Oxygen storage properties of La 1-xSr xFeO 3-δ for chemical-looping reactions–An in-situ neutron and synchrotron X-ray study

DOE PAGES

Taylor, Daniel D.; Schreiber, Nathaniel J.; Levitas, Benjamin D.; ...

2016-05-16

Oxygen storage materials (OSMs) provide lattice oxygen for a number of chemical-looping reactions including natural gas combustion and methane reforming. La 1–xSr xFeO 3-δ has shown promise for use as an OSM in methane reforming reactions due to its high product selectivity, fast oxide diffusion, and cycle stability. Here, we investigate the structural evolution of the series La 1–xSr xFeO 3-δ for x = 0, 1/3, 1/2, 2/3, and 1, using in situ synchrotron X-ray and neutron diffraction, as it is cycled under the conditions of a chemical-looping reactor (methane and oxygen atmospheres). In the compositions x = 1/3, 1/2,more » 2/3, and 1, we discover an envelope , or temperature range, of oxygen storage capacity (OSC), where oxygen can easily and reversibly be inserted and removed from the OSM. Our in situ X-ray and neutron diffraction results reveal that while samples with higher Sr contents had a higher OSC, those same samples suffered from slower reaction kinetics and some, such as the x = 1/2 and x = 2/3 compositions, had local variations in Sr content, which led to inhomogeneous regions with varying reaction rates. Therefore, we highlight the importance of in situ diffraction studies, and we propose that these measurements are required for the thorough evaluation of future candidate OSMs. Furthermore, we recommend La 2/3Sr 1/3FeO 3-δ as the optimal OSM in the series because its structure remains homogeneous throughout the reaction, and its OSC envelope is similar to that of the higher doped materials.« less

Class and Home Problems: Carbon Dioxide Capture from Coal-Fired Power Plants Using Calcium Looping

ERIC Educational Resources Information Center

Deshpande, Niranjani; Phalak, Nihar; Fan, Liang-Shih; Sundaresan, Sankaran

2015-01-01

Calcium looping is based on the simple premise of the reversible reaction between CO[subscript 2] and CaO. This reaction can be used for separation of CO2 from a mixture of gases; most notably the technology finds applications in CO[subscript 2] removal from gas streams in fossil fuel-based energy systems. This article gives a brief overview of…

Force modeling for incisions into various tissues with MRF haptic master

NASA Astrophysics Data System (ADS)

Kim, Pyunghwa; Kim, Soomin; Park, Young-Dai; Choi, Seung-Bok

2016-03-01

This study proposes a new model to predict the reaction force that occurs in incisions during robot-assisted minimally invasive surgery. The reaction force is fed back to the manipulator by a magneto-rheological fluid (MRF) haptic master, which is featured by a bi-directional clutch actuator. The reaction force feedback provides similar sensations to laparotomy that cannot be provided by a conventional master for surgery. This advantage shortens the training period for robot-assisted minimally invasive surgery and can improve the accuracy of operations. The reaction force modeling of incisions can be utilized in a surgical simulator that provides a virtual reaction force. In this work, in order to model the reaction force during incisions, the energy aspect of the incision process is adopted and analyzed. Each mode of the incision process is classified by the tendency of the energy change, and modeled for realistic real-time application. The reaction force model uses actual reaction force information with three types of actual tissues: hard tissue, medium tissue, and soft tissue. This modeled force is realized by the MRF haptic master through an algorithm based on the position and velocity of a scalpel using two different control methods: an open-loop algorithm and a closed-loop algorithm. The reaction forces obtained from the proposed model are compared with a desired force in time domain.

Conformational motions regulate phosphoryl transfer in related protein tyrosine phosphatases

PubMed Central

Whittier, Sean K.; Hengge, Alvan C.; Loria, J. Patrick

2014-01-01

Many studies have implicated a role for conformational motions during the catalytic cycle, acting to optimize the binding pocket or facilitate product release, but a more intimate role in the chemical reaction has not been described. We address this by monitoring active-site loop motion in two protein tyrosine phosphatases (PTPs) using NMR spectroscopy. The PTPs, YopH and PTP1B, have very different catalytic rates, however we find in both that the active-site loop closes to its catalytically competent position at rates that mirror the phosphotyrosine cleavage kinetics. This loop contains the catalytic acid, suggesting that loop closure occurs concomitantly with the protonation of the leaving group tyrosine and explains the different kinetics of two otherwise chemically and mechanistically indistinguishable enzymes. PMID:23970698

INTESTINAL OBSTRUCTION

PubMed Central

Whipple, G. H.; Stone, H. B.; Bernheim, B. M.

1913-01-01

Closed duodenal loops may be made in dogs by ligatures placed just below the pancreatic duct and just beyond the duodenojejunal junction, together with a posterior gastro-enterostomy. These closed duodenal loop dogs die with symptoms like those of patients suffering from volvulus or high intestinal obstruction. This duodenal loop may simulate closely a volvulus in which there has been no vascular disturbance. Dogs with closed duodenal loops which have been washed out carefully survive a little longer on the average than animals with unwashed loops. The duration of life in the first instance is one to three days, with an average of about forty-eight hours. The dogs usually lose considerable fluid by vomiting and diarrhea. A weak pulse, low blood pressure and temperature are usually conspicuous in the last stages. Autopsy shows more or less splanchnic congestion which may be most marked in the mucosa of the upper small intestine. The peritoneum is usually clear and the closed loop may be distended with thin fluid, or collapsed, and contain only a small amount of pasty brown material. The mucosa of the loop may show ulceration and even perforation, but in the majority of cases it is intact and exhibits only a moderate congestion. Simple intestinal obstruction added to a closed duodenal loop does not modify the result in any manner, but it may hasten the fatal outcome. The liver plays no essential role as a protective agent against this poison, for a dog with an Eck fistula may live three days with a closed loop. A normal dog reacts to intraportal injection and to intravenous injection of the toxic substance in an identical manner. Drainage of this loop under certain conditions may not interfere with the general health over a period of weeks or months. Excision of the part of the duodenum included in this loop causes no disturbance. The material from the closed duodenal loops contains no bile, pancreatic juice, gastric juice, or split products from the food. It can be formed in no other way than by the activity of the intestinal mucosa and the growth of the intestinal bacteria. This material after dilution, autolysis, sterilization, and filtration produces a characteristic effect when introduced intravenously. When in toxic doses it causes a profound drop in blood pressure, general collapse, drop in temperature, salivation, vomiting, and profuse diarrhea, which is often blood-stained. Splanchnic congestion is the conspicuous feature at autopsy and shows especially in the villi of the duodenal and jejunal mucosæ. Adrenalin, during this period of low blood pressure and splanchnic congestion, will cause the usual reaction when given intravenously, but applied locally or given intravenously it causes no bleaching of the engorged intestinal mucosa. Secretin is not found in the duodenal loop fluid, and the loop material does not influence the pancreatic secretion. Intraportal injection of the toxic material gives a reaction similar to intravenous injection. Intraperitoneal and subcutaneous injections produce a relatively slow reaction which closely resembles the picture seen in the closed duodenal loop dog. In both cases there is a relatively slow absorption, but the splanchnic congestion and other findings, though less intense, are present in both groups. There seems, therefore, to be no escape from the conclusion that a poisonous substance is formed in this closed duodenal loop which is absorbed from it and causes intoxication and death. Injection of this toxic substance into a normal dog gives intoxication and a reaction more intense but similar to that developing in a closed-loop dog. PMID:19867644

THE EFFECT OF THE {sup 14}N(p, {gamma}){sup 15}O REACTION ON THE BLUE LOOPS IN INTERMEDIATE-MASS STARS

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

Halabi, Ghina M.; El Eid, Mounib F.; Champagne, Arthur

2012-12-10

We present stellar evolutionary sequences of stars in the mass range 5-12 M{sub Sun }, having solar-like initial composition. The stellar models are obtained using updated input physics, including recent rates of thermonuclear reactions. We investigate the effects of a modification of the {sup 14}N(p, {gamma}){sup 15}O reaction rate, as suggested by recent evaluations, on the formation and extension of the blue loops encountered during the evolution of the stars in the above mass range. We find that a reduced {sup 14}N(p, {gamma}){sup 15}O rate, as described in the text, has a striking impact on the physical conditions of burningmore » and mixing during shell hydrogen burning when the blue loops are formed. In particular, we find that the efficiency of shell hydrogen burning is crucial for the formation of an extended blue loop. We show that a significantly reduced {sup 14}N(p, {gamma}){sup 15}O rate affects severely the extension of the blue loops and the time spent by the star in the blue part of the Hertzsprung-Russell diagram in the mass range 5-7 M{sub Sun} if the treatment of convection is based on the Schwarzschild criterion only. In this case, envelope overshooting helps to restore well-extended blue loops as supported by the observations of the Cepheid stars. If core overshooting is included during the core hydrogen and core helium burning phases, the loop formation and its properties depend on how this overshooting is treated for a given stellar mass range, as well as on its efficiency.« less

Assessment of the 3H and 7Be generation in the IFMIF lithium loop

NASA Astrophysics Data System (ADS)

Simakov, S. P.; Fischer, U.; von Möllendorff, U.

2004-08-01

A complete evaluation of the 7Be and tritium inventory induced in the IFMIF lithium loop by deuterons and neutrons was performed on the basis of 3D Monte Carlo calculations with the M CDeLicious code and evaluated d-Li and n-Li cross-section data. The associated reaction cross-sections and thick lithium target yields were checked against available experimental data. The IFMIF calculations showed that the deuteron beam will produce 1.5 g of 7Be and 6 g of 3H per full power year in the lithium jet. The tritium generation in the whole lithium loop due to neutron induced reactions is at a rate of 1.5 g/fpy. The radio-active decay results in an equilibrium concentration 0.3 mg of 7Be and 50 mg of 3H per 1 kg of circulating lithium if no radioactive products are removed from the loop.

Dissecting the hybridization of oligonucleotides to structured complementary sequences.

PubMed

Peracchi, Alessio

2016-06-01

When oligonucleotides hybridize to long target molecules, the process is slowed by the secondary structure in the targets. The phenomenon has been analyzed in several previous studies, but many details remain poorly understood. I used a spectrofluorometric strategy, focusing on the formation/breaking of individual base pairs, to study the kinetics of association between a DNA hairpin and >20 complementary oligonucleotides ('antisenses'). Hybridization rates differed by over three orders of magnitude. Association was toehold-mediated, both for antisenses binding to the target's ends and for those designed to interact with the loop. Binding of these latter, besides being consistently slower, was affected to variable, non-uniform extents by the asymmetric loop structure. Divalent metal ions accelerated hybridization, more pronouncedly when nucleation occurred at the loop. Incorporation of locked nucleic acid (LNA) residues in the antisenses substantially improved the kinetics only when LNAs participated to the earliest hybridization steps. The effects of individual LNAs placed along the antisense indicated that the reaction transition state occurred after invading at least the first base pair of the stem. The experimental approach helps dissect hybridization reactions involving structured nucleic acids. Toehold-dependent, nucleation-invasion models appear fully appropriate for describing such reactions. Estimating the stability of nucleation complexes formed at internal toeholds is the major hurdle for the quantitative prediction of hybridization rates. While analyzing the mechanisms of a fundamental biochemical process (hybridization), this work also provides suggestions for the improvement of technologies that rely on such process. Copyright © 2016 Elsevier B.V. All rights reserved.

Stopped-in-loop flow analysis of trace vanadium in water.

PubMed

Teshima, Norio; Ohno, Shinsuke; Sakai, Tadao

2007-01-01

The new concept of stopped-in-loop flow analysis (SIL-FA) is proposed, and an SIL-FA method for the catalytic determination of vanadium is demonstrated. In an SIL format, a sample solution merges with reagent(s), and the well-mixed solution is loaded into a loop. The solution in the loop is separated by a six-way switching valve from the main stream. While the reaction proceeds in the stationary loop, the SIL-FA system does not need to establish a baseline continuously. This leads to a reduction in reagent consumption and waste generation compared with traditional flow injection analysis.

Degradation pattern of photosystem II reaction center protein D1 in intact leaves. The major photoinhibition-induced cleavage site in D1 polypeptide is located amino terminally of the DE loop.

PubMed

Kettunen, R; Tyystjärvi, E; Aro, E M

1996-08-01

Photoinhibition-induced degradation of the D1 protein of the photosystem II reaction center was studied in intact pumpkin (Cucurbita pepo L.) leaves. Photoinhibition was observed to cause the cleavage of the D1 protein at two distinct sites. The main cleavage generated an 18-kD N-terminal and a 20-kD C-terminal degradation fragment of the D1 protein. this cleavage site was mapped to be located clearly N terminally of the DE loop. The other, less-frequent cleavage occurred at the DE loop and produced the well-documented 23-kD, N-terminal D1 degradation product. Furthermore, the 23-kD, N-terminal D1 fragment appears to be phosphorylated and can be detected only under severe photoinhibition in vivo. Comparison of the D1 degradation pattern after in vivo photoinhibition to that after in vitro acceptor-side and donor-side photoinhibition, performed with isolated photosystem II core particles, gives indirect evidence in support of donor-side photoinhibition in intact leaves.

Hardware-in-the-Loop Rendezvous Tests of a Novel Actuators Command Concept

NASA Astrophysics Data System (ADS)

Gomes dos Santos, Willer; Marconi Rocco, Evandro; Boge, Toralf; Benninghoff, Heike; Rems, Florian

2016-12-01

Integration, test and validation results, in a real-time environment, of a novel concept for spacecraft control are presented in this paper. The proposed method commands simultaneously a group of actuators optimizing a given set of objective functions based on a multiobjective optimization technique. Since close proximity maneuvers play an important role in orbital servicing missions, the entire GNC system has been integrated and tested at a hardware-in-the-loop (HIL) rendezvous and docking simulator known as European Proximity Operations Simulator (EPOS). During the test campaign at EPOS facility, a visual camera has been used to provide the necessary measurements for calculating the relative position with respect to the target satellite during closed-loop simulations. In addition, two different configurations of spacecraft control have been considered in this paper: a thruster reaction control system and a mixed actuators mode which includes thrusters, reaction wheels, and magnetic torqrods. At EPOS, results of HIL closed-loop tests have demonstrated that a safe and stable rendezvous approach can be achieved with the proposed GNC loop.

Active site loop dynamics of a class IIa fructose 1,6-bisphosphate aldolase from M. tuberculosis

PubMed Central

Pegan, Scott D.; Rukseree, Kamolchanok; Capodagli, Glenn C.; Baker, Erica A; Krasnykh, Olga; Franzblau, Scott G; Mesecar, Andrew D

2014-01-01

Class II fructose 1,6-bisphosphate aldolases (FBA; E.C. 4.1.2.13) comprise one of two families of aldolases. Instead of forming a Schiff-base intermediate using an ε-amino group of a lysine side chain, class II FBAs utilize Zn(II) to stabilize a proposed hydroxyenolate intermediate (HEI) in the reversible cleavage of fructose 1,6-bisphosphate forming glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). As class II FBAs has been shown to be essential in pathogenic bacteria, focus has been placed on these enzymes as potential antibacterial targets. Although structural studies on class II FBAs from Mycobacterium tuberculosis (MtFBA), other bacteria and protozoa have been reported, the structure of the active site loop responsible for catalyzing the protonation/deprotonation steps of the reaction for class II FBAs has not yet been observed. We therefore utilized the potent class II FBA inhibitor phosphoglycolohydroxamate (PGH) as a mimic of the HEI/DHAP bound form of the enzyme and determined the X-ray structure of MtFBA-PGH complex to 1.58 Å. Remarkably, we are able to observe well-defined electron density for the previously elusive active site loop of MtFBA trapped in a catalytically competent orientation. Utilization of this structural information plus site-directed mutagenesis and kinetic studies conducted on a series of residues within the active-site loop revealed that E169 facilitates a water mediated deprotonation/protonation step of the MtFBA reaction mechanism. Also, secondary isotope effects on MtFBA and catalytically relevant mutants were used to probe the effect of loop flexibility on catalytic efficiency. Additionally, we also reveal the structure of MtFBA in its holoenzyme form. PMID:23298222

Active site loop dynamics of a class IIa fructose 1,6-bisphosphate aldolase from Mycobacterium tuberculosis.

PubMed

Pegan, Scott D; Rukseree, Kamolchanok; Capodagli, Glenn C; Baker, Erica A; Krasnykh, Olga; Franzblau, Scott G; Mesecar, Andrew D

2013-02-05

Class II fructose 1,6-bisphosphate aldolases (FBAs, EC 4.1.2.13) comprise one of two families of aldolases. Instead of forming a Schiff base intermediate using an ε-amino group of a lysine side chain, class II FBAs utilize Zn(II) to stabilize a proposed hydroxyenolate intermediate (HEI) in the reversible cleavage of fructose 1,6-bisphosphate, forming glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). As class II FBAs have been shown to be essential in pathogenic bacteria, focus has been placed on these enzymes as potential antibacterial targets. Although structural studies of class II FBAs from Mycobacterium tuberculosis (MtFBA), other bacteria, and protozoa have been reported, the structure of the active site loop responsible for catalyzing the protonation-deprotonation steps of the reaction for class II FBAs has not yet been observed. We therefore utilized the potent class II FBA inhibitor phosphoglycolohydroxamate (PGH) as a mimic of the HEI- and DHAP-bound form of the enzyme and determined the X-ray structure of the MtFBA-PGH complex to 1.58 Å. Remarkably, we are able to observe well-defined electron density for the previously elusive active site loop of MtFBA trapped in a catalytically competent orientation. Utilization of this structural information and site-directed mutagenesis and kinetic studies conducted on a series of residues within the active site loop revealed that E169 facilitates a water-mediated deprotonation-protonation step of the MtFBA reaction mechanism. Also, solvent isotope effects on MtFBA and catalytically relevant mutants were used to probe the effect of loop flexibility on catalytic efficiency. Additionally, we also reveal the structure of MtFBA in its holoenzyme form.

Active Site Loop Dynamics of a Class IIa Fructose 1,6-Bisphosphate Aldolase from Mycobacterium tuberculosis

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

Pegan, Scott D.; Rukseree, Kamolchanok; Capodagli, Glenn C.

The class II fructose 1,6-bisphosphate aldolases (FBAs, EC 4.1.2.13) comprises one of two families of aldolases. Instead of forming a Schiff base intermediate using an ε-amino group of a lysine side chain, class II FBAs utilize Zn(II) to stabilize a proposed hydroxyenolate intermediate (HEI) in the reversible cleavage of fructose 1,6-bisphosphate, forming glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). As class II FBAs have been shown to be essential in pathogenic bacteria, focus has been placed on these enzymes as potential antibacterial targets. Although structural studies of class II FBAs from Mycobacterium tuberculosis (MtFBA), other bacteria, and protozoa have been reported,more » the structure of the active site loop responsible for catalyzing the protonation–deprotonation steps of the reaction for class II FBAs has not yet been observed. We therefore utilized the potent class II FBA inhibitor phosphoglycolohydroxamate (PGH) as a mimic of the HEI- and DHAP-bound form of the enzyme and determined the X-ray structure of the MtFBA–PGH complex to 1.58 Å. Remarkably, we are able to observe well-defined electron density for the previously elusive active site loop of MtFBA trapped in a catalytically competent orientation. Utilization of this structural information and site-directed mutagenesis and kinetic studies conducted on a series of residues within the active site loop revealed that E169 facilitates a water-mediated deprotonation–protonation step of the MtFBA reaction mechanism. Furthermore, solvent isotope effects on MtFBA and catalytically relevant mutants were used to probe the effect of loop flexibility on catalytic efficiency. Additionally, we also reveal the structure of MtFBA in its holoenzyme form.« less

Exclusive Meson Electroweak production off Bound Nucleons

NASA Astrophysics Data System (ADS)

Sato, Toru

2018-05-01

The effects of final state interaction in electroweak pion production reactions have been studied. The one loop corrections to the impulse approximation due to the nucleon and the pion rescattering is evaluated using the ANL-Osaka dynamical coupled channel model for the meson production reactions. It is found the final state interaction will affects the ν N cross section extracted in the previous analysis of the ν d data.

Natural selection for costly nutrient recycling in simulated microbial metacommunities.

PubMed

Boyle, Richard A; Williams, Hywel T P; Lenton, Timothy M

2012-11-07

Recycling of essential nutrients occurs at scales from microbial communities to global biogeochemical cycles, often in association with ecological interactions in which two or more species utilise each others' metabolic by-products. However, recycling loops may be unstable; sequences of reactions leading to net recycling may be parasitised by side-reactions causing nutrient loss, while some reactions in any closed recycling loop are likely to be costly to participants. Here we examine the stability of nutrient recycling loops in an individual-based ecosystem model based on microbial functional types that differ in their metabolism. A supplied nutrient is utilised by a "source" functional type, generating a secondary nutrient that is subsequently used by two other types-a "mutualist" that regenerates the initial nutrient at a growth rate cost, and a "parasite" that produces a refractory waste product but does not incur any additional cost. The three functional types are distributed across a metacommunity in which separate patches are linked by a stochastic diffusive migration process. Regions of high mutualist abundance feature high levels of nutrient recycling and increased local population density leading to greater export of individuals, allowing the source-mutualist recycling loop to spread across the system. Individual-level selection favouring parasites is balanced by patch-level selection for high productivity, indirectly favouring mutualists due to the synergistic productivity benefits of the recycling loop they support. This suggests that multi-level selection may promote nutrient cycling and thereby help to explain the apparent ubiquity and stability of nutrient recycling in nature.

Evaluation of driver reactions for effective use of dynamic message signs in Richmond, Virginia.

DOT National Transportation Integrated Search

2010-02-01

Dynamic message signs (DMS) are used in conjunction with other media to communicate traffic conditions, general information, and recommended diversion strategies to motorists. Previous studies using loop detector data to estimate diversion rates attr...

Vehicle load-equalization system

NASA Technical Reports Server (NTRS)

Creasy, W. K.

1976-01-01

System uses cables and associated pulleys to form closed-loop suspension system for terrain compensation. Loop causes reactions at each of three wheels in response to loading at remaining wheel. Simplicity of design should be of interest to designers and manufacturers of construction equipment and off-road vehicles.

Apparatus for and method of monitoring for breached fuel elements

DOEpatents

Gross, K.C.; Strain, R.V.

1981-04-28

This invention teaches improved apparatus for the method of detecting a breach in cladded fuel used in a nuclear reactor. The detector apparatus uses a separate bypass loop for conveying part of the reactor coolant away from the core, and at least three separate delayed-neutron detectors mounted proximate this detector loop. The detectors are spaced apart so that the coolant flow time from the core to each detector is different, and these differences are known. The delayed-neutron activity at the detectors is a function of the delay time after the reaction in the fuel until the coolant carrying the delayed-neutron emitter passes the respective detector. This time delay is broken down into separate components including an isotopic holdup time required for the emitter to move through the fuel from the reaction to the coolant at the breach, and two transit times required for the emitter now in the coolant to flow from the breach to the detector loop and then via the loop to the detector.

Stellar evolution of high mass based on the Ledoux criterion for convection

NASA Technical Reports Server (NTRS)

Stothers, R.; Chin, C.

1972-01-01

Theoretical evolutionary sequences of models for stars of 15 and 30 solar masses were computed from the zero-age main sequence to the end of core helium burning. During the earliest stages of core helium depletion, the envelope rapidly expands into the red-supergiant configuration. At 15 solar mass, a blue loop on the H-R diagram ensues if the initial metals abundance, initial helium abundance, or C-12 + alpha particle reaction rate is sufficiently large, or if the 3-alpha reaction rate is sufficiently small. These quantities affect the opacity of the base of the outer convection zone, the mass of the core, and the thermal properties of the core. The blue loop occurs abruptly and fully developed when the critical value of any of these quantities is exceeded, and the effective temperature range and fraction of the lifetime of core helium burning during the slow phase of the blue loop vary surprisingly little. At 30 solar mass no blue loop occurs for any reasonable set of input parameters.

Multiple roles of mobile active center loops in the E1 component of the Escherichia coli pyruvate dehydrogenase complex - Linkage of protein dynamics to catalysis

PubMed Central

Jordan, Frank; Arjunan, Palaniappa; Kale, Sachin; Nemeria, Natalia S.; Furey, William

2009-01-01

The region encompassing residues 401–413 on the E1 component of the pyruvate dehydrogenase multienzyme complex from Escherichia coli comprises a loop (the inner loop) which was not seen in the X-ray structure in the presence of thiamin diphosphate, the required cofactor for the enzyme. This loop is seen in the presence of a stable analogue of the pre-decarboxylation intermediate, the covalent adduct between the substrate analogue methyl acetylphosphonate and thiamin diphosphate, C2α-phosphonolactylthiamin diphosphate. It has been shown that the residue H407 and several other residues on this loop are required to reduce the mobility of the loop so electron density corresponding to it can be seen once the pre-decarboxylation intermediate is formed. Concomitantly, the loop encompassing residues 541–557 (the outer loop) appears to work in tandem with the inner loop and there is a hydrogen bond between the two loops ensuring their correlated motion. The inner loop was shown to: a) sequester the active center from carboligase side reactions; b) assist the interaction between the E1 and the E2 components, thereby affecting the overall reaction rate of the entire multienzyme complex; c) control substrate access to the active center. Using viscosity effects on kinetics it was shown that formation of the pre-decarboxylation intermediate is specifically affected by loop movement. A cysteine-less variant was created for the E1 component, onto which cysteines were substituted at selected loop positions. Introducing an electron spin resonance spin label and an 19F NMR label onto these engineered cysteines, the loop mobility was examined: a) both methods suggested that in the absence of ligand, the loop exists in two conformations; b) line-shape analysis of the NMR signal at different temperatures, enabled estimation of the rate constant for loop movement, and this rate constant was found to be of the same order of magnitude as the turnover number for the enzyme under the same conditions. Furthermore, this analysis gave important insights into rate-limiting thermal loop dynamics. Overall, the results suggest that the dynamic properties correlate with catalytic events on the E1 component of the pyruvate dehydrogenase complex. PMID:20160956

Chemical Looping Technology: Oxygen Carrier Characteristics.

PubMed

Luo, Siwei; Zeng, Liang; Fan, Liang-Shih

2015-01-01

Chemical looping processes are characterized as promising carbonaceous fuel conversion technologies with the advantages of manageable CO2 capture and high energy conversion efficiency. Depending on the chemical looping reaction products generated, chemical looping technologies generally can be grouped into two types: chemical looping full oxidation (CLFO) and chemical looping partial oxidation (CLPO). In CLFO, carbonaceous fuels are fully oxidized to CO2 and H2O, as typically represented by chemical looping combustion with electricity as the primary product. In CLPO, however, carbonaceous fuels are partially oxidized, as typically represented by chemical looping gasification with syngas or hydrogen as the primary product. Both CLFO and CLPO share similar operational features; however, the optimum process configurations and the specific oxygen carriers used between them can vary significantly. Progress in both CLFO and CLPO is reviewed and analyzed with specific focus on oxygen carrier developments that characterize these technologies.

Formation of prismatic loops from C15 Laves phase interstitial clusters in body-centered cubic iron

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

Zhang, Yongfeng; Bai, Xian-Ming; Tonks, Michael R.

2015-03-01

This Letter reports the transition of C15 phase self-interstitial clusters to loops in body-centered-cubic Iron. Molecular dynamics simulations are performed to evaluate the relative stabilities of difference interstitial cluster configurations including C15 phase structure and <100> and <111>/2 loops. Within a certain size range, C15 cluster are found more stable than loops, and the relative stabilities are reversed beyond that range. In accordance to the crossover in relative stabilities, C15 clusters may grow by absorbing individual interstitials at small sizes and transitions into loops eventually. The transition takes place by nucleation and reaction of <111>/2 loop segments. These observations explainmore » the absence of C15 phase interstitial clusters predicted by density-functional-theory calculations in previous experimental observations. More importantly, the current results provide a new formation mechanism of <100> loops which requires no interaction of loops.« less

Accelerated isothermal nucleic acid amplification in betaine-free reaction.

PubMed

Ma, Cuiping; Wang, Yifan; Zhang, Pansong; Shi, Chao

2017-08-01

Betaine was used as a common additive to isothermal nucleic acid amplification reactions because of lowering the melting temperature (Tm) of DNA. Herein, we reported a novel finding that betaine was inhibiting the reaction efficiency of isothermal amplification reactions. In this work, we have verified this finding by classical loop-mediated isothermal amplification that the addition of 0.8 M betaine inhibited the efficiency of reaction dropping to approximately 1%. Additionally, we clarified the mechanism of betaine hindering isothermal amplification reactions with a molecular barrier to lower associate rate constant K1 for intermolecular hybridization. This finding would be very significant for studies on the interaction between small molecule substance and DNA, and the development of point-of-care testing because of simplifying reaction system and increasing reaction efficiency. Copyright © 2017 Elsevier Inc. All rights reserved.

Techniques for Teachers Section

ERIC Educational Resources Information Center

Tait, A., Ed.

1973-01-01

Includes a simple technique to demonstrate Millikan's oil drop experiment, an environmental studies experiment to measure dissolved oxygen in water samples, and a technique to demonstrate action-reaction. Science materials described are the Pol-A-Star Tomiscope, Nuffield chemistry film loops, air pucks and pH meters. (JR)

One-Pot Reverse Transcriptional Loop-Mediated Isothermal Amplification (RT-LAMP) for Detecting MERS-CoV

PubMed Central

Lee, Se Hee; Baek, Yun Hee; Kim, Yang-Hoon; Choi, Young-Ki; Song, Min-Suk; Ahn, Ji-Young

2017-01-01

Due to the limitation of rapid development of specific antiviral drug or vaccine for novel emerging viruses, an accurate and rapid diagnosis is a key to manage the virus spread. We developed an efficient and rapid method with high specificity for the Middle East Respiratory Syndrome coronavirus (MERS-CoV), based on one-pot reverse transcription loop-mediated isothermal amplification (one-pot RT-LAMP). A set of six LAMP primers [F3, B3, FIP, BIP, LF (Loop-F), and LB (Loop-B)] were designed using the sequence of nucleocapsid (N) gene with optimized RT-LAMP enzyme conditions: 100 U M-MLV RTase and 4 U Bst polymerase, implying that the reaction was able to detect four infectious viral genome copies of MERS-CoV within a 60 min reaction time period. Significantly, EvaGreen dye has better signal read-out properties in one-pot RT-LAMP reaction and is more compatible with DNA polymerase than SYBR green I. Isothermally amplified specific N genes were further evaluated using field-deployable microchamber devices, leading to the specific identification of as few as 0.4 infectious viral genome copies, with no cross-reaction to the other acute respiratory disease viruses, including influenza type A (H1N1 and H3N2), type B, human coronavirus 229E, and human metapneumovirus. This sensitive, specific and feasible method provides a large-scale technical support in emergencies, and is also applied as a sample-to-detection module in Point of Care Testing devices. PMID:28119682

Detection of Fungi from an Indoor Environment using Loop-mediated Isothermal Amplification (LAMP) Method.

PubMed

Nakayama, Takako; Yamazaki, Takashi; Yo, Ayaka; Tone, Kazuya; Mahdi Alshahni, Mohamed; Fujisaki, Ryuichi; Makimura, Koichi

2017-01-01

　Loop-mediated isothermal amplification (LAMP) is a useful DNA detection method with high specificity and sensitivity. The LAMP reaction is carried out within a short time at a constant temperature without the need for thermal cycling. We developed a LAMP primer set for detecting a wide range of fungi by aligning the sequences of the large subunit ribosomal RNA gene of Candida albicans (Ascomycota), Cryptococcus neoformans (Basidiomycota), and Mucor racemosus (Mucorales). The threshold of C. albicans rDNA as template with our LAMP primer set was in the range of 10-100 copies per a reaction. In this study, we evaluated the correlation between colony forming units (CFU) and LAMP detection rate using the LAMP method for environmental fungi. The LAMP method should be a useful means of detecting fungi in indoor environments, disaster areas, or even in confined manned spacecraft to prevent allergies or infections caused by fungi.

Enzymatic function of loop movement in enolase: preparation and some properties of H159N, H159A, H159F, and N207A enolases.

PubMed

Brewer, John M; Glover, Claiborne V C; Holland, Michael J; Lebioda, Lukasz

2003-05-01

The hypothesis that His159 in yeast enolase moves on a polypeptide loop to protonate the phosphoryl of 2-phosphoglycerate to initiate its conversion to phosphoenolpyruvate was tested by preparing H159N, H159A, and H159F enolases. These have 0.07%-0.25% of the native activity under standard assay conditions and the pH dependence of maximum velocities of H159A and H159N mutants is markedly altered. Activation by Mg2+ is biphasic, with the smaller Mg2+ activation constant closer to that of the "catalytic" Mg2+ binding site of native enolase and the larger in the mM range in which native enolase is inhibited. A third Mg2+ may bind to the phosphoryl, functionally replacing proton donation by His159. N207A enolase lacks an intersubunit interaction that stabilizes the closed loop(s) conformation when 2-phosphoglycerate binds. It has 21% of the native activity, also exhibits biphasic Mg2+ activation, and its reaction with the aldehyde analogue of the substrate is more strongly inhibited than is its normal enzymatic reaction. Polypeptide loop(s) closure may keep a proton from His159 interacting with the substrate phosphoryl oxygen long enough to stabilize a carbanion intermediate.

Enzyme architecture: the effect of replacement and deletion mutations of loop 6 on catalysis by triosephosphate isomerase.

PubMed

Zhai, Xiang; Go, Maybelle K; O'Donoghue, AnnMarie C; Amyes, Tina L; Pegan, Scott D; Wang, Yan; Loria, J Patrick; Mesecar, Andrew D; Richard, John P

2014-06-03

Two mutations of the phosphodianion gripper loop in chicken muscle triosephosphate isomerase (cTIM) were examined: (1) the loop deletion mutant (LDM) formed by removal of residues 170-173 [Pompliano, D. L., et al. (1990) Biochemistry 29, 3186-3194] and (2) the loop 6 replacement mutant (L6RM), in which the N-terminal hinge sequence of TIM from eukaryotes, 166-PXW-168 (X = L or V), is replaced by the sequence from archaea, 166-PPE-168. The X-ray crystal structure of the L6RM shows a large displacement of the side chain of E168 from that for W168 in wild-type cTIM. Solution nuclear magnetic resonance data show that the L6RM results in significant chemical shift changes in loop 6 and surrounding regions, and that the binding of glycerol 3-phosphate (G3P) results in chemical shift changes for nuclei at the active site of the L6RM that are smaller than those of wild-type cTIM. Interactions with loop 6 of the L6RM stabilize the enediolate intermediate toward the elimination reaction catalyzed by the LDM. The LDM and L6RM result in 800000- and 23000-fold decreases, respectively, in kcat/Km for isomerization of GAP. Saturation of the LDM, but not the L6RM, by substrate and inhibitor phosphoglycolate is detected by steady-state kinetic analyses. We propose, on the basis of a comparison of X-ray crystal structures for wild-type TIM and the L6RM, that ligands bind weakly to the L6RM because a large fraction of the ligand binding energy is utilized to overcome destabilizing electrostatic interactions between the side chains of E168 and E129 that are predicted to develop in the loop-closed enzyme. Similar normalized yields of DHAP, d-DHAP, and d-GAP are formed in LDM- and L6RM-catalyzed reactions of GAP in D2O. The smaller normalized 12-13% yield of DHAP and d-DHAP observed for the mutant cTIM-catalyzed reactions compared with the 79% yield of these products for wild-type cTIM suggests that these mutations impair the transfer of a proton from O-2 to O-1 at the initial enediolate phosphate intermediate. No products are detected for the LDM-catalyzed isomerization reactions in D2O of [1-(13)C]GA and HPi, but the L6RM-catalyzed reaction in the presence of 0.020 M dianion gives a 2% yield of the isomerization product [2-(13)C,2-(2)H]GA.

A conserved loop-wedge motif moderates reaction site search and recognition by FEN1.

PubMed

Thompson, Mark J; Gotham, Victoria J B; Ciani, Barbara; Grasby, Jane A

2018-06-07

DNA replication and repair frequently involve intermediate two-way junction structures with overhangs, or flaps, that must be promptly removed; a task performed by the essential enzyme flap endonuclease 1 (FEN1). We demonstrate a functional relationship between two intrinsically disordered regions of the FEN1 protein, which recognize opposing sides of the junction and order in response to the requisite substrate. Our results inform a model in which short-range translocation of FEN1 on DNA facilitates search for the annealed 3'-terminus of a primer strand, which is recognized by breaking the terminal base pair to generate a substrate with a single nucleotide 3'-flap. This recognition event allosterically signals hydrolytic removal of the 5'-flap through reaction in the opposing junction duplex, by controlling access of the scissile phosphate diester to the active site. The recognition process relies on a highly-conserved 'wedge' residue located on a mobile loop that orders to bind the newly-unpaired base. The unanticipated 'loop-wedge' mechanism exerts control over substrate selection, rate of reaction and reaction site precision, and shares features with other enzymes that recognize irregular DNA structures. These new findings reveal how FEN1 precisely couples 3'-flap verification to function.

Studies of O18 impurity trapping at interstitial dislocation loops in ion implanted Fe (1 1 0) by ion channeling and ab initio calculations

NASA Astrophysics Data System (ADS)

Mathayan, Vairavel; Kothalamuthu, Saravanan; Gnanasekaran, Jaiganesh; Balakrishnan, Sundaravel; Panigrahi, Binaykumar

2018-01-01

The O18 and self ions are implanted at same depth in Fe (1 1 0) crystal and annealed to study the oxygen trapping under excess self interstitial defects. Rutherford backscattering spectrometry, nuclear reaction analysis and channeling measurements have been performed to determine the lattice site position of O18. The presence of dislocation loops is confirmed by energy-dependent dechanneling parameter measurements. From the tilt angular scans of Fe and O18 signals along 〈1 0 0〉, 〈1 1 0〉 axes, O18 is found to be displaced 0.2 Å from tetrahedral towards octahedral interstitial site in O18. Similar lattice site location of oxygen with the displacement of 0.37 Å is predicted by density functional theory calculations for the interaction of oxygen with 〈1 0 0〉 interstitial dislocation loop structure. Our results provide strong evidence on oxygen trapping at interstitial dislocation loops in the presence of excess interstitial defects in iron.

Rapid sex identification of papaya (Carica papaya) using multiplex loop-mediated isothermal amplification (mLAMP).

PubMed

Hsu, Te-Hua; Gwo, Jin-Chywan; Lin, Kuan-Hung

2012-10-01

Papaya (Carica papaya L.) is established as a cash crop throughout the tropical and subtropical regions due to its easy adaptation to diverse agricultural conditions, high yields, and prompt returns. The sex types of papaya plants are hermaphrodite, male, and female. Among them, hermaphroditic plants are the major type in papaya production, because the fruit has commercial advantages over that of the other sexes. Sex inheritance in papaya is determined by the M and M(h) dominant alleles in males and hermaphrodites, respectively, and a recessive m allele in females. Currently, all hermaphrodite seeds are not available due to the lethality of dominant homozygosity. Therefore, in this study, six male-hermaphrodite-specific markers were developed for a rapid sex identification using multiplex loop-mediated isothermal amplification (mLAMP) to efficiently and precisely select hermaphroditic individuals in the seedling or early growth stage. The LM1-LAMP assay consisted of two sex-LAMP reactions for amplifying two male-specific markers (T12 and Cpsm90) in one reaction, and showed several advantages in terms of a rapid reaction time (<1 h), isothermal conditions (less equipment required), a high efficiency (0.5 ng of DNA required in the reaction mixture), and an economical reaction system (5 μl in volume). The established method can be easily performed in the field by visual inspection and facilitates the selection of all hermaphroditic individuals in papaya production.

Analysis of fixed bed data for the extraction of a rate mechanism for the reaction of hematite with methane

DOE PAGES

Breault, Ronald W.; Monazam, Esmail R.

2015-04-01

In this study, chemical looping combustion is a promising technology for the capture of CO 2 involving redox materials as oxygen carriers. The effects of reduction conditions, namely, temperature and fuel partial pressure on the conversion products are investigated. The experiments were conducted in a laboratory fixed-bed reactor that was operated cyclically with alternating reduction and oxidation periods. Reactions are assumed to occur in the shell surrounding the particle grains with diffusion of oxygen to the surface from the grain core. Activation energies for the shell and core reactions range from 9 to 209 kJ/mol depending on the reaction step.

A reaction cell with sample laser heating for in situ soft X-ray absorption spectroscopy studies under environmental conditions.

PubMed

Escudero, Carlos; Jiang, Peng; Pach, Elzbieta; Borondics, Ferenc; West, Mark W; Tuxen, Anders; Chintapalli, Mahati; Carenco, Sophie; Guo, Jinghua; Salmeron, Miquel

2013-05-01

A miniature (1 ml volume) reaction cell with transparent X-ray windows and laser heating of the sample has been designed to conduct X-ray absorption spectroscopy studies of materials in the presence of gases at atmospheric pressures. Heating by laser solves the problems associated with the presence of reactive gases interacting with hot filaments used in resistive heating methods. It also facilitates collection of a small total electron yield signal by eliminating interference with heating current leakage and ground loops. The excellent operation of the cell is demonstrated with examples of CO and H2 Fischer-Tropsch reactions on Co nanoparticles.

Importance of Loop L1 Dynamics for Substrate Capture and Catalysis in Pseudomonas aeruginosa d-Arginine Dehydrogenase.

PubMed

Ouedraogo, Daniel; Souffrant, Michael; Vasquez, Sheena; Hamelberg, Donald; Gadda, Giovanni

2017-05-16

Mobile loops located at the active site entrance in enzymes often participate in conformational changes required to shield the reaction from bulk solvent, to control the access of the substrate to the active site, and to position residues for substrate binding and catalysis. In d-arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH), previous crystallographic data suggested that residues 45-47 in the FAD-binding domain and residues 50-56 in the substrate-binding domain in loop L1 could adopt two distinct conformations. In this study, we have used molecular dynamics, kinetics, and fluorescence spectroscopy on the S45A and A46G enzyme variants of PaDADH to investigate the impact of mutations in loop L1 on the catalytic function of the enzyme. Molecular dynamics showed that the mutant enzymes have probabilities of being in open conformations that are higher than that of wild-type PaDADH of loop L1, yielding an increased level of solvent exposure of the active site. In agreement, the flavin fluorescence intensity was ∼2-fold higher in the S45A and A46G enzymes than in wild-type PaDADH, with a 9 nm bathochromic shift of the emission band. In the variant enzymes, the k cat /K m values with d-arginine were ∼13-fold lower than in wild-type PaDADH. Moreover, the pH profiles for the k cat value with d-arginine showed a hollow, consistent with restricted proton movements in catalysis, and no saturation was achieved with the alternate substrate d-leucine in the reductive half-reaction of the variant enzymes. Taken together, the computational and experimental data are consistent with the dynamics of loop L1 being important for substrate capture and catalysis in PaDADH.

Lack of correlation between reaction speed and analytical sensitivity in isothermal amplification reveals the value of digital methods for optimization: validation using digital real-time RT-LAMP

PubMed Central

Khorosheva, Eugenia M.; Karymov, Mikhail A.; Selck, David A.; Ismagilov, Rustem F.

2016-01-01

In this paper, we asked if it is possible to identify the best primers and reaction conditions based on improvements in reaction speed when optimizing isothermal reactions. We used digital single-molecule, real-time analyses of both speed and efficiency of isothermal amplification reactions, which revealed that improvements in the speed of isothermal amplification reactions did not always correlate with improvements in digital efficiency (the fraction of molecules that amplify) or with analytical sensitivity. However, we observed that the speeds of amplification for single-molecule (in a digital device) and multi-molecule (e.g. in a PCR well plate) formats always correlated for the same conditions. Also, digital efficiency correlated with the analytical sensitivity of the same reaction performed in a multi-molecule format. Our finding was supported experimentally with examples of primer design, the use or exclusion of loop primers in different combinations, and the use of different enzyme mixtures in one-step reverse-transcription loop-mediated amplification (RT-LAMP). Our results show that measuring the digital efficiency of amplification of single-template molecules allows quick, reliable comparisons of the analytical sensitivity of reactions under any two tested conditions, independent of the speeds of the isothermal amplification reactions. PMID:26358811

Pitch Syntax Violations Are Linked to Greater Skin Conductance Changes, Relative to Timbral Violations - The Predictive Role of the Reward System in Perspective of Cortico-subcortical Loops.

PubMed

Gorzelańczyk, Edward J; Podlipniak, Piotr; Walecki, Piotr; Karpiński, Maciej; Tarnowska, Emilia

2017-01-01

According to contemporary opinion emotional reactions to syntactic violations are due to surprise as a result of the general mechanism of prediction. The classic view is that, the processing of musical syntax can be explained by activity of the cerebral cortex. However, some recent studies have indicated that subcortical brain structures, including those related to the processing of emotions, are also important during the processing of syntax. In order to check whether emotional reactions play a role in the processing of pitch syntax or are only the result of the general mechanism of prediction, the comparison of skin conductance levels reacting to three types of melodies were recorded. In this study, 28 subjects listened to three types of short melodies prepared in Musical Instrument Digital Interface Standard files (MIDI) - tonally correct, tonally violated (with one out-of-key - i.e., of high information content), and tonally correct but with one note played in a different timbre. The BioSemi ActiveTwo with two passive Nihon Kohden electrodes was used. Skin conductance levels were positively correlated with the presented stimuli (timbral changes and tonal violations). Although changes in skin conductance levels were also observed in response to the change in timbre, the reactions to tonal violations were significantly stronger. Therefore, despite the fact that timbral change is at least as equally unexpected as an out-of-key note, the processing of pitch syntax mainly generates increased activation of the sympathetic part of the autonomic nervous system. These results suggest that the cortico-subcortical loops (especially the anterior cingulate - limbic loop) may play an important role in the processing of musical syntax.

syk kinase activation by a src kinase-initiated activation loop phosphorylation chain reaction

PubMed Central

El-Hillal, O.; Kurosaki, T.; Yamamura, H.; Kinet, J.-P.; Scharenberg, A. M.

1997-01-01

Activation of the syk tyrosine kinase occurs almost immediately following engagement of many types of antigen receptors, including Fc receptors, but the mechanism through which syk is activated is currently unclear. Here we demonstrate that Fc receptor-induced syk activation occurs as the result of phosphorylation of the syk activation loop by both src family kinases and other molecules of activated syk, suggesting that syk activation occurs as the result of a src kinase-initiated activation loop phosphorylation chain reaction. This type of activation mechanism predicts that syk activation would exhibit exponential kinetics, providing a potential explanation for its rapid and robust activation by even weak antigen receptor stimuli. We propose that a similar mechanism may be responsible for generating rapid activation of other cytoplasmic tyrosine kinases, such as those of the Bruton tyrosine kinase/tec family, as well. PMID:9050880

Force-Manipulation Single-Molecule Spectroscopy Studies of Enzymatic Dynamics

NASA Astrophysics Data System (ADS)

Lu, H. Peter; He, Yufan; Lu, Maolin; Cao, Jin; Guo, Qing

2014-03-01

Subtle conformational changes play a crucial role in protein functions, especially in enzymatic reactions involving complex substrate-enzyme interactions and chemical reactions. We applied AFM-enhanced and magnetic tweezers-correlated single-molecule spectroscopy to study the mechanisms and dynamics of enzymatic reactions involved with kinase and lysozyme proteins. Enzymatic reaction turnovers and the associated structure changes of individual protein molecules were observed simultaneously in real-time by single-molecule FRET detections. Our single-molecule spectroscopy measurements of enzymatic conformational dynamics have revealed time bunching effect and intermittent coherence in conformational state change dynamics involving in enzymatic reaction cycles. The coherent conformational state dynamics suggests that the enzymatic catalysis involves a multi-step conformational motion along the coordinates of substrate-enzyme complex formation and product releasing. Our results support a multiple-conformational state model, being consistent with a complementary conformation selection and induced-fit enzymatic loop-gated conformational change mechanism in substrate-enzyme active complex formation.

Determination of Reaction Stoichiometries by Flow Injection Analysis.

ERIC Educational Resources Information Center

Rios, Angel; And Others

1986-01-01

Describes a method of flow injection analysis intended for calculation of complex-formation and redox reaction stoichiometries based on a closed-loop configuration. The technique is suitable for use in undergraduate laboratories. Information is provided for equipment, materials, procedures, and sample results. (JM)

Evaluation of Bosch-Based Systems Using Non-Traditional Catalysts at Reduced Temperatures

NASA Technical Reports Server (NTRS)

Abney, Morgan B.; Mansell, J. Matthew

2011-01-01

Oxygen and water resupply make open loop atmosphere revitalization (AR) systems unfavorable for long-term missions beyond low Earth orbit. Crucial to closing the AR loop are carbon dioxide reduction systems with low mass and volume, minimal power requirements, and minimal consumables. For this purpose, NASA is exploring using Bosch-based systems. The Bosch process is favorable over state-of-the-art Sabatier-based processes due to complete loop closure. However, traditional operation of the Bosch required high reaction temperatures, high recycle rates, and significant consumables in the form of catalyst resupply due to carbon fouling. A number of configurations have been proposed for next-generation Bosch systems. First, alternative catalysts (catalysts other than steel wool) can be used in a traditional single-stage Bosch reactor to improve reaction kinetics and increase carbon packing density. Second, the Bosch reactor may be split into separate stages wherein the first reactor stage is dedicated to carbon monoxide and water formation via the reverse water-gas shift reaction and the second reactor stage is dedicated to carbon formation. A series system will enable maximum efficiency of both steps of the Bosch reaction, resulting in optimized operation and maximum carbon formation rate. This paper details the results of testing of both single-stage and two-stage Bosch systems with alternative catalysts at reduced temperatures. These results are compared to a traditional Bosch system operated with a steel wool catalyst.

Accuracy of Loop-Mediated Isothermal Amplification for Diagnosis of Human Leptospirosis in Thailand

PubMed Central

Sonthayanon, Piengchan; Chierakul, Wirongrong; Wuthiekanun, Vanaporn; Thaipadungpanit, Janjira; Kalambaheti, Thareerat; Boonsilp, Siriphan; Amornchai, Premjit; Smythe, Lee D.; Limmathurotsakul, Direk; Day, Nicholas P.; Peacock, Sharon J.

2011-01-01

There is a lack of diagnostic tests for leptospirosis in technology-restricted settings. We developed loop-mediated isothermal amplification (LAMP) specific for the 16S ribosomal RNA gene (rrs) of pathogenic and intermediate group Leptospira species. The lower limit of detection was 10 genomic equivalents/reaction, and analytical specificity was high; we observed positive reactions for pathogenic/intermediate groups and negative reactions for non-pathogenic Leptospira species and other bacterial species. We evaluated this assay in Thailand by using a case–control study of 133 patients with laboratory-proven leptospirosis and 133 patients with other febrile illnesses. Using admission blood, we found that the rrs LAMP showed positive results in 58 of 133 cases (diagnostic sensitivity = 43.6, 95% confidence interval [CI] = 35.0–52.5) and in 22 of 133 controls (diagnostic specificity = 83.5, 95% CI = 76.0–89.3). Sensitivity was high for 39 patients who were culture positive for Leptospira spp. (84.6, 95% CI = 69.5–94.1). The rrs LAMP can provide an admission diagnosis in approximately half of patients with leptospirosis, but its clinical utility is reduced by a lower specificity. PMID:21460019

Accuracy of loop-mediated isothermal amplification for diagnosis of human leptospirosis in Thailand.

PubMed

Sonthayanon, Piengchan; Chierakul, Wirongrong; Wuthiekanun, Vanaporn; Thaipadungpanit, Janjira; Kalambaheti, Thareerat; Boonsilp, Siriphan; Amornchai, Premjit; Smythe, Lee D; Limmathurotsakul, Direk; Day, Nicholas P; Peacock, Sharon J

2011-04-01

There is a lack of diagnostic tests for leptospirosis in technology-restricted settings. We developed loop-mediated isothermal amplification (LAMP) specific for the 16S ribosomal RNA gene (rrs) of pathogenic and intermediate group Leptospira species. The lower limit of detection was 10 genomic equivalents/reaction, and analytical specificity was high; we observed positive reactions for pathogenic/intermediate groups and negative reactions for non-pathogenic Leptospira species and other bacterial species. We evaluated this assay in Thailand by using a case-control study of 133 patients with laboratory-proven leptospirosis and 133 patients with other febrile illnesses. Using admission blood, we found that the rrs LAMP showed positive results in 58 of 133 cases (diagnostic sensitivity = 43.6, 95% confidence interval [CI] = 35.0-52.5) and in 22 of 133 controls (diagnostic specificity = 83.5, 95% CI = 76.0-89.3). Sensitivity was high for 39 patients who were culture positive for Leptospira spp. (84.6, 95% CI = 69.5-94.1). The rrs LAMP can provide an admission diagnosis in approximately half of patients with leptospirosis, but its clinical utility is reduced by a lower specificity.

An improved external recycle reactor for determining gas-solid reaction kinetics

NASA Technical Reports Server (NTRS)

Miller, Irvin M.; Hoyt, Ronald F.

1987-01-01

These improvements in the recycle system effectively eliminate initial concentration variation by two modifications: (1) a vacuum line connection to the recycle loop which permits this loop to be evacuated and then filled with the test gas mixture to slightly above atmospheric pressure; and (2) a bypass line across the reactor which permits the reactor to be held under vacuum while the rest of the recycle loop is filled with test gas. A three-step procedure for bringing the feed gas mixture into contact with the catalyst at time zero is described.

Chemicl-looping combustion of coal with metal oxide oxygen carriers

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

Siriwardane, R.; Tian, H.; Richards, G.

2009-01-01

The combustion and reoxidation properties of direct coal chemical-looping combustion (CLC) over CuO, Fe2O3, Co3O4, NiO, and Mn2O3 were investigated using thermogravimetric analysis (TGA) and bench-scale fixed-bed flow reactor studies. When coal is heated in either nitrogen or carbon dioxide (CO2), 50% of weight loss was observed because of partial pyrolysis, consistent with the proximate analysis. Among various metal oxides evaluated, CuO showed the best reaction properties: CuO can initiate the reduction reaction as low as 500 °C and complete the full combustion at 700 °C. In addition, the reduced copper can be fully reoxidized by air at 700 °C.more » The combustion products formed during the CLC reaction of the coal/metal oxide mixture are CO2 and water, while no carbon monoxide was observed. Multicycle TGA tests and bench-scale fixed-bed flow reactor tests strongly supported the feasibility of CLC of coal by using CuO as an oxygen carrier. Scanning electron microscopy (SEM) images of solid reaction products indicated some changes in the surface morphology of a CuO-coal sample after reduction/oxidation reactions at 800 °C. However, significant surface sintering was not observed. The interactions of fly ash with metal oxides were investigated by X-ray diffraction and thermodynamic analysis. Overall, the results indicated that it is feasible to develop CLC with coal by metal oxides as oxygen carriers.« less

Development of Loop-Mediated Isothermal Amplification Assay for Detection of Entamoeba histolytica▿

PubMed Central

Liang, Shih-Yu; Chan, Yun-Hsien; Hsia, Kan-Tai; Lee, Jing-Lun; Kuo, Ming-Chu; Hwa, Kuo-Yuan; Chan, Chi-Wen; Chiang, Ting-Yi; Chen, Jung-Sheng; Wu, Fang-Tzy; Ji, Dar-Der

2009-01-01

A novel one-step, closed-tube, loop-mediated isothermal amplification (LAMP) assay for detecting Entamoeba histolytica, one of the leading causes of morbidity in developing countries, was developed. The sensitivity of the LAMP assay is 1 parasite per reaction. A total of 130 clinical samples were analyzed, and the results compared with those of conventional nested PCR to validate the practicability of this assay. No DNA was amplified from other diarrheal pathogens, such as other Entamoeba species, bacteria, and viruses. These results indicate that LAMP is a rapid, simple, and valuable diagnostic tool for epidemiological studies of amebiasis. PMID:19321720

Writing and compiling code into biochemistry.

PubMed

Shea, Adam; Fett, Brian; Riedel, Marc D; Parhi, Keshab

2010-01-01

This paper presents a methodology for translating iterative arithmetic computation, specified as high-level programming constructs, into biochemical reactions. From an input/output specification, we generate biochemical reactions that produce output quantities of proteins as a function of input quantities performing operations such as addition, subtraction, and scalar multiplication. Iterative constructs such as "while" loops and "for" loops are implemented by transferring quantities between protein types, based on a clocking mechanism. Synthesis first is performed at a conceptual level, in terms of abstract biochemical reactions - a task analogous to high-level program compilation. Then the results are mapped onto specific biochemical reactions selected from libraries - a task analogous to machine language compilation. We demonstrate our approach through the compilation of a variety of standard iterative functions: multiplication, exponentiation, discrete logarithms, raising to a power, and linear transforms on time series. The designs are validated through transient stochastic simulation of the chemical kinetics. We are exploring DNA-based computation via strand displacement as a possible experimental chassis.

Development of uracil-DNA-glycosylase-supplemented loop-mediated isothermal amplification coupled with nanogold probe (UDG-LAMP-AuNP) for specific detection of Pseudomonas aeruginosa.

PubMed

Manajit, Orapan; Longyant, Siwaporn; Sithigorngul, Paisarn; Chaivisuthangkura, Parin

2018-04-01

Pseudomonas aeruginosa (P. aeruginosa) is an important opportunistic pathogen that causes serious infections in humans, including keratitis in contact lens wearers. Therefore, establishing a rapid, specific and sensitive method for the identification of P. aeruginosa is imperative. In the present study, the uracil-DNA-glycosylase-supplemented loop-mediated isothermal amplification combined with nanogold labeled hybridization probe (UDG-LAMP-AuNP) was developed for the detection of P. aeruginosa. UDG-LAMP was performed to prevent carry over contamination and the LAMP reactions can be readily observed using the nanogold probe. A set of 4 primers and a hybridization probe were designed based on the ecfX gene. The UDG-LAMP reactions were performed at 65˚C for 60 min using the ratio of 40% deoxyuridine triphosphate to 60% deoxythymidine triphosphate. The detection of UDG-LAMP products using the nanogold labeled hybridization probe, which appeared as a red-purple color, was examined at 65˚C for 5 min with 40 mM MgSO4. The UDG-LAMP-AuNP demonstrated specificity to all tested isolates of P. aeruginosa without cross reaction to other bacteria. The sensitivity for the detection of pure culture was 1.6x103 colony-forming units (CFU) ml-1 or equivalent to 3 CFU per reaction while that of polymerase chain reaction was 30 CFU per reaction. The detection limit of spiked contact lenses was 1.1x103 CFU ml-1 or equivalent to 2 CFU per reaction. In conclusion, the UDG-LAMP-AuNP assay was rapid, simple, specific and was effective for the identification of P. aeruginosa in contaminated samples.

Development of uracil-DNA-glycosylase-supplemented loop-mediated isothermal amplification coupled with nanogold probe (UDG-LAMP-AuNP) for specific detection of Pseudomonas aeruginosa

PubMed Central

Manajit, Orapan; Longyant, Siwaporn; Sithigorngul, Paisarn; Chaivisuthangkura, Parin

2018-01-01

Pseudomonas aeruginosa (P. aeruginosa) is an important opportunistic pathogen that causes serious infections in humans, including keratitis in contact lens wearers. Therefore, establishing a rapid, specific and sensitive method for the identification of P. aeruginosa is imperative. In the present study, the uracil-DNA-glycosylase-supplemented loop-mediated isothermal amplification combined with nanogold labeled hybridization probe (UDG-LAMP-AuNP) was developed for the detection of P. aeruginosa. UDG-LAMP was performed to prevent carry over contamination and the LAMP reactions can be readily observed using the nanogold probe. A set of 4 primers and a hybridization probe were designed based on the ecfX gene. The UDG-LAMP reactions were performed at 65°C for 60 min using the ratio of 40% deoxyuridine triphosphate to 60% deoxythymidine triphosphate. The detection of UDG-LAMP products using the nanogold labeled hybridization probe, which appeared as a red-purple color, was examined at 65°C for 5 min with 40 mM MgSO4. The UDG-LAMP-AuNP demonstrated specificity to all tested isolates of P. aeruginosa without cross reaction to other bacteria. The sensitivity for the detection of pure culture was 1.6×103 colony-forming units (CFU) ml−1 or equivalent to 3 CFU per reaction while that of polymerase chain reaction was 30 CFU per reaction. The detection limit of spiked contact lenses was 1.1×103 CFU ml−1 or equivalent to 2 CFU per reaction. In conclusion, the UDG-LAMP-AuNP assay was rapid, simple, specific and was effective for the identification of P. aeruginosa in contaminated samples. PMID:29436623

Lack of correlation between reaction speed and analytical sensitivity in isothermal amplification reveals the value of digital methods for optimization: validation using digital real-time RT-LAMP.

PubMed

Khorosheva, Eugenia M; Karymov, Mikhail A; Selck, David A; Ismagilov, Rustem F

2016-01-29

In this paper, we asked if it is possible to identify the best primers and reaction conditions based on improvements in reaction speed when optimizing isothermal reactions. We used digital single-molecule, real-time analyses of both speed and efficiency of isothermal amplification reactions, which revealed that improvements in the speed of isothermal amplification reactions did not always correlate with improvements in digital efficiency (the fraction of molecules that amplify) or with analytical sensitivity. However, we observed that the speeds of amplification for single-molecule (in a digital device) and multi-molecule (e.g. in a PCR well plate) formats always correlated for the same conditions. Also, digital efficiency correlated with the analytical sensitivity of the same reaction performed in a multi-molecule format. Our finding was supported experimentally with examples of primer design, the use or exclusion of loop primers in different combinations, and the use of different enzyme mixtures in one-step reverse-transcription loop-mediated amplification (RT-LAMP). Our results show that measuring the digital efficiency of amplification of single-template molecules allows quick, reliable comparisons of the analytical sensitivity of reactions under any two tested conditions, independent of the speeds of the isothermal amplification reactions. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

New understanding of nano-scale interstitial dislocation loops in BCC iron

NASA Astrophysics Data System (ADS)

Gao, N.; Chen, J.; Kurtz, R. J.; Wang, Z. G.; Zhang, R. F.; Gao, F.

2017-11-01

Complex states of nanoscale interstitial dislocation loop can be described by its habit plane and Burgers vector. Using atomistic simulations, we provide direct evidences on the change of the habit plane of a 1/2〈1 1 1〉 loop from {1 1 1} to {1 1 0} and {2 1 1}, in agreement with TEM observations. A new {1 0 0} habit plane of this loop is also predicted by simulations. The non-conservation of the Burgers vector is approved theoretically for: (1) dislocation reactions between loops with different Burgers vectors and (2) the transition between 〈1 0 0〉 loops and 1/2〈1 1 1〉 loops. The rotation from a 1/2〈1 1 1〉 to a 〈1 0 0〉 loop has also been explored, which occurs at 570 K for time on the order of 10 s. The dislocation-precipitate phase duality and change of habit plane are then proposed as new features for nano-scale dislocation loops.

Auxiliary field loop expansion of the effective action for a class of stochastic partial differential equations

NASA Astrophysics Data System (ADS)

Cooper, Fred; Dawson, John F.

2016-02-01

We present an alternative to the perturbative (in coupling constant) diagrammatic approach for studying stochastic dynamics of a class of reaction diffusion systems. Our approach is based on an auxiliary field loop expansion for the path integral representation for the generating functional of the noise induced correlation functions of the fields describing these systems. The systems we consider include Langevin systems describable by the set of self interacting classical fields ϕi(x , t) in the presence of external noise ηi(x , t) , namely (∂t - ν∇2) ϕ - F [ ϕ ] = η, as well as chemical reaction annihilation processes obtained by applying the many-body approach of Doi-Peliti to the Master Equation formulation of these problems. We consider two different effective actions, one based on the Onsager-Machlup (OM) approach, and the other due to Janssen-deGenneris based on the Martin-Siggia-Rose (MSR) response function approach. For the simple models we consider, we determine an analytic expression for the Energy landscape (effective potential) in both formalisms and show how to obtain the more physical effective potential of the Onsager-Machlup approach from the MSR effective potential in leading order in the auxiliary field loop expansion. For the KPZ equation we find that our approximation, which is non-perturbative and obeys broken symmetry Ward identities, does not lead to the appearance of a fluctuation induced symmetry breakdown. This contradicts the results of earlier studies.

Partial deletion of beta9 loop in pancreatic lipase-related protein 2 reduces enzyme activity with a larger effect on long acyl chain substrates.

PubMed

Dridi, Kaouthar; Amara, Sawsan; Bezzine, Sofiane; Rodriguez, Jorge A; Carrière, Frédéric; Gaussier, Hélène

2013-07-01

Structural studies on pancreatic lipase have revealed a complex architecture of surface loops surrounding the enzyme active site and potentially involved in interactions with lipids. Two of them, the lid and beta loop, expose a large hydrophobic surface and are considered as acyl chain binding sites based on their interaction with an alkyl phosphonate inhibitor. While the role of the lid in substrate recognition and selectivity has been extensively studied, the implication of beta9 loop in acyl chain stabilization remained hypothetical. The characterization of an enzyme with a natural deletion of the lid, guinea pig pancreatic lipase-related protein 2 (GPLRP2), suggests however an essential contribution of the beta9 loop in the stabilization of the acyl enzyme intermediate formed during the lipolysis reaction. A GPLRP2 mutant with a seven-residue deletion of beta9 loop (GPLRP2-deltabeta9) was produced and its enzyme activity was measured using various substrates (triglycerides, monoglycerides, galactolipids, phospholipids, vinyl esters) with short, medium and long acyl chains. Whatever the substrate tested, GPLRP2-deltabeta9 activity is drastically reduced compared to that of wild-type GPLRP2 and this effect is more pronounced as the length of substrate acyl chain increases. Changes in relative substrate selectivity and stereoselectivity remained however weak. The deletion within beta9 loop has also a negative effect on the rate of enzyme inhibition by alkyl phosphonates. All these findings indicate that the reduced enzyme turnover observed with GPLRP2-deltabeta9 results from a weaker stabilization of the acyl enzyme intermediate due to a loss of hydrophobic interactions.

Architecture of a Diels-Alderase ribozyme with a preformed catalytic pocket.

PubMed

Keiper, Sonja; Bebenroth, Dirk; Seelig, Burckhard; Westhof, Eric; Jäschke, Andres

2004-09-01

Artificial ribozymes catalyze a variety of chemical reactions. Their structures and reaction mechanisms are largely unknown. We have analyzed a ribozyme catalyzing Diels-Alder cycloaddition reactions by comprehensive mutation analysis and a variety of probing techniques. New tertiary interactions involving base pairs between nucleotides of the 5' terminus and a large internal loop forming a pseudoknot fold were identified. The probing data indicate a preformed tertiary structure that shows no major changes on substrate or product binding. Based on these observations, a molecular architecture featuring a Y-shaped arrangement is proposed. The tertiary structure is formed in a rather unusual way; that is, the opposite sides of the asymmetric internal loop are clamped by the four 5'-terminal nucleotides, forming two adjacent two base-pair helices. It is proposed that the catalytic pocket is formed by a wedge within one of these helices.

Modal analysis of dislocation vibration and reaction attempt frequency

DOE PAGES

Sobie, Cameron; Capolungo, Laurent; McDowell, David L.; ...

2017-02-04

Transition state theory is a fundamental approach for temporal coarse-graining. It estimates the reaction rate for a transition processes by quantifying the activation free energy and attempt frequency for the unit process. To calculate the transition rate of a gliding dislocation, the attempt frequency is often obtained from line tension estimates of dislocation vibrations, a highly simplified model of dislocation behavior. This work revisits the calculation of attempt frequency for a dislocation bypassing an obstacle, in this case a self-interstitial atom (SIA) loop. First, a direct calculation of the vibrational characteristics of a finite pinned dislocation segment is compared tomore » line tension estimates before moving to the more complex case of dislocation-obstacle bypass. The entropic factor associated with the attempt frequency is calculated for a finite dislocation segment and for an infinite glide dislocation interacting with an SIA loop. Lastly, it is found to be dislocation length independent for three cases of dislocation-self interstitial atom (SIA) loop interactions.« less

Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes

PubMed Central

Sheng, Gang; Gogakos, Tasos; Wang, Jiuyu; Zhao, Hongtu; Serganov, Artem; Juranek, Stefan

2017-01-01

Abstract We have undertaken a systematic structural study of Thermus thermophilus Argonaute (TtAgo) ternary complexes containing single-base bulges positioned either within the seed segment of the guide or target strands and at the cleavage site. Our studies establish that single-base bulges 7T8, 5A6 and 4A5 on the guide strand are stacked-into the duplex, with conformational changes localized to the bulge site, thereby having minimal impact on the cleavage site. By contrast, single-base bulges 6’U7’ and 6’A7’ on the target strand are looped-out of the duplex, with the resulting conformational transitions shifting the cleavable phosphate by one step. We observe a stable alignment for the looped-out 6’N7’ bulge base, which stacks on the unpaired first base of the guide strand, with the looped-out alignment facilitated by weakened Watson–Crick and reversed non-canonical flanking pairs. These structural studies are complemented by cleavage assays that independently monitor the impact of bulges on TtAgo-mediated cleavage reaction. PMID:28911094

The interdigitating loop of the enolase superfamily as a specificity binding determinant or 'flying buttress'.

PubMed

Bearne, Stephen L

2017-05-01

Enzymes of the enolase superfamily (ENS) are mechanistically diverse, yet share a common partial reaction (abstraction of the α-proton from a carboxylate substrate). While the catalytic machinery responsible for the deprotonation reaction has been conserved, divergent evolution has led to numerous ENS members that catalyze different overall reactions. This rich functional diversity has made the ENS an excellent model system for developing the approaches necessary to validate enzyme function. However, enzymes of the ENS also share a common bidomain structure ((β/α) 7 β-barrel domain and α+β capping domain) which makes validation of function from structural information challenging. This review presents a comparative survey of the structural data obtained over the past decade for enzymes from all seven subgroups that comprise the ENS. Of the seven ENS subgroups (enolase, mandelate racemase (MR), muconate lactonizing enzyme, β-methylaspartate ammonia lyase, d-glucarate dehydratase, d-mannonate dehydratase (ManD), and galactarate dehydratase 2), only enzymes of the MR and ManD subgroups exhibit an additional feature of structural complexity-an interdigitating loop. This loop emanates from one protomer of a homodimeric pair and penetrates into the adjacent, symmetry-related protomer to either contribute a binding determinant to the active site of the adjacent protomer, or act as a 'flying buttress' to support residues of the active site. The analysis presented in this review suggests that the interdigitating loop is the only gross structural element that permits functional distinction between ENS subgroups at the tertiary level of protein structure. Copyright © 2017 Elsevier B.V. All rights reserved.

Oral insulin delivery using P(MAA-g-EG) hydrogels: effects of network morphology on insulin delivery characteristics.

PubMed

Nakamura, Koji; Murray, Robert J; Joseph, Jeffrey I; Peppas, Nicholas A; Morishita, Mariko; Lowman, Anthony M

2004-03-24

Hydrogels of poly(methacrylic acid-g-ethylene glycol) were prepared using different reaction water contents in order to vary the network mesh size, swelling behavior and insulin loading/release kinetics. Gels prepared with greater reaction solvent contents swelled to a greater degree and had a larger network mesh size. All of the hydrogels were able to incorporate insulin and protected it from release in acidic media. At higher pH (7.4), the release rates increased with reaction solvent content. Using a closed loop animal model, all of the insulin loaded formulations produced significant insulin absorption in the upper small intestine combined with hypoglycemic effects. In these studies, bioavailabilities ranged from 4.6% to 7.2% and were dependent on reaction solvent content.

Reaction of the rat tissues to implantation of polyhydroxyalkanoate films and ultrafine fibers.

PubMed

Maiborodin, I V; Shevela, A I; Morozov, V V; Novikova, Ya V; Matveeva, V A; Drovosekov, M N; Barannik, M I

2013-01-01

The reaction of various tissues of rats to implantation of polyhydroxyalkanoate films and ultrafine fibers was studied by optic microscopy. Implantation of polyhydroxyalkanoate films into the abdominal cavity caused a peritoneal reaction, leading after 1 month to the formation of fibrous adhesions between polyhydroxyalkanoate and intestinal loops. Under the skin and in the muscle tissue polyhydroxyalkanoate films were encapsulated in a thick fibrous capsule. Implantation of polyhydroxyalkanoate ultrathin fibers led to formation of foreign body granulomas in all tissues with perifocal inflammation and sclerosis of the adjacent tissues. The polymer was fragmented in these granulomas and phagocytosed by macrophages with the formation of giant foreign body cells. Hence, polyhydroxyalkanoate materials implanted in vivo caused chronic granulomatous inflammatory reaction and were very slowly destroyed by macrophages.

Reduction of Hematite to Magnetite in CO/CO2 Gas Mixtures Under Carbon Looping Combustion Conditions

NASA Astrophysics Data System (ADS)

Simmonds, Tegan; Hayes, Peter C.

2017-12-01

Iron oxides have been identified as promising materials for use as oxygen carriers in chemical looping combustion technologies as there are abundant resources available in the form of ore and in industrial wastes. The isothermal reduction of hematite (Fe2O3) in the fuel reactor and the subsequent oxidation of magnetite (Fe3O4) in air are the principal reactions of interest for these applications. Experimental investigations have been carried out to characterize the microstructural changes taking place as a result of the reduction reactions for a range of CO/CO2 gas compositions at temperatures between 1073 K and 1373 K (800 °C and 1100 °C). It has been shown that magnetite spinel is formed directly from hematite under these conditions and that porous magnetite or dense platelet or "lath" type morphologies can be formed depending on gas composition and reaction temperature. The conditions for the lath/pore transition are established. Dendritic gas pores are formed during the creation of the porous magnetite. This morphology allows continuous contact between the gas reactant and reaction interface and results in high reduction reaction rates.

Improved Performance of Loop-Mediated Isothermal Amplification Assays via Swarm Priming.

PubMed

Martineau, Rhett L; Murray, Sarah A; Ci, Shufang; Gao, Weimin; Chao, Shih-Hui; Meldrum, Deirdre R

2017-01-03

This work describes an enhancement to the loop-mediated isothermal amplification (LAMP) reaction which results in improved performance. Enhancement is achieved by adding a new set of primers to conventional LAMP reactions. These primers are termed "swarm primers" based on their relatively high concentration and their ability to create new amplicons despite the theoretical lack of single-stranded annealing sites. The primers target a region upstream of the FIP/BIP primer recognition sequences on opposite strands, substantially overlapping F1/B1 sites. Thus, despite the addition of a new primer set to an already complex assay, no significant increase in assay complexity is incurred. Swarm priming is presented for three DNA templates: Lambda phage, Synechocystis sp. PCC 6803 rbcL gene, and human HFE. The results of adding swarm primers to conventional LAMP reactions include increased amplification speed, increased indicator contrast, and increased reaction products. For at least one template, minor improvements in assay repeatability are also shown. In addition, swarm priming is shown to be effective at increasing the reaction speed for RNA amplification via RT-LAMP. Collectively, these results suggest that the addition of swarm primers will likely benefit most if not all existing LAMP assays based on state-of-the-art, six-primer reactions.

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

Taylor, Daniel D.; Schreiber, Nathaniel J.; Levitas, Benjamin D.

Oxygen storage materials (OSMs) provide lattice oxygen for a number of chemical-looping reactions including natural gas combustion and methane reforming. La 1–xSr xFeO 3-δ has shown promise for use as an OSM in methane reforming reactions due to its high product selectivity, fast oxide diffusion, and cycle stability. Here, we investigate the structural evolution of the series La 1–xSr xFeO 3-δ for x = 0, 1/3, 1/2, 2/3, and 1, using in situ synchrotron X-ray and neutron diffraction, as it is cycled under the conditions of a chemical-looping reactor (methane and oxygen atmospheres). In the compositions x = 1/3, 1/2,more » 2/3, and 1, we discover an envelope , or temperature range, of oxygen storage capacity (OSC), where oxygen can easily and reversibly be inserted and removed from the OSM. Our in situ X-ray and neutron diffraction results reveal that while samples with higher Sr contents had a higher OSC, those same samples suffered from slower reaction kinetics and some, such as the x = 1/2 and x = 2/3 compositions, had local variations in Sr content, which led to inhomogeneous regions with varying reaction rates. Therefore, we highlight the importance of in situ diffraction studies, and we propose that these measurements are required for the thorough evaluation of future candidate OSMs. Furthermore, we recommend La 2/3Sr 1/3FeO 3-δ as the optimal OSM in the series because its structure remains homogeneous throughout the reaction, and its OSC envelope is similar to that of the higher doped materials.« less

Automated stopped-in-dual-loop flow analysis system for catalytic determination of vanadium in drinking water.

PubMed

Teshima, Norio; Kuno, Masami; Ueda, Minoru; Ueda, Hisashi; Ohno, Shinsuke; Sakai, Tadao

2009-07-15

An automated stopped-in-dual-loop flow analysis (SIDL-FA) system is proposed for the determination of vanadium in drinking water. The chemistry is based on the vanadium-catalyzed oxidation reaction of p-anisidine by bromate in the presence of Tiron as an activator to produce a dye (lambda(max)=510 nm). A SIDL-FA system basically consists of a selection valve, three pumps (one is for delivering of standard/sample, and others are for reagents), two six-way injection valves, a spectrophotometric detector and a data acquisition device. A 100-microL coiled loop around a heated device is fitted onto each six-way injection valve. A well-mixed solution containing reagents and standard/sample is loaded into the first loop on a six-way valve, and then the same solution is loaded into the second loop on another six-way valve. The solutions are isolated by switching these two six-way valves, so that the catalytic reaction can be promoted. The net waste can be zero in this stage, because all pumps are turned off. Then each resulting solution is dispensed to the detector with suitable time lag. A touchscreen controller is developed to automatically carry out the original SIDL-FA protocol. The proposed SIDL-FA method allows vanadium to be quantified in the range of 0.1-2 microg L(-1) and is applied to the determination of vanadium in drinking water samples.

Cambium

NASA Technical Reports Server (NTRS)

Savidge, Rodney

2009-01-01

The Cambium investigation is one in a pair of investigations which utilizes the Advanced Biological Research System (ABRS). Cambium seeks definitive evidence that gravity has a direct effect on cambial cells (cells located under the inner bark where secondary growth occurs) in willow, Salix babylonica. The Cambium investigation uses willow plants flown on the International Space Station to better understand the fundamental processes by which plants produce cellulose and lignin, the two main structural materials found in plant matter. On Earth, the nature of wood within tree stems varies depending on position, and that within-tree variation includes differences in cell types and chemistry including lignin and cellulose, two major components of wood influencing wood strength, usefulness and carbon content. Reaction wood is an extreme example of such variation, and it is believed that reaction wood develops as a reaction to the influence of gravity. For the Cambium experiment, young willow plants will be launched to the ISS where their stems will be looped in an attempt to induce reaction wood formation. After on-orbit growth, the plants will be preserved and returned to Earth for analysis. Understanding the role of gravity in wood formation is expected to enable wiser management of forests for carbon sequestration as well as better utilization of trees for wood products. Detailed Research Description: The Cambium experiment will provide an understanding of physiological processes such as gene expression, metabolism and general plant development that are affected in plant systems exposed to space flight. Cambium seeks definitive evidence that gravity has a direct effect on the cambial cells (cells located under the inner bark where secondary growth occurs) that contribute to xylogenesis (reaction wood formation) in willow plants, Salix babylonica. Tension wood fibers differentiate on the upper sides of stems when the stem is altered from its normal (vertical) growth position by looping. This reaction wood response does not occur if the orientation of the plant stem with respect to gravity is not altered. If a localized zone of tension wood should be formed in looped stems under microgravity conditions, this would be the first conclusive evidence that gravity is not required. On the other hand, if a zone of tension wood is not produced in looped stems (subjected to tension on one side, compression on the other) in microgravity, this would be the first definitive evidence that gravity has a direct effect on the cambial cells which contribute to reaction wood formation. Following return to Earth the plants will be analyzed by microscopy and chemical methods.

Three-dimensional studies of pathogenic peptides from the c-terminal of Trypanosoma cruzi ribosomal P proteins and their interaction with a monoclonal antibody structural model

PubMed Central

Martín, Osvaldo A; Villegas, Myriam E; Aguilar, Carlos F

2009-01-01

The acidic C-terminal peptides from Trypanosoma cruzi ribosomal P proteins are the major target of the antibody response in patients suffering Chagas chronic heart disease. It has been proposed that the disease is triggered by the cross-reaction of these antibodies with the second extra cellular loop of the β1-adrenoreceptor, brought about by the molecular mimicry between the acidic C-terminal peptides and the receptor's loop. To improve the understanding of the structural basis of the autoimmune response against heart receptors, the 3-dimensional structure of the C-terminal peptides of Trypanosoma cruzi ribosomal proteins P0 (EDDDDDFGMGALF) and P2β (EEEDDDMGFGLFD) were solved using the Electrostaticaly Driven MonteCarlo method. Their structures were compared with the second extra-cellular loop of our homology model of human rhodopsin and the existing experimental NMR structures of the C-terminal peptides from human P0 (EESDDDMGFGLFD) and from Leishmania braziliensis P0 (EEADDDMGFGLFD). Docking of Trypanosoma cruzi peptides P0, P2β and human rhodopsin loop into our anti-P2β monoclonal antibody homology model allowed to explore their interactions. The solution structure of peptides P0 and P2β can be briefly described as a bend. Although the global conformations of the peptides are not identical they shared a common region of four residues (3 to 6) that have a similar structure. The structural alignment of the five peptides also showed a surprising conformational similarity for the same residues. The antibody model and docking studies revealed a most remarkable feature in the active site, a positively charged, narrow and deep cavity where the acidic residues 3 to 6 were accommodated. These results suggest that the most important elements in the molecular peptide recognition by the antibody may be the shape of the loop and the presence of negative charges in positions 3–5 (P0, P2β) or a negative charge in position 4 (rhodopsin loop). This work describes clearly the interactions of the structural elements involved in the autoimmune mechanism of anti-P auto-antibodies cross-reaction and stimulation of the β1-adrenoreceptor and the visual pigment rhodopsin. Results from this study could lead eventually to the development of treatments to abolish receptor mediated symptoms in Chagas. PACS code: 87.15.-v PMID:19473527

Sulphation of CaO-Based Sorbent Modified in CO2 Looping Cycles

NASA Astrophysics Data System (ADS)

Manovic, Vasilije; Anthony, Edward J.; Loncarevic, Davor

CaO-based looping cycles for CO2 capture at high temperatures are based on cyclical carbonation of CaO and regeneration of CaCO3. The main limitation of natural sorbents is the loss of carrying capacity with increasing numbers of reaction cycles, resulting in spent sorbent ballast. Use of spent sorbent from CO2 looping cycles for SO2 capture is a possible solution investigated in this study. Three limestones were investigated: Kelly Rock (Canada), La Blanca (Spain) and Katowice (Poland). Carbonation/calcination cycles were performed in a tube furnace with original limestones and samples thermally pretreated for different times (i.e., sintered). The spent sorbent samples were sulphated in a thermogravimetric analyzer. Changes in the resulting pore structure were then investigated using mercury porosimetry. Final conversions of both spent and pretreated sorbents after longer sulphation times were comparable or higher than those observed for the original sorbents. Maximum sulphation levels strongly depend on sorbent porosity and pore surface area. The shrinkage of sorbent particles during calcination/cycling resulted in a loss of sorbent porosity (≤48%), which corresponds to maximum sulphation levels ˜55% for spent Kelly Rock and Katowice. However, this is ˜10% higher than for the original samples. By contrast, La Blanca limestone had more pronounced particle shrinkage during pretreatment and cycling, leading to lower porosity, <35%, resulting in sulphation conversion of spent samples <30%, significantly lower than for the original sample (45%). These results showed that spent sorbent samples from CO2 looping cycles can be used as sorbents for SO2 retention if significant porosity loss does not occur during CO2 reaction cycles. For spent Kelly Rock and Katowice samples final conversions are determined by the total pore volume available for the bulky CaSO4 product.

Complete next-to-leading-order calculation for pion production in nucleon-nucleon collisions at threshold

NASA Astrophysics Data System (ADS)

Hanhart, C.; Kaiser, N.

2002-11-01

Based on a counting scheme that explicitly takes into account the large momentum (Mmπ) characteristic for pion production in nucleon-nucleon collisions we calculate all diagrams for the reaction NN-->NNπ at threshold up to next-to-leading-order. At this order there are no free parameters and the size of the next-to-leading- order contributions is in line with the expectation from power counting. The sum of loop corrections at that order vanishes for the process pp-->ppπ0 at threshold. The total contribution at next-to-leading-order from loop diagrams that include the delta degree of freedom vanishes at threshold in both reaction channels pp-->ppπ0,pnπ+.

Dynamic behavior of the bray-liebhafsky oscillatory reaction controlled by sulfuric acid and temperature

NASA Astrophysics Data System (ADS)

Pejić, N.; Vujković, M.; Maksimović, J.; Ivanović, A.; Anić, S.; Čupić, Ž.; Kolar-Anić, Lj.

2011-12-01

The non-periodic, periodic and chaotic regimes in the Bray-Liebhafsky (BL) oscillatory reaction observed in a continuously fed well stirred tank reactor (CSTR) under isothermal conditions at various inflow concentrations of the sulfuric acid were experimentally studied. In each series (at any fixed temperature), termination of oscillatory behavior via saddle loop infinite period bifurcation (SNIPER) as well as some kind of the Andronov-Hopf bifurcation is presented. In addition, it was found that an increase of temperature, in different series of experiments resulted in the shift of bifurcation point towards higher values of sulfuric acid concentration.

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

Phuthong, Witchukorn; Huang, Zubin; Wittkopp, Tyler M.

To investigate the dynamics of photosynthetic pigment-protein complexes in vascular plants at high resolution in an aqueous environment, membrane-protruding oxygen-evolving complexes (OECs) associated with photosystem II (PSII) on spinach ( Spinacia oleracea) grana membranes were examined using contact mode atomic force microscopy. This study represents, to our knowledge, the first use of atomic force microscopy to distinguish the putative large extrinsic loop of Photosystem II CP47 reaction center protein (CP47) from the putative oxygen-evolving enhancer proteins 1, 2, and 3 (PsbO, PsbP, and PsbQ) and large extrinsic loop of Photosystem II CP43 reaction center protein (CP43) in the PSII-OEC extrinsicmore » domains of grana membranes under conditions resulting in the disordered arrangement of PSII-OEC particles. Moreover, we observed uncharacterized membrane particles that, based on their physical characteristics and electrophoretic analysis of the polypeptides associated with the grana samples, are hypothesized to be a domain of photosystem I that protrudes from the stromal face of single thylakoid bilayers. Furthermore, our results are interpreted in the context of the results of others that were obtained using cryo-electron microscopy (and single particle analysis), negative staining and freeze-fracture electron microscopy, as well as previous atomic force microscopy studies.« less

Onset of multiferroicity in nickel and lithium co-substituted barium titanate ceramics

NASA Astrophysics Data System (ADS)

Alkathy, Mahmoud S.; James Raju, K. C.

2018-04-01

The structural, magnetic and ferroelectric properties of nickel and lithium co-substituted barium titanate were investigated in this work. Ba(1-x)LixNix/2TiO3 (x = 0, 0.02, 0.04 and 0.08) ceramics were synthesized via solid-state reaction with the assistance of microwave heating of the starting materials. The tetragonal structure has been observed in all samples, and it is confirmed by the Rietveld refinement study. The morphological study has been carried out by FE-SEM. Electron spin resonance (ESR) has been used to study the electron interaction and to verify the magnetism behavior of present samples. No resonance signal was observed in pure BaTiO3 samples. However, the resonance signal has appeared in the co-substituted samples. The result shows that the electron interactions are strongly affected by Ni2+ and Li+ concentrations. M-H loop was traced using VSM at room temperature. The results confirm that the sample with x = 0 shows an anti-ferromagnetic response. However, a ferromagnetic hysteresis loop arises with co-substitution. The emergence of M-H loops confirms the appearance of magnetic properties in Ni2+ and Li+ co-substituted BaTiO3 ceramics. The origin of magnetic behavior could be due to the carrier-mediated exchange interactions. Room temperature P-E hysteresis loop has been investigated at an applied electric field of 35 kV/cm and 33 Hz frequency. Measurements of room temperature ferroelectric and magnetic hysteresis loops indicate that the Ni2+ and Li+ co-substituted BaTiO3 ceramics show ferroelectricity and ferromagnetism simultaneously.

Novel recirculating loop reactor for studies on model catalysts: CO oxidation on Pt/TiO2(110)

NASA Astrophysics Data System (ADS)

Tenney, Samuel A.; Xie, Kangmin; Monnier, John R.; Rodriguez, Abraham; Galhenage, Randima P.; Duke, Audrey S.; Chen, Donna A.

2013-10-01

A novel recirculating loop microreactor coupled to an ultrahigh vacuum (UHV) chamber has been constructed for the kinetic evaluation of model catalysts, which can be fully characterized by UHV surface science techniques. The challenge for this reactor design is to attain sufficient sensitivity to detect reactions on model single-crystal surfaces, which have a low number of active sites compared to conventional catalysts of equivalent mass. To this end, the total dead volume of the reactor system is minimized (32 cm3), and the system is operated in recirculation mode so that product concentrations build up to detectable levels over time. The injection of gas samples into the gas chromatography column and the refilling of the recirculation loop with fresh feed gas are achieved with computer-controlled, automated switching valves. In this manner, product concentrations can be followed over short time intervals (15 min) for extended periods of time (24 h). A proof of principle study in this reactor for CO oxidation at 145-165 °C on Pt clusters supported on a rutile TiO2(110) single crystal yields kinetic parameters that are comparable to those reported in the literature for CO oxidation on Pt clusters on powdered oxide supports, as well as on Pt(100). The calculated activation energy is 16.4 ± 0.7 kcal/mol, the turnover frequency is 0.03-0.06 molecules/(site.s) over the entire temperature range, and the reaction orders in O2 and CO at 160 °C are 0.9 ± 0.2 and -0.82 ± 0.03, respectively.

Theoretical nuclear physics

NASA Astrophysics Data System (ADS)

Rost, E.; Shephard, J. R.

1992-08-01

This report discusses the following topics: Exact 1-loop vacuum polarization effects in 1 + 1 dimensional QHD; exact 1-fermion loop contributions in 1 + 1 dimensional solitons; exact scalar 1-loop contributions in 1 + 3 dimensions; exact vacuum calculations in a hyper-spherical basis; relativistic nuclear matter with self-consistent correlation energy; consistent RHA-RPA for finite nuclei; transverse response functions in the (triangle)-resonance region; hadronic matter in a nontopological soliton model; scalar and vector contributions to (bar p)p yields (bar lambda)lambda reaction; 0+ and 2+ strengths in pion double-charge exchange to double giant-dipole resonances; and nucleons in a hybrid sigma model including a quantized pion field.

Clearing the Air: New Approaches to Life Support in Outer Space

NASA Technical Reports Server (NTRS)

Knox, J.; Howard, D.

2008-01-01

This article reports on research into atmospheric revitalization systems for long-term space travel and the use ofCOMSOL Multiphysics to understand how structured sorbents can be used to improve the performance of adsorption processes via thermal management. We are developing the next generation of atmosphere revitalization systems, which will reach for new levels of resource conservation via a high percentage of loop closure. For example, a high percentage of carbon dioxide, exhaled by crew, can be converted via reaction to drinking water, closing the loop from human metabolic waste to supply. Adsorption processes play a lead role in these new/closed loop systems.

Simulations of Living Cell Origins Using a Cellular Automata Model

NASA Astrophysics Data System (ADS)

Ishida, Takeshi

2014-04-01

Understanding the generalized mechanisms of cell self-assembly is fundamental for applications in various fields, such as mass producing molecular machines in nanotechnology. Thus, the details of real cellular reaction networks and the necessary conditions for self-organized cells must be elucidated. We constructed a 2-dimensional cellular automata model to investigate the emergence of biological cell formation, which incorporated a looped membrane and a membrane-bound information system (akin to a genetic code and gene expression system). In particular, with an artificial reaction system coupled with a thermal system, the simultaneous formation of a looped membrane and an inner reaction process resulted in a more stable structure. These double structures inspired the primitive biological cell formation process from chemical evolution stage. With a model to simulate cellular self-organization in a 2-dimensional cellular automata model, 3 phenomena could be realized: (1) an inner reaction system developed as an information carrier precursor (akin to DNA); (2) a cell border emerged (akin to a cell membrane); and (3) these cell structures could divide into 2. This double-structured cell was considered to be a primary biological cell. The outer loop evolved toward a lipid bilayer membrane, and inner polymeric particles evolved toward precursor information carriers (evolved toward DNA). This model did not completely clarify all the necessary and sufficient conditions for biological cell self-organization. Further, our virtual cells remained unstable and fragile. However, the "garbage bag model" of Dyson proposed that the first living cells were deficient; thus, it would be reasonable that the earliest cells were more unstable and fragile than the simplest current unicellular organisms.

Simulations of living cell origins using a cellular automata model.

PubMed

Ishida, Takeshi

2014-04-01

Understanding the generalized mechanisms of cell self-assembly is fundamental for applications in various fields, such as mass producing molecular machines in nanotechnology. Thus, the details of real cellular reaction networks and the necessary conditions for self-organized cells must be elucidated. We constructed a 2-dimensional cellular automata model to investigate the emergence of biological cell formation, which incorporated a looped membrane and a membrane-bound information system (akin to a genetic code and gene expression system). In particular, with an artificial reaction system coupled with a thermal system, the simultaneous formation of a looped membrane and an inner reaction process resulted in a more stable structure. These double structures inspired the primitive biological cell formation process from chemical evolution stage. With a model to simulate cellular self-organization in a 2-dimensional cellular automata model, 3 phenomena could be realized: (1) an inner reaction system developed as an information carrier precursor (akin to DNA); (2) a cell border emerged (akin to a cell membrane); and (3) these cell structures could divide into 2. This double-structured cell was considered to be a primary biological cell. The outer loop evolved toward a lipid bilayer membrane, and inner polymeric particles evolved toward precursor information carriers (evolved toward DNA). This model did not completely clarify all the necessary and sufficient conditions for biological cell self-organization. Further, our virtual cells remained unstable and fragile. However, the "garbage bag model" of Dyson proposed that the first living cells were deficient; thus, it would be reasonable that the earliest cells were more unstable and fragile than the simplest current unicellular organisms.

Loop-mediated isothermal PCR (LAMP) for the diagnosis of falciparum malaria.

PubMed

Paris, Daniel H; Imwong, Mallika; Faiz, Abul M; Hasan, Mahtabuddin; Yunus, Emran Bin; Silamut, Kamolrat; Lee, Sue J; Day, Nicholas P J; Dondorp, Arjen M

2007-11-01

A recently described loop-mediated isothermal polymerase chain reaction (LAMP) for molecular detection of Plasmodium falciparum was compared with microscopy, PfHRP2-based rapid diagnostic test (RDT), and nested polymerase chain reaction (PCR) as the "gold standard" in 115 Bangladeshi in-patients with fever. DNA extraction for LAMP was conducted by conventional methods or simple heating of the sample; test results were either assessed visually or by gel electrophoresis. Conventional DNA extraction followed by gel electrophoresis had the highest agreement with the reference method (81.7%, kappa = 0.64), with a sensitivity (95% CI) of 76.1% (68.3-83.9%), comparable to RDT and microscopy, but a specificity of 89.6% (84.0-95.2%) compared with 100% for RDT and microscopy. DNA extraction by heat treatment deteriorated specificity to unacceptable levels. LAMP enables molecular diagnosis of falciparum malaria in settings with limited technical resources but will need further optimization. The results are in contrast with a higher accuracy reported in an earlier study comparing LAMP with a non-validated PCR method.

One loop back reaction on power law inflation

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

Abramo, L.R.; Woodard, R.P.

1999-08-01

We consider quantum-mechanical corrections to a homogeneous, isotropic, and spatially flat geometry whose scale factor expands classically as a general power of the comoving time. The effects of both gravitons and the scalar inflaton are computed at one loop using the manifestly causal formalism of Schwinger [J. Math. Phys. {bold 2}, 407 (1961); {ital Particles, Sources and Fields} (Addison, Wesley, Reading, MA, 1970)] with the Feynman rules recently developed by Iliopoulos {ital et al.} [Nucl. Phys. B {bold 534}, 419 (1998)]. We find no significant effect, in marked contrast to the result obtained by Mukhanov and co-workers [Phys. Rev. Lett.more » {bold 78}, 1624 (1998); Phys. Rev. D {bold 56}, 3248 (1997)] for chaotic inflation based on a quadratic potential. By applying the canonical technique of Mukhanov and co-workers to the exponential potentials of power law inflation, we show that the two methods produce the same results, within the approximations employed, for these backgrounds. We therefore conclude that the shape of the inflaton potential can have an enormous impact on the one loop back reaction. {copyright} {ital 1999} {ital The American Physical Society}« less

Structural, electrical, magnetic and magnetoelectric properties of composites

NASA Astrophysics Data System (ADS)

Rani, Renu; Juneja, J. K.; Singh, Sangeeta; Prakash, Chandra; Raina, K. K.

2013-11-01

The magnetoelectric (ME) composites with composition (y)Ni0.8Zn0.2Fe2O4+(1-y) Ba0.90Sr0.10Zr0.04Ti0.96O3 ((y)NZF+(1-y)BSZT) (where y=0.00-0.15 in wt%) were prepared by the conventional solid state reaction route. The existence of both phases was confirmed by the X-Ray diffraction technique and the lattice parameters for all samples were calculated. The dielectric properties such as dielectric constant and dielectric loss were measured as a function of temperature at different frequencies. P-E hysteresis loops and M-H hysteresis loops confirm the ferroelectric and ferrimagnetic nature of the composite samples. M-H loops for electrically poled and un-poled samples were compared to prove ME evidences. Variation of ME coefficient (α) with dc magnetic field was also studied for all composite samples. The maximum value of α (1.6 mV/cm Oe) was observed for y=0.10 at 750 Oe.

Space Station on-orbit solar array loads during assembly

NASA Astrophysics Data System (ADS)

Ghofranian, S.; Fujii, E.; Larson, C. R.

This paper is concerned with the closed-loop dynamic analysis of on-orbit maneuvers when the Space Shuttle is fully mated to the Space Station Freedom. A flexible model of the Space Station in the form of component modes is attached to a rigid orbiter and on-orbit maneuvers are performed using the Shuttle Primary Reaction Control System jets. The traditional approach for this type of problems is to perform an open-loop analysis to determine the attitude control system jet profiles based on rigid vehicles and apply the resulting profile to a flexible Space Station. In this study a closed-loop Structure/Control model was developed in the Dynamic Analysis and Design System (DADS) program and the solar array loads were determined for single axis maneuvers with various delay times between jet firings. It is shown that the Digital Auto Pilot jet selection is affected by Space Station flexibility. It is also shown that for obtaining solar array loads the effect of high frequency modes cannot be ignored.

Development and evaluation of a loop-mediated isothermal amplification assay for rapid detection of lymphocystis disease virus.

PubMed

Li, Qiong; Yue, Zhiqin; Liu, Hong; Liang, Chengzhu; Zheng, Xiaolong; Zhao, Yuran; Chen, Xiao; Xiao, Xizhi; Chen, Changfu

2010-02-01

A loop-mediated isothermal amplification (LAMP) assay was developed for the detection of lymphocystis disease virus (LCDV). A set of five specific primers, two inner and two outer primers and a loop primer, were designed on the basis of the major capsid protein gene of LCDV. The reaction time and temperatures were optimized for 60 min at 63 degrees C, respectively. LAMP amplification products were detected by a ladder-like appearance on agarose gel electrophoresis or a naked-eye inspection of a color change in the reaction tube by addition of SYBR Green I. The assay was specific for LCDV, and there was no cross-reactivity with white spot syndrome virus (WSSV) or six other Iridoviridae viruses (epizootic hematopoietic necrosis virus, EHNV; tiger frog virus, TFV; Bohle iridovirus, BIV; soft-shelled turtle iridovirus, STIV; infectious spleen and kidney necrosis virus, ISKNV; red sea bream iridovirus, RSIV). The detection limit of the LAMP assay was 15 fg, which was similar to that of real-time quantitative polymerase chain reaction (PCR) and 10-fold higher than the conventional PCR. The LAMP assay was evaluated using 109 clinical samples, and the results indicated the suitability and simplicity of the test as a rapid, field diagnostic tool for detection of LCDV. The LCDV LAMP assay has potential for early diagnosis of LCDV infection. 2009 Elsevier B.V. All rights reserved.

Development and application of reverse transcription loop-mediated isothermal amplification for detecting live Shewanella putrefaciens in preserved fish sample.

PubMed

Li, Chenghua; Ying, Qi; Su, Xiurong; Li, Taiwu

2012-04-01

Given that live Shewanella putrefaciens is one of the major causes of spoilage for aquatic products even in chill storage, the rapid and accurate detection process is the first priority. In the present study, a novel reverse transcription loop-mediated isothermal amplification (RT-LAMP) detecting assay was developed by targeting internal transcribed spacer (ITS) sequence between 16S and 23S rRNA. At the same time, a new procaryotic mRNA isolation strategy was also established by introducing a polyA tail to RNA during cDNA synthesis step. Under the optimal reaction time (60 min) and temperature (64.1 °C), S. putrefaciens could be specially identified from a variety of other tested bacteria by RT-LAMP. The sensitivity analysis showed that RT-LAMP could be identified as lower as 5.4 copies per reaction, which is over 200-fold higher than that of standard PCR (1.08 × 10³ copies per reaction). The method could be effectively identified S. putrefaciens in artificially contaminated or spoilaged fish samples with dose-dependent manners. To our knowledge, this is the first report using RT-LAMP assay to detect live S. putrefaciens in fish. The study provided a rapid and accurate detection method for live bacteria in aquatic food and established a new procaryotic mRNA isolation strategy at the same time, which will be useful for food preservation. © 2012 Institute of Food Technologists®

Liquid uranium alloy-helium fission reactor

DOEpatents

Minkov, V.

1984-06-13

This invention describes a nuclear fission reactor which has a core vessel and at least one tandem heat exchanger vessel coupled therewith across upper and lower passages to define a closed flow loop. Nuclear fuel such as a uranium alloy in its liquid phase fills these vessels and flow passages. Solid control elements in the reactor core vessel are adapted to be adjusted relative to one another to control fission reaction of the liquid fuel therein. Moderator elements in the other vessel and flow passages preclude fission reaction therein. An inert gas such as helium is bubbled upwardly through the heat exchanger vessel operable to move the liquid fuel upwardly therein and unidirectionally around the closed loop and downwardly through the core vessel. This helium gas is further directed to heat conversion means outside of the reactor vessels to utilize the heat from the fission reaction to generate useful output. The nuclear fuel operates in the 1200 to 1800/sup 0/C range, and even higher to 2500/sup 0/C.

Using "human state aware" robots to enhance physical human-robot interaction in a cooperative scenario.

PubMed

Guerrero, Carlos Rodriguez; Fraile Marinero, Juan Carlos; Turiel, Javier Perez; Muñoz, Victor

2013-11-01

Human motor performance, speed and variability are highly susceptible to emotional states. This paper reviews the impact of the emotions on the motor control performance, and studies the possibility of improving the perceived skill/challenge relation on a multimodal neural rehabilitation scenario, by means of a biocybernetic controller that modulates the assistance provided by a haptic controlled robot in reaction to undesirable physical and mental states. Results from psychophysiological, performance and self assessment data for closed loop experiments in contrast with their open loop counterparts, suggest that the proposed method had a positive impact on the overall challenge/skill relation leading to an enhanced physical human-robot interaction experience. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Unique phase identification of trimetallic copper iron manganese oxygen carrier using simultaneous differential scanning calorimetry/thermogravimetric analysis during chemical looping combustion reactions with methane

DOE PAGES

Benincosa, William; Siriwardane, Ranjani; Tian, Hanjing; ...

2017-07-05

Chemical looping combustion (CLC) is a promising combustion technology that generates heat and sequestration-ready carbon dioxide that is undiluted by nitrogen from the combustion of carbonaceous fuels with an oxygen carrier, or metal oxide. This process is highly dependent on the reactivity and stability of the oxygen carrier. The development of oxygen carriers remains one of the major barriers for commercialization of CLC. Synthetic oxygen carriers, consisting of multiple metal components, have demonstrated enhanced performance and improved CLC operation compared to single metal oxides. However, identification of the complex mixed metal oxide phases that form after calcination or during CLCmore » reactions has been challenging. Without an understanding of the dominant metal oxide phase, it is difficult to determine reaction parameters and the oxygen carrier reduction pathway, which are necessary for CLC reactor design. This is particularly challenging for complex multi-component oxygen carriers such as copper iron manganese oxide (CuFeMnO 4). This study aims to differentiate the unique phase formation of a highly reactive, complex trimetallic oxygen carrier, CuFeMnO 4, from its single and bimetallic counterparts using thermochemical and reaction data obtained from simultaneous differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA) during temperature programmed reductions (TPR) with methane. DSC/TGA experiments during TPR with methane provides heat flow data and corresponding reaction rate data that can be used to determine reaction routes and mechanisms during methane reduction. Furthermore, non-isothermal TPR data provides the advantage of distinguishing reactions that may not be observable in isothermal analysis. The detailed thermochemical and reaction data, obtained during TPR with methane, distinguished a unique reduction pathway for CuFeMnO 4 that differed from its single and bimetallic counterparts. This is remarkable since X-ray diffraction (XRD) data alone could not be used to distinguish the reactive trimetallic oxide phase due to overlapping peaks from various single and mixed metal oxides. The unique reduction pathway of CuFeMnO 4 was further characterized in this study using in-situ XRD TPR with methane to determine changes in the dominant trimetallic phase that influenced the thermochemical and reaction rate data.« less

Unique phase identification of trimetallic copper iron manganese oxygen carrier using simultaneous differential scanning calorimetry/thermogravimetric analysis during chemical looping combustion reactions with methane

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

Benincosa, William; Siriwardane, Ranjani; Tian, Hanjing

Chemical looping combustion (CLC) is a promising combustion technology that generates heat and sequestration-ready carbon dioxide that is undiluted by nitrogen from the combustion of carbonaceous fuels with an oxygen carrier, or metal oxide. This process is highly dependent on the reactivity and stability of the oxygen carrier. The development of oxygen carriers remains one of the major barriers for commercialization of CLC. Synthetic oxygen carriers, consisting of multiple metal components, have demonstrated enhanced performance and improved CLC operation compared to single metal oxides. However, identification of the complex mixed metal oxide phases that form after calcination or during CLCmore » reactions has been challenging. Without an understanding of the dominant metal oxide phase, it is difficult to determine reaction parameters and the oxygen carrier reduction pathway, which are necessary for CLC reactor design. This is particularly challenging for complex multi-component oxygen carriers such as copper iron manganese oxide (CuFeMnO 4). This study aims to differentiate the unique phase formation of a highly reactive, complex trimetallic oxygen carrier, CuFeMnO 4, from its single and bimetallic counterparts using thermochemical and reaction data obtained from simultaneous differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA) during temperature programmed reductions (TPR) with methane. DSC/TGA experiments during TPR with methane provides heat flow data and corresponding reaction rate data that can be used to determine reaction routes and mechanisms during methane reduction. Furthermore, non-isothermal TPR data provides the advantage of distinguishing reactions that may not be observable in isothermal analysis. The detailed thermochemical and reaction data, obtained during TPR with methane, distinguished a unique reduction pathway for CuFeMnO 4 that differed from its single and bimetallic counterparts. This is remarkable since X-ray diffraction (XRD) data alone could not be used to distinguish the reactive trimetallic oxide phase due to overlapping peaks from various single and mixed metal oxides. The unique reduction pathway of CuFeMnO 4 was further characterized in this study using in-situ XRD TPR with methane to determine changes in the dominant trimetallic phase that influenced the thermochemical and reaction rate data.« less

Comparison of Conventional PCR, Multiplex PCR, and Loop-Mediated Isothermal Amplification Assays for Rapid Detection of Arcobacter Species

PubMed Central

Wang, Xiaoyu; Seo, Dong Joo; Lee, Min Hwa

2014-01-01

This study aimed to develop a loop-mediated isothermal amplification (LAMP) method for the rapid detection of Arcobacter species. Specific primers targeting the 23S ribosomal RNA gene were used to detect Arcobacter butzleri, Arcobacter cryaerophilus, and Arcobacter skirrowii. The specificity of the LAMP primer set was assessed using DNA samples from a panel of Arcobacter and Campylobacter species, and the sensitivity was determined using serial dilutions of Arcobacter species cultures. LAMP showed a 10- to 1,000-fold-higher sensitivity than multiplex PCR, with a detection limit of 2 to 20 CFU per reaction in vitro. Whereas multiplex PCR showed cross-reactivity with Campylobacter species, the LAMP method developed in this study was more sensitive and reliable than conventional PCR or multiplex PCR for the detection of Arcobacter species. PMID:24478488

Adaptation of a visualized loop-mediated isothermal amplification technique for field detection of Plasmodium vivax infection.

PubMed

Tao, Zhi-Yong; Zhou, Hua-Yun; Xia, Hui; Xu, Sui; Zhu, Han-Wu; Culleton, Richard L; Han, Eun-Taek; Lu, Feng; Fang, Qiang; Gu, Ya-Ping; Liu, Yao-Bao; Zhu, Guo-Ding; Wang, Wei-Ming; Li, Ju-Lin; Cao, Jun; Gao, Qi

2011-06-21

Loop-mediated isothermal amplification (LAMP) is a high performance method for detecting DNA and holds promise for use in the molecular detection of infectious pathogens, including Plasmodium spp. However, in most malaria-endemic areas, which are often resource-limited, current LAMP methods are not feasible for diagnosis due to difficulties in accurately interpreting results with problems of sensitive visualization of amplified products, and the risk of contamination resulting from the high quantity of amplified DNA produced. In this study, we establish a novel visualized LAMP method in a closed-tube system, and validate it for the diagnosis of malaria under simulated field conditions. A visualized LAMP method was established by the addition of a microcrystalline wax-dye capsule containing the highly sensitive DNA fluorescence dye SYBR Green I to a normal LAMP reaction prior to the initiation of the reaction. A total of 89 blood samples were collected on filter paper and processed using a simple boiling method for DNA extraction, and then tested by the visualized LAMP method for Plasmodium vivax infection. The wax capsule remained intact during isothermal amplification, and released the DNA dye to the reaction mixture only when the temperature was raised to the melting point following amplification. Soon after cooling down, the solidified wax sealed the reaction mix at the bottom of the tube, thus minimizing the risk of aerosol contamination. Compared to microscopy, the sensitivity and specificity of LAMP were 98.3% (95% confidence interval (CI): 91.1-99.7%) and 100% (95% CI: 88.3-100%), and were in close agreement with a nested polymerase chain reaction method. This novel, cheap and quick visualized LAMP method is feasible for malaria diagnosis in resource-limited field settings.

Impact of a preoperative conversational hypnotic session on propofol consumption using closed-loop anesthetic induction guided by the bispectral index

PubMed Central

Bataille, Aurélien; Besset, Sébastien; Szekely, Barbara; Michel-Cherqui, Mireille; Dumans, Virginie; Liu, Ngai; Chazot, Thierry; Fischler, Marc; Le Guen, Morgan

2017-01-01

Abstract Objective: The automated administration of propofol in a closed loop could be used to objectively evaluate the nonpharmacological anesthetic action of hypnotherapy. The objective of this study was to evaluate the impact of a conversational hypnosis session on the consumption of propofol for anesthetic induction. Design: A randomized, usual care-controlled, single-center, patient-blind trial. Setting: Tertiary care center in France from November 2012 to December 2013. Participants: Adult patients scheduled for a surgical procedure under general anesthesia. Interventions: Before surgery, patients were randomized with a computer-generated random list for a preoperative conversational hypnosis session or for usual care. The conversational hypnosis session was conducted and individualized by the therapist with an academic degree in hypnosis in a quiet environment. Anesthetic induction was automatically performed by propofol without opioids and was assisted by the bispectral index in a closed loop. Outcome: Primary endpoint was the propofol dose required for anesthesia induction, defined as a Bispectral index less than 60 for at least 30 seconds. Results: The study included 48 patients in the hypnosis group and 49 patients in the control group. No difference in propofol consumption to obtain anesthesia induction was observed between the groups (total dose: 138.6 [67.5] and 130 [47.9] mg, P = .47; adjusted dose: 2.15 [1.09] and 1.95 [0.66] mg/kg, P = .28, for the hypnosis and control groups, respectively). Hetero-evaluation of arm movement during propofol injection (no reaction: 98% and 74%; P = .004, in the hypnosis and control groups, respectively) and face reaction at venous access placement (no reaction 59% and 30%; P = .017, in the hypnosis and control groups, respectively) were lower in the hypnosis group. No adverse event was reported. Conclusions: No difference in propofol consumption was observed in this study designed to evaluate the effect of a hypnotic conversational session on anesthesia induction using an automated tool for propofol administration. PMID:28489735

Detection of Coconut cadang-cadang viroid (CCCVd) in oil palm by reverse transcription loop-mediated isothermal amplification (RT-LAMP).

PubMed

Thanarajoo, Sathis Sri; Kong, Lih Ling; Kadir, Jugah; Lau, Wei Hongi; Vadamalai, Ganesan

2014-06-01

A reverse transcription loop-mediated isothermal amplification (RT-LAMP) detected Coconut cadang-cadang viroid (CCCVd) within 60 min at 60 °C in total nucleic acid extracted from oil palm leaves infected with CCCVd. Positive reactions showed colour change from orange to green in the reaction mix after the addition of fluorescent reagent, and a laddering pattern band on 2% agarose gel electrophoresis. Conventional RT-PCR with LAMP primers produced amplicons with a sequence identical to the 297-nt CCCVd oil palm variant with the primers being specific for CCCVd and not for other viroids such as PSTVd and CEVd. RT-LAMP was found to be rapid and specific for detecting oil palm CCCVd. Copyright © 2014 Elsevier B.V. All rights reserved.

Rational Design of Mixed-Metal Oxides for Chemical Looping Combustion of Coal via Coupled Computational-Experimental Studies

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

Mishra, Amit; Li, Fanxing; Santiso, Erik

Energy and global climate change are two grand challenges to the modern society. An urgent need exists for development of clean and efficient energy conversion processes. The chemical looping strategy, which utilizes regenerable oxygen carriers (OCs) to indirectly convert carbonaceous fuels via redox reactions, is considered to be one of the more promising approaches for CO2 capture by the U.S. Department of Energy (USDOE). To date, most long-term chemical looping operations were conducted using gaseous fuels, even though direct conversion of coal is more desirable from both economics and CO2 capture viewpoints. The main challenges for direct coal conversion residemore » in the stringent requirements on oxygen carrier performances. In addition, coal char and volatile compounds are more challenging to convert than gaseous fuels. A promising approach for direct conversion of coal is the so called chemical looping with oxygen uncoupling (CLOU) technique. In the CLOU process, a metal oxide that decomposes at the looping temperature, and releases oxygen to the gas phase is used as the OC. The overarching objective of this project was to discover the fundamental principles for rational design and optimization of oxygen carriers (OC) in coal chemical looping combustion (CLC) processes. It directly addresses Topic Area B of the funding opportunity announcement (FOA) in terms of “predictive description of the phase behavior and mechanical properties” of “mixed metal oxide” based OCs and rational development of new OC materials with superior functionality. This was achieved through studies exploring i) iron-containing mixed-oxide composites as oxygen carriers for CLOU, ii) Ca1-xAxMnO3-δ (A = Sr and Ba) as oxygen carriers for CLOU, iii) CaMn1-xBxO3-δ (B=Al, V, Fe, Co, and Ni) as oxygen carrier for CLOU and iv) vacancy creation energy in Mn-containing perovskites as an indicator chemical looping with oxygen uncoupling.« less

Topological dynamics of optical singularities in speckle-fields induced by photorefractive scattering in a LiNbO{sub 3} : Fe crystal

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

Vasil'ev, Vasilii I; Soskin, M S

2013-02-28

A natural singular dynamics of elliptically polarised speckle-fields induced by the 'optical damage' effect in a photorefractive crystal of lithium niobate by a passing beam of a helium - neon laser is studied by the developed methods of singular optics. For the polarisation singularities (C points), a new class of chain reactions, namely, singular chain reactions are discovered and studied. It is shown that they obey the topological charge and sum Poincare index conservation laws. In addition, they exist for all the time of crystal irradiation. They consist of a series of interlocking chains, where singularity pairs arising in amore » chain annihilate with singularities from neighbouring independently created chains. Less often singular 'loop' reactions are observed where arising pairs of singularities annihilate after reversible transformations in within the boundaries of a single speckle. The type of a singular reaction is determined by a topology and dynamics of the speckles, in which the reactions are developing. (laser optics 2012)« less

The Bosch process.

NASA Technical Reports Server (NTRS)

Meissner, H. P.; Reid, R. C.

1972-01-01

Many previous studies have been carried out to elucidate certain aspects of the Bosch process wherein CO2 is reacted over an iron catalyst to form carbon and water at temperatures around 1100 F. These results are assembled, and with the aid of new experimental data, are used to analyze the various reactions involved. It is shown that CO2 and H2 will not usually react to deposit carbon unless water is removed in a recycle loop. The critical importance of large catalyst areas is stressed relative to catalyst pretreatment processes. It is shown that in most operating Bosch reactions, mass transfer controls the rate of reaction, and it is suggested that the carbon filaments found are the expected result of such a rate limiting process. Typical recycle gas mixtures are considered, and maximum water yields are determined from various cases. A few suggestions are made to improve Bosch reaction performance, and a number of unresolved problems are noted.

Does the brain use sliding variables for the control of movements?

PubMed

Hanneton, S; Berthoz, A; Droulez, J; Slotine, J J

1997-12-01

Delays in the transmission of sensory and motor information prevent errors from being instantaneously available to the central nervous system (CNS) and can reduce the stability of a closed-loop control strategy. On the other hand, the use of a pure feedforward control (inverse dynamics) requires a perfect knowledge of the dynamic behavior of the body and of manipulated objects. Sensory feedback is essential both to accommodate unexpected errors and events and to compensate for uncertainties about the dynamics of the body. Experimental observations concerning the control of posture, gaze and limbs have shown that the CNS certainly uses a combination of closed-loop and open-loop control. Feedforward components of movement, such as eye saccades, occur intermittently and present a stereotyped kinematic profile. In visuo-manual tracking tasks, hand movements exhibit velocity peaks that occur intermittently. When a delay or a slow dynamics are inserted in the visuo-manual control loop, intermittent step-and-hold movements appear clearly in the hand trajectory. In this study, we investigated strategies used by human subjects involved in the control of a particular dynamic system. We found strong evidence for substantial nonlinearities in the commands produced. The presence of step-and-hold movements seemed to be the major source of nonlinearities in the control loop. Furthermore, the stereotyped ballistic-like kinematics of these rapid and corrective movements suggests that they were produced in an open-loop way by the CNS. We analyzed the generation of ballistic movements in the light of sliding control theory assuming that they occurred when a sliding variable exceeded a constant threshold. In this framework, a sliding variable is defined as a composite variable (a combination of the instantaneous tracking error and its temporal derivatives) that fulfills a specific stability criterion. Based on this hypothesis and on the assumption of a constant reaction time, the tracking error and its derivatives should be correlated at a particular time lag before movement onset. A peak of correlation was found for a physiologically plausible reaction time, corresponding to a stable composite variable. The direction and amplitude of the ongoing stereotyped movements seemed also be adjusted in order to minimize this variable. These findings suggest that, during visually guided movements, human subjects attempt to minimize such a composite variable and not the instantaneous error. This minimization seems to be obtained by the execution of stereotyped corrective movements.

The Development of Lyophilized Loop-mediated Isothermal Amplification Reagents for the Detection of Coxiella burnetii.

PubMed

Chen, Hua-Wei; Ching, Wei-Mei

2016-04-18

Coxiella burnetii, the agent causing Q fever, is an obligate intracellular bacterium. PCR based diagnostic assays have been developed for detecting C. burnetii DNA in cell cultures and clinical samples. PCR requires specialized equipment and extensive end user training, and therefore, it is not suitable for routine work especially in a resource-constrained area. We have developed a loop-mediated isothermal amplification (LAMP) assay to detect the presence of C. burnetii in patient samples. This method is performed at a single temperature around 60 °C in a water bath or heating block. The sensitivity of this LAMP assay is very similar to PCR with a detection limit of about 25 copies per reaction. This report describes the preparation of the reaction using lyophilized reagents and visualization of results using hydroxynaphthol blue (HNB) or a UV lamp with fluorescent intercalating dye in the reaction. The LAMP reagents were lyophilized and stored at room temperature (RT) for one month without loss of detection sensitivity. This LAMP assay is particularly robust because the reaction mixture preparation does not involve complex steps. This method is ideal for use in resource-limited settings where Q fever is endemic.

The mitochondrial C16069T polymorphism, not mitochondrial D310 (D-loop) mononucleotide sequence variations, is associated with bladder cancer.

PubMed

Shakhssalim, Nasser; Houshmand, Massoud; Kamalidehghan, Behnam; Faraji, Abolfazl; Sarhangnejad, Reza; Dadgar, Sepideh; Mobaraki, Maryam; Rosli, Rozita; Sanati, Mohammad Hossein

2013-12-05

Bladder cancer is a relatively common and potentially life-threatening neoplasm that ranks ninth in terms of worldwide cancer incidence. The aim of this study was to determine deletions and sequence variations in the mitochondrial displacement loop (D-loop) region from the blood specimens and tumoral tissues of patients with bladder cancer, compared to adjacent non-tumoral tissues. The DNA from blood, tumoral tissues and adjacent non-tumoral tissues of twenty-six patients with bladder cancer and DNA from blood of 504 healthy controls from different ethnicities were investigated to determine sequence variation in the mitochondrial D-loop region using multiplex polymerase chain reaction (PCR), DNA sequencing and southern blotting analysis. From a total of 110 variations, 48 were reported as new mutations. No deletions were detected in tumoral tissues, adjacent non-tumoral tissues and blood samples from patients. Although the polymorphisms at loci 16189, 16261 and 16311 were not significantly correlated with bladder cancer, the C16069T variation was significantly present in patient samples compared to control samples (p < 0.05). Interestingly, there was no significant difference (p > 0.05) of C variations, including C7TC6, C8TC6, C9TC6 and C10TC6, in D310 mitochondrial DNA between patients and control samples. Our study suggests that 16069 mitochondrial DNA D-Loop mutations may play a significant role in the etiology of bladder cancer and facilitate the definition of carcinogenesis-related mutations in human cancer.

Structural snapshots along the reaction pathway of Yersinia pestis RipA, a putative butyryl-CoA transferase

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

Torres, Rodrigo; Lan, Benson; Latif, Yama

2014-04-01

The crystal structures of Y. pestis RipA mutants were determined to provide insights into the CoA transferase reaction pathway. Yersinia pestis, the causative agent of bubonic plague, is able to survive in both extracellular and intracellular environments within the human host, although its intracellular survival within macrophages is poorly understood. A novel Y. pestis three-gene rip (required for intracellular proliferation) operon, and in particular ripA, has been shown to be essential for survival and replication in interferon γ-induced macrophages. RipA was previously characterized as a putative butyryl-CoA transferase proposed to yield butyrate, a known anti-inflammatory shown to lower macrophage-produced NOmore » levels. RipA belongs to the family I CoA transferases, which share structural homology, a conserved catalytic glutamate which forms a covalent CoA-thioester intermediate and a flexible loop adjacent to the active site known as the G(V/I)G loop. Here, functional and structural analyses of several RipA mutants are presented in an effort to dissect the CoA transferase mechanism of RipA. In particular, E61V, M31G and F60M RipA mutants show increased butyryl-CoA transferase activities when compared with wild-type RipA. Furthermore, the X-ray crystal structures of E61V, M31G and F60M RipA mutants, when compared with the wild-type RipA structure, reveal important conformational changes orchestrated by a conserved acyl-group binding-pocket phenylalanine, Phe85, and the G(V/I)G loop. Binary structures of M31G RipA and F60M RipA with two distinct CoA substrate conformations are also presented. Taken together, these data provide CoA transferase reaction snapshots of an open apo RipA, a closed glutamyl-anhydride intermediate and an open CoA-thioester intermediate. Furthermore, biochemical analyses support essential roles for both the catalytic glutamate and the flexible G(V/I)G loop along the reaction pathway, although further research is required to fully understand the function of the acyl-group binding pocket in substrate specificity.« less

Development of a loop-mediated isothermal amplification method for rapid mass-screening of sand flies for Leishmania infection.

PubMed

Nzelu, Chukwunonso O; Gomez, Eduardo A; Cáceres, Abraham G; Sakurai, Tatsuya; Martini-Robles, Luiggi; Uezato, Hiroshi; Mimori, Tatsuyuki; Katakura, Ken; Hashiguchi, Yoshihisa; Kato, Hirotomo

2014-04-01

Entomological monitoring of Leishmania infection in leishmaniasis endemic areas offers epidemiologic advantages for predicting the risk and expansion of the disease, as well as evaluation of the effectiveness of control programs. In this study, we developed a highly sensitive loop-mediated isothermal amplification (LAMP) method for the mass screening of sand flies for Leishmania infection based on the 18S rRNA gene. The LAMP technique could detect 0.01 parasites, which was more sensitive than classical PCR. The method was robust and could amplify the target DNA within 1h from a crude sand fly template without DNA purification. Amplicon detection could be accomplished by the newly developed colorimetric malachite green (MG)--mediated naked eye visualization. Pre-addition of MG to the LAMP reaction solution did not inhibit amplification efficiency. The field applicability of the colorimetric MG-based LAMP assay was demonstrated with 397 field-caught samples from the endemic areas of Ecuador and eight positive sand flies were detected. The robustness, superior sensitivity, and ability to produce better visual discriminatory reaction products than existing LAMP fluorescence and turbidity assays indicated the field potential usefulness of this new method for surveillance and epidemiological studies of leishmaniasis in developing countries. Copyright © 2013 Elsevier B.V. All rights reserved.

The Use of Contact Mode Atomic Force Microscopy in Aqueous Medium for Structural Analysis of Spinach Photosynthetic Complexes

DOE PAGES

Phuthong, Witchukorn; Huang, Zubin; Wittkopp, Tyler M.; ...

2015-07-28

To investigate the dynamics of photosynthetic pigment-protein complexes in vascular plants at high resolution in an aqueous environment, membrane-protruding oxygen-evolving complexes (OECs) associated with photosystem II (PSII) on spinach ( Spinacia oleracea) grana membranes were examined using contact mode atomic force microscopy. This study represents, to our knowledge, the first use of atomic force microscopy to distinguish the putative large extrinsic loop of Photosystem II CP47 reaction center protein (CP47) from the putative oxygen-evolving enhancer proteins 1, 2, and 3 (PsbO, PsbP, and PsbQ) and large extrinsic loop of Photosystem II CP43 reaction center protein (CP43) in the PSII-OEC extrinsicmore » domains of grana membranes under conditions resulting in the disordered arrangement of PSII-OEC particles. Moreover, we observed uncharacterized membrane particles that, based on their physical characteristics and electrophoretic analysis of the polypeptides associated with the grana samples, are hypothesized to be a domain of photosystem I that protrudes from the stromal face of single thylakoid bilayers. Furthermore, our results are interpreted in the context of the results of others that were obtained using cryo-electron microscopy (and single particle analysis), negative staining and freeze-fracture electron microscopy, as well as previous atomic force microscopy studies.« less

Quantitative mRNA analysis of muscarinic acetylcholine receptors in the intestine of dairy cows with spontaneous caecal dilatation-dislocation.

PubMed

Ontsouka, E C; Steiner, A; Bruckmaier, R M; Blum, J W; Meylan, M

2009-05-01

Muscarinic receptors mediate acetylcholine-induced muscular contractions. In this study, mRNA levels of muscarinic receptor subtypes 2 and 3 (M(2) and M(3)) in the ileum, caecum, proximal loop of the ascending colon (PLAC) and external loop of the spiral colon (ELSC) were determined by quantitative polymerase chain reaction in seven cows with caecal dilatation-dislocation (CDD) and seven healthy control cows. Levels of M(2) were significantly lower in the caecum, PLAC and ELSC and levels of M(3) were significantly lower in the ileum, caecum, PLAC and ELSC of cows with CDD compared to healthy cows (P<0.05). Down-regulation of M(3) may play a role in the pathogenesis of CDD.

A novel approach for evaluating the performance of real time quantitative loop-mediated isothermal amplification-based methods.

PubMed

Nixon, Gavin J; Svenstrup, Helle F; Donald, Carol E; Carder, Caroline; Stephenson, Judith M; Morris-Jones, Stephen; Huggett, Jim F; Foy, Carole A

2014-12-01

Molecular diagnostic measurements are currently underpinned by the polymerase chain reaction (PCR). There are also a number of alternative nucleic acid amplification technologies, which unlike PCR, work at a single temperature. These 'isothermal' methods, reportedly offer potential advantages over PCR such as simplicity, speed and resistance to inhibitors and could also be used for quantitative molecular analysis. However there are currently limited mechanisms to evaluate their quantitative performance, which would assist assay development and study comparisons. This study uses a sexually transmitted infection diagnostic model in combination with an adapted metric termed isothermal doubling time (IDT), akin to PCR efficiency, to compare quantitative PCR and quantitative loop-mediated isothermal amplification (qLAMP) assays, and to quantify the impact of matrix interference. The performance metric described here facilitates the comparison of qLAMP assays that could assist assay development and validation activities.

Different mutation patterns of mitochondrial DNA displacement-loop in hepatocellular carcinomas induced by N-nitrosodiethylamine and a choline-deficient l-amino acid-defined diet in rats.

PubMed

Onishi, Mariko; Sokuza, Yui; Nishikawa, Tomoki; Mori, Chiharu; Uwataki, Kimiko; Honoki, Kanya; Tsujiuchi, Toshifumi

2007-10-12

Mutations of the mitochondria DNA (mtDNA) displacement loop (D-loop) were investigated to clarify different changes of exogenous and endogenous liver carcinogenesis in rats. We induced hepatocellular carcinomas (HCCs) in rats with N-nitrosodiethylamine (DEN) and a choline-deficient l-amino acid-defined (CDAA) diet. DNAs were extracted from 10 HCCs induced by DEN and 10 HCCs induced by the CDAA diet. To identify mutations in mtDNA D-loop, polymerase chain reaction (PCR)-single strand conformation polymorphism (SSCP) analysis, followed by nucleotide sequencing, was performed. Mutations were detected in 5 out of 10 HCCs (50%) induced by DEN. Four out of 5 mutations were G/C to A/T transitions at positions 15707, 15717, 15930, and 16087, and one T/A to C/G transition at position 15559. By contrast, no mutations were found in 10 HCCs induced by the CDAA diet. These results demonstrated that mutations in mtDNA D-loop occur in rat HCCs induced by DEN but not by the CDAA diet, suggesting that mtDNA D-loop is a target of exogenous liver carcinogenesis in rats.

Tangled nonlinear driven chain reactions of all optical singularities

NASA Astrophysics Data System (ADS)

Vasil'ev, V. I.; Soskin, M. S.

2012-03-01

Dynamics of polarization optical singularities chain reactions in generic elliptically polarized speckle fields created in photorefractive crystal LiNbO3 was investigated in details Induced speckle field develops in the tens of minutes scale due to photorefractive 'optical damage effect' induced by incident beam of He-Ne laser. It was shown that polarization singularities develop through topological chain reactions of developing speckle fields driven by photorefractive nonlinearities induced by incident laser beam. All optical singularities (C points, optical vortices, optical diabolos,) are defined by instantaneous topological structure of the output wavefront and are tangled by singular optics lows. Therefore, they have develop in tangled way by six topological chain reactions driven by nonlinear processes in used nonlinear medium (photorefractive LiNbO3:Fe in our case): C-points and optical diabolos for right (left) polarized components domains with orthogonally left (right) polarized optical vortices underlying them. All elements of chain reactions consist from loop and chain links when nucleated singularities annihilated directly or with alien singularities in 1:9 ratio. The topological reason of statistics was established by low probability of far enough separation of born singularities pair from existing neighbor singularities during loop trajectories. Topology of developing speckle field was measured and analyzed by dynamic stokes polarimetry with few seconds' resolution. The hierarchy of singularities govern scenario of tangled chain reactions was defined. The useful space-time data about peculiarities of optical damage evolution were obtained from existence and parameters of 'islands of stability' in developing speckle fields.

System for thermal energy storage, space heating and cooling and power conversion

DOEpatents

Gruen, Dieter M.; Fields, Paul R.

1981-04-21

An integrated system for storing thermal energy, for space heating and cong and for power conversion is described which utilizes the reversible thermal decomposition characteristics of two hydrides having different decomposition pressures at the same temperature for energy storage and space conditioning and the expansion of high-pressure hydrogen for power conversion. The system consists of a plurality of reaction vessels, at least one containing each of the different hydrides, three loops of circulating heat transfer fluid which can be selectively coupled to the vessels for supplying the heat of decomposition from any appropriate source of thermal energy from the outside ambient environment or from the spaces to be cooled and for removing the heat of reaction to the outside ambient environment or to the spaces to be heated, and a hydrogen loop for directing the flow of hydrogen gas between the vessels. When used for power conversion, at least two vessels contain the same hydride and the hydrogen loop contains an expansion engine. The system is particularly suitable for the utilization of thermal energy supplied by solar collectors and concentrators, but may be used with any source of heat, including a source of low-grade heat.

Detection of Bar Transgenic Sugarcane with a Rapid and Visual Loop-Mediated Isothermal Amplification Assay.

PubMed

Zhou, Dinggang; Wang, Chunfeng; Li, Zhu; Chen, Yun; Gao, Shiwu; Guo, Jinlong; Lu, Wenying; Su, Yachun; Xu, Liping; Que, Youxiong

2016-01-01

Genetic engineering offers an attractive alternative in sugarcane breeding for increasing cane and sugar yields as well as disease and insect resistance. Bar transgenic sugarcane employing the herbicide tolerance is a useful agronomical trait in weed control. In this study, a loop-mediated isothermal amplification (LAMP) assay for rapid detection of the bar gene in transgenic sugarcane has been developed and evaluated. A set of six primers was designed for LAMP-based amplification of the bar gene. The LAMP reaction conditions were optimized as follows: 5.25 mM of Mg(2+), 6:1 ratio of inner vs. outer primer, and 6.0 U of Bst DNA polymerase in a reaction volume of 25.0 μL. The detection limit of the recombinant plasmid 1Ac0229 was as low as 10 copies in the developed LAMP, which was 10-fold higher sensitive than that of conventional PCR. In 100 putative transgenic lines, the bar gene was detected in 100/100 cases (100%) by LAMP and 97/100 cases (97%) by conventional PCR, respectively. In conclusion, the developed LAMP assay is visual, rapid, sensitive, reliable, and cost-effective for detection of the bar specific transgenic sugarcane.

Role of drinking water biofilms on residual chlorine decay and trihalomethane formation: An experimental and modeling study.

PubMed

Xu, Jianeng; Huang, Conghui; Shi, Xiaoyang; Dong, Shengkun; Yuan, Baoling; Nguyen, Thanh H

2018-06-13

PVC pipe loops were constructed to simulate household premise plumbing. These pipe loops were exposed to water treated by physical processes at three water treatment plants in Xiamen, China from August 2016 to June 2017. After the biofilms were allowed to develop inside the pipes, these pipes were deconstructed and exposed to organic-free chlorine solution buffered at pH 6.8 ± 0.2 for 48 h. The decay of chlorine by these biofilms was higher than by the effluent waters that were used to grow the biofilms. A chlorine consumption mass balance model elucidated the role of both the diffusion of chlorine into the biofilm and the reaction of chlorine with the biofilm matrix. Comparable concentrations of trihalomethanes were quantified from the reaction between chlorine and source water organic matters, and chlorine and the biofilm, further emphasizing the role of biofilms in the safety of disinfected drinking water. These findings imply that when chlorine is used in the drinking water distribution system, the ubiquitous presence of biofilms may cause the depletion of chlorine and the formation of non-negligible levels of toxic disinfection byproducts. Copyright © 2018 Elsevier B.V. All rights reserved.

Detection of Bar Transgenic Sugarcane with a Rapid and Visual Loop-Mediated Isothermal Amplification Assay

PubMed Central

Zhou, Dinggang; Wang, Chunfeng; Li, Zhu; Chen, Yun; Gao, Shiwu; Guo, Jinlong; Lu, Wenying; Su, Yachun; Xu, Liping; Que, Youxiong

2016-01-01

Genetic engineering offers an attractive alternative in sugarcane breeding for increasing cane and sugar yields as well as disease and insect resistance. Bar transgenic sugarcane employing the herbicide tolerance is a useful agronomical trait in weed control. In this study, a loop-mediated isothermal amplification (LAMP) assay for rapid detection of the bar gene in transgenic sugarcane has been developed and evaluated. A set of six primers was designed for LAMP-based amplification of the bar gene. The LAMP reaction conditions were optimized as follows: 5.25 mM of Mg2+, 6:1 ratio of inner vs. outer primer, and 6.0 U of Bst DNA polymerase in a reaction volume of 25.0 μL. The detection limit of the recombinant plasmid 1Ac0229 was as low as 10 copies in the developed LAMP, which was 10-fold higher sensitive than that of conventional PCR. In 100 putative transgenic lines, the bar gene was detected in 100/100 cases (100%) by LAMP and 97/100 cases (97%) by conventional PCR, respectively. In conclusion, the developed LAMP assay is visual, rapid, sensitive, reliable, and cost-effective for detection of the bar specific transgenic sugarcane. PMID:27014303

Rapid identification and differentiation of Fasciola hepatica and Fasciola gigantica by a loop-mediated isothermal amplification (LAMP) assay.

PubMed

Ai, L; Li, C; Elsheikha, H M; Hong, S J; Chen, J X; Chen, S H; Li, X; Cai, X Q; Chen, M X; Zhu, X Q

2010-12-15

The present study developed and validated a species-specific loop-mediated isothermal amplification (LAMP) assay for the rapid detection and discrimination of Fasciola hepatica and Fasciola gigantica. The LAMP assay is inexpensive, easy to perform and shows rapid reaction, wherein the amplification can be obtained in 45 min under isothermal conditions of 61 °C or 62 °C by employing a set of four species-specific primer mixtures and results can be checked through naked-eye visualization. The optimal assay conditions with no cross-reaction with other closely related trematodes (Clonorchis sinensis, Opisthorchis viverrini, Orientobilharzia turkestanicum and Schistosoma japonicum) as well as within the two Fasciola species were established. The assay was validated by examining F. gigantica DNA in the intermediate host snails and in faecal samples. The results indicated that the LAMP assay is approximately 10(4) times more sensitive than the conventional specific PCR assays. These findings indicate that this Fasciola species-specific LAMP assay may have a potential clinical application for detection and differentiation of Fasciola species, especially in endemic countries. Copyright © 2010 Elsevier B.V. All rights reserved.

Comparison of the structures of free and ribosome-bound tRNAPhe by using slow tritium exchange.

PubMed Central

Farber, N; Cantor, C R

1980-01-01

The rate of incorporation of tritium from the solvent into the C-8 position of purines in RNA is markedly sensitive to the microenvironment. This slow tritium exchange reaction has been used to study the structure and interactions of yeast tRNAPhe bound to poly(U)-programed tight-couple 70S ribosomes of Escherichia coli. The tritium incorporation into specific sites of the tRNA was determined by enzymatic digestion and measurement of the specific activity of each of the isolated radioactive fragments. Ribosome binding leads to marked suppression in the exchange rate of a number of fragments. This delineates extensive regions of tRNA-ribosome contact. No change in exchange rates is seen for fragments from the corner of the molecule, indicating that this region of bound tRNA is readily accessible to the solvent. Ribosome binding results in an enhanced exchange rate at the T loop. This appears to be the result of a conformational change that is most likely an unfolding of the T and D loops. Additional tritium exchange reactions suggest this conformational change is induced by ribosomes and not by messenger. PMID:7001473

Automated Droplet Manipulation Using Closed-Loop Axisymmetric Drop Shape Analysis.

PubMed

Yu, Kyle; Yang, Jinlong; Zuo, Yi Y

2016-05-17

Droplet manipulation plays an important role in a wide range of scientific and industrial applications, such as synthesis of thin-film materials, control of interfacial reactions, and operation of digital microfluidics. Compared to micron-sized droplets, which are commonly considered as spherical beads, millimeter-sized droplets are generally deformable by gravity, thus introducing nonlinearity into control of droplet properties. Such a nonlinear drop shape effect is especially crucial for droplet manipulation, even for small droplets, at the presence of surfactants. In this paper, we have developed a novel closed-loop axisymmetric drop shape analysis (ADSA), integrated into a constrained drop surfactometer (CDS), for manipulating millimeter-sized droplets. The closed-loop ADSA generalizes applications of the traditional drop shape analysis from a surface tension measurement methodology to a sophisticated tool for manipulating droplets in real time. We have demonstrated the feasibility and advantages of the closed-loop ADSA in three applications, including control of drop volume by automatically compensating natural evaporation, precise control of surface area variations for high-fidelity biophysical simulations of natural pulmonary surfactant, and steady control of surface pressure for in situ Langmuir-Blodgett transfer from droplets. All these applications have demonstrated the accuracy, versatility, applicability, and automation of this new ADSA-based droplet manipulation technique. Combining with CDS, the closed-loop ADSA holds great promise for advancing droplet manipulation in a variety of material and surface science applications, such as thin-film fabrication, self-assembly, and biophysical study of pulmonary surfactant.

Part-2: Analytical Expressions of Concentrations of Glucose, Oxygen, and Gluconic Acid in a Composite Membrane for Closed-Loop Insulin Delivery for the Non-steady State Conditions.

PubMed

Mehala, N; Rajendran, L; Meena, V

2017-02-01

A mathematical model developed by Abdekhodaie and Wu (J Membr Sci 335:21-31, 2009), which describes a dynamic process involving an enzymatic reaction and diffusion of reactants and product inside glucose-sensitive composite membrane has been discussed. This theoretical model depicts a system of non-linear non-steady state reaction diffusion equations. These equations have been solved using new approach of homotopy perturbation method and analytical solutions pertaining to the concentrations of glucose, oxygen, and gluconic acid are derived. These analytical results are compared with the numerical results, and limiting case results for steady state conditions and a good agreement is observed. The influence of various kinetic parameters involved in the model has been presented graphically. Theoretical evaluation of the kinetic parameters like the maximal reaction velocity (V max ) and Michaelis-Menten constants for glucose and oxygen (K g and K ox ) is also reported. This predicted model is very much useful for designing the glucose-responsive composite membranes for closed-loop insulin delivery.

Loop-mediated isothermal amplification for detection of Staphylococcus aureus in dairy cow suffering from mastitis.

PubMed

Tie, Zhang; Chunguang, Wang; Xiaoyuan, Wei; Xinghua, Zhao; Xiuhui, Zhong

2012-01-01

To develop a rapid detection method of Staphylococcus aureus using loop-mediated isothermal amplification (LAMP), four specific primers were designed according to six distinct sequences of the nuc gene. In addition, the specificity and sensitivity of LAMP were verified and compared with those of PCR. Results showed that the LAMP reaction was completed within 45 min at 62.5°C, and ladder bands were appeared in LAMP products analyzed by gel electrophoresis. After adding 1x SYBR Green l, the positive reaction tube showed green color and the negative reaction tube remained orange, indicating that the LAMP has high specificity. The minimal detectable concentration of LAMP was 1 × 10² CFU/mL and that of PCR was 1 × 10⁴ CFU/mL, indicating that the LAMP was 100 times more sensitive than the PCR. The LAMP method for detection of Staphylococcus aureus has many advantages, such as simple operation, high sensitivity, high specificity, and rapid analysis. Therefore, this method is more suitable for the rapid on-site detection of Staphylococcus aureus.

Site-Selective RNA Splicing Nanozyme: DNAzyme and RtcB Conjugates on a Gold Nanoparticle.

PubMed

Petree, Jessica R; Yehl, Kevin; Galior, Kornelia; Glazier, Roxanne; Deal, Brendan; Salaita, Khalid

2018-01-19

Modifying RNA through either splicing or editing is a fundamental biological process for creating protein diversity from the same genetic code. Developing novel chemical biology tools for RNA editing has potential to transiently edit genes and to provide a better understanding of RNA biochemistry. Current techniques used to modify RNA include the use of ribozymes, adenosine deaminase, and tRNA endonucleases. Herein, we report a nanozyme that is capable of splicing virtually any RNA stem-loop. This nanozyme is comprised of a gold nanoparticle functionalized with three enzymes: two catalytic DNA strands with ribonuclease function and an RNA ligase. The nanozyme cleaves and then ligates RNA targets, performing a splicing reaction that is akin to the function of the spliceosome. Our results show that the three-enzyme reaction can remove a 19 nt segment from a 67 nt RNA loop with up to 66% efficiency. The complete nanozyme can perform the same splice reaction at 10% efficiency. These splicing nanozymes represent a new promising approach for gene manipulation that has potential for applications in living cells.

Apparatus for and method of monitoring for breached fuel elements

DOEpatents

Gross, Kenny C.; Strain, Robert V.

1983-01-01

This invention teaches improved apparatus for the method of detecting a breach in cladded fuel used in a nuclear reactor. The detector apparatus uses a separate bypass loop for conveying part of the reactor coolant away from the core, and at least three separate delayed-neutron detectors mounted proximate this detector loop. The detectors are spaced apart so that the coolant flow time from the core to each detector is different, and these differences are known. The delayed-neutron activity at the detectors is a function of the dealy time after the reaction in the fuel until the coolant carrying the delayed-neutron emitter passes the respective detector. This time delay is broken down into separate components including an isotopic holdup time required for the emitter to move through the fuel from the reaction to the coolant at the breach, and two transit times required for the emitter now in the coolant to flow from the breach to the detector loop and then via the loop to the detector. At least two of these time components are determined during calibrated operation of the reactor. Thereafter during normal reactor operation, repeated comparisons are made by the method of regression approximation of the third time component for the best-fit line correlating measured delayed-neutron activity against activity that is approximated according to specific equations. The equations use these time-delay components and known parameter values of the fuel and of the part and emitting daughter isotopes.

Robust Decentralized Nonlinear Control for a Twin Rotor MIMO System

PubMed Central

Belmonte, Lidia María; Morales, Rafael; Fernández-Caballero, Antonio; Somolinos, José Andrés

2016-01-01

This article presents the design of a novel decentralized nonlinear multivariate control scheme for an underactuated, nonlinear and multivariate laboratory helicopter denominated the twin rotor MIMO system (TRMS). The TRMS is characterized by a coupling effect between rotor dynamics and the body of the model, which is due to the action-reaction principle originated in the acceleration and deceleration of the motor-propeller groups. The proposed controller is composed of two nested loops that are utilized to achieve stabilization and precise trajectory tracking tasks for the controlled position of the generalized coordinates of the TRMS. The nonlinear internal loop is used to control the electrical dynamics of the platform, and the nonlinear external loop allows the platform to be perfectly stabilized and positioned in space. Finally, we illustrate the theoretical control developments with a set of experiments in order to verify the effectiveness of the proposed nonlinear decentralized feedback controller, in which a comparative study with other controllers is performed, illustrating the excellent performance of the proposed robust decentralized control scheme in both stabilization and trajectory tracking tasks. PMID:27472338

Robust Decentralized Nonlinear Control for a Twin Rotor MIMO System.

PubMed

Belmonte, Lidia María; Morales, Rafael; Fernández-Caballero, Antonio; Somolinos, José Andrés

2016-07-27

This article presents the design of a novel decentralized nonlinear multivariate control scheme for an underactuated, nonlinear and multivariate laboratory helicopter denominated the twin rotor MIMO system (TRMS). The TRMS is characterized by a coupling effect between rotor dynamics and the body of the model, which is due to the action-reaction principle originated in the acceleration and deceleration of the motor-propeller groups. The proposed controller is composed of two nested loops that are utilized to achieve stabilization and precise trajectory tracking tasks for the controlled position of the generalized coordinates of the TRMS. The nonlinear internal loop is used to control the electrical dynamics of the platform, and the nonlinear external loop allows the platform to be perfectly stabilized and positioned in space. Finally, we illustrate the theoretical control developments with a set of experiments in order to verify the effectiveness of the proposed nonlinear decentralized feedback controller, in which a comparative study with other controllers is performed, illustrating the excellent performance of the proposed robust decentralized control scheme in both stabilization and trajectory tracking tasks.

Unmanned Aircraft Systems Human-in-the-Loop Controller and Pilot Acceptability Study: Collision Avoidance, Self-Separation, and Alerting Times (CASSAT)

NASA Technical Reports Server (NTRS)

Comstock, James R., Jr.; Ghatas, Rania W.; Vincent, Michael J.; Consiglio, Maria C.; Munoz, Cesar; Chamberlain, James P.; Volk, Paul; Arthur, Keith E.

2016-01-01

The Federal Aviation Administration (FAA) has been mandated by the Congressional funding bill of 2012 to open the National Airspace System (NAS) to Unmanned Aircraft Systems (UAS). With the growing use of unmanned systems, NASA has established a multi-center "UAS Integration in the NAS" Project, in collaboration with the FAA and industry, and is guiding its research efforts to look at and examine crucial safety concerns regarding the integration of UAS into the NAS. Key research efforts are addressing requirements for detect-and-avoid (DAA), self-separation (SS), and collision avoidance (CA) technologies. In one of a series of human-in-the-loop experiments, NASA Langley Research Center set up a study known as Collision Avoidance, Self-Separation, and Alerting Times (CASSAT). The first phase assessed active air traffic controller interactions with DAA systems and the second phase examined reactions to the DAA system and displays by UAS Pilots at a simulated ground control station (GCS). Analyses of the test results from Phase I and Phase II are presented in this paper. Results from the CASSAT study and previous human-in-the-loop experiments will play a crucial role in the FAA's establishment of rules, regulations, and procedures to safely, efficiently, and effectively integrate UAS into the NAS.

Synergies Between Quantum Mechanics and Machine Learning in Reaction Prediction.

PubMed

Sadowski, Peter; Fooshee, David; Subrahmanya, Niranjan; Baldi, Pierre

2016-11-28

Machine learning (ML) and quantum mechanical (QM) methods can be used in two-way synergy to build chemical reaction expert systems. The proposed ML approach identifies electron sources and sinks among reactants and then ranks all source-sink pairs. This addresses a bottleneck of QM calculations by providing a prioritized list of mechanistic reaction steps. QM modeling can then be used to compute the transition states and activation energies of the top-ranked reactions, providing additional or improved examples of ranked source-sink pairs. Retraining the ML model closes the loop, producing more accurate predictions from a larger training set. The approach is demonstrated in detail using a small set of organic radical reactions.

Control of transversal instabilities in reaction-diffusion systems

NASA Astrophysics Data System (ADS)

Totz, Sonja; Löber, Jakob; Totz, Jan Frederik; Engel, Harald

2018-05-01

In two-dimensional reaction-diffusion systems, local curvature perturbations on traveling waves are typically damped out and vanish. However, if the inhibitor diffuses much faster than the activator, transversal instabilities can arise, leading from flat to folded, spatio-temporally modulated waves and to spreading spiral turbulence. Here, we propose a scheme to induce or inhibit these instabilities via a spatio-temporal feedback loop. In a piecewise-linear version of the FitzHugh–Nagumo model, transversal instabilities and spiral turbulence in the uncontrolled system are shown to be suppressed in the presence of control, thereby stabilizing plane wave propagation. Conversely, in numerical simulations with the modified Oregonator model for the photosensitive Belousov–Zhabotinsky reaction, which does not exhibit transversal instabilities on its own, we demonstrate the feasibility of inducing transversal instabilities and study the emerging wave patterns in a well-controlled manner.

Disturbed P53-MDM2 Feedback Loop Contributes to Thoracic Aortic Dissection Formation and May be a Result of TRIM25 Overexpression.

PubMed

Gong, Bin; Wang, Zhiwei; Zhang, Min; Hu, Zhipeng; Ren, Zongli; Tang, Zheng; Jiang, Wanli; Cheng, Lianghao; Huang, Jun; Ren, Wei; Wang, Qingtao

2017-04-01

The development of thoracic aortic dissection (TAD) is attributed to a broad range of degenerative, genetic, structural, oxidative, apoptotic, and acquired disease states. In this study, we examined the role of the disturbed p53-MDM2 (murine double minute 2) feedback loop in the formation of TAD, and one of a potential feedback loop regulator, TRIM25 (tripartite motif protein-25). Surgical specimens of the aorta from TAD patients (n = 10) and controls (n = 10) were tested for α-smooth muscle actin (α-SMA), p53, MDM2, and TRIM25 by western blot, immunohistochemical staining, and quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR), respectively. When compared with controls, western blot shows that the protein levels of p53, MDM2, and TRIM25 were increased significantly in the aortic media of TAD patients. qRT-PCR further verified that the mRNA expression of MDM2 and TRIM25 was also increased 6- and 4-folds, respectively, in the TAD media of the aortic wall. Immunohistochemistry results showed significantly decreased staining of α-SMA, smooth muscle cells, and more collagen deposition in the media of the aortic wall from patients with TAD. This study provided a new insight into the disturbed p53-MDM2 feedback loop in the pathogenesis of TAD, and this may be because of the TRIM25 overexpression. Copyright © 2016 Elsevier Inc. All rights reserved.

A reentrant loop domain in the glutamate carrier EAAT1 participates in substrate binding and translocation.

PubMed

Seal, R P; Amara, S G

1998-12-01

To investigate the structural determinants underlying transport by the glutamate transporter EAAT1, we mutated each of 24 highly conserved residues (P392 to Q415) to cysteine. A majority of these substituted cysteines react with the sulfhydryl-modifying reagent MTSEA, suggesting that they reside in an aqueous environment. The impermeant reagents MTSES and MTSET react with residues at each end of the domain (A395C and A414C), supporting a model that places these residues near the extracellular surface. Substrates and inhibitors block the reaction between MTS derivatives and A395C, and the cosubstrate, sodium, slows reaction of MTSEA with Y405C and E406C. From these results, we propose that this domain forms a reentrant membrane loop at the cell surface and may comprise part of the translocation pore for substrates and cotransported ions.

Energy dissipation drives the gradient signal amplification through an incoherent type-1 feed-forward loop

NASA Astrophysics Data System (ADS)

Lan, Ganhui

2015-09-01

We present here the analytical relation between the gain of eukaryotic gradient sensing network and the associated thermodynamic cost. By analyzing a general incoherent type-1 feed-forward loop, we derive the gain function (G ) through the reaction network and explicitly show that G depends on the nonequilibrium factor (0 ≤γ ≤1 with γ =0 and 1 representing irreversible and equilibrium reaction systems, respectively), the Michaelis constant (KM), and the turnover ratio (rcat) of the participating enzymes. We further find the maximum possible gain is intrinsically determined by KM/Gmax=(1 /KM+2 ) /4 . Our model also indicates that the dissipated energy (measured by -lnγ ), from the intracellular energy-bearing bioparticles (e.g., ATP), is used to generate a force field Fγ∝(1 -√{γ }) that reshapes and disables the effective potential around the zero gain region, which leads to the ultrasensitive response to external chemical gradients.

Performance Evaluation of Staged Bosch Process for CO2 Reduction to Produce Life Support Consumables

NASA Technical Reports Server (NTRS)

Vilekar, Saurabh A.; Hawley, Kyle; Junaedi, Christian; Walsh, Dennis; Roychoudhury, Subir; Abney. Morgan B.; Mansell, James M.

2012-01-01

Utilizing carbon dioxide to produce water and hence oxygen is critical for sustained manned missions in space, and to support both NASA's cabin Atmosphere Revitalization System (ARS) and In-Situ Resource Utilization (ISRU) concepts. For long term missions beyond low Earth orbit, where resupply is significantly more difficult and costly, open loop ARS, like Sabatier, consume inputs such as hydrogen. The Bosch process, on the other hand, has the potential to achieve complete loop closure and is hence a preferred choice. However, current single stage Bosch reactor designs suffer from a large recycle penalty due to slow reaction rates and the inherent limitation in approaching thermodynamic equilibrium. Developmental efforts are seeking to improve upon the efficiency (hence reducing the recycle penalty) of current single stage Bosch reactors which employ traditional steel wool catalysts. Precision Combustion, Inc. (PCI), with support from NASA, has investigated the potential for utilizing catalysts supported over short-contact time Microlith substrates for the Bosch reaction to achieve faster reaction rates, higher conversions, and a reduced recycle flows. Proof-of-concept testing was accomplished for a staged Bosch process by splitting the chemistry in two separate reactors, first being the reverse water-gas-shift (RWGS) and the second being the carbon formation reactor (CFR) via hydrogenation and/or Boudouard. This paper presents the results from this feasibility study at various operating conditions. Additionally, results from two 70 hour durability tests for the RWGS reactor are discussed.

Rapid and Sensitive Detection of Vibrio parahaemolyticus and Vibrio vulnificus by Multiple Endonuclease Restriction Real-Time Loop-Mediated Isothermal Amplification Technique.

PubMed

Wang, Yi; Li, Dongxun; Wang, Yan; Li, Kewei; Ye, Changyun

2016-01-19

Vibrio parahaemolyticus and Vibrio vulnificus are two marine seafood-borne pathogens causing severe illnesses in humans and aquatic animals. In this study, a recently developed novel multiple endonuclease restriction real-time loop-mediated isothermal amplification technology (MERT-LAMP) were successfully developed and evaluated for simultaneous detection of V. parahaemolyticus and V. vulnificus strains in only a single reaction. Two MERT-LAMP primer sets were designed to specifically target toxR gene of V. parahaemolyticus and rpoS gene of V. vulnificus. The MERT-LAMP reactions were conducted at 62 °C, and the positive results were produced in as short as 19 min with the genomic DNA templates extracted from the V. parahaemolyticus and V. vulnificus strains. The two target pathogens present in the same sample could be simultaneously detected and correctly differentiated based on distinct fluorescence curves in a real-time format. The sensitivity of MERT-LAMP assay was 250 fg and 125 fg DNA per reaction with genomic templates of V. parahaemolyticus and V. vulnificus strains, which was in conformity with conventional LAMP detection. Compared with PCR-based techniques, the MERT-LAMP technology was 100- and 10-fold more sensitive than that of PCR and qPCR methods. Moreover, the limit of detection of MERT-LAMP approach for V. parahaemolyticus isolates and V. vulnificus isolates detection in artificially-contaminated oyster samples was 92 CFU and 83 CFU per reaction. In conclusion, the MERT-LAMP assay presented here was a rapid, specific, and sensitive tool for the detection of V. parahaemolyticus and V. vulnificus, and could be adopted for simultaneous screening of V. parahaemolyticus and V. vulnificus in a wide variety of samples.

Identification of Methicillin-Resistant Staphylococcus aureus (MRSA) Using Simultaneous Detection of mecA, nuc, and femB by Loop-Mediated Isothermal Amplification (LAMP).

PubMed

Chen, Changguo; Zhao, Qiangyuan; Guo, Jianwei; Li, Yanjun; Chen, Qiuyuan

2017-08-01

The aim of this study was to develop a rapid detection assay to identify methicillin-resistant Staphylococcus aureus by simultaneous testing for the mecA, nuc, and femB genes using the loop-mediated isothermal amplification (LAMP) method. LAMP primers were designed using online bio-software ( http://primerexplorer.jp/e/ ), and amplification reactions were performed in an isothermal temperature bath. The products were then examined using 2% agarose gel electrophoresis. MecA, nuc, and femB were confirmed by triplex TaqMan real-time PCR. For better naked-eye inspection of the reaction result, hydroxy naphthol blue (HNB) was added to the amplification system. Within 60 min, LAMP successfully amplified the genes of interest under isothermal conditions at 63 °C. The results of 2% gel electrophoresis indicated that when the Mg 2+ concentration in the reaction system was 6 μmol, the amplification of the mecA gene was relatively good, while the amplification of the nuc and femB genes was better at an Mg 2+ concentration of 8 μmol. Obvious color differences were observed by adding 1 μL (3.75 mM) of HNB into 25 μL reaction system. The LAMP assay was applied to 128 isolates cases of methicillin-resistant Staphylococcus aureus, which were separated from the daily specimens and identified by Vitek microbial identification instruments. The results were identical for both LAMP and PCR. LAMP offers an alternative detection assay for mecA, nuc, and femB and is faster than other methods.

Method-Unifying View of Loop-Formation Kinetics in Peptide and Protein Folding.

PubMed

Jacob, Maik H; D'Souza, Roy N; Schwarzlose, Thomas; Wang, Xiaojuan; Huang, Fang; Haas, Elisha; Nau, Werner M

2018-04-26

Protein folding can be described as a probabilistic succession of events in which the peptide chain forms loops closed by specific amino acid residue contacts, herein referred to as loop nodes. To measure loop rates, several photophysical methods have been introduced where a pair of optically active probes is incorporated at selected chain positions and the excited probe undergoes contact quenching (CQ) upon collision with the second probe. The quenching mechanisms involved triplet-triplet energy transfer, photoinduced electron transfer, and collision-induced fluorescence quenching, where the fluorescence of Dbo, an asparagine residue conjugated to 2,3-diazabicyclo[2.2.2]octane, is quenched by tryptophan. The discrepancy between the loop rates afforded from these three CQ techniques has, however, remained unresolved. In analyzing this discrepancy, we now report two short-distance FRET methods where Dbo acts as an energy acceptor in combination with tryptophan and naphtylalanine, two donors with largely different fluorescence lifetimes of 1.3 and 33 ns, respectively. Despite the different quenching mechanisms, the rates from FRET and CQ methods were, surprisingly, of comparable magnitude. This combination of FRET and CQ data led to a unifying physical model and to the conclusion that the rate of loop formation in folding reactions varies not only with the kind and number of residues that constitute the chain but also in particular with the size and properties of the residues that constitute the loop node.

Rapid detection of Puccinia triticina causing leaf rust of wheat by PCR and loop mediated isothermal amplification

PubMed Central

Kulshreshtha, Deepika; Gupta, Sangeeta; Singh, Kartar; Bhardwaj, Subhash C.

2018-01-01

Leaf rust of wheat caused by Puccinia triticina has significant impact on wheat production worldwide. Effective and quick detection methodologies are required to mitigate yield loss and time constraints associated with monitoring and management of leaf rust of wheat. In the present study, detection of P. triticina has been simplified by developing a rapid, reliable, efficient and visual colorimetric method i.e., loop mediated isothermal amplification of DNA (LAMP). Based on in silico analysis of P. triticina genome, PTS68, a simple sequence repeat was found highly specific to leaf rust fungus. A marker (PtRA68) was developed and its specificity was validated through PCR technique which gave a unique and sharp band of 919 bp in P. triticina pathotypes only. A novel gene amplification method LAMP which enables visual detection of pathogen by naked eye was developed for leaf rust pathogen. A set of six primers was designed from specific region of P. triticina and conditions were optimised to complete the observation process in 60 minutes at 65o C. The assay developed in the study could detect presence of P. triticina on wheat at 24 hpi (pre-symptomatic stage) which was much earlier than PCR without requiring thermal cycler. Sensitivity of LAMP assay developed in the study was 100 fg which was more sensitive than conventional PCR (50 pg) and equivalent to qPCR (100 fg). The protocol developed in the study was utilized for detection of leaf rust infected samples collected from different wheat fields. LAMP based colorimetric detection assay showed sky blue color in positive reaction and violet color in negative reaction after addition of 120 μM hydroxyl napthol blue (HNB) solution to reaction mixture. Similarly, 0.6 mg Ethidium bromide/ml was added to LAMP products, placed on transilluminator to witness full brightness in positive reaction and no such brightness could be seen in negative reaction mixture. Further, LAMP products spread in a ladder like banding pattern in gel electrophoresis. Our assay is significantly faster than the conventional methods used in the identification of P. triticina. The assay developed in the study shall be very much useful in the development of diagnostic kit for monitoring disease, creation of prediction model and efficient management of disease. PMID:29698484

Rapid detection of Puccinia triticina causing leaf rust of wheat by PCR and loop mediated isothermal amplification.

PubMed

Manjunatha, C; Sharma, Sapna; Kulshreshtha, Deepika; Gupta, Sangeeta; Singh, Kartar; Bhardwaj, Subhash C; Aggarwal, Rashmi

2018-01-01

Leaf rust of wheat caused by Puccinia triticina has significant impact on wheat production worldwide. Effective and quick detection methodologies are required to mitigate yield loss and time constraints associated with monitoring and management of leaf rust of wheat. In the present study, detection of P. triticina has been simplified by developing a rapid, reliable, efficient and visual colorimetric method i.e., loop mediated isothermal amplification of DNA (LAMP). Based on in silico analysis of P. triticina genome, PTS68, a simple sequence repeat was found highly specific to leaf rust fungus. A marker (PtRA68) was developed and its specificity was validated through PCR technique which gave a unique and sharp band of 919 bp in P. triticina pathotypes only. A novel gene amplification method LAMP which enables visual detection of pathogen by naked eye was developed for leaf rust pathogen. A set of six primers was designed from specific region of P. triticina and conditions were optimised to complete the observation process in 60 minutes at 65o C. The assay developed in the study could detect presence of P. triticina on wheat at 24 hpi (pre-symptomatic stage) which was much earlier than PCR without requiring thermal cycler. Sensitivity of LAMP assay developed in the study was 100 fg which was more sensitive than conventional PCR (50 pg) and equivalent to qPCR (100 fg). The protocol developed in the study was utilized for detection of leaf rust infected samples collected from different wheat fields. LAMP based colorimetric detection assay showed sky blue color in positive reaction and violet color in negative reaction after addition of 120 μM hydroxyl napthol blue (HNB) solution to reaction mixture. Similarly, 0.6 mg Ethidium bromide/ml was added to LAMP products, placed on transilluminator to witness full brightness in positive reaction and no such brightness could be seen in negative reaction mixture. Further, LAMP products spread in a ladder like banding pattern in gel electrophoresis. Our assay is significantly faster than the conventional methods used in the identification of P. triticina. The assay developed in the study shall be very much useful in the development of diagnostic kit for monitoring disease, creation of prediction model and efficient management of disease.

Loop-Mediated Isothermal Amplification for Salmonella Detection in Food and Feed: Current Applications and Future Directions

PubMed Central

Yang, Qianru; Domesle, Kelly J.

2018-01-01

Abstract Loop-mediated isothermal amplification (LAMP) has become a powerful alternative to polymerase chain reaction (PCR) for pathogen detection in clinical specimens and food matrices. Nontyphoidal Salmonella is a zoonotic pathogen of significant food and feed safety concern worldwide. The first study employing LAMP for the rapid detection of Salmonella was reported in 2005, 5 years after the invention of the LAMP technology in Japan. This review provides an overview of international efforts in the past decade on the development and application of Salmonella LAMP assays in a wide array of food and feed matrices. Recent progress in assay design, platform development, commercial application, and method validation is reviewed. Future perspectives toward more practical and wider applications of Salmonella LAMP assays in food and feed testing are discussed. PMID:29902082

Development of a loop-mediated isothermal amplification assay for rapid detection of Burkholderia mallei.

PubMed

Mirzai, S; Safi, S; Mossavari, N; Afshar, D; Bolourchian, M

2016-08-31

The present study was conducted to establish a Loop-mediated isothermal amplification (LAMP) technique for the rapid detection of B. mallei the etiologic agent of glanders, a highly contagious disease of equines. A set of six specific primers targeting integrase gene cluster were designed for the LAMP test. The reaction was optimized using different temperatures and time intervals. The specificity of the assay was evaluated using DNA from B.pseudomallei and Pseudomonas aeruginosa. The LAMP products were analyzed both visually and under UV light after electrophoresis. The optimized conditions were found to be at 63ºC for 60 min. The assay showed high specificity and sensitivity. It was concluded that the established LAMP assay is a rapid, sensitive and practical tool for detection of B. mallei and early diagnosis of glanders.

Single-Molecule Spectroscopy and Imaging Studies of Protein Dynamics

NASA Astrophysics Data System (ADS)

Lu, H. Peter

2012-04-01

Enzymatic reactions and protein-protein interactions are traditionally studied at the ensemble level, despite significant static and dynamic inhomogeneities. Subtle conformational changes play a crucial role in protein functions, and these protein conformations are highly dynamic rather than being static. We applied AFM-enhanced single-molecule spectroscopy to study the mechanisms and dynamics of enzymatic reactions involved with kinase and lysozyme proteins. Enzymatic reaction turnovers and the associated structure changes of individual protein molecules were observed simultaneously in real-time by single-molecule FRET detections. Our single-molecule spectroscopy measurements of T4 lysozyme and HPPK enzymatic conformational dynamics have revealed time bunching effect and intermittent coherence in conformational state change dynamics involving in enzymatic reaction cycles. The coherent conformational state dynamics suggests that the enzymatic catalysis involves a multi-step conformational motion along the coordinates of substrate-enzyme complex formation and product releasing, presenting as an extreme dynamic behavior intrinsically related to the time bunching effect that we have reported previously. Our results of HPPK interaction with substrate support a multiple-conformational state model, being consistent with a complementary conformation selection and induced-fit enzymatic loop-gated conformational change mechanism in substrate-enzyme active complex formation. Our new approach is applicable to a wide range of single-molecule FRET measurements for protein conformational changes under enzymatic reactions.

Role of the N*(1535) resonance and the {pi}{sup -}p{yields}KY amplitudes in the OZI forbidden {pi}N{yields}{phi}N reaction

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

Doering, M.; Oset, E.; Zou, B. S.

2008-08-15

We study the {pi}N{yields}{phi}N reaction close to the {phi}N threshold within the chiral unitary approach, by combining the {pi}{sup -}p{yields}K{sup +}{sigma}{sup -},{pi}{sup -}p{yields}K{sup 0}{sigma}{sup 0}, and {pi}{sup -}p{yields}K{sup 0}{lambda} amplitudes with the coupling of {phi} to the K components of the final states of these reactions via quantum loops. We obtain good agreement with experiment when the dominant {pi}{sup -}p{yields}K{sup 0}{lambda} amplitude is constrained with its experimental cross section. We also evaluate the coupling of N*(1535) to {phi}N and find a moderate coupling as a consequence of partial cancellation of the large KY components of N*(1535). We also show thatmore » the N*(1535) pole approximation is too small to reproduce the measured cross section for the {pi}{sup -}N{yields}{phi}N reaction.« less

Tip-enhanced fluorescence with radially polarized illumination for monitoring loop-mediated isothermal amplification on Hepatitis C virus cDNA

NASA Astrophysics Data System (ADS)

Wei, Shih-Chung; Chuang, Tsung-Liang; Wang, Da-Shin; Lu, Hui-Hsin; Gu, Frank X.; Sung, Kung-Bin; Lin, Chii-Wann

2015-02-01

A tip nanobiosensor for monitoring DNA replication was presented. The effects of excitation power and polarization on tip-enhanced fluorescence (TEF) were assessed with the tip immersed in fluorescein isothiocyanate solution first. The photon count rose on average fivefold with radially polarized illumination at 50 mW. We then used polymerase-functionalized tips for monitoring loop-mediated isothermal amplification on Hepatitis C virus cDNA. The amplicon-SYBR Green I complex was detected and compared to real-time loop-mediated isothermal amplification. The signals of the reaction using 4 and 0.004 ng/μl templates were detected 10 and 30 min earlier, respectively. The results showed the potential of TEF in developing a nanobiosensor for real-time DNA amplification.

Performance characterization of a Bosch CO sub 2 reduction subsystem

NASA Technical Reports Server (NTRS)

Heppner, D. B.; Hallick, T. M.; Schubert, F. H.

1980-01-01

The performance of Bosch hardware at the subsystem level (up to five-person capacity) in terms of five operating parameters was investigated. The five parameters were: (1) reactor temperature, (2) recycle loop mass flow rate, (3) recycle loop gas composition (percent hydrogen), (4) recycle loop dew point and (5) catalyst density. Experiments were designed and conducted in which the five operating parameters were varied and Bosch performance recorded. A total of 12 carbon collection cartridges provided over approximately 250 hours of operating time. Generally, one cartridge was used for each parameter that was varied. The Bosch hardware was found to perform reliably and reproducibly. No startup, reaction initiation or carbon containment problems were observed. Optimum performance points/ranges were identified for the five parameters investigated. The performance curves agreed with theoretical projections.

Label-free fluorescence strategy for sensitive detection of adenosine triphosphate using a loop DNA probe with low background noise.

PubMed

Lin, Chunshui; Cai, Zhixiong; Wang, Yiru; Zhu, Zhi; Yang, Chaoyong James; Chen, Xi

2014-07-15

A simple, rapid, label-free, and ultrasensitive fluorescence strategy for adenosine triphosphate (ATP) detection was developed using a loop DNA probe with low background noise. In this strategy, a loop DNA probe, which is the substrate for both ligation and digestion enzyme reaction, was designed. SYBR green I (SG I), a double-stranded specific dye, was applied for the readout fluorescence signal. Exonuclease I (Exo I) and exonuclease III (Exo III), sequence-independent nucleases, were selected to digest the loop DNA probe in order to minimize the background fluorescence signal. As a result, in the absence of ATP, the loop DNA was completely digested by Exo I and Exo III, leading to low background fluorescence owing to the weak electrostatic interaction between SG I and mononucleotides. On the other hand, ATP induced the ligation of the nicking site, and the sealed loop DNA resisted the digestion of Exo I and ExoIII, resulting in a remarkable increase of fluorescence response. Upon background noise reduction, the sensitivity of the ATP determination was improved significantly, and the detection limitation was found to be 1.2 pM, which is much lower than that in almost all the previously reported methods. This strategy has promise for wide application in the determination of ATP.

Spacecraft momentum management procedures. [large space telescope

NASA Technical Reports Server (NTRS)

Chen, L. C.; Davenport, P. B.; Sturch, C. R.

1980-01-01

Techniques appropriate for implementation onboard the space telescope and other spacecraft to manage the accumulation of momentum in reaction wheel control systems using magnetic torquing coils are described. Generalized analytical equations are derived for momentum control laws that command the magnetic torquers. These control laws naturally fall into two main categories according to the methods used for updating the magnetic dipole command: closed loop, in which the update is based on current measurements to achieve a desired torque instantaneously, and open-loop, in which the update is based on predicted information to achieve a desired momentum at the end of a period of time. Physical interpretations of control laws in general and of the Space Telescope cross product and minimum energy control laws in particular are presented, and their merits and drawbacks are discussed. A technique for retaining the advantages of both the open-loop and the closed-loop control laws is introduced. Simulation results are presented to compare the performance of these control laws in the Space Telescope environment.

Establishment and Application of a Loop-Mediated Isothermal Amplification Method for Simple, Specific, Sensitive and Rapid Detection of Toxoplasma gondii

PubMed Central

CAO, Lili; CHENG, Ronghua; YAO, Lin; YUAN, Shuxian; YAO, Xinhua

2013-01-01

ABSTRACT The Loop-mediated isothermal amplification (LAMP) method amplifies DNA with high simply, specificity, sensitivity and rapidity. In this study, A LAMP assay with 6 primers targeting a highly conserved region of the GRA1 gene was developed to diagnose Toxoplasma gondii. The reaction time of the LAMP assay was shortened to 30 min after optimizing the reaction system. The LAMP assay was found to be highly specific and stable. The detection limit of the LAMP assay was 10 copies, the same as that of the conventional PCR. We used the LAMP assay to develop a real-time fluorogenic protocol to quantitate T. gondii DNA and generated a log-linear regression plot by plotting the time-to-threshold values against genomic equivalent copies. Furthermore, the LAMP assay was applied to detect T. gondii DNA in 423 blood samples and 380 lymph node samples from 10 pig farms, and positive results were obtained for 7.8% and 8.2% of samples, respectively. The results showed that the LAMP method is slightly more sensitive than conventional PCR (6.1% and 7.6%). Positive samples obtained from 6 pig farms. The LAMP assay established in this study resulted in simple, specific, sensitive and rapid detection of T. gondii DNA and is expected to play an important role in clinical detection of T. gondii. PMID:23965849

Structural and magnetic properties of the products of the transformation of ferrihydrite: Effect of cobalt dications

NASA Astrophysics Data System (ADS)

Camacho, K. I.; Pariona, N.; Martinez, A. I.; Baggio-Saitovitch, E.; Herrera-Trejo, M.; Perry, Dale L.

2017-05-01

The effect of cobalt dications on the transformation of 2-line ferrihydrite (2LF) has been studied. The products of the transformation reaction were characterized by X-ray diffraction, Mössbauer spectroscopy (MS), transmission electron microscopy (TEM), magnetometry, and first-order reversal curve (FORC) diagrams. It was found that the concentration of cobalt dications plays an important role on the structural and magnetic properties of the products; i.e., for low cobalt concentrations, cobalt-substituted hematite is formed, while higher concentrations promote the formation of cobalt-substituted magnetite. Structural results revealed that formation of other iron oxide polymorphs is avoided and residual 2LF is always present in the final products. In this way, hematite/2LF and magnetite/2LF nanocomposites were formed. For all the samples, magnetic measurements yielded non-saturated hysteresis loops at a maximum field of 12 kOe. For cobalt-substituted hematite/2LF samples, FORC diagrams revealed the presence of multiple single-domain (SD) components which generate interaction coupling between SD with low and high coercivity. Moreover, for cobalt-substituted magnetite/2LF samples, the FORC diagrams revealed the components of wasp-waist hysteresis loops which consist of mixtures of SD and superparamagnetic particles. One of the goals of the present study is the rigorous, experimental documentation of ferrihydrite/hematite mixtures as a function of reaction conditions for use as analytical standards research.

Modulation of the Extent of Cooperative Structural Change During Protein Folding by Chemical Denaturant.

PubMed

Jethva, Prashant N; Udgaonkar, Jayant B

2017-09-07

Protein folding and unfolding reactions invariably appear to be highly cooperative reactions, but the structural and sequence determinants of cooperativity are poorly understood. Importantly, it is not known whether cooperative structural change occurs throughout the protein, or whether some parts change cooperatively and other parts change noncooperatively. In the current study, hydrogen exchange mass spectrometry has been used to show that the mechanism of unfolding of the PI3K SH3 domain is similar in the absence and presence of 5 M urea. The data are well described by a four state N ↔ I N ↔ I 2 ↔ U model, in which structural changes occur noncooperatively during the N ↔ I N and I N ↔ I 2 transitions, and occur cooperatively during the I 2 ↔ U transition. The nSrc-loop and RT-loop, as well as β strands 4 and 5 undergo noncooperative unfolding, while β strands 1, 2, and 3 unfold cooperatively in the absence of urea. However, in the presence of 5 M urea, the unfolding of β strand 4 switches to become cooperative, leading to an increase in the extent of cooperative structural change. The current study highlights the relationship between protein stability and cooperativity, by showing how the extent of cooperativity can be varied, using chemical denaturant to alter protein stability.

Structural Basis for the ATP-dependent Configuration of Adenylation Active Site in Bacillus subtilis o-Succinylbenzoyl-CoA Synthetase*

PubMed Central

Chen, Yaozong; Sun, Yueru; Song, Haigang; Guo, Zhihong

2015-01-01

o-Succinylbenzoyl-CoA synthetase, or MenE, is an essential adenylate-forming enzyme targeted for development of novel antibiotics in the menaquinone biosynthesis. Using its crystal structures in a ligand-free form or in complex with nucleotides, a conserved pattern is identified in the interaction between ATP and adenylating enzymes, including acyl/aryl-CoA synthetases, adenylation domains of nonribosomal peptide synthetases, and luciferases. It involves tight gripping interactions of the phosphate-binding loop (P-loop) with the ATP triphosphate moiety and an open-closed conformational change to form a compact adenylation active site. In MenE catalysis, this ATP-enzyme interaction creates a new binding site for the carboxylate substrate, allowing revelation of the determinants of substrate specificities and in-line alignment of the two substrates for backside nucleophilic substitution reaction by molecular modeling. In addition, the ATP-enzyme interaction is suggested to play a crucial catalytic role by mutation of the P-loop residues hydrogen-bonded to ATP. Moreover, the ATP-enzyme interaction has also clarified the positioning and catalytic role of a conserved lysine residue in stabilization of the transition state. These findings provide new insights into the adenylation half-reaction in the domain alteration catalytic mechanism of the adenylate-forming enzymes. PMID:26276389

Virtual solar field - An opportunity to optimize transient processes in line-focus CSP power plants

NASA Astrophysics Data System (ADS)

Noureldin, Kareem; Hirsch, Tobias; Pitz-Paal, Robert

2017-06-01

Optimizing solar field operation and control is a key factor to improve the competitiveness of line-focus solar thermal power plants. However, the risks of assessing new and innovative control strategies on operational power plants hinder such optimizations and result in applying more conservative control schemes. In this paper, we describe some applications for a whole solar field transient in-house simulation tool developed at the German Aerospace Centre (DLR), the Virtual Solar Field (VSF). The tool offers a virtual platform to simulate real solar fields while coupling the thermal and hydraulic conditions of the field with high computational efficiency. Using the tool, developers and operator can probe their control strategies and assess the potential benefits while avoiding the high risks and costs. In this paper, we study the benefits gained from controlling the loop valves and of using direct normal irradiance maps and forecasts for the field control. Loop valve control is interesting for many solar field operators since it provides a high degree of flexibility to the control of the solar field through regulating the flow rate in each loop. This improves the reaction to transient condition, such as passing clouds and field start-up in the morning. Nevertheless, due to the large number of loops and the sensitivity of the field control to the valve settings, this process needs to be automated and the effect of changing the setting of each valve on the whole field control needs to be taken into account. We used VSF to implement simple control algorithms to control the loop valves and to study the benefits that could be gained from using active loop valve control during transient conditions. Secondly, we study how using short-term highly spatially-resolved DNI forecasts provided by cloud cameras could improve the plant energy yield. Both cases show an improvement in the plant efficiency and outlet temperature stability. This paves the road for further investigations of new control strategies or for optimizations of the currently implemented ones.

Loop L1 governs the DNA-binding specificity and order for RecA-catalyzed reactions in homologous recombination and DNA repair

PubMed Central

Shinohara, Takeshi; Ikawa, Shukuko; Iwasaki, Wakana; Hiraki, Toshiki; Hikima, Takaaki; Mikawa, Tsutomu; Arai, Naoto; Kamiya, Nobuo; Shibata, Takehiko

2015-01-01

In all organisms, RecA-family recombinases catalyze homologous joint formation in homologous genetic recombination, which is essential for genome stability and diversification. In homologous joint formation, ATP-bound RecA/Rad51-recombinases first bind single-stranded DNA at its primary site and then interact with double-stranded DNA at another site. The underlying reason and the regulatory mechanism for this conserved binding order remain unknown. A comparison of the loop L1 structures in a DNA-free RecA crystal that we originally determined and in the reported DNA-bound active RecA crystals suggested that the aspartate at position 161 in loop L1 in DNA-free RecA prevented double-stranded, but not single-stranded, DNA-binding to the primary site. This was confirmed by the effects of the Ala-replacement of Asp-161 (D161A), analyzed directly by gel-mobility shift assays and indirectly by DNA-dependent ATPase activity and SOS repressor cleavage. When RecA/Rad51-recombinases interact with double-stranded DNA before single-stranded DNA, homologous joint-formation is suppressed, likely by forming a dead-end product. We found that the D161A-replacement reduced this suppression, probably by allowing double-stranded DNA to bind preferentially and reversibly to the primary site. Thus, Asp-161 in the flexible loop L1 of wild-type RecA determines the preference for single-stranded DNA-binding to the primary site and regulates the DNA-binding order in RecA-catalyzed recombinase reactions. PMID:25561575

Protein Arginine Methyltransferase Product Specificity Is Mediated by Distinct Active-site Architectures*

PubMed Central

Jain, Kanishk; Warmack, Rebeccah A.; Stavropoulos, Peter

2016-01-01

In the family of protein arginine methyltransferases (PRMTs) that predominantly generate either asymmetric or symmetric dimethylarginine (SDMA), PRMT7 is unique in producing solely monomethylarginine (MMA) products. The type of methylation on histones and other proteins dictates changes in gene expression, and numerous studies have linked altered profiles of methyl marks with disease phenotypes. Given the importance of specific inhibitor development, it is crucial to understand the mechanisms by which PRMT product specificity is conferred. We have focused our attention on active-site residues of PRMT7 from the protozoan Trypanosoma brucei. We have designed 26 single and double mutations in the active site, including residues in the Glu-Xaa8-Glu (double E) loop and the Met-Gln-Trp sequence of the canonical Thr-His-Trp (THW) loop known to interact with the methyl-accepting substrate arginine. Analysis of the reaction products by high resolution cation exchange chromatography combined with the knowledge of PRMT crystal structures suggests a model where the size of two distinct subregions in the active site determines PRMT7 product specificity. A dual mutation of Glu-181 to Asp in the double E loop and Gln-329 to Ala in the canonical THW loop enables the enzyme to produce SDMA. Consistent with our model, the mutation of Cys-431 to His in the THW loop of human PRMT9 shifts its product specificity from SDMA toward MMA. Together with previous results, these findings provide a structural basis and a general model for product specificity in PRMTs, which will be useful for the rational design of specific PRMT inhibitors. PMID:27387499

Rapid detection of all known ebolavirus species by reverse transcription-loop-mediated isothermal amplification (RT-LAMP).

PubMed

Oloniniyi, Olamide K; Kurosaki, Yohei; Miyamoto, Hiroko; Takada, Ayato; Yasuda, Jiro

2017-08-01

Ebola virus disease (EVD), a highly virulent infectious disease caused by ebolaviruses, has a fatality rate of 25-90%. Without a licensed chemotherapeutic agent or vaccine for the treatment and prevention of EVD, control of outbreaks requires accurate and rapid diagnosis of cases. In this study, five sets of six oligonucleotide primers targeting the nucleoprotein gene were designed for specific identification of each of the five ebolavirus species using reverse transcription-loop mediated isothermal amplification (RT-LAMP) assay. The detection limits of the ebolavirus species-specific primer sets were evaluated using in vitro transcribed RNAs. The detection limit of species-specific RT-LAMP assays for Zaire ebolavirus, Sudan ebolavirus, Taï Forest ebolavirus, and Bundibugyo ebolavirus was 256 copies/reaction, while the detection limit for Reston ebolavirus was 64 copies/reaction, and the detection time for each of the RT-LAMP assays was 13.3±3.0, 19.8±4.6, 14.3±0.6, 16.1±4.7, and 19.8±2.4min (mean±SD), respectively. The sensitivity of the species-specific RT-LAMP assays were similar to that of the established RT-PCR and quantitative RT-PCR assays for diagnosis of EVD and are suitable for field or point-of-care diagnosis. The RT-LAMP assays were specific for the detection of the respective species of ebolavirus with no cross reaction with other species of ebolavirus and other viral hemorrhagic fever viruses such as Marburg virus, Lassa fever virus, and Dengue virus. The species-specific RT-LAMP assays developed in this study are rapid, sensitive, and specific and could be useful in case of an EVD outbreak. Copyright © 2017 Elsevier B.V. All rights reserved.

groEL is a suitable genetic marker for detecting Vibrio parahaemolyticus by loop-mediated isothermal amplification assay.

PubMed

Siddique, M P; Jang, W J; Lee, J M; Ahn, S H; Suraiya, S; Kim, C H; Kong, I S

2017-08-01

A groEL gene-based loop-mediated isothermal amplification (LAMP) assay was developed to detect Vibrio parahaemolyticus in contaminated seafood and water. The assay was optimized and conducted at 63°C for 40 min using Bacillus stearothermophilus (Bst) DNA polymerase, large fragment. Amplification was analysed via multiple detection methods, including opacity, formation of white precipitate, DNA intercalating dyes (ethidium bromide and SYBR Green I), metal ion-binding indicator dye, calcein, and 2% agarose gel electrophoresis. A characteristic ladder-like band pattern on agarose gel and the desired colour changes when using different dyes were observed in positive cases, and these were species-specific for V. parahaemolyticus when compared with other closely related Vibrio spp. The limit of detection (LoD) of this assay was 100 fg per reaction, 100-fold higher than that for conventional polymerase chain reaction (PCR). When tested on artificially contaminated seafood and seawater, the LoDs of the LAMP assay were 120 and 150 fg per reaction respectively, and those of conventional PCR were 120 and 150 pg per reaction respectively. Based on our results, the groEL gene-based LAMP assay is rapid, specific, sensitive, and reliable for detecting V. parahaemolyticus, and it could be used in field diagnosis. The loop-mediated isothermal amplification (LAMP) assay using groEL gene (an abundant, highly conserved gene and member of the groESL chaperone gene family) provided rapid, species-specific and highly sensitive method for detecting Vibrio parahaemolyticus, the leading causal agent of seafood-borne diseases worldwide. Moreover, groEL LAMP revealed high efficiency than conventional PCR assay for V. parahaemolyticus using template both from pure culture and artificially contaminated seafood and water, which indicated the applicability in the field and environmental screening purpose for the organism. © 2017 The Society for Applied Microbiology.

Role of Loop-Clamping Side Chains in Catalysis by Triosephosphate Isomerase.

PubMed

Zhai, Xiang; Amyes, Tina L; Richard, John P

2015-12-09

The side chains of Y208 and S211 from loop 7 of triosephosphate isomerase (TIM) form hydrogen bonds to backbone amides and carbonyls from loop 6 to stabilize the caged enzyme-substrate complex. The effect of seven mutations [Y208T, Y208S, Y208A, Y208F, S211G, S211A, Y208T/S211G] on the kinetic parameters for TIM catalyzed reactions of the whole substrates dihydroxyacetone phosphate and d-glyceraldehyde 3-phosphate [(k(cat)/K(m))(GAP) and (k(cat)/K(m))DHAP] and of the substrate pieces glycolaldehyde and phosphite dianion (k(cat)/K(HPi)K(GA)) are reported. The linear logarithmic correlation between these kinetic parameters, with slope of 1.04 ± 0.03, shows that most mutations of TIM result in an identical change in the activation barriers for the catalyzed reactions of whole substrate and substrate pieces, so that the transition states for these reactions are stabilized by similar interactions with the protein catalyst. The second linear logarithmic correlation [slope = 0.53 ± 0.16] between k(cat) for isomerization of GAP and K(d)(⧧) for phosphite dianion binding to the transition state for wildtype and many mutant TIM-catalyzed reactions of substrate pieces shows that ca. 50% of the wildtype TIM dianion binding energy, eliminated by these mutations, is expressed at the wildtype Michaelis complex, and ca. 50% is only expressed at the wildtype transition state. Negative deviations from this correlation are observed when the mutation results in a decrease in enzyme reactivity at the catalytic site. The main effect of Y208T, Y208S, and Y208A mutations is to cause a reduction in the total intrinsic dianion binding energy, but the effect of Y208F extends to the catalytic site.

Displacement Fields and Self-Energies of Circular and Polygonal Dislocation Loops in Homogeneous and Layered Anisotropic Solids

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

Gao, Yanfei; Larson, Ben C.

There are large classes of materials problems that involve the solutions of stress, displacement, and strain energy of dislocation loops in elastically anisotropic solids, including increasingly detailed investigations of the generation and evolution of irradiation induced defect clusters ranging in sizes from the micro- to meso-scopic length scales. Based on a two-dimensional Fourier transform and Stroh formalism that are ideal for homogeneous and layered anisotropic solids, we have developed robust and computationally efficient methods to calculate the displacement fields for circular and polygonal dislocation loops. Using the homogeneous nature of the Green tensor of order -1, we have shown thatmore » the displacement and stress fields of dislocation loops can be obtained by numerical quadrature of a line integral. In addition, it is shown that the sextuple integrals associated with the strain energy of loops can be represented by the product of a pre-factor containing elastic anisotropy effects and a universal term that is singular and equal to that for elastic isotropic case. Furthermore, we have found that the self-energy pre-factor of prismatic loops is identical to the effective modulus of normal contact, and the pre-factor of shear loops differs from the effective indentation modulus in shear by only a few percent. These results provide a convenient method for examining dislocation reaction energetic and efficient procedures for numerical computation of local displacements and stresses of dislocation loops, both of which play integral roles in quantitative defect analyses within combined experimental–theoretical investigations.« less

Displacement Fields and Self-Energies of Circular and Polygonal Dislocation Loops in Homogeneous and Layered Anisotropic Solids

DOE PAGES

Gao, Yanfei; Larson, Ben C.

2015-06-19

There are large classes of materials problems that involve the solutions of stress, displacement, and strain energy of dislocation loops in elastically anisotropic solids, including increasingly detailed investigations of the generation and evolution of irradiation induced defect clusters ranging in sizes from the micro- to meso-scopic length scales. Based on a two-dimensional Fourier transform and Stroh formalism that are ideal for homogeneous and layered anisotropic solids, we have developed robust and computationally efficient methods to calculate the displacement fields for circular and polygonal dislocation loops. Using the homogeneous nature of the Green tensor of order -1, we have shown thatmore » the displacement and stress fields of dislocation loops can be obtained by numerical quadrature of a line integral. In addition, it is shown that the sextuple integrals associated with the strain energy of loops can be represented by the product of a pre-factor containing elastic anisotropy effects and a universal term that is singular and equal to that for elastic isotropic case. Furthermore, we have found that the self-energy pre-factor of prismatic loops is identical to the effective modulus of normal contact, and the pre-factor of shear loops differs from the effective indentation modulus in shear by only a few percent. These results provide a convenient method for examining dislocation reaction energetic and efficient procedures for numerical computation of local displacements and stresses of dislocation loops, both of which play integral roles in quantitative defect analyses within combined experimental–theoretical investigations.« less

Interstitial loop transformations in FeCr

DOE PAGES

Béland, Laurent Karim; Osetsky, Yuri N.; Stoller, Roger E.; ...

2015-03-27

Here, we improve the Self-Evolving Atomistic Kinetic Monte Carlo (SEAKMC) algorithm by integrating the Activation Relaxation Technique nouveau (ARTn), a powerful open-ended saddle-point search method, into the algorithm. We use it to investigate the reaction of 37-interstitial 1/2[1 1 1] and 1/2[View the MathML source] loops in FeCr at 10 at.% Cr. They transform into 1/2[1 1 1], 1/2[View the MathML source], [1 0 0] and [0 1 0] 74-interstitial clusters with an overall barrier of 0.85 eV. We find that Cr decoration locally inhibits the rotation of crowdions, which dictates the final loop orientation. Moreover, the final loop orientationmore » depends on the details of the Cr decoration. Generally, a region of a given orientation is favored if Cr near its interface with a region of another orientation is able to inhibit reorientation at this interface more than the Cr present at the other interfaces. Also, we find that substitutional Cr atoms can diffuse from energetically unfavorable to energetically favorable sites within the interlocked 37-interstitial loops conformation with barriers of less than 0.35 eV.« less

[Principle of LAMP method--a simple and rapid gene amplification method].

PubMed

Ushikubo, Hiroshi

2004-06-01

So far nucleic acid test (NAT) has been employed in various fields, including infectious disease diagnoses. However, due to its complicated procedures and relatively high cost, it has not been widely utilized in many actual diagnostic applications. We have therefore developed a simple and rapid gene amplification technology, Loop-mediated Isothermal Amplification (LAMP) method, which has shown prominent results of surpassing the performance of the conventional gene amplification methods. LAMP method acquires three main features: (1) all reaction can be carried out under isothermal conditions; (2) the amplification efficiency is extremely high and tremendous amount of amplification products can be obtained; and (3) the reaction is highly specific. Furthermore, developed from the standard LAMP method, a rapid LAMP method, by adding in the loop primers, can reduce the amplification time from the previous 1 hour to less than 30 minutes. Enormous amount of white precipitate of magnesium pyrophosphate is produced as a by-product of the amplification, therefore, direct visual detection is possible without using any reaction indicators and detection equipments. We believe LAMP technology, with the integration of these features, can rightly apply to clinical genetic testing, food and environmental analysis, as well as NAT in different fields.

A Digital Microfluidics Platform for Loop-Mediated Isothermal Amplification Detection

PubMed Central

Veigas, Bruno; Águas, Hugo; Fortunato, Elvira; Martins, Rodrigo; Baptista, Pedro Viana; Igreja, Rui

2017-01-01

Digital microfluidics (DMF) arises as the next step in the fast-evolving field of operation platforms for molecular diagnostics. Moreover, isothermal schemes, such as loop-mediated isothermal amplification (LAMP), allow for further simplification of amplification protocols. Integrating DMF with LAMP will be at the core of a new generation of detection devices for effective molecular diagnostics at point-of-care (POC), providing simple, fast, and automated nucleic acid amplification with exceptional integration capabilities. Here, we demonstrate for the first time the role of coupling DMF and LAMP, in a dedicated device that allows straightforward mixing of LAMP reagents and target DNA, as well as optimum temperature control (reaction droplets undergo a temperature variation of just 0.3 °C, for 65 °C at the bottom plate). This device is produced using low-temperature and low-cost production processes, adaptable to disposable and flexible substrates. DMF-LAMP is performed with enhanced sensitivity without compromising reaction efficacy or losing reliability and efficiency, by LAMP-amplifying 0.5 ng/µL of target DNA in just 45 min. Moreover, on-chip LAMP was performed in 1.5 µL, a considerably lower volume than standard bench-top reactions. PMID:29144379

Loop-mediated amplification of the Clavibacter michiganensis subsp. michiganensis micA gene is highly specific.

PubMed

Yasuhara-Bell, Jarred; Kubota, Ryo; Jenkins, Daniel M; Alvarez, Anne M

2013-12-01

Loop-mediated amplification (LAMP) was used to specifically identify Clavibacter michiganensis subsp. michiganensis, causal agent of bacterial canker of tomato. LAMP primers were developed to detect micA, a chromosomally stable gene that encodes a type II lantibiotic, michiganin A, which inhibits growth of other C. michiganensis subspecies. In all, 409 bacterial strains (351 C. michiganensis subsp. michiganensis and 58 non-C. michiganensis subsp. michiganensis) from a worldwide collection were tested with LAMP to determine its specificity. LAMP results were compared with genetic profiles established using polymerase chain reaction (PCR) amplification of seven genes (dnaA, ppaJ, pat-1, chpC, tomA, ppaA, and ppaC). C. michiganensis subsp. michiganensis strains produced eight distinct profiles. The LAMP reaction identified all C. michiganensis subsp. michiganensis strains and discriminated them from other C. michiganensis subspecies and non-Clavibacter bacteria. LAMP has advantages over immunodiagnostic and other molecular detection methods because of its specificity and isothermal nature, which allows for easy field application. The LAMP reaction is also not affected by as many inhibitors as PCR. This diagnostic tool has potential to provide an easy, one-step test for rapid identification of C. michiganensis subsp. michiganensis.

Rapid Detection of Haptoglobin Gene Deletion in Alkaline-Denatured Blood by Loop-Mediated Isothermal Amplification Reaction

PubMed Central

Soejima, Mikiko; Egashira, Kouichi; Kawano, Hiroyuki; Kawaguchi, Atsushi; Sagawa, Kimitaka; Koda, Yoshiro

2011-01-01

Anhaptoglobinemic patients run the risk of severe anaphylactic transfusion reaction because they produce serum haptoglobin antibodies. Being homozygous for the haptoglobin gene deletion allele (HPdel) is the only known cause of congenital anhaptoglobinemia, and detection of HPdel before transfusion is important to prevent anaphylactic shock. In this study, we developed a loop-mediated isothermal amplification (LAMP)-based screening for HPdel. Optimal primer sets and temperature for LAMP were selected for HPdel and the 5′ region of the HP using genomic DNA as a template. Then, the effects of diluent and boiling on LAMP amplification were examined using whole blood as a template. Blood samples diluted 1:100 with 50 mmol/L NaOH without boiling gave optimal results as well as those diluted 1:2 with water followed by boiling. The results from 100 blood samples were fully concordant with those obtained by real-time PCR methods. Detection of the HPdel allele by LAMP using alkaline-denatured blood samples is rapid, simple, accurate, and cost effective, and is readily applicable in various clinical settings because this method requires only basic instruments. In addition, the simple preparation of blood samples using NaOH saves time and effort for various genetic tests. PMID:21497293

Efficient H2O2/CH3COOH oxidative desulfurization/denitrification of liquid fuels in sonochemical flow-reactors.

PubMed

Calcio Gaudino, Emanuela; Carnaroglio, Diego; Boffa, Luisa; Cravotto, Giancarlo; Moreira, Elizabeth M; Nunes, Matheus A G; Dressler, Valderi L; Flores, Erico M M

2014-01-01

The oxidative desulfurization/denitrification of liquid fuels has been widely investigated as an alternative or complement to common catalytic hydrorefining. In this process, all oxidation reactions occur in the heterogeneous phase (the oil and the polar phase containing the oxidant) and therefore the optimization of mass and heat transfer is of crucial importance to enhancing the oxidation rate. This goal can be achieved by performing the reaction in suitable ultrasound (US) reactors. In fact, flow and loop US reactors stand out above classic batch US reactors thanks to their greater efficiency and flexibility as well as lower energy consumption. This paper describes an efficient sonochemical oxidation with H2O2/CH3COOH at flow rates ranging from 60 to 800 ml/min of both a model compound, dibenzotiophene (DBT), and of a mild hydro-treated diesel feedstock. Four different commercially available US loop reactors (single and multi-probe) were tested, two of which were developed in the authors' laboratory. Full DBT oxidation and efficient diesel feedstock desulfurization/denitrification were observed after the separation of the polar oxidized S/N-containing compounds (S≤5 ppmw, N≤1 ppmw). Our studies confirm that high-throughput US applications benefit greatly from flow-reactors. Copyright © 2013 Elsevier B.V. All rights reserved.

Development of mRNA-based body fluid identification using reverse transcription loop-mediated isothermal amplification.

PubMed

Satoh, Tetsuya; Kouroki, Seiya; Ogawa, Keita; Tanaka, Yorika; Matsumura, Kazutoshi; Iwase, Susumu

2018-04-25

Identifying body fluids from forensic samples can provide valuable evidence for criminal investigations. Messenger RNA (mRNA)-based body fluid identification was recently developed, and highly sensitive parallel identification using reverse transcription polymerase chain reaction (RT-PCR) has been described. In this study, we developed reverse transcription loop-mediated isothermal amplification (RT-LAMP) as a simple, rapid assay for identifying three common forensic body fluids, namely blood, semen, and saliva, and evaluated its specificity and sensitivity. Hemoglobin beta (HBB), transglutaminase 4 (TGM4), and statherin (STATH) were selected as marker genes for blood, semen, and saliva, respectively. RT-LAMP could be performed in a single step including both reverse transcription and DNA amplification under an isothermal condition within 60 min, and detection could be conveniently performed via visual fluorescence. Marker-specific amplification was performed in each assay, and no cross-reaction was observed among five representative forensically relevant body fluids. The detection limits of the assays were 0.3 nL, 30 nL, and 0.3 μL for blood, semen, and saliva, respectively, and their sensitivities were comparable with those of RT-PCR. Furthermore, RT-LAMP assays were applicable to forensic casework samples. It is considered that RT-LAMP is useful for body fluid identification.

Visual Detection of West Nile Virus Using Reverse Transcription Loop-Mediated Isothermal Amplification Combined with a Vertical Flow Visualization Strip.

PubMed

Cao, Zengguo; Wang, Hualei; Wang, Lina; Li, Ling; Jin, Hongli; Xu, Changping; Feng, Na; Wang, Jianzhong; Li, Qian; Zhao, Yongkun; Wang, Tiecheng; Gao, Yuwei; Lu, Yiyu; Yang, Songtao; Xia, Xianzhu

2016-01-01

West Nile virus (WNV) causes a severe zoonosis, which can lead to a large number of casualties and considerable economic losses. A rapid and accurate identification method for WNV for use in field laboratories is urgently needed. Here, a method utilizing reverse transcription loop-mediated isothermal amplification combined with a vertical flow visualization strip (RT-LAMP-VF) was developed to detect the envelope (E) gene of WNV. The RT-LAMP-VF assay could detect 10(2) copies/μl of an WNV RNA standard using a 40 min amplification reaction followed by a 2 min incubation of the amplification product on the visualization strip, and no cross-reaction with other closely related members of the Flavivirus genus was observed. The assay was further evaluated using cells and mouse brain tissues infected with a recombinant rabies virus expressing the E protein of WNV. The assay produced sensitivities of 10(1.5) TCID50/ml and 10(1.33) TCID50/ml for detection of the recombinant virus in the cells and brain tissues, respectively. Overall, the RT-LAMP-VF assay developed in this study is rapid, simple and effective, and it is therefore suitable for clinical application in the field.

Detection of Puccinia kuehnii Causing Sugarcane Orange Rust with a Loop-Mediated Isothermal Amplification-Based Assay.

PubMed

Chandra, Amaresh; Keizerweerd, Amber T; Grisham, Michael P

2016-03-01

Puccinia kuehnii is a fungal pathogen that causes orange rust in sugarcane, which is now prevalent in many countries. At the early stage of disease, it is almost indistinguishable from brown rust, which is caused by Puccinia melanocephala. Although several PCR assays are available to detect these diseases, the loop-mediated isothermal amplification (LAMP)-based assay has been reported to be more economical and easier to perform. Under isothermal conditions, DNA is amplified with high specificity and rapidity. Moreover, visual judgment of color change without further post-amplification processing makes the method convenient. The present study was undertaken to detect P. kuehnii genomic DNA using four primers corresponding to a unique DNA sequence of P. kuehnii. The LAMP assay was found to be optimal when 8 mM MgSO4 was used and the reaction was incubated at 63 °C for 90 min. Positive samples showed a color change from orange to green upon SYBR Green I dye addition. Specificity of the LAMP test was checked with DNA of P. melanocephala, which showed no reaction. Sensitivity of the LAMP method was observed to be the same as real-time PCR at 0.1 ng, thus providing a rapid and more affordable option for early disease detection.

Structure and phase formation behavior and dielectric and magnetic properties of lead iron tantalate-lead zirconate titanate multiferroic ceramics

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

Wongmaneerung, R., E-mail: re_nok@yahoo.com; Tipakontitikul, R.; Jantaratana, P.

2016-03-15

Highlights: • The multiferroic ceramics consisted of PFT and PZT. • Crystal structure changed from cubic to mixedcubic and tetragonal with increasing PZT content. • Dielectric showed the samples underwent a typical relaxor ferroelectric behavior. • Magnetic properties showed very interesting behavior with square saturated magnetic hysteresis loops. - Abstract: Multiferroic (1 − x)Pb(Fe{sub 0.5}Ta{sub 0.5})O{sub 3}–xPb(Zr{sub 0.53}Ti{sub 0.47})O{sub 3} (or PFT–PZT) ceramics were synthesized by solid-state reaction method. The crystal structure and phase formation of the ceramics were examined by X-ray diffraction (XRD). The local structure surrounding Fe and Ti absorbing atoms was investigated by synchrotron X-ray Absorption Near-Edgemore » Structure (XANES) measurement. Dielectric properties were studied as a function of frequency and temperature using a LCR meter. A vibrating sample magnetometer (VSM) was used to determine the magnetic hysteresis loops. XRD study indicated that the crystal structure of the sample changed from pure cubic to mixed cubic and tetragonal with increasing PZT content. XANES measurements showed that the local structure surrounding Fe and Ti ions was similar. Dielectric study showed that the samples underwent a typical relaxor ferroelectric behavior while the magnetic properties showed very interesting behavior with square saturated magnetic hysteresis loops.« less

Rapid detection of duck hepatitis A virus genotype C using reverse transcription loop-mediated isothermal amplification.

PubMed

Li, Chuanfeng; Chen, Zongyan; Meng, Chunchun; Liu, Guangqing

2014-02-01

A one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was used and optimized to develop a rapid and sensitive detection system for duck hepatitis A virus genotype C (DHAV-C) RNA. A set of four specific primers was designed against highly conserved sequences located within the 3D gene from DHAV (strain GX1201). Under optimal reaction conditions, the sensitivity of DHAV-C-specific RT-LAMP was 100-fold higher than that of reverse transcriptase-polymerase chain reaction (RT-PCR), with a detection limit of 0.3pg (6.59×10(4) copies) per reaction. No cross-reactivity was observed from the samples of other duck viruses, which is in good accordance with RT-PCR. Furthermore, a positive reaction can be visually inspected by observing turbidity or color change after the addition of SYBR green I dye. The DHAV-C-specific RT-LAMP assay was applied to the samples and compared with RT-PCR. The positive-sample ratios were 26.7% (12 of 45) by RT-LAMP and 20% (9 of 45) by RT-PCR. Therefore, the newly developed RT-LAMP assay is a rapid, specific, sensitive, and cost-effective method of DHAV-C detection. This assay has potential applications in both clinical diagnosis and field surveillance of DHAV-C infection. Copyright © 2013. Published by Elsevier B.V.

Design of an ammonia closed-loop storage system in a CSP power plant with a power tower cavity receiver

NASA Astrophysics Data System (ADS)

Abdiwe, Ramadan; Haider, Markus

2017-06-01

In this study the thermochemical system using ammonia as energy storage carrier is investigated and a transient mathematical model using MATLAB software was developed to predict the behavior of the ammonia closed-loop storage system including but not limited to the ammonia solar reactor and the ammonia synthesis reactor. The MATLAB model contains transient mass and energy balances as well as chemical equilibrium model for each relevant system component. For the importance of the dissociation and formation processes in the system, a Computational Fluid Dynamics (CFD) simulation on the ammonia solar and synthesis reactors has been performed. The CFD commercial package FLUENT is used for the simulation study and all the important mechanisms for packed bed reactors are taken into account, such as momentum, heat and mass transfer, and chemical reactions. The FLUENT simulation reveals the profiles inside both reactors and compared them with the profiles from the MATLAB code.

Evaluation of peristaltic micromixers for highly integrated microfluidic systems

PubMed Central

Kim, Duckjong; Rho, Hoon Suk; Jambovane, Sachin; Shin, Soojeong; Hong, Jong Wook

2016-01-01

Microfluidic devices based on the multilayer soft lithography allow accurate manipulation of liquids, handling reagents at the sub-nanoliter level, and performing multiple reactions in parallel processors by adapting micromixers. Here, we have experimentally evaluated and compared several designs of micromixers and operating conditions to find design guidelines for the micromixers. We tested circular, triangular, and rectangular mixing loops and measured mixing performance according to the position and the width of the valves that drive nanoliters of fluids in the micrometer scale mixing loop. We found that the rectangular mixer is best for the applications of highly integrated microfluidic platforms in terms of the mixing performance and the space utilization. This study provides an improved understanding of the flow behaviors inside micromixers and design guidelines for micromixers that are critical to build higher order fluidic systems for the complicated parallel bio/chemical processes on a chip. PMID:27036809

Evaluation of peristaltic micromixers for highly integrated microfluidic systems

NASA Astrophysics Data System (ADS)

Kim, Duckjong; Rho, Hoon Suk; Jambovane, Sachin; Shin, Soojeong; Hong, Jong Wook

2016-03-01

Microfluidic devices based on the multilayer soft lithography allow accurate manipulation of liquids, handling reagents at the sub-nanoliter level, and performing multiple reactions in parallel processors by adapting micromixers. Here, we have experimentally evaluated and compared several designs of micromixers and operating conditions to find design guidelines for the micromixers. We tested circular, triangular, and rectangular mixing loops and measured mixing performance according to the position and the width of the valves that drive nanoliters of fluids in the micrometer scale mixing loop. We found that the rectangular mixer is best for the applications of highly integrated microfluidic platforms in terms of the mixing performance and the space utilization. This study provides an improved understanding of the flow behaviors inside micromixers and design guidelines for micromixers that are critical to build higher order fluidic systems for the complicated parallel bio/chemical processes on a chip.

Development of Primer Sets for Loop-Mediated Isothermal Amplification that Enables Rapid and Specific Detection of Streptococcus dysgalactiae, Streptococcus uberis and Streptococcus agalactiae.

PubMed

Wang, Deguo; Liu, Yanhong

2015-05-26

Streptococcus dysgalactiae, Streptococcus uberis and Streptococcus agalactiae are the three main pathogens causing bovine mastitis, with great losses to the dairy industry. Rapid and specific loop-mediated isothermal amplification methods (LAMP) for identification and differentiation of these three pathogens are not available. With the 16S rRNA gene and 16S-23S rRNA intergenic spacers as targets, four sets of LAMP primers were designed for identification and differentiation of S. dysgalactiae, S. uberis and S. agalactiae. The detection limit of all four LAMP primer sets were 0.1 pg DNA template per reaction, the LAMP method with 16S rRNA gene and 16S-23S rRNA intergenic spacers as the targets can differentiate the three pathogens, which is potentially useful in epidemiological studies.

Rapid and Sensitive Detection of Lymphocystis Disease Virus Genotype VII by Loop-Mediated Isothermal Amplification.

PubMed

Valverde, Estefanía J; Cano, Irene; Castro, Dolores; Paley, Richard K; Borrego, Juan J

2017-03-01

Lymphocystis disease virus (LCDV) infections have been described in gilthead seabream (Sparus aurata L.) and Senegalese sole (Solea senegalensis, Kaup), two of the most important marine fish species in the Mediterranean aquaculture. In this study, a rapid, specific, and sensitive detection method for LCDV genotype VII based on loop-mediated isothermal amplification (LAMP) was developed. The LAMP assay, performed using an apparatus with real-time amplification monitoring, was able to specifically detect LCDV genotype VII from clinically positive samples in less than 12 min. In addition, the assay allowed the detection of LCDV in all asymptomatic carrier fish analysed, identified by qPCR, showing an analytical sensitivity of ten copies of viral DNA per reaction. The LCDV LAMP assay has proven to be a promising diagnostic method that can be used easily in fish farms to detect the presence and spread of this iridovirus.

Rapid detection of Prunus necrotic ringspot virus using magnetic nanoparticle-assisted reverse transcription loop-mediated isothermal amplification.

PubMed

Zong, Xiaojuan; Wang, Wenwen; Wei, Hairong; Wang, Jiawei; Chen, Xin; Xu, Li; Zhu, Dongzi; Tan, Yue; Liu, Qingzhong

2014-11-01

Prunus necrotic ringspot virus (PNRSV) has seriously reduced the yield of Prunus species worldwide. In this study, a highly efficient and specific two-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) was developed to detect PNRSV. Total RNA was extracted from sweet cherry leaf samples using a commercial kit based on a magnetic nanoparticle technique. Transcripts were used as the templates for the assay. The results of this assay can be detected using agarose gel electrophoresis or by assessing in-tube fluorescence after adding SYBR Green I. The assay is highly specific for PNRSV, and it is more sensitive than reverse-transcription polymerase chain reaction (RT-PCR). Restriction enzyme digestion verified further the reliability of this RT-LAMP assay. To our knowledge, this is the first report of the application of RT-LAMP to PNRSV detection in Prunus species. Copyright © 2014 Elsevier B.V. All rights reserved.

X-ray diffraction and TGA kinetic analyses for chemical looping combustion applications.

PubMed

Tijani, Mansour Mohammedramadan; Aqsha, Aqsha; Mahinpey, Nader

2018-04-01

Synthesis and characterization of supported metal-based oxygen carriers were carried out to provide information related to the use of oxygen carriers for chemical looping combustion processes. The Cu, Co, Fe, Ni metals supported with Al 2 O 3 , CeO 2 , TiO 2 , ZrO 2 were prepared using the wetness impregnation technique. Then, the X-ray Diffraction (XRD) characterization of oxidized and reduced samples was obtained and presented. The kinetic analysis using Thermogravimetric analyzer (TGA) of the synthesized samples was conducted. The kinetics of reduction reaction of all samples were estimated and explained.

Implementing Nonlinear Feedback Controllers Using DNA Strand Displacement Reactions.

PubMed

Sawlekar, Rucha; Montefusco, Francesco; Kulkarni, Vishwesh V; Bates, Declan G

2016-07-01

We show how an important class of nonlinear feedback controllers can be designed using idealized abstract chemical reactions and implemented via DNA strand displacement (DSD) reactions. Exploiting chemical reaction networks (CRNs) as a programming language for the design of complex circuits and networks, we show how a set of unimolecular and bimolecular reactions can be used to realize input-output dynamics that produce a nonlinear quasi sliding mode (QSM) feedback controller. The kinetics of the required chemical reactions can then be implemented as enzyme-free, enthalpy/entropy driven DNA reactions using a toehold mediated strand displacement mechanism via Watson-Crick base pairing and branch migration. We demonstrate that the closed loop response of the nonlinear QSM controller outperforms a traditional linear controller by facilitating much faster tracking response dynamics without introducing overshoots in the transient response. The resulting controller is highly modular and is less affected by retroactivity effects than standard linear designs.

Chlorine fate and transport in drinking water distribution systems: Results from experimental and modeling studies

NASA Astrophysics Data System (ADS)

Clark, Robert M.

2011-12-01

It has become generally accepted that water quality can deteriorate in a distribution system through microbiological and chemical reactions in the bulk phase and/or at the pipe wall. The most serious aspect of water quality deterioration in a network is the loss of the disinfectant residual that can weaken the barrier against microbial contamination. Studies have suggested that one factor contributing to the loss of disinfectant residuals is the reaction between bulk phase disinfectants and pipe wall material. Free chlorine loss in corroded metal and PVC pipes, subject to changes in velocity, was assessed during an experiment conducted under controlled conditions in a specially constructed pipe loop located at the US Environmental Protection Agency's (EPA's) Test and Evaluation (T&E) Facility in Cincinnati, Ohio (USA). These studies demonstrated that in older unlined metal pipes, the loss of chlorine residual increases with velocity but that wall demand in PVC was negligible.

The Use of the Ex Vivo Chandler Loop Apparatus to Assess the Biocompatibility of Modified Polymeric Blood Conduits

PubMed Central

Slee, Joshua B.; Alferiev, Ivan S.; Levy, Robert J.; Stachelek, Stanley J.

2014-01-01

The foreign body reaction occurs when a synthetic surface is introduced to the body. It is characterized by adsorption of blood proteins and the subsequent attachment and activation of platelets, monocyte/macrophage adhesion, and inflammatory cell signaling events, leading to post-procedural complications. The Chandler Loop Apparatus is an experimental system that allows researchers to study the molecular and cellular interactions that occur when large volumes of blood are perfused over polymeric conduits. To that end, this apparatus has been used as an ex vivo model allowing the assessment of the anti-inflammatory properties of various polymer surface modifications. Our laboratory has shown that blood conduits, covalently modified via photoactivation chemistry with recombinant CD47, can confer biocompatibility to polymeric surfaces. Appending CD47 to polymeric surfaces could be an effective means to promote the efficacy of polymeric blood conduits. Herein is the methodology detailing the photoactivation chemistry used to append recombinant CD47 to clinically relevant polymeric blood conduits and the use of the Chandler Loop as an ex vivo experimental model to examine blood interactions with the CD47 modified and control conduits. PMID:25178087

Toward a blueprint for UDP-glucose pyrophosphorylase structure/function properties: homology-modeling analyses.

PubMed

Geisler, Matt; Wilczynska, Malgorzata; Karpinski, Stanislaw; Kleczkowski, Leszek A

2004-11-01

UDP-glucose pyrophosphorylase (UGPase) is an important enzyme of synthesis of sucrose, cellulose, and several other polysaccharides in all plants. The protein is evolutionarily conserved among eukaryotes, but has little relation, aside from its catalytic reaction, to UGPases of prokaryotic origin. Using protein homology modeling strategy, 3D structures for barley, poplar, and Arabidopsis UGPases have been derived, based on recently published crystal structure of human UDP-N-acetylglucosamine pyrophosphorylase. The derived 3D structures correspond to a bowl-shaped protein with the active site at a central groove, and a C-terminal domain that includes a loop (I-loop) possibly involved in dimerization. Data on a plethora of earlier described UGPase mutants from a variety of eukaryotic organisms have been revisited, and we have, in most cases, verified the role of each mutation in enzyme catalysis/regulation/structural integrity. We have also found that one of two alternatively spliced forms of poplar UGPase has a very short I-loop, suggesting differences in oligomerization ability of the two isozymes. The derivation of the structural model for plant UGPase should serve as a useful blueprint for further function/structure studies on this protein.

Closed loop problems in biomechanics. Part II--an optimization approach.

PubMed

Vaughan, C L; Hay, J G; Andrews, J G

1982-01-01

A closed loop problem in biomechanics may be defined as a problem in which there are one or more closed loops formed by the human body in contact with itself or with an external system. Under certain conditions the problem is indeterminate--the unknown forces and torques outnumber the equations. Force transducing devices, which would help solve this problem, have serious drawbacks, and existing methods are inaccurate and non-general. The purposes of the present paper are (1) to develop a general procedure for solving closed loop problems; (2) to illustrate the application of the procedure; and (3) to examine the validity of the procedure. A mathematical optimization approach is applied to the solution of three different closed loop problems--walking up stairs, vertical jumping and cartwheeling. The following conclusions are drawn: (1) the method described is reasonably successful for predicting horizontal and vertical reaction forces at the distal segments although problems exist for predicting the points of application of these forces; (2) the results provide some support for the notion that the human neuromuscular mechanism attempts to minimize the joint torques and thus, to a certain degree, the amount of muscular effort; (3) in the validation procedure it is desirable to have a force device for each of the distal segments in contact with a fixed external system; and (4) the method is sufficiently general to be applied to all classes of closed loop problems.

Rapid and Simple Detection of Hot Spot Point Mutations of Epidermal Growth Factor Receptor, BRAF, and NRAS in Cancers Using the Loop-Hybrid Mobility Shift Assay

PubMed Central

Matsukuma, Shoichi; Yoshihara, Mitsuyo; Kasai, Fumio; Kato, Akinori; Yoshida, Akira; Akaike, Makoto; Kobayashi, Osamu; Nakayama, Haruhiko; Sakuma, Yuji; Yoshida, Tsutomu; Kameda, Yoichi; Tsuchiya, Eiju; Miyagi, Yohei

2006-01-01

A simple and rapid method to detect the epidermal growth factor receptor hot spot mutation L858R in lung adenocarcinoma was developed based on principles similar to the universal heteroduplex generator technology. A single-stranded oligonucleotide with an internal deletion was used to generate heteroduplexes (loop-hybrids) bearing a loop in the complementary strand derived from the polymerase chain reaction product of the normal or mutant allele. By placing deletion in the oligonucleotide adjacent to the mutational site, difference in electrophoretic mobility between loop-hybrids with normal and mutated DNA was distinguishable in a native polyacrylamide gel. The method was also modified to detect in-frame deletion mutations of epidermal growth factor receptor in lung adenocarcinomas. In addition, the method was adapted to detect hot spot mutations in the B-type Raf kinase (BRAF) at V600 and in a Ras-oncogene (NRAS) at Q61, the mutations commonly found in thyroid carcinomas. Our mutation detection system, designated the loop-hybrid mobility shift assay was sensitive enough to detect mutant DNA comprising 7.5% of the total DNA. As a simple and straightforward mutation detection technique, loop-hybrid mobility shift assay may be useful for the molecular diagnosis of certain types of clinical cancers. Other applications are also discussed. PMID:16931592

Recovery Act: Novel Oxygen Carriers for Coal-fueled Chemical Looping

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

Pan, Wei-Ping; Cao, Yan

2012-11-30

Chemical Looping Combustion (CLC) could totally negate the necessity of pure oxygen by using oxygen carriers for purification of CO{sub 2} stream during combustion. It splits the single fuel combustion reaction into two linked reactions using oxygen carriers. The two linked reactions are the oxidation of oxygen carriers in the air reactor using air, and the reduction of oxygen carriers in the fuel reactor using fuels (i.e. coal). Generally metal/metal oxides are used as oxygen carriers and operated in a cyclic mode. Chemical looping combustion significantly improves the energy conversion efficiency, in terms of the electricity generation, because it improvesmore » the reversibility of the fuel combustion process through two linked parallel processes, compared to the conventional combustion process, which is operated far away from its thermo-equilibrium. Under the current carbon-constraint environment, it has been a promising carbon capture technology in terms of fuel combustion for power generation. Its disadvantage is that it is less mature in terms of technological commercialization. In this DOE-funded project, accomplishment is made by developing a series of advanced copper-based oxygen carriers, with properties of the higher oxygen-transfer capability, a favorable thermodynamics to generate high purity of CO{sub 2}, the higher reactivity, the attrition-resistance, the thermal stability in red-ox cycles and the achievement of the auto-thermal heat balance. This will be achieved into three phases in three consecutive years. The selected oxygen carriers with final-determined formula were tested in a scaled-up 10kW coal-fueled chemical looping combustion facility. This scaled-up evaluation tests (2-day, 8-hour per day) indicated that, there was no tendency of agglomeration of copper-based oxygen carriers. Only trace-amount of coke or carbon deposits on the copper-based oxygen carriers in the fuel reactor. There was also no evidence to show the sulphidization of oxygen carriers in the system by using the high-sulfur-laden asphalt fuels. In all, the scaled-up test in 10 kW CLC facility demonstrated that the preparation method of copper-based oxygen carrier not only help to maintain its good reactivity, also largely minimize its agglomeration tendency.« less

Cell shape and negative links in regulatory motifs together control spatial information flow in signaling networks.

PubMed

Neves, Susana R; Tsokas, Panayiotis; Sarkar, Anamika; Grace, Elizabeth A; Rangamani, Padmini; Taubenfeld, Stephen M; Alberini, Cristina M; Schaff, James C; Blitzer, Robert D; Moraru, Ion I; Iyengar, Ravi

2008-05-16

The role of cell size and shape in controlling local intracellular signaling reactions, and how this spatial information originates and is propagated, is not well understood. We have used partial differential equations to model the flow of spatial information from the beta-adrenergic receptor to MAPK1,2 through the cAMP/PKA/B-Raf/MAPK1,2 network in neurons using real geometries. The numerical simulations indicated that cell shape controls the dynamics of local biochemical activity of signal-modulated negative regulators, such as phosphodiesterases and protein phosphatases within regulatory loops to determine the size of microdomains of activated signaling components. The model prediction that negative regulators control the flow of spatial information to downstream components was verified experimentally in rat hippocampal slices. These results suggest a mechanism by which cellular geometry, the presence of regulatory loops with negative regulators, and key reaction rates all together control spatial information transfer and microdomain characteristics within cells.

Giardia and Cryptosporidium spp. dissemination during wastewater treatment and comparative detection via immunofluorescence assay (IFA), nested polymerase chain reaction (nested PCR) and loop mediated isothermal amplification (LAMP).

PubMed

Gallas-Lindemann, Carmen; Sotiriadou, Isaia; Plutzer, Judit; Noack, Michael J; Mahmoudi, Mohammad Reza; Karanis, Panagiotis

2016-06-01

Environmental water samples from the Lower Rhine area in Germany were investigated via immunofluorescence assays (IFAs), nested polymerase chain reaction (nested PCR) and loop-mediated isothermal amplification (LAMP) to detect the presence of Giardia spp. (n=185) and Cryptosporidium spp. (n=227). The samples were concentrated through filtration or flocculation, and oocysts were purified via centrifugation through a sucrose density gradient. For all samples, IFA was performed first, followed by DNA extraction for the nested PCR and LAMP assays. Giardia cysts were detected in 105 samples (56.8%) by IFA, 62 samples (33.5%) by nested PCR and 79 samples (42.7%) by LAMP. Cryptosporidium spp. were detected in 69 samples (30.4%) by IFA, 95 samples (41.9%) by nested PCR and 99 samples (43.6%) by LAMP. According to these results, the three detection methods are complementary for monitoring Giardia and Cryptosporidium in environmental waters. Copyright © 2016 Elsevier B.V. All rights reserved.

The development of a loop-mediated isothermal amplification assay for rapid and sensitive detection of abalone herpesvirus DNA.

PubMed

Chen, M H; Kuo, S T; Renault, T; Chang, P H

2014-02-01

A loop-mediated isothermal amplification (LAMP) assay was developed for the detection of abalone herpesvirus DNA. Two pairs of primers were designed, based on the sequence of the DNA polymerase gene of abalone herpesvirus. The reaction temperature and time were optimized to 63°C and 60min, respectively. LAMP amplicons were analyzed by 2% agarose gel electrophoresis or by visual inspection of a colour change emitted by fluorescent dye. The method developed was specific for the detection of abalone herpesvirus, without cross-reactions with other tested herpesviruses including ostreid herpesvirus 1 (OsHV-1), European eel herpesvirus, koi herpesvirus (KHV) and an avian herpesvirus. The LAMP assay was 100 folds more sensitive than a conventional PCR and 10 folds less sensitive than a SYBR Green PCR. These results indicate that the developed LAMP assay is a simple, rapid, sensitive, specific and reliable technique for the detection of abalone herpesvirus. Copyright © 2013 Elsevier B.V. All rights reserved.

Mechanism of autophosphorylation of mycobacterial PknB explored by molecular dynamics simulations.

PubMed

Damle, Nikhil P; Mohanty, Debasisa

2014-07-22

Mycobacterial Ser/Thr kinase, PknB, is essential for the growth of the pathogen. Unphosphorylated PknB is catalytically inactive, and its activation requires autophosphorylation of Thr residues on the activation loop. Autophosphorylation can in principle take place via two distinct mechanisms. Intermolecular trans autophosphorylation involves dimerization and phosphorylation of the activation loop of one chain in the catalytic pocket of the other chain. On the other hand, intramolecular cis autophosphorylation involves phosphorylation of the activation loop of the kinases in its own catalytic pocket within a monomer. On the basis of the crystal structure of PknB in the front-to-front dimeric form, it is currently believed that activation of PknB involves trans autophosphorylation. However, because of the lack of coordinates of the activation loop in the crystal structures, atomic details of the conformational changes associated with activation are yet to be deciphered. Therefore, to understand the conformational transitions associated with activation via autophosphorylation, a series of explicit solvent molecular dynamics simulations with a duration of 1 μs have been performed on each of the phosphorylated and nonphosphorylated forms of the PknB catalytic domain in monomeric and dimeric states. Simulations on phosphorylated PknB revealed a differential network of crucial electrostatic and hydrophobic residues that stabilize the phosphorylated form in the active conformation. Interestingly, in our simulations on nonphosphorylated monomers, the activation loop was observed to fold into its own active site, thereby opening the novel possibility of activation through intramolecular cis autophosphorylation. Thus, our simulations suggest that autophosphorylation of PknB might also involve cis initiation followed by trans amplification as reported for other eukaryotic kinases based on recent reaction kinetics studies.

Protein Arginine Methyltransferase Product Specificity Is Mediated by Distinct Active-site Architectures.

PubMed

Jain, Kanishk; Warmack, Rebeccah A; Debler, Erik W; Hadjikyriacou, Andrea; Stavropoulos, Peter; Clarke, Steven G

2016-08-26

In the family of protein arginine methyltransferases (PRMTs) that predominantly generate either asymmetric or symmetric dimethylarginine (SDMA), PRMT7 is unique in producing solely monomethylarginine (MMA) products. The type of methylation on histones and other proteins dictates changes in gene expression, and numerous studies have linked altered profiles of methyl marks with disease phenotypes. Given the importance of specific inhibitor development, it is crucial to understand the mechanisms by which PRMT product specificity is conferred. We have focused our attention on active-site residues of PRMT7 from the protozoan Trypanosoma brucei We have designed 26 single and double mutations in the active site, including residues in the Glu-Xaa8-Glu (double E) loop and the Met-Gln-Trp sequence of the canonical Thr-His-Trp (THW) loop known to interact with the methyl-accepting substrate arginine. Analysis of the reaction products by high resolution cation exchange chromatography combined with the knowledge of PRMT crystal structures suggests a model where the size of two distinct subregions in the active site determines PRMT7 product specificity. A dual mutation of Glu-181 to Asp in the double E loop and Gln-329 to Ala in the canonical THW loop enables the enzyme to produce SDMA. Consistent with our model, the mutation of Cys-431 to His in the THW loop of human PRMT9 shifts its product specificity from SDMA toward MMA. Together with previous results, these findings provide a structural basis and a general model for product specificity in PRMTs, which will be useful for the rational design of specific PRMT inhibitors. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Accidental SUSY: enhanced bulk supersymmetry from brane back-reaction

NASA Astrophysics Data System (ADS)

Burgess, C. P.; van Nierop, L.; Parameswaran, S.; Salvio, A.; Williams, M.

2013-02-01

We compute how bulk loops renormalize both bulk and brane effective interactions for codimension-two branes in 6D gauged chiral supergravity, as functions of the brane tension and brane-localized flux. We do so by explicitly integrating out hyper- and gauge-multiplets in 6D gauged chiral supergravity compactified to 4D on a flux-stabilized 2D rugby-ball geometry, specializing the results of a companion paper, arXiv:1210.3753, to the supersymmetric case. While the brane back-reaction generically breaks supersymmetry, we show that the bulk supersymmetry can be preserved if the amount of brane- localized flux is related in a specific BPS-like way to the brane tension, and verify that the loop corrections to the brane curvature vanish in this special case. In these systems it is the brane-bulk couplings that fix the size of the extra dimensions, and we show that in some circumstances the bulk geometry dynamically adjusts to ensure the supersymmetric BPS-like condition is automatically satisfied. We investigate the robustness of this residual supersymmetry to loops of non-supersymmetric matter on the branes, and show that supersymmetry-breaking effects can enter only through effective brane-bulk interactions involving at least two derivatives. We comment on the relevance of this calculation to proposed applications of codimension-two 6D models to solutions of the hierarchy and cosmological constant problems.

Directional errors of movements and their correction in a discrete tracking task. [pilot reaction time and sensorimotor performance

NASA Technical Reports Server (NTRS)

Jaeger, R. J.; Agarwal, G. C.; Gottlieb, G. L.

1978-01-01

Subjects can correct their own errors of movement more quickly than they can react to external stimuli by using three general categories of feedback: (1) knowledge of results, primarily visually mediated; (2) proprioceptive or kinaesthetic such as from muscle spindles and joint receptors, and (3) corollary discharge or efference copy within the central nervous system. The effects of these feedbacks on simple reaction time, choice reaction time, and error correction time were studied in four normal human subjects. The movement used was plantarflexion and dorsiflexion of the ankle joint. The feedback loops were modified, by changing the sign of the visual display to alter the subject's perception of results, and by applying vibration at 100 Hz simultaneously to both the agonist and antagonist muscles of the ankle joint. The central processing was interfered with when the subjects were given moderate doses of alcohol (blood alcohol concentration levels of up to 0.07%). Vibration and alcohol increase both the simple and choice reaction times but not the error correction time.

Ligand-Dependent Disorder of Loop Observed in Extended-Spectrum SHV-Type beta-Lactamase

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

J Sampson; W Ke; C Bethel

2011-12-31

Among Gram-negative bacteria, resistance to {beta}-lactams is mediated primarily by {beta}-lactamases (EC 3.2.6.5), periplasmic enzymes that inactivate {beta}-lactam antibiotics. Substitutions at critical amino acid positions in the class A {beta}-lactamase families result in enzymes that can hydrolyze extended-spectrum cephalosporins, thus demonstrating an 'extended-spectrum' {beta}-lactamase (ESBL) phenotype. Using SHV ESBLs with substitutions in the {Omega} loop (R164H and R164S) as target enzymes to understand this enhanced biochemical capability and to serve as a basis for novel {beta}-lactamase inhibitor development, we determined the spectra of activity and crystal structures of these variants. We also studied the inactivation of the R164H and R164Smore » mutants with tazobactam and SA2-13, a unique {beta}-lactamase inhibitor that undergoes a distinctive reaction chemistry in the active site. We noted that the reduced K{sub i} values for the R164H and R164S mutants with SA2-13 are comparable to those with tazobactam (submicromolar). The apo enzyme crystal structures of the R164H and R164S SHV variants revealed an ordered {Omega} loop architecture that became disordered when SA2-13 was bound. Important structural alterations that result from the binding of SA2-13 explain the enhanced susceptibility of these ESBL enzymes to this inhibitor and highlight ligand-dependent {Omega} loop flexibility as a mechanism for accommodating and hydrolyzing {beta}-lactam substrates.« less

Watch what you type: the role of visual feedback from the screen and hands in skilled typewriting.

PubMed

Snyder, Kristy M; Logan, Gordon D; Yamaguchi, Motonori

2015-01-01

Skilled typing is controlled by two hierarchically structured processing loops (Logan & Crump, 2011): The outer loop, which produces words, commands the inner loop, which produces keystrokes. Here, we assessed the interplay between the two loops by investigating how visual feedback from the screen (responses either were or were not echoed on the screen) and the hands (the hands either were or were not covered with a box) influences the control of skilled typing. Our results indicated, first, that the reaction time of the first keystroke was longer when responses were not echoed than when they were. Also, the interkeystroke interval (IKSI) was longer when the hands were covered than when they were visible, and the IKSI for responses that were not echoed was longer when explicit error monitoring was required (Exp. 2) than when it was not required (Exp. 1). Finally, explicit error monitoring was more accurate when response echoes were present than when they were absent, and implicit error monitoring (i.e., posterror slowing) was not influenced by visual feedback from the screen or the hands. These findings suggest that the outer loop adjusts the inner-loop timing parameters to compensate for reductions in visual feedback. We suggest that these adjustments are preemptive control strategies designed to execute keystrokes more cautiously when visual feedback from the hands is absent, to generate more cautious motor programs when visual feedback from the screen is absent, and to enable enough time for the outer loop to monitor keystrokes when visual feedback from the screen is absent and explicit error reports are required.

Electric, Magnetic, and Magnetoelectric Properties of Yttrium-Containing BaY0.025Ti0.9625O3-SrFe12O19 Composite

NASA Astrophysics Data System (ADS)

Rather, Mehraj ud Din; Samad, Rubiya; Want, Basharat

2018-03-01

The physical properties of BaY0.025Ti0.9625O3, SrFe12O19, and 0.90BaY0.025Ti0.9625O3-0.10 SrFe12O19 composite have been studied. The proposed composite was synthesized by solid-state reaction method from yttrium barium titanate processed by solid-state reaction and strontium hexaferrite obtained by a sol-gel process. Microstructural analysis revealed monophasic grains for yttrium barium titanate phase, while loosely packed biphasic structure was observed for the composite. Powder x-ray analysis showed that the individual phases retained their crystal structure in the composite, without formation of any new additional phase. Measurement of magnetic hysteresis loops at room temperature indicated that the magnetic parameters of the composite were diluted by the presence of the ferroelectric phase. The ferroelectric hysteresis of yttrium barium titanate confirmed the ferroelectric transition at 119°C. Meanwhile, the symmetrical ferroelectric loops observed at different fields established the ferroelectric nature of the composite. Improved dielectric properties and low dielectric losses were observed due to yttrium doping in the composite. The diffuseness of the ferroelectric transitions for the composite was confirmed by the Curie-Weiss law. Activation energy calculations revealed the charge-hopping conduction mechanism in the composite. Magnetodielectric studies confirmed that the overall magnetocapacitance in the composite exhibited combined effects of magnetoresistance and magnetoelectric coupling.

Loop-mediated isothermal amplification (LAMP) method for detection of genetically modified maize T25.

PubMed

Xu, Junyi; Zheng, Qiuyue; Yu, Ling; Liu, Ran; Zhao, Xin; Wang, Gang; Wang, Qinghua; Cao, Jijuan

2013-11-01

The loop-mediated isothermal amplification (LAMP) assay indicates a potential and valuable means for genetically modified organism (GMO) detection especially for its rapidity, simplicity, and low cost. We developed and evaluated the specificity and sensitivity of the LAMP method for rapid detection of the genetically modified (GM) maize T25. A set of six specific primers was successfully designed to recognize six distinct sequences on the target gene, including a pair of inner primers, a pair of outer primers, and a pair of loop primers. The optimum reaction temperature and time were verified to be 65°C and 45 min, respectively. The detection limit of this LAMP assay was 5 g kg(-1) GMO component. Comparative experiments showed that the LAMP assay was a simple, rapid, accurate, and specific method for detecting the GM maize T25.

Loop-mediated isothermal amplification (LAMP) method for detection of genetically modified maize T25

PubMed Central

Xu, Junyi; Zheng, Qiuyue; Yu, Ling; Liu, Ran; Zhao, Xin; Wang, Gang; Wang, Qinghua; Cao, Jijuan

2013-01-01

The loop-mediated isothermal amplification (LAMP) assay indicates a potential and valuable means for genetically modified organism (GMO) detection especially for its rapidity, simplicity, and low cost. We developed and evaluated the specificity and sensitivity of the LAMP method for rapid detection of the genetically modified (GM) maize T25. A set of six specific primers was successfully designed to recognize six distinct sequences on the target gene, including a pair of inner primers, a pair of outer primers, and a pair of loop primers. The optimum reaction temperature and time were verified to be 65°C and 45 min, respectively. The detection limit of this LAMP assay was 5 g kg−1 GMO component. Comparative experiments showed that the LAMP assay was a simple, rapid, accurate, and specific method for detecting the GM maize T25. PMID:24804053

How to Achieve Learning Impact.

ERIC Educational Resources Information Center

Peterson, Bob

1978-01-01

Although learning can be defined in cognitive, affective, or behavioral terms, the specification of communication, planning, or evaluation skills in behavioral terms is most appropriate in management training. Learning objectives are most effectively reached in a closed rather than open loop learning design. In designs, the learner's reactions and…

Attrition Rate of Oxygen Carriers in Chemical Looping Combustion Systems

NASA Astrophysics Data System (ADS)

Feilen, Harry Martin

This project developed an evaluation methodology for determining, accurately and rapidly, the attrition resistance of oxygen carrier materials used in chemical looping technologies. Existing test protocols, to evaluate attrition resistance of granular materials, are conducted under non-reactive and ambient temperature conditions. They do not accurately reflect the actual behavior under the unique process conditions of chemical looping, including high temperatures and cyclic operation between oxidizing and reducing atmospheres. This project developed a test method and equipment that represented a significant improvement over existing protocols. Experimental results obtained from this project have shown that hematite exhibits different modes of attrition, including both due to mechanical stresses and due to structural changes in the particles due to chemical reaction at high temperature. The test methodology has also proven effective in providing reactivity changes of the material with continued use, a property, which in addition to attrition, determines material life. Consumption/replacement cost due to attrition or loss of reactivity is a critical factor in the economic application of the chemical looping technology. This test method will allow rapid evaluation of a wide range of materials that are best suited for this technology. The most important anticipated public benefit of this project is the acceleration of the development of chemical looping technology for lowering greenhouse gas emissions from fossil fuel combustion.

Multiferroic properties in NdFeO3-PbTiO3 solid solutions

NASA Astrophysics Data System (ADS)

Kumar, Sunil; Pal, Jaswinder; Kaur, Shubhpreet; Agrawal, P.; Singh, Mandeep; Singh, Anupinder

2018-05-01

The x(NdFeO3) - 1-x(PbTiO3) where x = 0.2 solid solution was prepared using solid state reaction route. The X-ray diffraction (XRD) data reveals the single phase formation. The microstructure shows grain growth with lesser porosity. The energy dispersive analysis confirms the presence of elements in stochiometric proportion. The polarization vs. Electric field loop estabilished a ferroelectric type behavior but lossy in nature. This lossy nature may be due to the presence of large leakage current in solid solution. The Magnetization vs. Magnetic field plot exhibits a unsaturated hysteriss loop indicates that the sample is not purely ferromagnetic.

Identification of ochratoxin A producing Aspergillus carbonarius and A. niger clade isolated from grapes using the loop-mediated isothermal amplification (LAMP) reaction.

PubMed

Storari, M; von Rohr, R; Pertot, I; Gessler, C; Broggini, G A L

2013-04-01

To develop two assays based on the loop-mediated isothermal amplification (LAMP) of DNA for the quick and specific identification of Aspergillus carbonarius and ochratoxigenic strains of the Aspergillus niger clade isolated from grapes. Two sets of primers were designed based on the polyketide synthase genes involved or putatively involved in ochratoxin A (OTA) biosynthesis in A. carbonarius and A. niger clade. Hydroxynaphthol blue was used as indirect method to indicate DNA amplification. The limit of detection of both assays was comparable to that of a PCR reaction. Specificities of the reactions were tested using DNA from different black aspergilli isolated from grapes. The two LAMP assays were then used to identify A. carbonarius and ochratoxigenic A. niger and A. awamori grown in pure cultures without a prior DNA extraction. The two LAMP assays permitted to quickly and specifically identify DNA from OTA-producing black aspergilli, as well as isolates grown in pure culture. Monitoring vineyards for the presence of OTA-producing strains is part of the measures to minimize the occurrence of OTA in grape products. The two LAMP assays developed here could be potentially used to speed the screening process of vineyards for the presence of OTA-producing black aspergilli. © 2013 The Society for Applied Microbiology.

Liquid uranium alloy-helium fission reactor

DOEpatents

Minkov, Vladimir

1986-01-01

This invention teaches a nuclear fission reactor having a core vessel and at least one tandem heat exchanger vessel coupled therewith across upper and lower passages to define a closed flow loop. Nuclear fuel such as a uranium alloy in its liquid phase fills these vessels and flow passages. Solid control elements in the reactor core vessel are adapted to be adjusted relative to one another to control fission reaction of the liquid fuel therein. Moderator elements in the other vessel and flow passages preclude fission reaction therein. An inert gas such as helium is bubbled upwardly through the heat exchanger vessel operable to move the liquid fuel upwardly therein and unidirectionally around the closed loop and downwardly through the core vessel. This helium gas is further directed to heat conversion means outside of the reactor vessels to utilize the heat from the fission reaction to generate useful output. The nuclear fuel operates in the 1200.degree.-1800.degree. C. range, and even higher to 2500.degree. C., limited only by the thermal effectiveness of the structural materials, increasing the efficiency of power generation from the normal 30-35% with 300.degree.-500.degree. C. upper limit temperature to 50-65%. Irradiation of the circulating liquid fuel, as contrasted to only localized irradiation of a solid fuel, provides improved fuel utilization.

Rapid screening method for male DNA by using the loop-mediated isothermal amplification assay.

PubMed

Kitamura, Masashi; Kubo, Seiji; Tanaka, Jin; Adachi, Tatsushi

2017-08-12

Screening for male-derived biological material from collected samples plays an important role in criminal investigations, especially those involving sexual assaults. We have developed a loop-mediated isothermal amplification (LAMP) assay targeting multi-repeat sequences of the Y chromosome for detecting male DNA. Successful amplification occurred with 0.5 ng of male DNA under isothermal conditions of 61 to 67 °C, but no amplification occurred with up to 10 ng of female DNA. Under the optimized conditions, the LAMP reaction initiated amplification within 10 min and amplified for 20 min. The LAMP reaction was sensitive at levels as low as 1-pg male DNA, and a quantitative LAMP assay could be developed because of the strong correlation between the reaction time and the amount of template DNA in the range of 10 pg to 10 ng. Furthermore, to apply the LAMP assay to on-site screening for male-derived samples, we evaluated a protocol using a simple DNA extraction method and a colorimetric intercalating dye that allows detection of the LAMP reaction by evaluating the change in color of the solution. Using this protocol, samples of male-derived blood and saliva stains were processed in approximately 30 min from DNA extraction to detection. Because our protocol does not require much hands-on time or special equipment, this LAMP assay promises to become a rapid and simple screening method for male-derived samples in forensic investigations.

Ca2+ improves organization of single-stranded DNA bases in human Rad51 filament, explaining stimulatory effect on gene recombination.

PubMed

Fornander, Louise H; Frykholm, Karolin; Reymer, Anna; Renodon-Cornière, Axelle; Takahashi, Masayuki; Nordén, Bengt

2012-06-01

Human RAD51 protein (HsRad51) catalyses the DNA strand exchange reaction for homologous recombination. To clarify the molecular mechanism of the reaction in vitro being more effective in the presence of Ca(2+) than of Mg(2+), we have investigated the effect of these ions on the structure of HsRad51 filament complexes with single- and double-stranded DNA, the reaction intermediates. Flow linear dichroism spectroscopy shows that the two ionic conditions induce significantly different structures in the HsRad51/single-stranded DNA complex, while the HsRad51/double-stranded DNA complex does not demonstrate this ionic dependence. In the HsRad51/single-stranded DNA filament, the primary intermediate of the strand exchange reaction, ATP/Ca(2+) induces an ordered conformation of DNA, with preferentially perpendicular orientation of nucleobases relative to the filament axis, while the presence of ATP/Mg(2+), ADP/Mg(2+) or ADP/Ca(2+) does not. A high strand exchange activity is observed for the filament formed with ATP/Ca(2+), whereas the other filaments exhibit lower activity. Molecular modelling suggests that the structural variation is caused by the divalent cation interfering with the L2 loop close to the DNA-binding site. It is proposed that the larger Ca(2+) stabilizes the loop conformation and thereby the protein-DNA interaction. A tight binding of DNA, with bases perpendicularly oriented, could facilitate strand exchange.

Effects of protonation state of Asp181 and position of active site water molecules on the conformation of PTP1B.

PubMed

Ozcan, Ahmet; Olmez, Elif Ozkirimli; Alakent, Burak

2013-05-01

In protein tyrosine phosphatase 1B (PTP1B), the flexible WPD loop adopts a closed conformation (WPDclosed ) in the active state of PTP1B, bringing the catalytic Asp181 close to the active site pocket, while WPD loop is in an open conformation (WPDopen ) in the inactive state. Previous studies showed that Asp181 may be protonated at physiological pH, and ordered water molecules exist in the active site. In the current study, molecular dynamics simulations are employed at different Asp181 protonation states and initial positions of active site water molecules, and compared with the existing crystallographic data of PTP1B. In WPDclosed conformation, the active site is found to maintain its conformation only in the protonated state of Asp181 in both free and liganded states, while Asp181 is likely to be deprotonated in WPDopen conformation. When the active site water molecule network that is a part of the free WPDclosed crystal structure is disrupted, intermediate WPD loop conformations, similar to that in the PTPRR crystal structure, are sampled in the MD simulations. In liganded PTP1B, one active site water molecule is found to be important for facilitating the orientation of Cys215 and the phosphate ion, thus may play a role in the reaction. In conclusion, conformational stability of WPD loop, and possibly catalytic activity of PTP1B, is significantly affected by the protonation state of Asp181 and position of active site water molecules, showing that these aspects should be taken into consideration both in MD simulations and inhibitor design. Copyright © 2013 Wiley Periodicals, Inc.

Microbial Abundances in Salt Marsh Soils: A Molecular Approach for Small Spatial Scales

NASA Astrophysics Data System (ADS)

Granse, Dirk; Mueller, Peter; Weingartner, Magdalena; Hoth, Stefan; Jensen, Kai

2016-04-01

The rate of biological decomposition greatly determines the carbon sequestration capacity of salt marshes. Microorganisms are involved in the decomposition of biomass and the rate of decomposition is supposed to be related to microbial abundance. Recent studies quantified microbial abundance by means of quantitative polymerase chain reaction (QPCR), a method that also allows determining the microbial community structure by applying specific primers. The main microbial community structure can be determined by using primers specific for 16S rRNA (Bacteria) and 18S rRNA (Fungi) of the microbial DNA. However, the investigation of microbial abundance pattern at small spatial scales, such as locally varying abiotic conditions within a salt-marsh system, requires high accuracy in DNA extraction and QPCR methods. Furthermore, there is evidence that a single extraction may not be sufficient to reliably quantify rRNA gene copies. The aim of this study was to establish a suitable DNA extraction method and stable QPCR conditions for the measurement of microbial abundances in semi-terrestrial environments. DNA was extracted from two soil samples (top WE{5}{cm}) by using the PowerSoil DNA Extraction Kit (Mo Bio Laboratories, Inc., Carlsbad, CA) and applying a modified extraction protocol. The DNA extraction was conducted in four consecutive DNA extraction loops from three biological replicates per soil sample by reusing the PowerSoil bead tube. The number of Fungi and Bacteria rRNA gene copies of each DNA extraction loop and a pooled DNA solution (extraction loop 1 - 4) was measured by using the QPCR method with taxa specific primer pairs (Bacteria: B341F, B805R; Fungi: FR1, FF390). The DNA yield of the replicates varied at DNA extraction loop 1 between WE{25 and 85}{ng

Preliminary approach of the MELiSSA loop energy balance

NASA Astrophysics Data System (ADS)

Poulet, Lucie; Lamaze, Brigitte; Lebrun, Jean

Long duration missions, such as the establishment of permanent bases on the lunar surface or the travel to Mars, require a huge amount of life support consumables (e.g. food, water and oxygen). Current rockets are at the moment unable to launch such a mass from Earth. Consequently Regenerative Life Support Systems are necessary to sustain long-term manned space mission to increase recycling rates and so reduce the launched mass. Thus the European and Canadian research has been concentrating on the MELiSSA (Micro-Ecological Life Support System Alternative) project over the last 20 years. MELiSSA is an Environmental Controlled Life Support System (ECLSS), i.e. a closed regenerative loop inspired of a lake ecosystem. Using light as a source of energy, MELiSSA's goal is the recovery of food, water and oxygen from CO2 and organic wastes, using microorganisms and higher plants. The architecture of a ECLSS depends widely on the mission scenario. To compare several ECLSS architectures and in order to be able to evaluate them, ESA is developing a multi criteria evaluation tool: ALISSE (Advanced LIfe Support System Evaluator). One of these criteria is the energy needed to operate the ECLSS. Unlike other criteria like the physical mass, the energy criterion has not been investigated yet and needs hence a detailed analysis. It will consequently be the focus of this study. The main objective of the work presented here is to develop a dynamic tool able to estimate the energy balance for several configurations of the MELiSSA loop. The first step consists in establishing the energy balance using concrete figures from the MELiSSA Pilot Plant (MPP). This facility located at the Universitat Autonoma de Barcelona (UAB) is aimed at the ground demonstration of the MELiSSA loop. The MELiSSA loop is structured on several subsystems; each of them is characterized by supplies, exhausts and process reactions. For the purpose of this study (i.e. a generic tool) the solver EES (Engineering Equation Solver) is used. As a result, several configurations of the MELiSSA loop are studied. The main issues in terms of energy costs are identified and in the meantime improvement opportunities, i.e. reduction of energy consumption, are diagnosed.

Surveillance for Western equine encephalitis St. Louis encephalitis and West Nile viruses using reverse transcription loop-mediated isothermal amplification

DOE PAGES

Meagher, Robert J.; Ball, Cameron Scott; Langevin, Stanley A.; ...

2016-01-25

In this study, collection of mosquitoes and testing for vector-borne viruses is a key surveillance activity that directly influences the vector control efforts of public health agencies, including determining when and where to apply insecticides. Vector control districts in California routinely monitor for three human pathogenic viruses including West Nile virus (WNV), Western equine encephalitis virus (WEEV), and St. Louis encephalitis virus (SLEV). Reverse transcription quantitative polymerase chain reaction (RT-qPCR) offers highly sensitive and specific detection of these three viruses in a single multiplex reaction, but this technique requires costly, specialized equipment that is generally only available in centralized publicmore » health laboratories. We report the use of reverse transcription loop-mediated isothermal amplification (RT-LAMP) to detect WNV, WEEV, and SLEV RNA extracted from pooled mosquito samples collected in California, including novel primer sets for specific detection of WEEV and SLEV, targeting the nonstructural protein 4 (nsP4) gene of WEEV and the 3’ untranslated region (3’-UTR) of SLEV. Our WEEV and SLEV RT-LAMP primers allowed detection of <0.1 PFU/reaction of their respective targets in <30 minutes, and exhibited high specificity without cross reactivity when tested against a panel of alphaviruses and flaviviruses. Furthermore, the SLEV primers do not cross-react with WNV, despite both viruses being closely related members of the Japanese encephalitis virus complex. The SLEV and WEEV primers can also be combined in a single RT-LAMP reaction, with discrimination between amplicons by melt curve analysis. Although RT-qPCR is approximately one order of magnitude more sensitive than RT-LAMP for all three targets, the RT-LAMP technique is less instrumentally intensive than RT-qPCR and provides a more cost-effective method of vector-borne virus surveillance.« less

PID Controller Settings Based on a Transient Response Experiment

ERIC Educational Resources Information Center

Silva, Carlos M.; Lito, Patricia F.; Neves, Patricia S.; Da Silva, Francisco A.

2008-01-01

An experimental work on controller tuning for chemical engineering undergraduate students is proposed using a small heat exchange unit. Based upon process reaction curves in open-loop configuration, system gain and time constant are determined for first order model with time delay with excellent accuracy. Afterwards students calculate PID…

The geometric phase controls ultracold chemistry

DOE PAGES

Kendrick, B. K.; Hazra, Jisha; Balakrishnan, N.

2015-07-30

In this study, the geometric phase is shown to control the outcome of an ultracold chemical reaction. The control is a direct consequence of the sign change on the interference term between two scattering pathways (direct and looping), which contribute to the reactive collision process in the presence of a conical intersection (point of degeneracy between two Born–Oppenheimer electronic potential energy surfaces). The unique properties of the ultracold energy regime lead to an effective quantization of the scattering phase shift enabling maximum constructive or destructive interference between the two pathways. By taking the O + OH → H + Omore » 2 reaction as an illustrative example, it is shown that inclusion of the geometric phase modifies ultracold reaction rates by nearly two orders of magnitude. Interesting experimental control possibilities include the application of external electric and magnetic fields that might be used to exploit the geometric phase effect reported here and experimentally switch on or off the reactivity.« less

Real-time fluorescence loop-mediated isothermal amplification assay for direct detection of egg drop syndrome virus.

PubMed

Zheney, Makay; Kaziyev, Zhambul; Kassenova, Gulmira; Zhao, Lingna; Liu, Wei; Liang, Lin; Li, Gang

2018-02-13

Egg drop syndrome (EDS), caused by the adenovirus "egg drop syndrome virus" (EDSV) causes severe economic losses through reduced egg production in breeder and layer flocks. The diagnosis of EDSV has been done by molecular tools since its complete genome sequence was identified. In order to enhance the capabilities of the real-time fluorescence loop-mediated isothermal amplification (RealAmp) assay, we aimed to apply the method for direct detection of the EDSV without viral DNA extraction. In order to detect the presence of the EDSV DNA, three pairs of primers were designed, from the conserved region of fiber gene of the EDSV. For our assay, test and control samples were directly used in the reaction mixture in 10-fold serial dilution. The target DNA was amplified at 65 °C, which yield positive results in a relatively short period of 40-45 min. The method reported in this study is highly sensitive as compared to polymerase chain reaction (PCR) and showed no sign of cross-reactivity or false positive results. The RealAmp accomplished specific identification of EDSV among a variety of poultry disease viruses. The direct RealAmp can be used to detect the presence of EDSV. As our result showed, the RealAmp method could be suitable for the direct detection of other DNA viruses.

Study of x CNFO + (1-x) PLZT magnetoelectric composites

NASA Astrophysics Data System (ADS)

Dipti, Singh, Sangeeta; Juneja, J. K.; Pant, R. P.; Raina, K. K.; Prakash, Chandra

2014-04-01

In the present paper, we are reporting the studies on structural, dielectric, ferroelectric and magnetic properties of Lanthanum (La) substituted Lead Zirconate Titanate (PZT) and Cobalt Nickel ferrite (CNFO) composites with compositional formula x(Co0.80Ni0.20Fe2O4)+(1-x)(Pb1.01625La0.0025Zr0.55Ti0.45O3) (x = 0.00,0.10). The materials were synthesized by solid state reaction route. XRD analysis confirms the presence of both ferrite and ferroelectric phases. Dielectric properties were studied as a function of frequency and temperature. Ferroelectric P-E and Magnetic M-H hysteresis loops were measured at room temperature.

An inexpensive and rapid diagnostic method of Koi Herpesvirus (KHV) infection by loop-mediated isothermal amplification

PubMed Central

Soliman, Hatem; El-Matbouli, Mansour

2005-01-01

Background Koi Herpesvirus (KHV) affects both juvenile and adult common carp and koi, and is especially lethal to fry. The high mortalities caused by the disease have had a negative impact on the international koi trade. Different diagnostic techniques have been used to detect KHV, including: isolation of the virus in cell culture, electron microscopy, several PCR tests, ELISA and in situ hybridisation. All of these methods are time consuming, laborious and require specialised equipment. Results A rapid field diagnosis of KHV in common and koi carp was developed using loop-mediated isothermal amplification (LAMP). The LAMP reaction rapidly amplified nucleic acid with high specificity and efficiency under isothermal conditions using a simple water bath. Two methods of extracting DNA from host tissue were compared: extraction by boiling and by using a commercial extraction kit. A set of six primers – two inner primers, two outer primers and two loop primers – was designed from a KHV amplicon. The reaction conditions were optimised for detection of KHV in 60 min at 65°C using Bst (Bacillus stearothermophilus) DNA polymerase. When visualised by gel electrophoresis, the products of the KHV LAMP assay appeared as a ladder pattern, with many bands of different sizes from 50 base-pairs (bp) up to the loading well. The KHV LAMP product could also be simply detected visually by adding SYBR Green I to the reaction tube and observing a colour change from orange to green. All samples positive for KHV by visual detection were confirmed positive by gel electrophoresis. The KHV LAMP had the same sensitivity as a standard PCR assay for the detection of KHV. Conclusion This paper describes an accelerated LAMP assay for diagnosis of KHV. The entire procedure took only 90 minutes to produce a result: 15 minutes for DNA extraction; 60 min for the LAMP reaction; 2 min for visual detection using SYBR Green I. The test can be used under field conditions because the only equipment it requires is a water bath. PMID:16216123

Pre-Steady State Kinetic Analysis of cis-3-Chloroacrylic Acid Dehalogenase: Analysis and Implications†

PubMed Central

Robertson, Brooklyn A.; Schroeder, Gottfried K.; Jin, Zhinan; Johnson, Kenneth A.; Whitman, Christian P.

2009-01-01

Isomer-specific 3-chloroacrylic acid dehalogenases catalyze the hydrolytic dehalogenation of the cis- and trans-isomers of 3-chloroacrylate to yield malonate semialdehyde. These reactions represent key steps in the degradation of the nematocide, 1,3-dichloropropene. The kinetic mechanism of cis-3-chloroacrylic acid dehalogenase (cis-CaaD) has now been examined using stopped-flow and chemical-quench techniques. Stopped-flow analysis of the reaction, following the fluorescence of an active site tryptophan, is consistent with a minimal three-step model involving substrate binding, chemistry, and product release. Chemical quench experiments show burst kinetics, indicating that product release is at least partially rate limiting. Global fitting of all of the kinetic results by simulation is best accommodated by a four-step mechanism. In the final kinetic model, the enzyme binds substrate and isomerizes to an alternate fluorescent form, chemistry occurs, and is followed by the ordered release of two products, with the release of the first product as the rate-limiting step. Bromide ion is a competitive inhibitor of the reaction indicating that it binds to the free enzyme rather than to the enzyme with one product still bound. This observation suggests that malonate semialdehyde is the first product released by the enzyme (rate limiting), followed by halide. A comparison of the unliganded cis-CaaD crystal structure with that of an inactivated cis-CaaD where the prolyl nitrogen of Pro-1 is covalently attached to (R)-2-hydroxypropanoate provides a possible explanation for the isomerization step. The structure of the covalently modified enzyme shows that a 7-residue loop comprised of residues 32-38 is closed down on the active site cavity where the backbone amides of two residues (Phe-37 and Leu-38) interact with the carboxylate group of the adduct. In the unliganded form, the same loop points away from the active site cavity. Similarly, substrate binding may cause this loop to close down on the active site and sequester the reaction from the external environment. PMID:19856961

Application of loop-mediated isothermal amplification with propidium monoazide treatment to detect live Salmonella in chicken carcasses.

PubMed

Youn, S Y; Jeong, O M; Choi, B K; Jung, S C; Kang, M S

2017-02-01

Raw chicken products are major causes of human foodborne salmonellosis worldwide. In particular, there is a significant risk of human exposure to Salmonella originating from the chicken slaughtering process. Controlling the contamination of chicken carcasses by Salmonella has been a considerable challenge in chicken-slaughtering facilities and involves routine microbiological monitoring using reliable detection methods. Simple and rapid detection methods, particularly those capable of determining cell viability, will significantly facilitate routine monitoring of Salmonella Here, we report an invA-based loop-mediated isothermal amplification method coupled with a simple propidium monoazide treatment (PMA-LAMP) for simple and rapid detection and quantification of viable Salmonella in rinse water of chicken carcasses. In this study, PMA-LAMP consistently gave negative results for isopropanol-killed Salmonella with concentrations up to 8.0 × 10 6 CFU/reaction. The detection limit of PMA-LAMP was 8.0 × 10 1 CFU/reaction with viable Salmonella in both pure culture and rinse water of chicken carcasses, and 10-fold lower than a conventional polymerase chain reaction coupled with PMA (PMA-PCR) targeting invA There was a high correlation (R 2 = 0.99 to 0.976) between LAMP time threshold (T T ) values and viable Salmonella with a quantification range of 1.0 × 10 3 to 1.0 × 10 8 CFU/mL in pure culture and rinse water of chicken carcasses. The PMA-LAMP assay took less than 2 h to detect Salmonella contaminated in test samples. Therefore, this simple and rapid method will be a very useful tool to detect live Salmonella contamination of chicken carcasses without pre-enrichment at the slaughterhouse where sanitizing treatments are commonly used. © 2016 Poultry Science Association Inc.

Real-time electrochemical LAMP: a rational comparative study of different DNA intercalating and non-intercalating redox probes.

PubMed

Martin, Alexandra; Bouffier, Laurent; Grant, Kathryn B; Limoges, Benoît; Marchal, Damien

2016-06-20

We present a comparative study of ten redox-active probes for use in real-time electrochemical loop-mediated isothermal amplification (LAMP). Our main objectives were to establish the criteria that need to be fulfilled for minimizing some of the current limitations of the technique and to provide future guidelines in the search for ideal redox reporters. To ensure a reliable comparative study, each redox probe was tested under similar conditions using the same LAMP reaction and the same entirely automatized custom-made real-time electrochemical device (designed for electrochemically monitoring in real-time and in parallel up to 48 LAMP samples). Electrochemical melt curve analyses were recorded immediately at the end of each LAMP reaction. Our results show that there are a number of intercalating and non-intercalating redox compounds suitable for real-time electrochemical LAMP and that the best candidates are those able to intercalate strongly into ds-DNA but not too much to avoid inhibition of the LAMP reaction. The strongest intercalating redox probes were finally shown to provide higher LAMP sensitivity, speed, greater signal amplitude, and cleaner-cut DNA melting curves than the non-intercalating molecules.

Loop-Mediated Isothermal Amplification Targeting Actin DNA of Trichomonas vaginalis.

PubMed

Goo, Youn-Kyoung; Shin, Won-Sik; Yang, Hye-Won; Joo, So-Young; Song, Su-Min; Ryu, Jae-Sook; Kong, Hyun-Hee; Lee, Won-Ki; Chung, Dong-Il; Hong, Yeonchul

2016-06-01

Trichomoniasis caused by Trichomonas vaginalis is a common sexually transmitted disease. Its association with several health problems, including preterm birth, pelvic inflammatory disease, cervical cancer, and transmission of human immunodeficiency virus, emphasizes the importance of improved access to early and accurate detection of T. vaginalis. In this study, a rapid and efficient loop-mediated isothermal amplification-based method for the detection of T. vaginalis was developed and validated, using vaginal swab specimens from subjects suspected to have trichomoniasis. The LAMP assay targeting the actin gene was highly sensitive with detection limits of 1 trichomonad and 1 pg of T. vaginalis DNA per reaction, and specifically amplified the target gene only from T. vaginalis. Validation of this assay showed that it had the highest sensitivity and better agreement with PCR (used as the gold standard) compared to microscopy and multiplex PCR. This study showed that the LAMP assay, targeting the actin gene, could be used to diagnose early infections of T. vaginalis. Thus, we have provided an alternative molecular diagnostic tool and a point-of-care test that may help to prevent trichomoniasis transmission and associated complications.

Chemical looping fluidized-bed concentrating solar power system and method

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

Ma, Zhiwen

A concentrated solar power (CSP) plant comprises a receiver configured to contain a chemical substance for a chemical reaction and an array of heliostats. Each heliostat is configured to direct sunlight toward the receiver. The receiver is configured to transfer thermal energy from the sunlight to the chemical substance in a reduction reaction. The CSP plant further comprises a first storage container configured to store solid state particles produced by the reduction reaction and a heat exchanger configured to combine the solid state particles and gas through an oxidation reaction. The heat exchanger is configured to transfer heat produced inmore » the oxidation reaction to a working fluid to heat the working fluid. The CSP plant further comprises a power turbine coupled to the heat exchanger, such that the heated working fluid turns the power turbine, and a generator coupled to and driven by the power turbine to generate electricity.« less

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

Alvarez-Ramirez, J.; Aguilar, R.; Lopez-Isunza, F.

FCC processes involve complex interactive dynamics which are difficult to operate and control as well as poorly known reaction kinetics. This work concerns the synthesis of temperature controllers for FCC units. The problem is addressed first for the case where perfect knowledge of the reaction kinetics is assumed, leading to an input-output linearizing state feedback. However, in most industrial FCC units, perfect knowledge of reaction kinetics and composition measurements is not available. To address the problem of robustness against uncertainties in the reaction kinetics, an adaptive model-based nonlinear controller with simplified reaction models is presented. The adaptive strategy makes usemore » of estimates of uncertainties derived from calorimetric (energy) balances. The resulting controller is similar in form to standard input-output linearizing controllers and can be tuned analogously. Alternatively, the controller can be tuned using a single gain parameter and is computationally efficient. The performance of the closed-loop system and the controller design procedure are shown with simulations.« less

Specific detection of the toxic dinoflagellates Alexandrium tamarense and Alexandrium catenella from single vegetative cells by a loop-mediated isothermal amplification method.

PubMed

Nagai, Satoshi; Itakura, Shigeru

2012-09-01

In this study, we succeeded in developing a loop-mediated isothermal amplification (LAMP) method that enables sensitive and specific detection of the toxic marine dinoflagellates Alexandrium tamarense and Alexandrium catenella from single cells of both laboratory cultures and naturally blooming cells within 25 min, by monitoring the turbidimeter from the start of the LAMP reaction. The fluorescence intensity was strong enough to allow discrimination between positive and negative results by naked eye under a UV lamp, even in amplified samples from a single cell, by using the LAMP method. Unambiguous detection by naked eye was possible even in half the volume of LAMP cocktail recommended by the manufacturer, suggesting the potential to significantly reduce the cost of Alexandrium monitoring. Therefore, we can conclude that this method is one of the most convenient, sensitive, and cost-effective molecular tools for Alexandrium monitoring. Copyright © 2012 Elsevier B.V. All rights reserved.

Loop-Mediated Isothermal Amplification (LAMP): Emergence As an Alternative Technology for Herbal Medicine Identification.

PubMed

Li, Jing-Jian; Xiong, Chao; Liu, Yue; Liang, Jun-Song; Zhou, Xing-Wen

2016-01-01

Correct identification of medicinal plant ingredients is essential for their safe use and for the regulation of herbal drug supply chain. Loop-mediated isothermal amplification (LAMP) is a recently developed approach to identify herbal medicine species. This novel molecular biology technique enables timely and accurate testing, especially in settings where infrastructures to support polymerase chain reaction facilities are lacking. Studies that used this method have altered our view on the extent and complexity of herbal medicine identification. In this review, we give an introduction into LAMP analysis, covers the basic principles and important aspects in the development of LAMP analysis method. Then we presented a critical review of the application of LAMP-based methods in detecting and identifying raw medicinal plant materials and their processed products. We also provide a practical standard operating procedure (SOP) for the utilization of the LAMP protocol in herbal authentication, and consider the prospects of LAMP technology in the future developments of herbal medicine identification and the challenges associated with its application.

Loop-Mediated Isothermal Amplification (LAMP): Emergence As an Alternative Technology for Herbal Medicine Identification

PubMed Central

Li, Jing-jian; Xiong, Chao; Liu, Yue; Liang, Jun-song; Zhou, Xing-wen

2016-01-01

Correct identification of medicinal plant ingredients is essential for their safe use and for the regulation of herbal drug supply chain. Loop-mediated isothermal amplification (LAMP) is a recently developed approach to identify herbal medicine species. This novel molecular biology technique enables timely and accurate testing, especially in settings where infrastructures to support polymerase chain reaction facilities are lacking. Studies that used this method have altered our view on the extent and complexity of herbal medicine identification. In this review, we give an introduction into LAMP analysis, covers the basic principles and important aspects in the development of LAMP analysis method. Then we presented a critical review of the application of LAMP-based methods in detecting and identifying raw medicinal plant materials and their processed products. We also provide a practical standard operating procedure (SOP) for the utilization of the LAMP protocol in herbal authentication, and consider the prospects of LAMP technology in the future developments of herbal medicine identification and the challenges associated with its application. PMID:28082999

Rapid and sensitive identification of the herbal tea ingredient Taraxacum formosanum using loop-mediated isothermal amplification.

PubMed

Lai, Guan-Hua; Chao, Jung; Lin, Ming-Kuem; Chang, Wen-Te; Peng, Wen-Huang; Sun, Fang-Chun; Lee, Meng-Shiunn; Lee, Meng-Shiou

2015-01-09

Taraxacum formosanum (TF) is a medicinal plant used as an important component of health drinks in Taiwan. In this study, a rapid, sensitive and specific loop-mediated isothermal amplification (LAMP) assay for authenticating TF was established. A set of four specific LAMP primers was designed based on the nucleotide sequence of the internal transcribed spacer 2 (ITS2) nuclear ribosomal DNA (nrDNA) of TF. LAMP amplicons were successfully amplified and detected when purified genomic DNA of TF was added in the LAMP reaction under isothermal condition (65 °C) within 45 min. These specific LAMP primers have high specificity and can accurately discriminate Taraxacum formosanum from other adulterant plants; 1 pg of genomic DNA was determined to be the detection limit of the LAMP assay. In conclusion, using this novel approach, TF and its misused plant samples obtained from herbal tea markets were easily identified and discriminated by LAMP assay for quality control.

Rapid and Sensitive Identification of the Herbal Tea Ingredient Taraxacum formosanum Using Loop-Mediated Isothermal Amplification

PubMed Central

Lai, Guan-Hua; Chao, Jung; Lin, Ming-Kuem; Chang, Wen-Te; Peng, Wen-Huang; Sun, Fang-Chun; Lee, Meng-Shiunn; Lee, Meng-Shiou

2015-01-01

Taraxacum formosanum (TF) is a medicinal plant used as an important component of health drinks in Taiwan. In this study, a rapid, sensitive and specific loop-mediated isothermal amplification (LAMP) assay for authenticating TF was established. A set of four specific LAMP primers was designed based on the nucleotide sequence of the internal transcribed spacer 2 (ITS2) nuclear ribosomal DNA (nrDNA) of TF. LAMP amplicons were successfully amplified and detected when purified genomic DNA of TF was added in the LAMP reaction under isothermal condition (65 °C) within 45 min. These specific LAMP primers have high specificity and can accurately discriminate Taraxacum formosanum from other adulterant plants; 1 pg of genomic DNA was determined to be the detection limit of the LAMP assay. In conclusion, using this novel approach, TF and its misused plant samples obtained from herbal tea markets were easily identified and discriminated by LAMP assay for quality control. PMID:25584616

High-throughput amplification of mature microRNAs in uncharacterized animal models using polyadenylated RNA and stem-loop reverse transcription polymerase chain reaction.

PubMed

Biggar, Kyle K; Wu, Cheng-Wei; Storey, Kenneth B

2014-10-01

This study makes a significant advancement on a microRNA amplification technique previously used for expression analysis and sequencing in animal models without annotated mature microRNA sequences. As research progresses into the post-genomic era of microRNA prediction and analysis, the need for a rapid and cost-effective method for microRNA amplification is critical to facilitate wide-scale analysis of microRNA expression. To facilitate this requirement, we have reoptimized the design of amplification primers and introduced a polyadenylation step to allow amplification of all mature microRNAs from a single RNA sample. Importantly, this method retains the ability to sequence reverse transcription polymerase chain reaction (RT-PCR) products, validating microRNA-specific amplification. Copyright © 2014 Elsevier Inc. All rights reserved.

Running with rugby balls: bulk renormalization of codimension-2 branes

NASA Astrophysics Data System (ADS)

Williams, M.; Burgess, C. P.; van Nierop, L.; Salvio, A.

2013-01-01

We compute how one-loop bulk effects renormalize both bulk and brane effective interactions for geometries sourced by codimension-two branes. We do so by explicitly integrating out spin-zero, -half and -one particles in 6-dimensional Einstein-Maxwell-Scalar theories compactified to 4 dimensions on a flux-stabilized 2D geometry. (Our methods apply equally well for D dimensions compactified to D - 2 dimensions, although our explicit formulae do not capture all divergences when D > 6.) The renormalization of bulk interactions are independent of the boundary conditions assumed at the brane locations, and reproduce standard heat-kernel calculations. Boundary conditions at any particular brane do affect how bulk loops renormalize this brane's effective action, but not the renormalization of other distant branes. Although we explicitly compute our loops using a rugby ball geometry, because we follow only UV effects our results apply more generally to any geometry containing codimension-two sources with conical singularities. Our results have a variety of uses, including calculating the UV sensitivity of one-loop vacuum energy seen by observers localized on the brane. We show how these one-loop effects combine in a surprising way with bulk back-reaction to give the complete low-energy effective cosmological constant, and comment on the relevance of this calculation to proposed applications of codimension-two 6D models to solutions of the hierarchy and cosmological constant problems.

A Pilot Model for the NASA Simplified Aid for EVA Rescue (SAFER) (Single-Axis Pitch Task)

NASA Astrophysics Data System (ADS)

Handley, Patrick Mark

This thesis defines, tests, and validates a descriptive pilot model for a single-axis pitch control task of the Simplified Aid for EVA Rescue (SAFER). SAFER is a small propulsive jetpack used by astronauts for self-rescue. Pilot model research supports development of improved self-rescue strategies and technologies through insights into pilot behavior.This thesis defines a multi-loop pilot model. The innermost loop controls the hand controller, the middle loop controls pitch rate, and the outer loop controls pitch angle. A human-in-the-loop simulation was conducted to gather data from a human pilot. Quantitative and qualitative metrics both indicate that the model is an acceptable fit to the human data. Fuel consumption was nearly identical; time to task completion matched very well. There is some evidence that the model responds faster to initial pitch rates than the human, artificially decreasing the model's time to task completion. This pilot model is descriptive, not predictive, of the human pilot. Insights are made into pilot behavior from this research. Symmetry implies that the human responds to positive and negative initial conditions with the same strategy. The human pilot appears indifferent to pitch angles within 0.5 deg, coasts at a constant pitch rate 1.09 deg/s, and has a reaction delay of 0.1 s.

Simulation of process identification and controller tuning for flow control system

NASA Astrophysics Data System (ADS)

Chew, I. M.; Wong, F.; Bono, A.; Wong, K. I.

2017-06-01

PID controller is undeniably the most popular method used in controlling various industrial processes. The feature to tune the three elements in PID has allowed the controller to deal with specific needs of the industrial processes. This paper discusses the three elements of control actions and improving robustness of controllers through combination of these control actions in various forms. A plant model is simulated using the Process Control Simulator in order to evaluate the controller performance. At first, the open loop response of the plant is studied by applying a step input to the plant and collecting the output data from the plant. Then, FOPDT of physical model is formed by using both Matlab-Simulink and PRC method. Then, calculation of controller’s setting is performed to find the values of Kc and τi that will give satisfactory control in closed loop system. Then, the performance analysis of closed loop system is obtained by set point tracking analysis and disturbance rejection performance. To optimize the overall physical system performance, a refined tuning of PID or detuning is further conducted to ensure a consistent resultant output of closed loop system reaction to the set point changes and disturbances to the physical model. As a result, the PB = 100 (%) and τi = 2.0 (s) is preferably chosen for setpoint tracking while PB = 100 (%) and τi = 2.5 (s) is selected for rejecting the imposed disturbance to the model. In a nutshell, selecting correlation tuning values is likewise depended on the required control’s objective for the stability performance of overall physical model.

Rapid detection of Piper yellow mottle virus and Cucumber mosaic virus infecting black pepper (Piper nigrum) by loop-mediated isothermal amplification (LAMP).

PubMed

Bhat, A I; Siljo, A; Deeshma, K P

2013-10-01

The loop-mediated isothermal amplification (LAMP) assay for Piper yellow mottle virus and the reverse transcription (RT) LAMP assay for Cucumber mosaic virus each consisted of a set of five primers designed against the conserved sequences in the viral genome. Both RNA and DNA isolated from black pepper were used as a template for the assay. The results were assessed visually by checking turbidity, green fluorescence and pellet formation in the reaction tube and also by gel electrophoresis. The assay successfully detected both viruses in infected plants whereas no cross-reactions were recorded with healthy plants. Optimum conditions for successful amplification were determined in terms of the concentrations of magnesium sulphate and betaine, temperature, and duration. The detection limit for both LAMP and RT-LAMP was up to 100 times that for conventional PCR and up to one-hundredth of that for real-time PCR. The optimal conditions arrived at were validated by testing field samples of infected vines of three species from different regions. Copyright © 2013 Elsevier B.V. All rights reserved.

Backstepping-based boundary control design for a fractional reaction diffusion system with a space-dependent diffusion coefficient.

PubMed

Chen, Juan; Cui, Baotong; Chen, YangQuan

2018-06-11

This paper presents a boundary feedback control design for a fractional reaction diffusion (FRD) system with a space-dependent (non-constant) diffusion coefficient via the backstepping method. The contribution of this paper is to generalize the results of backstepping-based boundary feedback control for a FRD system with a space-independent (constant) diffusion coefficient to the case of space-dependent diffusivity. For the boundary stabilization problem of this case, a designed integral transformation treats it as a problem of solving a hyperbolic partial differential equation (PDE) of transformation's kernel, then the well posedness of the kernel PDE is solved for the plant with non-constant diffusivity. Furthermore, by the fractional Lyapunov stability (Mittag-Leffler stability) theory and the backstepping-based boundary feedback controller, the Mittag-Leffler stability of the closed-loop FRD system with non-constant diffusivity is proved. Finally, an extensive numerical example for this closed-loop FRD system with non-constant diffusivity is presented to verify the effectiveness of our proposed controller. Copyright © 2018 ISA. Published by Elsevier Ltd. All rights reserved.

Loop-mediated isothermal amplification (LAMP) shield for Arduino DNA detection.

PubMed

Velders, Aldrik H; Schoen, Cor; Saggiomo, Vittorio

2018-02-01

Loop-mediated isothermal amplification (LAMP) of DNA is gaining relevance as a method to detect nucleic acids, as it is easier, faster, and more powerful than conventional Polymerase Chain Reaction. However, LAMP is still mostly used in laboratory settings, because of the lack of a cheap and easy, one-button device that can perform LAMP experiments. Here we show how to build and program an Arduino shield for a LAMP and detection of DNA. The here described Arduino Shield is cheap, easy to assemble, to program and use, it is battery operated and the detection of DNA is done by naked-eye so that it can be used in field.

Fine pointing control for a Next-Generation Space Telescope

NASA Astrophysics Data System (ADS)

Mosier, Gary E.; Femiano, Michael; Ha, Kong; Bely, Pierre Y.; Burg, Richard; Redding, David C.; Kissil, Andrew; Rakoczy, John; Craig, Larry

1998-08-01

The Next Generation Space Telescope will provide at least ten times the collecting area of the Hubble Space Telescope in a package that fits into the shroud of an expendable launch vehicle. The resulting large, flexible structure provides a challenge to the design of a pointing control system for which the requirements are at the milli-arcsecond level. This paper describes a design concept in which pointing stability is achieved by means of a nested-loop design involving an inertial attitude control system (ACS) and a fast steering mirror (FSM). A key to the integrated control design is that the ACS controllers has a bandwidth well below known structural modes and the FSM uses a rotationally balanced mechanism which should not interact with the flexible modes that are within its control bandwidth. The ACS controller provides stable pointing of the spacecraft bus with star trackers and gyros. This low bandwidth loop uses nearly co-located sensors and actuators to slew and acquire faint guide stars in the NIR camera. This controller provides a payload reference stable to the arcsecond level. Low-frequency pointing errors due to sensor noise and dynamic disturbances are suppressed by a 2-axis gimbaled FSM locate din the instrument module. The FSM servo bandwidth of 6 Hz is intended to keep the guide star position stable in the NIR focal plane to the required milli-arcsecond level. The mirror is kept centered in its range of travel by a low-bandwidth loop closed around the ACS. This paper presents the result of parametric trade studies designed to assess the performance of this control design in the presence of modeled reaction wheel disturbances, assumed to be the principle source of vibration for the NGST, and variations in structural dynamics. Additionally, requirements for reaction wheel disturbance levels and potential vibration isolation subsystems were developed.

Semi-quantitative visual detection of loop mediated isothermal amplification (LAMP)-generated DNA by distance-based measurement on a paper device.

PubMed

Hongwarittorrn, Irin; Chaichanawongsaroj, Nuntaree; Laiwattanapaisal, Wanida

2017-12-01

A distance-based paper analytical device (dPAD) for loop mediated isothermal amplification (LAMP) detection based on distance measurement was proposed. This approach relied on visual detection by the length of colour developed on the dPAD with reference to semi-quantitative determination of the initial amount of genomic DNA. In this communication, E. coli DNA was chosen as a template DNA for LAMP reaction. In accordance with the principle, the dPAD was immobilized by polyethylenimine (PEI), which is a strong cationic polymer, in the hydrophilic channel of the paper device. Hydroxynaphthol blue (HNB), a colourimetric indicator for monitoring the change of magnesium ion concentration in the LAMP reaction, was used to react with the immobilized PEI. The positive charges of PEI react with the negative charges of free HNB in the LAMP reaction, producing a blue colour deposit on the paper device. Consequently, the apparently visual distance appeared within 5min and length of distance correlated to the amount of DNA in the sample. The distance-based PAD for the visual detection of the LAMP reaction could quantify the initial concentration of genomic DNA as low as 4.14 × 10 3 copiesµL -1 . This distance-based visual semi-quantitative platform is suitable for choice of LAMP detection method, particular in resource-limited settings because of the advantages of low cost, simple fabrication and operation, disposability and portable detection of the dPAD device. Copyright © 2017 Elsevier B.V. All rights reserved.

Solar thermochemical process interface study

NASA Technical Reports Server (NTRS)

1984-01-01

The design and analyses of a subsystem of a hydrogen production process are described. The process is based on solar driven thermochemical reactions. The subject subsystem receives sulfuric acid of 60% concentration at 100 C, 1 atm pressure. The acid is further concentrated, vaporized, and decomposed (at a rate of 122 g moles/sec H2SO4) into SO2, O2, and water. The produce stream is cooled to 100 C. Three subsystem options, each being driven by direct solar energy, were designed and analyzed. The results are compared with a prior study case in which solar energy was provided indirectly through a helium loop.

Mechanical gating of a mechanochemical reaction cascade

NASA Astrophysics Data System (ADS)

Wang, Junpeng; Kouznetsova, Tatiana B.; Boulatov, Roman; Craig, Stephen L.

2016-11-01

Covalent polymer mechanochemistry offers promising opportunities for the control and engineering of reactivity. To date, covalent mechanochemistry has largely been limited to individual reactions, but it also presents potential for intricate reaction systems and feedback loops. Here we report a molecular architecture, in which a cyclobutane mechanophore functions as a gate to regulate the activation of a second mechanophore, dichlorocyclopropane, resulting in a mechanochemical cascade reaction. Single-molecule force spectroscopy, pulsed ultrasonication experiments and DFT-level calculations support gating and indicate that extra force of >0.5 nN needs to be applied to a polymer of gated gDCC than of free gDCC for the mechanochemical isomerization gDCC to proceed at equal rate. The gating concept provides a mechanism by which to regulate stress-responsive behaviours, such as load-strengthening and mechanochromism, in future materials designs.

Optimizing laboratory-based radon flux measurements for sediments.

PubMed

Chanyotha, Supitcha; Kranrod, Chutima; Kritsananuwat, Rawiwan; Lane-Smith, Derek; Burnett, William C

2016-07-01

Radon flux via diffusion from sediments and other materials may be determined in the laboratory by circulating air through the sample and a radon detector in a closed loop. However, this approach is complicated by the necessity of having to determine the total air volume in the system and accounting for any small air leaks that can arise if using extended measurement periods. We designed a simple open-loop configuration that includes a measured mass of wet sediment and water inside a gas-tight reaction flask connected to a drying system and a radon-in-air analyzer. Ambient air flows through two charcoal columns before entering the reaction vessel to eliminate incoming radon. After traveling through the reaction flask, the air passes the drier and the radon analyzer and is then vented. After some time, the radon activity will reach a steady state depending upon the airflow rate. With this approach, the radon flux via diffusion is simply the product of the steady-state radon activity (Bq/m(3)) multiplied by the airflow rate (mL/min). We demonstrated that this setup could produce good results for materials that produce relatively high radon fluxes. We also show that a modified closed system approach, including radon removal of the incoming air by charcoal filtration in a bypass, can produce very good results including samples with very low emission rates. Copyright © 2016 Elsevier Ltd. All rights reserved.

Loop-Mediated Isothermal Amplification of the sefA Gene for Rapid Detection of Salmonella Enteritidis and Salmonella Gallinarum in Chickens.

PubMed

Gong, Jiansen; Zhuang, Linlin; Zhu, Chunhong; Shi, Shourong; Zhang, Di; Zhang, Linji; Yu, Yan; Dou, Xinhong; Xu, Bu; Wang, Chengming

2016-04-01

Salmonella spp. pose a threat to both human and animal health, with more than 2600 serovars having been reported to date. Salmonella serovars are usually identified by slide agglutination tests, which are labor intensive and time consuming. In an attempt to develop a more rapid screening method for the major poultry Salmonella serovars, we developed a loop-mediated isothermal amplification (LAMP) assay, which directly detected the sefA gene, a fimbrial operon gene existing in several specific serovars of Salmonella enterica including the major poultry serovars, namely Salmonella enterica serovar Enteritidis (Salmonella Enteritidis) and Salmonella enterica serovar Gallinarum (Salmonella Gallinarum). With the 177 bacterial strains we tested, positive reactions were only observed with 85 strains of serovar Salmonella Enteritidis and Salmonella Gallinarum. The detection limit of the LAMP assay was 4 CFU/reaction with genomic DNAs of Salmonella Enteritidis (ATCC 13076) from pure culture and 400 CFU/ reaction with DNA extracted from spiked chicken feces. The LAMP assay was more sensitive than conventional culture, especially without enrichment, in detecting Salmonella Enteritidis (CMCC 50041) in the spiked fecal samples. The results show the sefA LAMP method is a rapid, sensitive, specific, and practical method for directly detection of Salmonella Enteritidis and Salmonella Gallinarum in chickens. The sefA LAMP assay can potentially serve as new on-site diagnostics in the poultry industry.

Stability of flat spacetime in quantum gravity

NASA Astrophysics Data System (ADS)

Jordan, R. D.

1987-12-01

In a previous paper, a modified effective-action formalism was developed which produces equations satisfied by the expectation value of the field, rather than the usual in-out average. Here this formalism is applied to a quantized scalar field in a background which is a small perturbation from Minkowski spacetime. The one-loop effective field equation describes the back reaction of created particles on the gravitational field, and is calculated in this paper to linear order in the perturbation. In this way we rederive an equation first found by Horowitz using completely different methods. This equation possesses exponentially growing solutions, so we confirm Horowitz's conclusion that flat spacetime is unstable in this approximation to the theory. The new derivation shows that the field equation is just as useful as the one-loop approximation to the in-out equation, contrary to earlier arguments. However, the instability suggests that the one-loop approximation cannot be trusted for gravity. These results are compared with the corresponding situation in QED and QCD.

[Possible mechanisms of learning, memory and attention impairment in consequence of sleep deprivation].

PubMed

Sil'kis, I G

2012-10-01

We proposed that impairment of learning, memory, and attention evoked by sleep deprivation could be a consequence of following changes in neuromodulator concentrations and intracellular processes that influence synaptic plasticity and functioning of the hippocampal formation and cortico--basal ganglia--thalamocortical loops. Firstly, a decrease in Ca2+ concentration and NMDA-receptor expression prevents induction of LTP of efficacy of synaptic transmissions in the neocortex and hippocampus. Secondly, a decrease in orexin concentration also worsens conditions for LTP induction and suppresses transmission of excitation in trisynaptic pathway through the hippocampus, thus worsening a creation of neural representations of "object-place" associations. Thirdly, a decrease in concentration of dopamine, and increase in level of adenosine and number of A1 receptors in the striatum worsen the functioning ofcortico-basal ganglia-thalamocortical loops. These lead to decrease in voluntary and involuntary attention, worsens processing of sensory information, and motor reactions. Excitation of neurons in reinforcement loops is also decreased thus suppressing the motivational significance of stimuli.

Mathematical modeling of planar cell polarity signaling in the Drosophila melanogaster wing

NASA Astrophysics Data System (ADS)

Amonlirdviman, Keith

Planar cell polarity (PCP) signaling refers to the coordinated polarization of cells within the plane of various epithelial tissues to generate sub-cellular asymmetry along an axis orthogonal to their apical-basal axes. For example, in the Drosophila wing, PCP is seen in the parallel orientation of hairs that protrude from each of the approximately 30,000 epithelial cells to robustly point toward the wing tip. Through a poorly understood mechanism, cell clones mutant for some PCP signaling components, including some, but not all alleles of the receptor frizzled, cause polarity disruptions of neighboring, wild-type cells, a phenomenon referred to as domineering nonautonomy. Previous models have proposed diffusible factors to explain nonautonomy, but no such factors have yet been found. This dissertation describes the mathematical modeling of PCP in the Drosophila wing, based on a contact dependent signaling hypothesis derived from experimental results. Intuition alone is insufficient to deduce that this hypothesis, which relies on a local feedback loop acting at the cell membrane, underlies the complex patterns observed in large fields of cells containing mutant clones, and others have argued that it cannot account for observed phenotypes. Through reaction-diffusion, partial differential equation modeling and simulation, the feedback loop is shown to fully reproduce PCP phenotypes, including domineering nonautonomy. The sufficiency of this model and the experimental validation of model predictions argue that previously proposed diffusible factors need not be invoked to explain PCP signaling and reveal how specific protein-protein interactions lead to autonomy or domineering nonautonomy. Based on these results, an ordinary differential equation model is derived to study the relationship of the feedback loop with upstream signaling components. The cadherin Fat transduces a cue to the local feedback loop, biasing the polarity direction of each cell toward the wing tip. The feedback loop then amplifies and propagates PCP across the pupal wing, but polarity information does not always propagate correctly across cells lacking Fat function. Using the simplified model, the presence and severity of polarity defects in fat clones is shown to be an inherent consequence of the feedback loop when confronted with irregular variations in cell geometry.

On-chip electrical detection of parallel loop-mediated isothermal amplification with DG-BioFETs for the detection of foodborne bacterial pathogens

USDA-ARS?s Scientific Manuscript database

The use of field effect transistors (FETs) as the transduction element for the detection of DNA amplification reactions will enable portable and inexpensive nucleic acid analysis. Transistors used as biological sensors,or BioFETs, minimize the cost and size of detection platforms by leveraging fabri...

Development of a Low-Cost Stem-Loop Real-Time Quantification PCR Technique for EBV miRNA Expression Analysis.

PubMed

Bergallo, Massimiliano; Merlino, Chiara; Montin, Davide; Galliano, Ilaria; Gambarino, Stefano; Mareschi, Katia; Fagioli, Franca; Montanari, Paola; Martino, Silvana; Tovo, Pier-Angelo

2016-09-01

MicroRNAs (miRNAs) are short, single stranded, non-coding RNA molecules. They are produced by many different species and are key regulators of several physiological processes. miRNAs are also encoded by the genomes of multiple virus families, such as herpesvirus family. In particular, miRNAs from Epstein Barr virus were found at high concentrations in different associated pathologies, such as Burkitt's lymphoma, Hodgkin disease, and nasopharyngeal carcinoma. Thanks to their stability, these molecules could possibly serve as biomarkers for EBV-associated diseases. In this study, a stem-loop real-time PCR for miR-BART2-5p, miR-BART15, and miR-BART22 EBV miRNAs detection and quantification has been developed. Evaluation of these miRNAs in 31 serum samples (12 from patients affected by primary immunodeficiency, 9 from X-linked agammaglobulinemia and 10 from healthy subjects) has been carried out. The amplification performance showed a wide dynamic range (10(8)-10(2) copies/reaction) and sensibility equal to 10(2) copies/reaction for all the target tested. Serum samples analysis, on the other hand, showed a statistical significant higher level of miR-BART22 in primary immunodeficiency patients (P = 0.0001) compared to other groups and targets. The results confirmed the potential use of this assay as a tool for monitoring EBV-associated disease and for miRNAs expression profile analysis.

Limestone calcination under calcium-looping conditions for CO2 capture and thermochemical energy storage in the presence of H2O: an in situ XRD analysis.

PubMed

Valverde, Jose Manuel; Medina, Santiago

2017-03-15

This work reports an in situ XRD analysis of whether the calcination/carbonation behavior of natural limestone (CaCO 3 ) is affected by the addition of H 2 O to the calciner at a very low concentration under relevant Calcium-Looping (CaL) conditions for CO 2 capture in coal fired power plants (CFPP) and Thermochemical Energy Storage (TCES) in Concentrated Solar Power plants (CSP). Previous studies have demonstrated that the presence of steam in the calciner at a high concentration yields a significant increase in the reaction rate. However, a further undesired consequence is the serious deterioration of the CaO mechanical strength, which would lead to particle attrition and mass loss in any CaL process based on the use of circulating fluidized beds. The results presented in this manuscript on the time evolution of the wt% and crystallite size of the phases involved in the calcination/carbonation reactions indicate that the calcination rate is still notably increased by the presence of H 2 O at very low concentrations whereas the reactivity toward carbonation and crystal structure of the formed CaO are not essentially affected, which suggests that the CaO mechanical strength is not impaired. Thus, the benefit of using steam for calcination in the CaL process could be still retained while at the same time particle attrition would not be promoted.

Mevalonate 5-diphosphate mediates ATP binding to the mevalonate diphosphate decarboxylase from the bacterial pathogen Enterococcus faecalis

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

Chen, Chun-Liang; Mermoud, James C.; Paul, Lake N.

The mevalonate pathway produces isopentenyl diphosphate (IPP), a building block for polyisoprenoid synthesis, and is a crucial pathway for growth of the human bacterial pathogen Enterococcus faecalis. The final enzyme in this pathway, mevalonate diphosphate decarboxylase (MDD), acts on mevalonate diphosphate (MVAPP) to produce IPP while consuming ATP. This essential enzyme has been suggested as a therapeutic target for the treatment of drug-resistant bacterial infections. Here, we report functional and structural studies on the mevalonate diphosphate decarboxylase from E. faecalis (MDDEF). The MDDEF crystal structure in complex with ATP (MDDEF–ATP) revealed that the phosphate-binding loop (amino acids 97–105) is notmore » involved in ATP binding and that the phosphate tail of ATP in this structure is in an outward-facing position pointing away from the active site. This suggested that binding of MDDEF to MVAPP is necessary to guide ATP into a catalytically favorable position. Enzymology experiments show that the MDDEF performs a sequential ordered bi-substrate reaction with MVAPP as the first substrate, consistent with the isothermal titration calorimetry (ITC) experiments. On the basis of ITC results, we propose that this initial prerequisite binding of MVAPP enhances ATP binding. In summary, our findings reveal a substrate-induced substrate-binding event that occurs during the MDDEF-catalyzed reaction. The disengagement of the phosphate-binding loop concomitant with the alternative ATP-binding configuration may provide the structural basis for antimicrobial design against these pathogenic enterococci.« less

Loop-mediated isothermal amplification (LAMP) assay for the diagnosis of fasciolosis in sheep and its application under field conditions.

PubMed

Martínez-Valladares, María; Rojo-Vázquez, Francisco Antonio

2016-02-05

Loop-mediated isothermal amplification (LAMP) is a very specific, efficient, and rapid gene amplification procedure in which the reaction can run at a constant temperature. In the current study we have developed a LAMP assay to improve the diagnosis of Fasciola spp. in the faeces of sheep. After the optimisation of the LAMP assay we have shown similar results between this technique and the standard PCR using the outer primers of the LAMP reaction. In both cases the limit of detection was 10 pg; also, the diagnosis of fasciolosis was confirmed during the first week post-infection in experimental infected sheep by both techniques. In eight naturally infected sheep, the infection with F. hepatica was confirmed in all animals before a treatment with triclabendazole and on day 30 post treatment in two sheep using the LAMP assay; however, when we carried out the standard PCR with the outer primers, the results before treatment were the same but on day 30 post-treatment the infection was only confirmed in one out of the two sheep. On the other hand, the standard PCR took around 3 h to obtain a result, comparing with 1 h and 10 min for the LAMP assay. The LAMP assay described here could be a good alternative to conventional diagnostic methods to detect F. hepatica in faeces since it solves the drawbacks of the standard PCR.

The reduction of carbon dioxide in iron biocatalyst catalytic hydrogenation reaction: a theoretical study.

PubMed

Yang, Longhua; Wang, Hongming; Zhang, Ning; Hong, Sanguo

2013-08-21

The reaction mechanism of CO₂ hydrogenation catalyzed by [FeH(PP₃)]BF₄ (PP₃ = P(CH₂CH₂PPh₂)₃) had been investigated by DFT calculations. Our calculations indicated that the reduction of carbon dioxide could be carried out via two spin states, the high-spin (HS) triplet state and the low-spin (LS) singlet state. The minimum energy crossing points (MECPs) on the seam of two intersecting PESs (potential energy surfaces) were searched out. Some interesting phenomena, such as the open-loop phenomenon, and the O-rebound process, were demonstrated to be the important causes of the spin crossover. All these calculations gave us insight into the essence of the related experiment from the macro point of view, and helped to verify which spin states the related complexes pertinent were in. All of these researches would help advance the development of efficient and structurally tailorable CO₂ hydrogenation catalysts.

Detection of Cucurbit chlorotic yellows virus from Bemisia tabaci captured on sticky traps using reverse transcription loop-mediated isothermal amplification (RT-LAMP) and simple template preparation.

PubMed

Okuda, Mitsuru; Okuda, Shiori; Iwai, Hisashi

2015-09-01

Cucurbit chlorotic yellows virus (CCYV) of the genus Crinivirus within the family Closteroviridae is an emerging infectious agent of cucurbits leading to severe disease and significant economic losses. Effective detection and identification methods for this virus are urgently required. In this study, a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed to detect CCYV from its vector Bemisia tabaci. LAMP primer sets to detect CCYV were evaluated for their sensitivity and specificity, and a primer set designed from the HSP70h gene with corresponding loop primers were selected. The RT-LAMP assay was applied to detect CCYV from viruliferous B. tabaci trapped on sticky traps. A simple extraction procedure using RNAsecure™ was developed for template preparation. CCYV was detected in all of the B. tabaci 0, 1, 7 and 14 days after they were trapped. Although the rise of turbidity was delayed in reactions using RNA from B. tabaci trapped for 7 and 14 days compared with those from 0 and 1 day, the DNA amplification was sufficient to detect CCYV in all of the samples. These findings therefore present a simple template preparation method and an effective RT-LAMP assay, which can be easily and rapidly performed to monitor CCYV-viruliferous B. tabaci in the field. Copyright © 2015 Elsevier B.V. All rights reserved.

Interfacial dislocations in (111) oriented (Ba 0.7Sr 0.3)TiO 3 films on SrTiO 3 single crystal

DOE PAGES

Shen, Xuan; Yamada, Tomoaki; Lin, Ruoqian; ...

2015-10-08

In this study, we have investigated the interfacial structure of epitaxial (Ba,Sr)TiO 3 films grown on (111)-oriented SrTiO 3 single-crystal substrates using transmission electron microscopy (TEM) techniques. Compared with the (100) epitaxial perovskite films, we observe dominant dislocation half-loop with Burgers vectors of a<110> comprised of a misfit dislocation along <112>, and threading dislocations along <110> or <100>. The misfit dislocation with Burgers vector of a <110> can dissociate into two ½ a <110> partial dislocations and one stacking fault. We found the dislocation reactions occur not only between misfit dislocations, but also between threading dislocations. Via three-dimensional electron tomography,more » we retrieved the configurations of the threading dislocation reactions. The reactions between threading dislocations lead to a more efficient strain relaxation than do the misfit dislocations alone in the near-interface region of the (111)-oriented (Ba 0.7Sr 0.3)TiO 3 films.« less

A Design Principle for an Autonomous Post-translational Pattern Formation.

PubMed

Sugai, Shuhei S; Ode, Koji L; Ueda, Hiroki R

2017-04-25

Previous autonomous pattern-formation models often assumed complex molecular and cellular networks. This theoretical study, however, shows that a system composed of one substrate with multisite phosphorylation and a pair of kinase and phosphatase can generate autonomous spatial information, including complex stripe patterns. All (de-)phosphorylation reactions are described with a generic Michaelis-Menten scheme, and all species freely diffuse without pre-existing gradients. Computational simulation upon >23,000,000 randomly generated parameter sets revealed the design motifs of cyclic reaction and enzyme sequestration by slow-diffusing substrates. These motifs constitute short-range positive and long-range negative feedback loops to induce Turing instability. The width and height of spatial patterns can be controlled independently by distinct reaction-diffusion processes. Therefore, multisite reversible post-translational modification can be a ubiquitous source for various patterns without requiring other complex regulations such as autocatalytic regulation of enzymes and is applicable to molecular mechanisms for inducing subcellular localization of proteins driven by post-translational modifications. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

POWER GENERATION FROM LIQUID METAL NUCLEAR FUEL

DOEpatents

Dwyer, O.E.

1958-12-23

A nuclear reactor system is described wherein the reactor is the type using a liquid metal fuel, such as a dispersion of fissile material in bismuth. The reactor is designed ln the form of a closed loop having a core sectlon and heat exchanger sections. The liquid fuel is clrculated through the loop undergoing flssion in the core section to produce heat energy and transferrlng this heat energy to secondary fluids in the heat exchanger sections. The fission in the core may be produced by a separate neutron source or by a selfsustained chain reaction of the liquid fuel present in the core section. Additional auxiliary heat exchangers are used in the system to convert water into steam which drives a turbine.

Physiological control of a rotary blood pump with selectable therapeutic options: control of pulsatility gradient.

PubMed

Arndt, Andreas; Nüsser, Peter; Graichen, Kurt; Müller, Johannes; Lampe, Bernhard

2008-10-01

A control strategy for rotary blood pumps meeting different user-selectable control objectives is proposed: maximum support with the highest feasible flow rate versus medium support with maximum ventricular washout and controlled opening of the aortic valve (AoV). A pulsatility index (PI) is calculated from the pressure difference, which is deduced from the axial thrust measured by the magnetic bearing of the pump. The gradient of PI with respect to pump speed (GPI) is estimated via online system identification. The outer loop of a cascaded controller regulates GPI to a reference value satisfying the selected control objective. The inner loop controls the PI to a reference value set by the outer loop. Adverse pumping states such as suction and regurgitation can be detected on the basis of the GPI estimates and corrected by the controller. A lumped-parameter computer model of the assisted circulation was used to simulate variations of ventricular contractility, pulmonary venous pressure, and aortic pressure. The performance of the outer control loop was demonstrated by transitions between the two control modes. Fast reaction of the inner loop was tested by stepwise reduction of venous return. For maximum support, a low PI was maintained without inducing ventricular collapse. For maximum washout, the pump worked at a high PI in the transition region between the opening and the permanently closed AoV. The cascaded control of GPI and PI is able to meet different control objectives and is worth testing in vitro and in vivo.

A Compact Self-Driven Liquid Lithium Loop for Industrial Neutron Generation

NASA Astrophysics Data System (ADS)

Stemmley, Steven; Szott, Matt; Kalathiparambil, Kishor; Ahn, Chisung; Jurczyk, Brian; Ruzic, David

2017-10-01

A compact, closed liquid lithium loop has been developed at the University of Illinois to test and utilize the Li-7(d,n) reaction. The liquid metal loop is housed in a stainless steel trench module with embedded heating and cooling. The system was designed to handle large heat and particle fluxes for use in neutron generators as well as fusion devices, solely operating via thermo-electric MHD. The objectives of this project are two-fold, 1) produce a high energy, MeV-level, neutron source and 2) provide a self-healing, low Z, low recycling plasma facing component. The flowing volume will keep a fresh, clean, lithium surface allowing Li-7(d,n) reactions to occur as well as deuterium adsorption in the fluid, increasing the overall neutron output. Expected yields of this system are 107 n/s for 13.5 MeV neutrons and 108 n/s for 2.45 MeV neutrons. Previous work has shown that using a tapered trench design prevents dry out and allows for an increase in velocity of the fluid at the particle strike point. For heat fluxes on the order of 10's MW/m2, COMSOL models have shown that high enough velocities ( 70 cm/s) are attainable to prevent significant lithium evaporation. Future work will be aimed at addressing wettability issues of lithium in the trenches, experimentally determine the velocities required to prevent dry out, and determine the neutron output of the system. The preliminary results and discussion will be presented. DOE SBIR project DE-SC0013861.

The Bosch Process-Performance of a Developmental Reactor and Experimental Evaluation of Alternative Catalysts

NASA Technical Reports Server (NTRS)

Abney, Morgan B.; Mansell, J. Matthew

2010-01-01

Bosch-based reactors have been in development at NASA since the 1960's. Traditional operation involves the reduction of carbon dioxide with hydrogen over a steel wool catalyst to produce water and solid carbon. While the system is capable of completely closing the loop on oxygen and hydrogen for Atmosphere Revitalization, steel wool requires a reaction temperature of 650C or higher for optimum performance. The single pass efficiency of the reaction over steel wool has been shown to be less than 10% resulting in a high recycle stream. Finally, the formation of solid carbon on steel wool ultimately fouls the catalyst necessitating catalyst resupply. These factors result in high mass, volume and power demands for a Bosch system. Interplanetary transportation and surface exploration missions of the moon, Mars, and near-earth objects will require higher levels of loop closure than current technology cannot provide. A Bosch system can provide the level of loop closure necessary for these long-term missions if mass, volume, and power can be kept low. The keys to improving the Bosch system lie in reactor and catalyst development. In 2009, the National Aeronautics and Space Administration refurbished a circa 1980's developmental Bosch reactor and built a sub-scale Bosch Catalyst Test Stand for the purpose of reactor and catalyst development. This paper describes the baseline performance of two commercially available steel wool catalysts as compared to performance reported in the 1960's and 80's. Additionally, the results of sub-scale testing of alternative Bosch catalysts, including nickel- and cobalt-based catalysts, are discussed.

Attachment of reporter groups to specific, selected cytidine residues in RNA using a bisulfite-catalyzed transamination reaction.

PubMed Central

Draper, D E

1984-01-01

Bisulfite catalyzes transamination of cytidine at the N4 position; the suitability of this reaction for attaching reporter groups to selected cytidine residues in RNA molecules has been investigated. Poly(C) is nearly quantitatively converted to the poly (N4 aminoethyl-C) derivative after 3 hrs at 42 degrees C with ethylene diamine (pK1 = 7.6) and bisulfite. This derivative reacts quantitatively with N-hydroxysuccinimide esters; the linkage of a fluorescent dye, nitrobenzofurazan, to cytidine by this reaction is demonstrated. To direct the bisulfite reaction to selected cytidines within a large RNA molecule, the RNA is hybridized to complementary DNA containing a deletion. Only the cytidines in the single strand RNA loop (corresponding to the DNA deletion) are reactive. Two cytidines in the middle of a 340 base RNA fragment from 16S ribosomal RNA have been modified by this technique. Images PMID:6198634

Understanding Which Residues of the Active Site and Loop Structure of a Tyrosine Aminomutase Define Its Mutase and Lyase Activities.

PubMed

Attanayake, Gayanthi; Walter, Tyler; Walker, Kevin D

2018-05-30

Site-directed mutations and substrate analogues were used to gain insights into the branch-point reaction of the 3,5-dihydro-5-methylidene-4 H-imidazol-4-one (MIO)-tyrosine aminomutase from Oryza sativa ( OsTAM). Exchanging the active residues of OsTAM (Y125C/N446K) for those in a phenylalanine aminomutase TcPAM altered its substrate specificity from tyrosine to phenylalanine. The aminomutase mechanism of OsTAM surprisingly changed almost exclusively to that of an ammonia lyase making cinnamic acid (>95%) over β-phenylalanine [Walter, T., et al. (2016) Biochemistry 55, 3497-3503]. We hypothesized that the missing electronics or sterics on the aryl ring of the phenylalanine substrate, compared with the sizable electron-donating hydroxyl of the natural tyrosine substrate, influenced the unexpected lyase reactivity of the OsTAM mutant. The double mutant was incubated with 16 α-phenylalanine substituent analogues of varying electronic strengths and sterics. The mutant converted each analogue principally to its acrylate with ∼50% conversion of the p-Br substrate, making only a small amount of the β-amino acid. The inner loop structure over the entrance to the active site was also mutated to assess how the lyase and mutase activities are affected. An OsTAM loop mutant, matching the loop residues of TcPAM, still chiefly made >95% of the acrylate from each substrate. A combined active site:loop mutant was most reactive but remained a lyase, making 10-fold more acrylates than other mutants did. While mutations within the active site changed the substrate specificity of OsTAM, continued exploration is needed to fully understand the interplay among the inner loop, the substrate, and the active site in defining the mutase and lyase activities.

Effect of urea and alkylureas on the stability and structural fluctuation of the M80-containing Ω-loop of horse cytochrome c.

PubMed

Kumar, Sandeep; Sharma, Deepak; Kumar, Rajesh

2014-03-01

The effect of denaturants on the structural fluctuation of M80-containing Ω-loop of ferrocytochrome c was determined by measuring the rate coefficient of CO-association with ferrocytochrome c under varying concentrations of urea and alkylureas (methylurea (MU), N,N'-dimethylurea (DMU), ethylurea (EU), tetramethylurea (TMU)) at pH7.0, 25°C. As denaturant concentration is increased within the subdenaturing limit, the CO-association reaction is decelerated indicating that subdenaturing concentrations of denaturant reduce the structural fluctuation of the Ω-loop. Structural fluctuation of the Ω-loop is reduced more for urea and least for TMU. Intermolecular docking between horse cytochrome c and denaturant molecule (urea, MU, DMU, EU and TMU) reveals that polyfunctional interactions between the denaturant and different groups of Ω-loop and other part of protein decrease with an increase of alkyl group on urea molecule, which suggests that the decrease in the extent of restricted dynamics of Ω-loop with a corresponding increase of alkyl groups on urea molecule is due to the decrease of denaturant-mediated cross-linking interactions. These denaturant-mediated interactions are expected to reduce the conformational entropy of protein. Analysis of rate-temperature data shows a progressive decrease in conformational entropy of protein in the native to subdenaturing region. Thermodynamic analysis of denaturant (urea, MU, DMU, EU, TMU) effects on the thermal unfolding of ferrocytochrome c reveals that (i) thermodynamic stability of protein decreases with increasing concentration of denaturant or hydrophobicity of urea derivatives, (ii) water activity plays an important role in stabilization of ferrocytochrome c, and (iii) destabilization of ferrocytochrome c by denaturant occurs through the disturbance of hydrophobic interactions and hydrogen-bonding. Copyright © 2014 Elsevier B.V. All rights reserved.

TRALI ASSOCIATED HNA-3a ANTIBODIES RECOGNIZE COMPLEX DETERMINANTS ON CHOLINE TRANSPORTER-LIKE PROTEIN 2 (CTL2)

PubMed Central

Bougie, Daniel W; Peterson, Julie A; Kanack, Adam J; Curtis, Brian R; Aster, Richard H

2014-01-01

Background HNA-3a specific antibodies can cause severe, sometimes fatal, transfusion related acute lung injury (TRALI) when present in transfused blood. The HNA3-a/b antigens are determined by an R154Q polymorphism in the first of five extracellular loops of the 10-membrane spanning choline transporter-like protein 2 (CTL2) expressed on neutrophils, lymphocytes and other tissues. About 50% of HNA-3a antibodies (Type 1) can be detected using CTL2 Loop 1 peptides containing R154; the remaining 50% (Type 2) fail to recognize this target. Understanding the basis for this difference could guide efforts to develop practical assays to screen blood donors for HNA-3 antibodies. Study design and methods Reactions of HNA-3a antibodies against recombinant versions of human, mouse, and human/mouse (chimeric) CTL2 were characterized using flow cytometry and various solid phase assays. Results Findings made show that, for binding to CTL2, Type 2 HNA-3a antibodies require non-polymorphic amino acid residues in the third, and possibly the second, extracellular loops of CTL2 to be in a configuration comparable to that found naturally in the cell membrane. In contrast, Type 1 antibodies require only peptides from the first extracellular loop that contain R154 for recognition. Conclusion Although Type 1 HNA-3a antibodies can readily be detected in solid phase assays that use a CTL2 peptide containing R154 as a target, development of a practical test to screen blood donors for Type 2 antibodies will pose a serious technical challenge because of the complex nature of the epitope(s) recognized by this antibody sub-group. PMID:24846273

Constitutive IDO expression in human cancer is sustained by an autocrine signaling loop involving IL-6, STAT3 and the AHR

PubMed Central

Sahm, Felix; Rauschenbach, Katharina J.; Trump, Saskia; Winter, Marcus; Ott, Martina; Ochs, Katharina; Lutz, Christian; Liu, Xiangdong; Anastasov, Natasa; Lehmann, Irina; Höfer, Thomas; von Deimling, Andreas; Wick, Wolfgang; Platten, Michael

2014-01-01

Indoleamine-2,3-dioxygenase (IDO) inhibitors have entered clinical trials based on their ability to restore anti-tumor immunity in preclinical studies. However, the mechanisms leading to constitutive expression of IDO in human tumors are largely unknown. Here we analyzed the pathways mediating constitutive IDO expression in human cancer. IDO-positive tumor cells and tissues showed basal phosphorylation and acetylation of STAT3 as evidenced by western blotting and immunoprecipitation. Inhibition of IL-6 or STAT3 using siRNA and/or pharmacological inhibitors reduced IDO mRNA and protein expression as well as kynurenine formation. In turn, IDO enzymatic activity activated the AHR as shown by the induction of AHR target genes. IDO-mediated AHR activation induced IL-6 expression, while inhibition or knockdown of the AHR reduced IL-6 expression. IDO activity thus sustains its own expression via an autocrine AHR–IL-6–STAT3 signaling loop. Inhibition of the AHR–IL-6–STAT3 signaling loop restored T-cell proliferation in mixed leukocyte reactions performed in the presence of IDO-expressing human cancer cells. Identification of the IDO-AHR-IL-6-STAT3 signaling loop maintaining IDO expression in human cancers reveals novel therapeutic targets for the inhibition of this core pathway promoting immunosuppression of human cancers. The relevance of the IDO-AHR-IL-6-STAT3 transcriptional circuit is underscored by the finding that high expression of its members IDO, STAT3 and the AHR target gene CYP1B1 is associated with reduced relapse-free survival in lung cancer patients. PMID:24657910

Neutron Tomography Using Mobile Neutron Generators for Assessment of Void Distributions in Thermal Hydraulic Test Loops

NASA Astrophysics Data System (ADS)

Andersson, P.; Bjelkenstedt, T.; Sundén, E. Andersson; Sjöstrand, H.; Jacobsson-Svärd, S.

Detailed knowledge of the lateral distribution of steam (void) and water in a nuclear fuel assembly is of great value for nuclear reactor operators and fuel manufacturers, with consequences for both reactor safety and economy of operation. Therefore, nuclear relevant two-phase flows are being studied at dedicated thermal-hydraulic test loop, using two-phase flow systems ranging from simplified geometries such as heated circular pipes to full scale mock-ups of nuclear fuel assemblies. Neutron tomography (NT) has been suggested for assessment of the lateral distribution of steam and water in such test loops, motivated by a good ability of neutrons to penetrate the metallic structures of metal pipes and nuclear fuel rod mock-ups, as compared to e.g. conventional X-rays, while the liquid water simultaneously gives comparatively good contrast. However, these stationary test loops require the measurement setup to be mobile, which is often not the case for NT setups. Here, it is acknowledged that fast neutrons of 14 MeV from mobile neutron generators constitute a viable option for a mobile NT system. We present details of the development of neutron tomography for this purpose at the division of Applied Nuclear Physics at Uppsala University. Our concept contains a portable neutron generator, exploiting the fusion reaction of deuterium and tritium, and a detector with plastic scintillator elements designed to achieveadequate spatial and energy resolution, all mounted in a light-weight frame without collimators or bulky moderation to allow for a mobile instrument that can be moved about the stationary thermal hydraulic test sections. The detector system stores event-to-event pulse-height information to allow for discrimination based on the energy deposition in the scintillator elements.

Fluoresceination of FepA during colicin B killing: effects of temperature, toxin and TonB.

PubMed

Smallwood, Chuck R; Marco, Amparo Gala; Xiao, Qiaobin; Trinh, Vy; Newton, Salete M C; Klebba, Phillip E

2009-06-01

We studied the reactivity of 35 genetically engineered Cys sulphydryl groups at different locations in Escherichia coli FepA. Modification of surface loop residues by fluorescein maleimide (FM) was strongly temperature-dependent in vivo, whereas reactivity at other sites was much less affected. Control reactions with bovine serum albumin showed that the temperature dependence of loop residue reactivity was unusually high, indicating that conformational changes in multiple loops (L2, L3, L4, L5, L7, L8, L10) transform the receptor to a more accessible form at 37 degrees C. At 0 degrees C colicin B binding impaired or blocked labelling at 8 of 10 surface loop sites, presumably by steric hindrance. Overall, colicin B adsorption decreased the reactivity of more than half of the 35 sites, in both the N- and C- domains of FepA. However, colicin B penetration into the cell at 37 degrees C did not augment the chemical modification of any residues in FepA. The FM modification patterns were similarly unaffected by the tonB locus. FepA was expressed at lower levels in a tonB host strain, but when we accounted for this decrease its FM labelling was comparable whether TonB was present or absent. Thus we did not detect TonB-dependent structural changes in FepA, either alone or when it interacted with colicin B at 37 degrees C. The only changes in chemical modification were reductions from steric hindrance when the bacteriocin bound to the receptor protein. The absence of increases in the reactivity of N-domain residues argues against the idea that the colicin B polypeptide traverses the FepA channel.

Fluoresceination of FepA during Colicin B Killing: Effects of Temperature, Toxin and TonB

PubMed Central

Smallwood, Chuck R.; Marco, Amparo Gala; Xiao, Qiaobin; Trinh, Vy; Newton, Salete M. C.; Klebba, Phillip E.

2009-01-01

We studied the reactivity of 35 genetically engineered Cys sulfhydryl groups at different locations in Escherichia coli FepA. Modification of surface loop residues by fluorescein maleimide (FM) was strongly temperature-dependent in vivo, whereas reactivity at other sites was much less affected. Control reactions with bovine serum albumin showed that the temperature dependence of loop residue reactivity was unusually high, indicating that conformational changes in multiple loops (L2, L3, L4, L5, L7, L8, L10) transform the receptor to a more accessible form at 37 °C. At 0 °C colicin B binding impaired or blocked labeling at 8 of 10 surface loop sites, presumably by steric hindrance. Overall, colicin B adsorption decreased the reactivity of more than half of the 35 sites, in both the N - and C- domains of FepA. However, colicin B penetration into the cell at 37 °C did not augment the chemical modification of any residues in FepA. The FM modification patterns were similarly unaffected by the tonB locus. FepA was expressed at lower levels in a tonB host strain, but when we accounted for this decrease its FM-labeling was comparable whether TonB was present or absent. Thus we did not detect TonB-dependent structural changes in FepA, either alone or when it interacted with colicin B at 37 °C. The only changes in chemical modification were reductions from steric hindrance when the bacteriocin bound to the receptor protein. The absence of increases in the reactivity of N-domain residues argues against the idea (Devanathan and Postle, Mol. Microbiol. 65: 441–453, 2007) that the colicin B polypeptide traverses the FepA channel. PMID:19432807

Real-time Detection and Monitoring of Loop Mediated Amplification (LAMP) Reaction Using Self-quenching and De-quenching Fluorogenic Probes.

PubMed

Gadkar, Vijay J; Goldfarb, David M; Gantt, Soren; Tilley, Peter A G

2018-04-03

Loop-mediated isothermal amplification (LAMP) is an isothermal nucleic acid amplification (iNAAT) technique known for its simplicity, sensitivity and speed. Its low-cost feature has resulted in its wide scale application, especially in low resource settings. The major disadvantage of LAMP is its heavy reliance on indirect detection methods like turbidity and non-specific dyes, which often leads to the detection of false positive results. In the present work, we have developed a direct detection approach, whereby a labelled loop probe quenched in its unbound state, fluoresces only when bound to its target (amplicon). Henceforth, referred to as Fluorescence of Loop Primer Upon Self Dequenching-LAMP (FLOS-LAMP), it allows for the sequence-specific detection of LAMP amplicons. The FLOS-LAMP concept was validated for rapid detection of the human pathogen, Varicella-zoster virus, from clinical samples. The FLOS-LAMP had a limit of detection of 500 copies of the target with a clinical sensitivity and specificity of 96.8% and 100%, respectively. The high level of specificity is a major advance and solves one of the main shortcomings of the LAMP technology, i.e. false positives. Self-quenching/de-quenching probes were further used with other LAMP primer sets and different fluorophores, thereby demonstrating its versatility and adaptability.

Electronic Maxwell demon in the coherent strong-coupling regime

NASA Astrophysics Data System (ADS)

Schaller, Gernot; Cerrillo, Javier; Engelhardt, Georg; Strasberg, Philipp

2018-05-01

We consider an external feedback control loop implementing the action of a Maxwell demon. Applying control actions that are conditioned on measurement outcomes, the demon may transport electrons against a bias voltage and thereby effectively converts information into electric power. While the underlying model—a feedback-controlled quantum dot that is coupled to two electronic leads—is well explored in the limit of small tunnel couplings, we can address the strong-coupling regime with a fermionic reaction-coordinate mapping. This exact mapping transforms the setup into a serial triple quantum dot coupled to two leads. We find that a continuous projective measurement of the central dot occupation would lead to a complete suppression of electronic transport due to the quantum Zeno effect. In contrast, by using a microscopic detector model we can implement a weak measurement, which allows for closure of the control loop without transport blockade. Then, in the weak-coupling regime, the energy flows associated with the feedback loop are negligible, and dominantly the information gained in the measurement induces a bound for the generated electric power. In the strong coupling limit, the protocol may require more energy for operating the control loop than electric power produced, such that the whole device is no longer information dominated and can thus not be interpreted as a Maxwell demon.

Biologically inspired design of feedback control systems implemented using DNA strand displacement reactions.

PubMed

Foo, Mathias; Sawlekar, Rucha; Kulkarni, Vishwesh V; Bates, Declan G

2016-08-01

The use of abstract chemical reaction networks (CRNs) as a modelling and design framework for the implementation of computing and control circuits using enzyme-free, entropy driven DNA strand displacement (DSD) reactions is starting to garner widespread attention in the area of synthetic biology. Previous work in this area has demonstrated the theoretical plausibility of using this approach to design biomolecular feedback control systems based on classical proportional-integral (PI) controllers, which may be constructed from CRNs implementing gain, summation and integrator operators. Here, we propose an alternative design approach that utilises the abstract chemical reactions involved in cellular signalling cycles to implement a biomolecular controller - termed a signalling-cycle (SC) controller. We compare the performance of the PI and SC controllers in closed-loop with a nonlinear second-order chemical process. Our results show that the SC controller outperforms the PI controller in terms of both performance and robustness, and also requires fewer abstract chemical reactions to implement, highlighting its potential usefulness in the construction of biomolecular control circuits.

Surveillance for Western Equine Encephalitis, St. Louis Encephalitis, and West Nile Viruses Using Reverse Transcription Loop-Mediated Isothermal Amplification

PubMed Central

Wheeler, Sarah S.; Ball, Cameron S.; Langevin, Stanley A.; Fang, Ying; Coffey, Lark L.; Meagher, Robert J.

2016-01-01

Collection of mosquitoes and testing for vector-borne viruses is a key surveillance activity that directly influences the vector control efforts of public health agencies, including determining when and where to apply insecticides. Vector control districts in California routinely monitor for three human pathogenic viruses including West Nile virus (WNV), Western equine encephalitis virus (WEEV), and St. Louis encephalitis virus (SLEV). Reverse transcription quantitative polymerase chain reaction (RT-qPCR) offers highly sensitive and specific detection of these three viruses in a single multiplex reaction, but this technique requires costly, specialized equipment that is generally only available in centralized public health laboratories. We report the use of reverse transcription loop-mediated isothermal amplification (RT-LAMP) to detect WNV, WEEV, and SLEV RNA extracted from pooled mosquito samples collected in California, including novel primer sets for specific detection of WEEV and SLEV, targeting the nonstructural protein 4 (nsP4) gene of WEEV and the 3’ untranslated region (3’-UTR) of SLEV. Our WEEV and SLEV RT-LAMP primers allowed detection of <0.1 PFU/reaction of their respective targets in <30 minutes, and exhibited high specificity without cross reactivity when tested against a panel of alphaviruses and flaviviruses. Furthermore, the SLEV primers do not cross-react with WNV, despite both viruses being closely related members of the Japanese encephalitis virus complex. The SLEV and WEEV primers can also be combined in a single RT-LAMP reaction, with discrimination between amplicons by melt curve analysis. Although RT-qPCR is approximately one order of magnitude more sensitive than RT-LAMP for all three targets, the RT-LAMP technique is less instrumentally intensive than RT-qPCR and provides a more cost-effective method of vector-borne virus surveillance. PMID:26807734

New closed tube loop mediated isothermal amplification assay for prevention of product cross-contamination

PubMed Central

Karthik, K.; Rathore, Rajesh; Thomas, Prasad; Arun, T.R.; Viswas, K.N.; Dhama, Kuldeep; Agarwal, R.K.

2014-01-01

Loop mediated isothermal amplification (LAMP) assay, a promising diagnostic test, has been developed for detection of different pathogens of human as well as animals. Various positive points support its use as a field level test but the major problem is product cross contamination leading to false positive results. Different methods were adopted by various researchers to control this false positive amplification due to cross contamination but all have their own advantages and disadvantages. A new closed tube LAMP assay based on agar dye capsule was developed in the present study and this technique has some advantages over the other closed tube technique.•Agar at the concentration of 1.5% was used to sandwich SYBR green dye I with the aid of intradermal syringe. This agar dye capsule was placed over the LAMP reaction mixture before it was amplified.•To eliminate the hazardous nature of Ultra Violet (UV) light during result visualization of LAMP products, the present study demonstrates the use of Light Emitting Diode (LED) lights for result visualization.•LAMP was carried out for Brucella species detection using this modified techniques yielding good results without any cross contamination and LED showed similar fluorescence compared to UV. PMID:26150945

New closed tube loop mediated isothermal amplification assay for prevention of product cross-contamination.

PubMed

Karthik, K; Rathore, Rajesh; Thomas, Prasad; Arun, T R; Viswas, K N; Dhama, Kuldeep; Agarwal, R K

2014-01-01

Loop mediated isothermal amplification (LAMP) assay, a promising diagnostic test, has been developed for detection of different pathogens of human as well as animals. Various positive points support its use as a field level test but the major problem is product cross contamination leading to false positive results. Different methods were adopted by various researchers to control this false positive amplification due to cross contamination but all have their own advantages and disadvantages. A new closed tube LAMP assay based on agar dye capsule was developed in the present study and this technique has some advantages over the other closed tube technique.•Agar at the concentration of 1.5% was used to sandwich SYBR green dye I with the aid of intradermal syringe. This agar dye capsule was placed over the LAMP reaction mixture before it was amplified.•To eliminate the hazardous nature of Ultra Violet (UV) light during result visualization of LAMP products, the present study demonstrates the use of Light Emitting Diode (LED) lights for result visualization.•LAMP was carried out for Brucella species detection using this modified techniques yielding good results without any cross contamination and LED showed similar fluorescence compared to UV.

The OGO attitude control subsystem redesign as a result of OGO 3 experience. Volume 1: System analysis and design studies

NASA Technical Reports Server (NTRS)

Mckenna, K. J.

1967-01-01

An oscillation in the OGO-3 roll control channel, resulting from the EP-5 and EP-6 boom motion coupling into the control channel and causing loss of attitude control, is investigated. The study includes (1) an analysis of the OGO-3 and OGO-2 flight data to determine the nature and extent of the roll oscillation phenomena, (2) design analysis of the complete attitude control subsystem (ACS) to evolve changes which would prevent recurrences of the coupled ACS boom oscillation observed on OGO-3, and (3) analog simulations to verify the performance of the design changes selected. Portions of OGO-3 and OGO-2 flight data are illustrated and the major flexible body oscillation are identified. A model of the major flexible appendage dynamics is developed and is shown analytically and through analog simulations to reproduce the OGO-3 oscillation phenomena. The design changes which were found necessary are: a reversal delay logic for the roll reaction wheels, widening of the solar array dead zone from 0.5 to 1.0 deg, and modification of the OPEP control loop to include a filter and stabilizing feedback loops.

Fabrication and processing of next-generation oxygen carrier materials for chemical looping combustion

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

Nadarajah, Arunan

Among numerous methods of controlling the global warming effect, Chemical Looping Combustion is known to be the most viable option currently. A key factor to a successful chemical looping process is the presence of highly effective oxygen carriers that enable fuel combustion by going through oxidation and reduction in the presence of air and fuel respectively. In this study, CaMnO 3-δ was used as the base material and doped on the A-site (Sr or La) and B-site (Fe, Ti, Zn and Al) by 10 mol % of dopants. Solid state reaction followed by mechanical extrusion (optimized paste formula) was usedmore » as the preparation method A series of novel doped perovskite-type oxygen carrier particles (Ca xLa (Or Sa) 1-x Mn 1-yByO 3-δ (B-site = Fe, Ti, Al, or Zr)) were synthesized by the proposed extrusion formula. The produced samples were characterized with XRD, SEM, BET and TGA techniques. According to the results obtained from TGA analysis, the oxygen capacity of the samples ranged between 1.2 for CLMZ and 1.75 for CSMF. Reactivity and oxygen uncoupling behaviors of the prepared samples were also evaluated using a fluidized bed chemical looping reactor using methane as the fuel at four different temperatures (800, 850, 900, 950 °C). All of the oxygen carriers showed oxygen uncoupling behavior and they were able to capture and release oxygen. Mass-based conversion of the perovskites was calculated and temperature increase proved to increase the mass-based conversion rate in all of the samples under study. Gas yield was calculated at 950 °C as well, and results showed that CLMZ, CM and CSMF showed 100% gas yields and CLMF and CSMZ showed approximately 85% yield in fluidized bed reactor, which is a high and acceptable quantity. Based on extended reactor tests the modified calcium manganese perovskite structures (CSMF) can be a good candidate for future pilot tests.« less

Absorption of carbon dioxide by solid hydroxide sorbent beds in closed-loop atmospheric revitalization system

NASA Technical Reports Server (NTRS)

Davis, S. H., Jr.; Kissinger, L. D.

1982-01-01

The reactions of carbon dioxide with various metals are discussed. The equations which govern the rates of CO2 removal from the atmosphere in spacecraft environmental control systems are discussed. Results from performance testing of various Space Shuttle environmental control systems are presented with the correlation of the equations to the performance given.

Joystick With Cable Springs Offers Better Feel

NASA Technical Reports Server (NTRS)

Kerley, James; Ecklund, Wayne

1992-01-01

Improved joystick allows motion in 6 degrees of freedom, biased toward central position and orientation by 16 segments of cable serving as springs. Improvement in feel and control results from nonlinear compliance of cable-spring assembly. Nonlinear variations accommodate natural reactions of hand and brain. Operator functions as part of feedback control loop. More comfortable, increases ability to exert control and reduces fatigue.

Initiator-catalyzed self-assembly of duplex-looped DNA hairpin motif based on strand displacement reaction for logic operations and amplified biosensing.

PubMed

Bi, Sai; Yue, Shuzhen; Wu, Qiang; Ye, Jiayan

2016-09-15

Here we program an initiator-catalyzed self-assembly of duplex-looped DNA hairpin motif based on strand displacement reaction. Due to the recycling of initiator and performance in a cascade manner, this system is versatilely extended to logic operations, including the construction of concatenated logic circuits with a feedback function and a biocomputing keypad-lock security system. Compared with previously reported molecular security systems, the prominent feature of our keypad lock is that it can be spontaneously reset and recycled with no need of any external stimulus and human intervention. Moreover, through integrating with an isothermal amplification technique of rolling circle amplification (RCA), this programming catalytic DNA self-assembly strategy readily achieves sensitive and selective biosensing of initiator. Importantly, a magnetic graphene oxide (MGO) is introduced to remarkably reduced background, which plays an important role in enhancing the signal-to-noise ratio and improving the detection sensitivity. Therefore, the proposed sophisticated DNA strand displacement-based methodology with engineering dynamic functions may find broad applications in the construction of programming DNA nanostructures, amplification biosensing platform, and large-scale DNA circuits. Copyright © 2016 Elsevier B.V. All rights reserved.

Detection of Brucellosis in Sika Deer ( Cervus nippon ) through Loop-mediated Isothermal Amplification (LAMP).

PubMed

Liu, Qianhong; Wei, Jie; Sun, Qingsong; Wang, Ben; Wang, Yuting; Hu, Ying; Wu, Wenrong

2017-07-01

Brucellosis (Brucella bovis) in sika deer ( Cervus nippon ) can cause enormous losses to stag breeding, especially in areas in which stag breeding has become an important industry. It also poses a threat to humans because it is a zoonotic disease. Use of the loop-mediated isothermal amplification (LAMP) assay has been poorly described in the diagnosis of brucellosis in deer. We developed a LAMP assay targeting the omp25 gene sequence to detect brucellosis in sika deer. The reaction can be completed in 60 min at 63 C and, with a detection limit of 17 pg, it was more sensitive than conventional PCR, with its detection limit of 1.7 ng. No cross-reactivity was observed with four bacteria: Escherichia coli , Salmonella enterica subsp. enterica, Clostridium pasteurianum , and Pseudomonas aeruginosa . We used 263 samples of blood to evaluate the reaction. The percentage of agreement between LAMP and PCR reached 91%; relative specificity reached 87%, and relative sensitivity reached 100%. The results indicate LAMP can be a simple and rapid diagnostic tool for detecting brucellosis in sika deer, particularly in the field, where it is essential to control brucellosis in deer with a rapid and accurate diagnosis for removal of positive animals.

Loop-mediated isothermal amplification (LAMP) assay for the rapid detection of the sexually-transmitted parasite, Trichomonas vaginalis.

PubMed

Adao, Davin Edric V; Rivera, Windell L

2016-01-01

A loop-mediated isothermal amplification (LAMP) assay was developed to detect the sexually-transmitted parasite, Trichomonas vaginalis in vaginal swabs. The presence of T. vaginalis was detected from 121 female sex workers attending a social hygiene clinic in Balibago, Angeles City, Pampanga, Philippines using culture, polymerase chain reaction (PCR), and the developed LAMP assay. The high analytical sensitivity of LAMP detected a higher prevalence of T. vaginalis (42.06%) compared to culture (8.26%) and PCR (7.44%). Additionally, this assay did not cross-react with DNAs of other trichomonads that can infect humans such as Trichomonas tenax and Pentatrichomonas hominis as well as the pathogens, Candida albicans and Staphylococcus aureus. The LAMP assay developed had a limit of detection (0.036 ng/μl) lower than that of PCR using the primers TvK3 and TvK7 (0.36 ng/μl). Prevalence of T. vaginalis in female sex workers in this area of the Philippines may be higher than previously estimated. Discordant results of PCR and LAMP may be due to different reactions to different kinds of inhibitors in the vaginal swabs.

Activation and reactivation of the RNA polymerase II trigger loop for intrinsic RNA cleavage and catalysis

PubMed Central

Čabart, Pavel; Jin, Huiyan; Li, Liangtao; Kaplan, Craig D

2014-01-01

In addition to RNA synthesis, multisubunit RNA polymerases (msRNAPs) support enzymatic reactions such as intrinsic transcript cleavage. msRNAP active sites from different species appear to exhibit differential intrinsic transcript cleavage efficiency and have likely evolved to allow fine-tuning of the transcription process. Here we show that a single amino-acid substitution in the trigger loop (TL) of Saccharomyces RNAP II, Rpb1 H1085Y, engenders a gain of intrinsic cleavage activity where the substituted tyrosine appears to participate in acid-base chemistry at alkaline pH for both intrinsic cleavage and nucleotidyl transfer. We extensively characterize this TL substitution for each of these reactions by examining the responses RNAP II enzymes to catalytic metals, altered pH, and factor inputs. We demonstrate that TFIIF stimulation of the first phosphodiester bond formation by RNAP II requires wild type TL function and that H1085Y substitution within the TL compromises or alters RNAP II responsiveness to both TFIIB and TFIIF. Finally, Mn2+ stimulation of H1085Y RNAP II reveals possible allosteric effects of TFIIB on the active center and cooperation between TFIIB and TFIIF. PMID:25764335

Development and evaluation of probe based real time loop mediated isothermal amplification for Salmonella: A new tool for DNA quantification.

PubMed

Mashooq, Mohmad; Kumar, Deepak; Niranjan, Ankush Kiran; Agarwal, Rajesh Kumar; Rathore, Rajesh

2016-07-01

A one step, single tube, accelerated probe based real time loop mediated isothermal amplification (RT LAMP) assay was developed for detecting the invasion gene (InvA) of Salmonella. The probe based RT LAMP is a novel method of gene amplification that amplifies nucleic acid with high specificity and rapidity under isothermal conditions with a set of six primers. The whole procedure is very simple and rapid, and amplification can be obtained in 20min. Detection of gene amplification was accomplished by amplification curve, turbidity and addition of DNA binding dye at the end of the reaction results in colour difference and can be visualized under normal day light and in UV. The sensitivity of developed assay was found 10 fold higher than taqman based qPCR. The specificity of the RT LAMP assay was validated by the absence of any cross reaction with other members of enterobacteriaceae family and other gram negative bacteria. These results indicate that the probe based RT LAMP assay is extremely rapid, cost effective, highly specific and sensitivity and has potential usefulness for rapid Salmonella surveillance. Crown Copyright © 2016. Published by Elsevier B.V. All rights reserved.

Development and application of loop-mediated isothermal amplification for detection of the F167Y mutation of carbendazim-resistant isolates in Fusarium graminearum

PubMed Central

Duan, Yabing; Zhang, Xiaoke; Ge, Changyan; Wang, Yong; Cao, Junhong; Jia, Xiaojing; Wang, Jianxin; Zhou, Mingguo

2014-01-01

Resistance of Fusarium graminearum to carbendazim is caused by point mutations in the β2-tubulin gene. The point mutation at codon 167 (TTT → TAT, F167Y) occurs in more than 90% of field resistant isolates in China. To establish a suitable method for rapid detection of the F167Y mutation in F. graminearum, an efficient and simple method with high specificity was developed based on loop-mediated isothermal amplification (LAMP). A set of four primers was designed and optimized to specially distinguish the F167Y mutation genotype. The LAMP reaction was optimal at 63°C for 60 min. When hydroxynaphthol blue dye (HNB) was added prior to amplification, samples with DNA of the F167Y mutation developed a characteristic sky blue color after the reaction but those without DNA or with different DNA did not. Results of HNB staining method were reconfirmed by gel electrophoresis. The developed LAMP had good specificity, stability and repeatability and was suitable for monitoring carbendazim-resistance populations of F. graminearum in agricultural production. PMID:25403277

Chemical reaction fouling model for single-phase heat transfer

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

Panchal, C.B.; Watkinson, A.P.

1993-08-01

A fouling model was developed on the premise that the chemical reaction for generation of precursor can take place in the bulk fluid, in the thermalboundary layer, or at the fluid/wall interface, depending upon the interactive effects of flu id dynamics, heat and mass transfer, and the controlling chemical reaction. The analysis was used to examine the experimental data for fouling deposition of polyperoxides produced by autoxidation of indene in kerosene. The effects of fluid and wall temperatures for two flow geometries were analyzed. The results showed that the relative effects of physical parameters on the fouling rate would differmore » for the three fouling mechanisms; therefore, it is important to identify the controlling mechanism in applying the closed-flow-loop data to industrial conditions.« less

Reaction Mechanism of Isopentenyl Phosphate Kinase: A QM/MM Study.

PubMed

McClory, James; Timson, David J; Singh, Warispreet; Zhang, Jian; Huang, Meilan

2017-12-14

Isopentenyl phosphate kinase (IPK) catalyzes the Mg 2+ -ATP dependent phosphorylation reactions to produce isopentenyl diphosphate, an important precursor in the synthesis of isopentenols. However, the position of the divalent metal ion in the crystal structures of IPK in complex with ATP and its native substrate IP has not been definitively resolved, and as a result ambiguity surrounds the catalytic mechanism of IP, limiting its exploitation as a biofuel and in drug design. Here we report the catalytically competent structure in complex with the metal ion Mg 2+ and elucidate the phosphorylation reaction mechanism using molecular dynamic simulations and density functional theory-based quantum mechanics/molecular mechanics calculations (B97d/AMBER99). Comparing the substrate-bound and substrate-free IPK complexes, we observed that substrate binding results in significant conformational change of three residues Lys204, Glu207, and Lys211 located on the αG helix to form a strong salt bridge network with Asp145, which in turn tethers the invariant Ser142 via H-bond interaction. The conformational change shuts the subtrate entrance channel formed between the αG and αE helices. Further, we demonstrate the phosphorylation reaction occurs with a reaction barrier of 17.58 kcal/mol, which is in agreement with the previous experimental kinetic data. We found that a highly conserved Gly8 on a glycine-rich loop, together with Lys14, stabilizes the transition state.

Chemical looping coal gasification with calcium ferrite and barium ferrite via solid--solid reactions

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

Siriwardane, Ranjani; Riley, Jarrett; Tian, Hanjing

Coal gasification to produce synthesis gas by chemical looping was investigated with two oxygen carriers, barium ferrite (BaFe2O4) and calcium ferrite (CaFe2O4). Thermo-gravimetric analysis (TGA) and fixed-bed flow reactor data indicated that a solid–solid interaction occurred between oxygen carriers and coal to produce synthesis gas. Both thermodynamic analysis and experimental data indicated that BaFe2O4 and CaFe2O4 have high reactivity with coal but have a low reactivity with synthesis gas, which makes them very attractive for the coal gasification process. Adding steam increased the production of hydrogen (H2) and carbon monoxide (CO), but carbon dioxide (CO2) remained low because these oxygenmore » carriers have minimal reactivity with H2 and CO. Therefore, the combined steam–oxygen carrier produced the highest quantity of synthesis gas. It appeared that neither the water–gas shift reaction nor the water splitting reaction promoted additional H2 formation with the oxygen carriers when steam was present. Wyodak coal, which is a sub-bituminous coal, had the best gasification yield with oxygen carrier–steam while Illinois #6 coal had the lowest. The rate of gasification and selectivity for synthesis gas production was significantly higher when these oxygen carriers were present during steam gasification of coal. The rates and synthesis gas yields during the temperature ramps of coal–steam with oxygen carriers were better than with gaseous oxygen.« less

Evaluation of a rapid detection for Coxsackievirus B3 using one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP).

PubMed

Monazah, A; Zeinoddini, M; Saeeidinia, A R

2017-08-01

Coxsackievirus B3 (CVB3) is a member of the genus Enterovirus within the family Picornaviridae and is an important pathogen of viral myocarditis, which accounts for more than 50% viral myocarditis cases. VP1 is major capsid protein that this region has a low homology in both amino acid and nucleotide sequences among Enteroviruses. Therefore we have chosen this region for designed a set of RT-LAMP primers for CVB3 detection. For this the total RNA was extracted from 24-h post infected-HeLa cells with complete cytopathic effect (CPE), and applied to a one-step reverse transcription loop-mediated isothermal amplification reaction (RT-LAMP) using CVB3-specific primers. The optimization of RT-LAMP reaction was carried out with three variables factors including MgSO 4 concentration, temperature and time of incubation. Amplification was analyzed by using 2% agarose gel electrophoresis and ethidium bromide and SYBR Green staining. Our results were shown the ladder-like pattern of the VP1 gene amplification. The LAMP reaction mix was optimized and the best result observed at 4mM MgSO 4 and 60°C for 90min incubation. RT-LAMP had high sensitivity and specificity for detection of CVB3 infection. This method can be used as a rapid and easy diagnostic test for detection of CVB3 in clinical laboratories. Copyright © 2017 Elsevier B.V. All rights reserved.

Detection of periodontal pathogen Porphyromonas gingivalis by loop-mediated isothermal amplification method.

PubMed

Maeda, Hiroshi; Kokeguchi, Susumu; Fujimoto, Chiyo; Tanimoto, Ichiro; Yoshizumi, Wakako; Nishimura, Fusanori; Takashiba, Shogo

2005-02-01

A method for nucleic acid amplification, loop-mediated isothermal amplification (LAMP) was employed to develop a rapid and simple detection system for periodontal pathogen, Porphyromonas gingivalis. A set of six primers was designed by targeting the 16S ribosomal RNA gene. By the detection system, target DNA was amplified and visualized on agarose gel within 30 min under isothermal condition at 64 degrees C with a detection limit of 20 cells of P. gingivalis. Without gel electrophoresis, the LAMP amplicon was directly visualized in the reaction tube by addition of SYBR Green I for a naked-eye inspection. The LAMP reaction was also assessed by white turbidity of magnesium pyrophosphate (a by-product of LAMP) in the tube. Detection limits of these naked-eye inspections were 20 cells and 200 cells, respectively. Although false-positive DNA amplification was observed from more than 10(7) cells of Porphyromonas endodontalis, no amplification was observed in other five related oral pathogens. Further, quantitative detection of P. gingivalis was accomplished by a real-time monitoring of the LAMP reaction using SYBR Green I with linearity over a range of 10(2)-10(6) cells. The real-time LAMP was then applied to clinical samples of dental plaque and demonstrated almost identical results to the conventional real-time PCR with an advantage of rapidity. These findings indicate the potential usefulness of LAMP for detecting and quantifying P. gingivalis, especially in its rapidity and simplicity.

Quenching of Unincorporated Amplification Signal Reporters in Reverse-Transcription Loop-Mediated Isothermal Amplification Enabling Bright, Single-Step, Closed-Tube, and Multiplexed Detection of RNA Viruses.

PubMed

Ball, Cameron S; Light, Yooli K; Koh, Chung-Yan; Wheeler, Sarah S; Coffey, Lark L; Meagher, Robert J

2016-04-05

Reverse-transcription-loop-mediated isothermal amplification (RT-LAMP) has frequently been proposed as an enabling technology for simplified diagnostic tests for RNA viruses. However, common detection techniques used for LAMP and RT-LAMP have drawbacks, including poor discrimination capability, inability to multiplex targets, high rates of false positives, and (in some cases) the requirement of opening reaction tubes postamplification. Here, we present a simple technique that allows closed-tube, target-specific detection, based on inclusion of a dye-labeled primer that is incorporated into a target-specific amplicon if the target is present. A short, complementary quencher hybridizes to unincorporated primer upon cooling down at the end of the reaction, thereby quenching fluorescence of any unincorporated primer. Our technique, which we term QUASR (for quenching of unincorporated amplification signal reporters, read "quasar"), does not significantly reduce the amplification efficiency or sensitivity of RT-LAMP. Equipped with a simple LED excitation source and a colored plastic gel filter, the naked eye or a camera can easily discriminate between positive and negative QUASR reactions, which produce a difference in signal of approximately 10:1 without background subtraction. We demonstrate that QUASR detection is compatible with complex sample matrices such as human blood, using a novel LAMP primer set for bacteriophage MS2 (a model RNA virus particle). Furthermore, we demonstrate single-tube duplex detection of West Nile virus (WNV) and chikungunya virus (CHIKV) RNA.

Evaluation of Loop-Mediated Isothermal Amplification Suitable for Molecular Monitoring of Schistosome-Infected Snails in Field Laboratories

PubMed Central

Hamburger, Joseph; Abbasi, Ibrahim; Kariuki, Curtis; Wanjala, Atsabina; Mzungu, Elton; Mungai, Peter; Muchiri, Eric; King, Charles H.

2013-01-01

We previously described loop-mediated isothermal amplification (LAMP) for detection of Schistosoma haematobium and S. mansoni DNA in infected snails. In the present study, we adapted the LAMP assay for application in field laboratories in schistosomiasis-endemic areas. Isolation of DNA was simplified by blotting snail tissue (extracted in NaOH/sodium dodecyl sulfate) onto treated membranes, which enabled preservation at ambient temperatures. A ready-mix of LAMP reagents, suitable for shipment at ambient temperature and storage in minimal refrigeration, was used. Local survey teams without experience in molecular biology acquired operational expertise with this test within a few hours. Fifty-four field-caught snails were tested locally by LAMP and 59 were tested at similar conditions in Jerusalem. The LAMP results were consistent with those of a polymerase chain reaction; only four samples showed false-negative results. Results indicate that LAMP assays are suitable for detection of S. haematobium and S. mansoni in low-technology parasitology laboratories in which schistosomiasis elimination activities are undertaken. PMID:23208875

Exploring the evolution of protein function in Archaea.

PubMed

Goncearenco, Alexander; Berezovsky, Igor N

2012-05-30

Despite recent progress in studies of the evolution of protein function, the questions what were the first functional protein domains and what were their basic building blocks remain unresolved. Previously, we introduced the concept of elementary functional loops (EFLs), which are the functional units of enzymes that provide elementary reactions in biochemical transformations. They are presumably descendants of primordial catalytic peptides. We analyzed distant evolutionary connections between protein functions in Archaea based on the EFLs comprising them. We show examples of the involvement of EFLs in new functional domains, as well as reutilization of EFLs and functional domains in building multidomain structures and protein complexes. Our analysis of the archaeal superkingdom yields the dominating mechanisms in different periods of protein evolution, which resulted in several levels of the organization of biochemical function. First, functional domains emerged as combinations of prebiotic peptides with the very basic functions, such as nucleotide/phosphate and metal cofactor binding. Second, domain recombination brought to the evolutionary scene the multidomain proteins and complexes. Later, reutilization and de novo design of functional domains and elementary functional loops complemented evolution of protein function.

Rapid and reliable diagnostic method to detect Zika virus by real-time fluorescence reverse transcription loop-mediated isothermal amplification.

PubMed

Guo, Xu-Guang; Zhou, Yong-Zhuo; Li, Qin; Wang, Wei; Wen, Jin-Zhou; Zheng, Lei; Wang, Qian

2018-04-18

To detect Zika virus more rapidly and accurately, we developed a novel method that utilized a real-time fluorescence reverse transcription loop-mediated isothermal amplification (LAMP) technique. The NS5 gene was amplified by a set of six specific primers that recognized six distinct sequences. The amplification process, including 60 min of thermostatic reaction with Bst DNA polymerase following real-time fluorescence reverse transcriptase using genomic Zika virus standard strain (MR766), was conducted through fluorescent signaling. Among the six pairs of primers that we designate here, NS5 was the most efficient with a high sensitivity of up to 3.3 ng/μl and reproducible specificity on eight pathogen samples that were used as negative controls. The real-time fluorescence reverse transcription LAMP detection process can be completed within 35 min. Our study demonstrated that real-time fluorescence reverse transcription LAMP could be highly beneficial and convenient clinical application to detect Zika virus due to its high specificity and stability.

Detection of Shigella in Milk and Clinical Samples by Magnetic Immunocaptured-Loop-Mediated Isothermal Amplification Assay

PubMed Central

Zhang, Liding; Wei, Qiujiang; Han, Qinqin; Chen, Qiang; Tai, Wenlin; Zhang, Jinyang; Song, Yuzhu; Xia, Xueshan

2018-01-01

Shigella is an important human food-borne zoonosis bacterial pathogen, and can cause clinically severe diarrhea. There is an urgent need to develop a specific, sensitive, and rapid methodology for detection of this pathogen. In this study, loop-mediated isothermal amplification (LAMP) combined with magnetic immunocapture assay (IC-LAMP) was first developed for the detection of Shigella in pure culture, artificial milk, and clinical stool samples. This method exhibited a detection limit of 8.7 CFU/mL. Compared with polymerase chain reaction, IC-LAMP is sensitive, specific, and reliable for monitoring Shigella. Additionally, IC-LAMP is more convenient, efficient, and rapid than ordinary LAMP, as it is more efficiently enriches pathogen cells without extraction of genomic DNA. Under isothermal conditions, the amplification curves and the green fluorescence were detected within 30 min in the presence of genomic DNA template. The overall analysis time was approximately 1 h, including the enrichment and lysis of the bacterial cells, a significantly short detection time. Therefore, the IC-LAMP methodology described here is potentially useful for the efficient detection of Shigella in various samples. PMID:29467730

Study on structural, dielectric, ferroelectric and piezoelectric properties of Ba doped Lead Zirconate Titanate Ceramics

NASA Astrophysics Data System (ADS)

Dipti; Juneja, J. K.; Singh, Sangeeta; Raina, K. K.; Prakash, Chandra

2013-12-01

The perovskite Pb(1-x)BaxZr0.55Ti0.45O3 material (x=0.00, 0.01, 0.02, 0.03, 0.05, and 0.07) was synthesized by solid state reaction route. Green bodies were sintered at 1250 °C. All samples were subjected to X-ray diffraction analysis and they were found to be in single phase. Dielectric properties were studied as a function of temperature and frequency. Ferroelectric properties were studied as a function of temperature. Remnant polarization, saturation polarization and coercive field were determined for all the samples using ferroelectric loops. Piezoelectric properties such as d33 and electromechanical coupling factor (kp) were also measured at room temperature for all samples.

A simple model of hysteresis behavior using spreadsheet analysis

NASA Astrophysics Data System (ADS)

Ehrmann, A.; Blachowicz, T.

2015-01-01

Hysteresis loops occur in many scientific and technical problems, especially as field dependent magnetization of ferromagnetic materials, but also as stress-strain-curves of materials measured by tensile tests including thermal effects, liquid-solid phase transitions, in cell biology or economics. While several mathematical models exist which aim to calculate hysteresis energies and other parameters, here we offer a simple model for a general hysteretic system, showing different hysteresis loops depending on the defined parameters. The calculation which is based on basic spreadsheet analysis plus an easy macro code can be used by students to understand how these systems work and how the parameters influence the reactions of the system on an external field. Importantly, in the step-by-step mode, each change of the system state, compared to the last step, becomes visible. The simple program can be developed further by several changes and additions, enabling the building of a tool which is capable of answering real physical questions in the broad field of magnetism as well as in other scientific areas, in which similar hysteresis loops occur.

Development of loop-mediated isothermal amplification (LAMP) assays for the rapid detection of allergic peanut in processed food.

PubMed

Sheu, Shyang-Chwen; Tsou, Po-Chuan; Lien, Yi-Yang; Lee, Meng-Shiou

2018-08-15

Peanut is a widely and common used in many cuisines around the world. However, peanut is also one of the most important food allergen for causing anaphylactic reaction. To prevent allergic reaction, the best way is to avoid the food allergen or food containing allergic ingredient such as peanut before food consuming. Thus, to efficient and precisely detect the allergic ingredient, peanut or related product, is essential and required for maintain consumer's health or their interest. In this study, a loop-mediated isothermal amplification (LAMP) assay was developed for the detection of allergic peanut using specifically designed primer sets. Two sets of the specific LAMP primers respectively targeted the internal transcribed sequence 1 (ITS1) of nuclear ribosomal DNA sequence regions and the ara h1 gene sequence of Arachia hypogeae (peanut) were used to address the application of LAMP for detecting peanut in processed food or diet. The results demonstrated that the identification of peanut using the newly designed primers for ITS 1 sequence is more sensitive rather than primers for sequence of Ara h1 gene when performing LAMP assay. Besides, the sensitivity of LAMP for detecting peanut is also higher than the traditional PCR method. These LAMP primers sets showed high specificity for the identification of the peanut and had no cross-reaction to other species of nut including walnut, hazelnut, almonds, cashew and macadamia nut. Moreover, when minimal 0.1% peanuts were mixed with other nuts ingredients at different ratios, no any cross-reactivity was evident during performing LAMP. Finally, genomic DNAs extracted from boiled and steamed peanut were used as templates; the detection of peanut by LAMP was not affected and reproducible. As to this established LAMP herein, not only can peanut ingredients be detected but commercial foods containing peanut can also be identified. This assay will be useful and potential for the rapid detection of peanut in practical food markets. Copyright © 2018 Elsevier Ltd. All rights reserved.

A Simple and Rapid Identification Method for Mycobacterium bovis BCG with Loop-Mediated Isothermal Amplification.

PubMed

Kouzaki, Yuji; Maeda, Takuya; Sasaki, Hiroaki; Tamura, Shinsuke; Hamamoto, Takaaki; Yuki, Atsushi; Sato, Akinori; Miyahira, Yasushi; Kawana, Akihiko

2015-01-01

Bacillus Calmette-Guérin (BCG) is widely used as a live attenuated vaccine against Mycobacterium tuberculosis and is an agent for standard prophylaxis against the recurrence of bladder cancer. Unfortunately, it can cause severe infectious diseases, especially in immunocompromised patients, and the ability to immediately distinguish BCG from other M. tuberculosis complexes is therefore important. In this study, we developed a simple and easy-to-perform identification procedure using loop-mediated amplification (LAMP) to detect deletions within the region of difference, which is deleted specifically in all M. bovis BCG strains. Reactions were performed at 64 °C for 30 min and successful targeted gene amplifications were detected by real-time turbidity using a turbidimeter and visual inspection of color change. The assay had an equivalent detection limit of 1.0 pg of genomic DNA using a turbidimeter whereas it was 10 pg with visual inspection, and it showed specificity against 49 strains of 44 pathogens, including M. tuberculosis complex. The expected LAMP products were confirmed through identical melting curves in real-time LAMP procedures. We employed the Procedure for Ultra Rapid Extraction (PURE) kit to isolate mycobacterial DNA and found that the highest sensitivity limit with a minimum total cell count of mycobacterium (including DNA purification with PURE) was up to 1 × 10(3) cells/reaction, based on color changes under natural light with FDA reagents. The detection limit of this procedure when applied to artificial serum, urine, cerebrospinal fluid, and bronchoalveolar lavage fluid samples was also about 1 × 10(3) cells/reaction. Therefore, this substitute method using conventional culture or clinical specimens followed by LAMP combined with PURE could be a powerful tool to enable the rapid identification of M. bovis BCG as point-of-care testing. It is suitable for practical use not only in resource-limited situations, but also in any clinical situation involving immunocompromised patients because of its convenience, rapidity, and cost effectiveness.

A Simple and Rapid Identification Method for Mycobacterium bovis BCG with Loop-Mediated Isothermal Amplification

PubMed Central

Kouzaki, Yuji; Maeda, Takuya; Sasaki, Hiroaki; Tamura, Shinsuke; Hamamoto, Takaaki; Yuki, Atsushi; Sato, Akinori; Miyahira, Yasushi; Kawana, Akihiko

2015-01-01

Bacillus Calmette-Guérin (BCG) is widely used as a live attenuated vaccine against Mycobacterium tuberculosis and is an agent for standard prophylaxis against the recurrence of bladder cancer. Unfortunately, it can cause severe infectious diseases, especially in immunocompromised patients, and the ability to immediately distinguish BCG from other M. tuberculosis complexes is therefore important. In this study, we developed a simple and easy-to-perform identification procedure using loop-mediated amplification (LAMP) to detect deletions within the region of difference, which is deleted specifically in all M. bovis BCG strains. Reactions were performed at 64°C for 30 min and successful targeted gene amplifications were detected by real-time turbidity using a turbidimeter and visual inspection of color change. The assay had an equivalent detection limit of 1.0 pg of genomic DNA using a turbidimeter whereas it was 10 pg with visual inspection, and it showed specificity against 49 strains of 44 pathogens, including M. tuberculosis complex. The expected LAMP products were confirmed through identical melting curves in real-time LAMP procedures. We employed the Procedure for Ultra Rapid Extraction (PURE) kit to isolate mycobacterial DNA and found that the highest sensitivity limit with a minimum total cell count of mycobacterium (including DNA purification with PURE) was up to 1 × 103 cells/reaction, based on color changes under natural light with FDA reagents. The detection limit of this procedure when applied to artificial serum, urine, cerebrospinal fluid, and bronchoalveolar lavage fluid samples was also about 1 × 103 cells/reaction. Therefore, this substitute method using conventional culture or clinical specimens followed by LAMP combined with PURE could be a powerful tool to enable the rapid identification of M. bovis BCG as point-of-care testing. It is suitable for practical use not only in resource-limited situations, but also in any clinical situation involving immunocompromised patients because of its convenience, rapidity, and cost effectiveness. PMID:26208001

Study of DNA extraction methods for use in loop-mediated isothermal amplification detection of single resting cysts in the toxic dinoflagellates Alexandrium tamarense and A. catenella.

PubMed

Nagai, Satoshi; Yamamoto, Keigo; Hata, Naotugu; Itakura, Shigeru

2012-09-01

In a previous study, we experienced instable amplification and a low amplification success in loop-mediated isothermal amplification (LAMP) reactions from naturally occurring vegetative cells or resting cysts of the toxic dinoflagellates Alexandrium tamarense and Alexandrium catenella. In this study, we examined 4 methods for extracting DNA from single resting cysts of A. tamarense and A. catenella to obtain more stable and better amplification success and to facilitate unambiguous detection using the LAMP method. Apart from comparing the 4 different DNA extraction methods, namely, (1) boiling in Tris-EDTA (TE) buffer, (2) heating at 65 °C in hexadecyltrimethylammonium bromide buffer, (3) boiling in 0.5% Chelex buffer, and (4) boiling in 5% Chelex buffer, we also examined the need for homogenization to crush the resting cysts before DNA extraction in each method. Homogenization of resting cysts was found to be essential for DNA extraction in all 4 methods. The detection time was significantly shorter in 5% Chelex buffer than in the other buffers and the amplification success was 100% (65/65), indicating the importance of DNA extraction and the effectiveness of 5% Chelex buffer in the Alexandrium LAMP. Copyright © 2012 Elsevier B.V. All rights reserved.

Accumulation of dislocation loops in the α phase of Zr Excel alloy under heavy ion irradiation

NASA Astrophysics Data System (ADS)

Yu, Hongbing; Yao, Zhongwen; Idrees, Yasir; Zhang, He K.; Kirk, Mark A.; Daymond, Mark R.

2017-08-01

In-situ heavy ion irradiations were performed on the high Sn content Zr alloy 'Excel', measuring type dislocation loop accumulation up to irradiation damage doses of 10 dpa at a range of temperatures. The high content of Sn, which diffuses slowly, and the thin foil geometry of the sample provide a unique opportunity to study an extreme case where displacement cascades dominate the loop formation and evolution. The dynamic observation of dislocation loop evolution under irradiation at 200 °C reveals that type dislocation loops can form at very low dose (0.0025 dpa). The size of the dislocation loops increases slightly with irradiation damage dose. The mechanism controlling loop growth in this study is different from that in neutron irradiation; in this study, larger dislocation loops can condense directly from the interaction of displacement cascades and the high concentration of point defects in the matrix. The size of the dislocation loop is dependent on the point defect concentration in the matrix. A negative correlation between the irradiation temperature and the dislocation loop size was observed. A comparison between cascade dominated loop evolution (this study), diffusion dominated loop evolution (electron irradiation) and neutron irradiation suggests that heavy ion irradiation alone may not be enough to accurately reproduce neutron irradiation induced loop structures. An alternative method is proposed in this paper. The effects of Sn on the displacement cascades, defect yield, and the diffusion behavior of point defects are established.

Methane Post-Processing for Oxygen Loop Closure

NASA Technical Reports Server (NTRS)

Greenwood, Zachary W.; Abney, Morgan B.; Miller, Lee

2016-01-01

State-of-the-art United States Atmospheric Revitalization carbon dioxide (CO2) reduction is based on the Sabatier reaction process, which recovers approximately 50% of the oxygen (O2) from crew metabolic CO2. Oxygen recovery from carbon dioxide is constrained by the limited availability of reactant hydrogen. Post-processing of methane to recover hydrogen with the Umpqua Research Company Plasma Pyrolysis Assembly (PPA) has the potential to further close the Atmospheric Revitalization oxygen loop. The PPA decomposes methane into hydrogen and hydrocarbons, predominantly acetylene, and a small amount of solid carbon. The hydrogen must then be purified before it can be recycled for additional oxygen recovery. Long duration testing and evaluation of a four crew-member sized PPA and a discussion of hydrogen recycling system architectures are presented.

First LIGO search for gravitational wave bursts from cosmic (super)strings

NASA Astrophysics Data System (ADS)

Abbott, B. P.; Abbott, R.; Adhikari, R.; Ajith, P.; Allen, B.; Allen, G.; Amin, R. S.; Anderson, S. B.; Anderson, W. G.; Arain, M. A.; Araya, M.; Armandula, H.; Armor, P.; Aso, Y.; Aston, S.; Aufmuth, P.; Aulbert, C.; Babak, S.; Baker, P.; Ballmer, S.; Barker, C.; Barker, D.; Barr, B.; Barriga, P.; Barsotti, L.; Barton, M. A.; Bartos, I.; Bassiri, R.; Bastarrika, M.; Behnke, B.; Benacquista, M.; Betzwieser, J.; Beyersdorf, P. T.; Bilenko, I. A.; Billingsley, G.; Biswas, R.; Black, E.; Blackburn, J. K.; Blackburn, L.; Blair, D.; Bland, B.; Bodiya, T. P.; Bogue, L.; Bork, R.; Boschi, V.; Bose, S.; Brady, P. R.; Braginsky, V. B.; Brau, J. E.; Bridges, D. O.; Brinkmann, M.; Brooks, A. F.; Brown, D. A.; Brummit, A.; Brunet, G.; Bullington, A.; Buonanno, A.; Burmeister, O.; Byer, R. L.; Cadonati, L.; Camp, J. B.; Cannizzo, J.; Cannon, K. C.; Cao, J.; Cardenas, L.; Caride, S.; Castaldi, G.; Caudill, S.; Cavaglià, M.; Cepeda, C.; Chalermsongsak, T.; Chalkley, E.; Charlton, P.; Chatterji, S.; Chelkowski, S.; Chen, Y.; Christensen, N.; Chung, C. T. Y.; Clark, D.; Clark, J.; Clayton, J. H.; Cokelaer, T.; Colacino, C. N.; Conte, R.; Cook, D.; Corbitt, T. R. C.; Cornish, N.; Coward, D.; Coyne, D. C.; Creighton, J. D. E.; Creighton, T. D.; Cruise, A. M.; Culter, R. M.; Cumming, A.; Cunningham, L.; Danilishin, S. L.; Danzmann, K.; Daudert, B.; Davies, G.; Daw, E. J.; Debra, D.; Degallaix, J.; Dergachev, V.; Desai, S.; Desalvo, R.; Dhurandhar, S.; Díaz, M.; Dietz, A.; Donovan, F.; Dooley, K. L.; Doomes, E. E.; Drever, R. W. P.; Dueck, J.; Duke, I.; Dumas, J.-C.; Dwyer, J. G.; Echols, C.; Edgar, M.; Effler, A.; Ehrens, P.; Espinoza, E.; Etzel, T.; Evans, M.; Evans, T.; Fairhurst, S.; Faltas, Y.; Fan, Y.; Fazi, D.; Fehrmann, H.; Finn, L. S.; Flasch, K.; Foley, S.; Forrest, C.; Fotopoulos, N.; Franzen, A.; Frede, M.; Frei, M.; Frei, Z.; Freise, A.; Frey, R.; Fricke, T.; Fritschel, P.; Frolov, V. V.; Fyffe, M.; Galdi, V.; Garofoli, J. A.; Gholami, I.; Giaime, J. A.; Giampanis, S.; Giardina, K. D.; Goda, K.; Goetz, E.; Goggin, L. M.; González, G.; Gorodetsky, M. L.; Goßler, S.; Gouaty, R.; Grant, A.; Gras, S.; Gray, C.; Gray, M.; Greenhalgh, R. J. S.; Gretarsson, A. M.; Grimaldi, F.; Grosso, R.; Grote, H.; Grunewald, S.; Guenther, M.; Gustafson, E. K.; Gustafson, R.; Hage, B.; Hallam, J. M.; Hammer, D.; Hammond, G. D.; Hanna, C.; Hanson, J.; Harms, J.; Harry, G. M.; Harry, I. W.; Harstad, E. D.; Haughian, K.; Hayama, K.; Heefner, J.; Heng, I. S.; Heptonstall, A.; Hewitson, M.; Hild, S.; Hirose, E.; Hoak, D.; Hodge, K. A.; Holt, K.; Hosken, D. J.; Hough, J.; Hoyland, D.; Hughey, B.; Huttner, S. H.; Ingram, D. R.; Isogai, T.; Ito, M.; Ivanov, A.; Johnson, B.; Johnson, W. W.; Jones, D. I.; Jones, G.; Jones, R.; Ju, L.; Kalmus, P.; Kalogera, V.; Kandhasamy, S.; Kanner, J.; Kasprzyk, D.; Katsavounidis, E.; Kawabe, K.; Kawamura, S.; Kawazoe, F.; Kells, W.; Keppel, D. G.; Khalaidovski, A.; Khalili, F. Y.; Khan, R.; Khazanov, E.; King, P.; Kissel, J. S.; Klimenko, S.; Kokeyama, K.; Kondrashov, V.; Kopparapu, R.; Koranda, S.; Kozak, D.; Krishnan, B.; Kumar, R.; Kwee, P.; Lam, P. K.; Landry, M.; Lantz, B.; Lazzarini, A.; Lei, H.; Lei, M.; Leindecker, N.; Leonor, I.; Li, C.; Lin, H.; Lindquist, P. E.; Littenberg, T. B.; Lockerbie, N. A.; Lodhia, D.; Longo, M.; Lormand, M.; Lu, P.; Lubiński, M.; Lucianetti, A.; Lück, H.; Machenschalk, B.; Macinnis, M.; Mageswaran, M.; Mailand, K.; Mandel, I.; Mandic, V.; Márka, S.; Márka, Z.; Markosyan, A.; Markowitz, J.; Maros, E.; Martin, I. W.; Martin, R. M.; Marx, J. N.; Mason, K.; Matichard, F.; Matone, L.; Matzner, R. A.; Mavalvala, N.; McCarthy, R.; McClelland, D. E.; McGuire, S. C.; McHugh, M.; McIntyre, G.; McKechan, D. J. A.; McKenzie, K.; Mehmet, M.; Melatos, A.; Melissinos, A. C.; Menéndez, D. F.; Mendell, G.; Mercer, R. A.; Meshkov, S.; Messenger, C.; Meyer, M. S.; Miller, J.; Minelli, J.; Mino, Y.; Mitrofanov, V. P.; Mitselmakher, G.; Mittleman, R.; Miyakawa, O.; Moe, B.; Mohanty, S. D.; Mohapatra, S. R. P.; Moreno, G.; Morioka, T.; Mors, K.; Mossavi, K.; Mowlowry, C.; Mueller, G.; Müller-Ebhardt, H.; Muhammad, D.; Mukherjee, S.; Mukhopadhyay, H.; Mullavey, A.; Munch, J.; Murray, P. G.; Myers, E.; Myers, J.; Nash, T.; Nelson, J.; Newton, G.; Nishizawa, A.; Numata, K.; O'Dell, J.; O'Reilly, B.; O'Shaughnessy, R.; Ochsner, E.; Ogin, G. H.; Ottaway, D. J.; Ottens, R. S.; Overmier, H.; Owen, B. J.; Pan, Y.; Pankow, C.; Papa, M. A.; Parameshwaraiah, V.; Patel, P.; Pedraza, M.; Penn, S.; Perreca, A.; Pierro, V.; Pinto, I. M.; Pitkin, M.; Pletsch, H. J.; Plissi, M. V.; Postiglione, F.; Principe, M.; Prix, R.; Prokhorov, L.; Punken, O.; Quetschke, V.; Raab, F. J.; Rabeling, D. S.; Radkins, H.; Raffai, P.; Raics, Z.; Rainer, N.; Rakhmanov, M.; Raymond, V.; Reed, C. M.; Reed, T.; Rehbein, H.; Reid, S.; Reitze, D. H.; Riesen, R.; Riles, K.; Rivera, B.; Roberts, P.; Robertson, N. A.; Robinson, C.; Robinson, E. L.; Roddy, S.; Röver, C.; Rollins, J.; Romano, J. D.; Romie, J. H.; Rowan, S.; Rüdiger, A.; Russell, P.; Ryan, K.; Sakata, S.; Sancho de La Jordana, L.; Sandberg, V.; Sannibale, V.; Santamaría, L.; Saraf, S.; Sarin, P.; Sathyaprakash, B. S.; Sato, S.; Satterthwaite, M.; Saulson, P. R.; Savage, R.; Savov, P.; Scanlan, M.; Schilling, R.; Schnabel, R.; Schofield, R.; Schulz, B.; Schutz, B. F.; Schwinberg, P.; Scott, J.; Scott, S. M.; Searle, A. C.; Sears, B.; Seifert, F.; Sellers, D.; Sengupta, A. S.; Sergeev, A.; Shapiro, B.; Shawhan, P.; Shoemaker, D. H.; Sibley, A.; Siemens, X.; Sigg, D.; Sinha, S.; Sintes, A. M.; Slagmolen, B. J. J.; Slutsky, J.; Smith, J. R.; Smith, M. R.; Smith, N. D.; Somiya, K.; Sorazu, B.; Stein, A.; Stein, L. C.; Steplewski, S.; Stochino, A.; Stone, R.; Strain, K. A.; Strigin, S.; Stroeer, A.; Stuver, A. L.; Summerscales, T. Z.; Sun, K.-X.; Sung, M.; Sutton, P. J.; Szokoly, G. P.; Talukder, D.; Tang, L.; Tanner, D. B.; Tarabrin, S. P.; Taylor, J. R.; Taylor, R.; Thacker, J.; Thorne, K. A.; Thorne, K. S.; Thüring, A.; Tokmakov, K. V.; Torres, C.; Torrie, C.; Traylor, G.; Trias, M.; Ugolini, D.; Ulmen, J.; Urbanek, K.; Vahlbruch, H.; Vallisneri, M.; van den Broeck, C.; van der Sluys, M. V.; van Veggel, A. A.; Vass, S.; Vaulin, R.; Vecchio, A.; Veitch, J.; Veitch, P.; Veltkamp, C.; Villar, A.; Vorvick, C.; Vyachanin, S. P.; Waldman, S. J.; Wallace, L.; Ward, R. L.; Weidner, A.; Weinert, M.; Weinstein, A. J.; Weiss, R.; Wen, L.; Wen, S.; Wette, K.; Whelan, J. T.; Whitcomb, S. E.; Whiting, B. F.; Wilkinson, C.; Willems, P. A.; Williams, H. R.; Williams, L.; Willke, B.; Wilmut, I.; Winkelmann, L.; Winkler, W.; Wipf, C. C.; Wiseman, A. G.; Woan, G.; Wooley, R.; Worden, J.; Wu, W.; Yakushin, I.; Yamamoto, H.; Yan, Z.; Yoshida, S.; Zanolin, M.; Zhang, J.; Zhang, L.; Zhao, C.; Zotov, N.; Zucker, M. E.; Zur Mühlen, H.; Zweizig, J.; Robinet, F.

2009-09-01

We report on a matched-filter search for gravitational wave bursts from cosmic string cusps using LIGO data from the fourth science run (S4) which took place in February and March 2005. No gravitational waves were detected in 14.9 days of data from times when all three LIGO detectors were operating. We interpret the result in terms of a frequentist upper limit on the rate of gravitational wave bursts and use the limits on the rate to constrain the parameter space (string tension, reconnection probability, and loop sizes) of cosmic string models. Many grand unified theory-scale models (with string tension Gμ/c2≈10-6) can be ruled out at 90% confidence for reconnection probabilities p≤10-3 if loop sizes are set by gravitational back reaction.

A loop-mediated isothermal amplification assay for rapid and sensitive detection of bovine papular stomatitis virus.

PubMed

Kurosaki, Yohei; Okada, Sayaka; Nakamae, Sayuri; Yasuda, Jiro

2016-12-01

Bovine papular stomatitis virus (BPSV) causes pustular cutaneous disease in cattle worldwide. This paper describes the development of a specific loop-mediated isothermal amplification (LAMP) assay to detect BPSV which did not cross-react with other parapoxviruses. To assess analytical sensitivity of this LAMP assay, DNA was extracted from serially diluted BPSV from which the infectious titer was determined by a novel assay based on calf kidney epithelial cells. The LAMP assay had equivalent analytical sensitivity to quantitative PCR, and could detect as few as 86 copies of viral DNA per reaction. These results suggest that the assay is a specific and sensitive technique to rapidly diagnose bovine papular stomatitis in domestic animals. Copyright © 2016 Elsevier B.V. All rights reserved.

Compact, closed-loop controlled waste incinerator

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

Schadow, K.C.; Seeker, W.R.

1999-07-01

Technologies for solid and liquid waste destruction in compact incinerators are being developed in collaboration between industry, universities, and a Government laboratory. This paper reviews progress on one technology, namely active combustion control to achieve efficient and controlled afterburning of air-starved reaction products. This technology which uses synchronized waste gas injection into acoustically stabilized air vortices was transitioned to a simplified afterburner design and practical operational conditions. The full-scale, simplified afterburner, which achieved CO and NO{sub x} emissions of about 30 ppm with a residence time of less than 50 msec, was integrated with a commercially available marine incinerator tomore » increase throughput and reduce emissions. Closed-loop active control with diode laser sensors and novel control strategies was demonstrated on a sub-scale afterburner.« less

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

PubMed Central

Tran, Tuan; Disney, Matthew D.

2011-01-01

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

Improved dual-loop detection system for collecting real-time truck data

DOT National Transportation Integrated Search

2005-02-01

The WSDOTs dual-loop detectors capability of measuring vehicle lengths makes the dual-loop detection system a potential real-time truck data source for freight movement study. However, a previous study found the WSDOT dual-loop detection system...

Crystal defect studies using x-ray diffuse scattering

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

Larson, B.C.

1980-01-01

Microscopic lattice defects such as point (single atom) defects, dislocation loops, and solute precipitates are characterized by local electronic density changes at the defect sites and by distortions of the lattice structure surrounding the defects. The effect of these interruptions of the crystal lattice on the scattering of x-rays is considered in this paper, and examples are presented of the use of the diffuse scattering to study the defects. X-ray studies of self-interstitials in electron irradiated aluminum and copper are discussed in terms of the identification of the interstitial configuration. Methods for detecting the onset of point defect aggregation intomore » dislocation loops are considered and new techniques for the determination of separate size distributions for vacancy loops and interstitial loops are presented. Direct comparisons of dislocation loop measurements by x-rays with existing electron microscopy studies of dislocation loops indicate agreement for larger size loops, but x-ray measurements report higher concentrations in the smaller loop range. Methods for distinguishing between loops and three-dimensional precipitates are discussed and possibilities for detailed studies considered. A comparison of dislocation loop size distributions obtained from integral diffuse scattering measurements with those from TEM show a discrepancy in the smaller sizes similar to that described above.« less

Development and Application of a Loop-Mediated Isothermal Amplification (LAMP) Approach for the Rapid Detection of Dirofilaria repens from Biological Samples

PubMed Central

Raele, Donato Antonio; Pugliese, Nicola; Galante, Domenico; Latorre, Laura Maria; Cafiero, Maria Assunta

2016-01-01

Dirofilariasis by Dirofilaria repens is an important mosquito vector borne parasitosis, and the dog represents the natural host and reservoir of the parasite. This filarial nematode can also induce disease in humans, and in the last decades an increasing number of cases have been being reported. The present study describes the first loop mediated isothermal amplification (LAMP) assay to detect D. repens DNA in blood and mosquitoes. Two versions of the technique have been developed and described: in the first, the amplification is followed point by point through a real time PCR instrument (ReT-LAMP); in the second, the amplification is visualized by checking UV fluorescence of the reaction mixture after addition of propidium iodide (PI-LAMP). The two variants use the same set of 4 primers targeting the D. repens cytochrome oxidase subunit I (COI) gene. To assess the specificity of the method, reactions were carried out by using DNA from the major zoonotic parasites of the family of Onchocercidae, and no amplification was observed. The lower limit of detection of the ReT-LAMP assay was 0.15 fg/μl (corresponding to about 50 copy of COI gene per μl). Results suggest that the described assay is specific, and its sensitivity is higher than the conventional PCR based on the same gene. It is also provide a rapid and cost-effective molecular detection of D. repens, mainly when PI-LAMP is applied, and it should be performed in areas where this emerging parasitosis is endemic. PMID:27341205

HIGH TEMPERATURE REACTOR

DOEpatents

Kulsrud, R.M.; Spitzer, L. Jr.

1961-12-12

An apparatus of the stellarator type for heating a plasma to high temperatures is designed. Circularizers at the end of then helical windings produce a circular magnetic surface and provide improved confining and heating of the plasma. Reverse curvature sections formed in the end loops of the reaction tube provide increased plasma pressure for a given magnetic field pressure and thereby minimize the current flow in the helical windings. (AEC)

Structures of NADH and CH[subscript 3]-H[subscript 4] Folate Complexes of Escherichia coli Methylenetetrahydrofolate Reductase Reveal a Spartan Strategy for a Ping-Pong Reaction

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

Pejchal, Robert; Sargeant, Ryan; Ludwig, Martha L.

Methylenetetrahydrofolate reductases (MTHFRs; EC 1.7.99.5) catalyze the NAD(P)H-dependent reduction of 5,10-methylenetetrahydrofolate (CH{sub 2}-H{sub 4}folate) to 5-methyltetrahydrofolate (CH{sub 3}-H{sub 4}folate) using flavin adenine dinucleotide (FAD) as a cofactor. The initial X-ray structure of Escherichia coli MTHFR revealed that this 33-kDa polypeptide is a ({beta}{alpha}){sub 8} barrel that aggregates to form an unusual tetramer with only 2-fold symmetry. Structures of reduced enzyme complexed with NADH and of oxidized Glu28Gln enzyme complexed with CH{sub 3}-H{sub 4}folate have now been determined at resolutions of 1.95 and 1.85 {angstrom}, respectively. The NADH complex reveals a rare mode of dinucleotide binding; NADH adopts a hairpin conformationmore » and is sandwiched between a conserved phenylalanine, Phe223, and the isoalloxazine ring of FAD. The nicotinamide of the bound pyridine nucleotide is stacked against the si face of the flavin ring with C4 adjoining the N5 of FAD, implying that this structure models a complex that is competent for hydride transfer. In the complex with CH{sub 3}-H{sub 4}folate, the pterin ring is also stacked against FAD in an orientation that is favorable for hydride transfer. Thus, the binding sites for the two substrates overlap, as expected for many enzymes that catalyze ping-pong reactions, and several invariant residues interact with both folate and pyridine nucleotide substrates. Comparisons of liganded and substrate-free structures reveal multiple conformations for the loops {beta}2-{alpha}2 (L2), {beta}3-{alpha}3 (L3), and {beta}4-{alpha}4 (L4) and suggest that motions of these loops facilitate the ping-pong reaction. In particular, the L4 loop adopts a 'closed' conformation that allows Asp120 to hydrogen bond to the pterin ring in the folate complex but must move to an 'open' conformation to allow NADH to bind.« less

Open Cascades as Simple Solutions to Providing Ultrasensitivity and Adaptation in Cellular Signaling

PubMed Central

Srividhya, Jeyaraman; Li, Yongfeng; Pomerening, Joseph R.

2011-01-01

Cell signaling is achieved predominantly by reversible phosphorylation-dephosphorylation reaction cascades. Up until now, circuits conferring adaptation have all required the presence of a cascade with some type of closed topology: negative–feedback loop with a buffering node, or incoherent feedforward loop with a proportioner node. In this paper—using Goldbeter and Koshland-type expressions—we propose a differential equation model to describe a generic, open signaling cascade that elicits an adaptation response. This is accomplished by coupling N phosphorylation–dephosphorylation cycles unidirectionally, without any explicit feedback loops. Using this model, we show that as the length of the cascade grows, the steady states of the downstream cycles reach a limiting value. In other words, our model indicates that there are a minimum number of cycles required to achieve a maximum in sensitivity and amplitude in the response of a signaling cascade. We also describe for the first time that the phenomenon of ultrasensitivity can be further subdivided into three sub–regimes, separated by sharp stimulus threshold values: OFF, OFF-ON-OFF, and ON. In the OFF-ON-OFF regime, an interesting property emerges. In the presence of a basal amount of activity, the temporal evolution of early cycles yields damped peak responses. On the other hand, the downstream cycles switch rapidly to a higher activity state for an extended period of time, prior to settling to an OFF state (OFF-ON-OFF). This response arises from the changing dynamics between a feed–forward activation module and dephosphorylation reactions. In conclusion, our model gives the new perspective that open signaling cascades embedded in complex biochemical circuits may possess the ability to show a switch–like adaptation response, without the need for any explicit feedback circuitry. PMID:21566270

Students' Understanding of Loops and Nested Loops in Computer Programming: An APOS Theory Perspective

ERIC Educational Resources Information Center

Cetin, Ibrahim

2015-01-01

The purpose of this study is to explore students' understanding of loops and nested loops concepts. Sixty-three mechanical engineering students attending an introductory programming course participated in the study. APOS (Action, Process, Object, Schema) is a constructivist theory developed originally for mathematics education. This study is the…

Difference in real-time magnetic image analysis of colonic looping patterns between males and females undergoing diagnostic colonoscopy.

PubMed

Lam, Jacob; Wilkinson, James; Brassett, Cecilia; Brown, Jonathan

2018-05-01

Background and study aim  Magnetic imaging technology is of proven benefit to trainees in colonoscopy, but few studies have examined its benefits in experienced hands. There is evidence that colonoscopy is more difficult in women. We set out to investigate (i) associations between the looping configurations in the proximal and distal colon and (ii) differences in the looping prevalence between the sexes. We have examined their significance in terms of segmental intubation times and position changes required for the completion of colonoscopy. Patients and methods  We analyzed 103 consecutive synchronized luminal and magnetic image videos of diagnostic colonoscopies with normal anatomy undertaken by a single experienced operator. Results  Deep transverse loops and sigmoid N-loops were more common in females. A deep transverse loop was more likely to be present if a sigmoid alpha-loop or N-loop had formed previously. Patients with sigmoid N-loops were turned more frequently from left lateral to supine before the sigmoid-descending junction was reached, but there was no statistical correlation between completion time and looping pattern. Conclusions  This study has reexamined the prevalence of the common looping patterns encountered during colonoscopy and has identified differences between the sexes. This finding may offer an explanation as to why colonoscopy has been shown to be more difficult in females. Although a deep transverse loop following a resolved sigmoid alpha-loop was the most commonly encountered pattern, no statistical correlation between completion time and looping pattern could be shown. It is the first study to examine segmental completion times using a magnetic imager in expert hands.

Structural, vibrational and magnetic studies of Pb(Fe0.585Nb0.25W0.165)O3 multiferroic solid solution

NASA Astrophysics Data System (ADS)

Nagaraja, T.; Dadami, Sunanda T.; Matteppanvar, Shidaling; Shivaraja, I.; Rayaprol, Sudhindra; Angadi, Basavaraj

2018-04-01

In this paper, the complex structured A(B'B''B''')O3 perovskite Pb(Fe0.585Nb0.25W0.165)O3(PFNW) type multiferroic, was successfully synthesized in a single phase by a single step solid state reaction method and optimized synthesis parameters are calcination at 700 °C/2hr and sintering at 800 °C/3hr. The detailed room temperature (RT) structural, vibrational and temperature dependent magnetization were carried out through the X ray diffraction, Raman spectroscopy and vibrating sample magnetometer (VSM). Rietveld refinement was carried out on RT XRD data it confirms the cubic structure with Pm-3m space group, the obtained lattice parameters: a = b = c = 3.9948 Å, and α = β = γ = 90°. The RT Raman spectroscopy confirms the formation of cubic structure broad peak at 820 cm-1, related to the A1g mode. PFNW exhibits a cusp at around 255 K in the temperature dependent magnetic susceptibility corresponding to the Néel temperature (TN) and another peak around 10 K (Tsg) corresponding to spin-glass like transition. The M-H loops were measured at few selected temperatures above and below TN. The M-H loop at 5 K shows the well saturated loop with significant coercive field compared to 260 and 300K data, due to the existence of spin-glass ordering.

Specific binding of a HeLa cell nuclear protein to RNA sequences in the human immunodeficiency virus transactivating region.

PubMed Central

Gaynor, R; Soultanakis, E; Kuwabara, M; Garcia, J; Sigman, D S

1989-01-01

The transactivator protein, tat, encoded by the human immunodeficiency virus is a key regulator of viral transcription. Activation by the tat protein requires sequences downstream of the transcription initiation site called the transactivating region (TAR). RNA derived from the TAR is capable of forming a stable stem-loop structure and the maintenance of both the stem structure and the loop sequences located between +19 and +44 is required for complete in vivo activation by tat. Gel retardation assays with RNA from both wild-type and mutant TAR constructs generated in vitro with SP6 polymerase indicated specific binding of HeLa nuclear proteins to the TAR. To characterize this RNA-protein interaction, a method of chemical "imprinting" has been developed using photoactivated uranyl acetate as the nucleolytic agent. This reagent nicks RNA under physiological conditions at all four nucleotides in a reaction that is independent of sequence and secondary structure. Specific interaction of cellular proteins with TAR RNA could be detected by enhanced cleavages or imprints surrounding the loop region. Mutations that either disrupted stem base-pairing or extensively changed the primary sequence resulted in alterations in the cleavage pattern of the TAR RNA. Structural features of the TAR RNA stem-loop essential for tat activation are also required for specific binding of the HeLa cell nuclear protein. Images PMID:2544877

Thermally multiplexed polymerase chain reaction.

PubMed

Phaneuf, Christopher R; Pak, Nikita; Saunders, D Curtis; Holst, Gregory L; Birjiniuk, Joav; Nagpal, Nikita; Culpepper, Stephen; Popler, Emily; Shane, Andi L; Jerris, Robert; Forest, Craig R

2015-07-01

Amplification of multiple unique genetic targets using the polymerase chain reaction (PCR) is commonly required in molecular biology laboratories. Such reactions are typically performed either serially or by multiplex PCR. Serial reactions are time consuming, and multiplex PCR, while powerful and widely used, can be prone to amplification bias, PCR drift, and primer-primer interactions. We present a new thermocycling method, termed thermal multiplexing, in which a single heat source is uniformly distributed and selectively modulated for independent temperature control of an array of PCR reactions. Thermal multiplexing allows amplification of multiple targets simultaneously-each reaction segregated and performed at optimal conditions. We demonstrate the method using a microfluidic system consisting of an infrared laser thermocycler, a polymer microchip featuring 1 μl, oil-encapsulated reactions, and closed-loop pulse-width modulation control. Heat transfer modeling is used to characterize thermal performance limitations of the system. We validate the model and perform two reactions simultaneously with widely varying annealing temperatures (48 °C and 68 °C), demonstrating excellent amplification. In addition, to demonstrate microfluidic infrared PCR using clinical specimens, we successfully amplified and detected both influenza A and B from human nasopharyngeal swabs. Thermal multiplexing is scalable and applicable to challenges such as pathogen detection where patients presenting non-specific symptoms need to be efficiently screened across a viral or bacterial panel.

Geometric phase effects in ultracold chemistry

NASA Astrophysics Data System (ADS)

Hazra, Jisha; Naduvalath, Balakrishnan; Kendrick, Brian K.

2016-05-01

In molecules, the geometric phase, also known as Berry's phase, originates from the adiabatic transport of the electronic wavefunction when the nuclei follow a closed path encircling a conical intersection between two electronic potential energy surfaces. It is demonstrated that the inclusion of the geometric phase has an important effect on ultracold chemical reaction rates. The effect appears in rotationally and vibrationally resolved integral cross sections as well as cross sections summed over all product quantum states. It arises from interference between scattering amplitudes of two reaction pathways: a direct path and a looping path that encircle the conical intersection between the two lowest adiabatic electronic potential energy surfaces. Illustrative results are presented for the O+ OH --> H+ O2 reaction and for hydrogen exchange in H+ H2 and D+HD reactions. It is also qualitatively demonstrated that the geometric phase effect can be modulated by applying an external electric field allowing the possibility of quantum control of chemical reactions in the ultracold regime. This work was supported in part by NSF Grant PHY-1505557 (N.B.) and ARO MURI Grant No. W911NF-12-1-0476 (N.B.).

Closing the tau loop: the missing tau mutation

PubMed Central

McCarthy, Allan; Lonergan, Roisin; Olszewska, Diana A.; O’Dowd, Sean; Cummins, Gemma; Magennis, Brian; Fallon, Emer M.; Pender, Niall; Huey, Edward D.; Cosentino, Stephanie; O’Rourke, Killian; Kelly, Brendan D.; O’Connell, Martin; Delon, Isabelle; Farrell, Michael; Spillantini, Maria Grazia; Rowland, Lewis P.; Fahn, Stanley; Craig, Peter; Hutton, Michael

2015-01-01

Frontotemporal lobar degeneration comprises a group of disorders characterized by behavioural, executive, language impairment and sometimes features of parkinsonism and motor neuron disease. In 1994 we described an Irish-American family with frontotemporal dementia linked to chromosome 17 associated with extensive tau pathology. We named this disinhibition-dementia-parkinsonism-amyotrophy complex. We subsequently identified mutations in the MAPT gene. Eleven MAPT gene splice site stem loop mutations were identified over time except for 5’ splice site of exon 10. We recently identified another Irish family with autosomal dominant early amnesia and behavioural change or parkinsonism associated with the ‘missing’ +15 mutation at the intronic boundary of exon 10. We performed a clinical, neuropsychological and neuroimaging study on the proband and four siblings, including two affected siblings. We sequenced MAPT and performed segregation analysis. We looked for a biological effect of the tau variant by performing real-time polymerase chain reaction analysis of RNA extracted from human embryonic kidney cells transfected with exon trapping constructs. We found a c.915+15A>C exon 10/intron 10 stem loop mutation in all affected subjects but not in the unaffected. The c.915+15A>C variant caused a shift in tau splicing pattern to a predominantly exon 10+ pattern presumably resulting in predominant 4 repeat tau and little 3 repeat tau. This strongly suggests that the c.915+15A>C variant is a mutation and that it causes frontotemporal dementia linked to chromosome 17 in this pedigree by shifting tau transcription and translation to +4 repeat tau. Tau (MAPT) screening should be considered in families where amnesia or atypical parkinsonism coexists with behavioural disturbance early in the disease process. We describe the final missing stem loop tau mutation predicted 15 years ago. Mutations have now been identified at all predicted sites within the ‘stem’ when the stem-loop model was first proposed and no mutations have been found within the ‘loop’ region as expected. Therefore we ‘close the tau loop’ having ‘opened the loop’ 21 years ago. PMID:26297556

Adaptive extended-state observer-based fault tolerant attitude control for spacecraft with reaction wheels

NASA Astrophysics Data System (ADS)

Ran, Dechao; Chen, Xiaoqian; de Ruiter, Anton; Xiao, Bing

2018-04-01

This study presents an adaptive second-order sliding control scheme to solve the attitude fault tolerant control problem of spacecraft subject to system uncertainties, external disturbances and reaction wheel faults. A novel fast terminal sliding mode is preliminarily designed to guarantee that finite-time convergence of the attitude errors can be achieved globally. Based on this novel sliding mode, an adaptive second-order observer is then designed to reconstruct the system uncertainties and the actuator faults. One feature of the proposed observer is that the design of the observer does not necessitate any priori information of the upper bounds of the system uncertainties and the actuator faults. In view of the reconstructed information supplied by the designed observer, a second-order sliding mode controller is developed to accomplish attitude maneuvers with great robustness and precise tracking accuracy. Theoretical stability analysis proves that the designed fault tolerant control scheme can achieve finite-time stability of the closed-loop system, even in the presence of reaction wheel faults and system uncertainties. Numerical simulations are also presented to demonstrate the effectiveness and superiority of the proposed control scheme over existing methodologies.

Efficient sampling of reversible cross-linking polymers: Self-assembly of single-chain polymeric nanoparticles

NASA Astrophysics Data System (ADS)

Oyarzún, Bernardo; Mognetti, Bortolo Matteo

2018-03-01

We present a new simulation technique to study systems of polymers functionalized by reactive sites that bind/unbind forming reversible linkages. Functionalized polymers feature self-assembly and responsive properties that are unmatched by the systems lacking selective interactions. The scales at which the functional properties of these materials emerge are difficult to model, especially in the reversible regime where such properties result from many binding/unbinding events. This difficulty is related to large entropic barriers associated with the formation of intra-molecular loops. In this work, we present a simulation scheme that sidesteps configurational costs by dedicated Monte Carlo moves capable of binding/unbinding reactive sites in a single step. Cross-linking reactions are implemented by trial moves that reconstruct chain sections attempting, at the same time, a dimerization reaction between pairs of reactive sites. The model is parametrized by the reaction equilibrium constant of the reactive species free in solution. This quantity can be obtained by means of experiments or atomistic/quantum simulations. We use the proposed methodology to study the self-assembly of single-chain polymeric nanoparticles, starting from flexible precursors carrying regularly or randomly distributed reactive sites. We focus on understanding differences in the morphology of chain nanoparticles when linkages are reversible as compared to the well-studied case of irreversible reactions. Intriguingly, we find that the size of regularly functionalized chains, in good solvent conditions, is non-monotonous as a function of the degree of functionalization. We clarify how this result follows from excluded volume interactions and is peculiar of reversible linkages and regular functionalizations.

A Compartmentalized Out-of-Equilibrium Enzymatic Reaction Network for Sustained Autonomous Movement

PubMed Central

2016-01-01

Every living cell is a compartmentalized out-of-equilibrium system exquisitely able to convert chemical energy into function. In order to maintain homeostasis, the flux of metabolites is tightly controlled by regulatory enzymatic networks. A crucial prerequisite for the development of lifelike materials is the construction of synthetic systems with compartmentalized reaction networks that maintain out-of-equilibrium function. Here, we aim for autonomous movement as an example of the conversion of feedstock molecules into function. The flux of the conversion is regulated by a rationally designed enzymatic reaction network with multiple feedforward loops. By compartmentalizing the network into bowl-shaped nanocapsules the output of the network is harvested as kinetic energy. The entire system shows sustained and tunable microscopic motion resulting from the conversion of multiple external substrates. The successful compartmentalization of an out-of-equilibrium reaction network is a major first step in harnessing the design principles of life for construction of adaptive and internally regulated lifelike systems. PMID:27924313

Experimental Studies on the Synthesis and Performance of Boron-containing High Temperature Resistant Resin Modified by Hydroxylated Tung Oil

NASA Astrophysics Data System (ADS)

Zhang, J. X.; Y Ren, Z.; Zheng, G.; Wang, H. F.; Jiang, L.; Fu, Y.; Yang, W. Q.; He, H. H.

2017-12-01

In this work, hydroxylated tung oil (HTO) modified high temperature resistant resin containing boron and benzoxazine was synthesized. HTO and ethylenediamine was used to toughen the boron phenolic resin with specific reaction. The structure of product was studied by Fourier-transform infrared spectroscopy(FTIR), and the heat resistance was tested by Differential Scanning Calorimetry (DSC) and Thermogravimetric Analysis(TGA). The results indicated that the conjugated triene structure of HTO was involved in the crosslinking of the heating curing progress, and in addition, the open-loop polymerization reaction of benzoxazine resin during heating can effectively reduce the curing temperature of the resin and reduce the release of small molecule volatiles, which is advantageous to follow-up processing. DSC data showed that the initial decomposition temperature of the resin is 350-400 °C, the carbon residue rate under 800 °C was 65%. It indicated that the resin has better heat resistance than normal boron phenolic resin. The resin can be used as an excellent ablative material and anti-friction material and has a huge application market in many fields.

Biochemical Frequency Control by Synchronisation of Coupled Repressilators: An In Silico Study of Modules for Circadian Clock Systems

PubMed Central

Hinze, Thomas; Schumann, Mathias; Bodenstein, Christian; Heiland, Ines; Schuster, Stefan

2011-01-01

Exploration of chronobiological systems emerges as a growing research field within bioinformatics focusing on various applications in medicine, agriculture, and material sciences. From a systems biological perspective, the question arises whether biological control systems for regulation of oscillatory signals and their technical counterparts utilise similar mechanisms. If so, modelling approaches and parameterisation adopted from building blocks can help to identify general components for frequency control in circadian clocks along with gaining insight into mechanisms of clock synchronisation to external stimuli like the daily rhythm of sunlight and darkness. Phase-locked loops could be an interesting candidate in this context. Both, biology and engineering, can benefit from a unified view resulting from systems modularisation. In a first experimental study, we analyse a model of coupled repressilators. We demonstrate its ability to synchronise clock signals in a monofrequential manner. Several oscillators initially deviate in phase difference and frequency with respect to explicit reaction and diffusion rates. Accordingly, the duration of the synchronisation process depends on dedicated reaction and diffusion parameters whose settings still lack to be sufficiently captured analytically. PMID:22046179

Chemical Looping Combustion Reactions and Systems

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

Sarofim, Adel; Lighty, JoAnn; Smith, Philip

2014-03-01

Chemical Looping Combustion (CLC) is one promising fuel-combustion technology, which can facilitate economic CO{sub 2} capture in coal-fired power plants. It employs the oxidation/reduction characteristics of a metal, or oxygen carrier, and its oxide, the oxidizing gas (typically air) and the fuel source may be kept separate. This topical report discusses the results of four complementary efforts: (5.1) the development of process and economic models to optimize important design considerations, such as oxygen carrier circulation rate, temperature, residence time; (5.2) the development of high-performance simulation capabilities for fluidized beds and the collection, parameter identification, and preliminary verification/uncertainty quantification; (5.3) themore » exploration of operating characteristics in the laboratoryscale bubbling bed reactor, with a focus on the oxygen carrier performance, including reactivity, oxygen carrying capacity, attrition resistance, resistance to deactivation, cost and availability; and (5.4) the identification of kinetic data for copper-based oxygen carriers as well as the development and analysis of supported copper oxygen carrier material. Subtask 5.1 focused on the development of kinetic expressions for the Chemical Looping with Oxygen Uncoupling (CLOU) process and validating them with reported literature data. The kinetic expressions were incorporated into a process model for determination of reactor size and oxygen carrier circulation for the CLOU process using ASPEN PLUS. An ASPEN PLUS process model was also developed using literature data for the CLC process employing an iron-based oxygen carrier, and the results of the process model have been utilized to perform a relative economic comparison. In Subtask 5.2, the investigators studied the trade-off between modeling approaches and available simulations tools. They quantified uncertainty in the high-performance computing (HPC) simulation tools for CLC bed applications. Furthermore, they performed a sensitivity analysis for velocity, height and polydispersity and compared results against literature data for experimental studies of CLC beds with no reaction. Finally, they present an optimization space using simple non-reactive configurations. In Subtask 5.3, through a series of experimental studies, behavior of a variety of oxygen carriers with different loadings and manufacturing techniques was evaluated under both oxidizing and reducing conditions. The influences of temperature, degree of carrier conversion and thermodynamic driving force resulting from the difference between equilibrium and system O{sub 2} partial pressures were evaluated through several experimental campaigns, and generalized models accounting for these influences were developed to describe oxidation and oxygen release. Conversion of three solid fuels with widely ranging reactivities was studied in a small fluidized bed system, and all but the least reactive fuel (petcoke) were rapidly converted by oxygen liberated from the CLOU carrier. Attrition propensity of a variety of carriers was also studied, and the carriers produced by freeze granulation or impregnation of preformed substrates displayed the lowest rates of attrition. Subtask 5.4 focused on gathering kinetic data for a copper-based oxygen carrier to assist with modeling of a functioning chemical looping reactor. The kinetics team was also responsible for the development and analysis of supported copper oxygen carrier material.« less

Low Speed and High Speed Correlation of SMART Active Flap Rotor Loads

NASA Technical Reports Server (NTRS)

Kottapalli, Sesi B. R.

2010-01-01

Measured, open loop and closed loop data from the SMART rotor test in the NASA Ames 40- by 80- Foot Wind Tunnel are compared with CAMRAD II calculations. One open loop high-speed case and four closed loop cases are considered. The closed loop cases include three high-speed cases and one low-speed case. Two of these high-speed cases include a 2 deg flap deflection at 5P case and a test maximum-airspeed case. This study follows a recent, open loop correlation effort that used a simple correction factor for the airfoil pitching moment Mach number. Compared to the earlier effort, the current open loop study considers more fundamental corrections based on advancing blade aerodynamic conditions. The airfoil tables themselves have been studied. Selected modifications to the HH-06 section flap airfoil pitching moment table are implemented. For the closed loop condition, the effect of the flap actuator is modeled by increased flap hinge stiffness. Overall, the open loop correlation is reasonable, thus confirming the basic correctness of the current semi-empirical modifications; the closed loop correlation is also reasonable considering that the current flap model is a first generation model. Detailed correlation results are given in the paper.

Assigning Peptide Disulfide Linkage Pattern Among Regio-Isomers via Methoxy Addition to Disulfide and Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Durand, Kirt L.; Tan, Lei; Stinson, Craig A.; Love-Nkansah, Chasity B.; Ma, Xiaoxiao; Xia, Yu

2017-06-01

Pinpointing disulfide linkage pattern is critical in the characterization of proteins and peptides consisting of multiple disulfide bonds. Herein, we report a method based on coupling online disulfide modification and tandem mass spectrometry (MS/MS) to distinguish peptide disulfide regio-isomers. Such a method relies on a new disulfide bond cleavage reaction in solution, involving methanol as a reactant and 254 nm ultraviolet (UV) irradiation. This reaction leads to selective cleavage of a disulfide bond and formation of sulfenic methyl ester (-SOCH3) at one cysteine residue and a thiol (-SH) at the other. Under low energy collision-induced dissociation (CID), cysteine sulfenic methyl ester motif produces a signature methanol loss (-32 Da), allowing its identification from other possible isomeric structures such as S-hydroxylmethyl (-SCH2OH) and methyl sulfoxide (-S(O)-CH3). Since disulfide bond can be selectively cleaved and modified upon methoxy addition, subsequent MS2 CID of the methoxy addition product provides enhanced sequence coverage as demonstrated by the analysis of bovine insulin. More importantly, this reaction does not induce disulfide scrambling, likely due to the fact that radical intermediates are not involved in the process. An approach based on methoxy addition followed by MS3 CID has been developed for assigning disulfide linkage patterns in peptide disulfide regio-isomers. This methodology was successfully applied to characterizing peptide systems having two disulfide bonds and three disulfide linkage isomers: side-by-side, overlapped, and looped-within-a-loop configurations. [Figure not available: see fulltext.

Quenching of unincorporated amplification signal reporters in reverse-transcription loop-mediated isothermal amplification enabling bright, single-step, closed-tube, and multiplexed detection of RNA viruses

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

Ball, Cameron S.; Light, Yooli K.; Koh, Chung -Yan

Reverse-transcription-loop-mediated isothermal amplification (RT-LAMP) has frequently been proposed as an enabling technology for simplified diagnostic tests for RNA viruses. However, common detection techniques used for LAMP and RT-LAMP have drawbacks, including poor discrimination capability, inability to multiplex targets, high rates of false positives, and (in some cases) the requirement of opening reaction tubes postamplification. Here, we present a simple technique that allows closed-tube, target-specific detection, based on inclusion of a dye-labeled primer that is incorporated into a target-specific amplicon if the target is present. A short, complementary quencher hybridizes to unincorporated primer upon cooling down at the end of themore » reaction, thereby quenching fluorescence of any unincorporated primer. Our technique, which we term QUASR (for quenching of unincorporated amplification signal reporters, read “quasar”), does not significantly reduce the amplification efficiency or sensitivity of RT-LAMP. Equipped with a simple LED excitation source and a colored plastic gel filter, the naked eye or a camera can easily discriminate between positive and negative QUASR reactions, which produce a difference in signal of approximately 10:1 without background subtraction. We demonstrate that QUASR detection is compatible with complex sample matrices such as human blood, using a novel LAMP primer set for bacteriophage MS2 (a model RNA virus particle). As a result, we demonstrate single-tube duplex detection of West Nile virus (WNV) and chikungunya virus (CHIKV) RNA.« less

Quenching of unincorporated amplification signal reporters in reverse-transcription loop-mediated isothermal amplification enabling bright, single-step, closed-tube, and multiplexed detection of RNA viruses

DOE PAGES

Ball, Cameron S.; Light, Yooli K.; Koh, Chung -Yan; ...

2016-03-16

Reverse-transcription-loop-mediated isothermal amplification (RT-LAMP) has frequently been proposed as an enabling technology for simplified diagnostic tests for RNA viruses. However, common detection techniques used for LAMP and RT-LAMP have drawbacks, including poor discrimination capability, inability to multiplex targets, high rates of false positives, and (in some cases) the requirement of opening reaction tubes postamplification. Here, we present a simple technique that allows closed-tube, target-specific detection, based on inclusion of a dye-labeled primer that is incorporated into a target-specific amplicon if the target is present. A short, complementary quencher hybridizes to unincorporated primer upon cooling down at the end of themore » reaction, thereby quenching fluorescence of any unincorporated primer. Our technique, which we term QUASR (for quenching of unincorporated amplification signal reporters, read “quasar”), does not significantly reduce the amplification efficiency or sensitivity of RT-LAMP. Equipped with a simple LED excitation source and a colored plastic gel filter, the naked eye or a camera can easily discriminate between positive and negative QUASR reactions, which produce a difference in signal of approximately 10:1 without background subtraction. We demonstrate that QUASR detection is compatible with complex sample matrices such as human blood, using a novel LAMP primer set for bacteriophage MS2 (a model RNA virus particle). As a result, we demonstrate single-tube duplex detection of West Nile virus (WNV) and chikungunya virus (CHIKV) RNA.« less

Use of reverse transcription loop-mediated isothermal amplification combined with lateral flow dipstick for an easy and rapid detection of Jembrana disease virus.

PubMed

Kusumawati, Asmarani; Tampubolon, Issabellina Dwades; Hendarta, Narendra Yoga; Salasia, Siti Isrina Oktavia; Wanahari, Tenri Ashari; Mappakaya, Basofi Ashari; Hartati, Sri

2015-09-01

Jembrana disease virus (JDV) is a viral pathogen that causes Jembrana disease in Bali cattle (Bos javanicus) with high mortality rate. An easy and rapid diagnostic method is essential for further control this disease. We used a reverse transcription loop-mediated isothermal amplification (RT-LAMP) combined with lateral flow dipstick (LFD), based on conserved tm subunit of Jembrana disease virus env gene. The RT-LAMP conditions were optimized by varying the concentration of MgSO4, betaine, dNTP, and temperature as well as the time and duration of reaction. The primers sensitivity for JDV was confirmed. The method was able to detect env-tm gene dilution which contained 2 × 10(-15) g of template. Comparatively, the sensitivity of RT-LAMP/LFD was 100-fold more sensitive than reverse transcription-polymerase chain reaction. The primers specificity for JDV was also confirmed using positive and negative controls. This work also showed that virus detection could be done not only on total RNA extracted from blood but various organs could also be analyzed for the presence of JDV using RT-LAMP/LFD method. The whole process, including the LAMP reaction and the LFD hybridization step only lasts approximately 75 min. Results of analysis can be easily observed with naked eyes without addition of any chemical or further analysis. The combination of RT-LAMP with LFD makes the method a more suitable diagnostic tool in conditions where sophisticated and expensive equipments are not available for field investigations on Jembrana disease in Bali cattle.

Uniform Free-Energy Profiles of the P-O Bond Formation and Cleavage Reactions Catalyzed by DNA Polymerases β and λ.

PubMed

Klvaňa, Martin; Bren, Urban; Florián, Jan

2016-12-29

Human X-family DNA polymerases β (Polβ) and λ (Polλ) catalyze the nucleotidyl-transfer reaction in the base excision repair pathway of the cellular DNA damage response. Using empirical valence bond and free-energy perturbation simulations, we explore the feasibility of various mechanisms for the deprotonation of the 3'-OH group of the primer DNA strand, and the subsequent formation and cleavage of P-O bonds in four Polβ, two truncated Polλ (tPolλ), and two tPolλ Loop1 mutant (tPolλΔL1) systems differing in the initial X-ray crystal structure and nascent base pair. The average calculated activation free energies of 14, 18, and 22 kcal mol -1 for Polβ, tPolλ, and tPolλΔL1, respectively, reproduce the trend in the observed catalytic rate constants. The most feasible reaction pathway consists of two successive steps: specific base (SB) proton transfer followed by rate-limiting concerted formation and cleavage of the P-O bonds. We identify linear free-energy relationships (LFERs) which show that the differences in the overall activation and reaction free energies among the eight studied systems are determined by the reaction free energy of the SB proton transfer. We discuss the implications of the LFERs and suggest pK a of the 3'-OH group as a predictor of the catalytic rate of X-family DNA polymerases.

Uniform Free-Energy Profiles of the P–O Bond Formation and Cleavage Reactions Catalyzed by DNA Polymerases β and λ

PubMed Central

2016-01-01

Human X-family DNA polymerases β (Polβ) and λ (Polλ) catalyze the nucleotidyl-transfer reaction in the base excision repair pathway of the cellular DNA damage response. Using empirical valence bond and free-energy perturbation simulations, we explore the feasibility of various mechanisms for the deprotonation of the 3′-OH group of the primer DNA strand, and the subsequent formation and cleavage of P–O bonds in four Polβ, two truncated Polλ (tPolλ), and two tPolλ Loop1 mutant (tPolλΔL1) systems differing in the initial X-ray crystal structure and nascent base pair. The average calculated activation free energies of 14, 18, and 22 kcal mol–1 for Polβ, tPolλ, and tPolλΔL1, respectively, reproduce the trend in the observed catalytic rate constants. The most feasible reaction pathway consists of two successive steps: specific base (SB) proton transfer followed by rate-limiting concerted formation and cleavage of the P–O bonds. We identify linear free-energy relationships (LFERs) which show that the differences in the overall activation and reaction free energies among the eight studied systems are determined by the reaction free energy of the SB proton transfer. We discuss the implications of the LFERs and suggest pKa of the 3′-OH group as a predictor of the catalytic rate of X-family DNA polymerases. PMID:27992186

Network Thermodynamic Curation of Human and Yeast Genome-Scale Metabolic Models

PubMed Central

Martínez, Verónica S.; Quek, Lake-Ee; Nielsen, Lars K.

2014-01-01

Genome-scale models are used for an ever-widening range of applications. Although there has been much focus on specifying the stoichiometric matrix, the predictive power of genome-scale models equally depends on reaction directions. Two-thirds of reactions in the two eukaryotic reconstructions Homo sapiens Recon 1 and Yeast 5 are specified as irreversible. However, these specifications are mainly based on biochemical textbooks or on their similarity to other organisms and are rarely underpinned by detailed thermodynamic analysis. In this study, a to our knowledge new workflow combining network-embedded thermodynamic and flux variability analysis was used to evaluate existing irreversibility constraints in Recon 1 and Yeast 5 and to identify new ones. A total of 27 and 16 new irreversible reactions were identified in Recon 1 and Yeast 5, respectively, whereas only four reactions were found with directions incorrectly specified against thermodynamics (three in Yeast 5 and one in Recon 1). The workflow further identified for both models several isolated internal loops that require further curation. The framework also highlighted the need for substrate channeling (in human) and ATP hydrolysis (in yeast) for the essential reaction catalyzed by phosphoribosylaminoimidazole carboxylase in purine metabolism. Finally, the framework highlighted differences in proline metabolism between yeast (cytosolic anabolism and mitochondrial catabolism) and humans (exclusively mitochondrial metabolism). We conclude that network-embedded thermodynamics facilitates the specification and validation of irreversibility constraints in compartmentalized metabolic models, at the same time providing further insight into network properties. PMID:25028891

Charged string loops in Reissner-Nordström black hole background

NASA Astrophysics Data System (ADS)

Oteev, Tursinbay; Kološ, Martin; Stuchlík, Zdeněk

2018-03-01

We study the motion of current carrying charged string loops in the Reissner-Nordström black hole background combining the gravitational and electromagnetic field. Introducing new electromagnetic interaction between central charge and charged string loop makes the string loop equations of motion to be non-integrable even in the flat spacetime limit, but it can be governed by an effective potential even in the black hole background. We classify different types of the string loop trajectories using effective potential approach, and we compare the innermost stable string loop positions with loci of the charged particle innermost stable orbits. We examine string loop small oscillations around minima of the string loop effective potential, and we plot radial profiles of the string loop oscillation frequencies for both the radial and vertical modes. We construct charged string loop quasi-periodic oscillations model and we compare it with observed data from microquasars GRO 1655-40, XTE 1550-564, and GRS 1915+105. We also study the acceleration of current carrying string loops along the vertical axis and the string loop ejection from RN black hole neighbourhood, taking also into account the electromagnetic interaction.

Effect of orientation of prismatic dislocation loops on interaction with free surfaces in BCC iron

NASA Astrophysics Data System (ADS)

Fikar, Jan; Gröger, Roman; Schäublin, Robin

2017-12-01

The prismatic loops appear in metals as a result of high-energy irradiation. Understanding their formation and interaction is important for quantification of irradiation-induced deterioration of mechanical properties. Characterization of dislocation loops in thin foils is commonly made using transmission electron microscopy (TEM), but the results are inevitably influenced by the proximity of free surfaces. The prismatic loops are attracted to free surfaces by image forces. Depending on the type, shape, size, orientation and depth of the loop in the foil, they can escape to the free surface creating denuded loop-free zones and thus invalidating TEM observations. In our previous studies we described a simple general method to determine the critical depth and the critical stress to move prismatic dislocation loops. The critical depths can be further used to correct measurements of the loop density by TEM. Here, we use this procedure to compare 〈100〉 loops and 1/2 〈111〉 loops in body-centered cubic (BCC) iron. The influences of the interatomic potential and the loop orientation are studied in detail. The difference between interstitial and vacancy type loop is also investigated.

[Assessment of the treatment with imiquimod in persistent infection by human papillomavirus with the polimerase chain reaction method].

PubMed

Hernández Quijano, Tomás; Illanes Aguiar, Berenice; Salas Linares, Natividad; Alarcón Romero, Luz del Carmen; Hernández Valencia, Marcelino

2006-06-01

Molecular studies have shown that oncogenic genotypes of human papillomavirus (HPV) are the main risk factor for cervical cancer development. Sub-clinical wound does not cause symptoms and is diagnosed by colposcopy or histology, in addition the latent infection is associated with the presence of DNA of the HPV, but when clinical and histological abnormalities are not presented only molecular techniques can detect this infection. To determine if complementary processing with imiquimod, recent medicament with powerful antiviral activity in vitro as in vivo, reduces the cervical persistence of HPV. This study was carried out with 87 patients, who had antecedents of HPV cervical and intraepithelial wound with low degree. Patients were divided as follows: treated with cryotherapy, cervical loop electrosurgical and imiquimod, all with diagnosis by cervical cytology, colposcopy and polymerase chain reaction (PCR) for HPV. At 3, 6 and 12 months after the processing, PCR, cervical cytology and colposcopy control were carried out again. Out of the 87 patients studied, 11% (10) patients treated with cervical cytology were positive for VPH; with colposcopy 8% (7) of patients and with PCR 40% (34) of patients; decreased persistence with combined methods of loop and imiquimod was obtained in 29% (5) patients; however, when utilized imiquimod alone, there were 55% (11) patients with persistence determined by PCR method. Imiquimod appears to be beneficial in 45% of the patients, in contrast with efficacy reported until 85% in genitals and annals warts, in addition, the capacity of eliminating the viruses has been shown, therefore it is possible that its potential effect could be observed long-time. It is evident that the percentages of viral detection are improved for PCR method, compared with indirect methods as cervical cytology and colposcopy, which is favorable when virus serotypes are of high degree of transformation and ablative methods should be conservatives due to fertility motives.

TRACING THE DEVELOPMENT OF TYPEWRITING SKILLS IN AN ADAPTIVE E-LEARNING ENVIRONMENT.

PubMed

van den Bergh, Mattis; Hofman, Abe D; Schmittmann, Verena D; van der Maas, Han L J

2015-12-01

Typewriting studies which compare novice and expert typists have suggested that highly trained typing skills involve cognitive process with an inner and outer loop, which regulate keystrokes and words, respectively. The present study investigates these loops longitudinally, using multi-level modeling of 1,091,707 keystroke latencies from 62 children (M age=12.6 yr.) following an online typing course. Using finger movement repetition as indicator of the inner loop and words typed as indicator of the outer loop, practicing keystroke latencies resulted in different developmental curves for each loop. Moreover, based on plateaus in the developmental curves, the inner loop seemed to require less practice to develop than the outer loop.

Active control: an investigation method for combustion instabilities

NASA Astrophysics Data System (ADS)

Poinsot, T.; Yip, B.; Veynante, D.; Trouvé, A.; Samaniego, J. M.; Candel, S.

1992-07-01

Closed-loop active control methods and their application to combustion instabilities are discussed. In these methods the instability development is impeded with a feedback control loop: the signal provided by a sensor monitoring the flame or pressure oscillations is processed and sent back to actuators mounted on the combustor or on the feeding system. Different active control systems tested on a non-premixed multiple-flame turbulent combustor are described. These systems can suppress all unstable plane modes of oscillation (i.e. low frequency modes). The active instability control (AIC) also constitutes an original and powerful technique for studies of mechanisms leading to instability or resulting from the instability. Two basic applications of this kind are described. In the first case the flame is initially controlled with AIC, the feedback loop is then switched off and the growth of the instability is analysed through high speed Schlieren cinematography and simultaneous sound pressure and reaction rate measurements. Three phases are identified during th growth of the oscillations: (1) a linear phase where acoustic waves induce a flapping motion of the flame sheets without interaction between sheets, (2) a modulation phase, where flame sheets interact randomly and (3) a nonlinear phase where the flame sheets are broken and a limit cycle is reached. In the second case we investigate different types of flame extinctions associated with combustion instability. It is shown that pressure oscillations may lead to partial or total extinctions. Extinctions occur in various forms but usually follow a rapid growth of pressure oscillations. The flame is extinguished during the modulation phase observed in the initiation experiments. In these studies devoted to transient instability phenomena, the control system constitutes a unique investigation tool because it is difficult to obtain the same information by other means. Implications for modelling and prediction of combustion instabilities are discussed.

Detection and differentiation of Fusarium oxysporum f. sp. lycopersici race 1 using loop-mediated isothermal amplification with three primer sets.

PubMed

Ayukawa, Y; Komatsu, K; Kashiwa, T; Akai, K; Yamada, M; Teraoka, T; Arie, T

2016-09-01

Fusarium oxysporum f. sp. lycopersici (Fol) causes tomato wilt. Based on the difference in pathogenicity towards tomato cultivars, Fol is classified into three races. In this study, a rapid method is developed for the detection and discrimination of Fol race 1 using a loop-mediated isothermal amplification (LAMP) assay with two primer sets targeting a region of the nucleotide sequence of the SIX4 gene specific for race 1 and a primer set targeting the SIX5 gene, conserved in all known Fol isolates. Upon LAMP reaction, amplification using all three primer sets was observed only when DNA of Fol race 1 was used as a template, and not when DNA of other Fol races or other fungal species was used. This method could detect 300 fg of Fol race 1 DNA, a 100-fold higher sensitivity than that obtained by conventional PCR. The method can also detect DNA extracted from soil artificially infested with Fol race 1. It is now possible to detect Fol race 1 in colonies and infected tomato stems without DNA isolation. This method is a rapid and simple tool for discrimination of Fol race 1. This study developed a loop-mediated isothermal amplification (LAMP) assay for detection and differentiation of Fusarium oxysporum f. sp. lycopersici (Fol) race 1 by using three primer sets targeting for the SIX4 and SIX5 genes. These genes are present together only in Fol race 1. This method can detect Fol race 1 in infected tomato stems without DNA extraction, affording an efficient diagnosis of Fusarium wilt on tomatoes in the field. © 2016 The Society for Applied Microbiology.

Noise induced oscillations and coherence resonance in a generic model of the nonisothermal chemical oscillator

PubMed Central

Simakov, David S. A.; Pérez-Mercader, Juan

2013-01-01

Oscillating chemical reactions are common in biological systems and they also occur in artificial non-biological systems. Generally, these reactions are subject to random fluctuations in environmental conditions which translate into fluctuations in the values of physical variables, for example, temperature. We formulate a mathematical model for a nonisothermal minimal chemical oscillator containing a single negative feedback loop and study numerically the effects of stochastic fluctuations in temperature in the absence of any deterministic limit cycle or periodic forcing. We show that noise in temperature can induce sustained limit cycle oscillations with a relatively narrow frequency distribution and some characteristic frequency. These properties differ significantly depending on the noise correlation. Here, we have explored white and colored (correlated) noise. A plot of the characteristic frequency of the noise induced oscillations as a function of the correlation exponent shows a maximum, therefore indicating the existence of autonomous stochastic resonance, i.e. coherence resonance. PMID:23929212

Neuro-estimator based GMC control of a batch reactive distillation.

PubMed

Prakash, K J Jithin; Patle, Dipesh S; Jana, Amiya K

2011-07-01

In this paper, an artificial neural network (ANN)-based nonlinear control algorithm is proposed for a simulated batch reactive distillation (RD) column. In the homogeneously catalyzed reactive process, an esterification reaction takes place for the production of ethyl acetate. The fundamental model has been derived incorporating the reaction term in the model structure of the nonreactive distillation process. The process operation is simulated at the startup phase under total reflux conditions. The open-loop process dynamics is also addressed running the batch process at the production phase under partial reflux conditions. In this study, a neuro-estimator based generic model controller (GMC), which consists of an ANN-based state predictor and the GMC law, has been synthesized. Finally, this proposed control law has been tested on the representative batch reactive distillation comparing with a gain-scheduled proportional integral (GSPI) controller and with its ideal performance (ideal GMC). Copyright © 2011 ISA. Published by Elsevier Ltd. All rights reserved.

Second Law of Thermodynamics Applied to Metabolic Networks

NASA Technical Reports Server (NTRS)

Nigam, R.; Liang, S.

2003-01-01

We present a simple algorithm based on linear programming, that combines Kirchoff's flux and potential laws and applies them to metabolic networks to predict thermodynamically feasible reaction fluxes. These law's represent mass conservation and energy feasibility that are widely used in electrical circuit analysis. Formulating the Kirchoff's potential law around a reaction loop in terms of the null space of the stoichiometric matrix leads to a simple representation of the law of entropy that can be readily incorporated into the traditional flux balance analysis without resorting to non-linear optimization. Our technique is new as it can easily check the fluxes got by applying flux balance analysis for thermodynamic feasibility and modify them if they are infeasible so that they satisfy the law of entropy. We illustrate our method by applying it to the network dealing with the central metabolism of Escherichia coli. Due to its simplicity this algorithm will be useful in studying large scale complex metabolic networks in the cell of different organisms.

Crystal plasticity modeling of irradiation growth in Zircaloy-2

NASA Astrophysics Data System (ADS)

Patra, Anirban; Tomé, Carlos N.; Golubov, Stanislav I.

2017-08-01

A physically based reaction-diffusion model is implemented in the visco-plastic self-consistent (VPSC) crystal plasticity framework to simulate irradiation growth in hcp Zr and its alloys. The reaction-diffusion model accounts for the defects produced by the cascade of displaced atoms, their diffusion to lattice sinks and the contribution to crystallographic strain at the level of single crystals. The VPSC framework accounts for intergranular interactions and irradiation creep, and calculates the strain in the polycrystalline ensemble. A novel scheme is proposed to model the simultaneous evolution of both, number density and radius, of irradiation-induced dislocation loops directly from experimental data of dislocation density evolution during irradiation. This framework is used to predict the irradiation growth behaviour of cold-worked Zircaloy-2 and trends compared to available experimental data. The role of internal stresses in inducing irradiation creep is discussed. Effects of grain size, texture and external stress on the coupled irradiation growth and creep behaviour are also studied and compared with available experimental data.

Development of loop-mediated isothermal amplification methods for detecting Taylorella equigenitalis and Taylorella asinigenitalis

PubMed Central

KINOSHITA, Yuta; NIWA, Hidekazu; KATAYAMA, Yoshinari; HARIU, Kazuhisa

2015-01-01

ABSTRACT Taylorella equigenitalis is a causative bacterium of contagious equine metritis (CEM), and Taylorella asinigenitalis is species belonging to genus Taylorella. The authors developed two loop-mediated isothermal amplification (LAMP) methods, Te-LAMP and Ta-LAMP, for detecting T. equigenitalis and T. asinigenitalis, respectively. Using experimentally spiked samples, Te-LAMP was as sensitive as a published semi-nested PCR method, and Ta-LAMP was more sensitive than conventional PCR. Multiplex LAMP worked well without nonspecific reactions, and the analytical sensitivities of multiplex LAMP in the spiked samples were almost equivalent to those of Te-LAMP and Ta-LAMP. Therefore, the LAMP methods are considered useful tools to detect T. equigenitalis and/or T. asinigenitalis, and preventive measures will be rapidly implemented if the occurrence of CEM is confirmed by the LAMP methods. PMID:25829868

Lethal Autonomous Weapons: Take the Human Out of the Loop

DTIC Science & Technology

2017-06-16

such as unrestricted submarine warfare and strategic bombing , both in WWII, without having had the chance to fully examine the potential ramifications...the trauma of battle. Kurt Vonnegut describes his experience as a POW during the bombing of Dresden: “I saw the destruction of Dresden...uncontrollable reaction to the stress he endured during the Dresden bombing . While laughter may not detrimentally affect decision making, he still loses

Ball Lightning–Aerosol Electrochemical Power Source or A Cloud of Batteries

PubMed Central

2007-01-01

Despite numerous attempts, an adequate theoretical and experimental simulation of ball lightning still remains incomplete. According to the model proposed here, the processes of electrochemical oxidation within separate aerosol particles are the basis for this phenomenon, and ball lightning is a cloud of composite nano or submicron particles, where each particle is a spontaneously formed nanobattery which is short-circuited by the surface discharge because it is of such a small size. As free discharge-shorted current loops, aerosol nanobatteries are exposed to a powerful mutual magnetic dipole–dipole attraction. The gaseous products and thermal energy produced by each nanobattery as a result of the intra-particle self-sustaining electrochemical reactions, cause a mutual repulsion of these particles over short distances and prevent their aggregation, while a collectivization of the current loops of separate particles, due to the electric arc overlapping between adjacent particles, weakens their mutual magnetic attraction over short distances. Discharge currents in the range of several amperes to several thousand amperes as well as the pre-explosive mega ampere currents, generated in the reduction–oxidation reactions and distributed between all the aerosol particles, explain both the magnetic attraction between the elements of the ball lightning substance and the impressive electromagnetic effects of ball lightning.

Loop-mediated isothermal amplification assay for detection of Haemophilus influenzae type b in cerebrospinal fluid.

PubMed

Kim, Dong Wook; Kilgore, Paul Evan; Kim, Eun Jin; Kim, Soon Ae; Anh, Dang Duc; Seki, Mitsuko

2011-10-01

Haemophilus influenzae type b (Hib) is one of the leading causes of meningitis in developing countries. To establish and evaluate a novel loop-mediated isothermal amplification (LAMP) assay for Hib, we designed a LAMP primer set targeting the Hib-specific capsulation locus. LAMP detected 10 copies of purified DNA in a 60-min reaction. This indicated that the detection limit of LAMP was >100-fold lower than the detection limits of both a PCR for the detection of bexA and a nested PCR for Hib (Hib PCR). No H. influenzae, other than Hib or control bacteria, was detected. Linear determination ranged from 10 to 1,000,000 microorganisms per reaction mixture using real-time turbidimetry. We evaluated the Hib LAMP assay using a set of 52 randomly selected cerebrospinal fluid (CSF) specimens obtained from children with suspected meningitis. For comparison, the CSF specimens were tested using a conventional Hib PCR assay. Hib was detected in 30 samples using LAMP and in 22 samples using the Hib PCR assay. The Hib PCR showed a clinical sensitivity of 73.3% and a clinical specificity of 100% relative to the Hib LAMP assay. These results suggest that further development and evaluation of the Hib LAMP will enhance the global diagnostic capability for Hib detection.

Approaches to flame resistant polymeric materials

NASA Technical Reports Server (NTRS)

Liepins, R.

1975-01-01

Four research and development areas are considered for further exploration in the quest of more flame-resistant polymeric materials. It is suggested that improvements in phenolphthalein polycarbonate processability may be gained through linear free energy relationship correlations. Looped functionality in the backbone of a polymer leads to both improved thermal resistance and increased solubility. The guidelines used in the pyrolytic carbon production constitute a good starting point for the development of improved flame-resistant materials. Numerous organic reactions requiring high temperatures and the techniques of protected functionality and latent functionality constitute the third area for exploration. Finally, some well-known organic reactions are suggested for the formation of polymers that were not made before.

Fluidics platform and method for sample preparation and analysis

DOEpatents

Benner, W. Henry; Dzenitis, John M.; Bennet, William J.; Baker, Brian R.

2014-08-19

Herein provided are fluidics platform and method for sample preparation and analysis. The fluidics platform is capable of analyzing DNA from blood samples using amplification assays such as polymerase-chain-reaction assays and loop-mediated-isothermal-amplification assays. The fluidics platform can also be used for other types of assays and analyzes. In some embodiments, a sample in a sealed tube can be inserted directly. The following isolation, detection, and analyzes can be performed without a user's intervention. The disclosed platform may also comprises a sample preparation system with a magnetic actuator, a heater, and an air-drying mechanism, and fluid manipulation processes for extraction, washing, elution, assay assembly, assay detection, and cleaning after reactions and between samples.

Ferroelectric and dielectric properties of BaTi0.9Zr0.1O3 doped with Li0.5Fe2.5O4 ceramics

NASA Astrophysics Data System (ADS)

Gajula, Ganapathi Rao; Buddiga, Lakshmi Rekha; Chidambara Kumar, K. N.; Ch, Arun Kumar; Samatha, K.; Kokkiragadda, Sreeramachandra Murthy; Dasari, Madhava Prasad

2018-06-01

We have prepared a composite BaTi0.9Zr0.1O3 (BTZr) doped with Li0.5Fe2.5O4 (LF) having chemical formulae (1- x) BTZr + (x) LF (x=0, 0.05, 0.1 and 0.15) conventional solid state reaction technique. We have sintered the grown composites at 1150 °C for 3 h. We have characterized the grown composites using XRD, FESEM, P-E loop tracer and LCR meter. The XRD measurements reveal the tetragonal nature of the composites. The morphological studies reveal that the composite exhibits dense microstructure with small pores. The P-E loops confirm that the composites exhibit remnant polarization and the coercive field increases with increasing concentration of Lithium Ferrite (LF). We have studied dielectric property of the composites by varying the temperature of the sample from 30 °C to 500 °C at 1 kHz, 10 kHz and also by varying the frequency from 1 Hz to 10 MHz at 30 °C. The dielectric property of BTZr has increased after doping LF in BTZr which reveals the enhancement of electrical properties of the grown composite.

Active site and loop 4 movements within human glycolate oxidase: implications for substrate specificity and drug design.

PubMed

Murray, Michael S; Holmes, Ross P; Lowther, W Todd

2008-02-26

Human glycolate oxidase (GO) catalyzes the FMN-dependent oxidation of glycolate to glyoxylate and glyoxylate to oxalate, a key metabolite in kidney stone formation. We report herein the structures of recombinant GO complexed with sulfate, glyoxylate, and an inhibitor, 4-carboxy-5-dodecylsulfanyl-1,2,3-triazole (CDST), determined by X-ray crystallography. In contrast to most alpha-hydroxy acid oxidases including spinach glycolate oxidase, a loop region, known as loop 4, is completely visible when the GO active site contains a small ligand. The lack of electron density for this loop in the GO-CDST complex, which mimics a large substrate, suggests that a disordered to ordered transition may occur with the binding of substrates. The conformational flexibility of Trp110 appears to be responsible for enabling GO to react with alpha-hydroxy acids of various chain lengths. Moreover, the movement of Trp110 disrupts a hydrogen-bonding network between Trp110, Leu191, Tyr134, and Tyr208. This loss of interactions is the first indication that active site movements are directly linked to changes in the conformation of loop 4. The kinetic parameters for the oxidation of glycolate, glyoxylate, and 2-hydroxy octanoate indicate that the oxidation of glycolate to glyoxylate is the primary reaction catalyzed by GO, while the oxidation of glyoxylate to oxalate is most likely not relevant under normal conditions. However, drugs that exploit the unique structural features of GO may ultimately prove to be useful for decreasing glycolate and glyoxylate levels in primary hyperoxaluria type 1 patients who have the inability to convert peroxisomal glyoxylate to glycine.

Closed-Loop Control Better than Open-Loop Control of Profofol TCI Guided by BIS: A Randomized, Controlled, Multicenter Clinical Trial to Evaluate the CONCERT-CL Closed-Loop System

PubMed Central

Zhang, Xuena; Wu, Anshi; Yao, Shanglong; Xue, Zhanggang; Yue, Yun

2015-01-01

Background The CONCERT-CL closed-loop infusion system designed by VERYARK Technology Co., Ltd. (Guangxi, China) is an innovation using TCI combined with closed-loop controlled intravenous anesthesia under the guide of BIS. In this study we performed a randomized, controlled, multicenter study to compare closed-loop control and open-loop control of propofol by using the CONCERT-CL closed-loop infusion system. Methods 180 surgical patients from three medical centers undergone TCI intravenous anesthesia with propofol and remifentanil were randomly assigned to propofol closed-loop group and propofol opened-loop groups. Primary outcome was global score (GS, GS = (MDAPE+Wobble)/% of time of bispectral index (BIS) 40-60). Secondary outcomes were doses of the anesthetics and emergence time from anesthesia, such as, time to tracheal extubation. Results There were 89 and 86 patients in the closed-loop and opened-loop groups, respectively. GS in the closed-loop groups (22.21±8.50) were lower than that in the opened-loop group (27.19±15.26) (p=0.009). The higher proportion of time of BIS between 40 and 60 was also observed in the closed-loop group (84.11±9.50%), while that was 79.92±13.17% in the opened-loop group, (p=0.016). No significant differences in propofol dose and time of tracheal extubation were observed. The frequency of propofol regulation in the closed-loop group (31.55±9.46 times/hr) was obverse higher than that in the opened-loop group (6.84±6.21 times/hr) (p=0.000). Conclusion The CONCERT-CL closed-loop infusion system can automatically regulate the TCI of propofol, maintain the BIS value in an adequate range and reduce the workload of anesthesiologists better than open-loop system. Trial Registration ChiCTR ChiCTR-OOR-14005551 PMID:25886041

A Flight-Calibrated Methodology for Determination of Cassini Thruster On-Times for Reaction Wheel Biases

NASA Technical Reports Server (NTRS)

Sarani, Sam

2010-01-01

The Cassini spacecraft, the largest and most complex interplanetary spacecraft ever built, continues to undertake unique scientific observations of planet Saturn, Titan, Enceladus, and other moons of the ring world. In order to maintain a stable attitude during the course of its mission, this three-axis stabilized spacecraft uses two different control systems: the Reaction Control System (or RCS) and the Reaction Wheel Assembly (RWA) control system. In the course of its mission, Cassini performs numerous reaction wheel momentum biases (or unloads) using its reaction control thrusters. The use of the RCS thrusters often imparts undesired velocity changes (delta Vs) on the spacecraft and it is crucial for Cassini navigation and attitude control teams to be able to, quickly but accurately, predict the hydrazine usage and delta V vector in Earth Mean Equatorial (J2000) inertial coordinates for reaction wheel bias events, without actually having to spend time and resources simulating the event in a dynamic or hardware-in-the-loop simulation environments. The flight-calibrated methodology described in this paper, and the ground software developed thereof, are designed to provide the RCS thruster on-times, with acceptable accuracy and without any form of dynamic simulation, for reaction wheel biases, along with the hydrazine usage and the delta V in EME-2000 inertial frame.

On higher order discrete phase-locked loops.

NASA Technical Reports Server (NTRS)

Gill, G. S.; Gupta, S. C.

1972-01-01

An exact mathematical model is developed for a discrete loop of a general order particularly suitable for digital computation. The deterministic response of the loop to the phase step and the frequency step is investigated. The design of the digital filter for the second-order loop is considered. Use is made of the incremental phase plane to study the phase error behavior of the loop. The model of the noisy loop is derived and the optimization of the loop filter for minimum mean-square error is considered.

Propulsive Reaction Control System Model

NASA Technical Reports Server (NTRS)

Brugarolas, Paul; Phan, Linh H.; Serricchio, Frederick; San Martin, Alejandro M.

2011-01-01

This software models a propulsive reaction control system (RCS) for guidance, navigation, and control simulation purposes. The model includes the drive electronics, the electromechanical valve dynamics, the combustion dynamics, and thrust. This innovation follows the Mars Science Laboratory entry reaction control system design, and has been created to meet the Mars Science Laboratory (MSL) entry, descent, and landing simulation needs. It has been built to be plug-and-play on multiple MSL testbeds [analysis, Monte Carlo, flight software development, hardware-in-the-loop, and ATLO (assembly, test and launch operations) testbeds]. This RCS model is a C language program. It contains two main functions: the RCS electronics model function that models the RCS FPGA (field-programmable-gate-array) processing and commanding of the RCS valve, and the RCS dynamic model function that models the valve and combustion dynamics. In addition, this software provides support functions to initialize the model states, set parameters, access model telemetry, and access calculated thruster forces.

Kinetics of Internal-Loop Formation in Polypeptide Chains: A Simulation Study

PubMed Central

Doucet, Dana; Roitberg, Adrian; Hagen, Stephen J.

2007-01-01

The speed of simple diffusional motions, such as the formation of loops in the polypeptide chain, places one physical limit on the speed of protein folding. Many experimental studies have explored the kinetics of formation of end-to-end loops in polypeptide chains; however, protein folding more often requires the formation of contacts between interior points on the chain. One expects that, for loops of fixed contour length, interior loops will form more slowly than end-to-end loops, owing to the additional excluded volume associated with the “tails”. We estimate the magnitude of this effect by generating ensembles of randomly coiled, freely jointed chains, and then using the theory of Szabo, Schulten, and Schulten to calculate the corresponding contact formation rates for these ensembles. Adding just a few residues, to convert an end-to-end loop to an internal loop, sharply decreases the contact rate. Surprisingly, the relative change in rate increases for a longer loop; sufficiently long tails, however, actually reverse the effect and accelerate loop formation slightly. Our results show that excluded volume effects in real, full-length polypeptides may cause the rates of loop formation during folding to depart significantly from the values derived from recent loop-formation experiments on short peptides. PMID:17208979

Stabilization of self-mode-locked quantum dash lasers by symmetric dual-loop optical feedback

NASA Astrophysics Data System (ADS)

Asghar, Haroon; Wei, Wei; Kumar, Pramod; Sooudi, Ehsan; McInerney, John. G.

2018-02-01

We report experimental studies of the influence of symmetric dual-loop optical feedback on the RF linewidth and timing jitter of self-mode-locked two-section quantum dash lasers emitting at 1550 nm. Various feedback schemes were investigated and optimum levels determined for narrowest RF linewidth and low timing jitter, for single-loop and symmetric dual-loop feedback. Two symmetric dual-loop configurations, with balanced and unbalanced feedback ratios, were studied. We demonstrate that unbalanced symmetric dual loop feedback, with the inner cavity resonant and fine delay tuning of the outer loop, gives narrowest RF linewidth and reduced timing jitter over a wide range of delay, unlike single and balanced symmetric dual-loop configurations. This configuration with feedback lengths 80 and 140 m narrows the RF linewidth by 4-67x and 10-100x, respectively, across the widest delay range, compared to free-running. For symmetric dual-loop feedback, the influence of different power split ratios through the feedback loops was determined. Our results show that symmetric dual-loop feedback is markedly more effective than single-loop feedback in reducing RF linewidth and timing jitter, and is much less sensitive to delay phase, making this technique ideal for applications where robustness and alignment tolerance are essential.

An optimal open/closed-loop control method with application to a pre-stressed thin duralumin plate

NASA Astrophysics Data System (ADS)

Nadimpalli, Sruthi Raju

The excessive vibrations of a pre-stressed duralumin plate, suppressed by a combination of open-loop and closed-loop controls, also known as open/closed-loop control, is studied in this thesis. The two primary steps involved in this process are: Step (I) with an assumption that the closed-loop control law is proportional, obtain the optimal open-loop control by direct minimization of the performance measure consisting of energy at terminal time and a penalty on open-loop control force via calculus of variations. If the performance measure also involves a penalty on closed-loop control effort then a Fourier based method is utilized. Step (II) the energy at terminal time is minimized numerically to obtain optimal values of feedback gains. The optimal closed-loop control gains obtained are used to describe the displacement and the velocity of open-loop, closed-loop and open/closed-loop controlled duralumin plate.

Evaluation of inertial devices for the control of large, flexible, space-based telerobotic arms

NASA Technical Reports Server (NTRS)

Montgomery, Raymond C.; Kenny, Sean P.; Ghosh, Dave; Shenhar, Joram

1993-01-01

Inertial devices, including sensors and actuators, offer the potential of improving the tracking of telerobotic commands for space-based robots by smoothing payload motions and suppressing vibrations. In this paper, inertial actuators (specifically, torque-wheels and reaction-masses) are studied for that potential application. Batch simulation studies are presented which show that torque-wheels can reduce the overshoot in abrupt stop commands by 82 percent for a two-link arm. For man-in-the-loop evaluation, a real-time simulator has been developed which samples a hand-controller, solves the nonlinear equations of motion, and graphically displays the resulting motion on a computer workstation. Currently, two manipulator models, a two-link, rigid arm and a single-link, flexible arm, have been studied. Results are presented which show that, for a single-link arm, a reaction-mass/torque-wheel combination at the payload end can yield a settling time of 3 s for disturbances in the first flexible mode as opposed to 10 s using only a hub motor. A hardware apparatus, which consists of a single-link, highly flexible arm with a hub motor and a torque-wheel, has been assembled to evaluate the concept and is described herein.

Evaluation of inertial devices for the control of large, flexible, space-based telerobotic arms

NASA Astrophysics Data System (ADS)

Montgomery, Raymond C.; Kenny, Sean P.; Ghosh, Dave; Shenhar, Joram

1993-02-01

Inertial devices, including sensors and actuators, offer the potential of improving the tracking of telerobotic commands for space-based robots by smoothing payload motions and suppressing vibrations. In this paper, inertial actuators (specifically, torque-wheels and reaction-masses) are studied for that potential application. Batch simulation studies are presented which show that torque-wheels can reduce the overshoot in abrupt stop commands by 82 percent for a two-link arm. For man-in-the-loop evaluation, a real-time simulator has been developed which samples a hand-controller, solves the nonlinear equations of motion, and graphically displays the resulting motion on a computer workstation. Currently, two manipulator models, a two-link, rigid arm and a single-link, flexible arm, have been studied. Results are presented which show that, for a single-link arm, a reaction-mass/torque-wheel combination at the payload end can yield a settling time of 3 s for disturbances in the first flexible mode as opposed to 10 s using only a hub motor. A hardware apparatus, which consists of a single-link, highly flexible arm with a hub motor and a torque-wheel, has been assembled to evaluate the concept and is described herein.

Low effective activation energies for oxygen release from metal oxides: evidence for mass-transfer limits at high heating rates.

PubMed

Jian, Guoqiang; Zhou, Lei; Piekiel, Nicholas W; Zachariah, Michael R

2014-06-06

Oxygen release from metal oxides at high temperatures is relevant to many thermally activated chemical processes, including chemical-looping combustion, solar thermochemical cycles and energetic thermite reactions. In this study, we evaluated the thermal decomposition of nanosized metal oxides under rapid heating (~10(5) K s(-1)) with time-resolved mass spectrometry. We found that the effective activation-energy values that were obtained using the Flynn-Wall-Ozawa isoconversional method are much lower than the values found at low heating rates, indicating that oxygen transport might be rate-determining at a high heating rate. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Feed forward and feedback control for over-ground locomotion in anaesthetized cats

NASA Astrophysics Data System (ADS)

Mazurek, K. A.; Holinski, B. J.; Everaert, D. G.; Stein, R. B.; Etienne-Cummings, R.; Mushahwar, V. K.

2012-04-01

The biological central pattern generator (CPG) integrates open and closed loop control to produce over-ground walking. The goal of this study was to develop a physiologically based algorithm capable of mimicking the biological system to control multiple joints in the lower extremities for producing over-ground walking. The algorithm used state-based models of the step cycle each of which produced different stimulation patterns. Two configurations were implemented to restore over-ground walking in five adult anaesthetized cats using intramuscular stimulation (IMS) of the main hip, knee and ankle flexor and extensor muscles in the hind limbs. An open loop controller relied only on intrinsic timing while a hybrid-CPG controller added sensory feedback from force plates (representing limb loading), and accelerometers and gyroscopes (representing limb position). Stimulation applied to hind limb muscles caused extension or flexion in the hips, knees and ankles. A total of 113 walking trials were obtained across all experiments. Of these, 74 were successful in which the cats traversed 75% of the 3.5 m over-ground walkway. In these trials, the average peak step length decreased from 24.9 ± 8.4 to 21.8 ± 7.5 (normalized units) and the median number of steps per trial increased from 7 (Q1 = 6, Q3 = 9) to 9 (8, 11) with the hybrid-CPG controller. Moreover, within these trials, the hybrid-CPG controller produced more successful steps (step length ≤ 20 cm ground reaction force ≥ 12.5% body weight) than the open loop controller: 372 of 544 steps (68%) versus 65 of 134 steps (49%), respectively. This supports our previous preliminary findings, and affirms that physiologically based hybrid-CPG approaches produce more successful stepping than open loop controllers. The algorithm provides the foundation for a neural prosthetic controller and a framework to implement more detailed control of locomotion in the future.

Feed forward and feedback control for over-ground locomotion in anaesthetized cats

PubMed Central

Mazurek, K A; Holinski, B J; Everaert, D G; Stein, R B; Etienne-Cummings, R; Mushahwar, V K

2012-01-01

The biological central pattern generator (CPG) integrates open and closed loop control to produce over-ground walking. The goal of this study was to develop a physiologically based algorithm capable of mimicking the biological system to control multiple joints in the lower extremities for producing over-ground walking. The algorithm used state-based models of the step cycle each of which produced different stimulation patterns. Two configurations were implemented to restore over-ground walking in five adult anaesthetized cats using intramuscular stimulation (IMS) of the main hip, knee and ankle flexor and extensor muscles in the hind limbs. An open loop controller relied only on intrinsic timing while a hybrid-CPG controller added sensory feedback from force plates (representing limb loading), and accelerometers and gyroscopes (representing limb position). Stimulation applied to hind limb muscles caused extension or flexion in the hips, knees and ankles. A total of 113 walking trials were obtained across all experiments. Of these, 74 were successful in which the cats traversed 75% of the 3.5 m over-ground walkway. In these trials, the average peak step length decreased from 24.9 ± 8.4 to 21.8 ± 7.5 (normalized units) and the median number of steps per trial increased from 7 (Q1=6, Q3 = 9) to 9 (8, 11) with the hybrid-CPG controller. Moreover, these trials, the hybrid-CPG controller produced more successful steps (step length ≤ 20 cm; ground reaction force ≥ 12.5% body weight) than the open loop controller: 372 of 544 steps (68%) versus 65 of 134 steps (49%), respectively. This supports our previous preliminary findings, and affirms that physiologically based hybrid-CPG approaches produce more successful stepping than open loop controllers. The algorithm provides the foundation for a neural prosthetic controller and a framework to implement more detailed control of locomotion in the future. PMID:22328615

A distal mutation perturbs dynamic amino acid networks in dihydrofolate reductase

PubMed Central

Bae, Sung-Hun; Duggan, Brendan M.; Benkovic, Stephen J.; Dyson, H. Jane; Wright, Peter E

2013-01-01

Correlated networks of amino acids have been proposed to play a fundamental role in allostery and enzyme catalysis. These networks of amino acids can be traced from surface-exposed residues all the way into the active site, and disruption of these networks can decrease enzyme activity. Substitution of the distal Gly121 residue in E.coli dihydrofolate reductase results in up to a 200-fold decrease in the hydride transfer rate despite the fact that the residue is located 15 Å from the active-site center. In the present study, NMR relaxation experiments are used to demonstrate that dynamics on the ps-ns and μs-ms timescales are changed significantly in the G121V mutant of dihydrofolate reductase. In particular, ps-ns timescale dynamics are decreased in the FG loop (containing the mutated residue 121) and the neighboring active-site loop (the Met20 loop) in the mutant compared to wild-type enzyme, suggesting that these loops are dynamically coupled. Changes in methyl order parameters reveal a pathway by which dynamic perturbations can be propagated more than 25 Å across the protein from the site of mutation. All of the enzyme complexes, including the model Michaelis complex with folate and NADP+ bound, assume an occluded ground state conformation, and we do not observe sampling of a higher energy closed conformation by 15N R2 relaxation dispersion. This is highly significant, since it is only in the closed conformation that the cofactor and substrate reactive centers are positioned for reaction. The mutation also impairs μs - ms timescale fluctuations that have been implicated in product release from the wild type enzyme. Our results are consistent with an important role for Gly121 in controlling protein dynamics critical for enzyme function and further validate the dynamic energy landscape hypothesis of enzyme catalysis. PMID:23758161

Molecular dynamics simulations reveal a new role for a conserved active site asparagine in a ubiquitin-conjugating enzyme.

PubMed

Wilson, R Hunter; Zamfir, Serban; Sumner, Isaiah

2017-09-01

The role of a highly conserved active site asparagine (N79) in the ubiquitin conjugating enzyme, Ubc13, is probed using molecular dynamics simulations. Both wild type and mutant enzymes (N79A and N79D) are studied. Contrary to a popular hypothesis, we show that it is unlikely that N79 stabilizes a reaction intermediate, but instead preferentially hydrogen bonds to a loop near the active site. This keeps the sidechain carboxylate of an aspartate in the loop (D119) near the sidechain amine of the substrate lysine. Our simulations show that this distance increases in the mutants. D119 has been hypothesized to play a variety of roles in the enzyme, including deprotonating the substrate lysine, so changing this distance can have an effect on the enzyme's efficiency. Finally, we show that it is possible for the aspartate to deprotonate the substrate even across long distances if short water wires form that connect the proton donor and acceptor. Short water wires form with greater probability in the wild type than in mutant enzymes. Copyright © 2017 Elsevier Inc. All rights reserved.

Direct detection of Mycobacterium avium in environmental water and scale samples by loop-mediated isothermal amplification.

PubMed

Nishiuchi, Yukiko; Tamaru, Aki; Suzuki, Yasuhiko; Kitada, Seigo; Maekura, Ryoji; Tateishi, Yoshitaka; Niki, Mamiko; Ogura, Hisashi; Matsumoto, Sohkichi

2014-06-01

We previously demonstrated the colonization of Mycobacterium avium complex in bathrooms by the conventional culture method. In the present study, we aimed to directly detect M. avium organisms in the environment using loop-mediated isothermal amplification (LAMP), and to demonstrate the efficacy of LAMP by comparing the results with those obtained by culture. Our data showed that LAMP analysis has detection limits of 100 fg DNA/reaction for M. avium. Using an FTA(®) elute card, DNA templates were extracted from environmental samples from bathrooms in the residences of 29 patients with pulmonary M. avium disease. Of the 162 environmental samples examined, 143 (88%) showed identical results by both methods; 20 (12%) and 123 (76%) samples were positive and negative, respectively, for M. avium. Of the remaining 19 samples (12%), seven (5%) and 12 (7%) samples were positive by the LAMP and culture methods, respectively. All samples that contained over 20 colony forming units/primary isolation plate, as measured by the culture method, were also positive by the LAMP method. Our data demonstrate that the combination of the FTA elute card and LAMP can facilitate prompt detection of M. avium in the environment.

Simple Identification of Human Taenia Species by Multiplex Loop-Mediated Isothermal Amplification in Combination with Dot Enzyme-Linked Immunosorbent Assay

PubMed Central

Nkouawa, Agathe; Sako, Yasuhito; Okamoto, Munehiro; Ito, Akira

2016-01-01

For differential detection of Taenia solium, Taenia saginata, and Taenia asiatica, loop-mediated isothermal amplification (LAMP) assay targeting the cytochrome c oxidase subunit 1 gene has been recently developed and shown to be sensitive, specific, and effective. However, to achieve differential identification, one specimen requires three reaction mixtures containing a primer set of each Taenia species separately, which is complex and time consuming and increases the risk of cross-contamination. In this study, we developed a simple differential identification of human Taenia species using multiplex LAMP (mLAMP) in combination with dot enzyme-linked immunosorbent assay (dot-ELISA). Forward inner primers of T. solium, T. saginata, and T. asiatica labeled with fluorescein isothiocyanate (FITC), digoxigenin (DIG), and tetramethylrhodamine (TAMRA), respectively, and biotin-labeled backward inner primers were used in mLAMP. The mLAMP assay succeeded in specific amplification of each respective target gene in a single tube. Furthermore, the mLAMP product from each species was easily distinguished by dot-ELISA with an antibody specific for FITC, DIG, or TAMRA. The mLAMP assay in combination with dot-ELISA will make identification of human Taenia species simpler, easier, and more practical. PMID:27044566

Chiral topological insulating phases from three-dimensional nodal loop semimetals

NASA Astrophysics Data System (ADS)

Li, Linhu; Yin, Chuanhao; Chen, Shu; Araujo, Miguel

We begin with a minimal model of three-dimensional nodal loop semimetals, and study the effect of anticommuting gap terms. The resulting topological insulating phases are protected by a chiral symmetry, and can be characterized by a winding number defined along the nodal loop. We illustrate the geometric relation between the nodal loop and the gap terms, which has a correspondence to the nodal loop winding number. We further investigate a lattice model and study its edge states under open boundary condition. The edge states hold Dirac cones with the same number as the summation of the winding numbers of each nodal loop in the first Brillouin zone.

Sulfur evolution in chemical looping combustion of coal with MnFe2O4 oxygen carrier.

PubMed

Wang, Baowen; Gao, Chuchang; Wang, Weishu; Zhao, Haibo; Zheng, Chuguang

2014-05-01

Chemical looping combustion (CLC) of coal has gained increasing attention as a novel combustion technology for its advantages in CO2 capture. Sulfur evolution from coal causes great harm from either the CLC operational or environmental perspective. In this research, a combined MnFe2O4 oxygen carrier (OC) was synthesized and its reaction with a typical Chinese high sulfur coal, Liuzhi (LZ) bituminous coal, was performed in a thermogravimetric analyzer (TGA)-Fourier transform infrared (FT-IR) spectrometer. Evolution of sulfur species during reaction of LZ coal with MnFe2O4 OC was systematically investigated through experimental means combined with thermodynamic simulation. TGA-FTIR analysis of the LZ reaction with MnFe2O4 indicated MnFe2O4 exhibited the desired superior reactivity compared to the single reference oxides Mn3O4 or Fe2O3, and SO2 produced was mainly related to oxidization of H2S by MnFe2O4. Experimental analysis of the LZ coal reaction with MnFe2O4, including X-ray diffraction and X-ray photoelectron spectroscopy analysis, verified that the main reduced counterparts of MnFe2O4 were Fe3O4 and MnO, in good agreement with the related thermodynamic simulation. The obtained MnO was beneficial to stabilize the reduced MnFe2O4 and avoid serious sintering, although the oxygen in MnO was not fully utilized. Meanwhile, most sulfur present in LZ coal was converted to solid MnS during LZ reaction with MnFe2O4, which was further oxidized to MnSO4. Finally, the formation of both MnS and such manganese silicates as Mn2SiO4 and MnSiO3 should be addressed to ensure the full regeneration of the reduced MnFe2O4. Copyright © 2014 The Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.

Active site remodeling during the catalytic cycle in metal-dependent fructose-1,6-bisphosphate aldolases.

PubMed

Jacques, Benoit; Coinçon, Mathieu; Sygusch, Jurgen

2018-03-28

Crystal structures of two bacterial metal (Zn) dependent D-fructose 1,6-bisphosphate (FBP) aldolases in complex with substrate, analogues, and triose-P reaction products were determined to 1.5-2.0 Å resolution. The ligand complexes cryotrapped in native or mutant H. pylori aldolase crystals enabled a novel mechanistic description of FBP C 3 -C 4 bond cleavage. The reaction mechanism uses active site remodelling during the catalytic cycle implicating relocation of the Zn cofactor that is mediated by conformational changes of active site loops. Substrate binding initiates conformational changes, triggered upon P 1 -phosphate binding, which liberates the Zn chelating His180, allowing it to act as a general base for the proton abstraction at the FBP C 4 -hydroxyl group. A second zinc chelating His83 hydrogen bonds the substrate C 4 - hydroxyl group and assists cleavage by stabilizing the developing negative charge during proton abstraction. Cleavage is concerted with relocation of the metal cofactor from an interior to a surface exposed site, thereby stabilizing the nascent enediolate form. Conserved residue Glu142 is essential for protonation of the enediolate form, prior to product release. A D-tagatose 1,6-bisphosphate enzymatic complex reveals how His180 mediated proton abstraction controls stereospecificity of the cleavage reaction. Recognition and discrimination of the reaction products, dihydroxyacetone-P and D-glyceraldehyde-3-P, occurs via charged hydrogen bonds between hydroxyl groups of the triose-Ps and conserved residues, Asp82 and Asp255, respectively, and are crucial aspects of the enzyme's role in gluconeogenesis. Conformational changes in mobile loops β5-α7 and β6-α8 (containing catalytic residues Glu142 and His180, respectively) drive active site remodelling enabling the relocation of the metal cofactor. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

Vancomycin-resistant gene identification from live bacteria on an integrated microfluidic system by using low temperature lysis and loop-mediated isothermal amplification

PubMed Central

Chang, Wen-Hsin; Yu, Ju-ching; Yang, Sung-Yi; Lin, Yi-Cheng; Wang, Chih-Hung; You, Huey-Ling; Wu, Jiunn-Jong; Lee, Gwo-Bin

2017-01-01

Vancomycin-resistant Enterococcus (VRE) is a kind of enterococci, which shows resistance toward antibiotics. It may last for a long period of time and meanwhile transmit the vancomycin-resistant gene (vanA) to other bacteria. In the United States alone, the resistant rate of Enterococcus to vancomycin increased from a mere 0.3% to a whopping 40% in the past two decades. Therefore, timely diagnosis and control of VRE is of great need so that clinicians can prevent patients from becoming infected. Nowadays, VRE is diagnosed by antibiotic susceptibility test or molecular diagnosis assays such as matrix-assisted laser desorption ionization/time-of-flight mass spectrometry and polymerase chain reaction. However, the existing diagnostic methods have some drawbacks, for example, time-consumption, no genetic information, or high false-positive rate. This study reports an integrated microfluidic system, which can automatically identify the vancomycin resistant gene (vanA) from live bacteria in clinical samples. A new approach using ethidium monoazide, nucleic acid specific probes, low temperature chemical lysis, and loop-mediated isothermal amplification (LAMP) has been presented. The experimental results showed that the developed system can detect the vanA gene from live Enterococcus in joint fluid samples with detection limit as low as 10 colony formation units/reaction within 1 h. This is the first time that an integrated microfluidic system has been demonstrated to detect vanA gene from live bacteria by using the LAMP approach. With its high sensitivity and accuracy, the proposed system may be useful to monitor antibiotic resistance genes from live bacteria in clinical samples in the near future. PMID:28798845

Loop-mediated isothermal amplification assay targeting the mpb70 gene for rapid differential detection of Mycobacterium bovis.

PubMed

Zhang, Hui; Wang, Zhen; Cao, Xudong; Wang, Zhengrong; Sheng, Jinliang; Wang, Yong; Zhang, Jing; Li, Zhiqiang; Gu, Xinli; Chen, Chuangfu

2016-11-01

Loop-mediated isothermal amplification (LAMP) is a highly sensitive, rapid, cost-effective nucleic acid amplification method. Tuberculosis (TB) is widely popular in the world and it is difficult to cure. The fundamental treatment is to clear the types of TB pathogens such as Mycobacterium bovis (M. bovis), Mycobacterium tuberculosis (M. tuberculosis). In order to detect and diagnose TB early, we constructed the differential diagnostic method of TB. In this study, we used LAMP for detection of M. bovis, based on amplification of the mpb70 gene which is a unique gene in M. bovis strain. The LAMP assay was able to detect only seven copies of the gene per reaction, whereas for the conventional PCR, it was 70 copies. The LAMP was evaluated for its specificity using six strains of five Mycobacterium species and 18 related non-Mycobacterium microorganism strains as controls. The target three Mycobacterium strains were all amplified, and no cross-reaction was found with 18 non-Mycobacterium microorganism strains. TB was detected by two methods, LAMP and conventional PCR (based on mpb70 gene); the positive rates of the two methods were 9.55 and 7.01 %, respectively. Our results indicate that the LAMP method should be a potential tool with high convenience, rapidity, sensitivity and specificity for the diagnosis of TB caused by M. bovis. Most importance is that the use of LAMP as diagnostic method in association with diagnostic tests based on mpb70 gene would allow the differentiation between M. bovis and other Mycobacterium in humans or animals. The LAMP method is actually in order to detect human TB, and it can be used for differential diagnosis in this paper.

Detection of Haemophilus parasuis isolates from South China by loop-mediated isothermal amplification and isolate characterisation.

PubMed

Zhang, Jian-Min; Shen, Hai-Yan; Liao, Ming; Ren, Tao; Guo, Li-Li; Xu, Cheng-Gang; Feng, Sai-Xiang; Fan, Hui-Ying; Li, Jing-Yi; Chen, Ji-Dang; Zhang, Bin

2012-04-24

Haemophilus parasuis is the etiological agent of Glässer's disease, which is characterised by fibrinous polyserositis, meningitis and polyarthritis, causing severe economic losses to the swine industry. In this study, a loop-mediated isothermal amplification (LAMP) test was developed to improve the specificity, facility and speed of diagnosis of H. parasuis isolates. The LAMP assay rapidly amplified the target gene within 50 min incubation at 63 °C in a laboratory water bath. The LAMP amplicon could be visualised directly in the reaction tubes following the addition of SYBR Green I dye. The detection limit of this LAMP method was 10 CFU/mL, which was 10 times more sensitive than the earlier 16S rRNA polymerase chain reaction (PCR) test conducted by Oliveira, Galina and Pijoan (2001), and no cross-reactivity was observed from other non-H. parasuis strains. This LAMP test was evaluated further on 187 clinical specimens from pigs suspected of being infected with H. parasuis. Forty-three were found positive by bacterial isolation of H. parasuis, as well as by the 16S rRNA PCR and LAMP tests. The 43 H. parasuis isolates were classified into 9 serovars and had 37 genetic patterns when analysed by pulsed-field gel electrophoresis (PFGE). This displayed that various H. parasuis serovars and genotypes were widely distributed in South China. Therefore, the speed, specificity and sensitivity of the LAMP test, the lack of a need for expensive equipment, and the visual readout showed great potential for a correct clinical diagnosis of H. parasuis in favour of controlling Glässer's disease.

Visual detection of Potato Leafroll virus by loop-mediated isothermal amplification of DNA with the GeneFinder™ dye.

PubMed

Almasi, Mohammad Amin; Erfan Manesh, Maryam; Jafary, Hossein; Dehabadi, Seyed Mohammad Hosseini

2013-09-01

The most common virus affecting potatoes in the field worldwide is Potato Leafroll virus (PLRV), belonging to the family Luteoviridae, genius Plerovirus. There are several molecular methods to detect PLRV including polymerase chain reaction (PCR), Multiplex AmpliDet RNA and double antibody sandwich ELISA (DAS-ELISA). But these techniques take a long time for 3h to two days, requiring sophisticated tools. The aim of this study was to reduce the time required to detect PLRV, using a newly designed loop-mediated isothermal amplification (LAMP) technique requiring only an ordinary water bath or thermoblock. PLRV RNA was extracted from overall 80 infected naturally potato leaves. A set of six novel primers for the LAMP reaction was designed according to the highly conserved sequence of the viral coat protein (CP) gene. LAMP was carried out under isothermal conditions, applying the Bst DNA polymerase enzyme; the LAMP products were detected visually using the GeneFinder™ florescence dye. A positive result using the GeneFinder™ dye was a color change from the original orange to green. Results confirmed LAMP with GeneFinder™ provides a rapid and safe assay for detection of PLRV. Since with other molecular methods, equipping laboratories with a thermocycler or expensive detector systems is unavoidable, this assay was found to be a simple, cost-effective molecular method that has the potential to replace other diagnostic methods in primary laboratories without the need for expensive equipment or specialized techniques. It can also be considered as a reliable alternative viral detection system in further investigations. Copyright © 2013 Elsevier B.V. All rights reserved.

Development of loop-mediated isothermal amplification (LAMP) assay for the rapid detection of Penicillium nordicum in dry-cured meat products.

PubMed

Ferrara, M; Perrone, G; Gallo, A; Epifani, F; Visconti, A; Susca, A

2015-06-02

The need of powerful diagnostic tools for rapid, simple, and cost-effective detection of food-borne fungi has become very important in the area of food safety. Currently, several isothermal nucleic acid amplification methods have been developed as an alternative to PCR-based analyses. Loop-mediated isothermal amplification (LAMP) is one of these innovative methods; it requires neither gel electrophoresis to separate and visualize the products nor expensive laboratory equipment and it has been applied already for detection of pathogenic organisms. In the current study, we developed a LAMP assay for the specific detection of Penicillium nordicum, the major causative agent of ochratoxin A contamination in protein-rich food, especially dry-cured meat products. The assay was based on targeting otapksPN gene, a key gene in the biosynthesis of ochratoxin A (OTA) in P. nordicum. Amplification of DNA during the reaction was detected directly in-tube by color transition of hydroxynaphthol blue from violet to sky blue, visible to the naked eye, avoiding further post amplification analyses. Only DNAs isolated from several P. nordicum strains led to positive results and no amplification was observed from non-target OTA and non OTA-producing strains. The assay was able to detect down to 100 fg of purified targeted genomic DNA or 10(2) conidia/reaction within 60 min. The LAMP assay for detection and identification of P. nordicum was combined with a rapid DNA extraction method set up on serially diluted conidia, providing an alternative rapid, specific and sensitive DNA-based method suitable for application directly "on-site", notably in key steps of dry-cured meat production. Copyright © 2015 Elsevier B.V. All rights reserved.

Role of Gts1p in regulation of energy-metabolism oscillation in continuous cultures of the yeast Saccharomyces cerevisiae.

PubMed

Xu, Zhaojun; Tsurugi, Kunio

2007-03-01

Energy-metabolism oscillation (EMO) in an aerobic chemostat culture of yeast is basically regulated by a feedback loop of redox reactions in energy metabolism and modulated by metabolism of storage carbohydrates. In this study, we investigated the role of Gts1p in the stabilization of EMO, using the GTS1-deleted transformant gts1Delta. We found that fluctuations in the redox state of the NAD co-factor and levels of redox-regulated metabolites in glycolysis, especially of ethanol, are markedly reduced in amplitude during EMO of gts1Delta, while respiration indicated by the oxygen uptake rate (OUR) and energy charge is not so affected throughout EMO in gts1Delta. Further, the transitions of the levels of OUR, NAD(+) : NADH ratio and intracellular pH between the two phases were apparently retarded compared with those in the wild-type, suggesting attenuation of EMO in gts1Delta. Furthermore, the mRNA levels of genes encoding enzymes for the synthesis of trehalose and glycogen are fairly reduced in gts1Delta, consistent with the decreased synthesis of storage carbohydrates. In addition, the level of inorganic phosphate, which is required for the reduction of NAD(+) and mainly supplied from trehalose synthesis, was decreased in the early respiro-fermentative phase in gts1Delta. Thus, we suggested that the deletion of GTS1 as a transcriptional co-activator for these genes inhibited the metabolism of storage carbohydrates, which causes attenuation of the feedback loop of dehydrogenase reactions in glycolysis with the restricted fluctuation of ethanol as a main synchronizing agent for EMO in a cell population.

Crystal structure of native and a mutant of Lampyris turkestanicus luciferase implicate in bioluminescence color shift.

PubMed

Kheirabadi, Mitra; Sharafian, Zohreh; Naderi-Manesh, Hossein; Heineman, Udo; Gohlke, Ulrich; Hosseinkhani, Saman

2013-12-01

Firefly bioluminescence reaction in the presence of Mg(2+), ATP and molecular oxygen is carried out by luciferase. The luciferase structure alterations or modifications of assay conditions determine the bioluminescence color of firefly luciferase. Among different beetle luciferases, Phrixothrix hirtus railroad worm emits either yellow or red bioluminescence color. Sequence alignment analysis shows that the red-emitter luciferase from Phrixothrix hirtus has an additional arginine residue at 353 that is absent in other firefly luciferases. It was reported that insertion of Arg in an important flexible loop350-359 showed changes in bioluminescence color from green to red and the optimum temperature activity was also increased. To explain the color tuning mechanism of firefly luciferase, the structure of native and a mutant (E354R/356R/H431Y) of Lampyris turkestanicus luciferase is determined at 2.7Å and 2.2Å resolutions, respectively. The comparison of structure of both types of Lampyris turkestanicus luciferases reveals that the conformation of this flexible loop is significantly changed by addition of two Arg in this region. Moreover, its surface accessibility is affected considerably and some ionic bonds are made by addition of two positive charge residues. Furthermore, we noticed that the hydrogen bonding pattern of His431 with the flexible loop is changed by replacing this residue with Tyr at this position. Juxtaposition of a flexible loop (residues 351-359) in firefly luciferase and corresponding ionic and hydrogen bonds are essential for color emission. © 2013.

Multilevel D-loop PCR identification of hunting game.

PubMed

Parkanyi, V; Ondruska, L; Vasicek, D; Slamecka, J

2014-03-01

The control region of mtDNA (D-loop) was used for hair samples of the five hunting game species identification: red deer (Cervus elaphus), roe deer (Capreolus capreolus), fallow deer (Dama dama), mouflon (Ovis aries musimon), and wild boar (Sus scrofa). For D-loop multilevel PCR detection scheme was applied in six primers (CE CVZV 1 = 5'-GATCACGAGCTTGATCACCA-3'; CE CVZV 2 = 5'-AGGAGTGGGCGATTTTAGGT-3'; DD CVZV 3 = 5'-CGCGTGAAACCAACAACCCGC-3'; DD CVZV 4 = 5'-CCGGGTCGGGGCCTTAGACG-3'; SSW CVZV 5 = 5'-ACACGTGCGTACACGCGCATA-3'; SSW CVZV 6 = 5'-GGTGCCTGCT T TCGTAGCACG-3') designed to identify unknown biological samples of the hunting game animals. The PCR reaction volume was 25 μl at conditions 95 °C for 2 min, 94 °C for 30 s, 60 °C for 30 s, 72 °C for 30 s, 35 cycles, with last extension at 72 °C for 10 min. D-loop mtDNA amplicons of the game animals are characterized with specific PCR product sizes depending on species: red deer = 163 bp and 140 bp, fallow deer = 280 bp and 138 bp, roe deer = 303 bp, 280 bp, 160 bp and 138 bp, mouflon = 299 bp and 178 bp, wild boar = 137 bp and 229 bp.

Evaluation of Effects and Effectiveness of Various α and β Angulations for Three Different Loop Made of Stainless Steel Arch Wires - A FEM Study.

PubMed

Kamisetty, Supradeep Kumar; N, Raghuveer; N, Rajavikram; N, Chakrapani; Dwaragesh; Praven

2014-07-01

Evaluations on retraction loop designs have been limited to describe the force systems applied to the buccal surfaces of the tooth that can be in different planes resulting undesirable effects, needing corrective action in future. By initially understanding these effects, modifications to the loop design can essentially counteract the undesired affects. To deter-mine Moments & M/F ratios produced by different gabling in the three retraction loops (Tear drop loop, T-loop, Open vertical loop) and movement of the anterior teeth and posterior teeth) of the maxillary arch in an extraction model, on activation of three retraction loops by1 mm. A PC with Quad core processor, 8GB RAM, 1TB storage space and Graphic Accelerator was used. Computer Software: ANSYS Version11, PRO/ENGINEER was used in the study. The first step is modeling, done by using Pro/Engineer software and for creating a model the CT scan data is required. The maxilla with teeth of a patient is scanned at various sections at regular intervals of 0.5 mm. These scanned images are then imported into Pro/E software to various offset planes. Once imported, the software can do an automatic meshing and establishes contact automatically. When angulations increases intrusive or extrusive movements and movements in horizontal direction of crown tip and root tip increases. All values of T-loop are more than Teardrop loop and less than Open vertical loop. FEM study concludes that Teardrop loop with 10-20(α-β) combination is preferred for Group A anchorage.

Method for taking into account hard-photon emission in four-fermion processes

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

Aleksejevs, A. G., E-mail: aaleksejevs@swgc.mun.ca; Barkanova, S. G., E-mail: svetlana.barkanova@acadiau.ca; Zykunov, V. A., E-mail: vladimir.zykunov@cern.ch

2016-01-15

A method for taking into account hard-photon emission in four-fermion processes proceeding in the s channel is described. The application of this method is exemplified by numerically estimating one-loop electroweak corrections to observables (cross sections and asymmetries) of the reaction e{sup −}e{sup +} → μ{sup −}μ{sup +}(γ) involving longitudinally polarized electrons and proceeding at energies below the Z-resonance energy.

Current systems of coronal loops in 3D MHD simulations

NASA Astrophysics Data System (ADS)

Warnecke, J.; Chen, F.; Bingert, S.; Peter, H.

2017-11-01

Aims: We study the magnetic field and current structure associated with a coronal loop. Through this we investigate to what extent the assumptions of a force-free magnetic field break down and where they might be justified. Methods: We analyze a three-dimensional (3D) magnetohydrodynamic (MHD) model of the solar corona in an emerging active region with the focus on the structure of the forming coronal loops. The lower boundary of this simulation is taken from a model of an emerging active region. As a consequence of the emerging magnetic flux and the horizontal motions at the surface a coronal loop forms self-consistently. We investigate the current density along magnetic field lines inside (and outside) this loop and study the magnetic and plasma properties in and around this loop. The loop is defined as the bundle of field lines that coincides with enhanced emission in extreme UV. Results: We find that the total current along the emerging loop changes its sign from being antiparallel to parallel to the magnetic field. This is caused by the inclination of the loop together with the footpoint motion. Around the loop, the currents form a complex non-force-free helical structure. This is directly related to a bipolar current structure at the loop footpoints at the base of the corona and a local reduction of the background magnetic field (I.e., outside the loop) caused by the plasma flow into and along the loop. Furthermore, the locally reduced magnetic pressure in the loop allows the loop to sustain a higher density, which is crucial for the emission in extreme UV. The action of the flow on the magnetic field hosting the loop turns out to also be responsible for the observed squashing of the loop. Conclusions: The complex magnetic field and current system surrounding it can only be modeled in 3D MHD models where the magnetic field has to balance the plasma pressure. A one-dimensional coronal loop model or a force-free extrapolation cannot capture the current system and the complex interaction of the plasma and the magnetic field in the coronal loop, despite the fact that the loop is under low-β conditions.

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

Xie, Haixia; Li, Bo; Huang, Zhenghua

How the solar corona is heated to high temperatures remains an unsolved mystery in solar physics. In the present study we analyze observations of 50 whole active region loops taken with the Extreme-ultraviolet Imaging Spectrometer on board the Hinode satellite. Eleven loops were classified as cool loops (<1 MK) and 39 as warm loops (1–2 MK). We study their plasma parameters, such as densities, temperatures, filling factors, nonthermal velocities, and Doppler velocities. We combine spectroscopic analysis with linear force-free magnetic field extrapolation to derive the 3D structure and positioning of the loops, their lengths and heights, and the magnetic fieldmore » strength along the loops. We use density-sensitive line pairs from Fe xii, Fe xiii, Si x, and Mg vii ions to obtain electron densities by taking special care of intensity background subtraction. The emission measure loci method is used to obtain the loop temperatures. We find that the loops are nearly isothermal along the line of sight. Their filling factors are between 8% and 89%. We also compare the observed parameters with the theoretical Rosner–Tucker–Vaiana (RTV) scaling law. We find that most of the loops are in an overpressure state relative to the RTV predictions. In a follow-up study, we will report a heating model of a parallel-cascade-based mechanism and will compare the model parameters with the loop plasma and structural parameters derived here.« less

Development of a rapid assay for the diagnosis of Myxobolus cerebralis in fish and oligochaetes using loop-mediated isothermal amplification.

PubMed

El-Matbouli, M; Soliman, H

2005-09-01

A loop-mediated isothermal amplification assay was developed for the rapid detection of Myxobolus cerebralis in both fish and oligochaete hosts. The assay was optimized to amplify parasitic DNA by incubation with Bst DNA polymerase and a set of six specially constructed primers at 65 degrees C for 60 min. The amplification products were detected visually using SYBR Green I dye which gave identical results to gel electrophoresis analysis. Parasite DNA was detected from infected oligochaetes, and from the anal fin, caudal fin, dorsal fin and operculum of clinically infected fish. This 'Myxo-LAMP' assay has a detection limit similar to that of a polymerase chain reaction assay (10(-6)), but is more rapid and only requires a water bath for amplification and is therefore practical for simple and rapid diagnosis of infected tissue.

Testing of the on-board attitude determination and control algorithms for SAMPEX

NASA Technical Reports Server (NTRS)

Mccullough, Jon D.; Flatley, Thomas W.; Henretty, Debra A.; Markley, F. Landis; San, Josephine K.

1993-01-01

Algorithms for on-board attitude determination and control of the Solar, Anomalous, and Magnetospheric Particle Explorer (SAMPEX) have been expanded to include a constant gain Kalman filter for the spacecraft angular momentum, pulse width modulation for the reaction wheel command, an algorithm to avoid pointing the Heavy Ion Large Telescope (HILT) instrument boresight along the spacecraft velocity vector, and the addition of digital sun sensor (DSS) failure detection logic. These improved algorithms were tested in a closed-loop environment for three orbit geometries, one with the sun perpendicular to the orbit plane, and two with the sun near the orbit plane - at Autumnal Equinox and at Winter Solstice. The closed-loop simulator was enhanced and used as a truth model for the control systems' performance evaluation and sensor/actuator contingency analysis. The simulations were performed on a VAX 8830 using a prototype version of the on-board software.

Deployment of a Reverse Transcription Loop-Mediated Isothermal Amplification Test for Ebola Virus Surveillance in Remote Areas in Guinea.

PubMed

Kurosaki, Yohei; Magassouba, N'Faly; Bah, Hadja Aïssatou; Soropogui, Barré; Doré, Amadou; Kourouma, Fodé; Cherif, Mahamoud Sama; Keita, Sakoba; Yasuda, Jiro

2016-10-15

To strengthen the laboratory diagnostic capacity for Ebola virus disease (EVD) in the remote areas of Guinea, we deployed a mobile field laboratory and implemented reverse transcription loop-mediated isothermal amplification (RT-LAMP) for postmortem testing. We tested 896 oral swab specimens and 21 serum samples, using both RT-LAMP and reverse transcription-polymerase chain reaction (RT-PCR). Neither test yielded a positive result, and the results from RT-LAMP and RT-PCR were consistent. More than 95% of the samples were tested within 2 days of sample collection. These results highlight the usefulness of the RT-LAMP assay as an EVD diagnostic testing method in the field or remote areas. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

Rapid and sensitive detection of Lily symptomless virus by reverse transcription loop-mediated isothermal amplification.

PubMed

He, Xiangfeng; Xue, Fei; Xu, Shufa; Wang, Wenhe

2016-12-01

Lily symptomless virus (LSV) is one of the most prevalent viruses that infect lily plants worldwide. A rapid and sensitive reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for detection of LSV, using two primer pairs that specifically amplified the conserved sequence of LSV coat protein. The optimum reaction conditions were as follows: 4mM MgCl 2 and 0.8M betaine with incubation at 64°C for 30min. The limit of detection of LSV from infected lily leaves was 10-fold higher for RT-LAMP than for conventional RT-PCR. Moreover, RT-LAMP detected LSV in not only symptomatic, but also in symptomless tissues of infected plants. These findings indicate that our RT-LAMP method for LSV can serve as a low-cost, simple, and rapid alternative to conventional detection assays. Copyright © 2016 Elsevier B.V. All rights reserved.

Thermal Control Utilizing an Thermal Control Utilizing an Two-Phase Loop with High Heat Flux Source

NASA Technical Reports Server (NTRS)

Jeong, Seong-Il; Didion, Jeffrey

2004-01-01

The electric field applied in dielectric fluids causes an imbalance in the dissociation-recombination reaction generated free space charges. The generated charges are redistributed by the applied electric field resulting in the heterocharge layers in the Vicinity of the electrodes. Proper design of the electrodes generates net axial flow motion pumping the fluid. The electrohydrodynamic (EHD) conduction pump is a new device that pumps dielectric fluids utilizing heterocharge layers formed by imposition of electrostatic fields. This paper evaluates the experimental performance of a two-phase breadboard thermal control loop consisting of an EHD conduction pump, condenser, pre-heater, high heat flux evaporator (HE), transport lines, and reservoir (accumulator). The generated pressure head and the maximum applicable heat flux are experimentally determined at various applied voltages and sink temperatures. Recovery from dryout condition by increasing the applied voltage to the pump is also demonstrated.

Insights into the O-Acetylation Reaction of Hydroxylated Heterocyclic Amines by Human Arylamine N-Acetyltransferases: A Computational Study

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

Lau, E Y; Felton, J S; Lightstone, F C

2006-06-06

A computational study was performed to better understand the differences between human arylamine N-acetyltransferase (NAT) 1 and 2. Homology models were constructed from available crystal structures and comparisons of the active site residues 125, 127, and 129 for these two enzymes provide insight into observed substrate differences. The NAT2 model provided a basis for understanding how some of the common mutations may affect the structure of the protein. Molecular dynamics simulations of the human NAT models and the template structure (NAT from Mycobacterium smegmatis) were performed and showed the models to be stable and reasonable. Docking studies of hydroxylated heterocyclicmore » amines in the models of NAT1 and NAT2 probed the differences exhibited by these two proteins with mutagenic agents. The hydroxylated heterocyclic amines were only able to fit into the NAT2 active site, and an alternative binding site by the P-loop was found using our models and will be discussed. Additionally, quantum mechanical calculations were performed to study the O-acetylation reaction of the hydroxylated heterocyclic amines N-OH MeIQx and N-OH PhIP. This study has given us insight into why there are substrate differences among isoenzymes and explains some of the polymorphic activity differences.« less

Innovative power conversion system for the French SFR prototype, ASTRID

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

Cachon, L.; Biscarrat, C.; Morin, F.

2012-07-01

In the framework of the French Act of 28 June 2006 about nuclear materials and waste management, the prototype ASTRID (Advanced Sodium Technological Reactor for Industrial Demonstration), foreseen in operation by the 20's, will have to demonstrate not only the minor actinide transmutation capability, but also the progress made in Sodium Fast Reactor (SFR) technology on an industrial scale, by qualifying innovative options. Some of these options still require improvements, especially in the field of operability and safety. In fact, one of the main issues with the standard steam/water Power Conversion System (PCS) of SFR is the fast and energeticmore » chemical reaction between water and sodium, which could occur in steam generators in case of tube failure. To manage the sodium/water reaction, one way consists in minimizing the impact of such event: hence studies are carried out on steam generator design, improvement of the physical knowledge of this phenomenon, development of numerical simulation to predict the reaction onset and consequences, and associated detection improvement. On the other hand, the other way consists in eliminating sodium/water reaction. In this frame, the CEA contribution to the feasibility evaluation of an alternative innovative PCS (replacing steam/water by 180 bar pressurised nitrogen) is focused on the following main topics: - The parametric study leading to nitrogen selection: the thermodynamic cycle efficiency optimisation on Brayton cycles is performed with several gases at different pressures. - The design of innovative compact heat exchangers for the gas loop: here the key points are the nuclear codification associated with inspection capability, the innovative welding process and the thermal-hydraulic and thermal-mechanic optimisations. After a general introduction of the ASTRID project, this paper presents in detail these different feasibility studies being led on the innovative gas PCS for an SFR. (authors)« less

Closed-Loop Multitarget Optimization for Discovery of New Emulsion Polymerization Recipes

PubMed Central

2015-01-01

Self-optimization of chemical reactions enables faster optimization of reaction conditions or discovery of molecules with required target properties. The technology of self-optimization has been expanded to discovery of new process recipes for manufacture of complex functional products. A new machine-learning algorithm, specifically designed for multiobjective target optimization with an explicit aim to minimize the number of “expensive” experiments, guides the discovery process. This “black-box” approach assumes no a priori knowledge of chemical system and hence particularly suited to rapid development of processes to manufacture specialist low-volume, high-value products. The approach was demonstrated in discovery of process recipes for a semibatch emulsion copolymerization, targeting a specific particle size and full conversion. PMID:26435638

Force modeling for incision surgery into tissue with haptic application

NASA Astrophysics Data System (ADS)

Kim, Pyunghwa; Kim, Soomin; Choi, Seung-Hyun; Oh, Jong-Seok; Choi, Seung-Bok

2015-04-01

This paper presents a novel force modeling for an incision surgery into tissue and its haptic application for a surgeon. During the robot-assisted incision surgery, it is highly urgent to develop the haptic system for realizing sense of touch in the surgical area because surgeons cannot sense sensations. To achieve this goal, the force modeling related to reaction force of biological tissue is proposed in the perspective on energy. The force model describes reaction force focused on the elastic feature of tissue during the incision surgery. Furthermore, the force is realized using calculated information from the model by haptic device using magnetorheological fluid (MRF). The performance of realized force that is controlled by PID controller with open loop control is evaluated.

The Effect of Phase Transitions, Surface Diffusion, and Defects on Heterogeneous Reactions: Multiplicities and Fluctuations

DTIC Science & Technology

1991-01-01

atoms. The isotherm obtained [35], shown also in fig. la. is called Fowler -Guggenheim (FG) and is given by 0.5 - 0 KP = 1 -- 0 20 exp(-z w/kT), 0.0t2 e0...average size of clusters formed on ," e surface loop is indicated, whenever it exists. by a pair of [33). lines of the same symbol. The reaction rate...K P , I solution 0 ... 𔃿 O . r. 1• & * .A Langmuir 0.1 0.5 mR 0 0.04 . 0.020-i 3 .A MF .."’, " .. e I k/kd 3 0 0’ 0 5 ---- 0.017 L 0.01 0.04 0.07 0

Space Station evolution study oxygen loop closure

NASA Technical Reports Server (NTRS)

Wood, M. G.; Delong, D.

1993-01-01

In the current Space Station Freedom (SSF) Permanently Manned Configuration (PMC), physical scars for closing the oxygen loop by the addition of oxygen generation and carbon dioxide reduction hardware are not included. During station restructuring, the capability for oxygen loop closure was deferred to the B-modules. As such, the ability to close the oxygen loop in the U.S. Laboratory module (LAB A) and the Habitation A module (HAB A) is contingent on the presence of the B modules. To base oxygen loop closure of SSF on the funding of the B-modules may not be desirable. Therefore, this study was requested to evaluate the necessary hooks and scars in the A-modules to facilitate closure of the oxygen loop at or subsequent to PMC. The study defines the scars for oxygen loop closure with impacts to cost, weight and volume and assesses the effects of byproduct venting. In addition, the recommended scenarios for closure with regard to topology and packaging are presented.

The Prevalence and Use of Walking Loops in Neighborhood Parks: A National Study.

PubMed

Cohen, Deborah A; Han, Bing; Evenson, Kelly R; Nagel, Catherine; McKenzie, Thomas L; Marsh, Terry; Williamson, Stephanie; Harnik, Peter

2017-02-01

Previous studies indicate that the design of streets and sidewalks can influence physical activity among residents. Park features also influence park use and park-based physical activity. Although individuals can walk on streets and sidewalks, walking loops in parks offer a setting to walk in nature and to avoid interruptions from traffic. Here we describe the use of walking loops in parks and compare the number of park users and their physical activity in urban neighborhood parks with and without walking loops. We analyzed data from the National Study of Neighborhood Parks in which a representative sample of neighborhood parks (n = 174) from 25 U.S. cities with > 100,000 population were observed systematically to document facilities and park users by age group and sex. We compared the number of people and their physical activity in parks with and without walking loops, controlling for multiple factors, including park size, facilities, and population density. Overall, compared with parks without walking loops, on average during an hourly observation, parks with walking loops had 80% more users (95% CI: 42, 139%), and levels of moderate-to-vigorous physical activity were 90% higher (95% CI: 49, 145%). The additional park use and park-based physical activity occurred not only on the walking loops but throughout the park. Walking loops may be a promising means of increasing population level physical activity. Further studies are needed to confirm a causal relationship. Citation: Cohen DA, Han B, Evenson KR, Nagel C, McKenzie TL, Marsh T, Williamson S, Harnik P. 2017. The prevalence and use of walking loops in neighborhood parks: a national study. Environ Health Perspect 125:170-174; http://dx.doi.org/10.1289/EHP293.

The Prevalence and Use of Walking Loops in Neighborhood Parks: A National Study

PubMed Central

Cohen, Deborah A.; Han, Bing; Evenson, Kelly R.; Nagel, Catherine; McKenzie, Thomas L.; Marsh, Terry; Williamson, Stephanie; Harnik, Peter

2016-01-01

Background: Previous studies indicate that the design of streets and sidewalks can influence physical activity among residents. Park features also influence park use and park-based physical activity. Although individuals can walk on streets and sidewalks, walking loops in parks offer a setting to walk in nature and to avoid interruptions from traffic. Objectives: Here we describe the use of walking loops in parks and compare the number of park users and their physical activity in urban neighborhood parks with and without walking loops. Methods: We analyzed data from the National Study of Neighborhood Parks in which a representative sample of neighborhood parks (n = 174) from 25 U.S. cities with > 100,000 population were observed systematically to document facilities and park users by age group and sex. We compared the number of people and their physical activity in parks with and without walking loops, controlling for multiple factors, including park size, facilities, and population density. Results: Overall, compared with parks without walking loops, on average during an hourly observation, parks with walking loops had 80% more users (95% CI: 42, 139%), and levels of moderate-to-vigorous physical activity were 90% higher (95% CI: 49, 145%). The additional park use and park-based physical activity occurred not only on the walking loops but throughout the park. Conclusions: Walking loops may be a promising means of increasing population level physical activity. Further studies are needed to confirm a causal relationship. Citation: Cohen DA, Han B, Evenson KR, Nagel C, McKenzie TL, Marsh T, Williamson S, Harnik P. 2017. The prevalence and use of walking loops in neighborhood parks: a national study. Environ Health Perspect 125:170–174; http://dx.doi.org/10.1289/EHP293 PMID:27517530

Stopped-in-loop flow analysis system for successive determination of trace vanadium and iron in drinking water using their catalytic reactions.

PubMed

Ayala Quezada, Alejandro; Ohara, Keisuke; Ratanawimarnwong, Nuanlaor; Nacapricha, Duangjai; Murakami, Hiroya; Teshima, Norio; Sakai, Tadao

2015-11-01

An automated stopped-in-loop flow analysis (SILFA) system is proposed for the successive catalytic determination of vanadium and iron. The determination of vanadium was based on the p-anisidine oxidation by potassium bromate in the presence of Tiron as an activator to form a reddish dye, which has an absorption maximum at 510 nm. The selectivity of the vanadium determination was greatly improved by adding diphosphate as a masking agent of iron. For the iron determination, an iron-catalyzed oxidative reaction of p-anisidine by hydrogen peroxide with 1,10-phenanthroline as an activator to produce a reddish dye (510 nm) was employed. The SILFA system consisted of two peristaltic pumps, two six-port injection valves, a four-port selection valve, a heater device, a spectrophotometric detector and a data acquisition device. One six-port injection valve was used for the isolation of a mixed solution of standard/sample and reagent to promote each catalytic reaction, and another six-port injection valve was used for switching the reagent for vanadium or iron to achieve selective determination of each analyte. The above mentioned four-port selection valve was used to select standard solutions or sample. These three valves and the two peristaltic pumps were controlled by a built-in programmable logic controller in a touchscreen controller. The obtained results showed that the proposed SILFA monitoring system constituted an effective approach for the selective determination of vanadium and iron. The limits of detection, 0.052 and 0.55 µg L(-1), were obtained for vanadium and iron, respectively. The proposed system was successfully applied to drinking water samples without any preconcentration procedures. Copyright © 2015 Elsevier B.V. All rights reserved.

Modulation of serpin reaction through stabilization of transient intermediate by ligands bound to alpha-helix F.

PubMed

Komissarov, Andrey A; Zhou, Aiwu; Declerck, Paul J

2007-09-07

Mechanism-based inhibition of proteinases by serpins involves enzyme acylation and fast insertion of the reactive center loop (RCL) into the central beta-sheet of the serpin, resulting in mechanical inactivation of the proteinase. We examined the effects of ligands specific to alpha-helix F (alphaHF) of plasminogen activator inhibitor-1 (PAI-1) on the stoichiometry of inhibition (SI) and limiting rate constant (k(lim)) of RCL insertion for reactions with beta-trypsin, tissue-type plasminogen activator (tPA), and urokinase. The somatomedin B domain of vitronectin (SMBD) did not affect SI for any proteinase or k(lim) for tPA but decreased the k(lim) for beta-trypsin. In contrast to SMBD, monoclonal antibodies MA-55F4C12 and MA-33H1F7, the epitopes of which are located at the opposite side of alphaHF, decreased k(lim) and increased SI for every enzyme. These effects were enhanced in the presence of SMBD. RCL insertion for beta-trypsin and tPA is limited by different subsequent steps of PAI-1 mechanism as follows: enzyme acylation and formation of a loop-displaced acyl complex (LDA), respectively. Stabilization of LDA through the disruption of the exosite interactions between PAI-1 and tPA induced an increase in the k(lim) but did not affect the SI. Thus it is unlikely that LDA contributes significantly to the outcome of the serpin reaction. These results demonstrate that the rate of RCL insertion is not necessarily correlated with SI and indicate that an intermediate, different from LDA, which forms during the late steps of PAI-1 mechanism, and could be stabilized by ligands specific to alphaHF, controls bifurcation between the inhibitory and the substrate pathways.

Mining protein loops using a structural alphabet and statistical exceptionality

PubMed Central

2010-01-01

Background Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. Results We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 Å). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a significant level of amino-acid conservation with at least four significant positions and 87% of long loops contain at least one such word. We complement our analysis with the detection of statistically over-represented patterns of structural letters as in conventional DNA sequence analysis. About 30% (930) of structural words are over-represented, and cover about 40% of loop lengths. Interestingly, these words exhibit lower structural variability and higher sequential specificity, suggesting structural or functional constraints. Conclusions We developed a method to systematically decompose and study protein loops using recurrent structural motifs. This method is based on the structural alphabet HMM-SA and not on structural alignment and geometrical parameters. We extracted meaningful structural motifs that are found in both short and long loops. To our knowledge, it is the first time that pattern mining helps to increase the signal-to-noise ratio in protein loops. This finding helps to better describe protein loops and might permit to decrease the complexity of long-loop analysis. Detailed results are available at http://www.mti.univ-paris-diderot.fr/publication/supplementary/2009/ACCLoop/. PMID:20132552

Mining protein loops using a structural alphabet and statistical exceptionality.

PubMed

Regad, Leslie; Martin, Juliette; Nuel, Gregory; Camproux, Anne-Claude

2010-02-04

Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 A). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a significant level of amino-acid conservation with at least four significant positions and 87% of long loops contain at least one such word. We complement our analysis with the detection of statistically over-represented patterns of structural letters as in conventional DNA sequence analysis. About 30% (930) of structural words are over-represented, and cover about 40% of loop lengths. Interestingly, these words exhibit lower structural variability and higher sequential specificity, suggesting structural or functional constraints. We developed a method to systematically decompose and study protein loops using recurrent structural motifs. This method is based on the structural alphabet HMM-SA and not on structural alignment and geometrical parameters. We extracted meaningful structural motifs that are found in both short and long loops. To our knowledge, it is the first time that pattern mining helps to increase the signal-to-noise ratio in protein loops. This finding helps to better describe protein loops and might permit to decrease the complexity of long-loop analysis. Detailed results are available at http://www.mti.univ-paris-diderot.fr/publication/supplementary/2009/ACCLoop/.

The development of loop-mediated isothermal amplification targeting alpha-tubulin DNA for the rapid detection of Plasmodium vivax.

PubMed

Dinzouna-Boutamba, Sylvatrie-Danne; Yang, Hye-Won; Joo, So-Young; Jeong, Sookwan; Na, Byoung-Kuk; Inoue, Noboru; Lee, Won-Ki; Kong, Hyun-Hee; Chung, Dong-Il; Goo, Youn-Kyoung; Hong, Yeonchul

2014-06-30

Malaria that is caused by Plasmodium vivax is the most widely distributed human malaria. Its recent resurgence in many parts of the world, including the Republic of Korea (ROK), emphasizes the importance of improved access to the early and accurate detection of P. vivax to reduce disease burden. In this study, a rapid and efficient loop-mediated isothermal amplification (LAMP)-based method was developed and validated using blood samples from malaria-suspected patients. A LAMP assay targeting the α-tubulin gene for the detection of P. vivax was developed with six primers that recognize different regions of the target gene. The diagnostic performance of the α-tubulin LAMP assay was compared to three other tests: microscopic examinations, rapid diagnostic tests (RDTs), and nested polymerase chain reactions (PCRs) using 177 whole blood specimens obtained from ROK military personnel from May to December 2011. The α-tubulin LAMP assay was highly sensitive with a detection limit of 100 copies of P. vivax α-tubulin gene per reaction within 50 min. It specifically amplified the target gene only from P. vivax. Validation of the α-tubulin LAMP assay showed that the assay had the highest sensitivity (P < 0.001 versus microscopy; P = 0.0023 versus RDT) when nested PCR was used as the gold standard and better agreement (concordance: 94.9%, kappa value: 0.865) with nested PCR than RDT and microscopy. A Receiver Operation Characteristics analysis showed that the diagnostic accuracy of the α-tubulin LAMP assay for vivax malaria was higher (Area Under Curve = 0.908) than RDT and microscopy. This study showed that the P. vivax α-tubulin LAMP assay, which can be used to diagnose early infections of vivax malaria, is an alternative molecular diagnostic tool and a point-of-care test that may help to prevent transmission in endemic areas.

Advanced uracil DNA glycosylase-supplemented real-time reverse transcription loop-mediated isothermal amplification (UDG-rRT-LAMP) method for universal and specific detection of Tembusu virus

PubMed Central

Tang, Yi; Chen, Hao; Diao, Youxiang

2016-01-01

Tembusu virus (TMUV) is a mosquito-borne flavivirus which threatens both poultry production and public health. In this study we developed a complete open reading frame alignment-based rRT-LAMP method for the universal detection of TUMV. To prevent false-positive results, the reaction was supplemented with uracil DNA glycosylase (UDG) to eliminate carryover contamination. The detection limit of the newly developed UDG-rRT-LAMP for TMUV was as low as 100 copies/reaction of viral RNA and 1 × 100.89 − 1 × 101.55 tissue culture infectious dose/100 μL of viruses. There were no cross-reactions with other viruses, and the reproducibility of the assay was confirmed by intra- and inter-assay tests with variability ranging from 0.22–3.33%. The new UDG-rRT-LAMP method for TMUV produced the same results as viral isolation combined with RT-PCR as the “gold standard” in 96.88% of cases for 81 clinical samples from subjects with suspected TMUV infection. The addition of UDG can eliminate as much as 1 × 10−16 g/reaction of contaminants, which can significantly reduce the likelihood of false-positive results during the rRT-LAMP reaction. Our result indicated that our UDG-rRT-LAMP is a rapid, sensitive, specific, and reliable method that can effectively prevent carryover contamination in the detection of TMUV. PMID:27270462

Network thermodynamic curation of human and yeast genome-scale metabolic models.

PubMed

Martínez, Verónica S; Quek, Lake-Ee; Nielsen, Lars K

2014-07-15

Genome-scale models are used for an ever-widening range of applications. Although there has been much focus on specifying the stoichiometric matrix, the predictive power of genome-scale models equally depends on reaction directions. Two-thirds of reactions in the two eukaryotic reconstructions Homo sapiens Recon 1 and Yeast 5 are specified as irreversible. However, these specifications are mainly based on biochemical textbooks or on their similarity to other organisms and are rarely underpinned by detailed thermodynamic analysis. In this study, a to our knowledge new workflow combining network-embedded thermodynamic and flux variability analysis was used to evaluate existing irreversibility constraints in Recon 1 and Yeast 5 and to identify new ones. A total of 27 and 16 new irreversible reactions were identified in Recon 1 and Yeast 5, respectively, whereas only four reactions were found with directions incorrectly specified against thermodynamics (three in Yeast 5 and one in Recon 1). The workflow further identified for both models several isolated internal loops that require further curation. The framework also highlighted the need for substrate channeling (in human) and ATP hydrolysis (in yeast) for the essential reaction catalyzed by phosphoribosylaminoimidazole carboxylase in purine metabolism. Finally, the framework highlighted differences in proline metabolism between yeast (cytosolic anabolism and mitochondrial catabolism) and humans (exclusively mitochondrial metabolism). We conclude that network-embedded thermodynamics facilitates the specification and validation of irreversibility constraints in compartmentalized metabolic models, at the same time providing further insight into network properties. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Run-time parallelization and scheduling of loops

NASA Technical Reports Server (NTRS)

Saltz, Joel H.; Mirchandaney, Ravi; Crowley, Kay

1991-01-01

Run-time methods are studied to automatically parallelize and schedule iterations of a do loop in certain cases where compile-time information is inadequate. The methods presented involve execution time preprocessing of the loop. At compile-time, these methods set up the framework for performing a loop dependency analysis. At run-time, wavefronts of concurrently executable loop iterations are identified. Using this wavefront information, loop iterations are reordered for increased parallelism. Symbolic transformation rules are used to produce: inspector procedures that perform execution time preprocessing, and executors or transformed versions of source code loop structures. These transformed loop structures carry out the calculations planned in the inspector procedures. Performance results are presented from experiments conducted on the Encore Multimax. These results illustrate that run-time reordering of loop indexes can have a significant impact on performance.

Loop equations and bootstrap methods in the lattice

DOE PAGES

Anderson, Peter D.; Kruczenski, Martin

2017-06-17

Pure gauge theories can be formulated in terms of Wilson Loops by means of the loop equation. In the large-N limit this equation closes in the expectation value of single loops. In particular, using the lattice as a regulator, it becomes a well defined equation for a discrete set of loops. In this paper we study different numerical approaches to solving this equation.

Stoichiometric network theory for nonequilibrium biochemical systems.

PubMed

Qian, Hong; Beard, Daniel A; Liang, Shou-dan

2003-02-01

We introduce the basic concepts and develop a theory for nonequilibrium steady-state biochemical systems applicable to analyzing large-scale complex isothermal reaction networks. In terms of the stoichiometric matrix, we demonstrate both Kirchhoff's flux law sigma(l)J(l)=0 over a biochemical species, and potential law sigma(l) mu(l)=0 over a reaction loop. They reflect mass and energy conservation, respectively. For each reaction, its steady-state flux J can be decomposed into forward and backward one-way fluxes J = J+ - J-, with chemical potential difference deltamu = RT ln(J-/J+). The product -Jdeltamu gives the isothermal heat dissipation rate, which is necessarily non-negative according to the second law of thermodynamics. The stoichiometric network theory (SNT) embodies all of the relevant fundamental physics. Knowing J and deltamu of a biochemical reaction, a conductance can be computed which directly reflects the level of gene expression for the particular enzyme. For sufficiently small flux a linear relationship between J and deltamu can be established as the linear flux-force relation in irreversible thermodynamics, analogous to Ohm's law in electrical circuits.

Run-time parallelization and scheduling of loops

NASA Technical Reports Server (NTRS)

Saltz, Joel H.; Mirchandaney, Ravi; Crowley, Kay

1990-01-01

Run time methods are studied to automatically parallelize and schedule iterations of a do loop in certain cases, where compile-time information is inadequate. The methods presented involve execution time preprocessing of the loop. At compile-time, these methods set up the framework for performing a loop dependency analysis. At run time, wave fronts of concurrently executable loop iterations are identified. Using this wavefront information, loop iterations are reordered for increased parallelism. Symbolic transformation rules are used to produce: inspector procedures that perform execution time preprocessing and executors or transformed versions of source code loop structures. These transformed loop structures carry out the calculations planned in the inspector procedures. Performance results are presented from experiments conducted on the Encore Multimax. These results illustrate that run time reordering of loop indices can have a significant impact on performance. Furthermore, the overheads associated with this type of reordering are amortized when the loop is executed several times with the same dependency structure.

Reaction Mechanism and Molecular Basis for Selenium/Sulfur Discrimination of Selenocysteine Lyase*

PubMed Central

Omi, Rie; Kurokawa, Suguru; Mihara, Hisaaki; Hayashi, Hideyuki; Goto, Masaru; Miyahara, Ikuko; Kurihara, Tatsuo; Hirotsu, Ken; Esaki, Nobuyoshi

2010-01-01

Selenocysteine lyase (SCL) catalyzes the pyridoxal 5′-phosphate-dependent removal of selenium from l-selenocysteine to yield l-alanine. The enzyme is proposed to function in the recycling of the micronutrient selenium from degraded selenoproteins containing selenocysteine residue as an essential component. The enzyme exhibits strict substrate specificity toward l-selenocysteine and no activity to its cognate l-cysteine. However, it remains unclear how the enzyme distinguishes between selenocysteine and cysteine. Here, we present mechanistic studies of selenocysteine lyase from rat. ESI-MS analysis of wild-type and C375A mutant SCL revealed that the catalytic reaction proceeds via the formation of an enzyme-bound selenopersulfide intermediate on the catalytically essential Cys-375 residue. UV-visible spectrum analysis and the crystal structure of SCL complexed with l-cysteine demonstrated that the enzyme reversibly forms a nonproductive adduct with l-cysteine. Cys-375 on the flexible loop directed l-selenocysteine, but not l-cysteine, to the correct position and orientation in the active site to initiate the catalytic reaction. These findings provide, for the first time, the basis for understanding how trace amounts of a selenium-containing substrate is distinguished from excessive amounts of its cognate sulfur-containing compound in a biological system. PMID:20164179

Topological insulating phases from two-dimensional nodal loop semimetals

NASA Astrophysics Data System (ADS)

Li, Linhu; Araújo, Miguel A. N.

2016-10-01

Starting from a minimal model for a two-dimensional nodal loop semimetal, we study the effect of chiral mass gap terms. The resulting Dirac loop anomalous Hall insulator's Chern number is the phase-winding number of the mass gap terms on the loop. We provide simple lattice models, analyze the topological phases, and generalize a previous index characterizing topological transitions. The responses of the Dirac loop anomalous Hall and quantum spin Hall insulators to a magnetic field's vector potential are also studied both in weak- and strong-field regimes, as well as the edge states in a ribbon geometry.

Reduced functional connectivity within the limbic cortico-striato-thalamo-cortical loop in unmedicated adults with obsessive-compulsive disorder.

PubMed

Posner, Jonathan; Marsh, Rachel; Maia, Tiago V; Peterson, Bradley S; Gruber, Allison; Simpson, H Blair

2014-06-01

Cortico-striato-thalamo-cortical (CSTC) loops project from the cortex to the striatum, then from the striatum to the thalamus via the globus pallidus, and finally from the thalamus back to the cortex again. These loops have been implicated in Obsessive-Compulsive Disorder (OCD) with particular focus on the limbic CSTC loop, which encompasses the orbitofrontal and anterior cingulate cortices, as well as the ventral striatum. Resting state functional-connectivity MRI (rs-fcMRI) studies, which examine temporal correlations in neural activity across brain regions at rest, have examined CSTC loop connectivity in patients with OCD and suggest hyperconnectivity within these loops in medicated adults with OCD. We used rs-fcMRI to examine functional connectivity within CSTC loops in unmedicated adults with OCD (n = 23) versus healthy controls (HCs) (n = 20). Contrary to prior rs-fcMRI studies in OCD patients on medications that report hyperconnectivity in the limbic CSTC loop, we found that compared with HCs, unmedicated OCD participants had reduced connectivity within the limbic CSTC loop. Exploratory analyses revealed that reduced connectivity within the limbic CSTC loop correlated with OCD symptom severity in the OCD group. Our finding of limbic loop hypoconnectivity in unmedicted OCD patients highlights the potential confounding effects of antidepressants on connectivity measures and the value of future examinations of the effects of pharmacological and/or behavioral treatments on limbic CSTC loop connectivity. Copyright © 2013 Wiley Periodicals, Inc.

Simulated countercurrent moving bed chromatographic reactor and method for use thereof

DOEpatents

Carr, Robert W.; Tonkovich, Anna Lee Y.

2001-01-01

A method and apparatus for continuously reacting a feed gas to form a product and separating the product from unreacted feed gas is provided. The apparatus includes a plurality of compartments and means for connecting the compartments in a series, with the last compartment in the series being connected to the first compartment in the series to provide a closed loop. Each compartment may include an upstream reaction zone and a downstream separation zone.

Closed Loop Adaptive Refinement of Dynamical Models for Complex Chemical Reactions

DTIC Science & Technology

2008-06-26

rotational energy Erot , bond length, or bond angle of the products, the corresponding RS-HDMR component functions, cf. eq. (??), can be constructed from a...rotational energy ∆ Erot , and (3) the H2O vibrational energy ∆Evib. The usually strong Coriolis coupling, for example, between H2O rotational and...averaged vibrational energy) is usually considered after the collision. On the other hand, the corresponding internal energy Eint = Evib+ Erot will remain

The Role of elF4E Activity in Breast Cancer

DTIC Science & Technology

2011-08-01

protein; ORF, open reading frame; qPCR, quantitative PCR; RACE, rapid amplification of cDNA ends; RT, reverse transcriptase ; uORF, upstream ORF; UTR...Reactions were also performed using template lacking RT ( reverse transcriptase ): products were either undetectable or greatly reduced (>30000-fold less...that a 5’UTR expressed from the human AXIN2 gene contains a sixty nucleotide sequence that is predicted to form a stable stem-loop structure6. This

Embryo Sexing and Sex Chromosomal Chimerism Analysis by Loop-Mediated Isothermal Amplification in Cattle and Water Buffaloes

PubMed Central

HIRAYAMA, Hiroki; KAGEYAMA, Soichi; MORIYASU, Satoru; SAWAI, Ken; MINAMIHASHI, Akira

2013-01-01

Abstract In domestic animals of the family Bovidae, sex preselection of offspring has been demanded for convenience of milk/beef production and animal breeding. Development of the nonsurgical embryo transfer technique and sexing methods of preimplantation embryos made it possible. Sexing based on detection of Y chromosome-specific DNA sequences is considered the most reliable method to date. PCR enables amplification of a target sequence from a small number of blastomeres. However, it requires technical skill and is time consuming. Furthermore, PCR has the risk of false positives because of DNA contamination during handling of the PCR products in duplicate PCR procedures and/or electrophoresis. Therefore, for embryo sexing to become widely used in the cattle embryo transfer industry, a simple, rapid and precise sexing method needs to be developed. Loop-mediated isothermal amplification (LAMP) is a novel DNA amplification method, and the reaction is carried out under isothermal conditions (range, 60 to 65 C) using DNA polymerase with strand displacement activity. When the target DNA is amplified by LAMP, a white precipitate derived from magnesium pyrophosphate (a by-product of the LAMP reaction) is observed. It is noteworthy that LAMP does not need special reagents or electrophoresis to detect the amplified DNA. This review describes the development and application of an embryo sexing method using LAMP in cattle and water buffaloes. PMID:23965599

Investigation of the recognition of an important uridine in an internal loop of a hairpin ribozyme prepared using post-synthetically modified oligonucleotides.

PubMed Central

Komatsu, Y; Kumagai, I; Ohtsuka, E

1999-01-01

We introduced 4-thio- ((4S)U), 2-thio- ((2S)U), 4- O -methyluridine ((4Me)U) and cytidine substitutions for U+2, which is an important base for cleavage in a substrate RNA. Oligonucleotides containing 4-thio- and 4- O -methyluridine were prepared by a new convenient post-synthetic modification method using a 4- O - p -nitrophenyl-uridine derivative. A hairpin ribozyme cleaved the substrate RNA with either C+2, (4S)U+2 or (4Me)U+2 at approximately 14-, 6- and 4-fold lower rates, respectively, than that of the natural substrate. In contrast, the substrate with a (2S)U+2 was cleaved with the same activity as the natural substrate. These results suggest that the O4 of U+2 is involved in hydrogen bonding at loop A, but the O2 of U+2 is not recognized by the active residues. Circular dichroism data of the ribozymes containing (4S)U+2 and (2S)U+2, as well as the susceptibility of the thiocarbonyl group to hydrogen peroxide, suggest that a conformational change of U+2 occurs during the domain docking in the cleavage reaction. We propose here the conformational change of U+2 from the ground state to the active molecule during the reaction. PMID:10536137

Positive Feedback Loops for Factor V and Factor VII Activation Supply Sensitivity to Local Surface Tissue Factor Density During Blood Coagulation

PubMed Central

Balandina, A.N.; Shibeko, A.M.; Kireev, D.A.; Novikova, A.A.; Shmirev, I.I.; Panteleev, M.A.; Ataullakhanov, F.I.

2011-01-01

Blood coagulation is triggered not only by surface tissue factor (TF) density but also by surface TF distribution. We investigated recognition of surface TF distribution patterns during blood coagulation and identified the underlying molecular mechanisms. For these investigations, we employed 1), an in vitro reaction-diffusion experimental model of coagulation; and 2), numerical simulations using a mathematical model of coagulation in a three-dimensional space. When TF was uniformly immobilized over the activating surface, the clotting initiation time in normal plasma increased from 4 min to >120 min, with a decrease in TF density from 100 to 0.7 pmol/m2. In contrast, surface-immobilized fibroblasts initiated clotting within 3–7 min, independently of fibroblast quantity and despite a change in average surface TF density from 0.5 to 130 pmol/m2. Experiments using factor V-, VII-, and VIII-deficient plasma and computer simulations demonstrated that different responses to these two TF distributions are caused by two positive feedback loops in the blood coagulation network: activation of the TF–VII complex by factor Xa, and activation of factor V by thrombin. This finding suggests a new role for these reactions: to supply sensitivity to local TF density during blood coagulation. PMID:22004734

Deduced catalytic mechanism of d-amino acid amidase from Ochrobactrum anthropi SV3

PubMed Central

Okazaki, Seiji; Suzuki, Atsuo; Komeda, Hidenobu; Asano, Yasuhisa; Yamane, Takashi

2008-01-01

d-Amino acid amidase (DAA) from Ochrobactrum anthropi SV3 catalyzes d-stereospecific hydrolysis of amino acid amides. DAA has attracted attention as a catalyst for the stereospecific production of d-amino acids, although the mechanism that drives the reaction has not been clear. Previously, the structure of DAA was classified into two types, a substrate-bound state with an ordered Ω loop, and a ground state with a disordered Ω loop. Because the binding of the substrate facilitates ordering, this transition was regarded to be induced fit motion. The angles and distances of hydrogen bonds at Tyr149 Oη, Ser60 Oγ and Lys63 Nζ revealed that Tyr149 Oη donates an H atom to a water molecule in the substrate-bound state, and that Tyr149 Oη donates an H atom to Ser60 Oγ or Lys63 Nζ in the ground state. Taking into consideration the locations of the H atoms of Tyr149 Oη, Ser60 Oγ and Lys63 Nζ, a catalytic mechanism of DAA activity is presented, wherein a shift of an H atom at Tyr149 Oη in the substrate-bound versus the ground state plays a significant role in the reaction. This mechanism explains well why acylation proceeds and deacylation does not proceed in the substrate-bound state. PMID:18421151

Establishment and application of a loop-mediated isothermal amplification (LAMP) system for detection of cry1Ac transgenic sugarcane

PubMed Central

Zhou, Dinggang; Guo, Jinlong; Xu, Liping; Gao, Shiwu; Lin, Qingliang; Wu, Qibin; Wu, Luguang; Que, Youxiong

2014-01-01

To meet the demand for detection of foreign genes in genetically modified (GM) sugarcane necessary for regulation of gene technology, an efficient method with high specificity and rapidity was developed for the cry1Ac gene, based on loop-mediated isothermal amplification (LAMP). A set of four primers was designed using the sequence of cry1Ac along with optimized reaction conditions: 5.25 mM of Mg2+, 4:1 ratio of inner primer to outer primer, 2.0 U of Bst DNA polymerase in a reaction volume of 25.0 μL. Three post-LAMP detection methods (precipitation, calcein (0.60 mM) with Mn2+ (0.05 mM) complex and SYBR Green I visualization), were shown to be effective. The sensitivity of the LAMP method was tenfold higher than that of conventional PCR when using templates of the recombinant cry1Ac plasmid or genomic DNA from cry1Ac transgenic sugarcane plants. More importantly, this system allowed detection of the foreign gene on-site when screening GM sugarcane without complex and expensive instruments, using the naked eye. This method can not only provide technological support for detection of cry1Ac, but can also further facilitate the use of this detection technique for other transgenes in GM sugarcane. PMID:24810230

Interdependence between electrical and magnetic properties of polycrystalline cobalt-substituted tungsten bronze multiferroic ceramics

NASA Astrophysics Data System (ADS)

Jindal, Shilpi; Devi, Sheela; Vasishth, Ajay; Batoo, Khalid Mujasam; Kumar, Gagan

Polycrystalline cobalt-substituted tungsten bronze ferroelectric ceramics with chemical composition Ba5CaTi2-xCoXNb8O30 (x=0.00, 0.02, 0.04 and 0.08) were synthesized by solid state reaction technique. X-ray diffraction (XRD) technique was used to confirm the phase formation and it revealed the formation of single phase tetragonal structure with space group P4bm. The surface morphology of the samples was studied by using the scanning electron microscopy (SEM) technique. The dielectric properties such as dielectric constant and dielectric loss have been investigated as a function of temperature and frequency. The P-E and M-H studies confirmed the coexistent of ferroelectricity and magnetism at room temperature. The P-E loop study indicated an increase in the coercive field while the M-H study depicted a decrease in the magnetization with the incorporation of cobalt ions.

Study of self-ion irradiated nanostructured ferritic alloy (NFA) and silicon carbide-nanostructured ferritic alloy (SiC-NFA) cladding materials

NASA Astrophysics Data System (ADS)

Ning, Kaijie; Bai, Xianming; Lu, Kathy

2018-07-01

Silicon carbide-nanostructured ferritic alloy (SiC-NFA) materials are expected to have the beneficial properties of each component for advanced nuclear claddings. Fabrication of pure NFA (0 vol% SiC-100 vol% NFA) and SiC-NFAs (2.5 vol% SiC-97.5 vol% NFA, 5 vol% SiC-95 vol% NFA) has been reported in our previous work. This paper is focused on the study of radiation damage in these materials under 5 MeV Fe++ ion irradiation with a dose up to ∼264 dpa. It is found that the material surfaces are damaged to high roughness with irregularly shaped ripples, which can be explained by the Bradley-Harper (B-H) model. The NFA matrix shows ion irradiation induced defect clusters and small dislocation loops, while the crystalline structure is maintained. Reaction products of Fe3Si and Cr23C6 are identified in the SiC-NFA materials, with the former having a partially crystalline structure but the latter having a fully amorphous structure upon irradiation. The different radiation damage behaviors of NFA, Fe3Si, and Cr23C6 are explained using the defect reaction rate theory.

Single amino acid insertions in extracellular loop 2 of Bombyx mori ABCC2 disrupt its receptor function for Bacillus thuringiensis Cry1Ab and Cry1Ac but not Cry1Aa toxins.

PubMed

Tanaka, Shiho; Miyamoto, Kazuhisa; Noda, Hiroaki; Endo, Haruka; Kikuta, Shingo; Sato, Ryoichi

2016-04-01

In a previous report, seven Cry1Ab-resistant strains were identified in the silkworm, Bombyx mori; these strains were shown to have a tyrosine insertion at position 234 in extracellular loop 2 of the ABC transporter C2 (BmABCC2). This insertion was confirmed to destroy the receptor function of BmABCC2 and confer the strains resistance against Cry1Ab and Cry1Ac. However, these strains were susceptible to Cry1Aa. In this report, we examined the mechanisms of the loss of receptor function of the transporter by expressing mutations in Sf9 cells. After replacement of one or two of the five amino acid residues in loop 2 of the susceptible BmABCC2 gene [BmABCC2_S] with alanine, cells still showed susceptibility, retaining the receptor function. Five mutants with single amino acid insertions at position 234 in BmABCC2 were also generated, resulting in loop 2 having six amino acids, which corresponds to replacing the tyrosine insertion in the resistant BmABCC2 gene [BmABCC2_R(+(234)Y)] with another amino acid. All five mutants exhibited loss of function against Cry1Ab and Cry1Ac. These results suggest that the amino acid sequence in loop 2 is less important than the loop size (five vs. six amino acids) or loop structure for Cry1Ab and Cry1Ac activity. Several domain-swapped mutant toxins were then generated among Cry1Aa, Cry1Ab, and Cry1Ac, which are composed of three domains. Swapped mutants containing domain II of Cry1Ab or Cry1Ac did not kill Sf9 cells expressing BmABCC2_R(+(234)Y), suggesting that domain II of the Cry toxin is related to the interaction with the receptor function of BmABCC2. This also suggests that different reactions against Bt-toxins in some B. mori strains, that is, Cry1Ab resistance or Cry1Aa susceptibility, are attributable to structural differences in domain II of Cry1A toxins. Copyright © 2016. Published by Elsevier Inc.

Loop Mediated Isothermal Amplification (LAMP) for Embryo Sex Determination in Pregnant Women at Eight Weeks of Pregnancy.

PubMed

Almasi, Mohammad Amin; Almasi, Galavizh

2017-01-01

In human, SRY (sex-determining region of the Y chromosome) is the major gene for the testis-determining factor which is found in normal XY males and in the rare XX males, and it is absent in normal XX females and many XY females. There are several methods which can indicate a male genotype by the presence of the amplified product of SRY gene. The aim of this study was to identify the SRY gene for embryo sex determination in human during pregnancy using loop mediated isothermal amplification (LAMP) method. A total of 15 blood samples from pregnant women at eight weeks of pregnancy were collected, and Plasma DNA was extracted. LAMP assay was performed using DNA obtained for detection of SRY gene. Furthermore, colorimetric LAMP assay for rapid and easy detection of SRY gene was developed. LAMP results revealed that the positive reaction was highly specific only with samples containing XY chromosomes, while no amplification was found in samples containing XX chromosomes. A total of 15 blood samples from pregnant women were seven male embryos (46.6%) and eight female embryos (53.4%). All used visual components in the colorimetric assay could successfully make a clear distinction between positive and negative ones. The LAMP assay developed in this study is a valuable tool capable of monitoring the purity and detection of SRY gene for sex determination.

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

Aranda, J. I.; Tututi, E. S.; Flores-Tlalpa, A.

Higgs mediated flavor violating electromagnetic interactions, induced at the one-loop level by a nondiagonal Hf{sub i}f{sub j} vertex, with f{sub i} and f{sub j} charged leptons or quarks, are studied within the context of a completely general effective Yukawa sector that comprises SU{sub L}(2)xU{sub Y}(1)-invariant operators of up to dimension-six. Exact formulae for the one-loop {gamma}f{sub i}f{sub j} and {gamma}{gamma}f{sub i}f{sub j} couplings are presented and their related processes used to study the phenomena of Higgs mediated lepton flavor violation. The experimental limit on the {mu}{yields}e{gamma} decay is used to derive a bound on the branching ratio of the {mu}{yields}e{gamma}{gamma}more » transition, which is 6 orders of magnitude stronger than the current experimental limit. Previous results on the {tau}{yields}{mu}{gamma} and {tau}{yields}{mu}{gamma}{gamma} decays are reproduced. The possibility of detecting signals of lepton flavor violation at {gamma}{gamma} colliders is explored through the {gamma}{gamma}{yields}l{sub i}l{sub j} reaction, putting special emphasis on the {tau}{mu} final state. Using the bound imposed on the H{tau}{mu} vertex by the current experimental data on the muon anomalous magnetic moment, it is found that about half a hundred events may be produced in the International Linear Collider.« less

Real-time control of walking using recordings from dorsal root ganglia.

PubMed

Holinski, B J; Everaert, D G; Mushahwar, V K; Stein, R B

2013-10-01

The goal of this study was to decode sensory information from the dorsal root ganglia (DRG) in real time, and to use this information to adapt the control of unilateral stepping with a state-based control algorithm consisting of both feed-forward and feedback components. In five anesthetized cats, hind limb stepping on a walkway or treadmill was produced by patterned electrical stimulation of the spinal cord through implanted microwire arrays, while neuronal activity was recorded from the DRG. Different parameters, including distance and tilt of the vector between hip and limb endpoint, integrated gyroscope and ground reaction force were modelled from recorded neural firing rates. These models were then used for closed-loop feedback. Overall, firing-rate-based predictions of kinematic sensors (limb endpoint, integrated gyroscope) were the most accurate with variance accounted for >60% on average. Force prediction had the lowest prediction accuracy (48 ± 13%) but produced the greatest percentage of successful rule activations (96.3%) for stepping under closed-loop feedback control. The prediction of all sensor modalities degraded over time, with the exception of tilt. Sensory feedback from moving limbs would be a desirable component of any neuroprosthetic device designed to restore walking in people after a spinal cord injury. This study provides a proof-of-principle that real-time feedback from the DRG is possible and could form part of a fully implantable neuroprosthetic device with further development.

Scroll wave filaments self-wrap around unexcitable heterogeneities.

PubMed

Jiménez, Zulma A; Steinbock, Oliver

2012-09-01

Scroll waves are three-dimensional excitation vortices rotating around one-dimensional phase singularities called filaments. In experiments with a chemical reaction-diffusion system and in numerical simulations, we study the pinning of closed filament loops to inert cylindrical heterogeneities. We show that the filament wraps itself around the heterogeneity and thus avoids contraction and annihilation. This entwining steadily increases the total length of the pinned filament and reshapes the entire rotation backbone of the vortex. Self-pinning is fastest for thin cylinders with radii not much larger than the core of the unpinned rotor. The process ends when the filament is attached to the entire length of the cylinder. The possible importance of self-pinning in cardiac systems is discussed.

Crystal plasticity modeling of irradiation growth in Zircaloy-2

DOE PAGES

Patra, Anirban; Tome, Carlos; Golubov, Stanislav I.

2017-05-10

A reaction-diffusion based mean field rate theory model is implemented in the viscoplastic self-consistent (VPSC) crystal plasticity framework to simulate irradiation growth in hcp Zr and its alloys. A novel scheme is proposed to model the evolution (both number density and radius) of irradiation-induced dislocation loops that can be informed directly from experimental data of dislocation density evolution during irradiation. This framework is used to predict the irradiation growth behavior of cold-worked Zircaloy-2 and trends compared to available experimental data. The role of internal stresses in inducing irradiation creep is discussed. Effects of grain size, texture, and external stress onmore » the coupled irradiation growth and creep behavior are also studied.« less

Crystal plasticity modeling of irradiation growth in Zircaloy-2

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

Patra, Anirban; Tome, Carlos; Golubov, Stanislav I.

A reaction-diffusion based mean field rate theory model is implemented in the viscoplastic self-consistent (VPSC) crystal plasticity framework to simulate irradiation growth in hcp Zr and its alloys. A novel scheme is proposed to model the evolution (both number density and radius) of irradiation-induced dislocation loops that can be informed directly from experimental data of dislocation density evolution during irradiation. This framework is used to predict the irradiation growth behavior of cold-worked Zircaloy-2 and trends compared to available experimental data. The role of internal stresses in inducing irradiation creep is discussed. Effects of grain size, texture, and external stress onmore » the coupled irradiation growth and creep behavior are also studied.« less

Structure of choline oxidase in complex with the reaction product glycine betaine.

PubMed

Salvi, Francesca; Wang, Yuan-Fang; Weber, Irene T; Gadda, Giovanni

2014-02-01

Choline oxidase from Arthrobacter globiformis, which is involved in the biosynthesis of glycine betaine from choline, has been extensively characterized in its mechanistic and structural properties. Despite the knowledge gained on the enzyme, the details of substrate access to the active site are not fully understood. The `loop-and-lid' mechanism described for the glucose-methanol-choline enzyme superfamily has not been confirmed for choline oxidase. Instead, a hydrophobic cluster on the solvent-accessible surface of the enzyme has been proposed by molecular dynamics to control substrate access to the active site. Here, the crystal structure of the enzyme was solved in complex with glycine betaine at pH 6.0 at 1.95 Å resolution, allowing a structural description of the ligand-enzyme interactions in the active site. This structure is the first of choline oxidase in complex with a physiologically relevant ligand. The protein structures with and without ligand are virtually identical, with the exception of a loop at the dimer interface, which assumes two distinct conformations. The different conformations of loop 250-255 define different accessibilities of the proposed active-site entrance delimited by the hydrophobic cluster on the other subunit of the dimer, suggesting a role in regulating substrate access to the active site.

Steady state statistical correlations predict bistability in reaction motifs.

PubMed

Chakravarty, Suchana; Barik, Debashis

2017-03-28

Various cellular decision making processes are regulated by bistable switches that take graded input signals and convert them to binary all-or-none responses. Traditionally, a bistable switch generated by a positive feedback loop is characterized either by a hysteretic signal response curve with two distinct signaling thresholds or by characterizing the bimodality of the response distribution in the bistable region. To identify the intrinsic bistability of a feedback regulated network, here we propose that bistability can be determined by correlating higher order moments and cumulants (≥2) of the joint steady state distributions of two components connected in a positive feedback loop. We performed stochastic simulations of four feedback regulated models with intrinsic bistability and we show that for a bistable switch with variation of the signal dose, the steady state variance vs. covariance adopts a signatory cusp-shaped curve. Further, we find that the (n + 1)th order cross-cumulant vs. nth order cross-cumulant adopts a closed loop structure for at least n = 3. We also propose that our method is capable of identifying systems without intrinsic bistability even though the system may show bimodality in the marginal response distribution. The proposed method can be used to analyze single cell protein data measured at steady state from experiments such as flow cytometry.

Impact of time delays on oscillatory dynamics of interlinked positive and negative feedback loops

NASA Astrophysics Data System (ADS)

Huang, Bo; Tian, Xinyu; Liu, Feng; Wang, Wei

2016-11-01

Interlinking a positive feedback loop (PFL) with a negative feedback loop (NFL) constitutes a typical motif in genetic networks, performing various functions in cell signaling. How time delay in feedback regulation affects the dynamics of such systems still remains unclear. Here, we investigate three systems of interlinked PFL and NFL with time delays: a synthetic genetic oscillator, a three-node circuit, and a simplified single-node model. The stability of steady states and the routes to oscillation in the single-node model are analyzed in detail. The amplitude and period of oscillations vary with a pointwise periodicity over a range of time delay. Larger-amplitude oscillations can be induced when the PFL has an appropriately long delay, in comparison with the PFL with no delay or short delay; this conclusion holds true for all the three systems. We unravel the underlying mechanism for the above effects via analytical derivation under a limiting condition. We also develop a stochastic algorithm for simulating a single reaction with two delays and show that robust oscillations can be maintained by the PFL with a properly long delay in the single-node system. This work presents an effective method for constructing robust large-amplitude oscillators and interprets why similar circuit architectures are engaged in timekeeping systems such as circadian clocks.

Study of the post-flare loops on 29 July 1973. I - Dynamics of the X-ray loops

NASA Technical Reports Server (NTRS)

Nolte, J. T.; Gerassimenko, M.; Krieger, A. S.; Petrasso, R. D.; Svestka, Z.

1979-01-01

We derive an empirical model of the X-ray emitting post-flare loops observed during the decay phase of the 29 July 1973 flare. We find that the loops are elliptical, with the brightest emitting region at the tops. We determine the height, velocity of growth, and ratio of height to width of the loops at times from 3 to 12 hr after the flare onset.

Effects of loop detector installation on the Portland cement concrete pavement lifespan : case study on I-5.

DOT National Transportation Integrated Search

2010-08-01

The installation of loop detectors in portland cement concrete pavement (PCCP) may shorten affected panel life, thus prematurely worsening the condition of the overall pavement. This study focuses on the performance of those loop embedded panels (LEP...

Shortening a loop can increase protein native state entropy.

PubMed

Gavrilov, Yulian; Dagan, Shlomi; Levy, Yaakov

2015-12-01

Protein loops are essential structural elements that influence not only function but also protein stability and folding rates. It was recently reported that shortening a loop in the AcP protein may increase its native state conformational entropy. This effect on the entropy of the folded state can be much larger than the lower entropic penalty of ordering a shorter loop upon folding, and can therefore result in a more pronounced stabilization than predicted by polymer model for loop closure entropy. In this study, which aims at generalizing the effect of loop length shortening on native state dynamics, we use all-atom molecular dynamics simulations to study how gradual shortening a very long or solvent-exposed loop region in four different proteins can affect their stability. For two proteins, AcP and Ubc7, we show an increase in native state entropy in addition to the known effect of the loop length on the unfolded state entropy. However, for two permutants of SH3 domain, shortening a loop results only with the expected change in the entropy of the unfolded state, which nicely reproduces the observed experimental stabilization. Here, we show that an increase in the native state entropy following loop shortening is not unique to the AcP protein, yet nor is it a general rule that applies to all proteins following the truncation of any loop. This modification of the loop length on the folded state and on the unfolded state may result with a greater effect on protein stability. © 2015 Wiley Periodicals, Inc.

N-Loop Learning: Part II--An Empirical Investigation

ERIC Educational Resources Information Center

Simonin, Bernard L.

2017-01-01

Purpose: Through a survey of firm's experiences with strategic alliances and a structural equation modeling approach, the aim of this study is to stimulate further interest in modeling and empirical research in the area of N-loop learning. Although the concepts of single-loop and double-loop learning, in particular, are well established in the…

GDP-bound and nucleotide-free intermediates of the guanine nucleotide exchange in the Rab5·Vps9 system.

PubMed

Uejima, Tamami; Ihara, Kentaro; Goh, Tatsuaki; Ito, Emi; Sunada, Mariko; Ueda, Takashi; Nakano, Akihiko; Wakatsuki, Soichi

2010-11-19

Many GTPases regulate intracellular transport and signaling in eukaryotes. Guanine nucleotide exchange factors (GEFs) activate GTPases by catalyzing the exchange of their GDP for GTP. Here we present crystallographic and biochemical studies of a GEF reaction with four crystal structures of Arabidopsis thaliana ARA7, a plant homolog of Rab5 GTPase, in complex with its GEF, VPS9a, in the nucleotide-free and GDP-bound forms, as well as a complex with aminophosphonic acid-guanylate ester and ARA7·VPS9a(D185N) with GDP. Upon complex formation with ARA7, VPS9 wedges into the interswitch region of ARA7, inhibiting the coordination of Mg(2+) and decreasing the stability of GDP binding. The aspartate finger of VPS9a recognizes GDP β-phosphate directly and pulls the P-loop lysine of ARA7 away from GDP β-phosphate toward switch II to further destabilize GDP for its release during the transition from the GDP-bound to nucleotide-free intermediates in the nucleotide exchange reaction.

The diversity of H3 loops determines the antigen-binding tendencies of antibody CDR loops.

PubMed

Tsuchiya, Yuko; Mizuguchi, Kenji

2016-04-01

Of the complementarity-determining regions (CDRs) of antibodies, H3 loops, with varying amino acid sequences and loop lengths, adopt particularly diverse loop conformations. The diversity of H3 conformations produces an array of antigen recognition patterns involving all the CDRs, in which the residue positions actually in contact with the antigen vary considerably. Therefore, for a deeper understanding of antigen recognition, it is necessary to relate the sequence and structural properties of each residue position in each CDR loop to its ability to bind antigens. In this study, we proposed a new method for characterizing the structural features of the CDR loops and obtained the antigen-binding ability of each residue position in each CDR loop. This analysis led to a simple set of rules for identifying probable antigen-binding residues. We also found that the diversity of H3 loop lengths and conformations affects the antigen-binding tendencies of all the CDR loops. © 2016 The Protein Society.

Atomistic study of the hardening of ferritic iron by Ni-Cr decorated dislocation loops

NASA Astrophysics Data System (ADS)

Bonny, G.; Bakaev, A.; Terentyev, D.; Zhurkin, E.; Posselt, M.

2018-01-01

The exact nature of the radiation defects causing hardening in reactor structural steels consists of several components that are not yet clearly determined. While generally, the hardening is attributed to dislocation loops, voids and secondary phases (radiation-induced precipitates), recent advanced experimental and computational studies point to the importance of solute-rich clusters (SRCs). Depending on the exact composition of the steel, SRCs may contain Mn, Ni and Cu (e.g. in reactor pressure vessel steels) or Ni, Cr, Si, Mn (e.g. in high-chromium steels for generation IV and fusion applications). One of the hypotheses currently implied to explain their formation is the process of radiation-induced diffusion and segregation of these elements to small dislocation loops (heterogeneous nucleation), so that the distinction between SRCs and loops becomes somewhat blurred. In this work, we perform an atomistic study to investigate the enrichment of loops by Ni and Cr solutes and their interaction with an edge dislocation. The dislocation loops decorated with Ni and Cr solutes are obtained by Monte Carlo simulations, while the effect of solute segregation on the loop's strength and interaction mechanism is then addressed by large scale molecular dynamics simulations. The synergy of the Cr-Ni interaction and their competition to occupy positions in the dislocation loop core are specifically clarified.

Fine flow structures in the transition region small-scale loops

NASA Astrophysics Data System (ADS)

Yan, L.; Peter, H.; He, J.; Wei, Y.

2016-12-01

The observation and model have suggested that the transition region EUV emission from the quiet sun region is contributed by very small scale loops which have not been resolved. Recently, the observation from IRIS has revealed that this kind of small scale loops. Based on the high resolution spectral and imaging observation from IRIS, much more detail work needs to be done to reveal the fine flow features in this kind of loop to help us understand the loop heating. Here, we present a detail statistical study of the spatial and temporal evolution of Si IV line profiles of small scale loops and report the spectral features: there is a transition from blue (red) wing enhancement dominant to red (blue) wing enhancement dominant along the cross-section of the loop, which is independent of time. This feature appears as the loop appear and disappear as the loop un-visible. This is probably the signature of helical flow along the loop. The result suggests that the brightening of this kind of loop is probably due to the current dissipation heating in the twisted magnetic field flux tube.

Structural features of the DNA hairpin d(ATCCTA-GTTA-TAGGAT): formation of a G-A base pair in the loop.

PubMed Central

van Dongen, M J; Mooren, M M; Willems, E F; van der Marel, G A; van Boom, J H; Wijmenga, S S; Hilbers, C W

1997-01-01

The three-dimensional structure of the hairpin formed by d(ATCCTA-GTTA-TAGGAT) has been determined by means of two-dimensional NMR studies, distance geometry and molecular dynamics calculations. The first and the last residues of the tetraloop of this hairpin form a sheared G-A base pair on top of the six Watson-Crick base pairs in the stem. The glycosidic torsion angles of the guanine and adenine residues in the G-A base pair reside in the anti and high- anti domain ( approximately -60 degrees ) respectively. Several dihedral angles in the loop adopt non-standard values to accommodate this base pair. The first and second residue in the loop are stacked in a more or less normal helical fashion; the fourth loop residue also stacks upon the stem, while the third residue is directed away from the loop region. The loop structure can be classified as a so-called type-I loop, in which the bases at the 5'-end of the loop stack in a continuous fashion. In this situation, loop stability is unlikely to depend heavily on the nature of the unpaired bases in the loop. Moreover, the present study indicates that the influence of the polarity of a closing A.T pair is much less significant than that of a closing C.G base pair. PMID:9092659

Te homogeneous precipitation in Ge dislocation loop vicinity

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

Perrin Toinin, J.; Portavoce, A., E-mail: alain.portavoce@im2np.fr; Texier, M.

2016-06-06

High resolution microscopies were used to study the interactions of Te atoms with Ge dislocation loops, after a standard n-type doping process in Ge. Te atoms neither segregate nor precipitate on dislocation loops, but form Te-Ge clusters at the same depth as dislocation loops, in contradiction with usual dopant behavior and thermodynamic expectations. Atomistic kinetic Monte Carlo simulations show that Te atoms are repulsed from dislocation loops due to elastic interactions, promoting homogeneous Te-Ge nucleation between dislocation loops. This phenomenon is enhanced by coulombic interactions between activated Te{sup 2+} or Te{sup 1+} ions.

Structures and functions in the crowded nucleus: new biophysical insights

NASA Astrophysics Data System (ADS)

Hancock, Ronald

2014-09-01

Concepts and methods from the physical sciences have catalysed remarkable progress in understanding the cell nucleus in recent years. To share this excitement with physicists and encourage their interest in this field, this review offers an overview of how the physics which underlies structures and functions in the nucleus is becoming more clear thanks to methods which have been developed to simulate and study macromolecules, polymers, and colloids. The environment in the nucleus is very crowded with macromolecules, making entropic (depletion) forces major determinants of interactions. Simulation and experiments are consistent with their key role in forming membraneless compartments such as nucleoli, PML and Cajal bodies, and discrete "territories" for chromosomes. The chromosomes, giant linear polyelectrolyte polymers, exist in vivo in a state like a polymer melt. Looped conformations are predicted in crowded conditions, and have been confirmed experimentally and are central to the regulation of gene expression. Polymer theory has revealed how the chromosomes are so highly compacted in the nucleus, forming a "crumpled globule" with fractal properties which avoids knots and entanglements in DNA while allowing facile accessibility for its replication and transcription. Entropic repulsion between looped polymers can explain the confinement of each chromosome to a discrete region of the nucleus. Crowding and looping are predicted to facilitate finding the specific targets of factors which modulate activities of DNA. Simulation shows that entropic effects contribute to finding and repairing potentially lethal double-strand breaks in DNA by increasing the mobility of the broken ends, favouring their juxtaposition for repair. Signaling pathways are strongly influenced by crowding, which favours a processive mode of response (consecutive reactions without releasing substrates). This new information contributes to understanding the sometimes counter-intuitive consequences.

Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways.

PubMed

Rydzewski, J; Jakubowski, R; Nowak, W; Grubmüller, H

2018-06-12

The dissociation of huperzine A (hupA) from Torpedo californica acetylcholinesterase ( TcAChE) was investigated by 4 μs unbiased and biased all-atom molecular dynamics (MD) simulations in explicit solvent. We performed our study using memetic sampling (MS) for the determination of reaction pathways (RPs), metadynamics to calculate free energy, and maximum-likelihood estimation (MLE) to recover kinetic rates from unbiased MD simulations. Our simulations suggest that the dissociation of hupA occurs mainly via two RPs: a front door along the axis of the active-site gorge (pwf) and through a new transient side door (pws), i.e., formed by the Ω-loop (residues 67-94 of TcAChE). An analysis of the inhibitor unbinding along the RPs suggests that pws is opened transiently after hupA and the Ω-loop reach a low free-energy transition state characterized by the orientation of the pyridone group of the inhibitor directed toward the Ω-loop plane. Unlike pws, pwf does not require large structural changes in TcAChE to be accessible. The estimated free energies and rates agree well with available experimental data. The dissociation rates along the unbinding pathways are similar, suggesting that the dissociation of hupA along pws is likely to be relevant. This indicates that perturbations to hupA- TcAChE interactions could potentially induce pathway hopping. In summary, our results characterize the slow-onset inhibition of TcAChE by hupA, which may provide the structural and energetic bases for the rational design of the next-generation slow-onset inhibitors with optimized pharmacokinetic properties for the treatment of Alzheimer's disease.

Interactions at the Dimer Interface Influence the Relative Efficiencies for Purine Nucleotide Synthesis and Pyrophosphorolysis in a Phosphoribosyltransferase

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

Canyuk, Bhutorn; Medrano, Francisco J.; Wenck, MaryAnne

2010-03-05

Enzymes that salvage 6-oxopurines, including hypoxanthine phosphoribosyltransferases (HPRTs), are potential targets for drugs in the treatment of diseases caused by protozoan parasites. For this reason, a number of high-resolution X-ray crystal structures of the HPRTs from protozoa have been reported. Although these structures did not reveal why HPRTs need to form dimers for catalysis, they revealed the existence of potentially relevant interactions involving residues in a loop of amino acid residues adjacent to the dimer interface, but the contributions of these interactions to catalysis remained poorly understood. The loop, referred to as active-site loop I, contains an unusual non-proline cis-peptidemore » and is composed of residues that are structurally analogous with Leu67, Lys68, and Gly69 in the human HPRT. Functional analyses of site-directed mutations (K68D, K68E, K68N, K68P, and K68R) in the HPRT from Trypanosoma cruzi, etiologic agent of Chagas disease, show that the side-chain at position 68 can differentially influence the K{sub m} values for all four substrates as well as the k{sub cat} values for both IMP formation and pyrophosphorolysis. Also, the results for the K68P mutant are inconsistent with a cis-trans peptide isomerization-assisted catalytic mechanism. These data, together with the results of structural studies of the K68R mutant, reveal that the side-chain of residue 68 does not participate directly in reaction chemistry, but it strongly influences the relative efficiencies for IMP formation and pyrophosphorolysis, and the prevalence of lysine at position 68 in the HPRT of the majority of eukaryotes is consistent with there being a biological role for nucleotide pyrophosphorolysis.« less

The β subunit of the high-conductance calcium-activated potassium channel contributes to the high-affinity receptor for charybdotoxin

PubMed Central

Hanner, Markus; Schmalhofer, William A.; Munujos, Petraki; Knaus, Hans-Günther; Kaczorowski, Gregory J.; Garcia, Maria L.

1997-01-01

Transient expression of either α or α+β subunits of the high-conductance Ca2+-activated K+ (maxi-K) channel has been achieved in COS-1 cells. Expression has been studied using charybdotoxin (ChTX), a peptidyl inhibitor that binds in the pore on the α subunit. Although some properties of monoiodotyrosine-ChTX (125I-ChTX) binding to membranes derived from each type of transfected cells appear to be identical, other parameters of the binding reaction are markedly different. Under low ionic strength conditions, the affinity constant for 125I-ChTX measured under equilibrium binding conditions is increased ca. 50-fold in the presence of the β subunit. The rate constant for 125I-ChTX association is enhanced ca. 5-fold, whereas the dissociation rate constant is decreased more than 7-fold when the β subunit is present. These data indicate that functional coassembly of maxi-K channel subunits can be obtained in a transient expression system, and that the β subunit has profound effects on 125I-ChTX binding. We postulate that certain negatively charged residues in the large extracellular loop of β attract the positively charged 125I-ChTX to its binding site on α through electrostatic interactions, and account for effects observed on ligand association kinetics. Moreover, another residue(s) in the loop of β must contribute to stabilization of the toxin-bound state, either by a direct interaction with toxin, or through an allosteric effect on the α subunit. Certain regions in the extracellular loop of the β subunit may be in close proximity to the pore of the channel, and could play an important role in maxi-K channel function. PMID:9096310

A toxic RNA catalyzes the in cellulo synthesis of its own inhibitor.

PubMed

Rzuczek, Suzanne G; Park, HaJeung; Disney, Matthew D

2014-10-06

Potent modulators of RNA function can be assembled in cellulo by using the cell as a reaction vessel and a disease-causing RNA as a catalyst. When designing small molecule effectors of function, a balance between permeability and potency must be struck. Low molecular weight compounds are more permeable whereas higher molecular weight compounds are more potent. The advantages of both types of compounds could be synergized if low molecular weight molecules could be transformed into potent, multivalent ligands by a reaction that is catalyzed by binding to a target in cells expressing a genetic defect. It was shown that this approach is indeed viable in cellulo. Small molecule modules with precisely positioned alkyne and azide moieties bind adjacent internal loops in r(CCUG)(exp), the causative agent of myotonic dystrophy type 2 (DM2), and are transformed into oligomeric, potent inhibitors of DM2 RNA dysfunction by a Huisgen 1,3-dipolar cycloaddition reaction, a variant of click chemistry. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Matthews, Melissa M.; Thomas, Justin M.; Zheng, Yuxuan

Adenosine deaminases acting on RNA (ADARs) are editing enzymes that convert adenosine to inosine in duplex RNA, a modification reaction with wide-ranging consequences in RNA function. Understanding of the ADAR reaction mechanism, the origin of editing-site selectivity, and the effect of mutations is limited by the lack of high-resolution structural data for complexes of ADARs bound to substrate RNAs. In this paper, we describe four crystal structures of the human ADAR2 deaminase domain bound to RNA duplexes bearing a mimic of the deamination reaction intermediate. These structures, together with structure-guided mutagenesis and RNA-modification experiments, explain the basis of the ADARmore » deaminase domain's dsRNA specificity, its base-flipping mechanism, and its nearest-neighbor preferences. In addition, we identified an ADAR2-specific RNA-binding loop near the enzyme active site, thus rationalizing differences in selectivity observed between different ADARs. In conclusion, our results provide a structural framework for understanding the effects of ADAR mutations associated with human disease.« less

Exponential isothermal amplification of nucleic acids and amplified assays for proteins, cells, and enzyme activities.

PubMed

Reid, Michael S; Le, X Chris; Zhang, Hongquan

2018-04-27

Isothermal exponential amplification techniques, such as strand-displacement amplification (SDA), rolling circle amplification (RCA), loop-mediated isothermal amplification (LAMP), nucleic acid sequence-based amplification (NASBA), helicase-dependent amplification (HDA), and recombinase polymerase amplification (RPA), have great potential for on-site, point-of-care, and in-situ assay applications. These amplification techniques eliminate the need for temperature cycling required for polymerase chain reaction (PCR) while achieving comparable amplification yield. We highlight here recent advances in exponential amplification reaction (EXPAR) for the detection of nucleic acids, proteins, enzyme activities, cells, and metal ions. We discuss design strategies, enzyme reactions, detection techniques, and key features. Incorporation of fluorescence, colorimetric, chemiluminescence, Raman, and electrochemical approaches enables highly sensitive detection of a variety of targets. Remaining issues, such as undesirable background amplification resulting from non-specific template interactions, must be addressed to further improve isothermal and exponential amplification techniques. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The pre-conceptual design of the nuclear island of ASTRID

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

Saez, M.; Menou, S.; Uzu, B.

The CEA is involved in a substantial effort on the ASTRID (Advanced Sodium Technological Reactor for Industrial Demonstration) pre-conceptual design in cooperation with EDF, as experienced Sodium-cooled Fast Reactor (SFR) operator, AREVA, as experienced SFR Nuclear Island engineering company and components designer, ALSTOM POWER as energy conversion system designer and COMEX NUCLEAIRE as mechanical systems designer. The CEA is looking for other partnerships, in France and abroad. The ASTRID preliminary design is based on a sodium-cooled pool reactor of 1500 MWth generating about 600 MWe, which is required to guarantee the representativeness of the reactor core and the main componentsmore » with regard to future commercial reactors. ASTRID lifetime target is 60 years. Two Energy Conversion Systems are studied in parallel until the end of 2012: Rankine steam cycle or Brayton gas based energy conversion cycle. ASTRID design is guided by the following major objectives: improved safety, simplification of structures, improved In Service Inspection and Repair (ISIR), improved manufacturing conditions for cost reduction and increased quality, reduction of risks related to sodium fires and water/sodium reaction, and improved robustness against external hazards. The core is supported by a diagrid, which lay on a strong back to transfer the weight to the main vessel. AREVA is involved in a substantial effort in order to improve the core support structure in particular regarding the ISIR and the connection to primary pump. In the preliminary design, the primary system is formed by the main vessel and the upper closure comprising the reactor roof, two rotating plugs - used for fuel handling - and the components plugs located in the roof penetrations. The Above Core Structure deflects the sodium flow in the hot pool and provides support to core instrumentation and guidance of the control rod drive mechanisms. The number of the major components in the main vessel, primary pumps, Intermediate Heat Exchangers, and Decay Heat Exchangers are now under consideration. Under normal conditions, power release is achieved using the steam/water plant (in case of Rankine steam cycle) or the gas plant (in case of Brayton gas cycle). The diverse design and operating modes of Decay Heat Removal systems provide protection against common cause failures. A Decay Heat Removal system through the reactor vault is in particular studied with the objective to complement Direct Reactor Cooling systems. At this stage of the studies, the secondary system comprises four independent sodium loops (two and three sodium loops configurations are also investigated). Each loop includes one mechanical pump (or a large capacity Annular Linear Induction Electromagnetic Pump), and three modular Steam Generator Units characterized by once through straight tube units with a ferritic tube bundle; nevertheless, helical coil steam generator with tubes made of Alloy 800, and inverted type steam generator with a ferritic tube bundle are also investigated. The limited power of each modular Steam Generator Unit allows the whole secondary loop to withstand a large water/sodium reaction consecutive to the postulated simultaneous rupture of all the heat exchange tubes of one module. The arrangement of the components is based on the 'Regain' concept, in which the secondary pump is situated at a low level in the circuit; conventional arrangement, as SUPERPHENIX type, is a back-up option. Alternative arrangements based on gas cycles are also studied together with Na-gas heat exchanger design. This paper presents a status of the ASTRID pre-conceptual design. The most promising options are highlighted as well as less risky and back-up options. (authors)« less

Experiments on Condensed Matter Nuclear Events in Kobe University

NASA Astrophysics Data System (ADS)

Minari, T.; Nishio, R.; Taniike, A.; Furuyama, Y.; Kitamura, A.

2006-02-01

We review three kinds of experimental works underway in our laboratory to investigate nuclear events in solid or liquid materials. The largest effort has been given to experiments to confirm the 7Li(d, n2α) reaction rate enhancement reaching 1015 in liquid lithium which was reported by H. Ikegami and R. Pettersson, Evidence of Enhanced Nonthermal Nuclear Fusion (Bulletin of Institute of Chemistry, BENF No. 3, Uppsala University, Sweden, September 2002). Li liquid droplets are formed as targets, and to keep them as pure as possible, we built a liquid Li loop. Thus far, in all cases of irradiation at the temperature from 520 to 570 K with 10-24 keV deuterons, we have not been able to reproduce the Ikegami enhancement for the 7Li(d, n2α) reaction.

ISO learning approximates a solution to the inverse-controller problem in an unsupervised behavioral paradigm.

PubMed

Porr, Bernd; von Ferber, Christian; Wörgötter, Florentin

2003-04-01

In "Isotropic Sequence Order Learning" (pp. 831-864 in this issue), we introduced a novel algorithm for temporal sequence learning (ISO learning). Here, we embed this algorithm into a formal nonevaluating (teacher free) environment, which establishes a sensor-motor feedback. The system is initially guided by a fixed reflex reaction, which has the objective disadvantage that it can react only after a disturbance has occurred. ISO learning eliminates this disadvantage by replacing the reflex-loop reactions with earlier anticipatory actions. In this article, we analytically demonstrate that this process can be understood in terms of control theory, showing that the system learns the inverse controller of its own reflex. Thereby, this system is able to learn a simple form of feedforward motor control.

Phase transitions between lower and higher level management learning in times of crisis: an experimental study based on synergetics.

PubMed

Liening, Andreas; Strunk, Guido; Mittelstadt, Ewald

2013-10-01

Much has been written about the differences between single- and double-loop learning, or more general between lower level and higher level learning. Especially in times of a fundamental crisis, a transition between lower and higher level learning would be an appropriate reaction to a challenge coming entirely out of the dark. However, so far there is no quantitative method to monitor such a transition. Therefore we introduce theory and methods of synergetics and present results from an experimental study based on the simulation of a crisis within a business simulation game. Hypothesized critical fluctuations - as a marker for so-called phase transitions - have been assessed with permutation entropy. Results show evidence for a phase transition during the crisis, which can be interpreted as a transition between lower and higher level learning.

Strength of Dislocation Junctions in FCC-monocrystals with a [\\overline{1}11] Deformation Axis

NASA Astrophysics Data System (ADS)

Kurinnaya, R. I.; Zgolich, M. V.; Starenchenko, V. A.

2017-07-01

The paper examines all dislocation reactions implemented in FCC-monocrystals with axis deformation oriented in the [\\overline{1}11] direction. It identifies the fracture stresses of dislocation junctions depending on intersection geometry of the reacting dislocation loop segments. Estimates are produced for the full spectrum of reacting forest dislocations. The paper presents the statistical data of the research performed and identifies the share of long strong dislocation junctions capable of limiting the zone of dislocation shift.

Fluid-loop reaction system

NASA Technical Reports Server (NTRS)

Lurie, Boris J. (Inventor); Schier, J. Alan (Inventor); Iskenderian, Theodore C. (Inventor)

1991-01-01

An improved fluid actuating system for imparting motion to a body such as a spacecraft is disclosed. The fluid actuating system consists of a fluid mass that may be controllably accelerated through at least one fluid path whereby an opposite acceleration is experienced by the spacecraft. For full control of the spacecraft's orientation, the system would include a plurality of fluid paths. The fluid paths may be circular or irregular, and the fluid paths may be located on the interior or exterior of the spacecraft.

Conserved Loop Cysteines of Vitamin K Epoxide Reductase Complex Subunit 1-like 1 (VKORC1L1) Are Involved in Its Active Site Regeneration*

PubMed Central

Tie, Jian-Ke; Jin, Da-Yun; Stafford, Darrel W.

2014-01-01

Vitamin K epoxide reductase complex subunit 1 (VKORC1) reduces vitamin K epoxide in the vitamin K cycle for post-translational modification of proteins that are involved in a variety of biological functions. However, the physiological function of VKORC1-like 1 (VKORC1L1), a paralogous enzyme sharing about 50% protein identity with VKORC1, is unknown. Here we determined the structural and functional differences of these two enzymes using fluorescence protease protection (FPP) assay and an in vivo cell-based activity assay. We show that in vivo VKORC1L1 reduces vitamin K epoxide to support vitamin K-dependent carboxylation as efficiently as does VKORC1. However, FPP assays show that unlike VKORC1, VKORC1L1 is a four-transmembrane domain protein with both its termini located in the cytoplasm. Moreover, the conserved loop cysteines, which are not required for VKORC1 activity, are essential for VKORC1L1's active site regeneration. Results from domain exchanges between VKORC1L1 and VKORC1 suggest that it is VKORC1L1's overall structure that uniquely allows for active site regeneration by the conserved loop cysteines. Intermediate disulfide trapping results confirmed an intra-molecular electron transfer pathway for VKORC1L1's active site reduction. Our results allow us to propose a concerted action of the four conserved cysteines of VKORC1L1 for active site regeneration; the second loop cysteine, Cys-58, attacks the active site disulfide, forming an intermediate disulfide with Cys-139; the first loop cysteine, Cys-50, attacks the intermediate disulfide resulting in active site reduction. The different membrane topologies and reaction mechanisms between VKORC1L1 and VKORC1 suggest that these two proteins might have different physiological functions. PMID:24532791

Conserved loop cysteines of vitamin K epoxide reductase complex subunit 1-like 1 (VKORC1L1) are involved in its active site regeneration.

PubMed

Tie, Jian-Ke; Jin, Da-Yun; Stafford, Darrel W

2014-03-28

Vitamin K epoxide reductase complex subunit 1 (VKORC1) reduces vitamin K epoxide in the vitamin K cycle for post-translational modification of proteins that are involved in a variety of biological functions. However, the physiological function of VKORC1-like 1 (VKORC1L1), a paralogous enzyme sharing about 50% protein identity with VKORC1, is unknown. Here we determined the structural and functional differences of these two enzymes using fluorescence protease protection (FPP) assay and an in vivo cell-based activity assay. We show that in vivo VKORC1L1 reduces vitamin K epoxide to support vitamin K-dependent carboxylation as efficiently as does VKORC1. However, FPP assays show that unlike VKORC1, VKORC1L1 is a four-transmembrane domain protein with both its termini located in the cytoplasm. Moreover, the conserved loop cysteines, which are not required for VKORC1 activity, are essential for VKORC1L1's active site regeneration. Results from domain exchanges between VKORC1L1 and VKORC1 suggest that it is VKORC1L1's overall structure that uniquely allows for active site regeneration by the conserved loop cysteines. Intermediate disulfide trapping results confirmed an intra-molecular electron transfer pathway for VKORC1L1's active site reduction. Our results allow us to propose a concerted action of the four conserved cysteines of VKORC1L1 for active site regeneration; the second loop cysteine, Cys-58, attacks the active site disulfide, forming an intermediate disulfide with Cys-139; the first loop cysteine, Cys-50, attacks the intermediate disulfide resulting in active site reduction. The different membrane topologies and reaction mechanisms between VKORC1L1 and VKORC1 suggest that these two proteins might have different physiological functions.

Two-loop renormalization of gaugino masses in general supersymmetric gauge models

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

Yamada, Y.

1994-01-03

We calculate the two-loop renormalization group equations for the running gaugino masses in general supersymmetry (SUSY) gauge models, improving our previous result. We also study its consequences on the unification of the gaugino masses in the SUSY SU(5) model. The two-loop correction to the one-loop relation [ital m][sub [ital i

Evaluating Mathematics Achievement of Middle School Students in a Looping Environment

ERIC Educational Resources Information Center

Franz, Dana Pomykal; Thompson, Nicole L.; Fuller, Bob; Hare, R. Dwight; Miller, Nicole C.; Walker, Jacob

2010-01-01

Looping, a school structure where students remain with one group of teachers for two or more school years, is used by middle schools to meet the diverse needs of young adolescents. However, little research exists on how looping effects the academic performance of students. This study was designed to determine if looping influenced middle school…

[What's new in clinical dermatology?].

PubMed

Janier, M

2013-11-01

2013 has been the year of large genetic studies of the GWAS type (Genome wide association studies) in common diseases such as psoriasis and atopic dermatitis, aimed at localization of candidate genes. It was also the year of population-based studies from huge public or private registers. Thus, epidemiologic correlations have been put forward: psoriasis and vascular risk, psoriasis and rhinosinusitis, rosacea and migraine, acne and food habits, eczema and basal-cell carcinoma, vitiligo and lower risk of skin cancer, cutaneous Ro/SS-A pos lupus and cancer, chronic eczema and calcium-channel inhlbitors, pemphigoid and loop diuretics. Risk of IBD induced by isotretinoin has not been confirmed but risk of skin cancer under azathioprine is real. New drug reactions have appeared (pigmentation due to interferon, hypodermitis and sarcoidosis to anti-BRAF, vandetanib) and old ones are revisited (patch-testing of Severe Cutaneous adverse cutaneous reactions, pigmentation due to anti-malarial drugs, neutrophilic dermatosis due to azathioprine). Diane35(®) has been transiently withdrawn in January 2013 but tetrazepam has been withdrawn definitively in July 2013. Original aspects of cutaneous infections will be discussed along with new data on STDs (meningococcemia in MSMs, HPV, Herpes, congenital syphilis). Finally, some important papers about dermoscopy, confocal microscopy and aesthetic dermatology will be presented. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Geometrical criteria for characterizing open and closed states of WPD-loop in PTP1B

NASA Astrophysics Data System (ADS)

Shinde, Ranajit Nivrutti; Elizabeth Sobhia, M.

2012-06-01

Distinctive movement of WPD-loop occurs during the catalysis of phosphotyrosine by protein tyrosine phosphatase 1B (PTP1B). This loop is in the "open" state in apo-form whereas it is catalytically competent in the "closed" state. During the closure of this loop, unique hydrogen bond interactions are formed between different residues of the PTP1B. Present study examines such interactions from the available 118 crystal structures of PTP1B. It gives insights into the five novel hydrogen bonds essentially formed in the "closed" loop structures. Additionally, the study provides distance ranges between the atoms involved in the hydrogen bonds. This information can be used as a geometrical criterion in the characterization of conformational state of the WPD-loop especially in the molecular dynamics simulations.

A dual-loop adaptive control for minimizing time response delay in real-time structural vibration control with magnetorheological (MR) devices

NASA Astrophysics Data System (ADS)

Chen, Xi; Li, Yancheng; Li, Jianchun; Gu, Xiaoyu

2018-01-01

Time delay is a challenge issue faced by the real-time control application of the magnetorheological (MR) devices. Not to deal with it properly may jeopardize the effectiveness of the control, even lead to instability of the control system or catastrophic failure. This paper proposes a dual-loop adaptive control to address the response time delay associated with MR devices. In the proposed dual-loop control, the inner loop is designed to compensate the time delay of MR device induced by the PWM current driver. While the outer loop control can be any structural control algorithm with aims to reducing structural responses of a building during extreme loadings. Here an adaptive control strategy is adopted. To verify the proposed dual-loop control, a smart base isolation system employing magnetorheological elastomer base isolators is used as an example to illustrate the control effect. Numerical study is then conducted using a 5 -storey shear building model equipped with smart base isolation system. The result shows that with the implementation of the inner loop, the control current can instantly follow the control command which reduce the possibility of instability caused by the time delay. Comparative studies are conducted between three control strategies, i.e. dual-loop control, Lyapunov’s direct method based control and optimal passive base isolation control. The results of the study have demonstrated that the proposed dual-loop control strategy can achieve much better performance than the other two control strategies.

A planar comparison of actuators for vibration control of flexible structures

NASA Technical Reports Server (NTRS)

Clark, William W.; Robertshaw, Harry H.; Warrington, Thomas J.

1989-01-01

The methods and results of an analytical study comparing the effectiveness of four actuators in damping the vibrations of a planar clamped-free beam are presented. The actuators studied are two inertia-type actuators, the proof mass and reaction wheel, and two variable geometry trusses, the planar truss and the planar truss proof mass (a combination variable geometry truss/inertia-type actuator). Actuator parameters used in the models were chosen based on the results of a parametric study. A full-state, LQR optimal feedback control law was used for control in each system. Numerical simulations of each beam/actuator system were performed in response to initial condition inputs. These simulations provided information such as time response of the closed-loop system and damping provided to the beam. This information can be used to determine the 'best' actuator for a given purpose.

Study of the Open Loop and Closed Loop Oscillator Techniques

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

Imel, George R.; Baker, Benjamin; Riley, Tony

This report presents the progress and completion of a five-year study undertaken at Idaho State University of the measurement of very small worth reactivity samples comparing open and closed loop oscillator techniques.The study conclusively demonstrated the equivalency of the two techniques with regard to uncertainties in reactivity values, i.e., limited by reactor noise. As those results are thoroughly documented in recent publications, in this report we will concentrate on the support work that was necessary. For example, we describe in some detail the construction and calibration of a pilot rod for the closed loop system. We discuss the campaign tomore » measure the required reactor parameters necessary for inverse-kinetics. Finally, we briefly discuss the transfer of the open loop technique to other reactor systems.« less

Study of the open loop and closed loop oscillator techniques

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

Baker, Benjamin; Riley, Tony; Langbehn, Adam

This paper presents some aspects of a five year study undertaken at Idaho State University of the measurement of very small worth reactivity samples comparing open and closed loop oscillator techniques. The study conclusively demonstrated the equivalency of the two techniques with regard to uncertainties in reactivity values, i.e., limited by reactor noise. As those results are thoroughly documented in recent publications, in this paper we will concentrate on the support work that was necessary. For example, we describe in some detail the construction and calibration of a pilot rod for the closed loop system. We discuss the campaign tomore » measure the required reactor parameters necessary for inverse-kinetics. Finally, we briefly discuss the transfer of the open loop technique to other reactor systems. (authors)« less

Development and application of a rapid and visual loop-mediated isothermal amplification for the detection of Sporisorium scitamineum in sugarcane

PubMed Central

Su, Yachun; Yang, Yuting; Peng, Qiong; Zhou, Dinggang; Chen, Yun; Wang, Zhuqing; Xu, Liping; Que, Youxiong

2016-01-01

Smut is a fungal disease with widespread prevalence in sugarcane planting areas. Early detection and proper identification of Sporisorium scitamineum are essential in smut management practices. In the present study, four specific primers targeting the core effector Pep1 gene of S. scitamineum were designed. Optimal concentrations of Mg2+, primer and Bst DNA polymerase, the three important components of the loop-mediated isothermal amplification (LAMP) reaction system, were screened using a single factor experiment method and the L16(45) orthogonal experimental design. Hence, a LAMP system suitable for detection of S. scitamineum was established. High specificity of the LAMP method was confirmed by the assay of S. scitamineum, Fusarium moniliforme, Pestalotia ginkgo, Helminthospcrium sacchari, Fusarium oxysporum and endophytes of Yacheng05-179 and ROC22. The sensitivity of the LAMP method was equal to that of the conventional PCR targeting Pep1 gene and was 100 times higher than that of the conventional PCR assay targeting bE gene in S. scitamineum. The results suggest that this novel LAMP system has strong specificity and high sensitivity. This method not only provides technological support for the epidemic monitoring of sugarcane smut, but also provides a good case for development of similar detection technology for other plant pathogens. PMID:27035751

Loop-mediated isothermal amplification (LAMP) based detection of Colletotrichum falcatum causing red rot in sugarcane.

PubMed

Chandra, Amaresh; Keizerweerd, Amber T; Que, Youxiong; Grisham, Michael P

2015-08-01

Red rot, caused by Colletotrichum falcatum, is a destructive disease prevalent in most sugarcane-producing countries. Disease-free sugarcane planting materials (setts) are essential as the pathogen spreads primarily through infected setts. The present study was undertaken to develop a loop-mediated isothermal amplification (LAMP) assay for the detection of C. falcatum. C. falcatum genomic DNA was isolated from pure mycelium culture and infected tissues. Four sets of primers corresponding to a unique DNA sequence specific to C. falcatum were designed. Specificity of the LAMP test was checked with DNA of another fungal pathogen of sugarcane, Puccinia melanocephala, as well as two closely-related species, Colletotrichum fructivorum and Colletotrichum acutatum. No reaction was found with the three pathogens. When C. falcatum DNA from pure culture was used in a detection limit analysis, sensitivity of the LAMP method was observed to be ten times higher than that of conventional PCR; however, sensitivity was only 5 times higher when DNA from C. falcatum-infected tissues was used. Using the LAMP assay, C. falcatum DNA is amplified with high specificity, efficiency, and rapidity under isothermal conditions. Moreover, visual judgment of color change in <1 h without further post-amplification processing makes the LAMP method convenient, economical, and useful in diagnostic laboratories and the field.

A novel diagnostic method for malaria using loop-mediated isothermal amplification (LAMP) and MinION™ nanopore sequencer.

PubMed

Imai, Kazuo; Tarumoto, Norihito; Misawa, Kazuhisa; Runtuwene, Lucky Ronald; Sakai, Jun; Hayashida, Kyoko; Eshita, Yuki; Maeda, Ryuichiro; Tuda, Josef; Murakami, Takashi; Maesaki, Shigefumi; Suzuki, Yutaka; Yamagishi, Junya; Maeda, Takuya

2017-09-13

A simple and accurate molecular diagnostic method for malaria is urgently needed due to the limitations of conventional microscopic examination. In this study, we demonstrate a new diagnostic procedure for human malaria using loop mediated isothermal amplification (LAMP) and the MinION™ nanopore sequencer. We generated specific LAMP primers targeting the 18S-rRNA gene of all five human Plasmodium species including two P. ovale subspecies (P. falciparum, P. vivax, P. ovale wallikeri, P. ovale curtisi, P. knowlesi and P. malariae) and examined human blood samples collected from 63 malaria patients in Indonesia. Additionally, we performed amplicon sequencing of our LAMP products using MinION™ nanopore sequencer to identify each Plasmodium species. Our LAMP method allowed amplification of all targeted 18S-rRNA genes of the reference plasmids with detection limits of 10-100 copies per reaction. Among the 63 clinical samples, 54 and 55 samples were positive by nested PCR and our LAMP method, respectively. Identification of the Plasmodium species by LAMP amplicon sequencing analysis using the MinION™ was consistent with the reference plasmid sequences and the results of nested PCR. Our diagnostic method combined with LAMP and MinION™ could become a simple and accurate tool for the identification of human Plasmodium species, even in resource-limited situations.

Simple Identification of Human Taenia Species by Multiplex Loop-Mediated Isothermal Amplification in Combination with Dot Enzyme-Linked Immunosorbent Assay.

PubMed

Nkouawa, Agathe; Sako, Yasuhito; Okamoto, Munehiro; Ito, Akira

2016-06-01

For differential detection of Taenia solium, Taenia saginata, and Taenia asiatica, loop-mediated isothermal amplification (LAMP) assay targeting the cytochrome c oxidase subunit 1 gene has been recently developed and shown to be sensitive, specific, and effective. However, to achieve differential identification, one specimen requires three reaction mixtures containing a primer set of each Taenia species separately, which is complex and time consuming and increases the risk of cross-contamination. In this study, we developed a simple differential identification of human Taenia species using multiplex LAMP (mLAMP) in combination with dot enzyme-linked immunosorbent assay (dot-ELISA). Forward inner primers of T. solium, T. saginata, and T. asiatica labeled with fluorescein isothiocyanate (FITC), digoxigenin (DIG), and tetramethylrhodamine (TAMRA), respectively, and biotin-labeled backward inner primers were used in mLAMP. The mLAMP assay succeeded in specific amplification of each respective target gene in a single tube. Furthermore, the mLAMP product from each species was easily distinguished by dot-ELISA with an antibody specific for FITC, DIG, or TAMRA. The mLAMP assay in combination with dot-ELISA will make identification of human Taenia species simpler, easier, and more practical. © The American Society of Tropical Medicine and Hygiene.

Specific detection of Angiostrongylus cantonensis in the snail Achatina fulica using a loop-mediated isothermal amplification (LAMP) assay.

PubMed

Liu, Chun-Yan; Song, Hui-Qun; Zhang, Ren-Li; Chen, Mu-Xin; Xu, Min-Jun; Ai, Lin; Chen, Xiao-Guang; Zhan, Xi-Mei; Liang, Shao-Hui; Yuan, Zi-Guo; Lin, Rui-Qing; Zhu, Xing-Quan

2011-08-01

Angiostrongylus cantonensis, a rat lungworm, can cause eosinophilic meningitis and angiostrongyliasis in humans following ingestion of contaminated foods or intermediate/paratenic hosts with infective larvae. The snail Achatina fulica is one of the important intermediate hosts of A. cantonensis and is commonly eaten by humans in some countries. In the present study, we developed a loop-mediated isothermal amplification (LAMP) method for the specific detection of A. cantonensis in Ac. fulica. Primers for LAMP were designed based on the first internal transcribed spacer (ITS-1) of nuclear ribosomal DNA (rDNA) of A. cantonensis. Specificity tests showed that only the products of A. cantonensis were detected when DNA samples of A. cantonensis and the heterologous control samples Anisakis simplex s.s, Trichuris trichiura, Toxocara canis, Trichinella spiralis and Ascaris lumbricoides were amplified by LAMP. Sensitivity evaluation indicated that the LAMP assay is 10 times more sensitive than the conventional polymerase chain reaction (PCR) assay. The established LAMP assay is rapid, inexpensive and easy to be performed. It can be used in clinical applications for rapid and sensitive detection of A. cantonensis in snails, which has implications for the effective control of angiostrongyliasis. Copyright © 2011 Elsevier Ltd. All rights reserved.

Functional Loop Dynamics of the Streptavidin-Biotin Complex

PubMed Central

Song, Jianing; Li, Yongle; Ji, Changge; Zhang, John Z. H.

2015-01-01

Accelerated molecular dynamics (aMD) simulation is employed to study the functional dynamics of the flexible loop3-4 in the strong-binding streptavidin-biotin complex system. Conventional molecular (cMD) simulation is also performed for comparison. The present study reveals the following important properties of the loop dynamics: (1) The transition of loop3-4 from open to closed state is observed in 200 ns aMD simulation. (2) In the absence of biotin binding, the open-state streptavidin is more stable, which is consistent with experimental evidences. The free energy (ΔG) difference is about 5 kcal/mol between two states. But with biotin binding, the closed state is more stable due to electrostatic and hydrophobic interactions between the loop3-4 and biotin. (3) The closure of loop3-4 is concerted to the stable binding of biotin to streptavidin. When the loop3-4 is in its open-state, biotin moves out of the binding pocket, indicating that the interactions between the loop3-4 and biotin are essential in trapping biotin in the binding pocket. (4) In the tetrameric streptavidin system, the conformational change of the loop3-4 in each monomer is independent of each other. That is, there is no cooperative binding for biotin bound to the four subunits of the tetramer. PMID:25601277

Evaluation of Different PCR-Based Assays and LAMP Method for Rapid Detection of Phytophthora infestans by Targeting the Ypt1 Gene

PubMed Central

Khan, Mehran; Li, Benjin; Jiang, Yue; Weng, Qiyong; Chen, Qinghe

2017-01-01

Late blight, caused by the oomycete Phytophthora infestans, is one of the most devastating diseases affecting potato and tomato worldwide. Early diagnosis of the P. infestans pathogen causing late blight should be the top priority for addressing disease epidemics and management. In this study, we performed a loop-mediated isothermal amplification (LAMP) assay, conventional polymerase chain reaction (PCR), nested PCR, and real-time PCR to verify and compare the sensitivity and specificity of the reaction based on the Ypt1 (Ras-related protein) gene of P. infestans. In comparison with the PCR-based assays, the LAMP technique led to higher specificity and sensitivity, using uncomplicated equipment with an equivalent time frame. All 43 P. infestans isolates, yielded positive detection results using LAMP assay showing no cross reaction with other Phytophthora spp., oomycetes or fungal pathogens. The LAMP assay yielded the lowest detectable DNA concentration (1.28 × 10-4 ng μL-1), being 10 times more sensitive than nested PCR (1.28 × 10-3 ng μL-1), 100 times more sensitive than real-time PCR (1.28 × 10-2 ng μL-1) and 103 times more sensitive than the conventional PCR assay (1.28 × 10-1 ng μL-1). In the field experiment, the LAMP assay outperformed the other tests by amplifying only diseased tissues (leaf and stem), and showing no positive reaction in healthy tissues. Overall, the LAMP assay developed in this study provides a specific, sensitive, simple, and effective visual method for detection of the P. infestans pathogen, and is therefore suitable for application in early prediction of the disease to reduce the risk of epidemics. PMID:29051751

Evaluation of Different PCR-Based Assays and LAMP Method for Rapid Detection of Phytophthora infestans by Targeting the Ypt1 Gene.

PubMed

Khan, Mehran; Li, Benjin; Jiang, Yue; Weng, Qiyong; Chen, Qinghe

2017-01-01

Late blight, caused by the oomycete Phytophthora infestans , is one of the most devastating diseases affecting potato and tomato worldwide. Early diagnosis of the P. infestans pathogen causing late blight should be the top priority for addressing disease epidemics and management. In this study, we performed a loop-mediated isothermal amplification (LAMP) assay, conventional polymerase chain reaction (PCR), nested PCR, and real-time PCR to verify and compare the sensitivity and specificity of the reaction based on the Ypt1 (Ras-related protein) gene of P. infestans. In comparison with the PCR-based assays, the LAMP technique led to higher specificity and sensitivity, using uncomplicated equipment with an equivalent time frame. All 43 P. infestans isolates, yielded positive detection results using LAMP assay showing no cross reaction with other Phytophthora spp., oomycetes or fungal pathogens. The LAMP assay yielded the lowest detectable DNA concentration (1.28 × 10 -4 ng μL -1 ), being 10 times more sensitive than nested PCR (1.28 × 10 -3 ng μL -1 ), 100 times more sensitive than real-time PCR (1.28 × 10 -2 ng μL -1 ) and 10 3 times more sensitive than the conventional PCR assay (1.28 × 10 -1 ng μL -1 ). In the field experiment, the LAMP assay outperformed the other tests by amplifying only diseased tissues (leaf and stem), and showing no positive reaction in healthy tissues. Overall, the LAMP assay developed in this study provides a specific, sensitive, simple, and effective visual method for detection of the P. infestans pathogen, and is therefore suitable for application in early prediction of the disease to reduce the risk of epidemics.

Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations.

PubMed

Di Palma, Francesco; Bottaro, Sandro; Bussi, Giovanni

2015-01-01

Riboswitches are cis-acting regulatory RNA elements prevalently located in the leader sequences of bacterial mRNA. An adenine sensing riboswitch cis-regulates adeninosine deaminase gene (add) in Vibrio vulnificus. The structural mechanism regulating its conformational changes upon ligand binding mostly remains to be elucidated. In this open framework it has been suggested that the ligand stabilizes the interaction of the distal "kissing loop" complex. Using accurate full-atom molecular dynamics with explicit solvent in combination with enhanced sampling techniques and advanced analysis methods it could be possible to provide a more detailed perspective on the formation of these tertiary contacts. In this work, we used umbrella sampling simulations to study the thermodynamics of the kissing loop complex in the presence and in the absence of the cognate ligand. We enforced the breaking/formation of the loop-loop interaction restraining the distance between the two loops. We also assessed the convergence of the results by using two alternative initialization protocols. A structural analysis was performed using a novel approach to analyze base contacts. Contacts between the two loops were progressively lost when larger inter-loop distances were enforced. Inter-loop Watson-Crick contacts survived at larger separation when compared with non-canonical pairing and stacking interactions. Intra-loop stacking contacts remained formed upon loop undocking. Our simulations qualitatively indicated that the ligand could stabilize the kissing loop complex. We also compared with previously published simulation studies. Kissing complex stabilization given by the ligand was compatible with available experimental data. However, the dependence of its value on the initialization protocol of the umbrella sampling simulations posed some questions on the quantitative interpretation of the results and called for better converged enhanced sampling simulations.

Influence of minor displacements in loops of the porcine parvovirus VP2 capsid on virus-like particles assembly and the induction of antibody responses.

PubMed

Pan, Qunxing; He, Kongwang; Wang, Yongshan; Wang, Xiaoli; Ouyang, Wei

2013-06-01

An antigen-delivery system based on hybrid virus-like particles (VLPs) formed by the self-assembly of the capsid VP2 protein of porcine parvovirus (PPV) and expressing foreign peptides offers an alternative method for vaccination. In this study, the three-dimensional structure of the PPV capsid protein and surface loops deletion mutants were analyzed to define essential domains in PPV VP2 for the assembly of VLPs. Electron microscopic analysis and SDS-PAGE analysis confirmed the presence of abundant VLPs in a loop2 deletion mutant of expected size and appropriate morphology. Loop4 and loop2-loop4 deletion mutants, however, resulted in a lower number of particles and the morphology of the particles was not well preserved. Furthermore, the green fluorescent protein (gfp) gene was used as a model. GFP was observed at the same level in displacements mutants. However, GFP displacement mutants in loop2 construct allowed better adaptation for the fusion GFP to be further displayed on the surface of the capsid-like structure. Immunogenicity study showed that there is no obvious difference in mice inoculated with rAd-VP2(Δloop2), rAd-VP2(Δloop4), rAd-VP2(Δloop2-Δloop4), and PPV inactivated vaccine. The results suggested the possibility of inserting simultaneously B and T cell epitopes in the surface loop2 and the N-terminus. The combination of different types of epitopes (B, CD4+, and CD8+) in different positions of the PPV particles opens the way to the development of highly efficient vaccines, able to stimulate at the same time the different branches of the immune system.

A molecular mechanism of P-loop pliability of Rho-kinase investigated by molecular dynamic simulation

NASA Astrophysics Data System (ADS)

Gohda, Keigo; Hakoshima, Toshio

2008-11-01

Rho-kinase is a leading player in the regulation of cytoskeletal events involving smooth muscle contraction and neurite growth-cone collapse and retraction, and is a promising drug target in the treatment of both vascular and neurological disorders. Recent crystal structure of Rho-kinase complexed with a small-molecule inhibitor fasudil has revealed structural details of the ATP-binding site, which represents the target site for the inhibitor, and showed that the conserved phenylalanine on the P-loop occupies the pocket, resulting in an increase of protein-ligand contacts. Thus, the P-loop pliability is considered to play an important role in inhibitor binding affinity and specificity. In this study, we carried out a molecular dynamic simulation for Rho-kinase-fasudil complexes with two different P-loop conformations, i.e., the extended and folded conformations, in order to understand the P-loop pliability and dynamics at atomic level. A PKA-fasudil complex was also used for comparison. In the MD simulation, the flip-flop movement of the P-loop conformation starting either from the extended or folded conformation was not able to be observed. However, a significant conformational change in a long loop region covering over the P-loop, and also alteration of ionic interaction-manner of fasudil with acidic residues in the ATP binding site were shown only in the Rho-kinase-fasudil complex with the extended P-loop conformation, while Rho-kinase with the folded P-loop conformation and PKA complexes did not show large fluctuations, suggesting that the Rho-kinase-fasudil complex with the extended P-loop conformation represents a meta-stable state. The information of the P-loop pliability at atomic level obtained in this study could provide valuable clues to designing potent and/or selective inhibitors for Rho-kinase.

The Natively Disordered Loop of Bcl-2 Undergoes Phosphorylation-Dependent Conformational Change and Interacts with Pin1

PubMed Central

Kang, CongBao; Bharatham, Nagakumar; Chia, Joel; Mu, Yuguang; Baek, Kwanghee; Yoon, Ho Sup

2012-01-01

Bcl-2 plays a central role in the regulation of apoptosis. Structural studies of Bcl-2 revealed the presence of a flexible and natively disordered loop that bridges the Bcl-2 homology motifs, BH3 and BH4. This loop is phosphorylated on multiple sites in response to a variety of external stimuli, including the microtubule-targeting drugs, paclitaxel and colchicine. Currently, the underlying molecular mechanism of Bcl-2 phosphorylation and its biological significance remain elusive. In this study, we investigated the molecular characteristics of this anti-apoptotic protein. To this end, we generated synthetic peptides derived from the Bcl-2 loop, and multiple Bcl-2 loop truncation mutants that include the phosphorylation sites. Our results demonstrate that S87 in the flexible loop of Bcl-2 is the primary phosphorylation site for JNK and ERK2, suggesting some sequence or structural specificity for the phosphorylation by these kinases. Our NMR studies and molecular dynamics simulation studies support indicate that phosphorylation of S87 induces a conformational change in the peptide. Finally, we show that the phosphorylated peptides of the Bcl-2 loop can bind Pin1, further substantiating the phosphorylation-mediated conformation change of Bcl-2. PMID:23272207

Man-in-the-control-loop simulation of manipulators

NASA Technical Reports Server (NTRS)

Chang, J. L.; Lin, Tsung-Chieh; Yae, K. Harold

1989-01-01

A method to achieve man-in-the-control-loop simulation is presented. Emerging real-time dynamics simulation suggests a potential for creating an interactive design workstation with a human operator in the control loop. The recursive formulation for multibody dynamics simulation is studied to determine requirements for man-in-the-control-loop simulation. High speed computer graphics techniques provides realistic visual cues for the simulator. Backhoe and robot arm simulations are implemented to demonstrate the capability of man-in-the-control-loop simulation.

THE CORONAL LOOP INVENTORY PROJECT: EXPANDED ANALYSIS AND RESULTS

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

Schmelz, J. T.; Christian, G. M.; Chastain, R. A., E-mail: jschmelz@usra.edu

We have expanded upon earlier work that investigates the relative importance of coronal loops with isothermal versus multithermal cross-field temperature distributions. These results are important for determining if loops have substructure in the form of unresolved magnetic strands. We have increased the number of loops targeted for temperature analysis from 19 to 207 with the addition of 188 new loops from multiple regions. We selected all loop segments visible in the 171 Å images of the Atmospheric Imaging Assembly (AIA) that had a clean background. Eighty-six of the new loops were rejected because they could not be reliably separated frommore » the background in other AIA filters. Sixty-one loops required multithermal models to reproduce the observations. Twenty-eight loops were effectively isothermal, that is, the plasma emission to which AIA is sensitive could not be distinguished from isothermal emission, within uncertainties. Ten loops were isothermal. Also, part of our inventory was one small flaring loop, one very cool loop whose temperature distribution could not be constrained by the AIA data, and one loop with inconclusive results. Our survey can confirm an unexpected result from the pilot study: we found no isothermal loop segments where we could properly use the 171-to-193 ratio method, which would be similar to the analysis done for many loops observed with TRACE and EIT. We recommend caution to observers who assume the loop plasma is isothermal, and hope that these results will influence the direction of coronal heating models and the effort modelers spend on various heating scenarios.« less

Canonical DNA Repair Pathways Influence R-Loop-Driven Genome Instability.

PubMed

Stirling, Peter C; Hieter, Philip

2017-10-27

DNA repair defects create cancer predisposition in humans by fostering a higher rate of mutations. While DNA repair is quite well characterized, recent studies have identified previously unrecognized relationships between DNA repair and R-loop-mediated genome instability. R-loops are three-stranded nucleic acid structures in which RNA binds to genomic DNA to displace a loop of single-stranded DNA. Mutations in homologous recombination, nucleotide excision repair, crosslink repair, and DNA damage checkpoints have all now been linked to formation and function of transcription-coupled R-loops. This perspective will summarize recent literature linking DNA repair to R-loop-mediated genomic instability and discuss how R-loops may contribute to mutagenesis in DNA-repair-deficient cancers. Copyright © 2016 Elsevier Ltd. All rights reserved.

Aviation Human-in-the-Loop Simulation Studies: Experimental Planning, Design, and Data Management

DTIC Science & Technology

2014-01-01

Aviation Human-in-the-Loop Simulation Studies: Experimental Planning, Design , and Data Management Kevin W. Williams1 Bonny Christopher2 Gena...Simulation Studies: Experimental Planning, Design , and Data Management January 2014 6. Performing Organization Code 7. Author(s) 8. Performing...describe the process by which we designed our human-in-the-loop (HITL) simulation study and the methodology used to collect and analyze the results

Virtual grasping: closed-loop force control using electrotactile feedback.

PubMed

Jorgovanovic, Nikola; Dosen, Strahinja; Djozic, Damir J; Krajoski, Goran; Farina, Dario

2014-01-01

Closing the control loop by providing somatosensory feedback to the user of a prosthesis is a well-known, long standing challenge in the field of prosthetics. Various approaches have been investigated for feedback restoration, ranging from direct neural stimulation to noninvasive sensory substitution methods. Although there are many studies presenting closed-loop systems, only a few of them objectively evaluated the closed-loop performance, mostly using vibrotactile stimulation. Importantly, the conclusions about the utility of the feedback were partly contradictory. The goal of the current study was to systematically investigate the capability of human subjects to control grasping force in closed loop using electrotactile feedback. We have developed a realistic experimental setup for virtual grasping, which operated in real time, included a set of real life objects, as well as a graphical and dynamical model of the prosthesis. We have used the setup to test 10 healthy, able bodied subjects to investigate the role of training, feedback and feedforward control, robustness of the closed loop, and the ability of the human subjects to generalize the control to previously "unseen" objects. Overall, the outcomes of this study are very optimistic with regard to the benefits of feedback and reveal various, practically relevant, aspects of closed-loop control.

Prevalence and Length of the Anterior Loop of the Inferior Alveolar Nerve in Iranians.

PubMed

Moghddam, Maryam Rastegar; Davoudmanesh, Zeinab; Azizi, Nasim; Rakhshan, Vahid; Shariati, Mahsa

2017-10-01

The anterior loop of the inferior alveolar nerve is a sensitive anatomical feature that should be taken into account during installation of dental implants anterior to the mental foramen. This study was conducted to explore the controversy regarding prevalence and length. A total of 452 mandible quadrants of 234 patients (age: 50.1 ± 13.3 years, 113 males, 121 females) were studied using cone-beam computerized tomography. After reconstructing axial, frontal, and sagittal slices, the region between the most anterior point on the mental foramen and the most anterior part of the mandibular nerve was inspected for signs of anterior loop presence. If positive, the length of the anterior loop was measured in mm as the distance between the anterior border of mental foramen and the anterior border of the loop. Prevalence and length of the anterior loop were compared statistically between sexes and age groups. The anterior loop was observed in 106 quadrants (23.5% of 451 quadrants) of 95 patients (40.6% of 234 patients), of whom 11 had bilateral anterior loops. Prevalences were similar in males (41%) and females (39%, chi-square P =.791). The mean anterior loop length was 2.77 ± 1.56 mm (95% CI: 2.5-3.1 mm), without significant sex (regression beta = -0.159, P = .134) or age (beta = -0.059, P = .578) differences. The anterior loop might exist in about 40% of patients, regardless of their gender. The mean safe anterior distance from the anterior loop is about 3 mm + (2.5-3.1 mm) = 5.5-6.1 mm, regardless of age.

Active site CP-loop dynamics modulate substrate binding, catalysis, oligomerization, stability, over-oxidation and recycling of 2-Cys Peroxiredoxins.

PubMed

Kamariah, Neelagandan; Eisenhaber, Birgit; Eisenhaber, Frank; Grüber, Gerhard

2018-04-01

Peroxiredoxins (Prxs) catalyse the rapid reduction of hydrogen peroxide, organic hydroperoxide and peroxynitrite, using a fully conserved peroxidatic cysteine (C P ) located in a conserved sequence Pxxx(T/S)xxC P motif known as C P -loop. In addition, Prxs are involved in cellular signaling pathways and regulate several redox-dependent process related disease. The effective catalysis of Prxs is associated with alterations in the C P -loop between reduced, Fully Folded (FF), and oxidized, Locally Unfolded (LU) conformations, which are linked to dramatic changes in the oligomeric structure. Despite many studies, little is known about the precise structural and dynamic roles of the C P -loop on Prxs functions. Herein, the comprehensive biochemical and biophysical studies on Escherichia coli alkyl hydroperoxide reductase subunit C (EcAhpC) and the C P -loop mutants, EcAhpC-F45A and EcAhpC-F45P reveal that the reduced form of the C P -loop adopts conformational dynamics, which is essential for effective peroxide reduction. Furthermore, the point mutants alter the structure and dynamics of the reduced form of the C P -loop and, thereby, affect substrate binding, catalysis, oligomerization, stability and overoxidiation. In the oxidized form, due to restricted C P -loop dynamics, the EcAhpC-F45P mutant favours a decamer formation, which enhances the effective recycling by physiological reductases compared to wild-type EcAhpC. In addition, the study reveals that residue F45 increases the specificity of Prxs-reductase interactions. Based on these studies, we propose an evolution of the C P -loop with confined sequence conservation within Prxs subfamilies that might optimize the functional adaptation of Prxs into various physiological roles. Copyright © 2018 Elsevier Inc. All rights reserved.

Non-Instrumented Nucleic Acid Amplification (NINA) for Rapid Detection of Ralstonia solanacearum Race 3 Biovar 2

PubMed Central

Kubota, Ryo; LaBarre, Paul; Singleton, Jered; Beddoe, Andy; Weigl, Bernhard H.; Alvarez, Anne M.; Jenkins, Daniel M.

2014-01-01

We report on the use of a non-instrumented device for the implementation of a loop-mediated amplification (LAMP) based assay for the select-agent bacterial-wilt pathogen Ralstonia solanacearum race 3 biovar 2. Heat energy is generated within the device by the exothermic hydration of calcium oxide, and the reaction temperature is regulated by storing latent energy at the melting temperature of a renewable lipid-based engineered phase-change material. Endpoint detection of the LAMP reaction is achieved without opening the reaction tube by observing the fluorescence of an innovative FRET-based hybridization probe with a simple custom fluorometer. Non-instrumented devices could maintain reactions near the design temperature of 63°C for at least an hour. Using this approach DNA extracted from the pathogen could be detected at fewer than ten copies within a 25 μL reaction mix, illustrating the potential of these technologies for simple, powerful agricultural diagnostics in the field. Furthermore, the assay was just as reliable when implemented in a tropical environment at 31°C as it was when implemented in an air-conditioned lab maintained at 22°C, illustrating the potential value of the technology for field conditions in the tropics and subtropics. PMID:25485176

Importance of geometric phase effects in ultracold chemistry

DOE PAGES

Hazra, Jisha; Kendrick, Brian K.; Balakrishnan, Naduvalath

2015-08-28

Here, it is demonstrated that the inclusion of the geometric phase has an important effect on ultracold chemical reaction rates. The effect appears in rotationally and vibrationally resolved integral cross sections as well as cross sections summed over all product quantum states. The effect arises from interference between scattering amplitudes of two reaction pathways: a direct path and a looping path that encircle the conical intersection between the two lowest adiabatic electronic potential energy surfaces. It is magnified when the two scattering amplitudes have comparable magnitude and they scatter into the same angular region which occurs in the isotropic scatteringmore » characteristic of the ultracold regime (s-wave scattering). Results are presented for the O + OH → H + O 2 reaction for total angular momentum quantum number J = 0–5. Large geometric phase effects occur for collision energies below 0.1 K, but the effect vanishes at higher energies when contributions from different partial waves are included. It is also qualitatively demonstrated that the geometric phase effect can be modulated by applying an external electric field allowing the possibility of quantum control of chemical reactions in the ultracold regime. In this case, the geometric phase plays the role of a “quantum switch” which can turn the reaction “on” or “off”.« less

Systems Performance Laboratory | Energy Systems Integration Facility | NREL

Science.gov Websites

array access Small Commercial Power Hardware in the Loop The small commercial power-hardware-in-the-loop (PHIL) test bay is dedicated to small-scale power hardware-in-the-loop studies of inverters and other , natural gas supply Multi-Inverter Power Hardware in the Loop The multi-inverter test bay is dedicated to

Runtime Assurance Framework Development for Highly Adaptive Flight Control Systems

DTIC Science & Technology

2015-12-01

performing a surveillance mission. The demonstration platform consisted of RTA systems for the inner- loop control, outer- loop guidance, ownship flight...For the inner- loop , the concept of employing multiple transition controllers in the reversionary control system was studied. For all feedback levels...5 RTA Protection Applied to Inner- Loop Control Systems .................................................61 5.1 General Description of Morphing Wing

Teachers' Attitudes and Perceptions of Looping and the Effect of Looping on Students' Academic Achievement

ERIC Educational Resources Information Center

Williams-Wright, Vera

2013-01-01

The purpose of this research study was two-fold. The first purpose was to investigate the impact of looping on academic achievement of students in selected public schools in Mississippi. The students' results on the 2010 and 2011 Mississippi Curriculum Test, Second Edition (MCT2) were used to determine whether looping students score differently in…

Overnight closed-loop insulin delivery with model predictive control: assessment of hypoglycemia and hyperglycemia risk using simulation studies.

PubMed

Wilinska, Malgorzata E; Budiman, Erwin S; Taub, Marc B; Elleri, Daniela; Allen, Janet M; Acerini, Carlo L; Dunger, David B; Hovorka, Roman

2009-09-01

Hypoglycemia and hyperglycemia during closed-loop insulin delivery based on subcutaneous (SC) glucose sensing may arise due to (1) overdosing and underdosing of insulin by control algorithm and (2) difference between plasma glucose (PG) and sensor glucose, which may be transient (kinetics origin and sensor artifacts) or persistent (calibration error [CE]). Using in silico testing, we assessed hypoglycemia and hyperglycemia incidence during over-night closed loop. Additionally, a comparison was made against incidence observed experimentally during open-loop single-night in-clinic studies in young people with type 1 diabetes mellitus (T1DM) treated by continuous SC insulin infusion. Simulation environment comprising 18 virtual subjects with T1DM was used to simulate overnight closed-loop study with a model predictive control (MPC) algorithm. A 15 h experiment started at 17:00 and ended at 08:00 the next day. Closed loop commenced at 21:00 and continued for 11 h. At 18:00, protocol included meal (50 g carbohydrates) accompanied by prandial insulin. The MPC algorithm advised on insulin infusion every 15 min. Sensor glucose was obtained by combining model-calculated noise-free interstitial glucose with experimentally derived transient and persistent sensor artifacts associated with FreeStyle Navigator (FSN). Transient artifacts were obtained from FSN sensor pairs worn by 58 subjects with T1DM over 194 nighttime periods. Persistent difference due to FSN CE was quantified from 585 FSN sensor insertions, yielding 1421 calibration sessions from 248 subjects with diabetes. Episodes of severe (PG < or = 36 mg/dl) and significant (PG < or = 45 mg/dl) hypoglycemia and significant hyperglycemia (PG > or = 300 mg/dl) were extracted from 18,000 simulated closed-loop nights. Severe hypoglycemia was not observed when FSN CE was less than 45%. Hypoglycemia and hyperglycemia incidence during open loop was assessed from 21 overnight studies in 17 young subjects with T1DM (8 males; 13.5 +/- 3.6 years of age; body mass index 21.0 +/- 4.0 kg/m2; duration diabetes 6.4 +/- 4.1 years; hemoglobin A1c 8.5% +/- 1.8%; mean +/- standard deviation) participating in the Artificial Pancreas Project at Cambridge. Severe and significant hypoglycemia during simulated closed loop occurred 0.75 and 17.11 times per 100 person years compared to 1739 and 3479 times per 100 person years during experimental open loop, respectively. Significant hyperglycemia during closed loop and open loop occurred 75 and 15,654 times per 100 person years, respectively. The incidence of severe and significant hypoglycemia reduced 2300- and 200-fold, respectively, during stimulated overnight closed loop with MPC compared to that observed during open-loop overnight clinical studies in young subjects with T1DM. Hyperglycemia was 200 times less likely. Overnight closed loop with the FSN and the MPC algorithm is expected to reduce substantially the risk of hypoglycemia and hyperglycemia. 2009 Diabetes Technology Society.

DNA–DNA kissing complexes as a new tool for the assembly of DNA nanostructures

PubMed Central

Barth, Anna; Kobbe, Daniela; Focke, Manfred

2016-01-01

Kissing-loop annealing of nucleic acids occurs in nature in several viruses and in prokaryotic replication, among other circumstances. Nucleobases of two nucleic acid strands (loops) interact with each other, although the two strands cannot wrap around each other completely because of the adjacent double-stranded regions (stems). In this study, we exploited DNA kissing-loop interaction for nanotechnological application. We functionalized the vertices of DNA tetrahedrons with DNA stem-loop sequences. The complementary loop sequence design allowed the hybridization of different tetrahedrons via kissing-loop interaction, which might be further exploited for nanotechnology applications like cargo transport and logical elements. Importantly, we were able to manipulate the stability of those kissing-loop complexes based on the choice and concentration of cations, the temperature and the number of complementary loops per tetrahedron either at the same or at different vertices. Moreover, variations in loop sequences allowed the characterization of necessary sequences within the loop as well as additional stability control of the kissing complexes. Therefore, the properties of the presented nanostructures make them an important tool for DNA nanotechnology. PMID:26773051

Inverted Temperature Loops in The Quiet Corona: Properties and Physical Origin

NASA Astrophysics Data System (ADS)

Huang, Z.; van der Holst, B.; Frazin, R. A.; Nuevo, F.; Vásquez, A. M.; Manchester, W.; Sokolov, I.; Gombosi, T. I.

2013-12-01

Huang et al. 2012 revealed the existence of inverted temperature ("down") loops, in which temperature decreases with height, as well as the usual ("up") loops, in which the temperature increases with height, in the quiet solar Corona. It was shown that the "down" loops are mostly located at low latitudes and "up" loops most often appear in high latitudes. A recent study by Nuevo et al. 2013 confirmed this discovery and further showed that the "down" loop population is greatest at solar minimum; and strongly decreases with solar activity. Moreover, the "down" loops were found to be associated with values of the plasma beta greater than about unity, while the "up" loops were associated with much smaller values of beta. Here, we review the properties of "up" and "down" loops, and employ a state-of-the-art global MHD model to understand the physics of these loops as well as to investigate their thermodynamic stability. The 3D MHD model uses a phenomenological wave dissipation model based on wave reflection (proportional to the Alfvén speed gradients) and turbulent dissipation.

Defining the location of promoter-associated R-loops at near-nucleotide resolution using bisDRIP-seq

PubMed Central

Dumelie, Jason G

2017-01-01

R-loops are features of chromatin consisting of a strand of DNA hybridized to RNA, as well as the expelled complementary DNA strand. R-loops are enriched at promoters where they have recently been shown to have important roles in modifying gene expression. However, the location of promoter-associated R-loops and the genomic domains they perturb to modify gene expression remain unclear. To resolve this issue, we developed a bisulfite-based approach, bisDRIP-seq, to map R-loops across the genome at near-nucleotide resolution in MCF-7 cells. We found the location of promoter-associated R-loops is dependent on the presence of introns. In intron-containing genes, R-loops are bounded between the transcription start site and the first exon-intron junction. In intronless genes, the 3' boundary displays gene-specific heterogeneity. Moreover, intronless genes are often associated with promoter-associated R-loop formation. Together, these studies provide a high-resolution map of R-loops and identify gene structure as a critical determinant of R-loop formation. PMID:29072160

Can arousing feedback rectify lapses in driving? Prediction from EEG power spectra.

PubMed

Lin, Chin-Teng; Huang, Kuan-Chih; Chuang, Chun-Hsiang; Ko, Li-Wei; Jung, Tzyy-Ping

2013-10-01

This study explores the neurophysiological changes, measured using an electroencephalogram (EEG), in response to an arousing warning signal delivered to drowsy drivers, and predicts the efficacy of the feedback based on changes in the EEG. Eleven healthy subjects participated in sustained-attention driving experiments. The driving task required participants to maintain their cruising position and compensate for randomly induced lane deviations using the steering wheel, while their EEG and driving performance were continuously monitored. The arousing warning signal was delivered to participants who experienced momentary behavioral lapses, failing to respond rapidly to lane-departure events (specifically the reaction time exceeded three times the alert reaction time). The results of our previous studies revealed that arousing feedback immediately reversed deteriorating driving performance, which was accompanied by concurrent EEG theta- and alpha-power suppression in the bilateral occipital areas. This study further proposes a feedback efficacy assessment system to accurately estimate the efficacy of arousing warning signals delivered to drowsy participants by monitoring the changes in their EEG power spectra immediately thereafter. The classification accuracy was up 77.8% for determining the need for triggering additional warning signals. The findings of this study, in conjunction with previous studies on EEG correlates of behavioral lapses, might lead to a practical closed-loop system to predict, monitor and rectify behavioral lapses of human operators in attention-critical settings.

Comparative assessment of the efficacy of closed helical loop and T-loop for space closure in lingual orthodontics-a finite element study.

PubMed

Chacko, Ajay; Tikku, Tripti; Khanna, Rohit; Maurya, Rana Pratap; Srivastava, Kamna

2018-05-28

Retraction in lingual orthodontics has biomechanical differences when compared to labial orthodontics, which is not yet established. Thus, we have intended to compare the biomechanical characteristics of closed helical loop and T-loop on 1 mm activation with 30° of compensatory curvatures during retraction in lingual orthodontics. STb lingual brackets were indirectly bonded to maxillary typhodont model that was scanned to obtain FEM model. Closed helical loop (2 × 7 mm) and T-loop (6 × 2 × 7 mm) of 0.016″ × 0.016″ TMA wire were modeled without preactivation bends. Preactivation bends at 30° were given in the software. Boundary conditions were set. The force (F) and moment (M) of both the loops were determined on 1 mm activation, using ANSYS software. M/F ratio was also calculated for both the loops. T-loop exerted less force, thus increased M/F ratio as compared to closed helical loop on 1 mm activation. When torque has to be preserved in the anterior segment during retraction in lingual orthodontics, T-loop can be preferred over closed helical loop.

Control-structure interaction in precision pointing servo loops

NASA Technical Reports Server (NTRS)

Spanos, John T.

1989-01-01

The control-structure interaction problem is addressed via stability analysis of a generic linear servo loop model. With the plant described by the rigid body mode and a single elastic mode, structural flexibility is categorized into one of three types: (1) appendage, (2) in-the-loop minimum phase, and (3) in-the-loop nonminimum phase. Closing the loop with proportional-derivative (PD) control action and introducing sensor roll-off dynamics in the feedback path, stability conditions are obtained. Trade studies are conducted with modal frequency, modal participation, modal damping, loop bandwidth, and sensor bandwidth treated as free parameters. Results indicate that appendage modes are most likely to produce instability if they are near the sensor rolloff, whereas in-the-loop modes are most dangerous near the loop bandwidth. The main goal of this paper is to provide a fundamental understanding of the control-structure interaction problem so that it may benefit the design of complex spacecraft and pointing system servo loops. In this framework, the JPL Pathfinder gimbal pointer is considered as an example.

Studies of uranium-sodium suspensions. Part I. Construction and operation of experimental loop

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

Bett, F L; Hilditch, R J; Mepham, R G

1961-08-01

An experimnental uranium- sodium suspension loop was operated for 4320 hr. The design, construction, commissioning, and operation of the loop to the point where a comnplete stable suspension was obtained is described.

Atomistic Simulation of Interstitial Dislocation Loop Evolution under Applied Stresses in BCC Iron

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

Long, Xue Hao; Wang, Dong; Setyawan, Wahyu

Evolution of an interstitial 1/2⟨111⟩ dislocation loop under tensile, shear, and torsion stresses is studied with molecular statics method. Under a tensile stress, the dependence of ultimate tensile strength on size of loop is calculated. The formation of small shear loops around the initial prismatic loop is confirmed as an intermediate state to form the final dislocation network. Under a shear stress, the rotation of a loop is observed not only by a change of the habit plane but also through a transformation between a shear and a prismatic loop. Under torsion, a perfect BCC crystal may undergo a BCCmore » to FCC or BCC to HCP transformation. The present work indicates that a 1/2⟨111⟩ loop can delay these transformations, resulting in the formation of micro-crack on the surface.« less

Human life support during interplanetary travel and domicile. III - Mars expedition system trade study

NASA Technical Reports Server (NTRS)

Seshan, P. K.; Ferrall, Joseph F.; Rohatgi, Naresh K.

1991-01-01

Several alternative configurations of life-support systems (LSSs) for a Mars missions are compared analytically on a quantitative basis in terms of weight, volume, and power. A baseline technology set is utilized for the illustrations of systems including totally open loop, carbon dioxide removal only, partially closed loop, and totally closed loop. The analytical model takes advantage of a modular, top-down hierarchical breakdown of LSS subsystems into functional elements that represent individual processing technologies. The open-loop systems are not competitive in terms of weight for both long-duration orbiters and short-duration lander vehicles, and power demands are lowest with the open loop and highest with the closed loop. The closed-loop system can reduce vehicle weight by over 70,000 lbs and thereby overcome the power penalty of 1600 W; the closed-loop variety is championed as the preferred system for a Mars expedition.

Coronal loops and active region structure

NASA Technical Reports Server (NTRS)

Webb, D. F.; Zirin, H.

1981-01-01

Synoptic H-alpha Ca K, magnetograph and Skylab soft X-ray and EUV data were compared for the purpose of identifying the basic coronal magnetic structure of loops in a 'typical' active region and studying its evolution. A complex of activity in July 1973, especially McMath 12417, was emphasized. The principal results are: (1) most of the brightest loops connected the bright f plage to either the sunspot penumbra or to p satellite spots; no non-flaring X-ray loops end in umbrae; (2) short, bright loops had one or both ends in regions of emergent flux, strong field or high field gradients; (3) stable, strongly sheared loop arcades formed over filaments; (4) EFRs were always associated with compact X-ray arcades; and (5) loops connecting to other active regions had their bases in outlying plage of weak field strength in McM 417 where H-alpha fibrils marked the direction of the loops

Structural Basis for Substrate Specificity in Phosphate Binding (beta/alpha)8-Barrels: D-Allulose 6-Phosphate 3-Epimerase from Escherichia coli K-12

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

Chan,K.; Fedorov, A.; Almo, S.

2008-01-01

Enzymes that share the ({beta}/{alpha})8-barrel fold catalyze a diverse range of reactions. Many utilize phosphorylated substrates and share a conserved C-terminal ({beta}/a)2-quarter barrel subdomain that provides a binding motif for the dianionic phosphate group. We recently reported functional and structural studies of d-ribulose 5-phosphate 3-epimerase (RPE) from Streptococcus pyogenes that catalyzes the equilibration of the pentulose 5-phosphates d-ribulose 5-phosphate and d-xylulose 5-phosphate in the pentose phosphate pathway [J. Akana, A. A. Fedorov, E. Fedorov, W. R. P. Novack, P. C. Babbitt, S. C. Almo, and J. A. Gerlt (2006) Biochemistry 45, 2493-2503]. We now report functional and structural studies ofmore » d-allulose 6-phosphate 3-epimerase (ALSE) from Escherichia coli K-12 that catalyzes the equilibration of the hexulose 6-phosphates d-allulose 6-phosphate and d-fructose 6-phosphate in a catabolic pathway for d-allose. ALSE and RPE prefer their physiological substrates but are promiscuous for each other's substrate. The active sites (RPE complexed with d-xylitol 5-phosphate and ALSE complexed with d-glucitol 6-phosphate) are superimposable (as expected from their 39% sequence identity), with the exception of the phosphate binding motif. The loop following the eighth {beta}-strand in ALSE is one residue longer than the homologous loop in RPE, so the binding site for the hexulose 6-phosphate substrate/product in ALSE is elongated relative to that for the pentulose 5-phosphate substrate/product in RPE. We constructed three single-residue deletion mutants of the loop in ALSE, ?T196, ?S197 and ?G198, to investigate the structural bases for the differing substrate specificities; for each, the promiscuity is altered so that d-ribulose 5-phosphate is the preferred substrate. The changes in kcat/Km are dominated by changes in kcat, suggesting that substrate discrimination results from differential transition state stabilization. In both ALSE and RPE, the phosphate group hydrogen bonds not only with the conserved motif but also with an active site loop following the sixth {beta}-strand, providing a potential structural mechanism for coupling substrate binding with catalysis.« less

Numerical Analysis of Combined Well and Open-Closed Loops Geothermal (CWG) Systems

NASA Astrophysics Data System (ADS)

Park, Yu-Chul

2016-04-01

Open-loop geothermal heat pump (GHP) system and closed-loop heat pump systems have been used in Korea to reduce emission of greenhouse gases such as carbon dioxide (CO2). The GHP systems have the pros and cons, for example, the open-loop GHP system is good energy-efficient and the closed-loop GHP system requires minimum maintenance costs. The open-loop GHP system can be used practically only with large amount of groundwater supply. The closed-loop GHP system can be used with high costs of initial installation. The performance and efficiency of the GHP system depend on the characteristics of the GHP system itself in addition to the geologic conditions. To overcome the cons of open-loop or closed-loop GHP system, the combined well and open-closed loops geothermal (CWG) system was designed. The open-loop GHP system is surrounded with closed-loop GHP systems in the CWG system. The geothermal energy in closed-loop GHP systems is supplied by the groundwater pumped by the open-loop GHP system. In this study, 2 different types of the CWG systems (small aperture hybrid CWG system and large aperture CWG system) are estimated using numerical simulation models in the aspect of energy efficiency. This work was supported by the New & Renewable Energy Core Technology Program of the Korea Institute of Energy Technology Evaluation and Planning (KETEP), granted financial resource from the Ministry of Trade, Industry & Energy, Republic of Korea. (No.20153030111120).

A minimal mathematical model combining several regulatory cycles from the budding yeast cell cycle.

PubMed

Sriram, K; Bernot, G; Képès, F

2007-11-01

A novel topology of regulatory networks abstracted from the budding yeast cell cycle is studied by constructing a simple nonlinear model. A ternary positive feedback loop with only positive regulations is constructed with elements that activates the subsequent element in a clockwise fashion. A ternary negative feedback loop with only negative regulations is constructed with the elements that inhibit the subsequent element in an anticlockwise fashion. Positive feedback loop exhibits bistability, whereas the negative feedback loop exhibits limit cycle oscillations. The novelty of the topology is that the corresponding elements in these two homogeneous feedback loops are linked by the binary positive feedback loops with only positive regulations. This results in the emergence of mixed feedback loops in the network that displays complex behaviour like the coexistence of multiple steady states, relaxation oscillations and chaos. Importantly, the arrangement of the feedback loops brings in the notion of checkpoint in the model. The model also exhibits domino-like behaviour, where the limit cycle oscillations take place in a stepwise fashion. As the aforementioned topology is abstracted from the budding yeast cell cycle, the events that govern the cell cycle are considered for the present study. In budding yeast, the sequential activation of the transcription factors, cyclins and their inhibitors form mixed feedback loops. The transcription factors that involve in the positive regulation in a clockwise orientation generates ternary positive feedback loop, while the cyclins and their inhibitors that involve in the negative regulation in an anticlockwise orientation generates ternary negative feedback loop. The mutual regulation between the corresponding elements in the transcription factors and the cyclins and their inhibitors generates binary positive feedback loops. The bifurcation diagram constructed for the whole system can be related to the different events of the cell cycle in terms of dynamical system theory. The checkpoint mechanism that plays an important role in different phases of the cell cycle are accounted for by silencing appropriate feedback loops in the model.