. A.

1973-01-01

The design of bearings for the control system of a fast reactor concept is presented. The bearings are required to operate at temperatures up to 2200 F in one of two fluids, lithium or argon. Basic bearing types are the same regardless of the fluid. Crowned cylindrical journals were selected for radially loaded bearings and modified spherical bearings were selected for bearings under combined thrust and radial loads. Graphite and aluminum oxide are the materials selected for the argon atmosphere bearings while cermet compositions (carbides or nitrides bonded with refractory metals) were selected for the lithium lubricated bearings. Mounting of components is by shrink fit or by axial clamping utilizing differential thermal expansion.

A dual switch controls bacterial enhancer-dependent transcription

PubMed Central

Wiesler, Simone C.; Burrows, Patricia C.; Buck, Martin

2012-01-01

Bacterial RNA polymerases (RNAPs) are targets for antibiotics. Myxopyronin binds to the RNAP switch regions to block structural rearrangements needed for formation of open promoter complexes. Bacterial RNAPs containing the major variant σ54 factor are activated by enhancer-binding proteins (bEBPs) and transcribe genes whose products are needed in pathogenicity and stress responses. We show that (i) enhancer-dependent RNAPs help Escherichia coli to survive in the presence of myxopyronin, (ii) enhancer-dependent RNAPs partially resist inhibition by myxopyronin and (iii) ATP hydrolysis catalysed by bEBPs is obligatory for functional interaction of the RNAP switch regions with the transcription start site. We demonstrate that enhancer-dependent promoters contain two barriers to full DNA opening, allowing tight regulation of transcription initiation. bEBPs engage in a dual switch to (i) allow propagation of nucleated DNA melting from an upstream DNA fork junction and (ii) complete the formation of the transcription bubble and downstream DNA fork junction at the RNA synthesis start site, resulting in switch region-dependent RNAP clamp closure and open promoter complex formation. PMID:22965125

Clamping characteristics study on different types of clamping unit

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiao, Zhiwei; Liu, Haichao; Xie, Pengcheng

2015-05-22

Plastic products are becoming more and more widely used in aerospace, IT, digital electronics and many other fields. With the development of technology, the requirement of product precision is getting higher and higher. However, type and working performance of clamping unit play a decisive role in product precision. Clamping characteristics of different types of clamping unit are discussed in this article, which use finite element numerical analysis method through the software ABAQUS to study the clamping uniformity, and detect the clamping force repeatability precision. The result shows that compared with toggled three-platen clamping unit, clamping characteristics of internal circulation two-platenmore » clamping unit are better, for instance, its mold cavity deformation and force that bars and mold parting surface suffered are more uniform, and its clamping uniformity and repeatability precision is also better.« less

Plasmid DNA loaded chitosan nanoparticles for nasal mucosal immunization against hepatitis B.

PubMed

Khatri, Kapil; Goyal, Amit K; Gupta, Prem N; Mishra, Neeraj; Vyas, Suresh P

2008-04-16

This work investigates the preparation and in vivo efficacy of plasmid DNA loaded chitosan nanoparticles for nasal mucosal immunization against hepatitis B. Chitosan pDNA nanoparticles were prepared using a complex coacervation process. Prepared nanoparticles were characterized for size, shape, surface charge, plasmid loading and ability of nanoparticles to protect DNA against nuclease digestion and for their transfection efficacy. Nasal administration of nanoparticles resulted in serum anti-HBsAg titre that was less compared to that elicited by naked DNA and alum adsorbed HBsAg, but the mice were seroprotective within 2 weeks and the immunoglobulin level was above the clinically protective level. However, intramuscular administration of naked DNA and alum adsorbed HBsAg did not elicit sIgA titre in mucosal secretions that was induced by nasal immunization with chitosan nanoparticles. Similarly, cellular responses (cytokine levels) were poor in case of alum adsorbed HBsAg. Chitosan nanoparticles thus produced humoral (both systemic and mucosal) and cellular immune responses upon nasal administration. The study signifies the potential of chitosan nanoparticles as DNA vaccine carrier and adjuvant for effective immunization through non-invasive nasal route.

Advanced Joining of Aerospace Metallic Materials.

DTIC Science & Technology

1986-07-01

uniaxial tensile test with varying temperature and cyclic loading. This simple test problem excercises maray aspects of the phenomena. suOn- ,Ual Yield...6vidence Ia seconde configuration apparait plus n~ faste . 5.3. Ents-e-igne-men-t-s s-u r a dyna-mique de. bain-s de fu-sion A lusage il svest r~vle que la...scanning system for fast and exact alignment of the EB-qun is used. In a fixture the cleaned detail parts are positioned exactly and clamped for welding. At

Feasibility Study of a Precision Cast Loading Machine for Small Ammunition Items

DTIC Science & Technology

1975-05-01

distribution unlimited. READ INStRUCTIONS BEFORE COMPLETING FORM 1. RECIPIENT’S CATALOG NUMBER S. TYRE OF REPORT « PERIOD COVERED S. PCRFORMINO ORO...through a short length rubber hose into the hemisphere. A clamp actuated by an air cylinder can close or open the rubber hose. Because of unknown... rubber hose in the recess on the face of the fixture, exposing opposite hole for observation by the TV monitor through the TV camera. 8. Release table

Rigid, Perfectly Plastic Analysis of Ring-Stiffened Shells Under Dynamic Loading

DTIC Science & Technology

1986-08-01

Elastic-Viscoplastic Response of Clamped Beams Under Uniformly Distributed Impulse, Technical Report AFML-TR-68-396, Jan 1969. 15. Save , M. A. and...Edition, 1959, pp. 466-471 (Chapter 15). A-4. Save , M. A. and Massonnett, C. E., Plastic Analysis and Design of Plates, Shells, and Discs, North-Holland...TYPE TYESHORT (2 ɞ) HIGH LOAnD p > I + CONDITIONS u C 2 (-1) 0 T 1 0 x < MOMENT m Ix, T) 2 +1 OR -RESULTANT Lxo u.=-g- MEMBRANE n,= RESULTANT

A numerical solution of Duffing's equations including the prediction of jump phenomena

NASA Technical Reports Server (NTRS)

Moyer, E. T., Jr.; Ghasghai-Abdi, E.

1987-01-01

Numerical methodology for the solution of Duffing's differential equation is presented. Algorithms for the prediction of multiple equilibrium solutions and jump phenomena are developed. In addition, a filtering algorithm for producing steady state solutions is presented. The problem of a rigidly clamped circular plate subjected to cosinusoidal pressure loading is solved using the developed algorithms (the plate is assumed to be in the geometrically nonlinear range). The results accurately predict regions of solution multiplicity and jump phenomena.

Strength Tests on Thin-walled Duralumin Cylinders in Torsion

NASA Technical Reports Server (NTRS)

Lundquist, Eugene E

1932-01-01

This report is the first of a series presenting the results of strength tests on thin-walled cylinders and truncated cones of circular and elliptical section; it comprises the results obtained to date from torsion (pure shear) tests on 65 thin-walled duralumin cylinders of circular section with ends clamped to rigid bulkheads. The effect of variations in the length/radius and radius/thickness ratios on the type of failure is indicated, and a semi-empirical equation for the shearing stress at maximum load is given.

Development and Testing of a Friction-Based Post-Installable Fiber-Optic Monitoring System for Subsea Applications

NASA Technical Reports Server (NTRS)

Bentley, Nicole L.; Brower, David V.; Le, Suy Q.; Seaman, Calvin H.; Tang, Henry H.

2017-01-01

This paper presents the design and development of a friction-based coupling device for a fiber-optic monitoring system capable of measuring pressure, strain, and temperature that can be deployed on existing subsea structures. A summary is provided of the design concept, prototype development, prototype performance testing, and subsequent design refinements of the device. The results of laboratory testing of the first prototype performed at the National Aeronautics and Space Administration (NASA) Johnson Space Center (JSC) are also included. Limitations of the initial concept were identified during testing and future design improvements were proposed and later implemented. These new features enhance the coupling of the sensor device and improve the monitoring system measurement capabilities. A major challenge of a post-installed instrumentation monitoring system is to ensure adequate coupling between the instruments and the structure of interest for reliable measurements. Friction-based devices have the potential to overcome coupling limitations caused by marine growth and soil contamination on flowlines, risers, and other subsea structures. The work described in this paper investigates the design and test of a friction-based coupling device (herein referred to as a friction clamp) which is suitable for pipelines and structures that are suspended in the water column as well as for those that are resting on the seabed. The monitoring elements consist of fiberoptic sensors that are bonded to a stainless steel clamshell assembly with a high-friction surface coating. The friction clamp incorporates a single hinge design to facilitate installation of the clamp and dual rows of opposing fasteners to distribute the clamping force along the structure. The friction clamp can be modified to be installed by commercial divers in shallow depths or by remotely operated vehicles in deep-water applications. NASA-JSC was involved in the selection and testing of the friction coating, and in the design and testing of the prototype clamp device. Four-inch diameter and eight-inch diameter sub-scale friction clamp prototypes were built and tested to evaluate the strain measuring capabilities of the design under different loading scenarios. The testing revealed some limitations of the initial design concept, and subsequent refinements were explored to improve the measurement performance of the system. This study was part of a collaboration between NASA-JSC and Astro Technology Inc. within a study called Clear Gulf. The primary objective of the Clear Gulf study is to develop advanced instrumentation technologies that will improve operational safety and reduce the risk of hydrocarbon spillage. NASA provided unique insights, expansive test facilities, and technical expertise to advance technologies that will benefit the environment, the public, and commercial industries.

LAMP-1-chimeric DNA vaccines enhance the antibody response in Japanese flounder, Paralichthys olivaceus.

PubMed

Rondón-Barragán, Iang; Nozaki, Reiko; Hirono, Ikuo; Kondo, Hidehiro

2017-08-01

DNA vaccination is one method to protect farmed fish from viral and bacterial diseases. Chimeric antigens encoded by DNA vaccines have been shown to increase the resistance to viral diseases. Here, we sequenced the gene encoding lysosome-associated membrane protein-1 from Japanese flounder, Paralichthys olivaceus, (JfLAMP-1) and assessed its use in a chimeric DNA vaccine fused with the major capsule protein (MCP) from red seabream iridovirus (RSIV). JfLAMP-1 cDNA has a length of 1248 bp encoding 415 aa, which contains transmembrane and cytoplasmic domains. JfLAMP-1 is constitutively expressed in several tissues and its expression in spleen was upregulated following injection of formalin-killed cells (FKC) of Edwardsiella tarda. Immunofluorescence analysis showed that JfLAMP-1 is distributed in the small and large granules in the cytoplasm and groups close to the nucleus. The DNA encoding the luminal domain of JfLAMP-1 was replaced with the gene for the RSIV MCP, and the construct was cloned in an expression vector (pCIneo). Fish vaccinated with pCLAMP-MCP had significantly higher antibody levels than fish vaccinated with pCIneo vector harboring the MCP gene (p < 0.05) at day 30 post-vaccination. Copyright © 2017 Elsevier Ltd. All rights reserved.

[Quantitative real-time PCR--usefulness in detection and monitoring of CMV infection after hematopeietic stem cells transplant].

PubMed

Grabarczyk, Piotr; Brojer, Ewa; Nasiłowska, Barbara; Mariańska, Bozena

2006-09-01

It is recommended that all patients after allogeneic hematopoietic stem cell transplantation (alloHSCT) should be monitored for CMV infection markers. The aim of the study was to check the usefulness of quantitative DNA CMV monitoring after alloHSCT. DNA CMV was tested by real-time PCR in sera and blood samples twice a week until 30th day after alloHSCT thereafter, once a week until 100th day and then, once every 2-3 weeks. 832 samples from 16 patients were tested. All patients were anti-CMV positive or/and received stem cells from seropositive donors. Introduction of antiviral treatment was based on initial viral load and its rate of increase. DNA CMV was detected in 13/16 patients; in 3 before 30h day after allo HSCT (group I) and in 10 (group II) after 30th day. In all patients from group I clinical symptoms were observed and DNA CMV was detected in sera and blood samples. Peak viral load was 2490-34 620 geq/ml. Although antiviral treatment was applied, reinfection was observed and infection lasted from 28 to 91 days. In 6 group II patients, clinical symptoms were observed and DNA CMV in sera and blood was detected for 16-56 days, DNA CMV peak load was 100-8950 geq/ml. In the remaining 4 patients, no clinical symptoms were observed--DNA CMV was detected in blood only for 7 to 14 days. In one patient with peak viral load 10,540 geq/ml, antiviral treatment was applied. In 3 with viral load of 400-2000 geq/ml, treatment was not introduced. The quantitative DNA CMV results were taken into account before the change of antiviral drugs for more effective drugs and the decrease of drug dose due to side effects. Application of quantititative DNA CMV testing allowed to optimise antiviral drug administration in immunosupressed patients after alloHSCT

Quantitative and Cost Comparison of Ultrasensitive Human Immunodeficiency Virus Type 1 RNA Viral Load Assays: Bayer bDNA Quantiplex Versions 3.0 and 2.0 and Roche PCR Amplicor Monitor Version 1.5

PubMed Central

Elbeik, Tarek; Charlebois, Edwin; Nassos, Patricia; Kahn, James; Hecht, Frederick M.; Yajko, David; Ng, Valerie; Hadley, Keith

2000-01-01

Quantification of human immunodeficiency virus type 1 (HIV-1) RNA as a measure of viral load has greatly improved the monitoring of therapies for infected individuals. With the significant reductions in viral load now observed in individuals treated with highly active anti-retroviral therapy (HAART), viral load assays have been adapted to achieve greater sensitivity. Two commercially available ultrasensitive assays, the Bayer Quantiplex HIV-1 bDNA version 3.0 (bDNA 3.0) assay and the Roche Amplicor HIV-1 Monitor Ultrasensitive version 1.5 (Amplicor 1.5) assay, are now being used to monitor HIV-1-infected individuals. Both of these ultrasensitive assays have a reported lower limit of 50 HIV-1 RNA copies/ml and were developed from corresponding older generation assays with lower limits of 400 to 500 copies/ml. However, the comparability of viral load data generated by these ultrasensitive assays and the relative costs of labor, disposables, and biohazardous wastes were not determined in most cases. In this study, we used matched clinical plasma samples to compare the quantification of the newer bDNA 3.0 assay with that of the older bDNA 2.0 assay and to compare the quantification and costs of the bDNA 3.0 assay and the Amplicor 1.5 assay. We found that quantification by the bDNA 3.0 assay was approximately twofold higher than that by the bDNA 2.0 assay and was highly correlated to that by the Amplicor 1.5 assay. Moreover, cost analysis based on labor, disposables, and biohazardous wastes showed significant savings with the bDNA 3.0 assay as compared to the costs of the Amplicor 1.5 assay. PMID:10699005

Quantitative and cost comparison of ultrasensitive human immunodeficiency virus type 1 RNA viral load assays: Bayer bDNA quantiplex versions 3.0 and 2.0 and Roche PCR Amplicor monitor version 1.5.

PubMed

Elbeik, T; Charlebois, E; Nassos, P; Kahn, J; Hecht, F M; Yajko, D; Ng, V; Hadley, K

2000-03-01

Quantification of human immunodeficiency virus type 1 (HIV-1) RNA as a measure of viral load has greatly improved the monitoring of therapies for infected individuals. With the significant reductions in viral load now observed in individuals treated with highly active anti-retroviral therapy (HAART), viral load assays have been adapted to achieve greater sensitivity. Two commercially available ultrasensitive assays, the Bayer Quantiplex HIV-1 bDNA version 3.0 (bDNA 3.0) assay and the Roche Amplicor HIV-1 Monitor Ultrasensitive version 1.5 (Amplicor 1.5) assay, are now being used to monitor HIV-1-infected individuals. Both of these ultrasensitive assays have a reported lower limit of 50 HIV-1 RNA copies/ml and were developed from corresponding older generation assays with lower limits of 400 to 500 copies/ml. However, the comparability of viral load data generated by these ultrasensitive assays and the relative costs of labor, disposables, and biohazardous wastes were not determined in most cases. In this study, we used matched clinical plasma samples to compare the quantification of the newer bDNA 3.0 assay with that of the older bDNA 2.0 assay and to compare the quantification and costs of the bDNA 3.0 assay and the Amplicor 1.5 assay. We found that quantification by the bDNA 3.0 assay was approximately twofold higher than that by the bDNA 2.0 assay and was highly correlated to that by the Amplicor 1.5 assay. Moreover, cost analysis based on labor, disposables, and biohazardous wastes showed significant savings with the bDNA 3.0 assay as compared to the costs of the Amplicor 1.5 assay.

Protein Phosphatase 2A Antagonizes ATM and ATR in a Cdk2- and Cdc7-Independent DNA Damage Checkpoint

PubMed Central

Petersen, Paris; Chou, Danny M.; You, Zhongsheng; Hunter, Tony; Walter, Johannes C.; Walter, Gernot

2006-01-01

We previously used a soluble cell-free system derived from Xenopus eggs to investigate the role of protein phosphatase 2A (PP2A) in chromosomal DNA replication. We found that immunodepletion of PP2A or inhibition of PP2A by okadaic acid (OA) inhibits initiation of DNA replication by preventing loading of the initiation factor Cdc45 onto prereplication complexes. Evidence was provided that PP2A counteracts an inhibitory protein kinase that phosphorylates and inactivates a crucial Cdc45 loading factor. Here, we report that the inhibitory effect of OA is abolished by caffeine, an inhibitor of the checkpoint kinases ataxia-telangiectasia mutated protein (ATM) and ataxia-telangiectasia related protein (ATR) but not by depletion of ATM or ATR from the extract. Furthermore, we demonstrate that double-strand DNA breaks (DSBs) cause inhibition of Cdc45 loading and initiation of DNA replication and that caffeine, as well as immunodepletion of either ATM or ATR, abolishes this inhibition. Importantly, the DSB-induced inhibition of Cdc45 loading is prevented by addition of the catalytic subunit of PP2A to the extract. These data suggest that DSBs and OA prevent Cdc45 loading through different pathways, both of which involve PP2A, but only the DSB-induced checkpoint implicates ATM and ATR. The inhibitory effect of DSBs on Cdc45 loading does not result from downregulation of cyclin-dependent kinase 2 (Cdk2) or Cdc7 activity and is independent of Chk2. However, it is partially dependent on Chk1, which becomes phosphorylated in response to DSBs. These data suggest that PP2A counteracts ATM and ATR in a DNA damage checkpoint in Xenopus egg extracts. PMID:16479016

Mechanism for verification of mismatched and homoduplex DNAs by nucleotides-bound MutS analyzed by molecular dynamics simulations.

PubMed

Ishida, Hisashi; Matsumoto, Atsushi

2016-09-01

In order to understand how MutS recognizes mismatched DNA and induces the reaction of DNA repair using ATP, the dynamics of the complexes of MutS (bound to the ADP and ATP nucleotides, or not) and DNA (with mismatched and matched base-pairs) were investigated using molecular dynamics simulations. As for DNA, the structure of the base-pairs of the homoduplex DNA which interacted with the DNA recognition site of MutS was intermittently disturbed, indicating that the homoduplex DNA was unstable. As for MutS, the disordered loops in the ATPase domains, which are considered to be necessary for the induction of DNA repair, were close to (away from) the nucleotide-binding sites in the ATPase domains when the nucleotides were (not) bound to MutS. This indicates that the ATPase domains changed their structural stability upon ATP binding using the disordered loop. Conformational analysis by principal component analysis showed that the nucleotide binding changed modes which have structurally solid ATPase domains and the large bending motion of the DNA from higher to lower frequencies. In the MutS-mismatched DNA complex bound to two nucleotides, the bending motion of the DNA at low frequency modes may play a role in triggering the formation of the sliding clamp for the following DNA-repair reaction step. Moreover, MM-PBSA/GBSA showed that the MutS-homoduplex DNA complex bound to two nucleotides was unstable because of the unfavorable interactions between MutS and DNA. This would trigger the ATP hydrolysis or separation of MutS and DNA to continue searching for mismatch base-pairs. Proteins 2016; 84:1287-1303. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Roughness evolution of metallic implant surfaces under contact loading and nanometer-scale chemical etching.

PubMed

Ryu, J J; Letchuman, S; Shrotriya, P

2012-10-01

Surface damage of metallic implant surface at taper lock and clamped interfaces may take place through synergistic interactions between repeated contact loading and corrosion. In the present research, we investigated the influence of surface roughness and contact loading on the mechanical and chemical damage phenomena. Cobalt-chromium (CoCrMo) specimens with two different roughness configurations created by milling and grinding process were subjected to normal and inclined contact loading. During repeated contact loading, amplitude of surface roughness reached a steady value after decreasing during the first few cycles. During the second phase, the alternating experiment of rough surface contact and micro-etching was conducted to characterize surface evolution behavior. As a result, surface roughness amplitude continuously evolved-decreasing during contact loading due to plastic deformation of contacting asperities and increasing on exposure to corrosive environment by the preferential corrosion attack on stressed area. Two different instabilities could be identified in the surface roughness evolution during etching of contact loaded surfaces: increase in the amplitude of dominant wavenumber and increase in amplitude of a small group of roughness modes. A damage mechanism that incorporates contact-induced residual stress development and stress-assisted dissolution is proposed to elucidate the measured instabilities in surface roughness evolution. Copyright © 2012 Elsevier Ltd. All rights reserved.

Buckling behavior of long symmetrically laminated plates subjected to combined loadings

NASA Technical Reports Server (NTRS)

Nemeth, Michael P.

1992-01-01

A parametric study is presented of the buckling behavior of infinitely long, symmetrically laminated anisotropic plates subjected to combined loadings. The loading conditions considered are axial tension and compression transverse tension and compression, and shear. Results obtained using a special-purpose analysis, well-suited for parametric studies, are presented for clamped and simply supported plates. Moreover, results are presented for some common laminate constructions, and generic buckling design charts are presented for a wide range of parameters. The generic design charts are presented in terms of useful nondimensional parameters, and the dependence of the nondimensional parameters on laminate fiber orientation, stacking sequence, and material properties is discussed. An important finding of the study is that the effects of anisotropy are much more pronounced in shear-loaded plates than in compression-loaded plates. In addition, the effects of anisotropy on plates subjected to combined loadings are generally manifested as a phase shift of self-similar buckling interaction curves. A practical application of this phase shift is that the buckling resistance of long plates can be improved by applying a shear loading with a specific orientation. In all cases considered in the study, the buckling coefficients of infinitely long plates are found to be independent of the bending stiffness ratio (D sub 11/D sub 22)(1/4).

Buckling behavior of long symmetrically laminated plates subjected to combined loads

NASA Technical Reports Server (NTRS)

Nemeth, Michael P.

1992-01-01

A parametric study of the buckling behavior of infinitely long symmetrically laminated anisotropic plates subjected to combined loadings is presented. The loading conditions considered are axial tension and compression, transverse tension and compression, and shear. Results obtained using a special purpose analysis, well suited for parametric studies are presented for clamped and simply supported plates. Moreover, results are presented for some common laminate constructions, and generic buckling design charts are presented for a wide range of parameters. The generic design charts are presented in terms of useful nondimensional parameters, and dependence of the nondimensional parameters on laminate fiber orientation, stacking sequence, and material properties is discussed. An important finding of the study is that the effects of anisotropy are much more pronounced in shear-loaded plates than in compression loaded plates. In addition, the effects of anisotropy on plates subjected to combined loadings are generally manifested as a phase shift of self-similar buckling interaction curves. A practical application of this phase shift is the buckling resistance of long plates can be improved by applying a shear loading with a specific orientation. In all cases considered, it is found that the buckling coefficients of infinitely long plates are independent of the bending stiffness ratio (D sub 11/D sub 22) sup 1/4.

Circulating, cell-free DNA as a marker for exercise load in intermittent sports.

PubMed

Haller, Nils; Helmig, Susanne; Taenny, Pascal; Petry, Julian; Schmidt, Sebastian; Simon, Perikles

2018-01-01

Attempts to establish a biomarker reflecting individual player load in intermittent sports such as football have failed so far. Increases in circulating DNA (cfDNA) have been demonstrated in various endurance sports settings. While it has been proposed that cfDNA could be a suitable marker for player load in intermittent sports, the effects on cfDNA of repeated sprinting as an essential feature in intermittent sports are unknown. For the first time, we assessed both alterations of cfDNA due to repeated maximal sprints and due to a professional football game. Nine participants were subjected to a standardised sprint training session with cross-over design of five maximal sprints of 40 meters with either "short" (1 minute) or "long" pauses (5 minutes). Capillary cfDNA and lactate were measured after every sprint and venous cfDNA before and after each series of sprints. Moreover, capillary cfDNA and lactate values were taken in 23 professional football players before and after incremental exercise testing, during the course of a training week at rest (baseline) and in all 17 enrolled players following a season game. Lactate and venous cfDNA increased more pronounced during "short" compared to "long" (1.4-fold, p = 0.032 and 1.7-fold, p = 0.016) and cfDNA correlated significantly with lactate (r = 0.69; p<0.001). Incremental exercise testing increased cfDNA 7.0-fold (p<0.001). The season game increased cfDNA 22.7-fold (p<0.0001), while lactate showed a 2.0-fold (p = 0.09) increase compared to baseline. Fold-changes in cfDNA correlated with distance covered during game (spearman's r = 0.87, p = 0.0012), while no correlation between lactate and the tracking data could be found. We show for the first time that cfDNA could be an objective marker for distance covered in elite intermittent sports. In contrast to the potential of more established blood-based markers like IL-6, CK, or CRP, cfDNA shows by far the strongest fold-change and a high correlation with a particular load related aspect in professional football.

Circulating, cell-free DNA as a marker for exercise load in intermittent sports

PubMed Central

Haller, Nils; Helmig, Susanne; Taenny, Pascal; Petry, Julian; Schmidt, Sebastian

2018-01-01

Background Attempts to establish a biomarker reflecting individual player load in intermittent sports such as football have failed so far. Increases in circulating DNA (cfDNA) have been demonstrated in various endurance sports settings. While it has been proposed that cfDNA could be a suitable marker for player load in intermittent sports, the effects on cfDNA of repeated sprinting as an essential feature in intermittent sports are unknown. For the first time, we assessed both alterations of cfDNA due to repeated maximal sprints and due to a professional football game. Methods Nine participants were subjected to a standardised sprint training session with cross-over design of five maximal sprints of 40 meters with either “short” (1 minute) or “long” pauses (5 minutes). Capillary cfDNA and lactate were measured after every sprint and venous cfDNA before and after each series of sprints. Moreover, capillary cfDNA and lactate values were taken in 23 professional football players before and after incremental exercise testing, during the course of a training week at rest (baseline) and in all 17 enrolled players following a season game. Results Lactate and venous cfDNA increased more pronounced during “short” compared to “long” (1.4-fold, p = 0.032 and 1.7-fold, p = 0.016) and cfDNA correlated significantly with lactate (r = 0.69; p<0.001). Incremental exercise testing increased cfDNA 7.0-fold (p<0.001). The season game increased cfDNA 22.7-fold (p<0.0001), while lactate showed a 2.0-fold (p = 0.09) increase compared to baseline. Fold-changes in cfDNA correlated with distance covered during game (spearman’s r = 0.87, p = 0.0012), while no correlation between lactate and the tracking data could be found. Discussion We show for the first time that cfDNA could be an objective marker for distance covered in elite intermittent sports. In contrast to the potential of more established blood-based markers like IL-6, CK, or CRP, cfDNA shows by far the strongest fold-change and a high correlation with a particular load related aspect in professional football. PMID:29370268

Tetramerization and interdomain flexibility of the replication initiation controller YabA enables simultaneous binding to multiple partners

PubMed Central

Felicori, Liza; Jameson, Katie H.; Roblin, Pierre; Fogg, Mark J.; Garcia-Garcia, Transito; Ventroux, Magali; Cherrier, Mickaël V.; Bazin, Alexandre; Noirot, Philippe; Wilkinson, Anthony J.; Molina, Franck; Terradot, Laurent; Noirot-Gros, Marie-Françoise

2016-01-01

YabA negatively regulates initiation of DNA replication in low-GC Gram-positive bacteria. The protein exerts its control through interactions with the initiator protein DnaA and the sliding clamp DnaN. Here, we combined X-ray crystallography, X-ray scattering (SAXS), modeling and biophysical approaches, with in vivo experimental data to gain insight into YabA function. The crystal structure of the N-terminal domain (NTD) of YabA solved at 2.7 Å resolution reveals an extended α-helix that contributes to an intermolecular four-helix bundle. Homology modeling and biochemical analysis indicates that the C-terminal domain (CTD) of YabA is a small Zn-binding domain. Multi-angle light scattering and SAXS demonstrate that YabA is a tetramer in which the CTDs are independent and connected to the N-terminal four-helix bundle via flexible linkers. While YabA can simultaneously interact with both DnaA and DnaN, we found that an isolated CTD can bind to either DnaA or DnaN, individually. Site-directed mutagenesis and yeast-two hybrid assays identified DnaA and DnaN binding sites on the YabA CTD that partially overlap and point to a mutually exclusive mode of interaction. Our study defines YabA as a novel structural hub and explains how the protein tetramer uses independent CTDs to bind multiple partners to orchestrate replication initiation in the bacterial cell. PMID:26615189

Prime-boost vaccination using DNA and whole inactivated virus vaccines provides limited protection against virulent feline immunodeficiency virus.

PubMed

Dunham, Stephen P; Bruce, Jennifer; Klein, Dieter; Flynn, J Norman; Golder, Matthew C; MacDonald, Susan; Jarrett, Oswald; Neil, James C

2006-11-30

Protection against feline immunodeficiency virus (FIV) has been achieved using a variety of vaccines notably whole inactivated virus (WIV) and DNA. However protection against more virulent isolates, typical of those encountered in natural infections, has been difficult to achieve. In an attempt to improve protection against virulent FIV(GL8), we combined both DNA and WIV vaccines in a "prime-boost" approach. Thirty cats were divided into four groups receiving vaccinations and one unvaccinated control group. Following viral challenge, two vaccinated animals, one receiving DNA alone and one the prime-boost vaccine remained free of viraemia, whilst all controls became viraemic. Animals vaccinated with WIV showed apparent early enhancement of infection at 2 weeks post challenge (pc) with higher plasma viral RNA loads than control animals or cats immunised with DNA alone. Despite this, animals vaccinated with WIV or DNA alone showed significantly lower proviral loads in peripheral blood mononuclear cells and mesenteric lymph node cells, whilst those receiving the DNA-WIV prime-boost vaccine showed significantly lower proviral loads in PBMC, than control animals, at 35 weeks pc. Therefore both DNA and WIV vaccines conferred limited protection against viral challenge but the combination of WIV and DNA in a prime-boost approach appeared to offer no significant advantage over either vaccine alone.

Human parvovirus B19, varicella zoster virus, and human herpesvirus-6 in mesenchymal stem cells of patients with osteoarthritis: analysis with quantitative real-time polymerase chain reaction.

PubMed

Rollín, R; Alvarez-Lafuente, R; Marco, F; Jover, J A; Hernández-García, C; Rodríguez-Navas, C; López-Durán, L; Fernández-Gutiérrez, B

2007-04-01

To investigate whether there is a possible viral transmission using mesenchymal stem cells (MSCs) in autologous or allogeneic transplantation in the context of osteoarthritis (OA) patients. The presence of parvovirus B19 (B19), varicella zoster virus (VZV), and human herpesvirus-6 (HHV-6) was studied in MSCs from bone marrow of patients with OA and healthy controls. MSCs were prepared from bone marrow aspirates obtained from 18 patients undergoing joint replacement as a result of OA and from 10 healthy controls. DNA was extracted from primary MSCs' culture established from these cells and quantitative real-time polymerase chain reaction was performed to analyse the prevalence and viral load of B19, VZV and HHV-6. The prevalence of total viral DNA among patients with OA was 16.7% (3/18), with a mean viral load of 29.7 copies/microg of DNA. One out of 18 was positive for B19 (viral load, 61.2 copies/microg of DNA), two for VZV (mean viral load, 14.4 copies/microg of DNA), and none for HHV-6. The prevalence of total viral DNA in the control group was 20% (2/10), with a mean viral load of 13.4 copies/microg of DNA. Both positive results were of B19 parvoviruses. There were no statistically significant differences among patients and controls. This first approach to the viral prevalence in MSCs of bone marrow in OA patients and healthy controls seems to show a very low risk of viral transmission or reactivation in a possible MSCs' transplantation.

DNA conformations in mismatch repair probed in solution by X-ray scattering from gold nanocrystals

PubMed Central

Hura, Greg L.; Tsai, Chi-Lin; Claridge, Shelley A.; Mendillo, Marc L.; Smith, Jessica M.; Williams, Gareth J.; Mastroianni, Alexander J.; Alivisatos, A. Paul; Putnam, Christopher D.; Kolodner, Richard D.; Tainer, John A.

2013-01-01

DNA metabolism and processing frequently require transient or metastable DNA conformations that are biologically important but challenging to characterize. We use gold nanocrystal labels combined with small angle X-ray scattering to develop, test, and apply a method to follow DNA conformations acting in the Escherichia coli mismatch repair (MMR) system in solution. We developed a neutral PEG linker that allowed gold-labeled DNAs to be flash-cooled and stored without degradation in sample quality. The 1,000-fold increased gold nanocrystal scattering vs. DNA enabled investigations at much lower concentrations than otherwise possible to avoid concentration-dependent tetramerization of the MMR initiation enzyme MutS. We analyzed the correlation scattering functions for the nanocrystals to provide higher resolution interparticle distributions not convoluted by the intraparticle distribution. We determined that mispair-containing DNAs were bent more by MutS than complementary sequence DNA (csDNA), did not promote tetramer formation, and allowed MutS conversion to a sliding clamp conformation that eliminated the DNA bends. Addition of second protein responder MutL did not stabilize the MutS-bent forms of DNA. Thus, DNA distortion is only involved at the earliest mispair recognition steps of MMR: MutL does not trap bent DNA conformations, suggesting migrating MutL or MutS/MutL complexes as a conserved feature of MMR. The results promote a mechanism of mismatch DNA bending followed by straightening in initial MutS and MutL responses in MMR. We demonstrate that small angle X-ray scattering with gold labels is an enabling method to examine protein-induced DNA distortions key to the DNA repair, replication, transcription, and packaging. PMID:24101514

The internal head protein Gp16 controls DNA ejection from the bacteriophage T7 virion.

PubMed

Struthers-Schlinke, J S; Robins, W P; Kemp, P; Molineux, I J

2000-08-04

A wild-type T7 virion ejects about 850 bp of the 40 kb genome into the bacterial cell by a transcription-independent process. Internalization of the remainder of the genome normally requires transcription. Inhibition of transcription-independent DNA translocation beyond the leading 850 bp is not absolute but the time taken by a population of phage genomes in overcoming the block averages about 20 minutes at 30 degrees C. There are additional blocks to transcription-independent translocation and less than 20 % of infecting DNA molecules completely penetrate the cell cytoplasm after four hours of infection. Mutant virions containing an altered gene 16 protein either prevent the blocks to transcription-independent DNA translocation or effect rapid release from blocking sites and allow the entire phage DNA molecule to enter the cell at a constant rate of about 75 bp per second. This rate is likely the same at which the leading 850 bp is ejected into the cell from a wild-type virion. All mutations fall into two clusters contained within 380 bp of the 4 kb gene 16, suggesting that a 127 residue segment of gp16 controls DNA ejection from the phage particle. We suggest that this segment of gp16 acts as a clamp to prevent transcription-independent DNA translocation. Copyright 2000 Academic Press.

DNA Methylation Profiles of Selected Pro-Inflammatory Cytokines in Alzheimer Disease.

PubMed

Nicolia, Vincenzina; Cavallaro, Rosaria A; López-González, Irene; Maccarrone, Mauro; Scarpa, Sigfrido; Ferrer, Isidre; Fuso, Andrea

2017-01-01

By means of functional genomics analysis, we recently described the mRNA expression profiles of various genes involved in the neuroinflammatory response in the brains of subjects with late-onset Alzheimer Disease (LOAD). Some of these genes, namely interleukin (IL)-1β and IL-6, showed distinct expression profiles with peak expression during the first stages of the disease and control-like levels at later stages. IL-1β and IL-6 genes are modulated by DNA methylation in different chronic and degenerative diseases; it is also well known that LOAD may have an epigenetic basis. Indeed, we and others have previously reported gene-specific DNA methylation alterations in LOAD and in related animal models. Based on these data, we studied the DNA methylation profiles, at single cytosine resolution, of IL-1β and IL-6 5'-flanking region by bisulphite modification in the cortex of healthy controls and LOAD patients at 2 different disease stages: Braak I-II/A and Braak V-VI/C. Our analysis provides evidence that neuroinflammation in LOAD is associated with (and possibly mediated by) epigenetic modifications. © 2017 American Association of Neuropathologists, Inc. All rights reserved.

Optimization of test parameters for quantitative stress measurements using the miniaturized disk-bend test

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meyers, D.E.; Chen, F.C.; Zhang, J.

A recently-developed miniaturized disk-bend test (MDBT) has been successfully used to evaluate the mechanical properties of a variety of materials, using specimens 3 mm in diameter. The load is applied either by a solid ball (the ball-on ring (BOR) mode), or by a hollow cylinder (the ring-on-ring (ROR) mode). They authors have reproduced the yield stresses of ordered intermetallic compounds and the fracture toughness of several ceramics using analytical solutions to the equations of elasticity theory. Despite this success there are several curious features involved in the analysis of data; for example, in previous tests conducted in the BOR modemore » correct values of the yield stress were obtained using the equations appropriate to clamped specimens, whether or not hey were actually clamped in the test fixture. They show that this is ubiquitous to tests in the BOR mode, and does not arise because of frictional constraints at the supporting ring. They have also completed a thorough evaluation of testing in the ROR mode, in which the yield stresses of cold-rolled or annealed AISI type 302 stainless steel were measured using various combinations of specimen thickness and radii of the loading and supporting rings, and compared to those of tensile specimens machined from the same material. The most accurate and reproducible measurements of the yield strength were obtained for specific combinations of specimen thickness and geometry of the apparatus.« less

Exact variational nonlocal stress modeling with asymptotic higher-order strain gradients for nanobeams

NASA Astrophysics Data System (ADS)

Lim, C. W.; Wang, C. M.

2007-03-01

This article presents a complete and asymptotic representation of the one-dimensional nanobeam model with nonlocal stress via an exact variational principle approach. An asymptotic governing differential equation of infinite-order strain gradient model and the corresponding infinite number of boundary conditions are derived and discussed. For practical applications, it explores and presents a reduced higher-order solution to the asymptotic nonlocal model. It is also identified here and explained at length that most publications on this subject have inaccurately employed an excessively simplified lower-order model which furnishes intriguing solutions under certain loading and boundary conditions where the results become identical to the classical solution, i.e., without the small-scale effect at all. Various nanobeam examples are solved to demonstrate the difference between using the simplified lower-order nonlocal model and the asymptotic higher-order strain gradient nonlocal stress model. An important conclusion is the discovery of significant over- or underestimation of stress levels using the lower-order model, particularly at the vicinity of the clamped end of a cantilevered nanobeam under a tip point load. The consequence is that the design of a nanobeam based on the lower-order strain gradient model could be flawed in predicting the nonlocal stress at the clamped end where it could, depending on the magnitude of the small-scale parameter, significantly over- or underestimate the failure criteria of a nanobeam which are governed by the level of stress.

Switch on the engine: how the eukaryotic replicative helicase MCM2-7 becomes activated.

PubMed

Tognetti, Silvia; Riera, Alberto; Speck, Christian

2015-03-01

A crucial step during eukaryotic initiation of DNA replication is the correct loading and activation of the replicative DNA helicase, which ensures that each replication origin fires only once. Unregulated DNA helicase loading and activation, as it occurs in cancer, can cause severe DNA damage and genomic instability. The essential mini-chromosome maintenance proteins 2-7 (MCM2-7) represent the core of the eukaryotic replicative helicase that is loaded at DNA replication origins during G1-phase of the cell cycle. The MCM2-7 helicase activity, however, is only triggered during S-phase once the holo-helicase Cdc45-MCM2-7-GINS (CMG) has been formed. A large number of factors and several kinases interact and contribute to CMG formation and helicase activation, though the exact mechanisms remain unclear. Crucially, upon DNA damage, this reaction is temporarily halted to ensure genome integrity. Here, we review the current understanding of helicase activation; we focus on protein interactions during CMG formation, discuss structural changes during helicase activation, and outline similarities and differences of the prokaryotic and eukaryotic helicase activation process.

Differences in Bordetella pertussis DNA load according to clinical and epidemiological characteristics of patients with whooping cough.

PubMed

Brotons, Pedro; de Paz, Hector D; Toledo, Diana; Villanova, Marta; Plans, Pedro; Jordan, Iolanda; Dominguez, Angela; Jane, Mireia; Godoy, Pere; Muñoz-Almagro, Carmen

2016-04-01

To identify associations between nasopharyngeal Bordetella pertussis DNA load and clinical and epidemiological characteristics and evaluate DNA load prognostic value in pertussis severity. Prospective observational multi-centre study including nasopharyngeal samples positive to pertussis DNA by real-time PCR collected from children and adult patients in more than 200 health centres of Catalonia (Spain) during 2012-2013. B. pertussis load was inversely correlated with age (rho = -0.32, p < 0.001), time to diagnosis (rho = -0.33, p < 0.001) and number of symptoms (rho = 0.13, p = 0.002). Median bacterial load was significantly higher in inpatients versus outpatients (4.91 vs. 2.55 log10 CFU/mL, p < 0.001), patients with complications versus those without (6.05 vs. 2.82 log10 CFU/mL, p < 0.001), disease incidence in summer and autumn versus spring and winter (3.50 vs. 2.21 log10 CFU/mL, p = 0.002), and unvaccinated-partially vaccinated patients versus vaccinated (4.20 vs. 2.76 log10 CFU/mL, p = 0.004). A logistic regression model including bacterial load and other candidate prognostic factors showed good prediction for hospital care (AUC = 0.94) although only age and unvaccinated status were found to be prognostic factors. We observed strong positive associations of nasopharyngeal bacterial load with severity outcomes of hospitalisation and occurrence of complications. Bacterial load and other independent variables contributed to an accurate prognostic model for hospitalisation. Copyright © 2016 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

Frame analysis of UNNES electric bus chassis construction using finite element method

NASA Astrophysics Data System (ADS)

Nugroho, Untoro; Anis, Samsudin; Kusumawardani, Rini; Khoiron, Ahmad Mustamil; Maulana, Syahdan Sigit; Irvandi, Muhammad; Mashdiq, Zia Putra

2018-03-01

Designing the chassis needs to be done element simulation analysis to gain chassis strength on an electric bus. The purpose of this research is to get the results of chassis simulation on an electric bus when having load use FEM (Finite element method). This research was conduct in several stages of process, such as modeling chassis by Autodesk Inventor and finite element simulation software. The frame is going to be simulated with static loading by determine fixed support and then will be given the vertical force. The fixed on the frame is clamped at both the front and rear suspensions. After the simulation based on FEM it can conclude that frame is still under elastic zone, until the frame design is safe to use.

First-Ply-Failure Performance of Composite Clamped Spherical Shells

NASA Astrophysics Data System (ADS)

Ghosh, A.; Chakravorty, D.

2018-05-01

The failure aspects of composites are available for plates, but studies of the literature on shells unveils that similar reports on them are very limited in number. The aim of this work was to investigate the first-ply-failure of industrially and aesthetically important spherical shells under uniform loadings. Apart from solving benchmark problems, numerical experiments were carried out with different variations of their parameters to obtain the first-ply-failure stresses by using the finite-element method. The load was increased in steps, and the lamina strains and stresses were put into well-established failure criteria to evaluate their first-ply-failure stress, the failed ply, the point of initiation of failure, and failure modes and tendencies. The results obtained are analyzed to extract the points of engineering significance.

Design of a Miniaturized RAD Hard Point-of-Load Converter

NASA Astrophysics Data System (ADS)

Lofgren, Henrik; Landstrom, Sven; Gunnarsson, Marcus; Hagstrom, Maria

2014-08-01

As an ARTES 5.2 activity, a miniaturized radiation hardened Point-Of-Load converter (uPOL) has been developed. Several different design options have been evaluated before the final system level design was selected. The selected topology is a buck regulator with synchronous rectification utilizing peak current mode control. The PWM logic is designed using discrete electronics. Inside the POL converter package, an independent latching current limiter and clamping over- voltage protection are included as protection devices. The converter has an input voltage range of 4.8-6.2V, output voltage range of 1.2-3.5V and an output current of 0-3.5A. The final converter will be a metal packaged hybrid built on LTCC technology with an operating case temperature range of -40 to +85 °C.

Viral load and genomic integration of HPV 16 in cervical samples from HIV-1-infected and uninfected women in Burkina Faso.

PubMed

Rousseau, Marie-Noelle Didelot; Costes, Valérie; Konate, Issouf; Nagot, Nicolas; Foulongne, Vincent; Ouedraogo, Abdoulaye; Van de Perre, Philippe; Mayaud, Philippe; Segondy, Michel

2007-06-01

The relationships between human papillomavirus type 16 (HPV 16) viral load, HPV 16 integration status, human immunodeficiency virus type 1 (HIV-1) status, and cervical cytology were studied among women enrolled in a cohort of female sex workers in Burkina Faso. The study focused on 24 HPV 16-infected women. The HPV 16 viral load in cervical samples was determined by real-time PCR. Integration ratio was estimated as the ratio between E2 and E6 genes DNA copy numbers. Integrated HPV16 viral load was defined as the product of HPV 16 viral load by the integration ratio. High HPV 16 viral load and high integration ratio were more frequent among women with squamous intraepithelial lesions compared with women with normal cytology (33% vs. 11%, and 33% vs. 0%, respectively), and among women with high-grade squamous intraepithelial lesions compared with women without high-grade squamous intraepithelial lesions (50% vs. 17%, and 50% vs. 11%, respectively). High HPV 16 DNA load, but not high integration ratio, was also more frequent among HIV-1-positive women (39% vs. 9%; and 23% vs. 18%, respectively). The absence of statistical significance of these differences might be explained by the small study sample size. High-integrated HPV 16 DNA load was significantly associated with the presence of high-grade squamous intraepithelial lesions (50% vs. 5%, P = 0.03) in univariate and multivariate analysis (adjusted odds-ratio: 19.05; 95% confidence interval (CI), 1.11-328.3, P = 0.03), but not with HIV-1 or other high-risk HPV types (HR-HPV). Integrated HPV 16 DNA load may be considered as a useful marker of high-grade cervical lesions in HPV 16-infected women. (c) 2007 Wiley-Liss, Inc.

Magnetic field-induced strain and magnetoelectric effects in sandwich composite of ferromagnetic shape memory Ni-Mn-Ga crystal and piezoelectric PVDF polymer.

PubMed

Zeng, Min; Or, Siu Wing; Chan, Helen Lai Wa

2010-10-01

A sandwich composite consisting of one layer of ferromagnetic shape memory Ni-Mn-Ga crystal plate bonded between two layers of piezoelectric PVDF polymer film was fabricated, and its magnetic field-induced strain (MFIS) and magnetoelectric (ME) effects were investigated, together with a monolithic Ni-Mn-Ga crystal, as functions of magnetic fields and mechanical load. The load-free dc- and ac-MFISs were 0.35 and 0.05% in the composite, and 5.6 and 0.3% in the monolithic crystal, respectively. The relatively smaller load-free MFISs in the composite than the monolithic crystal resulted from the clamping of martensitic twin-boundary motion in the Ni-Mn-Ga plate by the PVDF films. The largest ME coefficient (α(E)) was 0.58 V/cm·Oe at a magnetic bias field (H(Bias)) of 8.35 kOe under load-free condition. The mechanism of the ME effect originated from the mechanically mediated MFIS effect in the Ni-Mn-Ga plate and piezoelectric effect in the PVDF films. The measured α(E)-H(Bias) responses under different loads showed good agreement with the model prediction.

Roles of PCNA ubiquitination and TLS polymerases κ and η in the bypass of methyl methanesulfonate-induced DNA damage.

PubMed

Wit, Niek; Buoninfante, Olimpia Alessandra; van den Berk, Paul C M; Jansen, Jacob G; Hogenbirk, Marc A; de Wind, Niels; Jacobs, Heinz

2015-01-01

Translesion synthesis (TLS) provides a highly conserved mechanism that enables DNA synthesis on a damaged template. TLS is performed by specialized DNA polymerases of which polymerase (Pol) κ is important for the cellular response to DNA damage induced by benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide (BPDE), ultraviolet (UV) light and the alkylating agent methyl methanesulfonate (MMS). As TLS polymerases are intrinsically error-prone, tight regulation of their activity is required. One level of control is provided by ubiquitination of the homotrimeric DNA clamp PCNA at lysine residue 164 (PCNA-Ub). We here show that Polκ can function independently of PCNA modification and that Polη can function as a backup during TLS of MMS-induced lesions. Compared to cell lines deficient for PCNA modification (Pcna(K164R)) or Polκ, double mutant cell lines display hypersensitivity to MMS but not to BPDE or UV-C. Double mutant cells also displayed delayed post-replicative TLS, accumulate higher levels of replication stress and delayed S-phase progression. Furthermore, we show that Polη and Polκ are redundant in the DNA damage bypass of MMS-induced DNA damage. Taken together, we provide evidence for PCNA-Ub-independent activation of Polκ and establish Polη as an important backup polymerase in the absence of Polκ in response to MMS-induced DNA damage. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Viral load, integration and methylation of E2BS3 and 4 in human papilloma virus (HPV) 16-positive vaginal and vulvar carcinomas.

PubMed

Lillsunde Larsson, Gabriella; Helenius, Gisela; Sorbe, Bengt; Karlsson, Mats G

2014-01-01

To investigate if viral load, integration and methylation of E2BS3 and 4 represent different ways of tumor transformation in vaginal and vulvar carcinoma and to elucidate its clinical impact. Fifty-seven samples, positive for HPV16, were selected for the study. Detection of viral load was made with realtime-PCR using copy numbers of E6 and integration was calculated from comparing E2 to E6-copies. Methylation of E2BS3 and 4 was analysed using bisulphite treatment of tumor DNA, followed by PCR and pyrosequencing. Vaginal tumors were found to have a higher viral load (p = 0.024) compared to vulvar tumors but a high copy number (> median value, 15,000) as well as high methylation (>50%) was significantly (p = 0.010 and p = 0.045) associated with a worse cancer-specific survival rate in vulvar carcinoma, but not in vaginal carcinoma. Four groups could be defined for the complete series using a Cluster Two step analysis; (1) tumors holding episomal viral DNA, viral load below 150,000 copies not highly methylated (n = 25, 46.3%); (2) tumors harboring episomal viral DNA and being highly methylated (>50%; n = 6, 11.1%); (3) tumors with viral DNA fully integrated (n = 11, 20.4%), and (4) tumors harboring episomal viral DNA and being medium- or unmethylated (<50%) and having a high viral load (> total mean value 150,000; n = 12, 22.2%). The completely integrated tumors were found to be distinct group, whilst some overlap between the groups with high methylation and high viral load was observed. HPV16- related integration, methylation in E2BS3 and 4 and viral load may represent different viral characteristics driving vaginal and vulvar carcinogenesis. HPV16- related parameters were found to be of clinical importance in the vulvar series only.

Mechanism of action of hypoglycemic effects of an intestine-specific inhibitor of microsomal triglyceride transfer protein (MTP) in obese rats.

PubMed

Sakata, Shohei; Katsumi, Sohei; Mera, Yasuko; Kuroki, Yukiharu; Nashida, Reiko; Kakutani, Makoto; Ohta, Takeshi

2015-01-01

Diminished insulin sensitivity in the peripheral tissues and failure of pancreatic beta cells to secrete insulin are known major determinants of type 2 diabetes mellitus. JTT-130, an intestine-specific microsomal transfer protein inhibitor, has been shown to suppress high fat-induced obesity and ameliorate impaired glucose tolerance while enhancing glucagon-like peptide-1 (GLP-1) secretion. We investigated the effects of JTT-130 on glucose metabolism and elucidated the mechanism of action, direct effects on insulin sensitivity and glucose-stimulated insulin secretion in a high fat diet-induced obesity rat model. Male Sprague Dawley rats fed a high-fat diet were treated with a single administration of JTT-130. Glucose tolerance, hyperglycemic clamp and hyperinsulinemic-euglycemic testing were performed to assess effects on insulin sensitivity and glucose-stimulated insulin secretion, respectively. Plasma GLP-1 and tissue triglyceride content were also determined under the same conditions. A single administration of JTT-130 suppressed plasma glucose elevations after oral glucose loading and increased the disposition index while elevating GLP-1. JTT-130 also enhanced glucose-stimulated insulin secretion in hyperglycemic clamp tests, whereas increased insulin sensitivity was observed in hyperinsulinemic-euglycemic clamp tests. Single-dose administration of JTT-130 decreased lipid content in the liver and skeletal muscle. JTT-130 demonstrated acute and direct hypoglycemic effects by enhancing insulin secretion and/or insulin sensitivity. Copyright © 2014 Japanese Pharmacological Society. Production and hosting by Elsevier B.V. All rights reserved.

Influence of insulin on beta-endorphin plasma levels in obese and normal weight subjects.

PubMed

Brunani, A; Pincelli, A I; Pasqualinotto, L; Tibaldi, A; Baldi, G; Scacchi, M; Fatti, L M; Cavagnini, F

1996-08-01

To establish the possible role of hyperinsulinemia in the elevation of plasma beta-endorphin (beta-EP) levels observed in obese patients after an oral glucose load. Oral glucose tolerance test (OGTT) and euglycemic-hyperinsulinemic clamp. Two groups of six (age: 22-39 y, BMI: 30-48 kg/m2) and eight obese men (age: 18-37 y, BMI: 35-45 kg/m2), respectively, and five normal weight healthy men (age: 22-30 y, BMI 22-23 kg/m2). Glucose, insulin and beta-EP levels at baseline and every 30 min until 180 min during the OGTT; glucose, insulin, C-peptide and beta-EP concentrations at baseline and in steady state condition (i.e. during the last 30 min of insulin infusion) in the euglycemic-hyperinsulinemic clamp studies. In the six obese patients undergoing the OGTT a significant elevation of beta-EP plasma levels was observed between 60 and 90 min after glucose ingestion. In the clamp studies no significant differences in beta-EP plasma levels, blood glucose and serum insulin were observed between obese and normal weight subjects both at baseline and at steady state. A markedly diminished insulin sensitivity along with a lower inhibition of C-peptide during insulin infusion was observed in obese patients compared to control subjects. A rise in serum insulin levels unaccompanied by a concomitant increase in blood glucose concentration is unable to elicit a beta-EP response in obese patients.

[A study on the relationship between point mutation in pre-core region G1896A of hepatitis B virus and safety of breast feeding].

PubMed

Lu, Yin-ping; Cao, Wei; Hong, Mei; Zhu, Jian-fang; Liu, Zhao; Yang, Dong-liang

2008-10-01

To investigate the relationship between pre-core G1896A point mutation of hepatitis B virus (HBV) and safety of breast feeding. Serum and breast milk samples were collected from 62 pregnant women of HBV DNA positive/HBeAg negative. PCR-solid phase hybridization was used to detect the point mutation in pre-core region G1896A of HBV from pregnant women, and HBV DNA loads in sera and breast milk were determined by fluorescence quantitative PCR (FQ-PCR). The prevalence of point mutation was 61.3% (38/62) in 62 pregnant women with HBsAg positive/HBeAg negative. The positive rate of HBV DNA in breast milk of group with point mutation (28.9%) was similar to that of group without mutation (29.2%, chi2=0.0003, P>0.05). However, The positive rate of HBV DNA in breast milk of group with high HBV loads (56.0%) was significantly higher than that of group with low HBV loads (10.8%, chi2=14.79, P<0.01). The point mutation in pre-core region G1896A of HBV dose not affect the positive rate of HBV DNA in breast milk and higher HBV DNA loads in serum of pregnant women might increase the risk of mother-infant transmission.

Impact of Renal Hilar Control on Outcomes of Robotic Partial Nephrectomy: Systematic Review and Cumulative Meta-analysis.

PubMed

Cacciamani, Giovanni E; Medina, Luis G; Gill, Tania S; Mendelsohn, Alec; Husain, Fatima; Bhardwaj, Lokesh; Artibani, Walter; Sotelo, Renè; Gill, Inderbir S

2018-02-05

During robotic partial nephrectomy (RPN), various techniques of hilar control have been described, including on-clamp, early unclamping, selective/super-selective clamping, and completely-unclamped RPN. To evaluate the impact of various hilar control techniques on perioperative, functional, and oncological outcomes of RPN for tumors. We conducted a systematic literature review and meta-analysis of all comparative studies on various hilar control techniques during RPN using PubMed, Scopus, and Web of Science according to the Preferred Reporting Items for Systematic Review and Meta-analysis statement, and Methods and Guide for Effectiveness and Comparative Effectiveness Review of the Agency for Healthcare Research and Quality. Cumulative meta-analysis of comparative studies was conducted using Review Manager 5.3. Of 987 RPN publications in the literature, 19 qualified for this analysis. Comparison of off-clamp versus on-clamp RPN (n=9), selective clamping versus on-clamp RPN (n=3), super selective clamping versus on-clamp RPN (n=5), and early unclamped versus on-clamp (n=3) were reported. Patients undergoing RPN using off-clamp, selective/super selective, or early unclamp techniques had higher estimated blood loss compared with on-clamp RPN (weight mean difference [WMD]: 47.83, p=0.000, WMD: 41.06, p=0.02, and WMD: 37.50, p=0.47); however, this did not seem clinically relevant, since transfusion rates were similar (odds ratio [OR]: 0.98, p=0.95, OR: 0.72, p=0.7, and OR: 1.36, p=0.33, respectively). All groups appeared similar with regards to hospital stay, transfusions, overall and major complications, and positive cancer margin rates. Short- and long-term renal functional outcomes appeared superior in the off-clamp and super selective clamp groups compared with the on-clamp RPN cohort. Off-clamp, selective/super selective clamp, and early unclamp hilar control techniques are safe and feasible approaches for RPN surgery, with similar perioperative and oncological outcomes compared with on-clamp RPN. Minimizing global renal ischemia may provide superior renal function preservation. However, higher quality data are necessary for definitive conclusions in this regard. The objective of partial nephrectomy is to treat the cancer while maximizing renal function preservation. Clamping the main vessels is done primarily to reduce the blood loss during partial nephrectomy; however, vascular clamping can compromise kidney function. In order to avoid clamping, various techniques have been described. Our analysis showed that techniques that avoid main renal artery clamping during RPN are associated with better renal function preservation, yet deliver non-inferior perioperative and oncological outcomes as compared with robotic partial nephrectomy procedures that clamp the main vessels. Copyright © 2018 European Association of Urology. Published by Elsevier B.V. All rights reserved.

DNA Trojan Horses: Self-Assembled Floxuridine-Containing DNA Polyhedra for Cancer Therapy.

PubMed

Mou, Quanbing; Ma, Yuan; Pan, Gaifang; Xue, Bai; Yan, Deyue; Zhang, Chuan; Zhu, Xinyuan

2017-10-02

Based on their structural similarity to natural nucleobases, nucleoside analogue therapeutics were integrated into DNA strands through conventional solid-phase synthesis. By elaborately designing their sequences, floxuridine-integrated DNA strands were synthesized and self-assembled into well-defined DNA polyhedra with definite drug-loading ratios as well as tunable size and morphology. As a novel drug delivery system, these drug-containing DNA polyhedra could ideally mimic the Trojan Horse to deliver chemotherapeutics into tumor cells and fight against cancer. Both in vitro and in vivo results demonstrate that the DNA Trojan horse with buckyball architecture exhibits superior anticancer capability over the free drug and other formulations. With precise control over the drug-loading ratio and structure of the nanocarriers, the DNA Trojan horse may play an important role in anticancer treatment and exhibit great potential in translational nanomedicine. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Clamp usable as jig and lifting clamp

DOEpatents

Tsuyama, Yoshizo

1976-01-01

There is provided a clamp which is well suited for use as a lifting clamp for lifting and moving materials of assembly in a shipyard, etc. and as a pulling jig in welding and other operations. The clamp comprises a clamp body including a shackle for engagement with a pulling device and a slot for receiving an article, and a pair of jaws provided on the leg portions of the clamp body on the opposite sides of the slot to grip the article in the slot, one of said jaws consisting of a screw rod and the other jaw consisting of a swivel jaw with a spherical surface, whereby when the article clamped in the slot by the pair of jaws tends to slide in any direction with respect to the clamp body, the article is more positively gripped by the pair of jaws.

A pneumatic device for rapid loading of DNA sequencing gels.

PubMed

Panussis, D A; Cook, M W; Rifkin, L L; Snider, J E; Strong, J T; McGrane, R M; Wilson, R K; Mardis, E R

1998-05-01

This work describes the design and construction of a device that facilitates the loading of DNA samples onto polyacrylamide gels for detection in the Perkin Elmer/Applied Biosystems (PE/ABI) 373 and 377 DNA sequencing instruments. The device is mounted onto the existing gel cassettes and makes the process of loading high-density gels less cumbersome while the associated time and errors are reduced. The principle of operation includes the simultaneous transfer of the entire batch of samples, in which a spring-loaded air cylinder generates positive pressure and flexible silica capillaries transfer the samples. A retractable capillary array carrier allows the delivery ends of the capillaries to be held up clear of the gel during loader attachment on the gel plates, while enabling their insertion in the gel wells once the device is securely mounted. Gel-loading devices capable of simultaneously transferring 72 samples onto the PE/ABI 373 and 377 are currently being used in our production sequencing groups while a 96-sample transfer prototype undergoes testing.

Cable clamp bolt fixture facilitates assembly in close quarters

NASA Technical Reports Server (NTRS)

Sunderland, G. H.

1967-01-01

Cable clamp bolt holding fixture facilitates forming of electrical cable runs in limited equipment space. The fixture engages the threads of the short clamp bolt through the clamp and maintains tension against clamp tendency to open while the operator installs the nut without difficulty.

[Sequential monitoring of plasma EBV-DNA level in a patient with EBV-positive Hodgkin lymphoma].

PubMed

Uchida, Emi; Honma, Riko; Igarashi, Aiko; Kurata, Morito; Imadome, Ken-Ichi; Omoto, Eijiro; Miura, Osamu; Arai, Ayako

2012-01-01

A 58-year-old woman was admitted to our hospital because of fever, systemic lymphadenopathy with abnormal Epstein-Barr virus (EBV) antibody titers, and a high EBV-DNA load in the serum. She had been diagnosed as possibly having chronic active EBV infection (CAEBV) during a previous hospitalization. The EBV-DNA load of the plasma (pEBV-DNA), examined at our hospital, was elevated to 1.8×10(4) copies/ml, whereas that of the peripheral blood mononuclear cells was 3.4×10(1) copies/μg DNA, which was not clearly elevated, unlike in cases with CAEBV. Biopsy of the cervical lymph node was performed and the diagnosis of mixed cellularity classical Hodgkin lymphoma, Stage4B was made. Hodgkin cells were positive for EBV. COPP therapy was started and pEBV-DNA decreased drastically. The treatment was followed by ABVD therapy and pEBV-DNA turned negative after one course of ABVD therapy. She achieved complete response after 4 courses of the treatment. Reports from abroad indicate that pEBV-DNA parallels the disease state of EBV-positive Hodgkin lymphoma. Our results were consistent with these reports, and demonstrated that, in a Japanese patient, EBV-DNA load and its localization in the peripheral blood fractions could be useful tools for diagnosis as well as evaluating the disease status.

Split-tapered joint clamping device

DOEpatents

Olsen, Max J.; Schwartz, Jr., John F.

1988-01-01

This invention relates to a clamping device for removably attaching a tool element to a bracket element wherein a bracket element is disposed in a groove in the tool and a clamping member is disposed in said groove and in engagement with a clamping face of the bracket and a wall of the groove and with the clamping member having pivot means engaging the bracket and about which the clamping member rotates.

Effect of complete hilar versus only renal artery clamping on renal histomorphology following ischemia/reperfusion injury in an experimental model.

PubMed

Umul, M; Cal, A C; Turna, B; Oktem, G; Aydın, H H

2016-01-01

To evaluate the effect of temporary complete hilar versus only renal artery clamping with different duration of warm ischemia on renal functions, and possibly identify a "safe" clamping type and duration of renal ischemia. Fifty male rabbits have been incorporated to study. Rabbits were subjected to ischemia/reperfusion injury by temporary vascular clamping. Reagents were randomized to 3 experimental groups (only renal artery clamping, complete hilar clamping, sham surgery) and sub-groups were determined according to different clamping times (30 and 60 minutes). Median laparotomy and left renal hilus dissection were performed to sham group. Only artery or complete hilar clamping was performed for 30 or 60 minutes by microvascular bulldog clamps to other reagents. Rabbits were sacrificed 10 days after primary surgery and left nephrectomy performed. Nephrectomy materials were evaluated for the level of nitric-oxide synthase (NOS) immunoreactivity, malondialdehyde (MDA) level and superoxide dismutase (SOD) activity and an electron microscopic examination was performed. NOS immunoreactivity was correlated with the temporary clamping time. We also observed that complete hilar vascular clamping entails an increase on NOS immunoreactivity. MDA levels were similar for all experimental surgery groups (p = 0.42). The SOD activity was decreased among all subgroups compared with sham surgery. But the significant decrease occurred in 30 minutes only artery and 30 minutes complete hilar clamping groups in proportion to sham surgery (p = 0.026 and p = 0.019, respectively). This current study suggested that only renal artery clamping under 30 minutes is more appropriate during renal surgical procedures requiring temporary vascular clamping.

Comparative evaluation of the VERSANT HCV RNA 3.0, QUANTIPLEX HCV RNA 2.0, and COBAS AMPLICOR HCV MONITOR version 2.0 Assays for quantification of hepatitis C virus RNA in serum.

PubMed

Germer, Jeffrey J; Heimgartner, Paul J; Ilstrup, Duane M; Harmsen, W Scott; Jenkins, Greg D; Patel, Robin

2002-02-01

A comparison of quantitative results expressed in hepatitis C virus (HCV) international units per milliliter, obtained from the VERSANT HCV RNA 3.0 (bDNA-3.0) assay, the QUANTIPLEX HCV RNA 2.0 (bDNA-2.0) assay, and the COBAS AMPLICOR HCV MONITOR version 2.0 (HCM-2.0) test was performed. A total of 168 patient specimens submitted to the Mayo Clinic Molecular Microbiology Laboratory for HCV quantification or HCV genotyping were studied. Of the specimens tested, 97, 88, and 79% yielded quantitative results within the dynamic range of the bDNA-3.0, bDNA-2.0, and HCM-2.0 assays, respectively. Overall, there was substantial agreement between the results generated by all three assays. A total of 15 out of 29 (52%) of the specimens determined to contain viral loads of <31,746 IU/ml by the bDNA-3.0 assay were categorized as containing viral loads within the range of 31,746 to 500,000 IU/ml by the bDNA-2.0 assay. Although substantial agreement was noted between the results generated by the bDNA-2.0 and bDNA-3.0 assays, a bias toward higher viral titer by the bDNA-2.0 assay was noted (P = 0.001). Likewise, although substantial agreement was noted between the results generated by the HCM-2.0 and bDNA-3.0 assays, a bias toward higher viral titer by the bDNA-3.0 assay was noted (P < or = 0.001). The discrepancy between the HCM-2.0 and bDNA-3.0 results was more pronounced when viral loads were >500,000 IU/ml and resulted in statistically significant differences (P < or = 0.001) in determining whether viral loads were above or below 800,000 IU/ml of HCV RNA, the proposed threshold value for tailoring the duration of combination therapy. The expression of quantitative values in HCV international units per milliliter was a strength of both the bDNA-3.0 and HCM-2.0 assays.

Comparative Evaluation of the VERSANT HCV RNA 3.0, QUANTIPLEX HCV RNA 2.0, and COBAS AMPLICOR HCV MONITOR Version 2.0 Assays for Quantification of Hepatitis C Virus RNA in Serum

PubMed Central

Germer, Jeffrey J.; Heimgartner, Paul J.; Ilstrup, Duane M.; Harmsen, W. Scott; Jenkins, Greg D.; Patel, Robin

2002-01-01

A comparison of quantitative results expressed in hepatitis C virus (HCV) international units per milliliter, obtained from the VERSANT HCV RNA 3.0 (bDNA-3.0) assay, the QUANTIPLEX HCV RNA 2.0 (bDNA-2.0) assay, and the COBAS AMPLICOR HCV MONITOR version 2.0 (HCM-2.0) test was performed. A total of 168 patient specimens submitted to the Mayo Clinic Molecular Microbiology Laboratory for HCV quantification or HCV genotyping were studied. Of the specimens tested, 97, 88, and 79% yielded quantitative results within the dynamic range of the bDNA-3.0, bDNA-2.0, and HCM-2.0 assays, respectively. Overall, there was substantial agreement between the results generated by all three assays. A total of 15 out of 29 (52%) of the specimens determined to contain viral loads of <31,746 IU/ml by the bDNA-3.0 assay were categorized as containing viral loads within the range of 31,746 to 500,000 IU/ml by the bDNA-2.0 assay. Although substantial agreement was noted between the results generated by the bDNA-2.0 and bDNA-3.0 assays, a bias toward higher viral titer by the bDNA-2.0 assay was noted (P = 0.001). Likewise, although substantial agreement was noted between the results generated by the HCM-2.0 and bDNA-3.0 assays, a bias toward higher viral titer by the bDNA-3.0 assay was noted (P ≤ 0.001). The discrepancy between the HCM-2.0 and bDNA-3.0 results was more pronounced when viral loads were >500,000 IU/ml and resulted in statistically significant differences (P ≤ 0.001) in determining whether viral loads were above or below 800,000 IU/ml of HCV RNA, the proposed threshold value for tailoring the duration of combination therapy. The expression of quantitative values in HCV international units per milliliter was a strength of both the bDNA-3.0 and HCM-2.0 assays. PMID:11825962

Challenges to a molecular approach to prey identification in the Burmese python, Python molurus bivittatus

USGS Publications Warehouse

Falk, Bryan; Reed, Robert N.

2015-01-01

Molecular approaches to prey identification are increasingly useful in elucidating predator–prey relationships, and we aimed to investigate the feasibility of these methods to document the species identities of prey consumed by invasive Burmese pythons in Florida. We were particularly interested in the diet of young snakes, because visual identification of prey from this size class has proven difficult. We successfully extracted DNA from the gastrointestinal contents of 43 young pythons, as well as from several control samples, and attempted amplification of DNA mini-barcodes, a 130-bp region of COX1. Using a PNA clamp to exclude python DNA, we found that prey DNA was not present in sufficient quality for amplification of this locus in 86% of our samples. All samples from the GI tracts of young pythons contained only hair, and the six samples we were able to identify to species were hispid cotton rats. This suggests that young Burmese pythons prey predominantly on small mammals and that prey diversity among snakes of this size class is low. We discuss prolonged gastrointestinal transit times and extreme gastric breakdown as possible causes of DNA degradation that limit the success of a molecular approach to prey identification in Burmese pythons

Lifting clamp positively grips structural shapes

NASA Technical Reports Server (NTRS)

Reinhardt, E. C.

1966-01-01

Welded steel clamps securely grip structural shapes of various sizes for crane operations. The clamp has adjustable clamping jaws and screw-operated internal v-jaws and provides greater safety than hoisting slings presently used. The structural member can be rotated in any manner, angle, or direction without being released by the clamp.

Protection of Arabidopsis Blunt-Ended Telomeres Is Mediated by a Physical Association with the Ku Heterodimer[OPEN

PubMed Central

Valuchova, Sona; Prokop, Zbynek; Hofr, Ctirad

2017-01-01

Telomeres form specialized chromatin that protects natural chromosome termini from being recognized as DNA double-strand breaks. Plants possess unusual blunt-ended telomeres that are unable to form t-loops or complex with single-strand DNA binding proteins, raising the question of the mechanism behind their protection. We have previously suggested that blunt-ended telomeres in Arabidopsis thaliana are protected by Ku, a DNA repair factor with a high affinity for DNA ends. In nonhomologous end joining, Ku loads onto broken DNA via a channel consisting of positively charged amino acids. Here, we demonstrate that while association of Ku with plant telomeres also depends on this channel, Ku’s requirements for DNA binding differ between DNA repair and telomere protection. We show that a Ku complex proficient in DNA loading but impaired in translocation along DNA is able to protect blunt-ended telomeres but is deficient in DNA repair. This suggests that Ku physically sequesters blunt-ended telomeres within its DNA binding channel, shielding them from other DNA repair machineries. PMID:28584163

Conformational control and DNA-binding mechanism of the metazoan origin recognition complex.

PubMed

Bleichert, Franziska; Leitner, Alexander; Aebersold, Ruedi; Botchan, Michael R; Berger, James M

2018-06-26

In eukaryotes, the heterohexameric origin recognition complex (ORC) coordinates replication onset by facilitating the recruitment and loading of the minichromosome maintenance 2-7 (Mcm2-7) replicative helicase onto DNA to license origins. Drosophila ORC can adopt an autoinhibited configuration that is predicted to prevent Mcm2-7 loading; how the complex is activated and whether other ORC homologs can assume this state are not known. Using chemical cross-linking and mass spectrometry, biochemical assays, and electron microscopy (EM), we show that the autoinhibited state of Drosophila ORC is populated in solution, and that human ORC can also adopt this form. ATP binding to ORC supports a transition from the autoinhibited state to an active configuration, enabling the nucleotide-dependent association of ORC with both DNA and Cdc6. An unstructured N-terminal region adjacent to the conserved ATPase domain of Orc1 is shown to be required for high-affinity ORC-DNA interactions, but not for activation. ORC optimally binds DNA duplexes longer than the predicted footprint of the ORC ATPases associated with a variety of cellular activities (AAA + ) and winged-helix (WH) folds; cryo-EM analysis of Drosophila ORC bound to DNA and Cdc6 indicates that ORC contacts DNA outside of its central core region, bending the DNA away from its central DNA-binding channel. Our findings indicate that ORC autoinhibition may be common to metazoans and that ORC-Cdc6 remodels origin DNA before Mcm2-7 recruitment and loading.

Mechanical and thermal buckling analysis of sandwich panels under different edge conditions

NASA Technical Reports Server (NTRS)

Ko, William L.

1993-01-01

By using the Rayleigh-Ritz method of minimizing the total potential energy of a structural system, combined load (mechanical or thermal load) buckling equations are established for orthotropic rectangular sandwich panels supported under four different edge conditions. Two-dimensional buckling interaction curves and three dimensional buckling interaction surfaces are constructed for high-temperature honeycomb-core sandwich panels supported under four different edge conditions. The interaction surfaces provide easy comparison of the panel buckling strengths and the domains of symmetrical and antisymmetrical buckling associated with the different edge conditions. Thermal buckling curves of the sandwich panels also are presented. The thermal buckling conditions for the cases with and without thermal moments were found to be identical for the small deformation theory. In sandwich panels, the effect of transverse shear is quite large, and by neglecting the transverse shear effect, the buckling loads could be overpredicted considerably. Clamping of the edges could greatly increase buckling strength more in compression than in shear.

Analysis of progressive damage in thin circular laminates due to static-equivalent impact loads

NASA Technical Reports Server (NTRS)

Shivakumar, K. N.; Elber, W.; Illg, W.

1983-01-01

Clamped circular graphite/epoxy plates (25.4, 38.1, and 50.8 mm radii) with an 8-ply quasi-isotropic layup were analyzed for static-equivalent impact loads using the minimum-total-potential-energy method and the von Karman strain-displacement equations. A step-by-step incremental transverse displacement procedure was used to calculate plate load and ply stresses. The ply failure region was calculated using the Tsai-Wu criterion. The corresponding failure modes (splitting and fiber failure) were determined using the maximum stress criteria. The first-failure mode was splitting and initiated first in the bottom ply. The splitting-failure thresholds were relatively low and tended to be lower for larger plates than for small plates. The splitting-damage region in each ply was elongated in its fiber direction; the bottom ply had the largest damage region. The calculated damage region for the 25.4-mm-radius plate agreed with limited static test results from the literature.

Comparison between three quantitative assays in patients with chronic hepatitis C and their relevance in the prediction of response to therapy.

PubMed

Pradat, P; Chossegros, P; Bailly, F; Pontisso, P; Saracco, G; Sauleda, S; Thursz, M; Tillmann, H; Vlassopoulou, H; Alberti, A; Braconier, J H; Esteban, J I; Hadziyannis, S; Manns, M; Rizzetto, M; Thomas, H C; Trépo, C

2000-05-01

To compare three quantitative assays measuring viral load in patients with chronic hepatitis C and to determine their value in predicting response to interferon (IFN) therapy, we analysed serum from 896 patients from eight European Centres using QUANTIPLEXtrade mark bDNA, MONITOR AMPLICORtrade mark and SUPERQUANTtrade mark assays. Analyses were performed on the same sample. Viral genotype was assessed using INNO-LiPA HCV II kits. Intercentre variations were observed that were related to the handling of specimens not processed and stored within 6 h of blood sampling. Among sera with optimal handling, a stronger correlation was observed between bDNA and SUPERQUANT (0.806) than between bDNA and MONITOR (0.677) and between MONITOR and SUPERQUANT (0.632). These discrepancies were greatest with genotype 2 (bDNA/SUPERQUANT= 0.772; bDNA/MONITOR=0. 456; SUPERQUANT/MONITOR= 0.299). This correlation was influenced by viraemia level and was better at lower viral loads. The proportion of sera with undetectable viral load was 15% with bDNA, 9.7% with MONITOR and 7.7% with SUPERQUANT. For the three measurements, the best cut-offs of sustained response to IFN treatment were located at their detection threshold. Among patients with viral load below the detection level, a sustained response was observed in 35% tested with bDNA, 38% with MONITOR and 80% with SUPERQUANT. Hence a stronger correlation was observed between bDNA and SUPERQUANT than between either of these assays and MONITOR. SUPERQUANT was the most sensitive assay and this greater sensitivity was associated with a better predictive value of treatment response.

The Lagrangian Multiplier Method of Finding Upper and Lower Limits to Critical Stresses of Clamped Plates

DTIC Science & Technology

1946-01-01

geometrica ~ boundary condi- tions of the problem. (2) The energy of the load-plate system is computed for this deflection surface and is then minimized...and interpolating to find the k that makes the seriw vanish. The correct value of m is that which gives the lowest value of k. For two half waves (m=2...the square plate, the present rekdively simple upper- and lower-limit calcula- tions show that his est,imatd limit of error is correct for this case

IEEE Conference Record of 1973 Eleventh Modulator Symposium, New York City, 18-19 September 1973.

DTIC Science & Technology

1973-01-01

characteristics of High-Voltage, observed on am NPNP structure of 550 uN base thickness High- Power , Fast-Switching, Reverse- operating at 1.3 Kv I IA I KA/ us 30...of this which supplies four CFA’s. The odd-numered compact modulator are a shunt clamp regulator power supplies have an additional output going to a...three driver of HVPS filter banks. cabinets. Thus four of the power supplies have a 50% greater load than the other four. However, in AEGIS SPY-1

Destabilization of the Mg-H system through elastic constraints.

PubMed

Baldi, A; Gonzalez-Silveira, M; Palmisano, V; Dam, B; Griessen, R

2009-06-05

We tune the thermodynamics of hydrogen absorption in Mg by means of elastic clamping. The loading isotherms measured by hydrogenography show that Mg films covered with Mg-alloy-forming elements, such as Pd and Ni, have hydrogen plateau pressures more than 2 orders of magnitude higher than bulk Mg at the same temperature. An elastic model allows us to interpret the Mg thickness dependence of the hydrogen plateau pressure. Our results suggest an alternative route for the development of new hydrogen storage materials with optimized thermodynamic properties.

Destabilization of the Mg-H System through Elastic Constraints

NASA Astrophysics Data System (ADS)

Baldi, A.; Gonzalez-Silveira, M.; Palmisano, V.; Dam, B.; Griessen, R.

2009-06-01

We tune the thermodynamics of hydrogen absorption in Mg by means of elastic clamping. The loading isotherms measured by hydrogenography show that Mg films covered with Mg-alloy-forming elements, such as Pd and Ni, have hydrogen plateau pressures more than 2 orders of magnitude higher than bulk Mg at the same temperature. An elastic model allows us to interpret the Mg thickness dependence of the hydrogen plateau pressure. Our results suggest an alternative route for the development of new hydrogen storage materials with optimized thermodynamic properties.

Microbial load of umbilical cord blood Ureaplasma species and Mycoplasma hominis in preterm prelabor rupture of membranes.

PubMed

Kacerovsky, Marian; Pliskova, Lenka; Menon, Ramkumar; Kutova, Radka; Musilova, Ivana; Maly, Jan; Andrys, Ctirad

2014-11-01

To evaluate Ureaplasma species and M. hominis DNA in the umbilical cord blood and its correlation with its microbial load in the amniotic fluid, as a measure of microbial burden in fetal inflammatory response and neonatal outcome in pregnancies complicated by preterm prelabor rupture of membranes (pPROM). A retrospective study of 158 women with singleton pregnancies complicated by pPROM between 24(0/7) and 36(6/7) weeks was conducted. Amniotic fluid was obtained from all women by transabdominal amniocentesis, and umbilical cord blood was obtained by venipuncture from umbilical cords immediately after the delivery of the neonates. The Ureaplasma species and M. hominis DNA was quantitated using absolute quantification techniques. Ureaplasma species and M. hominis DNA was identified in 9% of the umbilical cord blood samples. No correlation between the amniotic fluid and umbilical cord blood microbial load was observed. The presence of Ureaplasma species and M. hominis DNA in the umbilical cord blood had no impact on short-term neonatal morbidity. A high microbial load of genital mycoplasma Ureaplasma species DNA in the umbilical cord in pregnancies complicated by pPROM is not associated with a high fetal inflammatory response and is therefore not associated with serious neonatal morbidity.

Selective Arterial Clamping Versus Hilar Clamping for Minimally Invasive Partial Nephrectomy.

PubMed

Yezdani, Mona; Yu, Sue-Jean; Lee, David I

2016-05-01

Partial nephrectomy has become an accepted treatment of cT1 renal masses as it provides improved long-term renal function compared to radical nephrectomy (Campbell et al. J Urol. 182:1271-9, 2009). Hilar clamping is utilized to help reduce bleeding and improve visibility during tumor resection. However, concern over risk of kidney injury with hilar clamping has led to new techniques to reduce length of warm ischemia time (WIT) during partial nephrectomy. These techniques have progressed over the years starting with early hilar unclamping, controlled hypotension during tumor resection, selective arterial clamping, minimal margin techniques, and off-clamp procedures. Selective arterial clamping has progressed significantly over the years. The main question is what are the exact short- and long-term renal effects from increasing clamp time. Moreover, does it make sense to perform these more time-consuming or more complex procedures if there is no long-term preservation of kidney function? More recent studies have shown no difference in renal function 6 months from surgery when selective arterial clamping or even hilar clamping is employed, although there is short-term improved decline in estimated glomerular filtration rate (eGFR) with selective clamping and off-clamp techniques (Komninos et al. BJU Int. 115:921-8, 2015; Shah et al. 117:293-9, 2015; Kallingal et al. BJU Int. doi: 10.1111/bju.13192, 2015). This paper reviews the progression of total hilar clamping to selective arterial clamping (SAC) and the possible difference its use makes on long-term renal function. SAC may be attempted based on surgeon's decision-making, but may be best used for more complex, larger, more central or hilar tumors and in patients who have renal insufficiency at baseline or a solitary kidney.

Whole-Cell Electrical Activity Under Direct Mechanical Stimulus by AFM Cantilever Using Planar Patch Clamp Chip Approach

PubMed Central

Upadhye, Kalpesh V.; Candiello, Joseph E.; Davidson, Lance A.; Lin, Hai

2011-01-01

Patch clamp is a powerful tool for studying the properties of ion-channels and cellular membrane. In recent years, planar patch clamp chips have been fabricated from various materials including glass, quartz, silicon, silicon nitride, polydimethyl-siloxane (PDMS), and silicon dioxide. Planar patch clamps have made automation of patch clamp recordings possible. However, most planar patch clamp chips have limitations when used in combination with other techniques. Furthermore, the fabrication methods used are often expensive and require specialized equipments. An improved design as well as fabrication and characterization of a silicon-based planar patch clamp chip are described in this report. Fabrication involves true batch fabrication processes that can be performed in most common microfabrication facilities using well established MEMS techniques. Our planar patch clamp chips can form giga-ohm seals with the cell plasma membrane with success rate comparable to existing patch clamp techniques. The chip permits whole-cell voltage clamp recordings on variety of cell types including Chinese Hamster Ovary (CHO) cells and pheochromocytoma (PC12) cells, for times longer than most available patch clamp chips. When combined with a custom microfluidics chamber, we demonstrate that it is possible to perfuse the extra-cellular as well as intra-cellular buffers. The chamber design allows integration of planar patch clamp with atomic force microscope (AFM). Using our planar patch clamp chip and microfluidics chamber, we have recorded whole-cell mechanosensitive (MS) currents produced by directly stimulating human keratinocyte (HaCaT) cells using an AFM cantilever. Our results reveal the spatial distribution of MS ion channels and temporal details of the responses from MS channels. The results show that planar patch clamp chips have great potential for multi-parametric high throughput studies of ion channel proteins. PMID:22174731

Design and testing of a novel piezoelectric micro-motor actuated by asymmetrical inertial impact driving principle.

PubMed

Zeng, Ping; Sun, Shujie; Li, Li'an; Xu, Feng; Cheng, Guangming

2014-03-01

In this paper, an asymmetrical inertial impact driving principle is first proposed, and accordingly a novel piezoelectrically actuated linear micro-motor is developed. It is driven by the inertial impact force generated by piezoelectric smart cantilever (PSC) with asymmetrical clamping locations during a driving cycle. When the PSC is excited by typical harmonic voltage signals, different equivalent stiffness will be induced due to its asymmetrical clamping locations when it is vibrating back and forth, leading to a tiny displacement difference on the two opposite directions in a cycle, and then the accumulation of tiny displacement difference will allow directional movements. A prototype of the proposed motor has been developed and investigated by means of experimental tests. The motion and dynamics characteristics of the prototype are well studied. The experimental results demonstrate that the resolution of the micro-motor is 0.02 μm, the maximum velocity is 16.87 mm/s, and the maximum loading capacity can reach up to 1 kg with a voltage of 100 V and 35 Hz.

Vibration isolation using extreme geometric nonlinearity

NASA Astrophysics Data System (ADS)

Virgin, L. N.; Santillan, S. T.; Plaut, R. H.

2008-08-01

A highly deformed, slender beam (or strip), attached to a vertically oscillating base, is used in a vibration isolation application to reduce the motion of a supported mass. The isolator is a thin strip that is bent so that the two ends are clamped together, forming a loop. The clamped ends are attached to an excitation source and the supported system is attached at the loop midpoint directly above the base. The strip is modeled as an elastica, and the resulting nonlinear boundary value problem is solved numerically using a shooting method. First the equilibrium shapes of the loop with varying static loads and lengths are studied. The analysis reveals a large degree of stiffness tunability; the stiffness is dependent on the geometric configuration, which itself is determined by the supported mass, loop length, and loop self-weight. Free vibration frequencies and mode shapes are also found. Finally, the case of forced vibration is studied, and the displacement transmissibility over a large range of forcing frequencies is determined for varying parameter values. Experiments using polycarbonate strips are conducted to verify equilibrium and dynamic behavior.

Pipe support for use in a nuclear system

DOEpatents

Pollono, Louis P.; Mello, Raymond M.

1977-01-01

A pipe support for high temperature, thin-walled vertical piping runs used in a nuclear system. A cylindrical pipe transition member, having the same inside diameter as the thin-walled piping, replaces a portion of the piping where support is desired. The outside diameter of the pipe transition member varies axially along its vertical dimension. For a section of the axial length adjacent the upper and lower terminations of the pipe transition member, the outside diameter is the same as the outside diameter of the thin-walled piping to which it is affixed. Intermediate of the termination sections, the outside diameter increases from the top of the member to the bottom. Adjacent the lower termination section, the diameter abruptly becomes the same as the piping. Thus, the cylindrical transition member is formed to have a generally triangular shaped cross-section along the axial dimension. Load-bearing insulation is installed next to the periphery of the member and is kept in place by an outer ring clamp. The outer ring clamp is connected to pipe hangers, which provide the desired support for the vertical thin-walled piping runs.

Effects of variables upon pyrotechnically induced shock response spectra, part 2

NASA Technical Reports Server (NTRS)

Smith, James Lee

1988-01-01

Throughout the aerospace industry, large variations of 50 percent (6 dB) or more in shock response spectra (SRS) derived from pyrotechnic separation events continue to be reported from actual spaceflight data and from laboratory tests. As a result of these variations, NASA funded a research program for 1984 through 1986. The purpose of the 1984 through 1986 project was to analyze variations in pyrotechnically induced SRS and to determine if and to what degree manufacturing and assembly variables and tolerances, distance from the shock source, data acquisition instrumentation, and shock energy propagation affect the SRS. Sixty-four free-free boundary plate tests were performed. NASA funded an additional study for 1987 through 1988. This paper is a summary of the additional study. The purpose was to evaluate shock dissipation through various spacecraft structural joint types, to evaluate shock variation for various manufacturing and assembly variables on clamped boundary test plates, and to verify data correction techniques. Five clamped boundary plate tests investigated manufacturing and assembly variables and mass loading effects. Six free-free boundary plate tests investigated shock dissipation across spacecraft joint structures.

The mechanism of the emergence of distinct overstretched DNA states

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, You-Liang; Sun, Zhao-Yan, E-mail: zysun@ciac.ac.cn; Lu, Zhong-Yuan

Although multiple overstretched DNA states were identified in experiments, the mechanism of the emergence of distinct states is still unclear. Molecular dynamics simulation is an ideal tool to clarify the mechanism, but the force loading rates in stretching achieved by conventional all-atom DNA models are much faster, which essentially affect overstretching states. We employed a modified coarse-grained DNA model with an unprecedented low loading rate in simulations to study the overstretching transitions of end-opened double-stranded DNA. We observed two-strand peeling off for DNA with low stability and the S-DNA with high stability under tension. By introducing a melting-forbidden model whichmore » prevents base-pair breaking, we still observed the overstretching transition induced by the formation of S-DNA due to the change of dihedral angle. Hence, we confirmed that the competition between the two strain-softening manners, i.e., base-pair breaking and dihedral angle variation, results in the emergence of distinct overstretched DNA states.« less

Quantification of Epstein-Barr virus DNA load, interleukin-6, interleukin-10, transforming growth factor-beta1 and stem cell factor in plasma of patients with nasopharyngeal carcinoma.

PubMed

Tan, Eng-lai; Selvaratnam, G; Kananathan, R; Sam, Choon-kook

2006-09-24

Nasopharyngeal carcinoma (NPC) is a common epithelial neoplasm among the Chinese populations in Southern China and South East Asia. Epstein-Barr virus (EBV) is known to be an important etiologic agent of NPC and the viral gene products are frequently detected in NPC tissues along with elevated antibody titres to the viral proteins (VCA and EA) in a majority of patients. Elevated plasma EBV DNA load is regarded as an important marker for the presence of the disease and for the monitoring of disease progression. However, other serum/plasma parameters such as the levels of certain interleukins and growth factors have also been implicated in NPC. The objectives of the present study are, 1) to investigate the correlations between plasma EBV DNA load and the levels of interleukin (IL)-6, IL-10, TGF-beta1 and SCF (steel factor) and 2) to relate these parameters to the stages of NPC and the effect of treatment. A total of 78 untreated NPC patients were enrolled in this study. Of these, 51 were followed-up after treatment. The remaining patients had irregular or were lost to follow-up. Plasma EBV DNA was quantified using real-time quantitative PCR. The levels of plasma interleukins and growth factors were quantified using ELISA. A significant decrease in EBV DNA load was detected in plasma of untreated NPC patients (1669 +/- 637 copies/mL; n = 51) following treatment (57 +/- 37 copies/mL, p < 0.05); n = 51). Plasma EBV DNA load was shown to be a good prognosticator for disease progression and clinical outcome in five of the follow-up patients. A significant difference in IL-6 levels was noted between the untreated patients (164 +/- 37 pg/mL; n = 51) and following treatment (58 +/- 16 pg/mL, p < 0.05; n = 51). Positive correlations between EBV DNA load and IL-10 (r(49) = 0.535, p < 0.01), between IL6 and IL-10 (r(49) = 0.474, p < 0.01) and between TGF and SCF (r(49) = 0.464, p < 0.01) were observed in patients following treatment. None of the parameters tested including IgA-VCA were associated with tumour stages. We conclude that among the parameters investigated, EBV DNA load and IL-6 levels were promising markers for the presence of NPC and for the assessment of treatment outcome.

Multilaboratory comparison of hepatitis C virus viral load assays.

PubMed

Caliendo, A M; Valsamakis, A; Zhou, Y; Yen-Lieberman, B; Andersen, J; Young, S; Ferreira-Gonzalez, A; Tsongalis, G J; Pyles, R; Bremer, J W; Lurain, N S

2006-05-01

We report a multilaboratory evaluation of hepatitis C virus (HCV) viral load assays to determine their linear range, reproducibility, subtype detection, and agreement. A panel of HCV RNA samples ranging in nominal concentration from 1.0 to 7.0 log10 IU/ml was constructed by diluting a clinical specimen (genotype 1b). Replicates of the panel were tested in multiple laboratories using the Abbott TaqMan analyte-specific reagent (Abbott reverse transcription-PCR [RT-PCR]), Roche TaqMan RUO (Roche RT-PCR), Roche Amplicor Monitor HCV 2.0 (Roche Monitor), and Bayer VERSANT HCV RNA 3.0 (Bayer bDNA) assays. Bayer bDNA-negative specimens were tested reflexively using the Bayer VERSANT HCV RNA qualitative assay (Bayer TMA). Abbott RT-PCR and Roche RT-PCR detected all 28 replicates with a concentration of 1.0 log10 IU/ml and were linear to 7.0 log10 IU/ml. Roche Monitor and Bayer bDNA detected 27 out of 28 and 13 out of 28 replicates, respectively, of 3.0 log10 IU/ml. Bayer TMA detected all seven replicates with 1.0 log10 IU/ml. Bayer bDNA was the most reproducible of the four assays. The mean viral load values for panel members in the linear ranges of the assays were within 0.5 log10 for the different tests. Eighty-nine clinical specimens of various genotypes (1 through 4) were tested in the Bayer bDNA, Abbott RT-PCR, and Roche RT-PCR assays. For Abbott RT-PCR, mean viral load values were 0.61 to 0.96 log10 greater than the values for Bayer bDNA assay for samples with genotype 1, 2, or 3 samples and 0.08 log10 greater for genotype 4 specimens. The Roche RT-PCR assay gave mean viral load values that were 0.28 to 0.82 log10 greater than those obtained with the Bayer bDNA assay for genotype 1, 2, and 3 samples. However, for genotype 4 samples the mean viral load value obtained with the Roche RT-PCR assay was, on average, 0.15 log10 lower than that of the Bayer bDNA. Based on these data, we conclude that the sensitivity and linear range of the Abbott and Roche RT-PCR assays enable them to be used for HCV diagnostics and therapeutic monitoring. However, the differences in the viral load values obtained with the different assays underscore the importance of using one assay when monitoring response to therapy.

Measuring beta-cell function relative to insulin sensitivity in youth: Does the hyperglycemic clamp suffice?

USDA-ARS?s Scientific Manuscript database

To compare beta-cell function relative to insulin sensitivity, disposition index (DI), calculated from two clamps (2cDI, insulin sensitivity from the hyperinsulinemic-euglycemic clamp and first-phase insulin from the hyperglycemic clamp) with the DI calculated from the hyperglycemic clamp alone (hcD...

21 CFR 882.4460 - Neurosurgical head holder (skull clamp).

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Neurosurgical head holder (skull clamp). 882.4460... holder (skull clamp). (a) Identification. A neurosurgical head holder (skull clamp) is a device used to clamp the patient's skull to hold head and neck in a particular position during surgical procedures. (b...

Microchip amplifier for in vitro, in vivo, and automated whole cell patch-clamp recording

PubMed Central

Kolb, Ilya; Kodandaramaiah, Suhasa B.; Chubykin, Alexander A.; Yang, Aimei; Bear, Mark F.; Boyden, Edward S.; Forest, Craig R.

2014-01-01

Patch clamping is a gold-standard electrophysiology technique that has the temporal resolution and signal-to-noise ratio capable of reporting single ion channel currents, as well as electrical activity of excitable single cells. Despite its usefulness and decades of development, the amplifiers required for patch clamping are expensive and bulky. This has limited the scalability and throughput of patch clamping for single-ion channel and single-cell analyses. In this work, we have developed a custom patch-clamp amplifier microchip that can be fabricated using standard commercial silicon processes capable of performing both voltage- and current-clamp measurements. A key innovation is the use of nonlinear feedback elements in the voltage-clamp amplifier circuit to convert measured currents into logarithmically encoded voltages, thereby eliminating the need for large high-valued resistors, a factor that has limited previous attempts at integration. Benchtop characterization of the chip shows low levels of current noise [1.1 pA root mean square (rms) over 5 kHz] during voltage-clamp measurements and low levels of voltage noise (8.2 μV rms over 10 kHz) during current-clamp measurements. We demonstrate the ability of the chip to perform both current- and voltage-clamp measurement in vitro in HEK293FT cells and cultured neurons. We also demonstrate its ability to perform in vivo recordings as part of a robotic patch-clamping system. The performance of the patch-clamp amplifier microchip compares favorably with much larger commercial instrumentation, enabling benchtop commoditization, miniaturization, and scalable patch-clamp instrumentation. PMID:25429119

Irradiation of DNA loaded with platinum containing molecules by fast atomic ions C(6+) and Fe(26+).

PubMed

Usami, N; Kobayashi, K; Furusawa, Y; Frohlich, H; Lacombe, S; Sech, C Le

2007-09-01

In order to study the role of the Linear Energy Transfer (LET) of fast atomic ions in platinum-DNA complexes inducing breaks, DNA Plasmids were irradiated by C(6+) and Fe(26+) ions. DNA Plasmids (pBR322) loaded with different amounts of platinum contained in a terpyridine-platinum molecule (PtTC) were irradiated by C(6+) ions and Fe(26+) ions. The LET values ranged between 13.4 keV/microm and 550 keV/microm. In some experiments, dimethyl sulfoxide (DMSO) was added. In all experiments, a significant increase in DNA strand breaks was observed when platinum was present. The yield of breaks induced per Gray decreased when the LET increased. The yield of single and double strand breaks per plasmid per track increased with the LET, indicating that the number of DNA breaks per Gray was related to the number of tracks through the medium. These findings show that more DNA breaks are induced by atomic ions when platinum is present. This effect increases for low LET heavy atoms. As DSB induction may induce cell death, these results could open new perspectives with the association of hadrontherapy and chemotherapy. Thus the therapeutic index might be improved by loading the tumour with platinum salts.

Photovoltaic panel clamp

DOEpatents

Mittan, Margaret Birmingham [Oakland, CA; Miros, Robert H. J. [Fairfax, CA; Brown, Malcolm P [San Francisco, CA; Stancel, Robert [Loss Altos Hills, CA

2012-06-05

A photovoltaic panel clamp includes an upper and lower section. The interface between the assembled clamp halves and the module edge is filled by a flexible gasket material, such as EPDM rubber. The gasket preferably has small, finger like protrusions that allow for easy insertion onto the module edge while being reversed makes it more difficult to remove them from the module once installed. The clamp includes mounting posts or an integral axle to engage a bracket. The clamp also may include a locking tongue to secure the clamp to a bracket.

Photovoltaic panel clamp

DOEpatents

Brown, Malcolm P.; Mittan, Margaret Birmingham; Miros, Robert H. J.; Stancel, Robert

2013-03-19

A photovoltaic panel clamp includes an upper and lower section. The interface between the assembled clamp halves and the module edge is filled by a flexible gasket material, such as EPDM rubber. The gasket preferably has small, finger like protrusions that allow for easy insertion onto the module edge while being reversed makes it more difficult to remove them from the module once installed. The clamp includes mounting posts or an integral axle to engage a bracket. The clamp also may include a locking tongue to secure the clamp to a bracket.

Real-time polymerase chain reaction detection of parvovirus B19 DNA in blood donations using a commercial and an in-house assay.

PubMed

Koppelman, M H G M; van Swieten, P; Cuijpers, H T M

2011-06-01

European regulations require testing of manufacturing plasma for parvovirus B19 (B19) DNA to limit the load of this virus to a maximum acceptable level of 10 IU/µL. To meet this requirement, most manufacturers introduced a test algorithm to identify and eliminate high-load donations before making large manufacturing pools of plasma units. Sanquin screens all donations using a commercial assay from Roche and an in-house assay. Between 2006 and 2009, 6.2 million donations were screened using two different polymerase chain reaction (PCR) assays targeting B19 DNA. Donations with B19 DNA loads of greater than 1 × 10(6) IU/mL showing significant differences in viral load between the two assays were further analyzed by sequencing analysis. A total of 396 donations with B19 DNA loads of greater than 1 × 10(6) IU/mL were identified. Fifteen samples (3.8%) had discordant test results; 10 samples (2.5%) were underquantified by the Roche assay, two samples (0.5%) were underquantified by the in-house assay, and three samples (0.8%) were not detected by the Roche assay. Sequencing analysis revealed mismatches in primer and probe-binding regions. Phylogenetic analysis showed that 12 samples were B19 Genotype 1. The three samples not detected by the Roche assay were B19 Genotype 2. This study shows that 3.8% of the viremic B19 DNA-positive donations are not quantified correctly by the Roche or in-house B19 DNA assays. B19 Genotype 1 isolates showing incorrect test results are more common than B19 Genotype 2 or 3 isolates. Newly designed B19 PCR assays for blood screening should preferably have multiplexed formats targeting multiple regions of the B19 genome. © 2010 American Association of Blood Banks.

DNA vaccination for cervical cancer: Strategic optimisation of RALA mediated gene delivery from a biodegradable microneedle system.

PubMed

Cole, Grace; Ali, Ahlam A; McCrudden, Cian M; McBride, John W; McCaffrey, Joanne; Robson, Tracy; Kett, Vicky L; Dunne, Nicholas J; Donnelly, Ryan F; McCarthy, Helen O

2018-06-01

Dissolvable microneedles can be employed to deliver DNA to antigen presenting cells within the skin. However, this technology faces two main challenges: the poor transfection efficacy of pDNA following release from the microneedle matrix, and the limited loading capacity of the micron-scale devices. Two-tier delivery systems combining microneedle platforms and DNA delivery vectors have increased efficacy but the challenge of increasing the loading capacity remains. This study utilised lyophilisation to increase the loading of RALA/pDNA nanoparticles within dissolvable PVA microneedles. As a result, delivery was significantly enhanced in vivo into an appropriate range for DNA vaccination (∼50 μg per array). Furthermore, modifying the manufacturing process was not detrimental to the microneedle mechanical properties or cargo functionality. It was demonstrated that arrays retained mechanical and functional stability over short term storage, and were able to elicit gene expression in vitro and in vivo. Finally, treatment with this novel formulation significantly retarded the growth of established tumours, and proved superior to standard intramuscular injection in a preclinical model of cervical cancer. Copyright © 2018 Elsevier B.V. All rights reserved.

MATLAB-based automated patch-clamp system for awake behaving mice

PubMed Central

Siegel, Jennifer J.; Taylor, William; Chitwood, Raymond A.; Johnston, Daniel

2015-01-01

Automation has been an important part of biomedical research for decades, and the use of automated and robotic systems is now standard for such tasks as DNA sequencing, microfluidics, and high-throughput screening. Recently, Kodandaramaiah and colleagues (Nat Methods 9: 585–587, 2012) demonstrated, using anesthetized animals, the feasibility of automating blind patch-clamp recordings in vivo. Blind patch is a good target for automation because it is a complex yet highly stereotyped process that revolves around analysis of a single signal (electrode impedance) and movement along a single axis. Here, we introduce an automated system for blind patch-clamp recordings from awake, head-fixed mice running on a wheel. In its design, we were guided by 3 requirements: easy-to-use and easy-to-modify software; seamless integration of behavioral equipment; and efficient use of time. The resulting system employs equipment that is standard for patch recording rigs, moderately priced, or simple to make. It is written entirely in MATLAB, a programming environment that has an enormous user base in the neuroscience community and many available resources for analysis and instrument control. Using this system, we obtained 19 whole cell patch recordings from neurons in the prefrontal cortex of awake mice, aged 8–9 wk. Successful recordings had series resistances that averaged 52 ± 4 MΩ and required 5.7 ± 0.6 attempts to obtain. These numbers are comparable with those of experienced electrophysiologists working manually, and this system, written in a simple and familiar language, will be useful to many cellular electrophysiologists who wish to study awake behaving mice. PMID:26084901

Synergetic approach for simple and rapid conjugation of gold nanoparticles with oligonucleotides.

PubMed

Li, Jiuxing; Zhu, Binqing; Yao, Xiujie; Zhang, Yicong; Zhu, Zhi; Tu, Song; Jia, Shasha; Liu, Rudi; Kang, Huaizhi; Yang, Chaoyong James

2014-10-08

Attaching thiolated DNA on gold nanoparticles (AuNPs) has been extremely important in nanobiotechnology because DNA-AuNPs combine the programmability and molecular recognition properties of the biopolymers with the optical, thermal, and catalytic properties of the inorganic nanomaterials. However, current standard protocols to attach thiolated DNA on AuNPs involve time-consuming, tedious steps and do not perform well for large AuNPs, thereby greatly restricting applications of DNA-AuNPs. Here we demonstrate a rapid and facile strategy to attach thiolated DNA on AuNPs based on the excellent stabilization effect of mPEG-SH on AuNPs. AuNPs are first protected by mPEG-SH in the presence of Tween 20, which results in excellent stability of AuNPs in high ionic strength environments and extreme pHs. A high concentration of NaCl can be applied to the mixture of DNA and AuNP directly, allowing highly efficient DNA attachment to the AuNP surface by minimizing electrostatic repulsion. The entire DNA loading process can be completed in 1.5 h with only a few simple steps. DNA-loaded AuNPs are stable for more than 2 weeks at room temperature, and they can precisely hybridize with the complementary sequence, which was applied to prepare core-satellite nanostructures. Moreover, cytotoxicity assay confirmed that the DNA-AuNPs synthesized by this method exhibit lower cytotoxicity than those prepared by current standard methods. The proposed method provides a new way to stabilize AuNPs for rapid and facile loading thiolated DNA on AuNPs and will find wide applications in many areas requiring DNA-AuNPs, including diagnosis, therapy, and imaging.

Flexible DNA Path in the MCM Double Hexamer Loaded on DNA.

PubMed

Hizume, Kohji; Kominami, Hiroaki; Kobayashi, Kei; Yamada, Hirofumi; Araki, Hiroyuki

2017-05-16

The formation of the pre-replicative complex (pre-RC) during the G1 phase, which is also called the licensing of DNA replication, is the initial and essential step of faithful DNA replication during the subsequent S phase. It is widely accepted that in the pre-RC, double-stranded DNA passes through the holes of two ring-shaped minichromosome maintenance (MCM) 2-7 hexamers; however, the spatial organization of the DNA and proteins involved in pre-RC formation is unclear. Here we reconstituted the pre-RC from purified DNA and proteins and visualized the complex using atomic force microscopy (AFM). AFM revealed that the MCM double hexamers formed elliptical particles on DNA. Analysis of the angle of binding of DNA to the MCM double hexamer suggests that the DNA does not completely pass through both holes of the MCM hexamers, possibly because the DNA exited from the gap between Mcm2 and Mcm5. A DNA loop fastened by the MCM double hexamer was detected in pre-RC samples reconstituted from purified proteins as well as those purified from yeast cells, suggesting a higher-order architecture of the loaded MCM hexamers and DNA strands.

Epstein-Barr viral load assessment in immunocompetent patients with fulminant infectious mononucleosis.

PubMed

van Laar, Jan A M; Buysse, Corinne M P; Vossen, Ann C T M; Hjálmarsson, Björn; van Den Berg, Bart; van Lom, Kirsten; Deinum, Jaap

2002-04-08

We describe 2 immunocompetent adolescents with fulminant infectious mononucleosis and virus-associated hemophagocytosis. A new quantitative polymerase chain reaction revealed high serum Epstein-Barr virus DNA levels in these patients. One patient died with an increasing viral load not responding to corticosteroids followed by antiviral and intensified immunomodulatory treatment. The other patient received corticosteroids and acyclovir at diagnosis; her rapid recovery was heralded by a steep decline of viral load. We propose monitoring the clinical course of fulminant infectious mononucleosis in immunocompetent patients by Epstein-Barr virus DNA quantification and prompt corticosteroid and antiviral therapy when viral load is high.

Gain-scheduled {{\\mathscr{H}}}_{\\infty } buckling control of a circular beam-column subject to time-varying axial loads

NASA Astrophysics Data System (ADS)

Schaeffner, Maximilian; Platz, Roland

2018-06-01

For slender beam-columns loaded by axial compressive forces, active buckling control provides a possibility to increase the maximum bearable axial load above that of a purely passive structure. In this paper, an approach for gain-scheduled {{\\mathscr{H}}}∞ buckling control of a slender beam-column with circular cross-section subject to time-varying axial loads is investigated experimentally. Piezo-elastic supports with integrated piezoelectric stack actuators at the beam-column ends allow an active stabilization in arbitrary lateral directions. The axial loads on the beam-column influence its lateral dynamic behavior and, eventually, cause the beam-column to buckle. A reduced modal model of the beam-column subject to axial loads including the dynamics of the electrical components is set up and calibrated with experimental data. Particularly, the linear parameter-varying open-loop plant is used to design a model-based gain-scheduled {{\\mathscr{H}}}∞ buckling control that is implemented in an experimental test setup. The beam-column is loaded by ramp- and step-shaped time-varying axial compressive loads that result in a lateral deformation of the beam-column due to imperfections, such as predeformation, eccentric loading or clamping moments. The lateral deformations and the maximum bearable loads of the beam-column are analyzed and compared for the beam-column with and without gain-scheduled {{\\mathscr{H}}}∞ buckling control or, respectively, active and passive configuration. With the proposed gain-scheduled {{\\mathscr{H}}}∞ buckling control it is possible to increase the maximum bearable load of the active beam-column by 19% for ramp-shaped axial loads and to significantly reduce the beam-column deformations for step-shaped axial loads compared to the passive structure.

Spontaneous sarcoplasmic reticulum calcium release and extrusion from bovine, not porcine, coronary artery smooth muscle.

PubMed Central

Stehno-Bittel, L; Sturek, M

1992-01-01

1. We tested the hypothesis that the Ca(2+)-loaded sarcoplasmic reticulum (SR) of coronary artery smooth muscle spontaneously releases Ca2+ preferentially toward the sarcolemma to be extruded from the cell without increasing the average free myoplasmic [Ca2+] (Ca(im)) concentration. 2. The SR of bovine cells was Ca(2+)-loaded by depolarization-induced Ca2+ influx. Release (unloading) of Ca2+ from the SR during recovery from depolarization was determined by Fura-2 microfluorometry of Ca(im). The SR Ca2+ unloading was maximal following a long (14 min) recovery from depolarization, as shown by the 66% decrease in the peak caffeine-induced Ca(im) transient compared to the Ca(im) transient after a short (2 min) recovery. No increase in Ca(im) occurred during the long recovery. No unloading of the SR Ca2+ store was noted in porcine cells. 3. Approximately 80% of the outward K+ current in bovine and porcine cells was sensitive to subsarcolemmal Ca2+ (Ca(is)) concentrations. Whole-cell voltage clamp using pipette solutions with Ca2+ concentrations clamped between 0 and 1000 nM with Ca(2+)-EGTA or Ca(2+)-BAPTA buffers showed increasing K+ currents (normalized for cell membrane surface area) as a function of both membrane potential and Ca(is). Clamping of Ca(im) and Ca(is) was verified by the lack of changes in K+ current and Fura-2 ratio in response to Ca2+ influx, Ca(2+)-free external solution, or caffeine-induced Ca2+ release. At +30 to +50 mV the K+ current amplitude showed a similar sensitivity to Ca2+ as Fura-2. These data indicate that in this experimental preparation Ca(2+)-activated K+ current is a valid estimate of Ca(is). 4. Simultaneous Ca(im) and Ca(is) measurements in bovine cells which were not Ca(2+)-clamped (2 x 10(-4) M-EGTA pipette solution) showed that during the long recovery period the K+ current (reflecting Ca(is)) increased 55%, while Ca(im) did not change. 5. In quiescent bovine cells the Ca(is) was higher than Ca(im), while the higher resting Ca(is) gradient was not apparent in porcine cells. 6. The Ca(is) concentration was directly related to the amount of Ca2+ in the SR in bovine, but not porcine cells. Depletion of the SR in bovine cells by caffeine resulted in a 58% decrease in K+ current compared to the resting K+ current. 7. Caffeine-induced Ca2+ release caused an increase in Ca(is) which preceded the increase in Ca(im) by approximately 2 s.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:1403820

Torque vs. induced load of A-286, and MP35N nuts and bolts with cadmium, dry film, and cetyl alcohol lubricants

NASA Technical Reports Server (NTRS)

Crispell, C.

1978-01-01

Data for specific joint design, utilizing various combinations of bolt, nut and lubricants in typical structure of the shuttle booster rocket is obtained. Requirements of the structure performance criteria were to withstand temperatures of 260 C (500 F) and to provide a nut lubricant which would be compatible with sealants used in the joint. Cadmium plating and dry film lubricant meeting the requirements of MIL-L-8937 were the lubricants specified. In a follow up effort, cadmium plating and cetyl alcohol were further specified The materials for the bolt and nut combinations were MP35N and A-286. These materials demand a lubricant to be used to prevent galling of the thread when tightened and also to help reduce the scatter of clamping load in application.

Perlecan and vascular endothelial growth factor-encoding DNA-loaded chitosan scaffolds promote angiogenesis and wound healing.

PubMed

Lord, Megan S; Ellis, April L; Farrugia, Brooke L; Whitelock, John M; Grenett, Hernan; Li, Chuanyu; O'Grady, Robert L; DeCarlo, Arthur A

2017-03-28

The repair of dermal wounds, particularly in the diabetic population, poses a significant healthcare burden. The impaired wound healing of diabetic wounds is attributed to low levels of endogenous growth factors, including vascular endothelial growth factor (VEGF), that normally stimulate multiple phases of wound healing. In this study, chitosan scaffolds were prepared via freeze drying and loaded with plasmid DNA encoding perlecan domain I and VEGF189 and analyzed in vivo for their ability to promote dermal wound healing. The plasmid DNA encoding perlecan domain I and VEGF189 loaded scaffolds promoted dermal wound healing in normal and diabetic rats. This treatment resulted in an increase in the number of blood vessels and sub-epithelial connective tissue matrix components within the wound beds compared to wounds treated with chitosan scaffolds containing control DNA or wounded controls. These results suggest that chitosan scaffolds containing plasmid DNA encoding VEGF189 and perlecan domain I have the potential to induce angiogenesis and wound healing. Copyright © 2017 Elsevier B.V. All rights reserved.

Saddle clamp assembly

NASA Technical Reports Server (NTRS)

Belrose, Charles R. (Inventor)

1994-01-01

A saddle clamp assembly is presented. The assembly is comprised of a hollow cylindrical body centered about a longitudinal axis and being diametrically split into semicircular top and bottom sections. Each section has a pair of connection flanges, at opposite ends, that project radially outward. A pair of bolts are retained on the top section flanges and are threadable into nuts retained on the bottom section flanges. A base member is anchored to a central underside portion of the bottom clamp body section and has a pair of connection tabs positioned beneath the bottom clamp body section connection flanges on opposite sides of the clamp axis. A pair of bolts are retained on the base member connection tabs and are threadable into a pair of nuts retainable on a support structure. The connection tab and connection flanges on each side of the clamp body are axially offset in a manner permitting downward installation/removable tool access to the lower bolts past the connection flanges. An elongated retention tether is used to connect the top clamp body section to the balance of the clamp assembly. This prevents loss of the top clamp body section when it is removed from the bottom clamp body section.

Clinical application of the Quantiplex HCV RNA 2.0 and Amplicor HCV Monitor assays for quantifying serum hepatitis C virus RNA.

PubMed

Yu, M L; Chuang, W L; Chen, S C; Lin, Z Y; Hsieh, M Y; Wang, L Y; Chang, W Y

1999-11-01

To compare the performance characteristics and clinical application of two different technologies for quantifying serum hepatitis C virus (HCV) RNA levels. HCV RNA was quantified by Amplicor HCV Monitor assay (Amplicor) and Quantiplex HCV RNA 2.0 assay (bDNA-2) in 119 sera from 107 HCV infected patients. Both assays had similar sensitivity (79.4% for Amplicor; 86.0% for bDNA-2), acceptable coefficients of variation (5.3% in Amplicor; 2.6% in bDNA-2), and good linearity (r2 > or = 0.98). There was a positive correlation between quantification values of both methods (r = 0.683, p < 0.001). The Amplicor values were on an average 1.76 log lower than bDNA-2 results. Male subjects and HCV genotype 1b were significantly associated with higher viral load determined by Amplicor, but not with viral load measured by bDNA-2. In 70 chronic HCV infected patients treated with interferon alfa, mean (SD) pretreatment viral load in 27 complete responders (3.47 (0.84) logs for Amplicor, 5.63 (0.58) for bDNA-2) was significantly lower than in non-responders (4.43 (1.01) logs for Amplicor, 6.10 (0.67) logs for bDNA-2; p < 0.001). Cut off points of 3.9 logs for Amplicor and 5.8 logs for bDNA-2 were determined to be the best for predicting response to interferon alfa, giving acceptable sensitivity (70.4%, 74.1%), specificity (72.1%, 65.1%), and accuracy (71.4%, 68.6%), respectively. Both the Amplicor and bDNA-2 assays are clinically useful methods for HCV RNA quantification and are reliable for predicting the outcome of treatment, despite differences in absolute quantification values and in the correlation between HCV genotypes and viral load.

A conserved MCM single-stranded DNA binding element is essential for replication initiation.

PubMed

Froelich, Clifford A; Kang, Sukhyun; Epling, Leslie B; Bell, Stephen P; Enemark, Eric J

2014-04-01

The ring-shaped MCM helicase is essential to all phases of DNA replication. The complex loads at replication origins as an inactive double-hexamer encircling duplex DNA. Helicase activation converts this species to two active single hexamers that encircle single-stranded DNA (ssDNA). The molecular details of MCM DNA interactions during these events are unknown. We determined the crystal structure of the Pyrococcus furiosus MCM N-terminal domain hexamer bound to ssDNA and define a conserved MCM-ssDNA binding motif (MSSB). Intriguingly, ssDNA binds the MCM ring interior perpendicular to the central channel with defined polarity. In eukaryotes, the MSSB is conserved in several Mcm2-7 subunits, and MSSB mutant combinations in S. cerevisiae Mcm2-7 are not viable. Mutant Mcm2-7 complexes assemble and are recruited to replication origins, but are defective in helicase loading and activation. Our findings identify an important MCM-ssDNA interaction and suggest it functions during helicase activation to select the strand for translocation. DOI: http://dx.doi.org/10.7554/eLife.01993.001.

A conserved MCM single-stranded DNA binding element is essential for replication initiation

PubMed Central

Froelich, Clifford A; Kang, Sukhyun; Epling, Leslie B; Bell, Stephen P; Enemark, Eric J

2014-01-01

The ring-shaped MCM helicase is essential to all phases of DNA replication. The complex loads at replication origins as an inactive double-hexamer encircling duplex DNA. Helicase activation converts this species to two active single hexamers that encircle single-stranded DNA (ssDNA). The molecular details of MCM DNA interactions during these events are unknown. We determined the crystal structure of the Pyrococcus furiosus MCM N-terminal domain hexamer bound to ssDNA and define a conserved MCM-ssDNA binding motif (MSSB). Intriguingly, ssDNA binds the MCM ring interior perpendicular to the central channel with defined polarity. In eukaryotes, the MSSB is conserved in several Mcm2-7 subunits, and MSSB mutant combinations in S. cerevisiae Mcm2-7 are not viable. Mutant Mcm2-7 complexes assemble and are recruited to replication origins, but are defective in helicase loading and activation. Our findings identify an important MCM-ssDNA interaction and suggest it functions during helicase activation to select the strand for translocation. DOI: http://dx.doi.org/10.7554/eLife.01993.001 PMID:24692448

Characterization and modification of phage T7 DNA polymerase for use in DNA sequencing; Progress report, June 1, 1990--May 31, 1993

DOE Office of Scientific and Technical Information (OSTI.GOV)

Richardson, C.C.

1993-12-31

This project focuses on the DNA polymerase (gene 5 protein) of phage T7 for use in DNA sequence analysis. Gene 5 protein interacts with accessory proteins to acquire properties essential for DNA replication. One goal is to understand these interactions in order to modify the proteins for use in DNA sequencing. E. coli thioredoxin, binds to gene 5 protein and clamps it to a primer-template. They have analyzed the binding of gene 5 protein-thioredoxin to primer-templates and have defined the optimal conditions to form an extremely stable complex with a dNTP in the polymerase catalytic site. The spatial proximity ofmore » these components has been determined using fluorescence emission anisotropy. The T7 DNA binding protein, the gene 2.5 protein, interacts with gene 5 protein and gene 4 protein to increase processivity and primer synthesis, respectively. Mutant gene 2.5 proteins have been isolated that do not interact with T7 DNA polymerase and can not support T7 growth. The nucleotide binding site of the T7 helicase has been identified and mutations affecting the site provide information on how the hydrolysis of NTPs fuel its unidirectional translocation. The sequence, GTC, has been shown to be necessary and sufficient for recognition by the T7 primase. The T7 gene 5.5 protein interacts with the E. coli nucleoid protein, H-NS, and also overcomes the phage {lambda} rex restriction system.« less

3D printing of surgical instruments for long-duration space missions.

PubMed

Wong, Julielynn Y; Pfahnl, Andreas C

2014-07-01

The first off-Earth fused deposition modeling (FDM) 3D printer will explore thermoplastic manufacturing capabilities in microgravity. This study evaluated the feasibility of FDM 3D printing 10 acrylonitrile butadiene styrene (ABS) thermoplastic surgical instruments on Earth. Three-point bending tests compared stiffness and yield strength between FDM 3D printed and conventionally manufactured ABS thermoplastic. To evaluate the relative speed of using four printed instruments compared to conventional instruments, 13 surgeons completed simulated prepping, draping, incising, and suturing tasks. Each surgeon ranked the performance of six printed instruments using a 5-point Likert scale. At a thickness of 5.75 mm or more, the FDM printing process had a less than 10% detrimental effect on the tested yield strength and stiffness of horizontally printed ABS thermoplastic relative to conventional ABS thermoplastic. Significant weakness was observed when a bending load was applied transversely to a 3D printed layer. All timed tasks were successfully performed using a printed sponge stick, towel clamp, scalpel handle, and toothed forceps. There was no substantial difference in time to completion of simulated surgical tasks with control vs. 3D printed instruments. Of the surgeons, 100%, 92%, 85%, 77%, 77%, and 69% agreed that the printed smooth and tissue forceps, curved and straight hemostats, tissue and right angle clamps, respectively, would perform adequately. It is feasible to 3D print ABS thermoplastic surgical instruments on Earth. Loadbearing structures were designed to be thicker, when possible. Printing orientations were selected so that the printing layering direction of critical structures would not be transverse to bending loads.

In vivo experimental study on laser welded ICG-loaded chitosan patches for vessel repair

NASA Astrophysics Data System (ADS)

Rossi, Francesca; Matteini, Paolo; Esposito, Giuseppe; Albanese, Alessio; Puca, Alfredo; Maira, Giulio; Rossi, Giacomo; Pini, Roberto

2011-03-01

Laser welding of microvessels provides several advantages over conventional suturing techniques: surgical times reduction, vascular healing process improvement, tissue damage reduction. We present the first application of biopolymeric patches in an in vivo laser assisted procedure for vessel repair. The study was performed in 20 New Zealand rabbits. After anesthesia, a 3-cm segment of the right common carotid artery was exposed and clamped proximally and distally. A linear lesion 3 mm in length was carried out. We used a diode laser emitting at 810 nm and equipped with a 300 μm diameter optical fiber. To close the cut, ICG-loaded chitosan films were prepared: chitosan is characterized by biodegradability, biocompatibility, antimicrobial, haemostatic and wound healing-promoting activity. ICG is an organic chromophore commonly used in the laser welding procedures to mediate the photothermal conversion at the basis of the welding effect. The membranes were used to wrap the whole length of the cut, and then they were welded in the correct position by delivering single laser spots to induce local patch/tissue adhesion. The result is an immediate closure of the wound, with no bleeding at clamps release. The animals were observed during follow-up and sacrificed after 2, 7, 30 and 90 days. All the repaired vessels were patent, no bleeding signs were documented. The carotid samples underwent histological examinations. The advantages of the proposed technique are: simplification of the surgical procedure and shortening of the operative time; good strength of the vessel repair; decreased foreign-body reaction, reduced inflammatory response and improved vascular healing process.

Chicken parvovirus and its associations with malabsorption syndrome.

PubMed

Finkler, F; Lima, D A; Cerva, C; Moraes, L B; Cibulski, S P; Teixeira, T F; Santos, H F; Almeida, L L; Roehe, P M; Franco, A C

2016-08-01

Malabsorption syndrome (MAS) is a multifactorial syndrome which is characterized by enteric disorders and reduced growth rates of broilers. Such condition is responsible for significant economic losses to the poultry industry. A possible association between chicken parvovirus (ChPV) infections and the occurrence of MAS has been proposed. However, such association has not to date been elucidated in view that ChPV has been detected in healthy as well as in MAS-affected chickens. This study aimed to detect and quantify ChPV loads in sera and tissues of MAS-affected, as well as in healthy broilers. Fifty nine, 39-day-old broilers (50 diseased, 9 healthy birds), obtained from the same flocks, were examined. The highest ChPV DNA loads were detected in MAS-affected broilers, particularly in fecal samples and intestinal tissues (~5500 genomic copies/300ng of total DNA). The average viral genome load in serum in MAS-affected birds was 1134copies/mL, whereas no viral DNA was found in sera and thymus tissues from healthy animals. These findings reveal that MAS-affected broilers consistently carry ChPV DNA is serum, whereas healthy animals do not. In addition, viral loads in tissues (bursa of Fabricius, spleen, intestine and liver) of MAS-affected birds were significantly higher in comparison to the same tissues from healthy broilers. Although preliminary, the results obtained here indicate an association between the detection of ChPV DNA in serum, in addition to high ChPV viral loads in tissues, and the occurrence of MAS in broilers. Further experiments should be performed to confirm such results. Copyright © 2016. Published by Elsevier Ltd.

46 CFR 128.420 - Keel cooler installations.

Code of Federal Regulations, 2013 CFR

2013-10-01

...-metallic hose-clamps may be used at machinery connections if— (1) The clamps are of a corrosion-resistant material; (2) The clamps do not depend on spring tension for their holding power; and (3) Two of the clamps...

Lactose-modified DNA tile nanostructures as drug carriers.

PubMed

Akkus Sut, Pinar; Tunc, Cansu Umran; Culha, Mustafa

2016-09-01

DNA hybridization allows the preparation of nanoscale DNA structures with desired shape and size. DNA structures using simple base pairing can be used for the delivery of drug molecules into the cells. Since DNA carries multiple negative charges, their cellular uptake efficiency is low. Thus, the modification of the DNA structures with molecules that may enhance the cellular internalization may be an option. The objective of this study is to construct DNA-based nanocarrier system and to investigate the cellular uptake of DNA tile with/without lactose modification. Doxorubicin was intercalated to DNA tile and cellular uptake of drug-loaded DNA-based carrier with/without lactose modification was investigated in vitro. HeLa, BT-474, and MDA-MB-231 cancer cells were used for cellular uptake studies and cytotoxicity assays. Using fluorescence spectroscopy, flow cytometry, and confocal microscopy, cellular uptake behavior of DNA tile was investigated. The cytotoxicity of DNA tile structures was determined with WST-1 assay. The results show that modification with lactose effectively increases the intracellular uptake of doxorubicin loaded DNA tile structure by cancer cells compared with the unmodified DNA tile. The findings of this study suggest that DNA-based nanostructures modified with carbohydrates can be used as suitable multifunctional nanocarriers with simple chemical modifications.

Random Mutagenesis, Clonal Events, and Embryonic or Somatic Origin Determine the mtDNA Variant Type and Load in Human Pluripotent Stem Cells.

PubMed

Zambelli, Filippo; Mertens, Joke; Dziedzicka, Dominika; Sterckx, Johan; Markouli, Christina; Keller, Alexander; Tropel, Philippe; Jung, Laura; Viville, Stephane; Van de Velde, Hilde; Geens, Mieke; Seneca, Sara; Sermon, Karen; Spits, Claudia

2018-06-07

In this study, we deep-sequenced the mtDNA of human embryonic and induced pluripotent stem cells (hESCs and hiPSCs) and their source cells and found that the majority of variants pre-existed in the cells used to establish the lines. Early-passage hESCs carried few and low-load heteroplasmic variants, similar to those identified in oocytes and inner cell masses. The number and heteroplasmic loads of these variants increased with prolonged cell culture. The study of 120 individual cells of early- and late-passage hESCs revealed a significant diversity in mtDNA heteroplasmic variants at the single-cell level and that the variants that increase during time in culture are always passenger to the appearance of chromosomal abnormalities. We found that early-passage hiPSCs carry much higher loads of mtDNA variants than hESCs, which single-fibroblast sequencing proved pre-existed in the source cells. Finally, we show that these variants are stably transmitted during short-term differentiation. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Epstein-Barr virus DNA loads in adult human immunodeficiency virus type 1-infected patients receiving highly active antiretroviral therapy

NASA Technical Reports Server (NTRS)

Ling, Paul D.; Vilchez, Regis A.; Keitel, Wendy A.; Poston, David G.; Peng, Rong Sheng; White, Zoe S.; Visnegarwala, Fehmida; Lewis, Dorothy E.; Butel, Janet S.

2003-01-01

Patients with human immunodeficiency virus type 1 (HIV-1) infection are at high risk of developing Epstein-Barr virus (EBV)-associated lymphoma. However, little is known of the EBV DNA loads in patients receiving highly active antiretroviral therapy (HAART). Using a real-time quantitative polymerase chain reaction assay, we demonstrated that significantly more HIV-1-infected patients receiving HAART than HIV-1-uninfected volunteers had detectable EBV DNA in blood (57 [81%] of 70 vs. 11 [16%] of 68 patients; P=.001) and saliva (55 [79%] of 68 vs. 37 [54%] of 68 patients; P=.002). The mean EBV loads in blood and saliva samples were also higher in HIV-1-infected patients than in HIV-1-uninfected volunteers (P=.001). The frequency of EBV detection in blood was associated with lower CD4+ cell counts (P=.03) among HIV-1-infected individuals, although no differences were observed in the EBV DNA loads in blood or saliva samples in the HIV-1-infected group. Additional studies are needed to determine whether EBV-specific CD4+ and CD8+ cells play a role in the pathogenesis of EBV in HIV-1-infected patients receiving HAART.

Dendritic cell targeted chitosan nanoparticles for nasal DNA immunization against SARS CoV nucleocapsid protein.

PubMed

Raghuwanshi, Dharmendra; Mishra, Vivek; Das, Dipankar; Kaur, Kamaljit; Suresh, Mavanur R

2012-04-02

This work investigates the formulation and in vivo efficacy of dendritic cell (DC) targeted plasmid DNA loaded biotinylated chitosan nanoparticles for nasal immunization against nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus (SARS-CoV) as antigen. The induction of antigen-specific mucosal and systemic immune response at the site of virus entry is a major challenge for vaccine design. Here, we designed a strategy for noninvasive receptor mediated gene delivery to nasal resident DCs. The pDNA loaded biotinylated chitosan nanoparticles were prepared using a complex coacervation process and characterized for size, shape, surface charge, plasmid DNA loading and protection against nuclease digestion. The pDNA loaded biotinylated chitosan nanoparticles were targeted with bifunctional fusion protein (bfFp) vector for achieving DC selective targeting. The bfFp is a recombinant fusion protein consisting of truncated core-streptavidin fused with anti-DEC-205 single chain antibody (scFv). The core-streptavidin arm of fusion protein binds with biotinylated nanoparticles, while anti-DEC-205 scFv imparts targeting specificity to DC DEC-205 receptor. We demonstrate that intranasal administration of bfFp targeted formulations along with anti-CD40 DC maturation stimuli enhanced magnitude of mucosal IgA as well as systemic IgG against N protein. The strategy led to the detection of augmented levels of N protein specific systemic IgG and nasal IgA antibodies. However, following intranasal delivery of naked pDNA no mucosal and systemic immune responses were detected. A parallel comparison of targeted formulations using intramuscular and intranasal routes showed that the intramuscular route is superior for induction of systemic IgG responses compared with the intranasal route. Our results suggest that targeted pDNA delivery through a noninvasive intranasal route can be a strategy for designing low-dose vaccines.

Detachable clamps for minimal access surgery.

PubMed

Frank, T; Willetts, G J; Cuschieri, A

1995-01-01

A detachable clamp and applicator have been developed for use in minimal access surgical operations involving hollow visceral transection and anastomosis. The clamp has parallel jaws which ensure uniform distribution of the occlusive force. Following application on the bowel, the clamp is released from the applicator, thus freeing the access port. On completion of the anastomosis, the clamp is docked to the applicator, its jaws opened for release from the bowel and then closed prior to removal. The jaws of the clamp are kept closed by a pseudoelastic nickel-titanium (NiTi) alloy spring which imparts advantageous force characteristics when compared to stainless steel. The excellent holding and atraumatic characteristics of the detachable clamp have been confirmed by use in laparoscopic and thoracoscopic surgery on the gastrointestinal tract.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morris, John; Gilchrist, Phillip Charles

Processes, systems, devices, and articles of manufacture are provided. Each may include adapting micro-inverters initially configured for frame-mounting to mounting on a frameless solar panel. This securement may include using an adaptive clamp or several adaptive clamps secured to a micro-inverter or its components, and using compressive forces applied directly to the solar panel to secure the adaptive clamp and the components to the solar panel. The clamps can also include compressive spacers and safeties for managing the compressive forces exerted on the solar panels. Friction zones may also be used for managing slipping between the clamp and the solarmore » panel during or after installation. Adjustments to the clamps may be carried out through various means and by changing the physical size of the clamps themselves.« less

A clamp fixture with interdigital capacitive sensor for in situ evaluation of wire insulation

NASA Astrophysics Data System (ADS)

Sheldon, Robert T.; Bowler, Nicola

2014-02-01

An interdigital capacitive sensor has been designed and optimized for testing aircraft wires by applying a quasinumerical model developed and reported previously. The sensor consists of two patches of interdigitated electrodes, connected by a long signal bus strip, that are intended to conform to two sides of an insulated wire. The electrodes are deposited using photolithography upon a 25.4-μm-thick Kapton® polyimide film. The two electrode patches are attached to the two jaws of a plastic spring-loaded clamp, with each jaw having a milled groove designed such that the electrodes conform to the curved surface of the insulated wire. An SMA connector and cable connect between the electrodes on the clamp and an LCR meter. Segments of pristine M5086/2 aircraft wire, each 10 cm long, were immersed in fluids commonly found in aircraft environments, to cause accelerated chemical degradation. The effects of Jet A fuel, deicing fluid, hydraulic fluid, aircraft cleaner, isopropyl alcohol and distilled water were studied. The frequency-dependent capacitance and dissipation factor of one pristine wire segment and of those degraded in the six fluid environments were measured within the frequency range 100 Hz to 1 MHz. Significant changes in capacitance and dissipation factor were observed for all degraded wires, compared with results for the pristine sample, suggesting the feasibility of detecting insulation degradation in the field. The results were also consistent with those of a similar experiment performed on sheets of Nylon 6, the material that comprises the outermost layer of M5086/2 wire.

Targeting of loaded Sendai virus envelopes by covalently attached insulin molecules to virus receptor-depleted cells: fusion-mediated microinjection of ricin A and simian virus 40 DNA.

PubMed

Gitman, A G; Graessmann, A; Loyter, A

1985-11-01

Insulin molecules were covalently attached to detergent-solubilized Sendai virus envelope glycoproteins (HN and F polypeptides) by the use of the crosslinking reagent succinimidyl 4-(p-maleimidophenyl)butyrate (SMPB). Reconstitution of modified viral glycoproteins (carrying covalently attached insulin) together with unmodified viral glycoproteins resulted in the formation of "fusogenic" viral envelopes bearing insulin molecules. Reconstitution of such fusogenic viral envelopes in the presence of ricin A or simian virus 40 (SV40) DNA resulted in the formation of viral envelopes bearing insulin molecules and loaded with ricin A or SV40 DNA. Such viral envelopes were able to bind to hepatoma tissue culture cells (HTCC) from which Sendai virus receptors were removed by treatment with neuraminidase. Incubation of viral envelopes loaded with ricin A with virus receptor-depleted HTCC resulted in fusion-mediated injection of the toxin, as inferred from inhibition of protein synthesis and decrease in cell viability of the microinjected cells. Fusion-mediated injection of SV40 DNA was inferred from the appearance of SV40 tumor antigen in microinjected cells. Binding and fusion of the loaded viral envelopes to neuraminidase-treated HTCC was mediated solely by the virus-associated insulin molecules. Addition of free insulin molecules inhibited binding of the viral envelopes and, consequently, the microinjection of ricin A and SV40 DNA.

Targeting of loaded Sendai virus envelopes by covalently attached insulin molecules to virus receptor-depleted cells: fusion-mediated microinjection of ricin A and simian virus 40 DNA.

PubMed Central

Gitman, A G; Graessmann, A; Loyter, A

1985-01-01

Insulin molecules were covalently attached to detergent-solubilized Sendai virus envelope glycoproteins (HN and F polypeptides) by the use of the crosslinking reagent succinimidyl 4-(p-maleimidophenyl)butyrate (SMPB). Reconstitution of modified viral glycoproteins (carrying covalently attached insulin) together with unmodified viral glycoproteins resulted in the formation of "fusogenic" viral envelopes bearing insulin molecules. Reconstitution of such fusogenic viral envelopes in the presence of ricin A or simian virus 40 (SV40) DNA resulted in the formation of viral envelopes bearing insulin molecules and loaded with ricin A or SV40 DNA. Such viral envelopes were able to bind to hepatoma tissue culture cells (HTCC) from which Sendai virus receptors were removed by treatment with neuraminidase. Incubation of viral envelopes loaded with ricin A with virus receptor-depleted HTCC resulted in fusion-mediated injection of the toxin, as inferred from inhibition of protein synthesis and decrease in cell viability of the microinjected cells. Fusion-mediated injection of SV40 DNA was inferred from the appearance of SV40 tumor antigen in microinjected cells. Binding and fusion of the loaded viral envelopes to neuraminidase-treated HTCC was mediated solely by the virus-associated insulin molecules. Addition of free insulin molecules inhibited binding of the viral envelopes and, consequently, the microinjection of ricin A and SV40 DNA. PMID:2997783

A novel high performance ESD power clamp circuit with a small area

NASA Astrophysics Data System (ADS)

Zhaonian, Yang; Hongxia, Liu; Li, Li; Qingqing, Zhuo

2012-09-01

A MOSFET-based electrostatic discharge (ESD) power clamp circuit with only a 10 ns RC time constant for a 0.18-μm process is proposed. A diode-connected NMOSFET is used to maintain a long delay time and save area. The special structure overcomes other shortcomings in this clamp circuit. Under fast power-up events, the gate voltage of the clamp MOSFET does not rise as quickly as under ESD events, the special structure can keep the clamp MOSFET thoroughly off. Under a falsely triggered event, the special structure can turn off the clamp MOSFET in a short time. The clamp circuit can also reject the power supply noise effectively. Simulation results show that the clamp circuit avoids fast false triggering events such as a 30 ns/1.8 V power-up, maintains a 1.2 μs delay time and a 2.14 μs turn-off time, and reduces to about 70% of the RC time constant. It is believed that the proposed clamp circuit can be widely used in high-speed integrated circuits.

Cytokine and iNOS profiles in lymph nodes of dogs naturally infected with Leishmania infantum and their association with the parasitic DNA load and clinical and histopathological features.

PubMed

de Vasconcelos, Tassia Cristina Bello; Doyen, Noelle; Cavaillon, Jean-Marc; Bruno, Sávio Freire; de Campos, Monique Paiva; de Miranda, Luisa Helena Monteiro; Madeira, Maria de Fátima; Belo, Vinícius Silva; Figueiredo, Fabiano Borges

2016-08-30

In South America, visceral leishmaniasis is a zoonotic disease with severe evolution characteristics in humans, and dogs are its main reservoir. In this context, this study aimed to evaluate the clinical status of dogs from a Brazilian endemic area naturally, at Barra Mansa municipality, infected with Leishmania infantum, in conjunction with their histopathological profile and, in order to determine possible markers of susceptibility or resistance to the disease, parasitic DNA load, cytokine and iNOS mRNA expression profiles were investigated in lymph nodes. High levels of IFN-ɣ and IL-6 mRNA were detected. Both IFN-ɣ and IL-6 mRNA were associated with disorganization of the corticomedullary region. IFN-ɣ and TNF-α mRNA were associated with the absence of follicular hyperplasia. The regulatory pathway was remarkable with IL-10 mRNA detection and its significant association with the severity of the disease. Plasmacytosis and sinus histiocytosis were associated with high loads of parasitic DNA, but there was no significant association between the parasite DNA load and animal clinical alterations. Since high parasitic loads were found in animals with or without symptoms, clinical examination cannot be considered as a criterion for disease susceptibility assessment. Copyright © 2016 Elsevier B.V. All rights reserved.

A Wide Range of 3243A>G/tRNALeu(UUR) (MELAS) Mutation Loads May Segregate in Offspring through the Female Germline Bottleneck

PubMed Central

Pallotti, Francesco; Binelli, Giorgio; Fabbri, Raffaella; Valentino, Maria L.; Vicenti, Rossella; Macciocca, Maria; Cevoli, Sabina; Baruzzi, Agostino; DiMauro, Salvatore; Carelli, Valerio

2014-01-01

Segregation of mutant mtDNA in human tissues and through the germline is debated, with no consensus about the nature and size of the bottleneck hypothesized to explain rapid generational shifts in mutant loads. We investigated two maternal lineages with an apparently different inheritance pattern of the same pathogenic mtDNA 3243A>G/tRNALeu(UUR) (MELAS) mutation. We collected blood cells, muscle biopsies, urinary epithelium and hair follicles from 20 individuals, as well as oocytes and an ovarian biopsy from one female mutation carrier, all belonging to the two maternal lineages to assess mutant mtDNA load, and calculated the theoretical germline bottleneck size (number of segregating units). We also evaluated “mother-to-offspring” segregations from the literature, for which heteroplasmy assessment was available in at least three siblings besides the proband. Our results showed that mutation load was prevalent in skeletal muscle and urinary epithelium, whereas in blood cells there was an inverse correlation with age, as previously reported. The histoenzymatic staining of the ovarian biopsy failed to show any cytochrome-c-oxidase defective oocyte. Analysis of four oocytes and one offspring from the same unaffected mother of the first family showed intermediate heteroplasmic mutant loads (10% to 75%), whereas very skewed loads of mutant mtDNA (0% or 81%) were detected in five offspring of another unaffected mother from the second family. Bottleneck size was 89 segregating units for the first mother and 84 for the second. This was remarkably close to 88, the number of “segregating units” in the “mother-to-offspring” segregations retrieved from literature. In conclusion, a wide range of mutant loads may be found in offspring tissues and oocytes, resulting from a similar theoretical bottleneck size. PMID:24805791

Effects of vegetation and sewage load on mangrove crab condition using experimental mesocosms

NASA Astrophysics Data System (ADS)

Amaral, Valter; Penha-Lopes, Gil; Paula, José

2009-09-01

Constructed wetlands, especially mangroves, have been studied for their usefulness in sewage treatment but the effects of mangrove vegetation and a sewage load on mangrove macrofauna have been given little attention. Ocypodid crabs are important components of mangrove forests and constitute good bioindicators of the functioning of the ecosystem as a whole. In constructed mangrove mesocosms, three vegetation treatments (bare substratum, and Avicennia marina and Rhizophora mucronata seedlings) were subjected to 0, 20, 60 and 100% sewage loads from a nearby hotel. The physiological condition of introduced Uca annulipes and Uca inversa was evaluated in terms of their RNA/DNA ratio after one, five and twelve months, and used as an indicator of ecological function in the system. Crab condition in 0% sewage load was similar to that of wild crabs throughout, suggesting no significant effects of the mesocosms on their RNA/DNA ratio. Overall, both species coped well with the administered sewage loads, suggesting good ecological function in the system. Both species manifested similar patterns in RNA/DNA ratio, being more affected by seasonal fluctuations than by sewage load and vegetation presence and type. Higher RNA/DNA ratios were recorded in the long compared to the short rainy season. Sewage enhanced crab condition in the bare substratum and R. mucronata treatments, especially after one year, probably as a result of enhanced food availability. Uca inversa may be more sensitive to sewage pollution than U. annulipes. In A. marina, no difference in crab condition was observed between sewage loads, and this mangrove yielded the best reduction in sewage impacts. Our results support the usefulness of constructed mangrove areas in sewage treatment, especially if planted with A. marina and inhabited by physiologically healthy ocypodid crabs to enhance the system's performance.

Drum ring removal/installation tool

DOEpatents

Andrade, William Andrew [Livermore, CA

2006-11-14

A handheld tool, or a pair of such tools, such as for use in removing/installing a bolt-type clamping ring on a container barrel/drum, where the clamping ring has a pair of clamping ends each with a throughbore. Each tool has an elongated handle and an elongated lever arm transversely connected to one end of the handle. The lever arm is capable of being inserted into the throughbore of a selected clamping end and leveraged with the handle to exert a first moment on the selected clamping end. Each tool also has a second lever arm, such as a socket with an open-ended slot, which is suspended alongside the first lever arm. The second lever arm is capable of engaging the selected clamping end and being leveraged with the handle to exert a second moment which is orthogonal to the first moment. In this manner, the first and second moments operate to hold the selected clamping end fixed relative to the tool so that the selected clamping end may be controlled with the handle. The pair of clamping ends may also be simultaneously and independently controlled with the use of two handles/tools so as to contort the geometry of the drum clamping ring and enable its removal/installation.

Prediction of Fretting Crack Location and Orientation in a Single Crystal Nickel Alloy

NASA Technical Reports Server (NTRS)

Matlik, J. F.; Farris, T. N.; Haynes, J.; Swanson, G. R.; Ham-Battista, G.

2005-01-01

Fretting is a structural damage mechanism arising between two nominally clamped surfaces subjected to an oscillatory loading. A critical location for fretting induced damage has been identified at the blade/disk and blade/damper interfaces of gas turbine engine turbomachinery and space propulsion components. The high- temperature, high-frequency loading environment seen by these components lead to severe stress gradients at the edge-of-contact that could potentially foster crack growth leading to component failure. These contact stresses drive crack nucleation in fretting and are very sensitive to the geometry of the contacting bodies, the contact loads, materials, temperature, and contact surface tribology (friction). Recently, a high-frequency, high-temperature load frame has been designed for experimentally investigating fretting damage of single crystal nickel materials employed in aircraft and spacecraft turbomachinery. A modeling method for characterizing the fretting stresses of the spherical fretting contact stress behavior in this experiment is developed and described. The calculated fretting stresses for a series of experiments are then correlated to the observed fretting damage. Results show that knowledge of the normal stresses and resolved shear stresses on each crystal plane can aid in predicting crack locations and orientations.

Quantitative analysis of herpes virus sequences from normal tissue and fibropapillomas of marine turtles with real-time PCR

USGS Publications Warehouse

Quackenbush, S.L.; Casey, R.N.; Murcek, R.J.; Paul, T.A.; Work, Thierry M.; Limpus, C.J.; Chaves, A.; duToit, L.; Perez, J.V.; Aguirre, A.A.; Spraker, T.R.; Horrocks, J.A.; Vermeer, L.A.; Balazs, G.S.; Casey, J.W.

2001-01-01

Quantitative real-time PCR has been used to measure fibropapilloma-associated turtle herpesvirus (FPTHV) pol DNA loads in fibropapillomas, fibromas, and uninvolved tissues of green, loggerhead, and olive ridley turtles from Hawaii, Florida, Costa Rica, Australia, Mexico, and the West Indies. The viral DNA loads from tumors obtained from terminal animals were relatively homogenous (range 2a??20 copies/cell), whereas DNA copy numbers from biopsied tumors and skin of otherwise healthy turtles displayed a wide variation (range 0.001a??170 copies/cell) and may reflect the stage of tumor development. FPTHV DNA loads in tumors were 2.5a??4.5 logs higher than in uninvolved skin from the same animal regardless of geographic location, further implying a role for FPTHV in the etiology of fibropapillomatosis. Although FPTHV pol sequences amplified from tumors are highly related to each other, single signature amino acid substitutions distinguish the Australia/Hawaii, Mexico/Costa Rica, and Florida/Caribbean groups.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Patel, Asmita; Shuman, Stewart; Mondragon, Alfonso

Type IB DNA topoisomerases are found in all eukarya, two families of eukaryotic viruses (poxviruses and mimivirus), and many genera of bacteria. They alter DNA topology by cleaving and resealing one strand of duplex DNA via a covalent DNA-(3-phosphotyrosyl)-enzyme intermediate. Bacterial type IB enzymes were discovered recently and are described as poxvirus-like with respect to their small size, primary structures, and bipartite domain organization. Here we report the 1.75-{angstrom} crystal structure of Deinococcus radiodurans topoisomerase IB (DraTopIB), a prototype of the bacterial clade. DraTopIB consists of an amino-terminal (N) {beta}-sheet domain (amino acids 1-90) and a predominantly {alpha}-helical carboxyl-terminal (C)more » domain (amino acids 91-346) that closely resemble the corresponding domains of vaccinia virus topoisomerase IB. The five amino acids of DraTopIB that comprise the catalytic pentad (Arg-137, Lys-174, Arg-239, Asn-280, and Tyr-289) are preassembled into the active site in the absence of DNA in a manner nearly identical to the pentad configuration in human topoisomerase I bound to DNA. This contrasts with the apoenzyme of vaccinia topoisomerase, in which three of the active site constituents are either displaced or disordered. The N and C domains of DraTopIB are splayed apart in an 'open' conformation, in which the surface of the catalytic domain containing the active site is exposed for DNA binding. A comparison with the human topoisomerase I-DNA cocrystal structure suggests how viral and bacterial topoisomerase IB enzymes might bind DNA circumferentially via movement of the N domain into the major groove and clamping of a disordered loop of the C domain around the helix.« less

The Ctf18RFC Clamp Loader Is Essential for Telomere Stability in Telomerase-Negative and mre11 Mutant Alleles

PubMed Central

Parke, Courtney; Tatum, Danielle; Lustig, Arthur J.

2014-01-01

The function of the replication clamp loaders in the semi-conservative telomere replication and their relationship to telomerase- and recombination mechanisms of telomere addition remains ambiguous. We have investigated the variant clamp loader Ctf18 RFC (Replication Factor C). To understand the role of Ctf18 at the telomere, we first investigated genetic interactions after loss of Ctf18 and TLC1 (the yeast telomerase RNA). We find that the tlc1▵ ctf18▵ double mutant confers a rapid >1000-fold decrease in viability. The rate of loss was similar to the kinetics of cell death in rad52▵ tlc1▵ cells. However, the Ctf18 pathway is distinct from Rad52, required for the repair of DSBs, as demonstrated by the synthetic lethality of rad52▵ tlc1▵ ctf18▵ triple mutants. These data suggest that each mutant elicits non-redundant defects acting on the same substrate. Second, interactions of the yeast hyper-recombinational mutant, mre11A470T, with ctf18▵ confer a synergistic cold sensitivity. The phenotype of these double mutants ultimately results in telomere loss and the generation of recombinational survivors. We observed a similar synergism between single mutants that led to hypersensitivity to the DNA alkylating agent, methane methyl sulphonate (MMS), the replication fork inhibitor hydroxyurea (HU), and to a failure to separate telomeres of sister chromatids. Hence, ctf18▵ and mre11A470T act in different pathways on telomere substrates for multiple phenotypes. The mre11A470T cells also displayed a DNA damage response (DDR) at 15°C but not at 30°C while ctf18▵ mutants conferred a constitutive DDR activity. Both the 15°C DDR pattern and growth rate were reversible at 30°C and displayed telomerase activity in vivo. We hypothesize that Ctf18 confers protection against stalling and/or breaks at the replication fork in cells that either lack, or are compromised for, telomerase activity. This Ctf18-based function is likely to contribute another level to telomere size homeostasis. PMID:24533124

Polyplex-microbubble hybrids for ultrasound-guided plasmid DNA delivery to solid tumors.

PubMed

Sirsi, Shashank R; Hernandez, Sonia L; Zielinski, Lukasz; Blomback, Henning; Koubaa, Adel; Synder, Milo; Homma, Shunichi; Kandel, Jessica J; Yamashiro, Darrell J; Borden, Mark A

2012-01-30

Microbubble ultrasound contrast agents are being developed as image-guided gene carriers for targeted delivery in vivo. In this study, novel polyplex-microbubbles were synthesized, characterized and evaluated for systemic circulation and tumor transfection. Branched polyethylenimine (PEI; 25 kDa) was modified with polyethylene glycol (PEG; 5 kDa), thiolated and covalently attached to maleimide groups on lipid-coated microbubbles. The PEI-microbubbles demonstrated increasingly positive surface charge and DNA loading capacity with increasing maleimide content. The in vivo ultrasound contrast persistence of PEI-microbubbles was measured in the healthy mouse kidney, and a two-compartment pharmacokinetic model accounting for free and adherent microbubbles was developed to describe the anomalous time-intensity curves. The model suggested that PEI loading dramatically reduced free circulation and increased nonspecific adhesion to the vasculature. However, DNA loading to form polyplex-microbubbles increased circulation in the bloodstream and decreased nonspecific adhesion. PEI-microbubbles coupled to a luciferase bioluminescence reporter plasmid DNA were shown to transfect tumors implanted in the mouse kidney. Site-specific delivery was achieved using ultrasound applied over the tumor area following bolus injection of the DNA/PEI-microbubbles. In vivo imaging showed over 10-fold higher bioluminescence from the tumor region compared to untreated tissue. Ex vivo analysis of excised tumors showed greater than 40-fold higher expression in tumor tissue than non-sonicated control (heart) tissue. These results suggest that the polyplex-microbubble platform offers improved control of DNA loading and packaging suitable for ultrasound-guided tissue transfection. Copyright © 2011 Elsevier B.V. All rights reserved.

Welding fixture for joining bar-wound stator conductors

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Souza, Urban J.; Rhoads, Frederick W.; Hanson, Justin

A fixture assembly for welding a plurality of stator wire end pairs may include an anvil, a movable clamp configured to translate between an unclamped state and a clamped state, a first grounding electrode, and a second grounding electrode. The movable clamp may be configured to urge the plurality of stator wire ends against the anvil when in the clamped state. The moveable clamp includes a separator feature that generally extends toward the anvil. Each of the first grounding electrode and second grounding electrodes may be configured to translate between a clamped state and an unclamped state. When in themore » clamped state, each of the first and second grounding electrodes is configured to urge a pair of the plurality of stator wire end pairs against the separator feature.« less

Renal Vascular Clamp Placement: A Potential Cause of Incomplete Hilar Control during Partial Nephrectomy.

PubMed

Tryon, David; Myklak, Kristene; Alsyouf, Muhannad; Conceicao, Carol; Peplinski, Brandon; Arenas, Javier L; Faaborg, Daniel; Ruckle, Herbert C; Baldwin, D Duane

2016-03-01

Previous benchtop studies have shown that robotic bulldog clamps provide incomplete vascular control of a Penrose drain. We determined the efficacy of robotic and laparoscopic bulldog clamps to ensure hemostasis on the human renal artery. The effect of clamp position on vascular control was also examined. Fresh human cadaveric renal arteries were used to determine the leak point pressure of 7 bulldog clamps from a total of 3 manufacturers. Five trials were performed per clamp at 4 locations, including the fulcrum, proximal, middle and distal positions. Comparison was done using the Kruskal-Wallis test with p <0.05 considered significant. None of the bulldog clamps leaked at a pressure less than 215 mm Hg when applied at the proximal, middle or distal position. In general leak point pressure decreased as the artery was positioned more distal along the clamp. The exception was when the vessel was placed at the fulcrum position. At that position 80% to 100% of trials with the Klein laparoscopic, 100% with the Klein robotic (Klein Robotic, San Antonio, Texas) and 60% to 80% with the Scanlan robotic (Scanlan International, Saint Paul, Minnesota) clamp leaked at pressure below 215 mm Hg. Each vascular clamp adequately occluded flow at physiological pressure when placed at the proximal, middle or distal position. Furthermore, these results demonstrate that there is leakage at physiological pressure when the artery is placed at the fulcrum of certain clamp types. These results suggest that applying a bulldog clamp at the fulcrum could potentially lead to inadequate vessel occlusion and intraoperative bleeding. Copyright © 2016 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

A comparison between the minimal model and the glucose clamp in the assessment of insulin sensitivity across the spectrum of glucose tolerance. Insulin Resistance Atherosclerosis Study.

PubMed

Saad, M F; Anderson, R L; Laws, A; Watanabe, R M; Kades, W W; Chen, Y D; Sands, R E; Pei, D; Savage, P J; Bergman, R N

1994-09-01

An insulin-modified frequently sampled intravenous glucose tolerance test (FSIGTT) with minimal model analysis was compared with the glucose clamp in 11 subjects with normal glucose tolerance (NGT), 20 with impaired glucose tolerance (IGT), and 24 with non-insulin-dependent diabetes mellitus (NIDDM). The insulin sensitivity index (SI) was calculated from FSIGTT using 22- and 12-sample protocols (SI(22) and SI(12), respectively). Insulin sensitivity from the clamp was expressed as SI(clamp) and SIP(clamp). Minimal model parameters were similar when calculated with SI(22) and SI(12). SI could not be distinguished from 0 in approximately 50% of diabetic patients with either protocol. SI(22) correlated significantly with SI(clamp) in the whole group (r = 0.62), and in the NGT (r = 0.53), IGT (r = 0.48), and NIDDM (r = 0.41) groups (P < 0.05 for each). SI(12) correlated significantly with SI(clamp) in the whole group (r = 0.55, P < 0.001) and in the NGT (r = 0.53, P = 0.046) and IGT (r = 0.58, P = 0.008) but not NIDDM (r = 0.30, P = 0.085) groups. When SI(22), SI(clamp), and SIP(clamp) were expressed in the same units, SI(22) was 66 +/- 5% (mean +/- SE) and 50 +/- 8% lower than SI(clamp) and SIP(clamp), respectively. Thus, minimal model analysis of the insulin-modified FSIGTT provides estimates of insulin sensitivity that correlate significantly with those from the glucose clamp. The correlation was weaker, however, in NIDDM. The insulin-modified FSIGTT can be used as a simple test for assessment of insulin sensitivity in population studies involving nondiabetic subjects. Additional studies are needed before using this test routinely in patients with NIDDM.

Arterial waves in humans during peripheral vascular surgery.

PubMed

Khir, A W; Henein, M Y; Koh, T; Das, S K; Parker, K H; Gibson, D G

2001-12-01

The purpose of this study was to investigate the effect of aortic clamping on arterial waves during peripheral vascular surgery. We measured pressure and velocity simultaneously in the ascending aorta, in ten patients (70+/-5 years) with aortic-iliac disease intra-operatively. Pressure was measured using a catheter tip manometer, and velocity was measured using Doppler ultrasound. Data were collected before aortic clamping, during aortic clamping and after unclamping. Hydraulic work in the aortic root was calculated from the measured data, the reflected waves were determined by wave-intensity analysis and wave speed was determined by the PU-loop (pressure-velocity-loop) method; a new technique based on the 'water-hammer' equation. The wave speed is approx. 32% (P<0.05) higher during clamping than before clamping. Although the peak intensity of the reflected wave does not alter with clamping, it arrives 30 ms (P<0.05) earlier and its duration is 25% (P<0.05) longer than before clamping. During clamping, left ventricule (LV) hydraulic systolic work and the energy carried by the reflected wave increased by 27% (P<0.05) and 20% (P<0.05) respectively, compared with before clamping. The higher wave speed during clamping explains the earlier arrival of the reflected waves suggesting an increase in the afterload, since the LV has to overcome earlier reflected compression waves. The longer duration of the reflected wave during clamping is associated with an increase in the total energy carried by the wave, which causes an increase in hydraulic work. Increased hydraulic work during clamping may increase LV oxygen consumption, provoke myocardial ischaemia and hence contribute to the intra-operative impairment of LV function known in patients with peripheral vascular disease.

Comparison of oral fluid collection methods for the molecular detection of hepatitis B virus.

PubMed

Portilho, M M; Mendonça, Acf; Marques, V A; Nabuco, L C; Villela-Nogueira, C A; Ivantes, Cap; Lewis-Ximenez, L L; Lampe, E; Villar, L M

2017-11-01

This study aims to compare the efficiency of four oral fluid collection methods (Salivette, FTA Card, spitting and DNA-Sal) to detect HBV DNA by qualitative PCR. Seventy-four individuals (32 HBV reactive and 42 with no HBV markers) donated serum and oral fluid. In-house qualitative PCR to detect HBV was used for both samples and commercial quantitative PCR for serum. HBV DNA was detected in all serum samples from HBV-infected individuals, and it was not detected in control group. HBV DNA from HBV group was detected in 17 samples collected with Salivette device, 16 samples collected by FTA Card device, 16 samples collected from spitting and 13 samples collected by DNA-Sal device. Samples that corresponded to a higher viral load in their paired serum sample could be detected using all oral fluid collection methods, but Salivette collection device yielded the largest numbers of positive samples and had a wide range of viral load that was detected. It was possible to detect HBV DNA using all devices tested, but higher number of positive samples was observed when samples were collected using Salivette device, which shows high concordance to viral load observed in the paired serum samples. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd. All rights reserved.

Structure of the Small Outer Capsid Protein, Soc: A Clamp for Stabilizing Capsids of T4-like Phages

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qin, Li; Fokine, Andrei; O'Donnell, Erin

2010-07-22

Many viruses need to stabilize their capsid structure against DNA pressure and for survival in hostile environments. The 9-kDa outer capsid protein (Soc) of bacteriophage T4, which stabilizes the virus, attaches to the capsid during the final stage of maturation. There are 870 Soc molecules that act as a 'glue' between neighboring hexameric capsomers, forming a 'cage' that stabilizes the T4 capsid against extremes of pH and temperature. Here we report a 1.9 {angstrom} resolution crystal structure of Soc from the bacteriophage RB69, a close relative of T4. The RB69 crystal structure and a homology model of T4 Soc weremore » fitted into the cryoelectron microscopy reconstruction of the T4 capsid. This established the region of Soc that interacts with the major capsid protein and suggested a mechanism, verified by extensive mutational and biochemical studies, for stabilization of the capsid in which the Soc trimers act as clamps between neighboring capsomers. The results demonstrate the factors involved in stabilizing not only the capsids of T4-like bacteriophages but also many other virus capsids.« less

Quantum dot-loaded monofunctionalized DNA icosahedra for single-particle tracking of endocytic pathways.

PubMed

Bhatia, Dhiraj; Arumugam, Senthil; Nasilowski, Michel; Joshi, Himanshu; Wunder, Christian; Chambon, Valérie; Prakash, Ved; Grazon, Chloé; Nadal, Brice; Maiti, Prabal K; Johannes, Ludger; Dubertret, Benoit; Krishnan, Yamuna

2016-12-01

Functionalization of quantum dots (QDs) with a single biomolecular tag using traditional approaches in bulk solution has met with limited success. DNA polyhedra consist of an internal void bounded by a well-defined three-dimensional structured surface. The void can house cargo and the surface can be functionalized with stoichiometric and spatial precision. Here, we show that monofunctionalized QDs can be realized by encapsulating QDs inside DNA icosahedra and functionalizing the DNA shell with an endocytic ligand. We deployed the DNA-encapsulated QDs for real-time imaging of three different endocytic ligands-folic acid, galectin-3 (Gal3) and the Shiga toxin B-subunit (STxB). Single-particle tracking of Gal3- or STxB-functionalized QD-loaded DNA icosahedra allows us to monitor compartmental dynamics along endocytic pathways. These DNA-encapsulated QDs, which bear a unique stoichiometry of endocytic ligands, represent a new class of molecular probes for quantitative imaging of endocytic receptor dynamics.

Clamp-mount device

NASA Technical Reports Server (NTRS)

Clark, K. H. (Inventor)

1983-01-01

A clamp-mount device is disclosed for mounting equipment to an associated I-beam and the like structural member of the type having oppositely extending flanges wherein the device comprises a base and a pair of oppositely facing clamping members carried diagonally on the base clamping flanges therebetween and having flange receiving openings facing one another. Lock means are carried diagonally by the base opposite the clamping members locking the flanges in the clamping members. A resilient hub is carried centrally of the base engaging and biasing a back side of the flanges maintaining tightly clamped and facilitating use on vertical as well as horizontal members. The base turns about the hub to receive the flanges within the clamping members. Equipment may be secured to the base by any suitable means such as bolts in openings. Slidable gate latches secure the hinged locks in an upright locking position. The resilient hub includes a recess opening formed in the base and a rubber-like pad carried in this opening being depressably and rotatably carried therein.

The RNA polymerase clamp interconverts dynamically among three states and is stabilized in a partly closed state by ppGpp.

PubMed

Duchi, Diego; Mazumder, Abhishek; Malinen, Anssi M; Ebright, Richard H; Kapanidis, Achillefs N

2018-06-06

RNA polymerase (RNAP) contains a mobile structural module, the 'clamp,' that forms one wall of the RNAP active-center cleft and that has been linked to crucial aspects of the transcription cycle, including promoter melting, transcription elongation complex stability, transcription pausing, and transcription termination. Using single-molecule FRET on surface-immobilized RNAP molecules, we show that the clamp in RNAP holoenzyme populates three distinct conformational states and interconvert between these states on the 0.1-1 s time-scale. Similar studies confirm that the RNAP clamp is closed in open complex (RPO) and in initial transcribing complexes (RPITC), including paused initial transcribing complexes, and show that, in these complexes, the clamp does not exhibit dynamic behaviour. We also show that, the stringent-response alarmone ppGpp, which reprograms transcription during amino acid starvation stress, selectively stabilizes the partly-closed-clamp state and prevents clamp opening; these results raise the possibility that ppGpp controls promoter opening by modulating clamp dynamics.

Evaluation of Introduction of a Delayed Cord Clamping Protocol for Premature Neonates in a High-Volume Maternity Center.

PubMed

Liu, Lilly Y; Feinglass, Joe M; Khan, Janine Y; Gerber, Susan E; Grobman, William A; Yee, Lynn M

2017-05-01

To evaluate adherence to a delayed cord clamping protocol for preterm births in the first 2 years after its introduction, perform a quality improvement assessment, and determine neonatal outcomes associated with protocol implementation and adherence. This is a retrospective cohort study of women delivering singleton neonates at 23-32 weeks of gestation in the 2 years before (preprotocol) and 2 years after (postprotocol) introduction of a 30-second delayed cord clamping protocol at a large-volume academic center. This policy was communicated to obstetric and pediatric health care providers and nurses and reinforced with intermittent educational reviews. Barriers to receiving delayed cord clamping were assessed using χ tests and multivariable logistic regression. Neonatal outcomes then were compared between all neonates in the preprotocol period and all neonates in the postprotocol period and between all neonates in the preprotocol period and neonates receiving delayed cord clamping in the postprotocol period using multivariable linear and logistic regression analyses. Of the 427 eligible neonates, 187 were born postprotocol. Of these, 53.5% (n=100) neonates received delayed cord clamping according to the protocol. The rate of delayed cord clamping preprotocol was 0%. Protocol uptake and frequency of delayed cord clamping increased over the 2 years after its introduction. In the postprotocol period, cesarean delivery was the only factor independently associated with failing to receive delayed cord clamping (adjusted odds ratio [OR] 0.49, 95% confidence interval [CI] 0.25-0.96). In comparison with the preprotocol period, those who received delayed cord clamping in the postprotocol period had significantly higher birth hematocrit (β=2.46, P=.007) and fewer blood transfusions in the first week of life (adjusted OR 0.49, 95% CI 0.25-0.96). After introduction of an institutional delayed cord clamping protocol followed by continued health care provider education and quality feedback, the frequency of delayed cord clamping progressively increased. Compared with historical controls, performing delayed cord clamping in eligible preterm neonates was associated with improved neonatal hematologic indices, demonstrating the effectiveness of delayed cord clamping in a large-volume maternity unit.

Construction of a novel peptide nucleic acid piezoelectric gene sensor microarray detection system.

PubMed

Chen, Ming; Liu, Minghua; Yu, Lili; Cai, Guoru; Chen, Qinghai; Wu, Rong; Wang, Feng; Zhang, Bo; Jiang, Tianlun; Fu, Welling

2005-08-01

A novel 2 x 5 clamped style piezoelectric gene sensor microarray has been successfully constructed. Every crystal unit of the fabricated gene sensor can oscillate independently without interfering with each other. The bis-peptide nucleic acid (bis-PNA) probe, which can combine with target DNA or RNA sequences more effectively and specifically than a DNA probe, was designed and immobilized on the surface of the gene sensor microarray to substitute the conventional DNA probe for direct detection of the hepatitis B virus (HBV) genomic DNA. Detection conditions were then explored and optimized. Results showed that PBS buffer of pH 6.8, an ion concentration of 20 mmol/liter, and a probe concentration of 1.5 micromol/liter were optimal for the detection system. Under such optimized experimental conditions, the specificity of bis-PNA was proved much higher than that of DNA probe. The relationship between quantity of target and decrease of frequency showed a typical saturation curve when concentrations of target HBV DNA varied from 10 pg/liter to 100 microg/liter, and 10 microg/liter was the watershed, with a statistic linear regression equation of I gC = -2.7455 + 0.0691 deltaF and the correlating coefficient of 0.9923. Fortunately, this is exactly the most ordinary variant range of the HBV virus concentration in clinical hepatitis samples. So, a good technical platform is successfully constructed and it will be applied to detect HBV quantitatively in clinical samples.

Single-molecule visualization of Saccharomyces cerevisiae leading-strand synthesis reveals dynamic interaction between MTC and the replisome

PubMed Central

Lewis, Jacob S.; Spenkelink, Lisanne M.; Schauer, Grant D.; Hill, Flynn R.; Georgescu, Roxanna E.; O’Donnell, Michael E.; van Oijen, Antoine M.

2017-01-01

The replisome, the multiprotein system responsible for genome duplication, is a highly dynamic complex displaying a large number of different enzyme activities. Recently, the Saccharomyces cerevisiae minimal replication reaction has been successfully reconstituted in vitro. This provided an opportunity to uncover the enzymatic activities of many of the components in a eukaryotic system. Their dynamic behavior and interactions in the context of the replisome, however, remain unclear. We use a tethered-bead assay to provide real-time visualization of leading-strand synthesis by the S. cerevisiae replisome at the single-molecule level. The minimal reconstituted leading-strand replisome requires 24 proteins, forming the CMG helicase, the Pol ε DNA polymerase, the RFC clamp loader, the PCNA sliding clamp, and the RPA single-stranded DNA binding protein. We observe rates and product lengths similar to those obtained from ensemble biochemical experiments. At the single-molecule level, we probe the behavior of two components of the replication progression complex and characterize their interaction with active leading-strand replisomes. The Minichromosome maintenance protein 10 (Mcm10), an important player in CMG activation, increases the number of productive replication events in our assay. Furthermore, we show that the fork protection complex Mrc1–Tof1–Csm3 (MTC) enhances the rate of the leading-strand replisome threefold. The introduction of periods of fast replication by MTC leads to an average rate enhancement of a factor of 2, similar to observations in cellular studies. We observe that the MTC complex acts in a dynamic fashion with the moving replisome, leading to alternating phases of slow and fast replication. PMID:28923950

The formulation and immunisation of oral poly(DL-lactide-co-glycolide) microcapsules containing a plasmid vaccine against lymphocystis disease virus in Japanese flounder (Paralichthys olivaceus).

PubMed

Tian, Jiyuan; Sun, Xiuqin; Chen, Xiguang; Yu, Juan; Qu, Lingyun; Wang, Lingchong

2008-06-01

Nucleic acid-based immunotherapy is a new treatment option for fish immunisation in intensive culture. However, DNA-based vaccines would be hydrolyzed or denaturized because of the existence of nucleases and severe gastrointestinal conditions. Poly(DL-lactide-co-glycolide) (PLGA) microcapsules, loaded with plasmid DNA (pDNA) against lymphocystis disease virus (LCDV), were prepared by modified water in oil in water (W/O/W) double emulsion method in our laboratory. Encapsulation efficiency, loading percent and diameter of microcapsules were 78-88%, 0.5-0.7% and less than 10 mum, respectively. In simulated gastric fluid (SGF), less than 10% of pDNA was released from microcapsules in 12 h, and about 6.5% of pDNA was released in 12 h in simulated intestinal fluid (SIF). The content of the supercoiled of pDNA in microcapsules and control was 80% and 89% respectively, which indicated that a little supercoiled pDNA degradation occurred during encapsulation. RT-PCR showed that lots of RNA containing information of MCP gene existed in all tissues of fish vaccinated with microcapsules 10-90 days after oral administration. SDS-PAGE and immunoblots, as well as immunofluorescence images, displayed that major capsid protein (MCP) of LCDV was expressed in tissues of fish vaccinated with pDNA-loaded microcapsules. In addition, indirect enzyme-linked immunosorbent assay (ELISA) showed that the immune responses of sera were positive (O.D> or =0.3) from week 1 to week 24 for fish vaccinated with microcapsules, in comparison with fish vaccinated with naked pDNA. Our results suggested that PLGA microcapsules were promising oral carriers for pDNA delivery. This encapsulation technique had potential for drug delivery applications due to its ease of operation and notable immunisation efficacy.

Loading capacity and interaction of DNA binding on catanionic vesicles with different cationic surfactants.

PubMed

Xu, Lu; Chen, Jingfei; Feng, Lei; Dong, Shuli; Hao, Jingcheng

2014-12-07

Cationic and anionic (catanionic) vesicles were constructed from the mixtures of sodium laurate (SL) and alkyltrimethylammonium bromide (CnTAB, n = 12, 14, and 16) and were used to control the loading capacity of DNA. The binding saturation point (BSP) of DNA to catanionic vesicles increases with the chain length of cationic surfactants, which is at 1.0, 1.3 and 1.5 for CnTAB with n = 12, 14, and 16, respectively. Our measurements showed that the loading capacity and affinity of DNA can be controlled by catanionic vesicles. It increases with the chain length of cationic surfactants. Because of a large reduction in surface charge density, catanionic vesicles are prone to undergo re-aggregation or fusion with the addition of DNA. DNA molecules can still maintain original coil state during the interaction with catanionic CnTAL vesicles. (1)H NMR data reveals that the obvious dissociation of anionic ions, L(-), from catanionic C14TAL vesicles is due to the interaction with DNA; however, this phenomenon cannot be observed in C12TAB-SL vesicles. Agarose gel electrophoresis (AGE) results demonstrate that the electrostatic interaction between the two oppositely charged cationic and anionic surfactants is stronger than that between DNA and cationic surfactant, CnTAB (n = 12, 14, and 16). Not only is the dissociation of L(-) simply determined by the charge competition, but it also depends largely on the variations in the surface charge density as well as the cationic and anionic surfactant competing ability in geometry configuration of catanionic vesicles. The complicated interaction between DNA and catanionic vesicles induces the deformation of cationic vesicles. Our results should provide clear guidance for choosing more proper vectors for DNA delivery and gene therapy in cell experiments.

A composite thin vacuum window for the CLAS photon tagger at Jefferson lab

NASA Astrophysics Data System (ADS)

Matthews, S. K.; Crannell, Hall; O'Brien, J. T.; Sober, D. I.

1999-01-01

The construction of a thin vacuum window, currently in use on the CLAS photon tagging system at the Thomas Jefferson National Accelerator Facility, is described. A layer of woven Kevlar cloth supports a much thinner membrane of aluminized Mylar. Notable features of this particular window include its overall length (9.6 m), and the fact that the entire load is supported by the epoxy seal with no mechanical clamping around the edges. Results from a diverse program of materials testing, including a clear dependence of leak rate on relative humidity, are also reported.

Polymer Piezoelectric Energy Harvesters for Low Wind Speed

DOE PAGES

Li, Dong Jun; Hong, Seungbum; Gu, Shiyuan; ...

2014-01-06

We fabricated polymer piezoelectric energy harvesters (PEHs) that can generate electric power at wind speed of less than 4.7 m/s due to their high sensitivity to wind. In order to optimize their operating conditions, we evaluated three distinct PEH operation modes under the boundary conditions of single-side clamping. We found that a PEH connected to an external load of 120 kΩ shows the largest output power of 0.98 μW at 3.9m/s, with wind incident on its side (mode I). We attribute this result to large bending and torsion involved in this operation mode.

A clamped rectangular plate containing a crack

NASA Technical Reports Server (NTRS)

Tang, R.; Erdogan, F.

1985-01-01

The general problem of a rectangular plate clamped along two parallel sides and containing a crack parallel to the clamps is considered. The problem is formulated in terms of a system of singular integral equations and the asymptotic behavior of the stress state near the corners is investigated. Numerical examples are considered for a clamped plate without a crack and with a centrally located crack, and the stress intensity factors and the stresses along the clamps are calculated.

Force-Measuring Clamp

NASA Technical Reports Server (NTRS)

Nunnelee, Mark (Inventor)

2004-01-01

A precision clamp that accurately measures force over a wide range of conditions is described. Using a full bridge or other strain gage configuration. the elastic deformation of the clamp is measured or detected by the strain gages. Thc strain gages transmit a signal that corresponds to the degree of stress upon the clamp. Thc strain gage signal is converted to a numeric display. Calibration is achieved by ero and span potentiometers which enable accurate measurements by the force-measuring clamp.

Current and past Epstein-Barr virus infection in risk of initial CNS demyelination.

PubMed

Lucas, R M; Ponsonby, A-L; Dear, K; Valery, P; Pender, M P; Burrows, J M; Burrows, S R; Chapman, C; Coulthard, A; Dwyer, D E; Dwyer, T; Kilpatrick, T; Lay, M-L J; McMichael, A J; Taylor, B V; van der Mei, I A F; Williams, D

2011-07-26

To assess risk of a first clinical diagnosis of CNS demyelination (FCD) in relation to measures of Epstein-Barr virus (EBV) infection within the context of other known risk factors. This was a multicenter incident case-control study. FCD cases (n = 282) aged 18-59 years and controls (n = 558, matched on age, sex, and region) were recruited from 4 Australian centers between November 1, 2003, and December 31, 2006. A nested study (n = 215 cases, n = 216 controls) included measurement of whole blood quantitative EBV DNA load and serum EBV-specific antibodies. Conditional logistic regression was used to analyze case-control differences. There were no significant case-control differences in the proportion with detectable EBV DNA (55.8% vs 50.5%, respectively, p = 0.28), or in quantitative EBV DNA load (p = 0.33). Consistent with previous work, higher anti-EBV-specific immunoglobulin G (IgG) titers and a history of infectious mononucleosis were associated with increased FCD risk and there was an additive interaction with HLA-DRB1*1501 status. We found additional interactions between high anti-EBNA IgG titer and SNPs in HLA-A (adjusted odds ratios [AOR] = 19.84 [95% confidence interval (CI) 5.95 to 66.21] for both factors compared to neither) and CTLA-4 genes (AOR = 0.31 [95% CI 0.13 to 0.76] for neither factor compared to both). EBV DNA load was lower at higher serum 25-hydroxyvitamin D concentrations in controls (r = -0.17, p = 0.01). An adverse effect of higher EBV DNA load on FCD risk was increased with higher 25-hydroxyvitamin D concentration (p[interaction] = 0.02). Past infection with EBV, but not current EBV DNA load in whole blood, is significantly associated with increased FCD risk. These associations appear to be modified by immune-related gene variants.

Towards development of novel immunization strategies against leishmaniasis using PLGA nanoparticles loaded with kinetoplastid membrane protein-11.

PubMed

Santos, Diego M; Carneiro, Marcia W; de Moura, Tatiana R; Fukutani, Kiyoshi; Clarencio, Jorge; Soto, Manuel; Espuelas, Socorro; Brodskyn, Claudia; Barral, Aldina; Barral-Netto, Manoel; de Oliveira, Camila I

2012-01-01

Vaccine development has been a priority in the fight against leishmaniases, which are vector-borne diseases caused by Leishmania protozoa. Among the different immunization strategies employed to date is inoculation of plasmid DNA coding for parasite antigens, which has a demonstrated ability to induce humoral and cellular immune responses. In this sense, inoculation of plasmid DNA encoding Leishmania kinetoplasmid membrane protein-11 (KMP-11) was able to confer protection against visceral leishmaniasis. However, recently the use of antigen delivery systems such as poly(lactic-co-glycolic acid) (PLGA) nanoparticles has also proven effective for eliciting protective immune responses. In the present work, we tested two immunization strategies with the goal of obtaining protection, in terms of lesion development and parasite load, against cutaneous leishmaniasis caused by L. braziliensis. One strategy involved immunization with plasmid DNA encoding L. infantum chagasi KMP-11. Alternatively, mice were primed with PLGA nanoparticles loaded with the recombinant plasmid DNA and boosted using PLGA nanoparticles loaded with recombinant KMP-11. Both immunization strategies elicited detectable cellular immune responses with the presence of both proinflammatory and anti-inflammatory cytokines; mice receiving the recombinant PLGA nanoparticle formulations also demonstrated anti-KMP-11 IgG1 and IgG2a. Mice were then challenged with L. braziliensis, in the presence of sand fly saliva. Lesion development was not inhibited following either immunization strategy. However, immunization with PLGA nanoparticles resulted in a more prominent reduction in parasite load at the infection site when compared with immunization using plasmid DNA alone. This effect was associated with a local increase in interferon-gamma and in tumor necrosis factor-alpha. Both immunization strategies also resulted in a lower parasite load in the draining lymph nodes, albeit not significantly. Our results encourage the pursuit of immunization strategies employing nanobased delivery systems for vaccine development against cutaneous leishmaniasis caused by L. braziliensis infection.

Delayed clamping of the umbilical cord after delivery and implications for public cord blood banking.

PubMed

Allan, David S; Scrivens, Nicholas; Lawless, Tiffany; Mostert, Karen; Oppenheimer, Lawrence; Walker, Mark; Petraszko, Tanya; Elmoazzen, Heidi

2016-03-01

Public banking of umbilical cord blood units (CBUs) containing higher numbers of cells ensures timely engraftment after transplantation for increasing numbers of patients. Delayed clamping of the umbilical cord after birth may benefit some infants by preventing iron deficiency. Implications of delayed cord clamping for public cord blood banking remains unclear. CBUs collected by Canadian Blood Services at one collection site between November 1, 2014, and March 17, 2015, were analyzed. The delay in cord clamping after birth was timed and classified as "no delay," 20 to 60 seconds, more than 60 seconds, or more than 120 seconds. Of 367 collections, 100 reported no delay in clamping while clamping was delayed by 20 to 60 seconds (n = 69), more than 60 seconds (n = 98), or more than 120 seconds (n = 100) in the remaining cases. The mean volume and total nucleated cells (TNCs) in units with no delay in clamping were significantly greater than mean volumes for all categories of delayed clamping (Tukey's test, p < 0.05 for each comparison). The proportion of units with more than 1.5 × 10(9) TNCs was significantly reduced when clamping was delayed (p = 5.5 × 10(-8) ). The difference was most marked for cords that were clamped more than 120 seconds after delivery (6.2% compared with 39%). Delayed cord clamping greatly diminishes the volume and TNC count of units collected for a public cord blood bank. Creating an inventory of CBUs with high TNC content may take more time than expected. © 2015 AABB.

Serial monitoring of Mucorales DNA load in serum samples of a patient with disseminated mucormycosis after allogeneic bone marrow transplantation.

PubMed

Shigemura, Tomonari; Nakazawa, Yozo; Matsuda, Kazuyuki; Sano, Kenji; Yaguchi, Takashi; Motobayashi, Mitsuo; Saito, Shoji; Noda, Shunsuke; Kobayashi, Norimoto; Agematsu, Kazunaga; Honda, Takayuki; Koike, Kenichi

2014-08-01

Mucormycosis is a fatal complication in immunocompromised patients, and is additionally difficult to diagnose due to the lack of useful serum biomarkers. Using a quantitative PCR approach, we retrospectively analyzed Mucorales DNA load in sera collected serially from a 3-year-old patient with chronic granulomatous disease, who died of multi-organ failure probably due to dissemination of Rhizomucor pusillus, which was detected from necropsy specimens. Mucorales DNA load was below the detection limit on days 9, 2, and 4 after unrelated bone marrow transplantation. Rhizomucor DNA was first detected on day 14 (1.6 × 10(3) copies/mL), and subsequently fluctuated between 1.3 × 10(3) and 37.2 × 10(3) copies/mL until day 43. Rhizomucor achieved a peak value of 940.0 × 10(3) copies/mL on day 48 the day before death. The detection or fluctuation of Rhizomucor DNA appeared to be associated with corticosteroid dosages or C-reactive protein levels. This specific, noninvasive, and highly quantitative assay may be useful for the early diagnosis of mucormycosis and prediction of disease progression.

Theory of equilibria of elastic 2-braids with interstrand interaction

NASA Astrophysics Data System (ADS)

Starostin, E. L.; van der Heijden, G. H. M.

2014-03-01

Motivated by continuum models for DNA supercoiling we formulate a theory for equilibria of 2-braids, i.e., structures formed by two elastic rods winding around each other in continuous contact and subject to a local interstrand interaction. No assumption is made on the shape of the contact curve. The theory is developed in terms of a moving frame of directors attached to one of the strands. The other strand is tracked by including in this frame the normalised closest-approach chord connecting the two strands. The kinematic constant-distance constraint is formulated at strain level through the introduction of what we call braid strains. As a result the total potential energy involves arclength derivatives of these strains, thus giving rise to a second-order variational problem. The Euler-Lagrange equations for this problem give balance equations for the overall braid force and moment referred to the moving frame as well as differential equations that can be interpreted as effective constitutive relations encoding the effect that the second strand has on the first as the braid deforms under the action of end loads. Hard contact models are used to obtain the normal contact pressure between strands that has to be non-negative for a physically realisable solution without the need for external devices such as clamps or glue to keep the strands together. The theory is first illustrated by a number of problems that can be solved analytically and then applied to several new problems that have not hitherto been treated.

The bacteriorhodopsin model membrane system as a prototype molecular computing element.

PubMed

Hong, F T

1986-01-01

The quest for more sophisticated integrated circuits to overcome the limitation of currently available silicon integrated circuits has led to the proposal of using biological molecules as computational elements by computer scientists and engineers. While the theoretical aspect of this possibility has been pursued by computer scientists, the research and development of experimental prototypes have not been pursued with an equal intensity. In this survey, we make an attempt to examine model membrane systems that incorporate the protein pigment bacteriorhodopsin which is found in Halobacterium halobium. This system was chosen for several reasons. The pigment/membrane system is sufficiently simple and stable for rigorous quantitative study, yet at the same time sufficiently complex in molecular structure to permit alteration of this structure in an attempt to manipulate the photosignal. Several methods of forming the pigment/membrane assembly are described and the potential application to biochip design is discussed. Experimental data using these membranes and measured by a tunable voltage clamp method are presented along with a theoretical analysis based on the Gouy-Chapman diffuse double layer theory to illustrate the usefulness of this approach. It is shown that detailed layouts of the pigment/membrane assembly as well as external loading conditions can modify the time course of the photosignal in a predictable manner. Some problems that may arise in the actual implementation and manufacturing, as well as the use of existing technology in protein chemistry, immunology, and recombinant DNA technology are discussed.

30 CFR 75.605 - Clamping of trailing cables to equipment.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Clamping of trailing cables to equipment. 75... MINE SAFETY AND HEALTH MANDATORY SAFETY STANDARDS-UNDERGROUND COAL MINES Trailing Cables § 75.605 Clamping of trailing cables to equipment. [Statutory Provisions] Trailing cables shall be clamped to...

Rapid DNA replication origin licensing protects stem cell pluripotency

PubMed Central

Matson, Jacob Peter; Dumitru, Raluca; Coryell, Philip; Baxley, Ryan M; Chen, Weili; Twaroski, Kirk; Webber, Beau R; Tolar, Jakub; Bielinsky, Anja-Katrin; Purvis, Jeremy E

2017-01-01

Complete and robust human genome duplication requires loading minichromosome maintenance (MCM) helicase complexes at many DNA replication origins, an essential process termed origin licensing. Licensing is restricted to G1 phase of the cell cycle, but G1 length varies widely among cell types. Using quantitative single-cell analyses, we found that pluripotent stem cells with naturally short G1 phases load MCM much faster than their isogenic differentiated counterparts with long G1 phases. During the earliest stages of differentiation toward all lineages, MCM loading slows concurrently with G1 lengthening, revealing developmental control of MCM loading. In contrast, ectopic Cyclin E overproduction uncouples short G1 from fast MCM loading. Rapid licensing in stem cells is caused by accumulation of the MCM loading protein, Cdt1. Prematurely slowing MCM loading in pluripotent cells not only lengthens G1 but also accelerates differentiation. Thus, rapid origin licensing is an intrinsic characteristic of stem cells that contributes to pluripotency maintenance. PMID:29148972

Effect of potentially interfering substances on the measurement of HIV-1 viral load by the bDNA assay.

PubMed

Alonso, R; García de Viedma, D; Rodríguez-Creixems, M; Bouza, E

1999-03-01

As high heterogeneity of plasma composition may be responsible for interference with HIV-1 viral load determination by the bDNA assay, the potential interference caused by a number of plasma components was examined. Among the biochemical substances assayed, cholesterol, bilirubin, and triglycerides did not affect viral load quantification. Hemoglobin did not interfere with the assay at concentrations lower than or equal to 14 g/dl. Above this concentration, measurements decreased by up to 0.78 log, but these hemoglobin levels do not usually occur in the clinical setting. None of the antiretroviral drugs assayed (AZT, dDC, d4T, 3TC and Indinavir) interfered with the measurement. HIV bDNA is a robust assay even in those frequent circumstances in which plasma composition differs notably from normal.

Effects of microbial DNA on human DNA profiles generated using the PowerPlex® 16 HS system.

PubMed

Dembinski, Gina M; Picard, Christine J

2017-11-01

Most crime scenes are not sterile and therefore may be contaminated with environmental DNA, especially if a decomposing body is found. Collecting biological evidence from this individual will yield DNA samples mixed with microbial DNA. This also becomes important if postmortem swabs are collected from sexually assaulted victims. Although genotyping kits undergo validation tests, including bacterial screens, they do not account for the diverse microbial load during decomposition. We investigated the effect of spiking human DNA samples with known concentrations of DNA from 17 microbe species associated with decomposition on DNA profiles produced using the Promega PowerPlex ® HS system. Two species, Bacillus subtilis and Mycobacterium smegmatis, produced an extraneous allele at the TPOX locus. When repeated with the PowerPlex ® Fusion kit, the extra allele no longer amplified with these two species. This experiment demonstrates that caution should be exhibited if microbial load is high and the PowerPlex ® 16HS system is used. Copyright © 2017 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Fully localized post-buckling states of cylindrical shells under axial compression

NASA Astrophysics Data System (ADS)

Kreilos, Tobias; Schneider, Tobias M.

2017-09-01

We compute nonlinear force equilibrium solutions for a clamped thin cylindrical shell under axial compression. The equilibrium solutions are dynamically unstable and located on the stability boundary of the unbuckled state. A fully localized single dimple deformation is identified as the edge state-the attractor for the dynamics restricted to the stability boundary. Under variation of the axial load, the single dimple undergoes homoclinic snaking in the azimuthal direction, creating states with multiple dimples arranged around the central circumference. Once the circumference is completely filled with a ring of dimples, snaking in the axial direction leads to further growth of the dimple pattern. These fully nonlinear solutions embedded in the stability boundary of the unbuckled state constitute critical shape deformations. The solutions may thus be a step towards explaining when the buckling and subsequent collapse of an axially loaded cylinder shell is triggered.

A universal procedure for evaluation and application of surge-protective devices

NASA Technical Reports Server (NTRS)

1980-01-01

The source, nature, and frequency of occurrence of transients must be identified and a representative standard test wave chosen for proof testing. The performance of candidate suppressor devices then can be evaluated against the withstand goals set for the equipment. The various suppressors divide into two classes of generic behavior. The key to a universal procedure for evaluating both classes lies in representing transients as quasi-current sources of defined current impulse duration. The available surge current is established by the Thevenin equivalent transient voltage and source impedance. A load line drawn on the V-I characteristic graph of the suppressor quickly determines the clamping voltage and peak current. These values then can be compared to the requirement. The deposited energy and average power dissipation for multiple transients also can be calculated. The method is illustrated with a design example for motor vehicle alternator load dump suppression.

Wnt-Mediated Repression via Bipartite DNA Recognition by TCF in the Drosophila Hematopoietic System

PubMed Central

Zhang, Chen U.; Blauwkamp, Timothy A.; Burby, Peter E.; Cadigan, Ken M.

2014-01-01

The Wnt/β-catenin signaling pathway plays many important roles in animal development, tissue homeostasis and human disease. Transcription factors of the TCF family mediate many Wnt transcriptional responses, promoting signal-dependent activation or repression of target gene expression. The mechanism of this specificity is poorly understood. Previously, we demonstrated that for activated targets in Drosophila, TCF/Pangolin (the fly TCF) recognizes regulatory DNA through two DNA binding domains, with the High Mobility Group (HMG) domain binding HMG sites and the adjacent C-clamp domain binding Helper sites. Here, we report that TCF/Pangolin utilizes a similar bipartite mechanism to recognize and regulate several Wnt-repressed targets, but through HMG and Helper sites whose sequences are distinct from those found in activated targets. The type of HMG and Helper sites is sufficient to direct activation or repression of Wnt regulated cis-regulatory modules, and protease digestion studies suggest that TCF/Pangolin adopts distinct conformations when bound to either HMG-Helper site pair. This repressive mechanism occurs in the fly lymph gland, the larval hematopoietic organ, where Wnt/β-catenin signaling controls prohemocytic differentiation. Our study provides a paradigm for direct repression of target gene expression by Wnt/β-catenin signaling and allosteric regulation of a transcription factor by DNA. PMID:25144371

Mechanical support of a ceramic gas turbine vane ring

DOEpatents

Shi, Jun; Green, Kevin E.; Mosher, Daniel A.; Holowczak, John E.; Reinhardt, Gregory E.

2010-07-27

An assembly for mounting a ceramic turbine vane ring onto a turbine support casing comprises a first metal clamping ring and a second metal clamping ring. The first metal clamping ring is configured to engage with a first side of a tab member of the ceramic turbine vane ring. The second metal clamping ring is configured to engage with a second side of the tab member such that the tab member is disposed between the first and second metal clamping rings.

Active energy recovery clamping circuit to improve the performance of power converters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Whitaker, Bret; Barkley, Adam

2017-05-09

A regenerative clamping circuit for a power converter using clamping diodes to transfer charge to a clamping capacitor and a regenerative converter to transfer charge out of the clamping capacitor back to the power supply input connection. The regenerative converter uses a switch connected to the midpoint of a series connected inductor and capacitor. The ends of the inductor and capacitor series are connected across the terminals of the power supply to be in parallel with the power supply.

Payload Launch Lock Mechanism

NASA Technical Reports Server (NTRS)

Young, Ken (Inventor); Hindle, Timothy (Inventor)

2014-01-01

A payload launch lock mechanism includes a base, a preload clamp, a fastener, and a shape memory alloy (SMA) actuator. The preload clamp is configured to releasibly restrain a payload. The fastener extends, along an axis, through the preload clamp and into the base, and supplies a force to the preload clamp sufficient to restrain the payload. The SMA actuator is disposed between the base and the clamp. The SMA actuator is adapted to receive electrical current and is configured, upon receipt of the electrical current, to supply a force that causes the fastener to elongate without fracturing. The preload clamp, in response to the fastener elongation, either rotates or pivots to thereby release the payload.

Distribution and load of elephant endotheliotropic herpesviruses in tissues from associated fatalities of Asian elephants.

PubMed

Seilern-Moy, Katharina; Darpel, Karin; Steinbach, Falko; Dastjerdi, Akbar

2016-07-15

Elephant Endotheliotropic Herpesviruses (EEHVs) are the cause of a highly fatal haemorrhagic disease in elephants primarily affecting young Asian elephants (Elephas maximus) in both captivity and in the wild. The viruses have emerged as a significant threat to Asian elephant conservation, critically affecting overall sustainability of their population. So far insight into the pathogenesis of EEHV infections has been restricted to examination of EEHV-infected tissues. However, little is known about distribution and burden of the viruses within the organs of fatal cases, crucial elements in the understanding of the virus pathogenesis. This study was therefore undertaken to assess the extent of organ and cell involvement in fatal cases of EEHV-1A, 1B and 5 using a quantitative real-time PCR. EEHV-1 and 5 DNA were detectable in all the tissues examined, albeit with substantial differences in the viral DNA load. The highest EEHV-1A DNA load was observed in the liver, followed by the heart, thymus and tongue. EEHV-1B and 5 showed the highest DNA load in the heart, followed by tongue and liver. This study provides new insights into EEHV pathogenicity and has implications in choice of sample type for disease investigation and virus isolation. Crown Copyright © 2016. Published by Elsevier B.V. All rights reserved.

Relationship between locking-bolt torque and load pre-tension in the Ilizarov frame.

PubMed

Osei, N A; Bradley, B M; Culpan, P; Mitchell, J B; Barry, M; Tanner, K E

2006-10-01

The wire-bolt interface in an Ilizarov frame has been mechanically tested. The optimal torque to be applied to the frame locking-bolts during physiological loading has been defined. The set-up configuration was as is used clinically except a copper tube was used to simulate bone. The force-displacement curves of the Ilizarov wires are not altered by locking-bolt torque. The force in the bone model at which pre-tension is lost increases as the locking-bolts are tightened to 14 Nm torque, but decreases if torque exceeds 14 Nm. Thus, 14 Nm is the optimal locking-bolt torque in frame. The relationship between pre-tension versus load for different locking-bolt torques arises because at low and high clamping torques poor wire holding and plastic deformation respectively occur. Wire damage was seen under light and electron microscopy. Clinically, over or under-tightening locking-bolts will cause loss of pre-tension, reduction in frame stiffness and excessive movement at the fracture site, which may be associated with delayed union.

Biomechanical evaluation of various suture configurations in side-to-side tenorrhaphy.

PubMed

Wagner, Emilio; Ortiz, Cristian; Wagner, Pablo; Guzman, Rodrigo; Ahumada, Ximena; Maffulli, Nicola

2014-02-05

Side-to-side tenorrhaphy is increasingly used, but its mechanical performance has not been studied. Two porcine flexor digitorum tendon segments of equal length (8 cm) and thickness (1 cm) were placed side by side. Eight tenorrhaphies (involving sixteen tendons) were performed with each of four suture techniques (running locked, simple eight, vertical mattress, and pulley suture). The resulting constructs underwent cyclic loading on a tensile testing machine, followed by monotonically increasing tensile load if failure during cyclic loading did not occur. Clamps secured the tendons on each side of the repair, and specimens were mounted vertically. Cyclic loading varied between 15 N and 35 N, with a distension rate of 1 mm/sec. Cyclic loading strength was determined by applying a force of 70 N. The cause of failure and tendon distension during loading were recorded. All failures occurred in the monotonic loading phase and resulted from tendon stripping. No suture or knot failure was observed. The mean loads resisted by the configurations ranged from 138 to 398 N. The mean load to failure, maximum load resisted prior to 1 cm of distension, and load resisted at 1 cm of distension were significantly lower for the vertical mattress suture group than for any of the other three groups (p < 0.031). All four groups sustained loads well above the physiologic loads expected to occur in tendons in the foot and ankle (e.g., in tendon transfer for tibialis posterior tendon insufficiency). None of the four side-to-side configurations distended appreciably during the cyclic loading phase. The vertical mattress suture configuration appeared to be weaker than the other configurations. For surgeons who advocate immediate loading or motion of a side-to-side tendon repair, a pulley, running locked, or simple eight suture technique appears to provide a larger safety margin compared with a vertical mattress suture technique.

21 CFR 876.5160 - Urological clamp for males.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Urological clamp for males. 876.5160 Section 876...) MEDICAL DEVICES GASTROENTEROLOGY-UROLOGY DEVICES Therapeutic Devices § 876.5160 Urological clamp for males. (a) Identification. A urological clamp for males is a device used to close the urethra of a male to...

Experimental Modal Analysis of Rectangular and Circular Beams

ERIC Educational Resources Information Center

Emory, Benjamin H.; Zhu, Wei Dong

2006-01-01

Analytical and experimental methods are used to determine the natural frequencies and mode shapes of Aluminum 6061-T651 beams with rectangular and circular cross-sections. A unique test stand is developed to provide the rectangular beam with different boundary conditions including clamped-free, clamped-clamped, clamped-pinned, and pinned-pinned.…

How do type II topoisomerases use ATP hydrolysis to simplify DNA topology beyond equilibrium? Investigating the relaxation reaction of non-supercoiling type II topoisomerases

PubMed Central

Stuchinskaya, Tanya; Mitchenall, Lesley A.; Schoeffler, Allyn J.; Corbett, Kevin D.; Berger, James M.; Bates, Andrew D.; Maxwell, Anthony

2015-01-01

DNA topoisomerases control the topology of DNA (e.g. the level of supercoiling) in all cells. Type IIA topoisomerases are ATP-dependent enzymes that have been shown to simplify the topology of their DNA substrates to a level beyond that expected at equilibrium (i.e. more relaxed than the product of relaxation by ATP-independent enzymes, such as type I topoisomerases, or a lower than equilibrium level of catenation). The mechanism of this effect is currently unknown, although several models have been suggested. We have analysed the DNA relaxation reactions of type II topoisomerases to further explore this phenomenon. We find that all type IIA topoisomerases tested exhibit the effect to a similar degree and that it is not dependent on the C-terminal domains of the enzymes. As recently reported, the type IIB topoisomerase, topo VI (which is only distantly related to the type IIA enzymes), does not exhibit topology simplification. We find that topology simplification is not significantly dependent on circle size in the range ~2–9 kbp, and is not altered by reducing the free energy available from ATP hydrolysis by varying the ATP:ADP ratio. A direct test of one model (DNA tracking, i.e. sliding of a protein clamp along DNA to trap supercoils) suggests that this is unlikely to be the explanation for the effect. We conclude that geometric selection of DNA segments by the enzymes is likely to be a primary source of the effect but that it is possible that other factors contribute. We also speculate whether topology simplification might simply be an evolutionary relic, with no adaptive significance. PMID:19094994

How do type II topoisomerases use ATP hydrolysis to simplify DNA topology beyond equilibrium? Investigating the relaxation reaction of nonsupercoiling type II topoisomerases.

PubMed

Stuchinskaya, Tanya; Mitchenall, Lesley A; Schoeffler, Allyn J; Corbett, Kevin D; Berger, James M; Bates, Andrew D; Maxwell, Anthony

2009-02-06

DNA topoisomerases control the topology of DNA (e.g., the level of supercoiling) in all cells. Type IIA topoisomerases are ATP-dependent enzymes that have been shown to simplify the topology of their DNA substrates to a level beyond that expected at equilibrium (i.e., more relaxed than the product of relaxation by ATP-independent enzymes, such as type I topoisomerases, or a lower-than-equilibrium level of catenation). The mechanism of this effect is currently unknown, although several models have been suggested. We have analyzed the DNA relaxation reactions of type II topoisomerases to further explore this phenomenon. We find that all type IIA topoisomerases tested exhibit the effect to a similar degree and that it is not dependent on the supercoil-sensing C-terminal domains of the enzymes. As recently reported, the type IIB topoisomerase, topoisomerase VI (which is only distantly related to type IIA enzymes), does not exhibit topology simplification. We find that topology simplification is not significantly dependent on circle size in the range approximately 2-9 kbp and is not altered by reducing the free energy available from ATP hydrolysis by varying the ADP:ATP ratio. A direct test of one model (DNA tracking; i.e., sliding of a protein clamp along DNA to trap supercoils) suggests that this is unlikely to be the explanation for the effect. We conclude that geometric selection of DNA segments by the enzymes is likely to be a primary source of the effect, but that it is possible that other kinetic factors contribute. We also speculate whether topology simplification might simply be an evolutionary relic, with no adaptive significance.

Solutions for transients in arbitrarily branching cables: III. Voltage clamp problems.

PubMed

Major, G

1993-07-01

Branched cable voltage recording and voltage clamp analytical solutions derived in two previous papers are used to explore practical issues concerning voltage clamp. Single exponentials can be fitted reasonably well to the decay phase of clamped synaptic currents, although they contain many underlying components. The effective time constant depends on the fit interval. The smoothing effects on synaptic clamp currents of dendritic cables and series resistance are explored with a single cylinder + soma model, for inputs with different time courses. "Soma" and "cable" charging currents cannot be separated easily when the soma is much smaller than the dendrites. Subtractive soma capacitance compensation and series resistance compensation are discussed. In a hippocampal CA1 pyramidal neurone model, voltage control at most dendritic sites is extremely poor. Parameter dependencies are illustrated. The effects of series resistance compound those of dendritic cables and depend on the "effective capacitance" of the cell. Plausible combinations of parameters can cause order-of-magnitude distortions to clamp current waveform measures of simulated Schaeffer collateral inputs. These voltage clamp problems are unlikely to be solved by the use of switch clamp methods.

Real-Time linux dynamic clamp: a fast and flexible way to construct virtual ion channels in living cells.

PubMed

Dorval, A D; Christini, D J; White, J A

2001-10-01

We describe a system for real-time control of biological and other experiments. This device, based around the Real-Time Linux operating system, was tested specifically in the context of dynamic clamping, a demanding real-time task in which a computational system mimics the effects of nonlinear membrane conductances in living cells. The system is fast enough to represent dozens of nonlinear conductances in real time at clock rates well above 10 kHz. Conductances can be represented in deterministic form, or more accurately as discrete collections of stochastically gating ion channels. Tests were performed using a variety of complex models of nonlinear membrane mechanisms in excitable cells, including simulations of spatially extended excitable structures, and multiple interacting cells. Only in extreme cases does the computational load interfere with high-speed "hard" real-time processing (i.e., real-time processing that never falters). Freely available on the worldwide web, this experimental control system combines good performance. immense flexibility, low cost, and reasonable ease of use. It is easily adapted to any task involving real-time control, and excels in particular for applications requiring complex control algorithms that must operate at speeds over 1 kHz.

Cellular HIV-1 DNA Levels in Drug Sensitive Strains Are Equivalent to Those in Drug Resistant Strains in Newly-Diagnosed Patients in Europe

PubMed Central

Demetriou, Victoria L.; van de Vijver, David A. M. C.; Kousiappa, Ioanna; Balotta, Claudia; Clotet, Bonaventura; Grossman, Zehava; Jørgensen, Louise B.; Lepej, Snjezana Z.; Levy, Itzchak; Nielsen, Claus; Paraskevis, Dimitrios; Poljak, Mario; Roman, Francois; Ruiz, Lidia; Schmidt, Jean-Claude; Vandamme, Anne-Mieke; Van Laethem, Kristel; Vercauteren, Jurgen; Kostrikis, Leondios G.

2010-01-01

Background HIV-1 genotypic drug resistance is an important threat to the success of antiretroviral therapy and transmitted resistance has reached 9% prevalence in Europe. Studies have demonstrated that HIV-1 DNA load in peripheral blood mononuclear cells (PBMC) have a predictive value for disease progression, independently of CD4 counts and plasma viral load. Methodology/Principal Findings Molecular-beacon-based real-time PCR was used to measure HIV-1 second template switch (STS) DNA in PBMC in newly-diagnosed HIV-1 patients across Europe. These patients were representative for the HIV-1 epidemic in the participating countries and were carrying either drug-resistant or sensitive viral strains. The assay design was improved from a previous version to specifically detect M-group HIV-1 and human CCR5 alleles. The findings resulted in a median of 3.32 log10 HIV-1 copies/106 PBMC and demonstrated for the first time no correlation between cellular HIV-1 DNA load and transmitted drug-resistance. A weak association between cellular HIV-1 DNA levels with plasma viral RNA load and CD4+ T-cell counts was also reconfirmed. Co-receptor tropism for 91% of samples, whether or not they conferred resistance, was CCR5. A comparison of pol sequences derived from RNA and DNA, resulted in a high similarity between the two. Conclusions/Significance An improved molecular-beacon-based real-time PCR assay is reported for the measurement of HIV-1 DNA in PBMC and has investigated the association between cellular HIV-1 DNA levels and transmitted resistance to antiretroviral therapy in newly-diagnosed patients from across Europe. The findings show no correlation between these two parameters, suggesting that transmitted resistance does not impact disease progression in HIV-1 infected individuals. The CCR5 co-receptor tropism predominance implies that both resistant and non-resistant strains behave similarly in early infection. Furthermore, a correlation found between RNA- and DNA-derived sequences in the pol region suggests that genotypic drug-resistance testing could be carried out on either template. PMID:20544014

Application of active electrode compensation to perform continuous voltage-clamp recordings with sharp microelectrodes.

PubMed

Gómez-González, J F; Destexhe, A; Bal, T

2014-10-01

Electrophysiological recordings of single neurons in brain tissues are very common in neuroscience. Glass microelectrodes filled with an electrolyte are used to impale the cell membrane in order to record the membrane potential or to inject current. Their high resistance induces a high voltage drop when passing current and it is essential to correct the voltage measurements. In particular, for voltage clamping, the traditional alternatives are two-electrode voltage-clamp technique or discontinuous single electrode voltage-clamp (dSEVC). Nevertheless, it is generally difficult to impale two electrodes in a same neuron and the switching frequency is limited to low frequencies in the case of dSEVC. We present a novel fully computer-implemented alternative to perform continuous voltage-clamp recordings with a single sharp-electrode. To reach such voltage-clamp recordings, we combine an active electrode compensation algorithm (AEC) with a digital controller (AECVC). We applied two types of control-systems: a linear controller (proportional plus integrative controller) and a model-based controller (optimal control). We compared the performance of the two methods to dSEVC using a dynamic model cell and experiments in brain slices. The AECVC method provides an entirely digital method to perform continuous recording and smooth switching between voltage-clamp, current clamp or dynamic-clamp configurations without introducing artifacts.

A new balancing three level three dimensional space vector modulation strategy for three level neutral point clamped four leg inverter based shunt active power filter controlling by nonlinear back stepping controllers.

PubMed

Chebabhi, Ali; Fellah, Mohammed Karim; Kessal, Abdelhalim; Benkhoris, Mohamed F

2016-07-01

In this paper is proposed a new balancing three-level three dimensional space vector modulation (B3L-3DSVM) strategy which uses a redundant voltage vectors to realize precise control and high-performance for a three phase three-level four-leg neutral point clamped (NPC) inverter based Shunt Active Power Filter (SAPF) for eliminate the source currents harmonics, reduce the magnitude of neutral wire current (eliminate the zero-sequence current produced by single-phase nonlinear loads), and to compensate the reactive power in the three-phase four-wire electrical networks. This strategy is proposed in order to gate switching pulses generation, dc bus voltage capacitors balancing (conserve equal voltage of the two dc bus capacitors), and to switching frequency reduced and fixed of inverter switches in same times. A Nonlinear Back Stepping Controllers (NBSC) are used for regulated the dc bus voltage capacitors and the SAPF injected currents to robustness, stabilizing the system and to improve the response and to eliminate the overshoot and undershoot of traditional PI (Proportional-Integral). Conventional three-level three dimensional space vector modulation (C3L-3DSVM) and B3L-3DSVM are calculated and compared in terms of error between the two dc bus voltage capacitors, SAPF output voltages and THDv, THDi of source currents, magnitude of source neutral wire current, and the reactive power compensation under unbalanced single phase nonlinear loads. The success, robustness, and the effectiveness of the proposed control strategies are demonstrated through simulation using Sim Power Systems and S-Function of MATLAB/SIMULINK. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.

Optimal Surgical Therapy in a Porcine (Sus scrofa) Model of Extra-Thoracic Penetrating Trauma Resulting in Hemorrhagic Shock: ED Thoracotomy vs. Immediate Trans-Abdominal Vascular Control. A Porcine Model for Evaluating the Management of Non-Compressible Torso Hemorrhage

DTIC Science & Technology

2010-11-08

celiac aortic clamping (n=6), direct vascular control (n=6), and endovascular aortic occlusion n=6). This study presents a large animal model of class...including thoracic aortic clamping, supra- celiac aortic clamping, direct vascular control, and proximal endovascular balloon occlusion. Following vascular...subsequently underwent non-compressible hemorrhage with thoracic aortic clamping (n=6), supra- celiac aortic clamping (n=6), direct vascular control (n=6

Device for remote operation of electrical disconnect

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coleman, Jody Rustyn; Bobbitt, III, John Thomas

Provided is a device for remote operation of an electrical disconnect. The device can include a handle clamp configured to be secured to an extending member of the electrical disconnect. The device can further include a case clamp configured to be secured to a rigid portion of the electrical disconnect. The device can further include a cable having an exterior sheath coaxially surrounding an inner cable. The inner cable can be coaxially slidable with respect to the exterior sheath. The inner cable can extend through an opening of the case clamp and be secured to the handle clamp. The devicemore » can further include an actuator configured to coaxially slide the inner cable such that the handle clamp is actuated towards the case clamp.« less

[Investigation of RNA viral genome amplification by multiple displacement amplification technique].

PubMed

Pang, Zheng; Li, Jian-Dong; Li, Chuan; Liang, Mi-Fang; Li, De-Xin

2013-06-01

In order to facilitate the detection of newly emerging or rare viral infectious diseases, a negative-strand RNA virus-severe fever with thrombocytopenia syndrome bunyavirus, and a positive-strand RNA virus-dengue virus, were used to investigate RNA viral genome unspecific amplification by multiple displacement amplification technique from clinical samples. Series of 10-fold diluted purified viral RNA were utilized as analog samples with different pathogen loads, after a series of reactions were sequentially processed, single-strand cDNA, double-strand cDNA, double-strand cDNA treated with ligation without or with supplemental RNA were generated, then a Phi29 DNA polymerase depended isothermal amplification was employed, and finally the target gene copies were detected by real time PCR assays to evaluate the amplification efficiencies of various methods. The results showed that multiple displacement amplification effects of single-strand or double-strand cDNA templates were limited, while the fold increases of double-strand cDNA templates treated with ligation could be up to 6 X 10(3), even 2 X 10(5) when supplemental RNA existed, and better results were obtained when viral RNA loads were lower. A RNA viral genome amplification system using multiple displacement amplification technique was established in this study and effective amplification of RNA viral genome with low load was achieved, which could provide a tool to synthesize adequate viral genome for multiplex pathogens detection.

Error analysis and assessment of unsteady forces acting on a flapping wing micro air vehicle: free flight versus wind-tunnel experimental methods.

PubMed

Caetano, J V; Percin, M; van Oudheusden, B W; Remes, B; de Wagter, C; de Croon, G C H E; de Visser, C C

2015-08-20

An accurate knowledge of the unsteady aerodynamic forces acting on a bio-inspired, flapping-wing micro air vehicle (FWMAV) is crucial in the design development and optimization cycle. Two different types of experimental approaches are often used: determination of forces from position data obtained from external optical tracking during free flight, or direct measurements of forces by attaching the FWMAV to a force transducer in a wind-tunnel. This study compares the quality of the forces obtained from both methods as applied to a 17.4 gram FWMAV capable of controlled flight. A comprehensive analysis of various error sources is performed. The effects of different factors, e.g., measurement errors, error propagation, numerical differentiation, filtering frequency selection, and structural eigenmode interference, are assessed. For the forces obtained from free flight experiments it is shown that a data acquisition frequency below 200 Hz and an accuracy in the position measurements lower than ± 0.2 mm may considerably hinder determination of the unsteady forces. In general, the force component parallel to the fuselage determined by the two methods compares well for identical flight conditions; however, a significant difference was observed for the forces along the stroke plane of the wings. This was found to originate from the restrictions applied by the clamp to the dynamic oscillations observed in free flight and from the structural resonance of the clamped FWMAV structure, which generates loads that cannot be distinguished from the external forces. Furthermore, the clamping position was found to have a pronounced influence on the eigenmodes of the structure, and this effect should be taken into account for accurate force measurements.

Single aortic clamping in coronary artery bypass surgery reduces cerebral embolism and improves neurocognitive outcomes.

PubMed

Gasparovic, Hrvoje; Borojevic, Marko; Malojcic, Branko; Gasparovic, Kristina; Biocina, Bojan

2013-10-01

Aortic manipulation releases embolic material, thereby enhancing the probability of adverse neurologic outcomes following coronary artery bypass grafting (CABG). We prospectively evaluated 59 patients undergoing CABG. Patients in the single (SC, n = 37) and multiple clamp (MC, n = 22) groups were comparable in relation to age and operative risk (p > 0.05). Neurocognitive evaluation consisted of the Auditory Verbal Learning Test (AVLT), Color Trails Test A, the Grooved Pegboard test and the Mini-Mental State Examination. Data acquisition was performed preoperatively, early postoperatively and at the 4-month follow-up. Intraoperative transcranial Doppler (TCD) monitoring was used to quantify the embolic load in relation to different aortic clamping strategies. Preoperative neurocognitive results were similar between the groups (p > 0.05). The incidence of postoperative delirium was greater in the MC group but this failed to reach statistical significance (23% vs 8%, p = 0.14). SC patients had fewer embolization signals (270 ± 181 vs 465 ± 160, p < 0.0001). Early postoperative neurocognitive results were depressed in comparison to preoperative values in both groups (p < 0.05 for multiple comparisons). The magnitude of this cognitive depression was greater in the MC group (p < 0.05 for multiple comparisons). Preoperative levels of neurocognition were restored at follow-up in the SC group in all tests except the AVLT. A trend towards improvements in neurocognitive performances at follow-up was also observed in the MC group. Residual attention, motor skill and memory deficits were, however, documented with multiple tests. In conclusion, the embolic burden was significantly lower in the SC group. This TCD imaging outcome translated into fewer early cognition deficits and superior late restoration of function.

Direct and quantitative detection of HIV-1 RNA in human plasma with a branched DNA signal amplification assay.

PubMed

Urdea, M S; Wilber, J C; Yeghiazarian, T; Todd, J A; Kern, D G; Fong, S J; Besemer, D; Hoo, B; Sheridan, P J; Kokka, R

1993-11-01

To determine the relative effect of sample matrix on the quantitation of HIV RNA in plasma. Two HIV-positive specimens were diluted into five and 10 different HIV-negative plasma samples, respectively. Branched DNA signal amplification technology and reverse-transcriptase polymerase chain reaction were used to measure the viral load. In one sample the viral load by polymerase chain reaction ranged from undetectable to 1.9 x 10(5) copies/ml, and the branched DNA results ranged from 2.6 x 10(4) to 4.2 x 10(4) HIV RNA equivalent/ml. In the other sample the corresponding figures were 6.3 x 10(4) to 5.5 x 10(5) copies/ml and 5.7 x 10(4) to 7.5 x 10(4) HIV RNA equivalents/ml. In contrast to reverse-transcriptase polymerase chain reaction the branched DNA signal amplification assay does not require a separate extraction step or enzymatic amplification of the target. Therefore this measurement is less affected by the sample matrix and the signal generated is directly proportional to the viral load.

Comparative evaluation of three automated systems for DNA extraction in conjunction with three commercially available real-time PCR assays for quantitation of plasma Cytomegalovirus DNAemia in allogeneic stem cell transplant recipients.

PubMed

Bravo, Dayana; Clari, María Ángeles; Costa, Elisa; Muñoz-Cobo, Beatriz; Solano, Carlos; José Remigia, María; Navarro, David

2011-08-01

Limited data are available on the performance of different automated extraction platforms and commercially available quantitative real-time PCR (QRT-PCR) methods for the quantitation of cytomegalovirus (CMV) DNA in plasma. We compared the performance characteristics of the Abbott mSample preparation system DNA kit on the m24 SP instrument (Abbott), the High Pure viral nucleic acid kit on the COBAS AmpliPrep system (Roche), and the EZ1 Virus 2.0 kit on the BioRobot EZ1 extraction platform (Qiagen) coupled with the Abbott CMV PCR kit, the LightCycler CMV Quant kit (Roche), and the Q-CMV complete kit (Nanogen), for both plasma specimens from allogeneic stem cell transplant (Allo-SCT) recipients (n = 42) and the OptiQuant CMV DNA panel (AcroMetrix). The EZ1 system displayed the highest extraction efficiency over a wide range of CMV plasma DNA loads, followed by the m24 and the AmpliPrep methods. The Nanogen PCR assay yielded higher mean CMV plasma DNA values than the Abbott and the Roche PCR assays, regardless of the platform used for DNA extraction. Overall, the effects of the extraction method and the QRT-PCR used on CMV plasma DNA load measurements were less pronounced for specimens with high CMV DNA content (>10,000 copies/ml). The performance characteristics of the extraction methods and QRT-PCR assays evaluated herein for clinical samples were extensible at cell-based standards from AcroMetrix. In conclusion, different automated systems are not equally efficient for CMV DNA extraction from plasma specimens, and the plasma CMV DNA loads measured by commercially available QRT-PCRs can differ significantly. The above findings should be taken into consideration for the establishment of cutoff values for the initiation or cessation of preemptive antiviral therapies and for the interpretation of data from clinical studies in the Allo-SCT setting.

Comparative evaluation of hepatitis C virus RNA quantitation by branched DNA, NASBA, and monitor assays.

PubMed

Lunel, F; Cresta, P; Vitour, D; Payan, C; Dumont, B; Frangeul, L; Reboul, D; Brault, C; Piette, J C; Huraux, J M

1999-02-01

Several studies have shown a relationship between pretreatment hepatitis C virus (HCV) viral load and the response to interferon (IFN) therapy, creating a need for quantitative HCV-RNA assays. Here, we compared three commercial methods: nucleic acid sequence-based amplification NASBA (Organon), branched DNA 2.0 (bDNA) (Chiron), and Monitor (Roche), with reverse-transcription polymerase chain reaction (RT-PCR) as the reference. We assessed sensitivity and reproducibility on a well-characterized panel of sera (EUROHEP), a Chimp Rodney plasma pool, and samples from IFN-treated and -untreated patients with chronic hepatitis C caused by different HCV genotypes. The reproducibility of the NASBA and bDNA methods was slightly better than that of Monitor, especially for genotypes 2 and 4. NASBA had the highest sensitivity (99% vs. 94% and 88% with Monitor and bDNA, respectively), especially for the follow-up of patients on IFN. NASBA gave the highest HCV-RNA concentrations, which were approximately 10-fold more than with the bDNA assay and 100-fold more than with the Monitor kit. The linearity, tested on the chimp Rodney plasma pool, was better with bDNA for high viral load than with NASBA and Monitor, although for low concentration of HCV RNA, bDNA was negative. Pretreatment viral load was lower in patients who had a sustained virological response to IFN, although the bDNA method was not sensitive enough to quantify all pretreatment samples. This study indicates that gene amplification methods (NASBA or Monitor) have better sensitivity than bDNA assays for quantification of HCV RNA in patients with chronic HCV infection, although the bDNA and NASBA methods are more likely to quantify all genotypes. Prospective studies are needed to demonstrate the usefulness of quantitative assays for the follow-up of patients with chronic hepatitis C.

Recovery and separation of rare earth elements using columns loaded with DNA-filter hybrid.

PubMed

Takahashi, Yoshio; Kondo, Kazuhiro; Miyaji, Asami; Umeo, Miyuki; Honma, Tetsuo; Asaoka, Satoshi

2012-01-01

Given that the supply of several rare earth elements (REEs) is sometimes limited, recycling REEs used in various advanced materials, such as Nd magnets, is important for realizing efficient use of REE resources. In the present work, the feasibility of using DNA for REE recovery and separation was examined, along with the identification of the binding site of REEs in DNA. In particular, a DNA-cellulose filter paper hybrid was prepared so that DNA-based materials can be used for the separation of REEs using columns loaded with DNA. N,N'-Disuccinimidyl was used as a cross-linker reagent for the fixation of DNA onto a fibrous cellulose filter. The results showed that (i) the DNA-filter hybrid has a sufficiently high affinity to adsorb REEs; (ii) the adsorption capacity was 0.182 mg/g for Nd; and (iii) the affinity of REEs for DNA was stronger for REEs with larger atomic numbers. The difference of the affinity among REEs in the third result was compared with the adsorption patterns of REEs discussed in the literature. The comparison suggests that phosphate in the DNA-filter paper hybrid was responsible for REE adsorption onto the hybrid. The results were supported by the Nd, Dy, and Lu L(III)-edge EXAFS; the REE-P shell was identified for the second neighboring atom, showing the importance of the phosphate site as REE binding sites. The difference in the affinity among REEs suggest that group separation of REEs (such as La, Ce, (Pr and Nd), (Ho, Dy, and Er), (Tb and Gd), (Sm, Eu), Tm, Yb, and Lu) is possible, although complete isolation of each REE from a solution containing all REEs may be difficult. For practical applications, Nd and Fe(III) were successfully separated from a synthetic solution of Nd magnet waste using columns loaded with the DNA-filter hybrid.

Comparison of Standardized Cytomegalovirus (CMV) Viral Load Thresholds in Whole Blood and Plasma of Solid Organ and Hematopoietic Stem Cell Transplant Recipients with CMV Infection and Disease.

PubMed

Dioverti, M Veronica; Lahr, Brian D; Germer, Jeffrey J; Yao, Joseph D; Gartner, Michelle L; Razonable, Raymund R

2017-01-01

Quantification of cytomegalovirus (CMV) deoxyribonucleic acid (DNA) has important diagnostic, prognostic, and therapeutic implications in the management of transplant recipients. We aimed to assess a viral load in plasma and whole blood that distinguishes CMV disease from asymptomatic infection in a cohort of solid organ and hematopoietic stem cell transplantation. We prospectively measured and compared CMV viral load in paired plasma and whole blood samples collected from transplant recipients with CMV infection and disease. Cytomegalovirus viral loads were determined by a commercially available US Food and Drug Administration-approved quantitative assay (COBAS AmpliPrep/COBAS TaqMan CMV Test [CAP/CTM CMV]) calibrated to the first World Health Organization International Standard for CMV DNA quantification. Moderate agreement of CMV viral load was observed between plasma and whole blood, with 31% of samples having discordant findings, particularly among samples with low DNA levels. Among the subset of samples where both paired samples had quantifiable levels, we observed a systematic bias that reflected higher viral load in whole blood compared with plasma. Based on receiver operating curve analysis, an initial plasma CMV viral load threshold of 1700 IU/mL in solid organ transplant recipients (sensitivity 80%, specificity 74%) and 1350 IU/mL in allogeneic hematopoietic stem cell transplant recipients (sensitivity 87%, specificity 87%) distinguished CMV disease and asymptomatic infection. This study identifies standardized viral load thresholds that distinguish CMV disease from asymptomatic infection using CAP/CTM CMV assay. We propose these thresholds as potential triggers to be evaluated in prospective studies of preemptive therapy. Plasma was better than whole blood for measuring viral load using the CAP/CTM CMV assay.

Risk factors and long-term outcomes of pediatric liver transplant recipients with chronic high Epstein-Barr virus loads.

PubMed

Kamei, Hideya; Ito, Yoshinori; Kawada, Junichi; Ogiso, Satoshi; Onishi, Yasuharu; Komagome, Masahiko; Kurata, Nobuhiko; Ogura, Yasuhiro

2018-04-20

Serial monitoring of Epstein-Barr virus (EBV) reveals that certain pediatric liver transplant (LT) recipients exhibit high EBV loads for long periods. We investigated the incidence and risk factors of chronic high EBV (CHEBV) loads (continuous EBV DNA >10 000 IU/mL of whole blood for ≥6 months) and long-term outcomes. This single center, retrospective observational study investigated pediatric LT recipients who survived ≥6 months. We quantitated EBV DNA weekly during hospitalization and subsequently every 4 or 6 weeks at the outpatient clinic. Tacrolimus was maintained at a low trough level (<3 ng/mL, EBV DNA load >5000 IU/mL). Thirty-one of 77 LT recipients developed CHEBV. Univariate analysis revealed that age <2 years and body weight <10 kg upon LT, operation time <700 minutes, warm ischemia time (WIT) >35 minutes, graft-to-recipient weight ratio (GRWR) >2.7%, and preoperative EBV seronegativity were significantly associated with the development of CHEBV loads. Multivariate analysis identified significant associations of CHEBV with WIT >35 minutes, GRWR >2.7%, and preoperative seronegative. None of the recipients developed post-transplantation lymphoproliferative disorder. Survival rates of patients with and without CHEBV loads were not significantly different. A significant number of pediatric LT recipients developed CHEBV loads. Long WIT, high GRWR, and preoperative EBV seronegativity were significantly associated with the development of CHEBV loads. Although the long-term outcomes of patients with or without CHEBV loads were not significantly different, further studies of more subjects are warranted. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Incorporation of Active DNA/Cationic Polymer Polyplexes into Hydrogel Scaffolds

PubMed Central

Lei, Yuguo; Huang, Suxian; Sharif-Kashani, Pooria; Chen, Yong; Kavehpour, Pirouz; Segura, Tatiana

2010-01-01

The effective and sustained delivery of DNA and siRNAs locally would increase the applicability of gene therapy in tissue regeneration and cancer therapy. One promising approach is to use hydrogel scaffolds to encapsulate and deliver nucleotides in the form of nanoparticles to the disease sites. However, this approach is currently limited by the inability to load concentrated and active gene delivery nanoparticles into the hydrogels due to the severe nanoparticle aggregation during the loading process. Here, we present a process to load concentrated and un-aggregated non-viral gene delivery nanoparticles, using DNA/polyethylene imine (PEI) polyplexes as an example, into neutral polyethylene glycol (PEG), negatively charged hyaluronic acid (HA) and protein fibrin hydrogels crosslinked through various chemistries. The encapsulated polyplexes are highly active both in vitro and in vivo. We believe this process will significantly advance the applications of hydrogel scaffold mediated non-viral gene delivery in tissue regeneration and cancer therapy. PMID:20822811

Leaf extract of Wasabia japonica relieved oxidative stress induced by Helicobacter pylori infection and stress loading in Mongolian gerbils.

PubMed

Sekiguchi, Hirotaka; Takabayashi, Fumiyo; Deguchi, Yuya; Masuda, Hideki; Toyoizumi, Tomoyasu; Masuda, Shuichi; Kinae, Naohide

2010-01-01

Infection with Helicobacter pylori (H. pylori) can induce gastric disorders, and though its presence cannot explain disease pathogenesis and does not have associations with other factors, it is well known that H. pylori infection causes stomach inflammation following oxidative stress. We examined the suppressive effects of a leaf extract of Wasabia japonica on H. pylori infection and on stress loading in Mongolian gerbils. Following oral administration of wasabi extract of 50 and 200 mg/kg B.W./d for 10 d, the animals were exposed to restraint stress for 90 and 270 min. As for the results, the level of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) in the stomach and oxidative DNA damage in peripheral erythrocytes at 270 min significantly increased. That elevation was significantly suppressed by the addition of the leaf extract. We concluded that the simultaneous loading of H. pylori infection and physical stress loading might induce oxidative DNA damage additively, while a leaf extract attenuated this DNA damage in the stomach as well as the peripheral erythrocytes.

Validation of Marek's disease diagnosis and monitoring of Marek's disease vaccines from samples collected in FTA cards.

PubMed

Cortes, Aneg L; Montiel, Enrique R; Gimeno, Isabel M

2009-12-01

The use of Flinders Technology Associates (FTA) filter cards to quantify Marek's disease virus (MDV) DNA for the diagnosis of Marek's disease (MD) and to monitor MD vaccines was evaluated. Samples of blood (43), solid tumors (14), and feather pulp (FP; 36) collected fresh and in FTA cards were analyzed. MDV DNA load was quantified by real-time PCR. Threshold cycle (Ct) ratios were calculated for each sample by dividing the Ct value of the internal control gene (glyceraldehyde-3-phosphate dehydrogenase) by the Ct value of the MDV gene. Statistically significant correlation (P < 0.05) within Ct ratios was detected between samples collected fresh and in FTA cards by using Pearson's correlation test. Load of serotype 1 MDV DNA was quantified in 24 FP, 14 solid tumor, and 43 blood samples. There was a statistically significant correlation between FP (r = 0.95), solid tumor (r = 0.94), and blood (r = 0.9) samples collected fresh and in FTA cards. Load of serotype 2 MDV DNA was quantified in 17 FP samples, and the correlation between samples collected fresh and in FTA cards was also statistically significant (Pearson's coefficient, r = 0.96); load of serotype 3 MDV DNA was quantified in 36 FP samples, and correlation between samples taken fresh and in FTA cards was also statistically significant (r = 0.84). MDV DNA samples extracted 3 days (t0) and 8 months after collection (t1) were used to evaluate the stability of MDV DNA in archived samples collected in FTA cards. A statistically significant correlation was found for serotype 1 (r = 0.96), serotype 2 (r = 1), and serotype 3 (r = 0.9). The results show that FTA cards are an excellent media to collect, transport, and archive samples for MD diagnosis and to monitor MD vaccines. In addition, FTA cards are widely available, inexpensive, and adequate for the shipment of samples nationally and internationally.

Synthesis and characterization of DNA nano-meso-microspheres as drug delivery carriers for intratumoral chemotherapy

NASA Astrophysics Data System (ADS)

Enriquez Schumacher, Iris Vanessa

Conventional cancer chemotherapy results in systemic toxicity which severely limits effectiveness and often adversely affects patient quality of life. There is a need to find new drugs and delivery methods for less toxic therapy. Previous studies concerning DNA complexing with chemotherapy drugs suggest unique opportunities for DNA as a mesosphere drug carrier. The overall objective of this research was devoted to the synthesis and evaluation of novel DNA-drug nano-mesospheres designed for localized chemotherapy via intratumoral injection. My research presents DNA nano-meso-microspheres (DNA-MS) that were prepared using a modified steric stabilization method originally developed in this lab for the preparation of albumin MS. DNA-MS were prepared with glutaraldehyde covalent crosslinking (genipin crosslinking was attempted) through the DNA base pairs. In addition, novel crosslinking of DNA-MS was demonstrated using chromium, gadolinium, or iron cations through the DNA phosphate groups. Covalent and ionic crosslinked DNA-MS syntheses yielded smooth and spherical particle morphologies with multimodal size distributions. Optimized DNA-MS syntheses produced particles with narrow and normal size distributions in the 50nm to 5mum diameter size range. In aqueous dispersions approximately 200% swelling was observed with dispersion stability for more than 48 hours. Typical process conditions included a 1550rpm initial mixing speed and particle filtration through 20mum filters to facilitate preparation. DNA-MS were in situ loaded during synthesis for the first time with mitoxantrone, 5-fluorouracil, and methotrexate. DNA-MS drug incorporation was 12%(w/w) for mitoxantrone, 9%(w/w) for methotrexate, and 5%(w/w) for 5-fluorouracil. In vitro drug release into phosphate buffered saline was observed for over 35 days by minimum sink release testing. The effect of gadolinium crosslink concentration on mitoxantrone release was evaluated at molar equivalences in the range of 20% to 120%. The most highly crosslinked DNA-MS exhibited the longest sustained release. The drug efficacy of mitoxantrone loaded DNA-MS was evaluated in vitro using a murine Lewis lung carcinoma cell line and a significant cytotoxic response was found at mitoxantrone doses as low as 1ppm. Drug release properties, DNA biodegradability, and observed cancer cell cytotoxicity of drug loaded DNA-MS suggest that they are appropriate for intratumoral chemotherapy evaluation aimed at improved and less toxic cancer therapy.

Light-Responsive and pH-Responsive DNA Microcapsules for Controlled Release of Loads.

PubMed

Huang, Fujian; Liao, Wei-Ching; Sohn, Yang Sung; Nechushtai, Rachel; Lu, Chun-Hua; Willner, Itamar

2016-07-20

A method to assemble light-responsive or pH-responsive microcapsules loaded with different loads (tetramethylrhodamine-modified dextran, TMR-D; microperoxidase-11, MP-11; CdSe/ZnS quantum dots; or doxorubicin-modified dextran, DOX-D) is described. The method is based on the layer-by-layer deposition of sequence-specific nucleic acids on poly(allylamine hydrochloride)-functionalized CaCO3 core microparticles, loaded with the different loads, that after the dissolution of the core particles with EDTA yields the stimuli-responsive microcapsules that include the respective loads. The light-responsive microcapsules are composed of photocleavable o-nitrobenzyl-phosphate-modified DNA shells, and the pH-responsive microcapsules are made of a cytosine-rich layer cross-linked by nucleic acid bridges. Irradiating the o-nitrobenzyl phosphate-functionalized microcapsules, λ = 365 nm, or subjecting the pH-responsive microcapsules to pH = 5.0, results in the cleavage of the microcapsule shells and the release of the loads. Preliminary studies address the cytotoxicity of the DOX-D-loaded microcapsules toward MDA-MB-231 breast cancer cells and normal MCF-10A breast epithelial cells. Selective cytotoxicity of the DOX-D-loaded microcapsules toward cancer cells is demonstrated.

A structural and mechanistic study of π-clamp-mediated cysteine perfluoroarylation.

PubMed

Dai, Peng; Williams, Jonathan K; Zhang, Chi; Welborn, Matthew; Shepherd, James J; Zhu, Tianyu; Van Voorhis, Troy; Hong, Mei; Pentelute, Bradley L

2017-08-11

Natural enzymes use local environments to tune the reactivity of amino acid side chains. In searching for small peptides with similar properties, we discovered a four-residue π-clamp motif (Phe-Cys-Pro-Phe) for regio- and chemoselective arylation of cysteine in ribosomally produced proteins. Here we report mutational, computational, and structural findings directed toward elucidating the molecular factors that drive π-clamp-mediated arylation. We show the significance of a trans conformation prolyl amide bond for the π-clamp reactivity. The π-clamp cysteine arylation reaction enthalpy of activation (ΔH ‡ ) is significantly lower than a non-π-clamp cysteine. Solid-state NMR chemical shifts indicate the prolyl amide bond in the π-clamp motif adopts a 1:1 ratio of the cis and trans conformation, while in the reaction product Pro3 was exclusively in trans. In two structural models of the perfluoroarylated product, distinct interactions at 4.7 Å between Phe1 side chain and perfluoroaryl electrophile moiety are observed. Further, solution 19 F NMR and isothermal titration calorimetry measurements suggest interactions between hydrophobic side chains in a π-clamp mutant and the perfluoroaryl probe. These studies led us to design a π-clamp mutant with an 85-fold rate enhancement. These findings will guide us toward the discovery of small reactive peptides to facilitate abiotic chemistry in water.

Cardiovascular transition at birth: a physiological sequence.

PubMed

Hooper, Stuart B; Te Pas, Arjan B; Lang, Justin; van Vonderen, Jeroen J; Roehr, Charles Christoph; Kluckow, Martin; Gill, Andrew W; Wallace, Euan M; Polglase, Graeme R

2015-05-01

The transition to newborn life at birth involves major cardiovascular changes that are triggered by lung aeration. These include a large increase in pulmonary blood flow (PBF), which is required for pulmonary gas exchange and to replace umbilical venous return as the source of preload for the left heart. Clamping the umbilical cord before PBF increases reduces venous return and preload for the left heart and thereby reduces cardiac output. Thus, if ventilation onset is delayed following cord clamping, the infant is at risk of superimposing an ischemic insult, due to low cardiac output, on top of an asphyxic insult. Much debate has centered on the timing of cord clamping at birth, focusing mainly on the potential for a time-dependent placental to infant blood transfusion. This has prompted recommendations for delayed cord clamping for a set time after birth in infants not requiring resuscitation. However, recent evidence indicates that ventilation onset before cord clamping mitigates the adverse cardiovascular consequences caused by immediate cord clamping. This indicates that the timing of cord clamping should be based on the infant's physiology rather than an arbitrary period of time and that delayed cord clamping may be of greatest benefit to apneic infants.

Planar patch clamp for neuronal networks--considerations and future perspectives.

PubMed

Bosca, Alessandro; Martina, Marzia; Py, Christophe

2014-01-01

The patch-clamp technique is generally accepted as the gold standard for studying ion channel activity allowing investigators to either "clamp" membrane voltage and directly measure transmembrane currents through ion channels, or to passively monitor spontaneously occurring intracellular voltage oscillations. However, this resulting high information content comes at a price. The technique is labor-intensive and requires highly trained personnel and expensive equipment. This seriously limits its application as an interrogation tool for drug development. Patch-clamp chips have been developed in the last decade to overcome the tedious manipulations associated with the use of glass pipettes in conventional patch-clamp experiments. In this chapter, we describe some of the main materials and fabrication protocols that have been developed to date for the production of patch-clamp chips. We also present the concept of a patch-clamp chip array providing high resolution patch-clamp recordings from individual cells at multiple sites in a network of communicating neurons. On this chip, the neurons are aligned with the aperture-probes using chemical patterning. In the discussion we review the potential use of this technology for pharmaceutical assays, neuronal physiology and synaptic plasticity studies.

Clinical aspects of incorporating cord clamping into stabilisation of preterm infants.

PubMed

Knol, Ronny; Brouwer, Emma; Vernooij, Alex S N; Klumper, Frans J C M; DeKoninck, Philip; Hooper, Stuart B; Te Pas, Arjan B

2018-04-21

Fetal to neonatal transition is characterised by major pulmonary and haemodynamic changes occurring in a short period of time. In the international neonatal resuscitation guidelines, comprehensive recommendations are available on supporting pulmonary transition and delaying clamping of the cord in preterm infants. Recent experimental studies demonstrated that the pulmonary and haemodynamic transition are intimately linked, could influence each other and that the timing of umbilical cord clamping should be incorporated into the respiratory stabilisation. We reviewed the current knowledge on how to incorporate cord clamping into stabilisation of preterm infants and the physiological-based cord clamping (PBCC) approach, with the infant's transitional status as key determinant of timing of cord clamping. This approach could result in optimal timing of cord clamping and has the potential to reduce major morbidities and mortality in preterm infants. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Sound absorption by clamped poroelastic plates.

PubMed

Aygun, H; Attenborough, K

2008-09-01

Measurements and predictions have been made of the absorption coefficient and the surface acoustic impedance of poroelastic plates clamped in a large impedance tube and separated from the rigid termination by an air gap. The measured and predicted absorption coefficient and surface impedance spectra exhibit low frequency peaks. The peak frequencies observed in the absorption coefficient are close to those predicted and measured in the deflection spectra of the clamped poroelastic plates. The influences of the rigidity of the clamping conditions and the width of the air gap have been investigated. Both influences are found to be important. Increasing the rigidity of clamping reduces the low frequency absorption peaks compared with those measured for simply supported plates or plates in an intermediate clamping condition. Results for a closed cell foam plate and for two open cell foam plates made from recycled materials are presented. For identical clamping conditions and width of air gap, the results for the different materials differ as a consequence mainly of their different elasticity, thickness, and cell structure.

BUCKO- A BUCKLING ANALYSIS FOR RECTANGULAR PLATES WITH CENTRALLY LOCATED CUTOUTS

NASA Technical Reports Server (NTRS)

Nemeth, M. P.

1994-01-01

BUCKO is a computer program developed to predict the buckling load of a rectangular compression-loaded orthotropic plate with a centrally located cutout. The plate is assumed to be a balanced, symmetric laminate of uniform thickness. The cutout shape can be elliptical, circular, rectangular, or square. The BUCKO package includes sample data that demonstrates the essence of the program and its ease of usage. BUCKO uses an approximate one-dimensional formulation of the classical two-dimensional buckling problem following the Kantorovich method. The boundary conditions are considered to be simply supported unloaded edges and either clamped or simply supported loaded edges. The plate is loaded in uniaxial compression by either uniformly displacing or uniformly stressing two opposite edges of the plate. The BUCKO analysis consists of two parts: calculation of the inplane stress distribution prior to buckling, and calculation of the plate axial load and displacement at buckling. User input includes plate planform and cutout geometry, plate membrane and bending stiffnesses, finite difference parameters, boundary condition data, and loading data. Results generated by BUCKO are the prebuckling strain energy, inplane stress resultants, buckling mode shape, critical end shortening, and average axial and transverse strains at buckling. BUCKO is written in FORTRAN V for batch execution and has been implemented on a CDC CYBER 170 series computer operating under NOS with a central memory requirement of approximately 343K of 60 bit words. This program was developed in 1984 and was last updated in 1990.

Cytomegalovirus Pneumonia in Patients with Rheumatic Diseases After Immunosuppressive Therapy: A Single Center Study in China.

PubMed

Xue, Yu; Jiang, Li; Wan, Wei-Guo; Chen, Yu-Ming; Zhang, Jiong; Zhang, Zhen-Chun

2016-02-05

Rheumatic diseases involve multiple organs that are affected by immunological mechanisms. Treatment with corticosteroids and immunosuppressive agents may also increase the frequency of infection. Cytomegalovirus (CMV) is a widespread herpes virus and a well-recognized pathogen, which causes an opportunistic and potentially fatal infection in immunocompromised patients. This retrospective study aimed to investigate the clinical and laboratory characteristics of CMV pneumonia in patients with rheumatic diseases after immunosuppressive therapy in a single center in Shanghai, China. Eight hundred and thirty-four patients with rheumatic diseases who had undergone CMV-DNA viral load tests were included, and the medical records of 142 patients who were positive for CMV-DNA in plasma samples were evaluated. GraphPad Prism version 5.013 (San Diego, CA, USA) was used to conduct statistical analysis. The correlation between CMV-DNA viral loads and lymphocyte counts was assessed using the Spearman rank correlation coefficient test. Significance between qualitative data was analyzed using Pearson's Chi-squared test. The cut-off thresholds for CMV-DNA viral load and lymphocyte count were determined by receiver operating characteristic (ROC) curve analysis. One hundred and forty-two patients had positive CMV viral load tests. Of these 142 patients, 73 patients with CMV pneumonia were regarded as symptomatic, and the other 69 were asymptomatic. The symptomatic group received higher doses of prednisolone (PSL) and more frequently immunosuppressants than the asymptomatic group (P < 0.01). The symptomatic group had lower lymphocyte counts, especially CD4+ T-cells, than the asymptomatic group (P < 0.01). By ROC curve analysis, when CD4+ T-cell count was <0.39 × 109/L, patients with rheumatic diseases were at high risk for symptomatic CMV infection. The CMV-DNA load was significantly higher in the symptomatic patients than that in asymptomatic patients (P < 0.01; threshold viral loads: 1.75 × 104 copies/ml). Seven patients had a fatal outcome, and they had lower peripheral lymphocyte counts (P < 0.01), including CD4+ and CD8+ T-cells (P < 0.01). When CD4+ T-cell count is <0.39 × 109/L, patients are at high risk for pulmonary CMV infection. Patients are prone to be symptomatic with CMV-DNA load >1.75 × 104 copies/ml. Lymphopenia (especially CD4+ T-cells), presence of symptoms, and other infections, especially fungal infection, are significant risk factors for poor outcome, and a higher PSL dosage combined with immunosuppressants may predict CMV pneumonia.

[The risk of neoplastic processes transformation in cervix uteri].

PubMed

Kiseleva, V I; Krikunova, L I; Mkrtchian, L S; Liubina, L V; Beziaeva, G P; Panarina, L V; Zamuliaeva, I A

2014-01-01

There was performed a comparative analysis of quantitative load and physical status of human papillomavirus (HPV) type 16 in groups of patients with cervical intraepithelial neoplasia (CIN)--25 people and cervical cancer (CC)--85 people. According to the analysis there were selected criteria appropriate to a combination of adverse factors that characterized HPV- infection and at the same time estimated both quantitative load and physical status of the virus: high viral load (> 6,5 lg copies of HPV DNA per 100000 cells) in episomal form or low load (< 6,5 lg copies of HPV DNA per 100000 cells) in integrated form of the virus. According to calculations a relative chance of appearing of CC in CIN patients with unfavorable combination of factors was 7,5 times higher than in other patients.

Srs2 overexpression reveals a helicase-independent role at replication forks that requires diverse cell functions

PubMed Central

León Ortiz, Ana María; Reid, Robert J. D.; Dittmar, John C.; Rothstein, Rodney; Nicolas, Alain

2011-01-01

Srs2 is a 3’ to 5’ DNA helicase that regulates many aspects of DNA metabolism in Saccharomyces cerevisiae. It is best known for its ability to counteract homologous recombination by dismantling Rad51 filaments, but is also involved in checkpoint activation, adaptation and recovery, and in resolution of late recombination intermediates. To further address its biological roles and uncover new genetic interactions, we examined the consequences of overexpressing SRS2 as well as two helicase-dead mutants, srs2-K41A and srs2-K41R, in the collection of 4827 yeast haploid deletion mutants. We identified 274 genes affecting a large variety of cellular functions that are required for cell growth when SRS2 or its mutants are overexpressed. Further analysis of these interactions reveals that Srs2 acts independently of its helicase function at replication forks likely through its recruitment by the sumoylated PCNA replication clamp. This helicase-independent function is responsible for the negative interactions with DNA metabolism genes and for the toxicity of SRS2 overexpression in many of the diverse cellular pathways revealed in our screens. PMID:21459050

DOE Office of Scientific and Technical Information (OSTI.GOV)

Altieri, Amanda S.; Ladner, Jane E.; Li, Zhuo

Proliferating cell nuclear antigen (PCNA) forms a trimeric ring that encircles duplex DNA and acts as an anchor for a number of proteins involved in DNA metabolic processes. PCNA has two structurally similar domains (I and II) linked by a long loop (inter-domain connector loop, IDCL) on the outside of each monomer of the trimeric structure that makes up the DNA clamp. All proteins that bind to PCNA do so via a PCNA-interacting peptide (PIP) motif that binds near the IDCL. A small protein, called TIP, binds to PCNA and inhibits PCNA-dependent activities although it does not contain a canonicalmore » PIP motif. The X-ray crystal structure of TIP bound to PCNA reveals that TIP binds to the canonical PIP interaction site, but also extends beyond it through a helix that relocates the IDCL. TIP alters the relationship between domains I and II within the PCNA monomer such that the trimeric ring structure is broken, while the individual domains largely retain their native structure. Small angle X-ray scattering (SAXS) confirms the disruption of the PCNA trimer upon addition of the TIP protein in solution and together with the X-ray crystal data, provides a structural basis for the mechanism of PCNA inhibition by TIP.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Altieri, Amanda S.; Ladner, Jane E.; Li, Zhuo

Here, proliferating cell nuclear antigen (PCNA) forms a trimeric ring that encircles duplex DNA and acts as an anchor for a number of proteins involved in DNA metabolic processes. PCNA has two structurally similar domains (I and II) linked by a long loop (inter-domain connector loop, IDCL) on the outside of each monomer of the trimeric structure that makes up the DNA clamp. All proteins that bind to PCNA do so via a PCNA-interacting peptide (PIP) motif that binds near the IDCL. A small protein, called TIP, binds to PCNA and inhibits PCNA-dependent activities although it does not contain amore » canonical PIP motif. The X-ray crystal structure of TIP bound to PCNA reveals that TIP binds to the canonical PIP interaction site, but also extends beyond it through a helix that relocates the IDCL. TIP alters the relationship between domains I and II within the PCNA monomer such that the trimeric ring structure is broken, while the individual domains largely retain their native structure. Small angle X-ray scattering (SAXS) confirms the disruption of the PCNA trimer upon addition of the TIP protein in solution and together with the X-ray crystal data, provides a structural basis for the mechanism of PCNA inhibition by TIP.« less

Rigid clamp

DOEpatents

Benavides, G.L.; Burt, J.D.

1994-07-12

The invention relates to a clamp mechanism that can be used to attach or temporarily support objects inside of tubular goods. The clamp mechanism can also be modified so that it grips objects. The clamp has a self-centering feature to accommodate out-of-roundness or other internal defections in tubular objects such as pipe. A plurality of clamping shoes are expanded by a linkage which is preferably powered by a motor to contact the inside of a pipe. The motion can be reversed and jaw elements can be connected to the linkage so as to bring the jaws together to grab an object. 12 figs.

Rigid clamp

DOEpatents

Benavides, Gilbert L.; Burt, Jack D.

1994-01-01

The invention relates to a clamp mechanism that can be used to attach or temporarily support objects inside of tubular goods. The clamp mechanism can also be modified so that it grips objects. The clamp has a self-centering feature to accommodate out-of-roundness or other internal defections in tubular objects such as pipe. A plurality of clamping shoes are expanded by a linkage which is preferably powered by a motor to contact the inside of a pipe. The motion can be reversed and jaw elements can be connected to the linkage so as to bring the jaws together to grab an object.

Advanced motor driven clamped borehole seismic receiver

DOEpatents

Engler, Bruce P.; Sleefe, Gerard E.; Striker, Richard P.

1993-01-01

A borehole seismic tool including a borehole clamp which only moves perpendicular to the borehole. The clamp is driven by an electric motor, via a right angle drive. When used as a seismic receiver, the tool has a three part housing, two of which are hermetically sealed. Accelerometers or geophones are mounted in one hermetically sealed part, the electric meter in the other hermetically sealed part, and the clamp and right angle drive in the third part. Preferably the tool includes cable connectors at both ends. Optionally a shear plate can be added to the clamp to extend the range of the tool.

Radial wedge flange clamp

DOEpatents

Smith, Karl H.

2002-01-01

A radial wedge flange clamp comprising a pair of flanges each comprising a plurality of peripheral flat wedge facets having flat wedge surfaces and opposed and mating flat surfaces attached to or otherwise engaged with two elements to be joined and including a series of generally U-shaped wedge clamps each having flat wedge interior surfaces and engaging one pair of said peripheral flat wedge facets. Each of said generally U-shaped wedge clamps has in its opposing extremities apertures for the tangential insertion of bolts to apply uniform radial force to said wedge clamps when assembled about said wedge segments.

Germline mitochondrial DNA mutations aggravate ageing and can impair brain development.

PubMed

Ross, Jaime M; Stewart, James B; Hagström, Erik; Brené, Stefan; Mourier, Arnaud; Coppotelli, Giuseppe; Freyer, Christoph; Lagouge, Marie; Hoffer, Barry J; Olson, Lars; Larsson, Nils-Göran

2013-09-19

Ageing is due to an accumulation of various types of damage, and mitochondrial dysfunction has long been considered to be important in this process. There is substantial sequence variation in mammalian mitochondrial DNA (mtDNA), and the high mutation rate is counteracted by different mechanisms that decrease maternal transmission of mutated mtDNA. Despite these protective mechanisms, it is becoming increasingly clear that low-level mtDNA heteroplasmy is quite common and often inherited in humans. We designed a series of mouse mutants to investigate the extent to which inherited mtDNA mutations can contribute to ageing. Here we report that maternally transmitted mtDNA mutations can induce mild ageing phenotypes in mice with a wild-type nuclear genome. Furthermore, maternally transmitted mtDNA mutations lead to anticipation of reduced fertility in mice that are heterozygous for the mtDNA mutator allele (PolgA(wt/mut)) and aggravate premature ageing phenotypes in mtDNA mutator mice (PolgA(mut/mut)). Unexpectedly, a combination of maternally transmitted and somatic mtDNA mutations also leads to stochastic brain malformations. Our findings show that a pre-existing mutation load will not only allow somatic mutagenesis to create a critically high total mtDNA mutation load sooner but will also increase clonal expansion of mtDNA mutations to enhance the normally occurring mosaic respiratory chain deficiency in ageing tissues. Our findings suggest that maternally transmitted mtDNA mutations may have a similar role in aggravating aspects of normal human ageing.

Detection of active human papilloma virus-16 in head and neck cancers of Asian North Indian patients.

PubMed

Sannigrahi, M K; Singh, V; Sharma, R; Panda, N K; Radotra, B D; Khullar, M

2016-01-01

Head and neck cancers (HNC) are one of the most common cancers in India. Human papillomavirus (HPV) has been identified as an emerging risk factor for HNC. The present study was carried out to determine the active form of HPV-16 using a combination of PCR, viral load determination, HPV-16 E7 mRNA expression, p16, p53, and pRB immuno-histochemistry (IHC). A total of 226 HNC patients were enrolled in the present study. Sixty-seven (29.7%) of HNC cases were found to be HPV DNA positive. Thirty-two (14%) cases were HPV-16 DNA positive and 20 (9%) cases expressed HPV-16 E7 mRNA. HPV-16 mRNA/p16 positive cases had significantly increased viral load and integrated HPV-16 DNA. In summary, of total HNC patients, 6% cases were positive for both HPV-16 DNA and p16, and 5% were positive for both E7 mRNA and p16 IHC. We observed similar HPV-16 DNA/E7mRNA prevalence in oropharynx and oral cavity sites, however, oropharynx SCC had significantly higher viral load. Our results show low prevalence of active HPV-16 in North Indian HNC patients. HPV-16 E7 mRNA expression correlated with p16 nuclear positivity and increased viral load. Therefore, E7 mRNA expression may be used as a good surrogate indicator for active form of HPV-16 infection. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Development of a nanostructured DNA delivery scaffold via electrospinning of PLGA and PLA-PEG block copolymers

NASA Technical Reports Server (NTRS)

Luu, Y. K.; Kim, K.; Hsiao, B. S.; Chu, B.; Hadjiargyrou, M.; Hadjiargyou, M. (Principal Investigator)

2003-01-01

The present work utilizes electrospinning to fabricate synthetic polymer/DNA composite scaffolds for therapeutic application in gene delivery for tissue engineering. The scaffolds are non-woven, nano-fibered, membranous structures composed predominantly of poly(lactide-co-glycolide) (PLGA) random copolymer and a poly(D,L-lactide)-poly(ethylene glycol) (PLA-PEG) block copolymer. Release of plasmid DNA from the scaffolds was sustained over a 20-day study period, with maximum release occurring at approximately 2 h. Cumulative release profiles indicated amounts released were approximately 68-80% of the initially loaded DNA. Variations in the PLGA to PLA-PEG block copolymer ratio vastly affected the overall structural morphology, as well as both the rate and efficiency of DNA release. Results indicated that DNA released directly from these electrospun scaffolds was indeed intact, capable of cellular transfection, and successfully encoded the protein beta-galactosidase. When tested under tensile loads, the electrospun polymer/DNA composite scaffolds exhibited tensile moduli of approximately 35 MPa, with approximately 45% strain initially. These values approximate those of skin and cartilage. Taken together, this work represents the first successful demonstration of plasmid DNA incorporation into a polymer scaffold using electrospinning.

A Delicate Balance Between Repair and Replication Factors Regulates Recombination Between Divergent DNA Sequences in Saccharomyces cerevisiae

PubMed Central

Chakraborty, Ujani; George, Carolyn M.; Lyndaker, Amy M.; Alani, Eric

2016-01-01

Single-strand annealing (SSA) is an important homologous recombination mechanism that repairs DNA double strand breaks (DSBs) occurring between closely spaced repeat sequences. During SSA, the DSB is acted upon by exonucleases to reveal complementary sequences that anneal and are then repaired through tail clipping, DNA synthesis, and ligation steps. In baker’s yeast, the Msh DNA mismatch recognition complex and the Sgs1 helicase act to suppress SSA between divergent sequences by binding to mismatches present in heteroduplex DNA intermediates and triggering a DNA unwinding mechanism known as heteroduplex rejection. Using baker’s yeast as a model, we have identified new factors and regulatory steps in heteroduplex rejection during SSA. First we showed that Top3-Rmi1, a topoisomerase complex that interacts with Sgs1, is required for heteroduplex rejection. Second, we found that the replication processivity clamp proliferating cell nuclear antigen (PCNA) is dispensable for heteroduplex rejection, but is important for repairing mismatches formed during SSA. Third, we showed that modest overexpression of Msh6 results in a significant increase in heteroduplex rejection; this increase is due to a compromise in Msh2-Msh3 function required for the clipping of 3′ tails. Thus 3′ tail clipping during SSA is a critical regulatory step in the repair vs. rejection decision; rejection is favored before the 3′ tails are clipped. Unexpectedly, Msh6 overexpression, through interactions with PCNA, disrupted heteroduplex rejection between divergent sequences in another recombination substrate. These observations illustrate the delicate balance that exists between repair and replication factors to optimize genome stability. PMID:26680658

Hepatitis B virus serosurvey and awareness of mother-to-child transmission among pregnant women in Shenyang, China: An observational study.

PubMed

Sheng, Qiu-Ju; Wang, Sui-Jing; Wu, Yu-Yu; Dou, Xiao-Guang; Ding, Yang

2018-06-01

Preventing hepatitis B virus (HBV) mother-to-child transmission (MTCT) is the key to controlling the prevalence of chronic HBV infection. Adequate awareness of hepatitis B in hepatitis B s antigen (HBsAg) positive pregnant women may be helpful to reduce HBV MTCT.The aim of this study was to explore HBV seroprevalence among pregnant women and investigate the level of hepatitis B awareness among HBsAg positive pregnant women.HBV serum biomarkers were tested among pregnant women visiting Shengjing Hospital of China Medical University. HBsAg-positive pregnant women received a HBV DNA test and completed a questionnaire. The different HBV DNA loads were interpreted as follows: 20 to  < 2 × 10 IU/mL was low viral load, 2 × 10 to  < 2 × 10 IU/mL was intermediate viral load and ≥2 × 10 IU/mL was high viral load. The pregnant women with high viral load were treated with telbivudine (LdT). HBV DNA at different times was tested. The rate of HBV MTCT was confirmed at 28 weeks postpartum.HBsAg prevalence among pregnant women was 3.1% (441/14314). There was significant difference in comparing HBsAg prevalence in different age groups (χ = 13.86, P < .01). Among 441 HBsAg-positive pregnant women, 151 (34.2%) were hepatitis B e antigen (HBeAg) positive and 112 (25.4%) had high viral load. After 4 weeks of treatment, the average HBV DNA load of 66 cases with high viral load was (5.0 ± 0.8) log10 IU/mL. The average HBV DNA load at 4 weeks postpartum rebounded to (7.9 ± 1.0) log10 IU/mL, which was not significantly different from that at baseline (t = 1.23, P = .22). At 28 weeks postpartum, the rate of HBV MTCT in the treatment group was significantly lower than that in the observation group (0% vs 12.2%; P = .02). Only 23.4% of pregnant women knew their HBV status before gestation and 17.7% of pregnant women knew the HBV status before delivery. However, only 21.3% of pregnant women realized to need antiviral treatment to prevent MTCT.The pregnant women in Shenyang had a low HBsAg prevalence. Antiviral treatment for pregnant women with high viral load can effectively reduce the rate of HBV MTCT. HBV screening and education among HBsAg-positive pregnant women should be strengthened.

Urinary urea nitrogen excretion during the hyperinsulinemic euglycemic clamp in type 1 diabetic patients and healthy subjects.

PubMed

Wohl, P; Krusinová, E; Klementová, M; Wohl, P; Kratochvílová, S; Pelikánová, T

2008-01-01

The hyperinsulinemic euglycemic clamp (HEC) combined with indirect calorimetry (IC) is used for estimation of insulin-stimulated substrate utilization. Calculations are based on urinary urea nitrogen excretion (UE), which is influenced by correct urine collection. The aims of our study were to improve the timing of urine collection during the clamp and to test the effect of insulin on UE in patients with type 1 diabetes (DM1; n=11) and healthy subjects (C; n=11). Urine samples were collected (a) over 24 h divided into 3-h periods and (b) before and during two-step clamp (1 and 10 mIU.kg(-1).min(-1); period 1 and period 2) combined with IC. The UE during the clamp was corrected for changes in urea pool size (UEc). There were no significant differences in 24-h UE between C and DM1 and no circadian variation in UE in either group. During the clamp, serum urea decreased significantly in both groups (p<0.01). Therefore, UEc was significantly lower as compared to UE not adjusted for changes in urea pool size both in C (p<0.001) and DM1 (p<0.001). While UE did not change during the clamp, UEc decreased significantly in both groups (p<0.01). UEc during the clamp was significantly higher in DM1 compared to C both in period 1 (p<0.05) and period 2 (p<0.01). The UE over 24 h and UEc during the clamp were statistically different in both C and DM1. We conclude that urine collection performed during the clamp with UE adjusted for changes in urea pool size is the most suitable technique for measuring substrate utilization during the clamp both in DM1 and C. Urine collections during the clamp cannot be replaced either by 24-h sampling (periods I-VII) or by a single 24-h urine collection. Attenuated insulin-induced decrease in UEc in DM1 implicates the impaired insulin effect on proteolysis.

Twisting short dsDNA with applied tension

NASA Astrophysics Data System (ADS)

Zoli, Marco

2018-02-01

The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair fluctuations. The latter are all the more important at short length scales in which DNA fragments maintain an intrinsic flexibility. The presented computational method simulates a broad ensemble of possible molecule conformations characterized by a specific average twist and determines the energetically most convenient helical twist by free energy minimization. As this is done for any external load, the method yields the characteristic twist-stretch profile of the molecule and also computes the changes in the macroscopic helix parameters i.e. average diameter and rise distance. It is predicted that short molecules under stretching should first over-twist and then untwist by increasing the external load. Moreover, applying a constant load and simulating a torsional strain which over-twists the helix, it is found that the average helix diameter shrinks while the molecule elongates, in agreement with the experimental trend observed in kilo-base long sequences. The quantitative relation between percent relative elongation and superhelical density at fixed load is derived. The proposed theoretical model and computational method offer a general approach to characterize specific DNA fragments and predict their macroscopic elastic response as a function of the effective potential parameters of the mesoscopic Hamiltonian.

A universal real-time PCR assay for the quantification of group-M HIV-1 proviral load.

PubMed

Malnati, Mauro S; Scarlatti, Gabriella; Gatto, Francesca; Salvatori, Francesca; Cassina, Giulia; Rutigliano, Teresa; Volpi, Rosy; Lusso, Paolo

2008-01-01

Quantification of human immunodeficiency virus type-1 (HIV-1) proviral DNA is increasingly used to measure the HIV-1 cellular reservoirs, a helpful marker to evaluate the efficacy of antiretroviral therapeutic regimens in HIV-1-infected individuals. Furthermore, the proviral DNA load represents a specific marker for the early diagnosis of perinatal HIV-1 infection and might be predictive of HIV-1 disease progression independently of plasma HIV-1 RNA levels and CD4(+) T-cell counts. The high degree of genetic variability of HIV-1 poses a serious challenge for the design of a universal quantitative assay capable of detecting all the genetic subtypes within the main (M) HIV-1 group with similar efficiency. Here, we describe a highly sensitive real-time PCR protocol that allows for the correct quantification of virtually all group-M HIV-1 strains with a higher degree of accuracy compared with other methods. The protocol involves three stages, namely DNA extraction/lysis, cellular DNA quantification and HIV-1 proviral load assessment. Owing to the robustness of the PCR design, this assay can be performed on crude cellular extracts, and therefore it may be suitable for the routine analysis of clinical samples even in developing countries. An accurate quantification of the HIV-1 proviral load can be achieved within 1 d from blood withdrawal.