CFD simulations of Rapid Compression Machines using detailed chemistry: Evaluation of the ‘crevice containment’ concept

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

Bourgeois, Nicolas; Goldsborough, S. Scott; Jeanmart, Herve

The use of creviced pistons in Rapid Compression Machines (RCMs) has proven to be very effcient in making the temperature homogeneous inside the reaction chamber but has the disadvantage of inducing a mass transfer from the reaction chamber to the crevice, especially during the preliminary heat release of two- stage ignition processes. Aiming to mitigate this mass transfer, the technique of `crevice containment' (CC) has been proposed. It consists of a physical separa- tion between the reaction chamber and the crevice region that is engaged at the end of the compression, physically preventing any mass transfer between both parts ofmore » the geometry. In order to numerically assess this novel design concept across a broader range of conditions than previously investigated, reactive simu- lations using detailed chemical kinetic mechanisms are performed for n-heptane and iso-octane. For compressed temperatures outside of the NTC (negative temperature coeffcient) region, the CC approach is very effective in suppress- ing the influence of the crevice mass transfer and thus increases the validity of the widely-used 0-D model based on the adiabatic core assumption. Still, for most of the temperature cases inside the NTC region, the ignition appears to be precipitately initiated in the residual vortex region formed after the seal engagement, possibly inducing very significant differences with the 0-D model. The benefits of eliminating the post-compression crevice mass transfer appear to be counter-balanced by effects that have not been previously investigated in detail.« less

CFD simulations of Rapid Compression Machines using detailed chemistry: Evaluation of the ‘crevice containment’ concept

DOE PAGES

Bourgeois, Nicolas; Goldsborough, S. Scott; Jeanmart, Herve; ...

2018-01-17

The use of creviced pistons in Rapid Compression Machines (RCMs) has proven to be very effcient in making the temperature homogeneous inside the reaction chamber but has the disadvantage of inducing a mass transfer from the reaction chamber to the crevice, especially during the preliminary heat release of two- stage ignition processes. Aiming to mitigate this mass transfer, the technique of `crevice containment' (CC) has been proposed. It consists of a physical separa- tion between the reaction chamber and the crevice region that is engaged at the end of the compression, physically preventing any mass transfer between both parts ofmore » the geometry. In order to numerically assess this novel design concept across a broader range of conditions than previously investigated, reactive simu- lations using detailed chemical kinetic mechanisms are performed for n-heptane and iso-octane. For compressed temperatures outside of the NTC (negative temperature coeffcient) region, the CC approach is very effective in suppress- ing the influence of the crevice mass transfer and thus increases the validity of the widely-used 0-D model based on the adiabatic core assumption. Still, for most of the temperature cases inside the NTC region, the ignition appears to be precipitately initiated in the residual vortex region formed after the seal engagement, possibly inducing very significant differences with the 0-D model. The benefits of eliminating the post-compression crevice mass transfer appear to be counter-balanced by effects that have not been previously investigated in detail.« less

Cockroaches traverse crevices, crawl rapidly in confined spaces, and inspire a soft, legged robot.

PubMed

Jayaram, Kaushik; Full, Robert J

2016-02-23

Jointed exoskeletons permit rapid appendage-driven locomotion but retain the soft-bodied, shape-changing ability to explore confined environments. We challenged cockroaches with horizontal crevices smaller than a quarter of their standing body height. Cockroaches rapidly traversed crevices in 300-800 ms by compressing their body 40-60%. High-speed videography revealed crevice negotiation to be a complex, discontinuous maneuver. After traversing horizontal crevices to enter a vertically confined space, cockroaches crawled at velocities approaching 60 cm⋅s(-1), despite body compression and postural changes. Running velocity, stride length, and stride period only decreased at the smallest crevice height (4 mm), whereas slipping and the probability of zigzag paths increased. To explain confined-space running performance limits, we altered ceiling and ground friction. Increased ceiling friction decreased velocity by decreasing stride length and increasing slipping. Increased ground friction resulted in velocity and stride length attaining a maximum at intermediate friction levels. These data support a model of an unexplored mode of locomotion--"body-friction legged crawling" with body drag, friction-dominated leg thrust, but no media flow as in air, water, or sand. To define the limits of body compression in confined spaces, we conducted dynamic compressive cycle tests on living animals. Exoskeletal strength allowed cockroaches to withstand forces 300 times body weight when traversing the smallest crevices and up to nearly 900 times body weight without injury. Cockroach exoskeletons provided biological inspiration for the manufacture of an origami-style, soft, legged robot that can locomote rapidly in both open and confined spaces.

Boulder Clusters as Flow Refugia for Juvenile Salmonids and Aquatic Invertebrates in Steep Mountain Streams, Klamath Mountains, Northern California

NASA Astrophysics Data System (ADS)

Cover, M. R.; May, C. L.; Dietrich, W. E.; Resh, V. H.

2005-12-01

The availability of flow refugia and cover is an important factor affecting habitat suitability for fish and invertebrates, especially in steep, turbulent streams. In some channels, crevices beneath and between large rocks may be the only available flow refugia that allow rainbow trout (Oncorhynchus mykiss) to conserve energy and escape from high velocity flow during large storm events. Many aquatic invertebrates, especially large or crawling taxa, require cover that is provided by unembedded crevice space underneath large stones. To investigate the influence of channel type on habitat availability, we performed intensive surveys of crevice habitat for salmonids and benthic invertebrates in 12 reaches in Walker Creek, a 25 square km basin in the Klamath Mountains of Northern California. We identified four reaches in each of three channel types: plane bed (3.1% - 3.7% slope), step-pool (5.4% - 6.5% slope), and cascade (6.3% - 8.5% slope). We used 4 realistic fish models (5, 10, 15, and 20 cm length) to assess the size of crevices and presence of flow refugia associated with all cobble (64 - 256 mm) and boulder (> 256 mm) grains within five 0.5 m-wide diagonal transects. The total abundance of crevices was similar among plane bed (6.3 +/- 1.1 m-2) (Mean +/- SD), step-pool (6.2 +/- 0.25 m-2), and cascade (6.7 +/- 1.2 m-2) reaches. Small (5 cm) crevices made up the majority of crevices in all three reach types. While the presence of 5 cm and 10 cm crevices was not significantly different between the three channel types, there were significantly more large (20 cm) crevices in cascade (0.73 +/- 0.33 m-2) and step-pool (0.68 +/- 0.1 m-2) reaches than in plane bed (0.26 +/- 0.14 m-2) reaches (AVOVA, p < 0.05). Moderately sized (15 cm) crevices were more common in step-pool reaches (0.91 +/- 0.13 m-2) than either cascade (0.54 +/- 0.15 m-2) or plane bed (0.42 +/- 0.13 m-2) reaches. Based on these results we conclude that step-pool reaches provide the most favorable habitat for larger (15 to 20 cm) fish, probably due to the channel-spawning clusters of large cobbles and boulders that define this channel type. Understanding the processes that develop and maintain these open-framework clusters is important for basin-scale assessment of potential aquatic habitat.

Plasmonic-Field Interactions at Nanoparticle Interfaces for Infrared Thermal-Shielding Applications Based on Transparent Oxide Semiconductors.

PubMed

Matsui, Hiroaki; Furuta, Shinya; Hasebe, Takayuki; Tabata, Hitoshi

2016-05-11

This paper describes infrared plasmonic responses in three-dimensional (3D) assembled films of In2O3:Sn nanoparticles (NPs). The introduction of surface modifications to NPs can facilitate the production of electric-field interactions between NPs due to the creation of narrow crevices in the NP interfaces. In particular, the electric-field interactions along the in-plane and out-of-plane directions in the 3D assembled NP films allow for resonant splitting of plasmon excitations to the quadrupole and dipole modes, thereby realizing selective high reflections in the near- and mid-infrared range, respectively. The origins of these plasmonic properties were revealed from electric-field distributions calculated by electrodynamic simulations that agreed well with experimental results. The interparticle gaps and their derived plasmon couplings play an important role in producing high reflective performances in assembled NP films. These 3D assemblies of NPs can be further extended to produce large-size flexible films with high infrared reflectance, which simultaneously exhibit microwave transmittance essential for telecommunications. This study provides important insights for harnessing infrared optical responses using plasmonic technology for the fabrication of infrared thermal-shielding applications.

Rail assembly for use in a radioactive environment

DOEpatents

Watts, Ralph E.

1989-01-01

An improved rail assembly and method of construction thereof is disclosed herein that is particularly adapted for use with a crane trolley in a hot cell environment which is exposed to airborne and liquidborne radioactive contaminants. The rail assembly is generally comprised of a support wall having an elongated, rail-housing recess having a floor, side wall and ceiling. The floor of the recess is defined at least in part by the load-bearing surface of a rail, and is substantially flat, level and crevice-free to facilitate the drainage of liquids out of the recess. The ceiling of the recess overhangs and thereby captures trolley wheels within the recess to prevent them from becoming dislodged from the recess during a seismic disturbance. Finally, the interior of the recess includes a power track having a slot for receiving a sliding electrical connector from the crane trolley. The power track is mounted in an upper corner of the recess with its connector-receiving groove oriented downwardly to facilitate the drainage of liquidborne contaminants and to discourage the collection of airborne contaminants within the track.

Survey of degradation modes of candidate materials for high-level radioactive-waste disposal containers

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

Farmer, J.C.; Van Konynenburg, R.A.; McCright, R.D.

1988-04-01

Three iron- to nickel-based austenitic alloys (Types 304L and 316L stainless steels and Alloy 825) are being considered as candidate materials for the fabrication of high-level radioactive-waste containers. Waste will include fuel assemblies from reactors as well as high-level waste in borosilicate glass forms, and will be sent to the prospective repository at Yucca Mountain, Nevada. The decay of radionuclides in the repository will result in the generation of substantial heat and in fluences of gamma radiation. Container materials may undergo any of several modes of degradation in this environment, including atmospheric oxidation; uniform aqueous phase corrosion; pitting; crevice corrosion;more » sensitization and intergranular stress corrosion cracking (IGSCC); and transgranular stress corrosion cracking (TGSCC). This report is an analysis of data relevant to the pitting, crevice corrosion, and stress corrosion cracking (SCC) of the three austenitic candidate alloys. The candidates are compared in terms of their susceptibilities to these forms of corrosion. Although all three candidates have demonstrated pitting and crevice corrosion in chloride-containing environments, Alloy 825 has the greatest resistance to these types of localized corrosion (LC); such resistance is important because pits can penetrate the metal and serve as crack initiation sites. Both Types 304L and 316L stainless steels are susceptible to SCC in acidic chloride media. In contrast, SCC has not been documented in Alloy 825 under comparable conditions. Gamma radiation has been found to enhance SCC in Types 304 and 304L stainless steels, but it has no detectable effect on the resistance of Alloy 825 to SCC. Furthermore, while the effects of microbiologically induced corrosion have been observed for 300-series stainless steels, nickel-based alloys such as Alloy 825 seem to be immune to such problems. 211 refs., 49 figs., 10 tabs.« less

The corrosion effect of ozonated seawater solution on titanium in polymer generated crevice environments

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

Leveillee, S.Y.

1998-01-01

Two different tests were designed to evaluate the reaction of various polymers and grade-2 titanium in ozonated seawater in conjunction with a comparative analysis in an aerated seawater solution. The first was a weight loss test measuring the weight change of Polyvinyl chloride (PVC), Polyethylene and Teflon{trademark} in both ozonated and aerated artificial seawater baths. The second test was designed to induce crevice corrosion on the titanium test samples using various crevice generating materials in both ozonated and aerated solutions. The materials used to create the crevices were grade-2 titanium washers, PVC, Polyethylene, Saran and Teflon{trademark}. The weight loss testmore » showed that all three polymers lost weight in the ozonated bath. The results of the titanium washer crevice test provided no indication of corrosion or surface discoloration in either the ozonated or aerated solutions. Energy dispersive spectrometry (EDS) analysis found no fluorine, chlorine or other corrosion product. The PVC samples in the aerated bath also showed no signs of corrosion, but the PVC samples in the ozonated tank had light brown rings of surface discoloration. One of the ozonated PVC samples did show evidence of chlorine in the corrosion product. The outer circumference of the ozonated PVC washers exhibited the same type bleaching effect as in the weight loss samples, but the whitening of these samples were more pronounced. The polyethylene samples under aeration showed no discoloration or presence of fluorine or chlorine. The polyethylene crevice samples in the ozonated solution all exhibited the distinct brilliant blue color of titanium oxide. Fluorine was found in the corrosion product on only one of the samples. Chlorine was found on the surface of one of the other corrosion coupons. The results of the Teflon{trademark} crevice samples substantiated the previous Rensselaer study.« less

Modeling local chemistry in PWR steam generator crevices

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

Millett, P.J.

1997-02-01

Over the past two decades steam generator corrosion damage has been a major cost impact to PWR owners. Crevices and occluded regions create thermal-hydraulic conditions where aggressive impurities can become highly concentrated, promoting localized corrosion of the tubing and support structure materials. The type of corrosion varies depending on the local conditions, with stress corrosion cracking being the phenomenon of most current concern. A major goal of the EPRI research in this area has been to develop models of the concentration process and resulting crevice chemistry conditions. These models may then be used to predict crevice chemistry based on knowledgemore » of bulk chemistry, thereby allowing the operator to control corrosion damage. Rigorous deterministic models have not yet been developed; however, empirical approaches have shown promise and are reflected in current versions of the industry-developed secondary water chemistry guidelines.« less

Gimme shelter: The importance of crevices to some fish species inhabiting a deeper-water rocky outcrop in Southern California

USGS Publications Warehouse

Love, M.S.; Schroeder, D.M.; Lenarz, B.; Cochrane, G.R.

2006-01-01

Federal law governing fisheries management recognizes the role habitat plays in structuring fish assemblages and achieving sustainable fisheries. However, in most instances it is not known which aspects of habitat are important to the lives of fish species. In 2004, we examined the importance of sheltering sites (crevices) to fishes living along low ledges in deeper waters off Anacapa Island, southern California. We found that patterns of fish-habitat relationships varied among the eight most abundant species. Three species, bocaccio (Sebastes paucispinis), vermilion (S. miniatus), and flag (S. rubrivinctus) rockfishes, had densities one to three orders of magnitude greater in the deep crevice habitat compared to low relief rock or shallow crevice habitats. Density and mean size of the two most abundant fishes, halfbanded (S. semicinctus) and squarespot (S. hopkinsi) rockfishes, generally increased as complexity of rock habitat increased. Not all species had the highest densities in deep crevice habitat. Greenspotted rockfish (S. chlorostictus) and blackeye goby (Rhinogobiops nicholsii) showed no significant difference in density among rock habitats. Pink seaperch (Zalembius rosaceus) were absent in the deep crevice habitat and abundant only in low relief rock habitats. Our study implies that it is not sufficient to distinguish only between soft and hard bottom types when using habitat to guide fisheries management strategies. Finer-scale investigations of fish-habitat relationships, paired with habitat mapping and groundtruthing, aid in the design and positioning of Marine Park Areas (MPAs) and are necessary to facilitate understanding of how a particular MPA may contribute to fisheries management.

Application of ANS fluorescent probes to identify hydrophobic sites on the surface of DREAM.

PubMed

Gonzalez, Walter G; Miksovska, Jaroslava

2014-09-01

DREAM (calsenilin or KChIP-3) is a calcium sensor involved in regulation of diverse physiological processes by interactions with multiple intracellular partners including DNA, Kv4 channels, and presenilin, however the detailed mechanism of the recognition of the intracellular partners remains unclear. To identify the surface hydrophobic surfaces on apo and Ca(2+)DREAM as a possible interaction sites for target proteins and/or specific regulators of DREAM function the binding interactions of 1,8-ANS and 2,6-ANS with DREAM were characterized by fluorescence and docking studies. Emission intensity of ANS-DREAM complexes increases upon Ca(2+) association which is consistent with an overall decrease in surface polarity. The dissociation constants for ANS binding to apoDREAM and Ca(2+)DREAM were determined to be 195±20μM and 62±4μM, respectively. Fluorescence lifetime measurements indicate that two ANS molecules bind in two independent binding sites on DREAM monomer. One site is near the exiting helix of EF-4 and the second site is located in the hydrophobic crevice between EF-3 and EF-4. 1,8-ANS displacement studies using arachidonic acid demonstrate that the hydrophobic crevice between EF-3 and EF-4 serves as a binding site for fatty acids that modulate functional properties of Kv4 channel:KChIP complexes. Thus, the C-terminal hydrophobic crevice may be involved in DREAM interactions with small hydrophobic ligands as well as other intracellular proteins. Copyright © 2014 Elsevier B.V. All rights reserved.

Small-Molecule-Based Self-Assembled Ligands for G-Quadruplex DNA Surface Recognition.

PubMed

Rivera-Sánchez, María Del C; García-Arriaga, Marilyn; Hobley, Gerard; Morales-de-Echegaray, Ana V; Rivera, José M

2017-10-31

Most drugs are small molecules because of their attractive pharmacokinetics, manageable development and manufacturing, and effective binding into the concave crevices of bio-macromolecules. Despite these features, they often fall short when it comes to effectively recognizing the surfaces of bio-macromolecules. One way to overcome the challenge of biomolecular surface recognition is to develop small molecules that become self-assembled ligands (SALs) prior to binding. Herein, we report SALs made from 8-aryl-2'-deoxyguanosine derivatives forming precise hydrophilic supramolecular G-quadruplexes (SGQs) with excellent size, shape, and charge complementarity to G-quadruplex DNA (QDNA). We show that only those compounds forming SGQs act as SALs, which in turn differentially stabilize QDNAs from selected oncogene promoters and the human telomeric regions. Fluorescence resonance energy-transfer melting assays are consistent with spectroscopic, calorimetric, and light scattering studies, showing the formation of a "sandwichlike" complex QDNA·SGQ·QDNA. These results open the door for the advent of SALs that recognize QDNAs and potentially the surfaces of other bio-macromolecules such as proteins.

Autumn migration and selection of rock crevices as hibernacula by big brown bats in Colorado

USGS Publications Warehouse

Neubaum, D.J.; O'Shea, T.J.; Wilson, K.R.

2006-01-01

Movements, distribution, and roosting requirements of most species of temperate-zone bats in autumn are poorly understood. We conducted the 1st radiotelemetry study of autumn migrations and prehibernation roost selection of bats in western North America. Big brown bats (Eptesicus fuscus, n = 55) in the Poudre River watershed, Colorado, moved from low-elevation summer ranges to high-elevation locations in autumn, where they roosted in rock crevices during the period leading up to winter hibernation. We characterized rock crevices used as roosts in autumn at these higher elevations at microhabitat and landscape scales. We used logistic regression combined with an information theoretic approach to determine which variables were most important in roost selection. At the microhabitat scale, autumn roosts were higher to the ground above and below the exit point and were in deeper crevices that had more constant temperatures than randomly selected crevices. At the landscape scale, aspect of the hillside was important, with autumn roosts typically facing north-northwest. Autumn roosts fell into 2 categories: those used for a few days (transient roosts) and those used for ≥7 days and presumed to be hibernacula. Temperature regimes in the presumed hibernacula appear to provide optimal conditions for use of winter torpor, whereas transient roosts may offer passive rewarming and energy savings for bats still active in early autumn. Elevational segregation of sexes also was documented in our region, with a preponderance of females found at lower elevations and males at higher elevations in summer. Sex ratios at higher elevations became even in autumn. Use of short elevational migrations and selection of hibernation sites in rock crevices may be a common overwintering strategy of insectivorous bats of western North America.

Visualization and Analysis of Biomaterial-Centered Thrombus Formation within a Defined Crevice Under Flow

PubMed Central

Jamiolkowski, Megan A.; Pedersen, Drake D.; Wu, Wei-Tao; Antaki, James F.; Wagner, William R.

2016-01-01

The blood flow pathway within a device, together with the biomaterial surfaces and status of the patient’s blood, are well-recognized factors in the development of thrombotic deposition and subsequent embolization. Blood flow patterns are of particular concern for devices such as blood pumps (i.e. ventricular assist devices, VADs) where shearing forces can be high, volumes are relatively large, and the flow fields can be complex. However, few studies have examined the effect of geometric irregularities on thrombus formation on clinically relevant opaque materials under flow. The objective of this study was to quantify human platelet deposition onto Ti6Al4V alloys, as well as positive and negative control surfaces, in the region of defined crevices (~50–150 µm in width) that might be encountered in many VADs or other cardiovascular devices. To achieve this, reconstituted fresh human blood with hemoglobin-depleted red blood cells (to achieve optical clarity while maintaining relevant rheology), long working optics, and a custom designed parallel plate flow chamber were employed. The results showed that the least amount of platelet deposition occurred in the largest crevice size examined, which was counterintuitive. The greatest levels of deposition occurred in the 90 µm and 53 µm crevices at the lower wall shear rate. The results suggest that while crevices may be unavoidable in device manufacturing, the crevice size might be tailored, depending on the flow conditions, to reduce the risk of thromboembolic events. Further, these data might be used to improve the accuracy of predictive models of thrombotic deposition in cardiovascular devices to help optimize the blood flow path and reduce device thrombogenicity. PMID:27156141

Clonality of bacterial consortia in root canals and subjacent gingival crevices.

PubMed

Parahitiyawa, Nipuna B; Chu, Frederick C S; Leung, Wai K; Yam, Wing C; Jin, Li Jian; Samaranayake, Lakshman P

2015-02-01

No oral niche can be considered to be segregated from the subjacent milieu because of the complex community behavior and nature of the oral biofilms. The aim of this study was to address the paucity of information on how these species are clonally related to the subjacent gingival crevice bacteria. We utilized a metagenomic approach of amplifying 16S rDNA from genomic DNA, cloning, sequencing and analysis using LIBSHUFF software to assess the genetic homogeneity of the bacterial species from two infected root canals and subjacent gingival crevices. The four niches studied yielded 186 clones representing 54 phylotypes. Clone library comparisons using LIBSHUFF software indicated that each niche was inhabited by a unique flora. Further, 42% of the clones were of hitherto unknown phylotypes indicating the extent of bacterial diversity, especially in infected root canals and subjacent gingival crevices. We believe data generated through this novel analytical tool shed new light on understanding oral microbial ecosystems. © 2014 Wiley Publishing Asia Pty Ltd.

The seating mechanics of head-neck modular tapers in vitro: Load-displacement measurements, moisture, and rate effects.

PubMed

Ouellette, Eric S; Shenoy, Aarti A; Gilbert, Jeremy L

2018-04-01

The mechanically assisted crevice corrosion performance of head-neck modular tapers is a significant concern in orthopedic biomaterials. Fretting crevice corrosion processes in modular tapers are thought to be influenced by a wide array of factors including seating mechanics of the junction, hence there is a need for in vitro test methods that can assess their performance. This study presented a test method to directly measure the load-displacement seating mechanics of modular tapers and used this method to compare the seating mechanics for different tapers, moisture, seating loads and seating rates. Seating mechanics were explored whereby the instantaneous load-displacement behavior of the head seating onto the neck is captured and used to define the mechanics of seating. Two distinct taper design/material combinations were assembled wet or dry using axially applied loads (500, 1,000, 2,000, and 4,000 N) at two loading rates of 100 and 10 4  N/s (n = 5 for each condition) using a servohydraulic test frame. The results showed that pull-off strength scaled with seating load and ranged between 43% and 68% of seating load depending on sample and wetness. Tapers seated wet had higher pull-off strengths (2,200 ± 300 N) than those seated dry (1,800 ± 200 N, p < 0.05). Seating mechanics (load-displacement plots) varied due to sample type and due to wetness with differences in seating energy, seating stiffness, and seating displacement. These results show the detailed mechanics of seating during assembly and provide significant insight into the complex interplay of factors associated with even "ideal" seating (axial, quasistatic) loading. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:1164-1172, 2018. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

Crevice corrosion - NaCl concentration map for grade-2 titanium at elevated temperature

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

Tsujikawa, Shigeo; Kojima, Yoichi

1993-12-31

The repassivation potential, ER, for metal/metal-crevice of Commercially Pure Titanium, C.P.Ti, was determined in NaCl solutions at temperatures up to 250C. The ER has its least noble value near 100C and becomes more noble as the temperature increases. As shown in previous research, the shrinkage of the repassivation region should continue with increasing temperatures. However, in conducting this same experiment at temperatures higher than 100C, an examination of the NaCl concentration - temperature - crevice corrosion map verifies that the repassivation region began to expand again when the temperature exceeded 140C. This expansion continued as the temperature continued to increase.

The role of trapped bubbles in kidney stone detection with the color Doppler ultrasound twinkling artifact.

PubMed

Simon, Julianna C; Sapozhnikov, Oleg A; Kreider, Wayne; Breshock, Michael; Williams, James C; Bailey, Michael R

2018-01-09

The color Doppler ultrasound twinkling artifact, which highlights kidney stones with rapidly changing color, has the potential to improve stone detection; however, its inconsistent appearance has limited its clinical utility. Recently, it was proposed stable crevice bubbles on the kidney stone surface cause twinkling; however, the hypothesis is not fully accepted because the bubbles have not been directly observed. In this paper, the micron or submicron-sized bubbles predicted by the crevice bubble hypothesis are enlarged in kidney stones of five primary compositions by exposure to acoustic rarefaction pulses or hypobaric static pressures in order to simultaneously capture their appearance by high-speed photography and ultrasound imaging. On filming stones that twinkle, consecutive rarefaction pulses from a lithotripter caused some bubbles to reproducibly grow from specific locations on the stone surface, suggesting the presence of pre-existing crevice bubbles. Hyperbaric and hypobaric static pressures were found to modify the twinkling artifact; however, the simple expectation that hyperbaric exposures reduce and hypobaric pressures increase twinkling by shrinking and enlarging bubbles, respectively, largely held for rough-surfaced stones but was inadequate for smoother stones. Twinkling was found to increase or decrease in response to elevated static pressure on smooth stones, perhaps because of the compression of internal voids. These results support the crevice bubble hypothesis of twinkling and suggest the kidney stone crevices that give rise to the twinkling phenomenon may be internal as well as external.

The role of trapped bubbles in kidney stone detection with the color Doppler ultrasound twinkling artifact

NASA Astrophysics Data System (ADS)

Simon, Julianna C.; Sapozhnikov, Oleg A.; Kreider, Wayne; Breshock, Michael; Williams, James C., Jr.; Bailey, Michael R.

2018-01-01

The color Doppler ultrasound twinkling artifact, which highlights kidney stones with rapidly changing color, has the potential to improve stone detection; however, its inconsistent appearance has limited its clinical utility. Recently, it was proposed stable crevice bubbles on the kidney stone surface cause twinkling; however, the hypothesis is not fully accepted because the bubbles have not been directly observed. In this paper, the micron or submicron-sized bubbles predicted by the crevice bubble hypothesis are enlarged in kidney stones of five primary compositions by exposure to acoustic rarefaction pulses or hypobaric static pressures in order to simultaneously capture their appearance by high-speed photography and ultrasound imaging. On filming stones that twinkle, consecutive rarefaction pulses from a lithotripter caused some bubbles to reproducibly grow from specific locations on the stone surface, suggesting the presence of pre-existing crevice bubbles. Hyperbaric and hypobaric static pressures were found to modify the twinkling artifact; however, the simple expectation that hyperbaric exposures reduce and hypobaric pressures increase twinkling by shrinking and enlarging bubbles, respectively, largely held for rough-surfaced stones but was inadequate for smoother stones. Twinkling was found to increase or decrease in response to elevated static pressure on smooth stones, perhaps because of the compression of internal voids. These results support the crevice bubble hypothesis of twinkling and suggest the kidney stone crevices that give rise to the twinkling phenomenon may be internal as well as external.

Electrochemical characterization of cerium-based conversion coatings on aluminum alloy 7075-T6

NASA Astrophysics Data System (ADS)

Joshi, Simon

This research used electrochemical techniques to characterize the deposition and corrosion protection behavior of cerium-based conversion coatings on Al 7075-T6. Alkaline activation decreased native oxide impedance (5.9 kO-cm2) by ˜25% promoting deposition of 250--500 nm coatings. Activation in NaOH solutions deposited coatings with large cracks and craters, whereas Na2CO3 activation resulted in uniform coatings, i.e., fewer cracks and almost no craters. Uniformly deposited coatings exhibited better cathodic inhibition and higher impedance (˜200 kO-cm 2) than on NaOH activated substrates (˜100 kO-cm 2). Subsurface crevices, caused by Cl- and H 2O2 in the deposition solution, were found under large cracks and craters. Thus, Na2CO3 activation produced fewer subsurface crevices. To reduce subsurface crevice formation, Ce(NO3) 3 and CeCl3 were used in different ratios. Coatings made using 100% Ce(NO3)3 solutions were ˜60 nm thick without subsurface crevices, but the coatings offered little corrosion protection. Despite formation of subsurface crevices, Cl- was necessary as impedance increased linearly with Cl- concentration in the deposition solution. To characterize the different non-uniform features of the coatings, microelectrochemical testing was performed and it showed three distinct regions: active, intermediate, and passive. Humidity experiments were performed to understand the effect of moisture during salt spray testing and showed an increase in coating impedance by making the exposed substrate oxide more passive. However, this passive oxide could not provide corrosion resistance in a chloride environment. Dissolution studies showed that cerium migration was only possible at pH ≤2. Overall, deposition of uniform 250--500 nm thick outings was essential to make it an effective barrier to Cl - attach and prevent subsurface crevices on Al 7075-T6.

THE DISTRIBUTION OF CHLORPYRIFOS FOLLOWING A CRACK AND CREVICE TYPE APPLICATION IN THE U.S. EPA INDOOR AIR QUALITY RESEARCH HOUSE

EPA Science Inventory

A study was conducted in the U.S. EPA Indoor Air Quality Research House to determine the spatial and temporal distribution of chlorpyrifos following a professional crack and crevice application in the kitchen. Following the application, measurements were made in the kitchen, de...

CHLORPYRIFOS ACCUMULATION PATTERNS FOR CHILD ACCESSIBLE SURFACES AND OBJECTIVES AND URINARY METABOLITE EXCRETION BY CHILDREN FOR TWO-WEEKS AFTER CRACK-AND-CREVICE APPLICATION

EPA Science Inventory

The Children's-Post-Pesticide-Application-Exposure-Study (CPPAES) was conducted to look at the distribution of chlorpyrifos within a home environment for a 2-week period following a routine professional crack-and-crevice application, and to determine the amount of the chlorpyrifo...

THE DISTRIBUTION OF CHLORPYRIFOS FOLLOWING A CRACK AND CREVICE TYPE APPLICATION IN THE U.S. EPA INDOOR AIR QUALITY RESEARCH HOUSE

EPA Science Inventory

The paper gives results of a study to determine the spatial and temporal distribution of chlorpyrifos following a professional crack-and-crevice application in the kitchen of the U.S. EPA's indoor air quality research house in North Carolina. Following the application, measuremen...

THE DISTRIBUTION OF CHLORPYRIFOS FOLLOWING A CRACK AND CREVICE TYPE APPLICATION IN THE U.S. EPA INDOOR AIR QUALITY TEST HOUSE

EPA Science Inventory

A study was conducted in the U.S. EPA Indoor Air Quality Test House to determine the spatial and temporal distribution of chlorpyrifos following a professional crack and crevice application in the kitchen. Following the application, measurements were made in the kitchen, den a...

Disruption of a hydrogen bond network in human versus spider monkey cytochrome c affects heme crevice stability.

PubMed

Goldes, Matthew E; Jeakins-Cooley, Margaret E; McClelland, Levi J; Mou, Tung-Chung; Bowler, Bruce E

2016-05-01

The hypothesis that the recent rapid evolution of primate cytochromes c, which primarily involves residues in the least stable Ω-loop (Ω-loop C, residues 40-57), stabilizes the heme crevice of cytochrome c relative to other mammals, is tested. To accomplish this goal, we have compared the properties of human and spider monkey cytochrome c and a set of four variants produced in the process of converting human cytochrome c into spider monkey cytochrome c. The global stability of all variants has been measured by guanidine hydrochloride denaturation. The stability of the heme crevice has been assessed with the alkaline conformational transition. Structural insight into the effects of the five amino acid substitutions needed to convert human cytochrome c into spider monkey cytochrome c is provided by a 1.15Å resolution structure of spider monkey cytochrome c. The global stability for all variants is near 9.0kcal/mol at 25°C and pH7, which is higher than that observed for other mammalian cytochromes c. The heme crevice stability is more sensitive to the substitutions required to produce spider monkey cytochrome c with decreases of up to 0.5 units in the apparent pKa of the alkaline conformational transition relative to human cytochrome c. The structure of spider monkey cytochrome c indicates that the Y46F substitution destabilizes the heme crevice by disrupting an extensive hydrogen bond network that connects three surface loops including Ω-loop D (residues 70-85), which contains the Met80 heme ligand. Copyright © 2015 Elsevier Inc. All rights reserved.

Marine Corrosion.

DTIC Science & Technology

1985-04-24

cor- rosion resistant alloys such as molybdenum -containing stainless steels. For the latter the high degree of aeration in the splashing water...imposed by marine technology, such as elevated temperatures , tensile stresses, cyclic stresses, severe (tight) crevices, galvanic coupling and high ...corrosion in seawater in tight metal-to-non-metal crevices are titanium alloys 4, the high molybdenum nickel base alloys Hastelloy alloy C-276 and

Roost selection by western long-eared myotis (Myotis evotis) in burned and unburned piñon–juniper woodlands of southwestern Colorado

USGS Publications Warehouse

Snider, E. Apple; Cryan, Paul M.; Wilson, Kenneth R.

2013-01-01

All 16 species of bats known to occur in western Colorado are found at Mesa Verde National Park (MVNP) in the southwestern United States. Since 1996, wildfires have burned more than 70% of MVNP (> 15,000 ha), potentially altering food and roosting resources for bats. During the summers of 2006–2007, we investigated roost use by reproductive female western long-eared myotis (Myotis evotis). We located 33 bat roosts in rock crevices and 1 in a juniper snag. All but 2 of the roosts were in unburned habitat. Bats roosted alone or in small groups (≤3 individuals) and switched roosts frequently (1–7 roosts per bat, median = 1.5 roosts per bat, SE = 0.5 roosts per bat). We compared occupied roosts with randomly selected unoccupied crevices and used an information theoretic approach to determine which variables were most important in determining roost use at microhabitat and landscape scales. At the microhabitat scale, maternity roosts were higher above the ground and deeper than random, unoccupied rock crevices. At the landscape scale, roosts were closer to water and farther from burned habitat than random crevices, providing reproductive female M. evotis with the best opportunities to drink and forage for insects. Tree roosts are apparently not a vital resource for reproductive female M. evotis during the summer months at our study site, presumably because of the extensive availability of rock crevices. Understanding site-specific roosting behavior is important for proper management of bat populations because differences can exist between geographic regions, even among areas with similar plant communities.

Characterization of the corrosion protection mechanism of cerium-based conversion coatings on high strength aluminum alloys

NASA Astrophysics Data System (ADS)

Pinc, William Ross

The aim of the work presented in this dissertation is to investigate the corrosion protection mechanism of cerium-based conversion coatings (CeCCs) used in the corrosion protection of high strength aluminum alloys. The corrosion resistance of CeCCs involves two general mechanisms; barrier and active. The barrier protection mechanism was influenced by processing parameters, specifically surface preparation, post-treatment, and the use of gelatin. Post-treatment and the addition of gelatin to the coating solution resulted in fewer cracks and transformation of the coating to CePO4, which increased the corrosion resistance by improving the barrier aspect of CeCCs. CeCCs were found to best act as barriers when crack size was limited and CePO4 was present in the coating. CeCCs were found to protect areas of the substrate that were exposed in the coating, indicating that the coatings were more than simple barriers. CeCCs contained large cracks, underneath which subsurface crevices were connected to the surface by the cracks. Despite the observation that no cerium was present in crevices, coatings with crevices exhibited significant corrosion protection. The impedance of post-treated coatings with crevices increased during salt spray exposure. The increase in impedance was associated with the formation of protective oxides / hydroxides; however, crevice-free coatings also exhibited active protection leading to the conclusion that the formation of interfacial layers between the CeCC and the substrate also contributed to the active protection. Based on the overall results of the study, the optimal corrosion protection of CeCCs occurred when processing conditions produced coatings with morphologies and compositions that facilitated both the barrier and active protection mechanisms.

Relative stress corrosion susceptibilities of alloys 690 and 600 in simulated boiling water reactor environments

NASA Astrophysics Data System (ADS)

Page, R. A.; McMinn, A.

1986-05-01

The relative susceptibilities of alloys 600 and 690 to intergranular stress corrosion cracking (IGSCC) in pure water and a simulated resin intrusion environment at 288 °C were evaluated. A combination of creviced and noncreviced slow-strain-rate, and precracked fracture mechanics tests were employed in the evaluation. Susceptibility was determined as a function of dissolved oxygen content, degree of sensitization, and crevice condition. The results indicated that alloy 600 was susceptible to various degrees of IGSCC in oxygen containing pure water when creviced, and immune to IGSCC when uncreviced. Alloy 690 was immune to IGSCC under all pure water conditions examined. Alloy 600 and alloy 690 were both susceptible to cracking in the simulated resin intrusion environment. Alloy 690, however, exhibited the greatest resistance to SCC of the two alloys.

Structure of the Minor Pseudopilin EpsH From the Type 2 Secretion System of Vibrio Cholerae

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

Yanez, M.E.; Korotkov, K.V.; Abendroth, J.

2009-05-28

Many Gram-negative bacteria use the multi-protein type II secretion system (T2SS) to selectively translocate virulence factors from the periplasmic space into the extracellular environment. In Vibrio cholerae the T2SS is called the extracellular protein secretion (Eps) system, which translocates cholera toxin and several enzymes in their folded state across the outer membrane. Five proteins of the T2SS, the pseudopilins, are thought to assemble into a pseudopilus, which may control the outer membrane pore EpsD, and participate in the active export of proteins in a 'piston-like' manner. We report here the 2.0 {angstrom} resolution crystal structure of an N-terminally truncated variantmore » of EpsH, a minor pseudopilin from Vibrio cholerae. While EpsH maintains an N-terminal {alpha}-helix and C-terminal {beta}-sheet consistent with the type 4a pilin fold, structural comparisons reveal major differences between the minor pseudopilin EpsH and the major pseudopilin GspG from Klebsiella oxytoca: EpsH contains a large {beta}-sheet in the variable domain, where GspG contains an {alpha}-helix. Most importantly, EpsH contains at its surface a hydrophobic crevice between its variable and conserved {beta}-sheets, wherein a majority of the conserved residues within the EpsH family are clustered. In a tentative model of a T2SS pseudopilus with EpsH at its tip, the conserved crevice faces away from the helix axis. This conserved surface region may be critical for interacting with other proteins from the T2SS machinery.« less

IN VIVO SEVERE CORROSION AND HYDROGEN EMBRITTLEMENT OF RETRIEVED MODULAR BODY TITANIUM ALLOY HIP-IMPLANTS

PubMed Central

Rodrigues, Danieli C.; Urban, Robert M.; Jacobs, Joshua J.; Gilbert, Jeremy L.

2009-01-01

Titanium alloys are widely used in total-joint replacements due to a combination of outstanding mechanical properties, biocompatibility, passivity and corrosion resistance. Nevertheless, retrieval studies have pointed out that these materials can be subjected to localized or general corrosion in modular interfaces when mechanical abrasion of the oxide film (fretting) occurs. Modularity adds large crevice environments, which are subject to micromotion between contacting interfaces and differential aeration of the surface. Titanium alloys are also known to be susceptible to hydrogen absorption, which can induce precipitation of hydrides and subsequent brittle failure. In this work, the surface of three designs of retrieved hip-implants with Ti-6Al-4V/Ti-6Al-4V modular taper interfaces in the stem were investigated for evidence of severe corrosion and precipitation of brittle hydrides during fretting-crevice corrosion in the modular connections. The devices were retrieved from patients and studied by means of scanning electron microscopy (SEM), x-ray diffraction (XRD) and chemical analysis. The surface qualitative investigation revealed severe corrosion attack in the mating interfaces with evidence of etching, pitting, delamination and surface cracking. In vivo hydrogen embrittlement was shown to be a mechanism of degradation in modular connections resulting from electrochemical reactions induced in the crevice environment of the tapers during fretting-crevice corrosion. PMID:18683224

Sensitivity of coral recruitment to subtle shifts in early community succession.

PubMed

Doropoulos, Christopher; Roff, George; Visser, Mart-Simone; Mumby, Peter J

2017-02-01

Community succession following disturbance depends on positive and negative interactions, the strength of which change along environmental gradients. To investigate how early succession affects coral reef recovery, we conducted an 18-month experiment in Palau, using recruitment tiles and herbivore exclusion cages. One set of reefs has higher wave exposure and had previously undergone a phase shift to macroalgae following a major typhoon, whereas the other set of reefs have lower wave exposure and did not undergo a macroalgal phase shift. Similar successional trajectories were observed at all sites when herbivores were excluded: turf algae dominated early succession, followed by shifts to foliose macroalgae and heterotrophic invertebrates. However, trajectories differed in the presence of herbivores. At low wave exposure reefs, herbivores promoted coralline algae and limited turf and encrusting fleshy algae in crevice microhabitats, facilitating optimal coral recruitment. Under medium wave exposure, relatively higher but still low coverage of turf and encrusting fleshy algae (15-25%) found in crevice microhabitats inhibited coral recruitment, persisting throughout multiple recruitment events. Our results indicate that altered interaction strength in different wave environments following disturbance can drive subtle changes in early succession that cascade to alter secondary succession to coral recruitment and system recovery. © 2016 by the Ecological Society of America.

Monitoring planktivorous seabird populations: Validating surface counts of crevice-nesting auklets using mark-resight techniques

USGS Publications Warehouse

Sheffield, L.M.; Gall, Adrian E.; Roby, D.D.; Irons, D.B.; Dugger, K.M.

2006-01-01

Least Auklets (Aethia pusilla (Pallas, 1811)) are the most abundant species of seabird in the Bering Sea and offer a relatively efficient means of monitoring secondary productivity in the marine environment. Counting auklets on surface plots is the primary method used to track changes in numbers of these crevice-nesters, but counts can be highly variable and may not be representative of the number of nesting individuals. We compared average maximum counts of Least Auklets on surface plots with density estimates based on mark–resight data at a colony on St. Lawrence Island, Alaska, during 2001–2004. Estimates of breeding auklet abundance from mark–resight averaged 8 times greater than those from maximum surface counts. Our results also indicate that average maximum surface counts are poor indicators of breeding auklet abundance and do not vary consistently with auklet nesting density across the breeding colony. Estimates of Least Auklet abundance from mark–resight were sufficiently precise to meet management goals for tracking changes in seabird populations. We recommend establishing multiple permanent banding plots for mark–resight studies on colonies selected for intensive long-term monitoring. Mark–resight is more likely to detect biologically significant changes in size of auklet breeding colonies than traditional surface count techniques.

Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth

PubMed Central

Marcy, Yann; Ouverney, Cleber; Bik, Elisabeth M.; Lösekann, Tina; Ivanova, Natalia; Martin, Hector Garcia; Szeto, Ernest; Platt, Darren; Hugenholtz, Philip; Relman, David A.; Quake, Stephen R.

2007-01-01

We have developed a microfluidic device that allows the isolation and genome amplification of individual microbial cells, thereby enabling organism-level genomic analysis of complex microbial ecosystems without the need for culture. This device was used to perform a directed survey of the human subgingival crevice and to isolate bacteria having rod-like morphology. Several isolated microbes had a 16S rRNA sequence that placed them in candidate phylum TM7, which has no cultivated or sequenced members. Genome amplification from individual TM7 cells allowed us to sequence and assemble >1,000 genes, providing insight into the physiology of members of this phylum. This approach enables single-cell genetic analysis of any uncultivated minority member of a microbial community. PMID:17620602

Great Lakes Regional Phase 3 Commercialization Conference, Held in Detroit, Michigan on May 23 - 25, 1994

DTIC Science & Technology

1994-05-25

small highly efficient power systems to provide electricity for space applications. These converters are solar heated for near earth orbit applications...processing in NASA’s Wake Shield Facility. AMPS plans to complete product development in each of these specific technology areas utilizing SBIR...Corrosion: Crevice corrosion is a form of localized corrosion that occurs within crevices or shielded surfaces where stagnant solution is present

Laboratory Investigation of a Leaking Type 316 Socket Weld in a Boron Injection Tank Sampling Line

NASA Astrophysics Data System (ADS)

Xu, Hongqing; Fyfitch, Steve; Hosier, Ryan; Hyres, James

A leak was discovered in a Type 316 stainless steel socket weld in the sampling line for the boron injection tank. A section of the pipeline containing the leaking weld was removed for laboratory investigation that included visual and Stereovisual inspections, liquid penetrant (PT) testing, metallography, scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), and ferrite content determinations. The leak path was a through-wall transgranular crack in the socket weld. Cracking initiated along the weld-metal-to-base-metal interface at the tip of the crevice between the socket and pipe. The crevice was exposed to oxygenated boron solution at <180°F. Shallow intergranular attack (IGA) was found in the exposed base metal inside the crevice. Based on the investigation results, it was concluded that transgranular stress corrosion cracking (TGSCC) is the primary cracking mechanism.

Anode for a secondary, high-temperature electrochemical cell

DOEpatents

Vissers, Donald R.; Tani, Benjamin S.

1976-01-01

A high-temperature, secondary electrochemical cell includes an anode containing lithium, an electrolyte containing lithium ions and a cathode containing a chalcogen material such as sulfur or a metallic sulfide. The anode includes a porous substrate formed of, for instance, a compacted mass of entangled metallic fibers providing interstitial crevices for receiving molten lithium metal. The surfaces of the interstitial crevices are provided with a coating of cobalt metal to enhance the retention of the molten lithium metal within the substrate.

Holocene seasonal variability inferred from multiple proxy records from Crevice Lake, Yellowstone National Park, USA

USGS Publications Warehouse

Whitlock, Cathy; Dean, Walter E.; Fritz, Sherilyn C.; Stevens, Lora R.; Stone, Jeffery R.; Power, Mitchell J.; Rosenbaum, Joseph R.; Pierce, Kenneth L.; Bracht-Flyr, Brandi B.

2012-01-01

A 9400-yr-old record from Crevice Lake, a semi-closed alkaline lake in northern Yellowstone National Park, was analyzed for pollen, charcoal, geochemistry, mineralogy, diatoms, and stable isotopes to develop a nuanced understanding of Holocene environmental history in a region of northern Rocky Mountains that receives both summer and winter precipitation. The limited surface area, conical bathymetry, and deep water (> 31 m) of Crevice Lake create oxygen-deficient conditions in the hypolimnion and preserve annually laminated sediment (varves) for much of the record. Pollen data indicate that the watershed supported a closed Pinus-dominated forest and low fire frequency prior to 8200 cal yr BP, followed by open parkland until 2600 cal yr BP, and open mixed-conifer forest thereafter. Fire activity shifted from infrequent stand-replacing fires initially to frequent surface fires in the middle Holocene and stand-replacing events in recent centuries. Low values of δ18O suggest high winter precipitation in the early Holocene, followed by steadily drier conditions after 8500 cal yr BP. Carbonate-rich sediments before 5000 cal yr BP imply warmer summer conditions than after 5000 cal yr BP. High values of molybdenum (Mo), uranium (U), and sulfur (S) indicate anoxic bottom-waters before 8000 cal yr BP, between 4400 and 3900 cal yr BP, and after 2400 cal yr BP. The diatom record indicates extensive water-column mixing in spring and early summer through much of the Holocene, but a period between 2200 and 800 cal yr BP had strong summer stratification, phosphate limitation, and oxygen-deficient bottom waters. Together, the proxy data suggest wet winters, protracted springs, and warm effectively wet summers in the early Holocene and less snowpack, cool springs, warm dry summers in the middle Holocene. In the late Holocene, the region and lake experienced extreme changes in winter, spring, and summer conditions, with particularly short springs and dry summers and winters during the Roman Warm Period (~ 2000 cal yr BP) and Medieval Climate Anomaly (1200–800 cal yr BP). Long springs and mild summers occurred during the Little Ice Age, and these conditions persist to the present. Although the proxy data indicate effectively wet summer conditions in the early Holocene and drier conditions in the middle and late Holocene, none point specifically to changes in summer precipitation as the cause. Instead, summer conditions were governed by multi-seasonal controls on effective moisture that operated over multiple time scales.

Earthquakes Promote Bacterial Genetic Exchange in Serpentinite Crevices

NASA Astrophysics Data System (ADS)

Naoto, Yoshida; Fujiura, Nori

2009-04-01

We report the results of our efforts to study the effects of seismic shaking on simulated biofilms within serpentinite fissures. A colloidal solution consisting of recipient bacterial cells (Pseudomonas sp. or Bacillus subtilis), donor plasmid DNA encoded for antibiotic resistance, and chrysotile (an acicular clay mineral that forms in crevices of serpentinite layers) were placed onto an elastic body made from gellan gum, which acted as the biofilm matrix. Silica beads, as rock analogues (i.e., chemically inert mechanical serpentinite), were placed on the gellan surface, which was coated with the colloidal solution. A rolling vibration similar to vibrations generated by earthquakes was applied, and the silica beads moved randomly across the surface of the gellan. This resulted in the recipient cells' acquiring plasmid DNA and thus becoming genetically transformed to demonstrate marked antibiotic resistance. Neither Pseudomonas sp. nor B. subtilis were transformed by plasmid DNA when chrysotile was substituted for by kaolinite or bentonite in the colloidal solution. Tough gellan (1.0%) promoted the introduction of plasmid DNA into Pseudomonas sp., but soft gellan (0.3%) had no such effect. Genetic transformation of bacteria on the surface of gellan by exposure to exogenous plasmid DNA required seismic shaking and exposure to the acicular clay mineral chrysotile. These experimental results suggest that bacterial genetic exchange readily occurs when biofilms that form in crevices of serpentinite are exposed to seismic shaking. Seismic activity may be a key factor in bacterial evolution along with the formation of biofilms within crevices of serpentinite.

Aerodynamics inside a rapid compression machine

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

Mittal, Gaurav; Sung, Chih-Jen

2006-04-15

The aerodynamics inside a rapid compression machine after the end of compression is investigated using planar laser-induced fluorescence (PLIF) of acetone. To study the effect of reaction chamber configuration on the resulting aerodynamics and temperature field, experiments are conducted and compared using a creviced piston and a flat piston under varying conditions. Results show that the flat piston design leads to significant mixing of the cold vortex with the hot core region, which causes alternate hot and cold regions inside the combustion chamber. At higher pressures, the effect of the vortex is reduced. The creviced piston head configuration is demonstratedmore » to result in drastic reduction of the effect of the vortex. Experimental conditions are also simulated using the Star-CD computational fluid dynamics package. Computed results closely match with experimental observation. Numerical results indicate that with a flat piston design, gas velocity after compression is very high and the core region shrinks quickly due to rapid entrainment of cold gases. Whereas, for a creviced piston head design, gas velocity after compression is significantly lower and the core region remains unaffected for a long duration. As a consequence, for the flat piston, adiabatic core assumption can significantly overpredict the maximum temperature after the end of compression. For the creviced piston, the adiabatic core assumption is found to be valid even up to 100 ms after compression. This work therefore experimentally and numerically substantiates the importance of piston head design for achieving a homogeneous core region inside a rapid compression machine. (author)« less

Socket welds in nuclear facilities

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

Anderson, P.A.; Torres, L.L.

1995-12-31

Socket welds are easier and faster to make than are butt welds. However, they are often not used in nuclear facilities because the crevices between the pipes and the socket sleeves may be subject to crevice corrosion. If socket welds can be qualified for wider use in facilities that process nuclear materials, the radiation exposures to welders can be significantly reduced. The current tests at the Idaho Chemical Processing Plant (ICPP) are designed to determine if socket welds can be qualified for use in the waste processing system at a nuclear fuel processing plant.

Investigation of Local Hydrogen Uptake in Rescaled Model Occluded Sites Using Crevice Scaling Laws

DTIC Science & Technology

2005-04-01

13- 8 Mo . Under anodic polarization, there is a combination of x and G in a crevice or crack where the stainless steel would be passive and remain...2004). 8 . G.A. Young, Jr., J.R. Scully, "The Effects of Test Temperature , Temper and Alloyed Copper on Hydrogen Controlled Crack Growth of an A1-Zn-Mg...sharp crack tip.[16] Precipitation-aged hardened martensitic stainless steels (i.e., Fe-Cr-Ni- Mo alloys) that release hydrolysable Cr and Fe cations

Variability in colony attendance of crevice-nesting horned puffins: Implications for population monitoring

USGS Publications Warehouse

Harding, A.M.A.; Piatt, John F.; Byrd, G.V.; Hatch, Shyla A.; Konyukhov, N.B.; Golubova, E.U.; Williams, J.C.

2005-01-01

It is difficult to survey crevice-nesting seabirds because nest-sites are hard to identify and count, and the number of adult birds attending a colony can be extremely variable within and between days. There is no standardized method for surveying crevice-nesting horned puffins (Fratercula corniculata), and consequently little is known about abundance or changes in their numbers. We examined the variability in colony attendance of horned puffins at 5 breeding colonies in the North Pacific to assess whether variation in count data can be reduced to a level that would allow us to detect changes in the number of birds attending a colony. We used within-year measures of variation in attendance to examine the power to detect a change in numbers between 2 years, and we used measures of among-year variation to examine the power to detect trends over multiple years. Diurnal patterns of attendance differed among colonies, and among-day variation in attendance was generally lowest from mid- to late-incubation to early chick rearing. Within-year variation in water counts was lower than in land counts, and variation was lower using a daily index based on 5 counts per day than it was using 1 count per day. Measures of among-year variation in attendance also were higher for land-based than water-based counts, and they were higher when we used a 10-day survey period than when we used a 30-day period. The use of either 1 or 5 counts a day during the colony-specific diurnal peak of attendance had little influence on levels of among-year variation. Overall, our study suggests that variation in count data may be reduced to a level that allows detection of trends in numbers. However, more studies of interannual variability in horned puffin attendance are needed. Further, the relationship between count data and breeding population size needs more study before the number of birds present at the colony can be used with confidence as an index of population trend.

Characterisation of Crevice and Pit Solution Chemistries Using Capillary Electrophoresis with Contactless Conductivity Detector

PubMed Central

Nie, Mengyan; Wharton, Julian A.; Cranny, Andy; Harris, Nick R.; Wood, Robert J.K.; Stokes, Keith R.

2013-01-01

The ability to predict structural degradation in-service is often limited by a lack of understanding of the evolving chemical species occurring within a range of different microenvironments associated with corrosion sites. Capillary electrophoresis (CE) is capable of analysing nanolitre solution volumes with widely disparate concentrations of ionic species, thereby producing accurate and reliable results for the analysis of the chemical compositions found within microenvironment corrosion solutions, such as those found at crevice and pit corrosion sites. In this study, CE with contactless conductivity detection (CCD) has been used to characterize pitting and crevice corrosion solution chemistries for the first time. By using the capillary electrophoresis with contactless conductivity detection (CE-CCD) system, direct and simultaneous detection of seven metal cations (Cu2+, Ni2+, Fe3+, Fe2+, Cr3+, Mn2+, and Al3+) and chloride anions was achieved with a buffer solution of 10 mM 2,6-pyridinedicarboxylic acid and 0.5 mM cetyltrimethylammonium hydroxide at pH 4 using a pre-column complexation method. The detection limits obtained for the metal cations and chloride anions were 100 and 10 ppb, respectively. The CE-CCD methodology has been demonstrated to be a versatile technique capable of speciation and quantifying the ionic species generated within artificial pit (a pencil electrode) and crevice corrosion geometries for carbon steels and nickel-aluminium bronze, thus allowing the evolution of the solution chemistry to be assessed with time and the identification of the key corrosion analyte targets for structural health monitoring. PMID:28788335

Initiation criteria for crevice corrosion of titanium alloys used for HLW disposal overpack

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

Akashi, Masatsune; Nakayama, Guen; Fukuda, Takanori

1998-12-31

The overpack that geologically stores the canisters containing vitrified high-level radioactive waste (HLW) for super-long term disposal is demanded of being able to hold the canisters securely for at least 1,000 years. For such a service, the greatest as well as essentially the sole factor that can mar the overpack`s working is corrosion by the groundwater. This paper discusses the notion and the methodology to prove for overpacks made of titanium (Ti) alloys that they are capable of stably maintaining the state of passivity indefinitely long time so as to be immune to the initiation of localized corrosion. it ismore » shown that (1) the critical potential for corrosion-crevice initiation, V{sub C,CREV}, can be substituted rationally by the corrosion-crevice repassivation potential, E{sub R,CREV}, which can be determined by the cyclic polarization test, and (2) the limits of safety usage of Ti alloys can be determined quantitatively by comparing E{sub R,CREV} and E{sub SP}, the steady-state corrosion potential.« less

Partial-Vacuum-Gasketed Electrochemical Corrosion Cell

NASA Technical Reports Server (NTRS)

Bonifas, Andrew P.; Calle, Luz M.; Hintze, Paul E.

2006-01-01

An electrochemical cell for making corrosion measurements has been designed to prevent or reduce crevice corrosion, which is a common source of error in prior such cells. The present cell (see figure) includes an electrolyte reservoir with O-ring-edged opening at the bottom. In preparation for a test, the reservoir, while empty, is pressed down against a horizontal specimen surface to form an O-ring seal. A purge of air or other suitable gas is begun in the reservoir, and the pressure in the reservoir is regulated to maintain a partial vacuum. While maintaining the purge and partial vacuum, and without opening the interior of the reservoir to the atmosphere, the electrolyte is pumped into the reservoir. The reservoir is then slowly lifted a short distance off the specimen. The level of the partial vacuum is chosen such that the differential pressure is just sufficient to keep the electrolyte from flowing out of the reservoir through the small O-ring/specimen gap. Electrochemical measurements are then made. Because there is no gasket (and, hence, no crevice between the specimen and the gasket), crevice corrosion is unlikely to occur.

Niche partitioning of feeding microhabitats produces a unique function for herbivorous rabbitfishes (Perciformes, Siganidae) on coral reefs

NASA Astrophysics Data System (ADS)

Fox, R. J.; Bellwood, D. R.

2013-03-01

Niche theory predicts that coexisting species minimise competition by evolving morphological or behavioural specialisations that allow them to spread out along resource axes such as space, diet and temporal activity. These specialisations define how a species interacts with its environment and, by extension, determine its functional role. Here, we examine the feeding niche of three species of coral reef-dwelling rabbitfishes (Siganidae, Siganus). By comparing aspects of their feeding behaviour (bite location, bite rate, foraging distance) with that of representative species from two other abundant herbivorous fish families, the parrotfishes (Labridae, Scarus) and surgeonfishes (Acanthuridae, Acanthurus), we examine whether rabbitfishes have a feeding niche distinct from other members of the herbivore guild. Measurements of the penetration of the fishes' snouts and bodies into reef concavities when feeding revealed that rabbitfish fed to a greater degree from reef crevices and interstices than other herbivores. There was just a 40 % overlap in the penetration-depth niche between rabbitfish and surgeonfish and a 45 % overlap between rabbitfish and parrotfish, compared with the almost complete niche overlap (95 %) recorded for parrotfish and surgeonfish along this spatial niche axis. Aspects of the morphology of rabbitfish which may contribute to this niche segregation include a comparatively longer, narrower snout and narrower head. Our results suggest that sympatric coexistence of rabbitfish and other reef herbivores is facilitated by segregation along a spatial (and potentially dietary) axis. This segregation results in a unique functional role for rabbitfishes among roving herbivores that of "crevice-browser": a group that specifically feeds on crevice-dwelling algal or benthic organisms. This functional trait may have implications for reef ecosystem processes in terms of controlling the successional development of crevice-based algal communities, reducing their potential to trigger macroalgal outbreaks.

Review of corrosion in 10- and 14-ton mild steel depleted UF{sub 6} storage cylinders

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

Lykins, M.L.

1995-08-01

A literature review was conducted to determine the type, extent and severity of corrosion found in the 10- and 14-ton mild steel depleted UF{sub 6} storage cylinders. Also discussed in this review is corrosion found in the valves and plugs used in the cylinders. Corrosion of the cylinders is a gradual process which occurs slowly over time. Understanding corrosion of the cylinders is an important concern for long term storage of the UF{sub 6} in the cylinder yards, as well as the final disposition of the depleted UF{sub 6} tails inventory in the future. The following conclusions are made frommore » the literature review: (1) The general external corrosion rate of the cylinders is about 1 to 2 mils per year (1 mil = 0.001{double_prime}). The highest general external corrosion rate was over 5 mpy on the 48G type cylinders. (2) General internal corrosion from the depleted UF{sub 6} is negligible under normal storage conditions. Crevice corrosion can occur at the cylinder/saddle interface from the retention of water in this area. Crevice corrosion can occur at the cylinder/skirt interface on the older skirted cylinders due to the lack of water drainage in this area. Crevice corrosion can occur on cylinders that have been in ground contact. Crevice corrosion and galvanic corrosion can occur where the stainless steel I.D. nameplates are attached to the cylinder. The packing nuts on the bronze one-inch valves used in the cylinders are susceptible to stress corrosion cracking (SCC). Mechanical damage from routine handling can lead to a breach in a cylinder with subsequent accelerated corrosion of the mild steel due to attack from HF and other UF{sub 6} hydrolysis by-products.« less

Nonuniform Grain Boundary Corrosion and the Local Electrode Potential in Crevicing. Types and Models of Precipitation Induced Nonuniform Grain Boundary Corrosion. Investigation of Sensitization and Grain Boundary Corrosion in Ferritic Stainless Steel. The Local Electrode Potential in Cavities, Crevices and Cracks and Its Role in Causing Degradation of Structural Materials.

DTIC Science & Technology

1987-02-01

J.R. Pickens Dept. of Metallurgy & Mining Eng. Martin Marietta Laboratories % University of Illinois 1450 South Rolling Rd. Urbana, EIl 61801...AND MINERAL DEPARTMENT OF MATERIALS SCIENCE SCIENCES METALLURGY PROGRAM 00 00 TECHNICAL REPORT February 1987 OFFICE OF NAVAL RESEARCH IContract No...725 % ~ ~ ’. -~ ~AS~~jX.%......... !1CUlnITY CLASSIFICATION OF THIS PAGE (When n#e& Entered) REPORT DOCUMENTATION PAGE READ INSTRUCTIONS

ECLSS Universal Waste Management System (UWMS) Metal Materials Compatibility Study- Electrochemical and Crevice Corrosion Evaluation

NASA Technical Reports Server (NTRS)

Lee, R. E.

2017-01-01

Electrochemical and crevice corrosion laboratory test results are presented for three noble metal candidates with possible application on the Universal Waste Management System (UWMS) in support of the Environmental Control and Life Support System (ECLSS) aboard the International Space Station (ISS). The three metal candidates, which included Inconel 625, Hastelloy C276 and Titanium 6Al-4V, were evaluated in two solutions representative of the acidic pretreatment formulations utilized during processing of waste liquids within the ECLSS. Final test results and data analysis indicated that the passive layer on all three metals provides excellent corrosion protection in both solutions under standard test conditions.

Dovetail spoke internal permanent magnet machine

DOEpatents

Alexander, James Pellegrino [Ballston Lake, NY; EL-Refaie, Ayman Mohamed Fawzi [Niskayuna, NY; Lokhandwalla, Murtuza [Clifton Park, NY; Shah, Manoj Ramprasad [Latham, NY; VanDam, Jeremy Daniel [West Coxsackie, NY

2011-08-23

An internal permanent magnet (IPM) machine is provided. The IPM machine includes a stator assembly and a stator core. The stator core also includes multiple stator teeth. The stator assembly is further configured with stator windings to generate a stator magnetic field when excited with alternating currents and extends along a longitudinal axis with an inner surface defining a cavity. The IPM machine also includes a rotor assembly and a rotor core. The rotor core is disposed inside the cavity and configured to rotate about the longitudinal axis. The rotor assembly further includes a shaft. The shaft further includes multiple protrusions alternately arranged relative to multiple bottom structures provided on the shaft. The rotor assembly also includes multiple stacks of laminations disposed on the protrusions and dovetailed circumferentially around the shaft. The rotor assembly further includes multiple pair of permanent magnets for generating a magnetic field, which magnetic field interacts with the stator magnetic field to produce a torque. The multiple pair of permanent magnets are disposed between the stacks. The rotor assembly also includes multiple middle wedges mounted between each pair of the multiple permanent magnets.

High speed internal permanent magnet machine and method of manufacturing the same

DOEpatents

Alexander, James Pellegrino [Ballston Lake, NY; EL-Refaie, Ayman Mohamed Fawzi [Niskayuna, NY; Lokhandwalla, Murtuza [Clifton Park, NY; Shah, Manoj Ramprasad [Latham, NY; VanDam, Jeremy Daniel [West Coxsackie, NY

2011-09-13

An internal permanent magnet (IPM) machine is provided. The IPM machine includes a stator assembly and a stator core. The stator core also includes multiple stator teeth. The stator assembly is further configured with stator windings to generate a magnetic field when excited with alternating currents and extends along a longitudinal axis with an inner surface defining a cavity. The IPM machine also includes a rotor assembly and a rotor core. The rotor core is disposed inside the cavity and configured to rotate about the longitudinal axis. The rotor assembly further includes a shaft. The shaft further includes multiple protrusions alternately arranged relative to multiple bottom structures provided on the shaft. The rotor assembly also includes multiple stacks of laminations disposed on the protrusions and dovetailed circumferentially around the shaft. The rotor assembly further includes multiple permanent magnets for generating a magnetic field, which interacts with the stator magnetic field to produce torque. The permanent magnets are disposed between the stacks. The rotor assembly also includes multiple bottom wedges disposed on the bottom structures of the shaft and configured to hold the multiple stacks and the multiple permanent magnets.

The MARVEL assembly for neutron multiplication.

PubMed

Chichester, David L; Kinlaw, Mathew T

2013-10-01

A new multiplying test assembly is under development at Idaho National Laboratory to support research, validation, evaluation, and learning. The item is comprised of three stacked, highly-enriched uranium (HEU) cylinders, each 11.4 cm in diameter and having a combined height of up to 11.7 cm. The combined mass of all three cylinders is 20.3 kg of HEU. Calculations for the bare configuration of the assembly indicate a multiplication level of >3.5 (k(eff)=0.72). Reflected configurations of the assembly, using either polyethylene or tungsten, are possible and have the capability of raising the assembly's multiplication level to greater than 10. This paper describes simulations performed to assess the assembly's multiplication level under different conditions and describes the resources available at INL to support the use of these materials. We also describe some preliminary calculations and test activities using the assembly to study neutron multiplication. Copyright © 2013 Elsevier Ltd. All rights reserved.

Periodontitis and periimplantitis: one and the same?

PubMed

Meffert, R M

1993-12-01

Research shows that the same anaerobic, gram-negative pathogens are present in the periodontal and implant pocket or crevice. The implants in a partially edentulous case are probably more at risk due to the bacteria being more pathogenic and a seeding mechanism from the tooth pocket to the implant crevice. In the face of a normal microbial flora, retrograde periimplantitis or radiographic bone loss without gingival changes may be due to trauma because of overloading, loading too soon, and/or loading in a lateral direction. Finally, the combination of an infective process (periimplantitis) and noninfective or traumatic process (retrograde periimplantitis) will result in rapid osseous destruction and, possibly, loss of the implant fixture(s).

Automated ensemble assembly and validation of microbial genomes.

PubMed

Koren, Sergey; Treangen, Todd J; Hill, Christopher M; Pop, Mihai; Phillippy, Adam M

2014-05-03

The continued democratization of DNA sequencing has sparked a new wave of development of genome assembly and assembly validation methods. As individual research labs, rather than centralized centers, begin to sequence the majority of new genomes, it is important to establish best practices for genome assembly. However, recent evaluations such as GAGE and the Assemblathon have concluded that there is no single best approach to genome assembly. Instead, it is preferable to generate multiple assemblies and validate them to determine which is most useful for the desired analysis; this is a labor-intensive process that is often impossible or unfeasible. To encourage best practices supported by the community, we present iMetAMOS, an automated ensemble assembly pipeline; iMetAMOS encapsulates the process of running, validating, and selecting a single assembly from multiple assemblies. iMetAMOS packages several leading open-source tools into a single binary that automates parameter selection and execution of multiple assemblers, scores the resulting assemblies based on multiple validation metrics, and annotates the assemblies for genes and contaminants. We demonstrate the utility of the ensemble process on 225 previously unassembled Mycobacterium tuberculosis genomes as well as a Rhodobacter sphaeroides benchmark dataset. On these real data, iMetAMOS reliably produces validated assemblies and identifies potential contamination without user intervention. In addition, intelligent parameter selection produces assemblies of R. sphaeroides comparable to or exceeding the quality of those from the GAGE-B evaluation, affecting the relative ranking of some assemblers. Ensemble assembly with iMetAMOS provides users with multiple, validated assemblies for each genome. Although computationally limited to small or mid-sized genomes, this approach is the most effective and reproducible means for generating high-quality assemblies and enables users to select an assembly best tailored to their specific needs.

A Composite Depth Scale for Sediments from Crevice Lake, Montana

USGS Publications Warehouse

Rosenbaum, J.G.; Skipp, G.; Honke, J.; Chapman, C.

2010-01-01

As part of a study to derive records of past environmental change from lake sediments in the western United States, a set of cores was collected from Crevice Lake, Montana, in late February and early March 2001. Crevice Lake (latitude 45.000N, longitude 110.578W, elevation 1,713 meters) lies adjacent to the Yellowstone River at the north edge of Yellowstone National Park. The lake is more than 31 meters deep and has a surface area of 7.76 hectares. The combination of small surface area and significant depth promote anoxic bottom-water conditions that preserve annual laminations (varves) in the sediment. Three types of cores were collected through the ice. The uppermost sediments were obtained in freeze cores that preserved the sediment water interface. Two sites were cored with a 5-centimeter diameter corer. Five cores were taken with a 2-meter-long percussion piston corer. The percussion core uses a plastic core liner with an inside diameter of 9 centimeters. Coring was done at two sites. Because of the relatively large diameter of the percussion cores, samples from these cores were used for a variety of analyses including pollen, charcoal, diatoms, stable isotopes, organic and inorganic carbon, elemental analyses, and magnetic properties.

Density-dependent coral recruitment displays divergent responses during distinct early life-history stages

PubMed Central

Evensen, Nicolas R.; Gómez-Lemos, Luis A.; Babcock, Russell C.

2017-01-01

Population growth involves demographic bottlenecks that regulate recruitment success during various early life-history stages. The success of each early life-history stage can vary in response to population density, interacting with intrinsic (e.g. behavioural) and environmental (e.g. competition, predation) factors. Here, we used the common reef-building coral Acropora millepora to investigate how density-dependence influences larval survival and settlement in laboratory experiments that isolated intrinsic effects, and post-settlement survival in a field experiment that examined interactions with environmental factors. Larval survival was exceptionally high (greater than 80%) and density-independent from 2.5 to 12 days following spawning. By contrast, there was a weak positive effect of larval density on settlement, driven by gregarious behaviour at the highest density. When larval supply was saturated, settlement was three times higher in crevices compared with exposed microhabitats, but a negative relationship between settler density and post-settlement survival in crevices and density-independent survival on exposed surfaces resulted in similar recruit densities just one month following settlement. Moreover, a negative relationship was found between turf algae and settler survival in crevices, whereas gregarious settlement improved settler survival on exposed surfaces. Overall, our findings reveal divergent responses by coral larvae and newly settled recruits to density-dependent regulation, mediated by intrinsic and environmental interactions. PMID:28573015

Mitigating Localized Corrosion Using Thermally Sprayed Aluminum (TSA) Coatings on Welded 25% Cr Superduplex Stainless Steel

NASA Astrophysics Data System (ADS)

Paul, S.; Lu, Q.; Harvey, M. D. F.

2015-04-01

Thermally sprayed aluminum (TSA) coating has been increasingly used for the protection of carbon steel offshore structures, topside equipment, and flowlines/pipelines exposed to both marine atmospheres and seawater immersion conditions. In this paper, the effectiveness of TSA coatings in preventing localized corrosion, such as pitting and crevice corrosion of 25% Cr superduplex stainless steel (SDSS) in subsea applications, has been investigated. Welded 25% Cr SDSS (coated and uncoated) with and without defects, and surfaces coated with epoxy paint were also examined. Pitting and crevice corrosion tests, on welded 25% Cr SDSS specimens with and without TSA/epoxy coatings, were conducted in recirculated, aerated, and synthetic seawater at 90 °C for 90 days. The tests were carried out at both the free corrosion potentials and an applied cathodic potential of -1100 mV saturated calomel electrode. The acidity (pH) of the test solution was monitored daily and adjusted to between pH 7.5 and 8.1, using dilute HCl solution or dilute NaOH, depending on the pH of the solution measured during the test. The test results demonstrated that TSA prevented pitting and crevice corrosion of 25% Cr SDSS in artificial seawater at 90 °C, even when 10-mm-diameter coating defect exposing the underlying steel was present.

Wave field features of shallow vertical discontinuity and their application in non-destructive detection

USGS Publications Warehouse

Liu, J.; Xia, J.; Luo, Y.; Chen, C.; Li, X.; Huang, Y.

2007-01-01

The geotechnical integrity of critical infrastructure can be seriously compromised by the presence of fractures or crevices. Non-destructive techniques to accurately detect fractures in critical infrastructure such as dams and highways could be of significant benefit to the geotechnical industry. This paper investigates the application of shallow seismic and georadar methods to the detection of a vertical discontinuity using numerical simulations. The objective is to address the kinematical analysis of a vertical discontinuity, determine the resulting wave field characteristics, and provide the basis for determining the existence of vertical discontinuities based on the recorded signals. Simulation results demonstrate that: (1) A reflection from a vertical discontinuity produces a hyperbolic feature on a seismic or georadar profile; (2) In order for a reflection from a vertical discontinuity to be produced, a reflecting horizon below the discontinuity must exist, the offset between source and receiver (x0) must be non-zero, on the same side of the vertical discontinuity; (3) The range of distances from the vertical discontinuity where a reflection event is observed is proportional to its length and to x0; (4) Should the vertical crevice (or fracture) pass through a reflecting horizon, dual hyperbolic features can be observed on the records, and this can be used as a determining factor that the vertical crevice passes through the interface; and (5) diffractions from the edges of the discontinuity can be recorded with relatively smaller amplitude than reflections and their ranges are not constrained by the length of discontinuity. If the length of discontinuity is short enough, diffractions are the dominant feature. Real-world examples show that the shallow seismic reflection method and the georadar method are capable of recording the hyperbolic feature, which can be interpreted as vertical discontinuity. Thus, these methods show some promise as effective non-destructive detection methods for locating vertical discontinuities (e.g., fractures or crevices) in infrastructure such as dams and highway pavement. ?? 2007 Elsevier B.V. All rights reserved.

The A-chain of insulin contacts the insert domain of the insulin receptor. Photo-cross-linking and mutagenesis of a diabetes-related crevice.

PubMed

Huang, Kun; Chan, Shu Jin; Hua, Qing-xin; Chu, Ying-Chi; Wang, Run-ying; Klaproth, Birgit; Jia, Wenhua; Whittaker, Jonathan; De Meyts, Pierre; Nakagawa, Satoe H; Steiner, Donald F; Katsoyannis, Panayotis G; Weiss, Michael A

2007-11-30

The contribution of the insulin A-chain to receptor binding is investigated by photo-cross-linking and nonstandard mutagenesis. Studies focus on the role of Val(A3), which projects within a crevice between the A- and B-chains. Engineered receptor alpha-subunits containing specific protease sites ("midi-receptors") are employed to map the site of photo-cross-linking by an analog containing a photoactivable A3 side chain (para-azido-Phe (Pap)). The probe cross-links to a C-terminal peptide (residues 703-719 of the receptor A isoform, KTFEDYLHNVVFVPRPS) containing side chains critical for hormone binding (underlined); the corresponding segment of the holoreceptor was shown previously to cross-link to a Pap(B25)-insulin analog. Because Pap is larger than Val and so may protrude beyond the A3-associated crevice, we investigated analogs containing A3 substitutions comparable in size to Val as follows: Thr, allo-Thr, and alpha-aminobutyric acid (Aba). Substitutions were introduced within an engineered monomer. Whereas previous studies of smaller substitutions (Gly(A3) and Ser(A3)) encountered nonlocal conformational perturbations, NMR structures of the present analogs are similar to wild-type insulin; the variant side chains are accommodated within a native-like crevice with minimal distortion. Receptor binding activities of Aba(A3) and allo-Thr(A3) analogs are reduced at least 10-fold; the activity of Thr(A3)-DKP-insulin is reduced 5-fold. The hormone-receptor interface is presumably destabilized either by a packing defect (Aba(A3)) or by altered polarity (allo-Thr(A3) and Thr(A3)). Our results provide evidence that Val(A3), a site of mutation causing diabetes mellitus, contacts the insert domain-derived tail of the alpha-subunit in a hormone-receptor complex.

Thermoregulatory challenges in the habitat of the world's smallest tortoise, Chersobius signatus.

PubMed

Loehr, Victor J T

2018-01-01

Ectotherms have various means of dealing with low environmental temperatures, but relatively few species have been rigorously investigated. Consequently, we have little information to predict how ectotherm populations might respond to global temperature changes. Tortoises from temperate and subtropical regions often overcome periodically cool conditions by hibernation, but speckled dwarf tortoises (Chersobius signatus) need to remain active to exploit ephemeral resources in their arid winter-rainfall habitat. This study investigated how dwarf tortoises cope with low temperatures in winter and spring, by measuring thermal habitat quality and thermoregulation based on differently-sized operative temperature models in sun, shade, and in deep crevices. Investigations continued in summer and autumn to obtain a year-round picture of thermoregulatory challenges. Although large models (i.e., larger than dwarf tortoises) were expected to have lower operative temperatures than smaller models, due to the former's larger thermal inertia, all model sizes had similar temperatures. Hence, the species' small body size does not appear constrained by obtainable body temperatures in cool seasons. Nevertheless, low operative temperatures in winter posed a challenge for the tortoises, which reached their field-preferred body temperature for an average of only 0.8-0.9h per day. Moreover, a low thermoregulation effectiveness suggested that tortoises traded-off physiological benefits of favourable body temperatures against predation risk. Spring and autumn provided higher temperatures, but summer caused the greatest thermoregulatory challenge. Although summer body temperatures were closer to field-preferred body temperature than in any other season, tortoises required rock crevices to avoid overheating. The small size of dwarf tortoises might help them utilise crevices. In summer, maximum operative temperatures in crevices were similar to field-preferred body temperature, indicating that an increase in environmental temperatures might be detrimental to dwarf tortoises. In light of projected temperature rises, future studies should assess if dwarf tortoises can cope with higher environmental temperatures in summer. Copyright © 2017 Elsevier Ltd. All rights reserved.

Possibilities of fish passage through the block ramp: Model-based estimation of permeability.

PubMed

Plesiński, Karol; Bylak, Aneta; Radecki-Pawlik, Artur; Mikołajczyk, Tomasz; Kukuła, Krzysztof

2018-08-01

Block ramps offer an opportunity to combine hydrotechnical structures with fish passages. The primary study objective was to evaluate the effectiveness of a block ramp for upstream fish movement in a mountain stream. Geodetic measurements of the bottom surface and water level were taken for three cross-sections. The description of the geometric and hydrodynamic parameters of the block ramp was supplemented with information on the width and length of crevices between boulders. Measurements of the geometric and hydrodynamic parameters of the block ramp were performed at 76 measurement sites, at three different types of discharge. Ichthyological data were collected in the analyzed stream. Measurements covered among others total length, width, and height of caught fish. Salmonid, cottid, balitorid, and cyprinid fish were studied. The determination of the main effects of the geometric and hydrodynamic parameters of the block ramp on the possibilities of use by target fish species employed generalized linear models (GLMs). The study shows that the block ramp cannot provide longitudinal connectivity and migration of fish occurring in the mountain stream. According to estimates, the block ramp did not meet the permeability expectations. The reason for low usefulness of the ramp for fish is particularly excessively strong water current. The stream concentration constituted an unsurmountable velocity barrier for fish moving upstream for each of the analyzed discharges. The developed model suggests that some crevices in the side zones of the ramp could be parts of the migration corridor, but only for small and medium-sized fish. At medium and high water stages, movement of fish in crevices was difficult due to fast water current, and at low and very low discharges, some crevices lost their permeability, and could become ecological traps for fish. The necessity of estimation of ramp permeability during pre-construction phase was emphasized. Copyright © 2018 Elsevier B.V. All rights reserved.

Investigation of Stainless Steel Corrosion in Ultrahigh-Purity Water and Steam Systems by Surface Analytical Techniques

NASA Astrophysics Data System (ADS)

Dong, Xia; Iacocca, Ronald G.; Bustard, Bethany L.; Kemp, Craig A. J.

2010-02-01

Stainless steel pipes with different degrees of rouging and a Teflon®-coated rupture disc with severe corrosion were thoroughly investigated by combining multiple surface analytical techniques. The surface roughness and iron oxide layer thickness increase with increasing rouge severity, and the chromium oxide layer coexists with the iron oxide layer in samples with various degrees of rouging. Unlike the rouging observed for stainless steel pipes, the fast degradation of the rupture disc was caused by a crevice corrosion environment created by perforations in the protective Teflon coating. This failure analysis clearly shows the highly corrosive nature of ultrapure water used in the manufacture of pharmaceutical products, and demonstrates some of the unexpected corrosion mechanisms that can be encountered in these environments.

Ants learn to rely on more informative attributes during decision-making.

PubMed

Sasaki, Takao; Pratt, Stephen C

2013-01-01

Evolutionary theory predicts that animals act to maximize their fitness when choosing among a set of options, such as what to eat or where to live. Making the best choice is challenging when options vary in multiple attributes, and animals have evolved a variety of heuristics to simplify the task. Many of these involve ranking or weighting attributes according to their importance. Because the importance of attributes can vary across time and place, animals might benefit by adjusting weights accordingly. Here, we show that colonies of the ant Temnothorax rugatulus use their experience during nest site selection to increase weights on more informative nest attributes. These ants choose their rock crevice nests on the basis of multiple features. After exposure to an environment where only one attribute differentiated options, colonies increased their reliance on this attribute relative to a second attribute. Although many species show experience-based changes in selectivity based on a single feature, this is the first evidence in animals for adaptive changes in the weighting of multiple attributes. These results show that animal collectives, like individuals, change decision-making strategies according to experience. We discuss how these colony-level changes might emerge from individual behaviour.

A new finding on the in-vivo crevice corrosion damage in a CoCrMo hip implant.

PubMed

Oskouei, Reza H; Barati, Mohammad Reza; Farhoudi, Hamidreza; Taylor, Mark; Solomon, Lucian Bogdan

2017-10-01

A detailed investigation was performed to characterize the fretting wear and corrosion damage to the neck component of a CoCrMo stem from a metal-on-polyethylene implant retrieved after 99months. The stem was a low-carbon (0.07wt%) wrought Co-28Cr-6Mo alloy with no secondary carbide phases in the matrix (γ-phase). The original design of the neck surface contained an intentionally fabricated knurled profile with a valley-to-peak range of approximately 11μm. Roughness measurements indicated that the tip of the knurled profile was significantly damaged, especially in the distal medial region of the neck, with up to a 22% reduction in the mean peak-to-valley height (R a ) compared to the original profile. As a new finding, the channels between the peaks of the profile created an additional crevice site in the presence of stagnant body fluid within the head-neck taper junction. These channels were observed to contain the most severe corroded areas and surface oxide layers with micro-cracks. SEM/EDS, XRD and XPS evaluations identified the formation of Cr 2 O 3 as a corrosion product. Also, decobaltification was found to occur in these corroded areas. The findings of this work indicate the important role of the knurled profile in inducing additional crevice corrosion. Copyright © 2017 Elsevier B.V. All rights reserved.

Structure and dynamics of protein waters revealed by radiolysis and mass spectrometry

PubMed Central

Gupta, Sayan; D’Mello, Rhijuta; Chance, Mark R.

2012-01-01

Water is critical for the structure, stability, and functions of macromolecules. Diffraction and NMR studies have revealed structure and dynamics of bound waters at atomic resolution. However, localizing the sites and measuring the dynamics of bound waters, particularly on timescales relevant to catalysis and macromolecular assembly, is quite challenging. Here we demonstrate two techniques: first, temperature-dependent radiolytic hydroxyl radical labeling with a mass spectrometry (MS)-based readout to identify sites of bulk and bound water interactions with surface and internal residue side chains, and second, H218O radiolytic exchange coupled MS to measure the millisecond dynamics of bound water interactions with various internal residue side chains. Through an application of the methods to cytochrome c and ubiquitin, we identify sites of water binding and measure the millisecond dynamics of bound waters in protein crevices. As these MS-based techniques are very sensitive and not protein size limited, they promise to provide unique insights into protein–water interactions and water dynamics for both small and large proteins and their complexes. PMID:22927377

Development of sustained release antipsychotic tablets using novel polysaccharide isolated from Delonix regia seeds and its pharmacokinetic studies

PubMed Central

Krishnaraj, Kaliaperumal; Chandrasekar, Mulla Joghi Nanjan; Nanjan, Mulla Joghi; Muralidharan, Selvadurai; Manikandan, Duraikannu

2011-01-01

A natural polysaccharide was isolated from the seeds of Delonix regia. The isolated polysaccharide could maintain aqueous equilibrium between the dosage form and the surrounding medium due to its massive competence of water absorption (80.72%) and swelling index (266.7%). The Scanning Electron Micrograph of a polysaccharide exhibits rough surface with pores and crevices, hence, the drug release will be retarded because of the drug particles entrapment in the pores and crevices. Further, the surface tension of polysaccharide is higher than that of water, which may facilitate sustained release of drugs from dosage forms. An antipsychotic drug, quetiapine fumarate has a short half-life of 6 h and administered multiple times per day. Hence the quetiapine fumarate oral sustained release tablets were formulated using this polysaccharide in the concentration of 5–30% to avoid the side effects and increase patient compliance. Dissolution of the developed tablets with 25% polysaccharide content showed a better release profile than the other batches (5–20%) at the end of 12 h. The strong matrix complex has low solubility in water, it does not dissolve rapidly and the drug continues to diffuse through the gel layer at a consistent rate. Drug release from the matrix tablets follows matrix type except F-4 and F-5 which follow first order and Hix.crow type. The bioavailability study was carried out using healthy male New Zealand white rabbits that show the AUC(0–inf) value for developed SR tablets is 1.44 times higher than the reference thus, indicating more efficient and sustained drug delivery capable of maintaining plasma drug levels better. PMID:24115903

40 CFR 144.3 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... facility” Improved sinkhole means a naturally occurring karst depression or other natural crevice found in... the Administrator under the “appropriate Act and regulations.” Major facility means any UIC “facility...

Influence of the Supramolecular Micro-Assembly of Multiple Emulsions on their Biopharmaceutical Features and In vivo Therapeutic Response.

PubMed

Cilurzo, Felisa; Cristiano, Maria Chiara; Di Marzio, Luisa; Cosco, Donato; Carafa, Maria; Ventura, Cinzia Anna; Fresta, Massimo; Paolino, Donatella

2015-01-01

The ability of some surfactants to self-assemble in a water/oil bi-phase environment thus forming supramolecular structure leading to the formation of w/o/w multiple emulsions was investigated. The w/o/w multiple emulsions obtained by self-assembling (one-step preparation method) were compared with those prepared following the traditional two-step procedure. Methyl-nicotinate was used as a hydrophilic model drug. The formation of the multiple emulsion structure was evidenced by optical microscopy, which showed a mean size of the inner oil droplets of 6 μm and 10 μm for one-step and two-step multiple emulsions, respectively. The in vitrobiopharmaceutical features of the various w/o/w multiple emulsion formulations were evaluated by means of viscosimetry studies, drug release and in vitro percutaneous permeation experiments through human stratum corneum and viable epidermis membranes. The self-assembled multiple emulsions allowed a more gradual percutaneous permeation (a zero-order permeation rate) than the two-step ones. The in vivotopical carrier properties of the two different multiple emulsions were evaluated on healthy human volunteers by using the spectrophotometry of reflectance, an in vivonon invasive method. These multiple emulsion systems were also compared with conventional emulsion formulations. Our findings demonstrated that the multiple emulsions obtained by self-assembling were able to provide a more sustained drug delivery into the skin and hence a longer therapeutic action than two-step multiple emulsions and conventional emulsion formulations. Finally, our findings showed that the supramolecular micro-assembly of multiple emulsions was able to influence not only the biopharmaceutical characteristics but also the potential in vivotherapeutic response.

How Dangerous Can Localized Corrosion Be? An Experiment that Studies Its Effects.

ERIC Educational Resources Information Center

Celdran, R.; Gonzalo, P.

1988-01-01

Considers three common cases of localized corrosion of metals: pitting, crevice, and stress corrosion. Provides experimental methods for studying all three methods. Includes a discussion of expected results. (ML)

NATURE'S WAY HS

EPA Pesticide Factsheets

Technical product bulletin: aka MICRO CLEAN or POWERCLEAN, this surface washing agent used in oil spill cleanups should be applied full strength to surfaces such as shorelines and beaches, pressure sprayed into cracks/crevices, and scrubbed well.

FINAL ANALYTICAL RESULTS FROM THE EXAMINATION OF CORROSION ON SECTIONS OF CORROSION PROBE REMOVED FROM TANK 241-AN-107 ON 08/10/2006

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

DUNCAN JB; COOKE GA

2007-03-22

Tank Farms Operations removed an electrochemical noise probe from Tank 241-AN-107. In the field, the probe was cut into four sections, wrapped, and placed in a 55-gallon drum, This drum was delivered to the 222-S Laboratory. The 222 S Laboratory unpackaged the sections of the AN-107 electrochemical noise probe and examined the material for evidence of corrosion. Each of the four sections contained three C-ring and three bullet specimens. The specimens were examined for pitting corrosion, crevice corrosion, and stress corrosion cracking. No evidence of stress corrosion cracking was found in the stressed C-ring specimens. Minor pitting was evident onmore » some surfaces. Crevice corrosion was the dominant type of corrosion observed.« less

Colony mapping: A new technique for monitoring crevice-nesting seabirds

USGS Publications Warehouse

Renner, H.M.; Renner, M.; Reynolds, J.H.; Harping, A.M.A.; Jones, I.L.; Irons, D.B.; Byrd, G.V.

2006-01-01

Monitoring populations of auklets and other crevice-nesting seabirds remains problematic, although numerous methods have been attempted since the mid-1960s. Anecdotal evidence suggests several large auklet colonies have recently decreased in both abundance and extent, concurrently with vegetation encroachment and succession. Quantifying changes in the geographical extent of auklet colonies may be a useful alternative to monitoring population size directly. We propose a standardized method for colony mapping using a randomized systematic grid survey with two components: a simple presence/absence survey and an auklet evidence density survey. A quantitative auklet evidence density index was derived from the frequency of droppings and feathers. This new method was used to map the colony on St. George Island in the southeastern Bering Sea and results were compared to previous colony mapping efforts. Auklet presence was detected in 62 of 201 grid cells (each grid cell = 2500 m2) by sampling a randomly placed 16 m2 plot in each cell; estimated colony area = 155 000 m2. The auklet evidence density index varied by two orders of magnitude across the colony and was strongly correlated with means of replicated counts of birds socializing on the colony surface. Quantitatively mapping all large auklet colonies is logistically feasible using this method and would provide an important baseline for monitoring colony status. Regularly monitoring select colonies using this method may be the best means of detecting changes in distribution and population size of crevice-nesting seabirds. ?? The Cooper Ornithological Society 2006.

Corrosion behavior of 2205 duplex stainless steel.

PubMed

Platt, J A; Guzman, A; Zuccari, A; Thornburg, D W; Rhodes, B F; Oshida, Y; Moore, B K

1997-07-01

The corrosion of 2205 duplex stainless steel was compared with that of AISI type 316L stainless steel. The 2205 stainless steel is a potential orthodontic bracket material with low nickel content (4 to 6 wt%), whereas the 316L stainless steel (nickel content: 10 to 14 wt%) is a currently used bracket material. Both stainless steels were subjected to electrochemical and immersion (crevice) corrosion tests in 37 degrees C, 0.9 wt% sodium chloride solution. Electrochemical testing indicates that 2205 has a longer passivation range than 316L. The corrosion rate of 2205 was 0.416 MPY (milli-inch per year), whereas 316L exhibited 0.647 MPY. When 2205 was coupled to 316L with equal surface area ratio, the corrosion rate of 2205 reduced to 0.260 MPY, indicating that 316L stainless steel behaved like a sacrificial anode. When 316L is coupled with NiTi, TMA, or stainless steel arch wire and was subjected to the immersion corrosion test, it was found that 316L suffered from crevice corrosion. On the other hand, 2205 stainless steel did not show any localized crevice corrosion, although the surface of 2205 was covered with corrosion products, formed when coupled to NiTi and stainless steel wires. This study indicates that considering corrosion resistance, 2205 duplex stainless steel is an improved alternative to 316L for orthodontic bracket fabrication when used in conjunction with titanium, its alloys, or stainless steel arch wires.

Measuring the Multiplication of Spent Fuel Assemblies – It’s easier than you think!

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

Tobin, Stephen Joseph

This is a set of eight slides which advertise how easy it can be to measure the multiplication of a spent fuel assembly. A robust (fission chambers), rapid (under 15 minutes), direct (multiplication is measured, not photons from fission fragments) measurement of multiplication is possible.

Integrating genome assemblies with MAIA

PubMed Central

Nijkamp, Jurgen; Winterbach, Wynand; van den Broek, Marcel; Daran, Jean-Marc; Reinders, Marcel; de Ridder, Dick

2010-01-01

Motivation: De novo assembly of a eukaryotic genome with next-generation sequencing data is still a challenging task. Over the past few years several assemblers have been developed, often suitable for one specific type of sequencing data. The number of known genomes is expanding rapidly, therefore it becomes possible to use multiple reference genomes for assembly projects. We introduce an assembly integrator that makes use of all available data, i.e. multiple de novo assemblies and mappings against multiple related genomes, by optimizing a weighted combination of criteria. Results: The developed algorithm was applied on the de novo sequencing of the Saccharomyces cerevisiae CEN.PK 113-7D strain. Using Solexa and 454 read data, two de novo and three comparative assemblies were constructed and subsequently integrated, yielding 29 contigs, covering more than 12 Mbp; a drastic improvement compared with the single assemblies. Availability: MAIA is available as a Matlab package and can be downloaded from http://bioinformatics.tudelft.nl Contact: j.f.nijkamp@tudelft.nl PMID:20823304

5 CFR 532.279 - Special wage schedules for printing positions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... Opaquer 4 Offset Press Helper 5 Bindery Machine Operator (Helper) 5 Film Assembler-Stripper (Single Flat-Single Color) 5 Platemaker (Single Color) 5 Film Assembler-Stripper (Partial and Composite Flats) 7... Cutter) 8 Bindery Machine Operator (Power Folder) 8 Film Assembler-Stripper (Multiple Flat-Multiple Color...

5 CFR 532.279 - Special wage schedules for printing positions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... Opaquer 4 Offset Press Helper 5 Bindery Machine Operator (Helper) 5 Film Assembler-Stripper (Single Flat-Single Color) 5 Platemaker (Single Color) 5 Film Assembler-Stripper (Partial and Composite Flats) 7... Cutter) 8 Bindery Machine Operator (Power Folder) 8 Film Assembler-Stripper (Multiple Flat-Multiple Color...

40 CFR 180.513 - Chlorfenapyr; tolerances for residues.

Code of Federal Regulations, 2011 CFR

2011-07-01

... greater than a 0.5% active ingredient solution for spot crack and crevice use in food/feed handling.... Application excludes any direct application to any food, food packaging, or any food contact surfaces. (v) To...

Tandem mobile robot system

DOEpatents

Buttz, James H.; Shirey, David L.; Hayward, David R.

2003-01-01

A robotic vehicle system for terrain navigation mobility provides a way to climb stairs, cross crevices, and navigate across difficult terrain by coupling two or more mobile robots with a coupling device and controlling the robots cooperatively in tandem.

Multicriteria Analysis of Assembling Buildings from Steel Frame Structures

NASA Astrophysics Data System (ADS)

Miniotaite, Ruta

2017-10-01

Steel frame structures are often used in the construction of public and industrial buildings. They are used for: all types of slope roofs; walls of newly-built public and industrial buildings; load bearing structures; roofs of renovated buildings. The process of assembling buildings from steel frame structures should be analysed as an integrated process influenced by such factors as construction materials and machinery used, the qualification level of construction workers, complexity of work, available finance. It is necessary to find a rational technological design solution for assembling buildings from steel frame structures by conducting a multiple criteria analysis. The analysis provides a possibility to evaluate the engineering considerations and find unequivocal solutions. The rational alternative of a complex process of assembling buildings from steel frame structures was found through multiple criteria analysis and multiple criteria evaluation. In multiple criteria evaluation of technological solutions for assembling buildings from steel frame structures by pairwise comparison method the criteria by significance are distributed as follows: durability is the most important criterion in the evaluation of alternatives; the price (EUR/unit of measurement) of a part of assembly process; construction workers’ qualification level (category); mechanization level of a part of assembling process (%), and complexity of assembling work (in points) are less important criteria.

The Influence of Contamination and Cleaning on the Strength of Modular Head Taper Fixation in Total Hip Arthroplasty.

PubMed

Krull, Annika; Morlock, Michael M; Bishop, Nicholas E

2017-10-01

Intraoperative interface contamination of modular head-stem taper junctions of hip implants can lead to poor fixation strength, causing fretting and crevice corrosion or even stem taper fracture. Careful cleaning before assembly should help to reduce these problems. The purpose of this study was to determine the effect of cleaning (with and without drying) contaminated taper interfaces on the taper fixation strength. Metal or ceramic heads were impacted onto titanium alloy stem tapers with cleaned or contaminated (fat or saline solution) interfaces. The same procedure was performed after cleaning and drying the contaminated interfaces. Pull-off force was used to determine the influence of contamination and cleaning on the taper strength. Pull-off forces after contamination with fat were significantly lower than those for uncontaminated interfaces for both head materials. Pull-off forces after application of saline solution were not significantly different from those for uncontaminated tapers. However, a large variation in taper strength was observed, pull-off forces for cleaned and dried tapers were similar to those for uncontaminated tapers for both head materials. Intraoperative contamination of taper interfaces may be difficult to detect but has a major influence on taper fixation strength. Cleaning of the stem taper with saline solution and drying with gauze directly before assembly allows the taper strength of the pristine components to be achieved. Not drying the taper results in a large variation in pull-off forces, emphasizing that drying is essential for sufficient and reproducible fixation strength. Copyright © 2017 Elsevier Inc. All rights reserved.

33 CFR 159.121 - Sewage processing test.

Code of Federal Regulations, 2010 CFR

2010-07-01

... crevices that could come in contact with a person using the device or servicing the device in accordance..., the device must be tilted to the maximum angles specified by the manufacturer under §§ 159.55 and 159...

Friction enhancement in concertina locomotion of snakes

PubMed Central

Marvi, Hamidreza; Hu, David L.

2012-01-01

Narrow crevices are challenging terrain for most organisms and biomimetic robots. Snakes move through crevices using sequential folding and unfolding of their bodies in the manner of an accordion or concertina. In this combined experimental and theoretical investigation, we elucidate this effective means of moving through channels. We measure the frictional properties of corn snakes, their body kinematics and the transverse forces they apply to channels of varying width and inclination. To climb channels inclined at 60°, we find snakes use a combination of ingenious friction-enhancing techniques, including digging their ventral scales to double their frictional coefficient and pushing channel walls transversely with up to nine times body weight. Theoretical modelling of a one-dimensional n-linked crawler is used to calculate the transverse force factor of safety: we find snakes push up to four times more than required to prevent sliding backwards, presumably trading metabolic energy for an assurance of wall stability. PMID:22728386

Susceptibility of steam generator tubes in secondary conditions: Effects of lead and sulphate

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

Gomez Briceno, D.; Garcia, M.S.; Castano, M.L.

1997-02-01

IGA/SCC on the secondary side of steam generators is increasing every year, and represents the cause of some steam generator replacements. Until recently, caustic and acidic environments have been accepted as causes of IGA/SCC, particulary in certain environments: in sludge pile on the tube sheet; at support crevices; in free span. Lead and sulfur have been identified as significant impurities. Present thoughts are that some IGA/SCC at support crevices may have occurred in nearly neutral or mildly alkaline environments. Here the authors present experimental work aimed at studying the influence of lead and sulfur on the behaviour of steam generatormore » tube alloys in different water environments typical of steam generators. Most test results ran for at least 2000 hours, and involved visual and detailed surface analysis during and following the test procedures.« less

Friction enhancement in concertina locomotion of snakes.

PubMed

Marvi, Hamidreza; Hu, David L

2012-11-07

Narrow crevices are challenging terrain for most organisms and biomimetic robots. Snakes move through crevices using sequential folding and unfolding of their bodies in the manner of an accordion or concertina. In this combined experimental and theoretical investigation, we elucidate this effective means of moving through channels. We measure the frictional properties of corn snakes, their body kinematics and the transverse forces they apply to channels of varying width and inclination. To climb channels inclined at 60°, we find snakes use a combination of ingenious friction-enhancing techniques, including digging their ventral scales to double their frictional coefficient and pushing channel walls transversely with up to nine times body weight. Theoretical modelling of a one-dimensional n-linked crawler is used to calculate the transverse force factor of safety: we find snakes push up to four times more than required to prevent sliding backwards, presumably trading metabolic energy for an assurance of wall stability.

Halogen-Enriched Fragment Libraries as Leads for Drug Rescue of Mutant p53

PubMed Central

2012-01-01

The destabilizing p53 cancer mutation Y220C creates a druggable surface crevice. We developed a strategy exploiting halogen bonding for lead discovery to stabilize the mutant with small molecules. We designed halogen-enriched fragment libraries (HEFLibs) as starting points to complement classical approaches. From screening of HEFLibs and subsequent structure-guided design, we developed substituted 2-(aminomethyl)-4-ethynyl-6-iodophenols as p53-Y220C stabilizers. Crystal structures of their complexes highlight two key features: (i) a central scaffold with a robust binding mode anchored by halogen bonding of an iodine with a main-chain carbonyl and (ii) an acetylene linker, enabling the targeting of an additional subsite in the crevice. The best binders showed induction of apoptosis in a human cancer cell line with homozygous Y220C mutation. Our structural and biophysical data suggest a more widespread applicability of HEFLibs in drug discovery. PMID:22439615

Polycrystalline and Mesoporous 3-D Bi2O3 Nanostructured Negatrodes for High-Energy and Power-Asymmetric Supercapacitors: Superfast Room-Temperature Direct Wet Chemical Growth.

PubMed

Shinde, Nanasaheb M; Xia, Qi Xun; Yun, Je Moon; Mane, Rajaram S; Kim, Kwang Ho

2018-04-04

Superfast (≤10 min) room-temperature (300 K) chemical synthesis of three-dimensional (3-D) polycrystalline and mesoporous bismuth(III) oxide (Bi 2 O 3 ) nanostructured negatrode (as an abbreviation of negative electrode) materials, viz., coconut shell, marigold, honey nest cross section and rose with different surface areas, charge transfer resistances, and electrochemical performances essential for energy storage, harvesting, and even catalysis devices, are directly grown onto Ni foam without and with poly(ethylene glycol), ethylene glycol, and ammonium fluoride surfactants, respectively. Smaller diffusion lengths, caused by the involvement of irregular crevices, allow electrolyte ions to infiltrate deeply, increasing the utility of inner active sites for the following electrochemical performance. A marigold 3-D Bi 2 O 3 electrode of 58 m 2 ·g -1 surface area has demonstrated a specific capacitance of 447 F·g -1 at 2 A·g -1 and chemical stability of 85% even after 5000 redox cycles at 10 A·g -1 in a 6 M KOH electrolyte solution, which were higher than those of other morphology negatrode materials. An asymmetric supercapacitor (AS) device assembled with marigold Bi 2 O 3 negatrode and manganese(II) carbonate quantum dots/nickel hydrogen-manganese(II)-carbonate (MnCO 3 QDs/NiH-Mn-CO 3 ) positrode corroborates as high as 51 Wh·kg -1 energy at 1500 W·kg -1 power and nearly 81% cycling stability even after 5000 cycles. The obtained results were comparable or superior to the values reported previously for other Bi 2 O 3 morphologies. This AS assembly glowed a red-light-emitting diode for 20 min, demonstrating the scientific and industrial credentials of the developed superfast Bi 2 O 3 nanostructured negatrodes in assembling various energy storage devices.

Chlorpyrifos accumulation patterns for child-accessible surfaces and objects and urinary metabolite excretion by children for 2 weeks after crack-and-crevice application.

PubMed

Hore, Paromita; Robson, Mark; Freeman, Natalie; Zhang, Jim; Wartenberg, Daniel; Ozkaynak, Halûk; Tulve, Nicolle; Sheldon, Linda; Needham, Larry; Barr, Dana; Lioy, Paul J

2005-02-01

The Children's Post-Pesticide Application Exposure Study (CPPAES) was conducted to look at the distribution of chlorpyrifos within a home environment for 2 weeks after a routine professional crack-and-crevice application and to determine the amount of the chlorpyrifos that is absorbed by a child living within the home. Ten residential homes with a 2- to 5-year-old child in each were selected for study, and the homes were treated with chlorpyrifos. Pesticide measurements were made from the indoor air, indoor surfaces, and plush toys. In addition, periodic morning urine samples were collected from each of the children throughout the 2-week period. We analyzed the urine samples for 3,5,6-trichloropyridinol, the primary urinary metabolite of chlorpyrifos, and used the results to estimate the children's absorbed dose. Average chlorpyrifos levels in the indoor air and surfaces were 26 (pretreatment)/120 (posttreatment) ng/m3 and 0.48 (pretreatment)/2.8 (posttreatment) ng/cm2, respectively, reaching peak levels between days 0 and 2; subsequently, concentrations decreased throughout the 2-week period. Chlorpyrifos in/on the plush toys ranged from 7.3 to 1,949 ng/toy postapplication, with concentrations increasing throughout the 2-week period, demonstrating a cumulative adsorption/absorption process indoors. The daily amount of chlorpyrifos estimated to be absorbed by the CPPAES children postapplication ranged from 0.04 to 4.8 microg/kg/day. During the 2 weeks after the crack-and-crevice application, there was no significant increase in the amount of chlorpyrifos absorbed by the CPPAES children.

A 2650-year-long record of environmental change from northern Yellowstone National Park based on a comparison of multiple proxy data

USGS Publications Warehouse

Whitlock, C.; Dean, W.; Rosenbaum, J.; Stevens, L.; Fritz, S.; Bracht, B.; Power, M.

2008-01-01

Geochemical, stable-isotope, pollen, charcoal, and diatom records were analyzed at high-resolution in cores obtained from Crevice Lake, a varved-sediment lake in northern Yellowstone National Park. The objective was to reconstruct the ecohydrologic, vegetation, and fire history of the watershed for the last 2650 years to better understand past climate variations at the forest-steppe transition. The data suggest a period of limited bottom-water anoxia, relatively wet winters, and cool springs and summers from 2650 to 2100 cal yr BP (700-150 BC). Dry warm conditions occurred between 2100 and 850-800 cal yr BP (150 BC and AD 1100-1150), when the lake was anoxic, winter precipitation was low, and summer stratification was protracted. The data are consistent with overall warmer/drier conditions during the Medieval Climate Anomaly, although they suggest a shift towards wetter winters within that period. The period from 850 to 800 cal yr BP (AD 1100-1150) to 250 cal yr BP (AD 1700) was characterized by greater water-column mixing and cooler spring/summer conditions than before. In addition, fire activity shifted towards infrequent large events and pollen production was low. From 250 to 150 cal yr BP (AD 1700-1800), winter precipitation was moderate compared to previous conditions, and the lake was again stratified, suggesting warm summers. Between 150 and 42 cal yr BP (AD 1800-1908), winter precipitation increased and spring and summer conditions became moderate. Metal pollution, probably from regional mining operations, is evident in the 1870s. Large fires occurred between ca. 1800-1880, but in general the forests were more closed than before. The Crevice Lake record suggests that the last 150 years of Yellowstone's environmental history were characterized by intermediate conditions when compared with the previous 2500 years. ?? 2007 Elsevier Ltd and INQUA.

R102Q mutation shifts the salt-bridge network and reduces the structural flexibility of human neuronal calcium sensor-1 protein.

PubMed

Zhu, Yuzhen; Wu, Ying; Luo, Yin; Zou, Yu; Ma, Buyong; Zhang, Qingwen

2014-11-20

Neuronal calcium sensor-1 (NCS-1) protein has a variety of different neuronal functions and interacts with multiple binding partners mostly through a large solvent-exposed hydrophobic crevice (HC). A single R102Q mutation in human NCS-1 protein was demonstrated to be associated with autism disease. Solution NMR study reported that this R102Q mutant had long-range chemical shift effects on the HC and the C-terminal tail (L3). To understand the influence of the R102Q mutation on the HC and L3 of NCS-1, we have investigated the conformational dynamics and the structural flexibility of wild type (WT) NCS-1 and its R102Q mutant by conducting extensive all-atom molecular dynamics (MD) simulations. On the basis of six independent 450 ns MD simulations, we have found that the R102Q mutation in NCS-1 protein (1) dramatically reduces the flexibility of loops L2 and L3, (2) facilitates L3 in a more extended state to occupy the hydrophobic crevice to a larger extent, (3) significantly affects the intersegment salt bridges, and (4) changes the subspace of the free energy landscape of NCS-1 protein. Analysis of the salt bridge network in both WT and the R102Q variant demonstrates that the R102Q-mutation-induced salt bridge alternations play a critical role on the reduced flexibility of L2 and L3. These results reveal the important role of salt bridges on the structural properties of NCS-1 protein and that R102Q mutation disables the dynamic relocation of C-terminus, which may block the binding of NCS-1 protein to its receptors. This study may provide structural insights into the autistic spectrum disorder associated with R102Q mutation.

MOVEMENT AND DEPOSITION OF PESTICIDES WITHIN RESIDENCES AFTER INTERIOR AND EXTERIOR APPLICATIONS

EPA Science Inventory

In a study begun in 1999, the Environmental Protection Agency (EPA) investigated the temporal and spatial distributions of pesticides applied by homeowners and commercial applicators for indoor crack and crevice and exterior perimeter treatments. In each participating househol...

Effects of Corrosion and Fatigue on the Load-Carrying Capacity of Structural and Reinforcing Steel

DOT National Transportation Integrated Search

1994-03-01

Pitting and crevice corrosion have profound effects on the fatigue life of structural and reinforcing steels used in bridge construction. Stress concentration factors were measured on actual corroded plates with strain gage instrumentation. Using cor...

Chlorpyrifos Accumulation Patterns for Child-Accessible Surfaces and Objects and Urinary Metabolite Excretion by Children for 2 Weeks after Crack-and-Crevice Application

PubMed Central

Hore, Paromita; Robson, Mark; Freeman, Natalie; Zhang, Jim; Wartenberg, Daniel; Özkaynak, Halûk; Tulve, Nicolle; Sheldon, Linda; Needham, Larry; Barr, Dana; Lioy, Paul J.

2005-01-01

The Children’s Post-Pesticide Application Exposure Study (CPPAES) was conducted to look at the distribution of chlorpyrifos within a home environment for 2 weeks after a routine professional crack-and-crevice application and to determine the amount of the chlorpyrifos that is absorbed by a child living within the home. Ten residential homes with a 2- to 5-year-old child in each were selected for study, and the homes were treated with chlorpyrifos. Pesticide measurements were made from the indoor air, indoor surfaces, and plush toys. In addition, periodic morning urine samples were collected from each of the children throughout the 2-week period. We analyzed the urine samples for 3,5,6-trichloropyridinol, the primary urinary metabolite of chlorpyrifos, and used the results to estimate the children’s absorbed dose. Average chlorpyrifos levels in the indoor air and surfaces were 26 (pretreatment)/120 (posttreatment) ng/m3 and 0.48 (pretreatment)/2.8 (posttreatment) ng/cm2, respectively, reaching peak levels between days 0 and 2; subsequently, concentrations decreased throughout the 2-week period. Chlorpyrifos in/on the plush toys ranged from 7.3 to 1,949 ng/toy postapplication, with concentrations increasing throughout the 2-week period, demonstrating a cumulative adsorption/absorption process indoors. The daily amount of chlorpyrifos estimated to be absorbed by the CPPAES children postapplication ranged from 0.04 to 4.8 μg/kg/day. During the 2 weeks after the crack-and-crevice application, there was no significant increase in the amount of chlorpyrifos absorbed by the CPPAES children. PMID:15687060

Does the extracorporeal circulation worsen anemia in hemodialysis patients? Investigation with advanced microscopes of red blood cells drawn at the beginning and end of dialysis.

PubMed

Stamopoulos, Dimosthenis; Bakirtzi, Nerantzoula; Manios, Efthymios; Grapsa, Eirini

2013-01-01

In hemodialysis (HD) patients, anemia relates to three main factors: insufficient production of erythropoietin; impaired management of iron; and decreased lifespan of red blood cells (RBCs). The third factor can relate to structural deterioration of RBCs due to extrinsic (extracorporeal circuit; biochemical activation and/or mechanical stress during dialysis) and intrinsic (uremic milieu; biochemical interference of the RBC membrane constituents with toxins) mechanisms. Herein, we evaluate information accessed with advanced imaging techniques at the cellular level. Atomic force and scanning electron microscopes were employed to survey intact RBCs (iRBCs) of seven HD patients in comparison to seven healthy donors. The extrinsic factor was investigated by contrasting pre- and post-HD samples. The intrinsic environment was investigated by comparing the microscopy data with the clinical ones. The iRBC membranes of the enrolled HD patients were overpopulated with orifice-like (high incidence; typical size within 100-1,000 nm) and crevice-like (low incidence; typical size within 500-4,000 nm) defects that exhibited a statistically significant (P < 0.05) relative increase (+55% and +350%, respectively) in respect to healthy donors. The relative variation of the orifice and crevice indices (mean population of orifices and crevices per top membrane surface) between pre- and post-HD was not statistically significant (-3.3% and +4.5%, respectively). The orifice index correlates with the concentrations of urea, calcium, and phosphorus, but not, however, with that of creatinine. Extracorporeal circulation is not detrimental to the structural integrity of RBC membranes. Uremic milieu is a candidate cause of RBC membrane deterioration, which possibly worsens anemia.

Does the extracorporeal circulation worsen anemia in hemodialysis patients? Investigation with advanced microscopes of red blood cells drawn at the beginning and end of dialysis

PubMed Central

Stamopoulos, Dimosthenis; Bakirtzi, Nerantzoula; Manios, Efthymios; Grapsa, Eirini

2013-01-01

Background In hemodialysis (HD) patients, anemia relates to three main factors: insufficient production of erythropoietin; impaired management of iron; and decreased lifespan of red blood cells (RBCs). The third factor can relate to structural deterioration of RBCs due to extrinsic (extracorporeal circuit; biochemical activation and/or mechanical stress during dialysis) and intrinsic (uremic milieu; biochemical interference of the RBC membrane constituents with toxins) mechanisms. Herein, we evaluate information accessed with advanced imaging techniques at the cellular level. Methods Atomic force and scanning electron microscopes were employed to survey intact RBCs (iRBCs) of seven HD patients in comparison to seven healthy donors. The extrinsic factor was investigated by contrasting pre- and post-HD samples. The intrinsic environment was investigated by comparing the microscopy data with the clinical ones. Results The iRBC membranes of the enrolled HD patients were overpopulated with orifice-like (high incidence; typical size within 100–1,000 nm) and crevice-like (low incidence; typical size within 500–4,000 nm) defects that exhibited a statistically significant (P < 0.05) relative increase (+55% and +350%, respectively) in respect to healthy donors. The relative variation of the orifice and crevice indices (mean population of orifices and crevices per top membrane surface) between pre- and post-HD was not statistically significant (−3.3% and +4.5%, respectively). The orifice index correlates with the concentrations of urea, calcium, and phosphorus, but not, however, with that of creatinine. Conclusion Extracorporeal circulation is not detrimental to the structural integrity of RBC membranes. Uremic milieu is a candidate cause of RBC membrane deterioration, which possibly worsens anemia. PMID:24143093

Inhibition of dog and human gastric lipases by enantiomeric phosphonate inhibitors: a structure-activity study.

PubMed

Miled, Nabil; Roussel, Alain; Bussetta, Cécile; Berti-Dupuis, Liliane; Rivière, Mireille; Buono, Gérard; Verger, Robert; Cambillau, Christian; Canaan, Stéphane

2003-10-14

The crystal structures of gastric lipases in the apo form [Roussel, A., et al. (1999) J. Biol. Chem. 274, 16995-17002] or in complex with the (R(P))-undecyl butyl phosphonate [C(11)Y(4)(+)] [Roussel, A., et al. (2002) J. Biol. Chem. 277, 2266-2274] have improved our understanding of the structure-activity relationships of acid lipases. In this report, we have performed a kinetic study with dog and human gastric lipases (DGL and HGL, respectively) using several phosphonate inhibitors by varying the absolute configuration of the phosphorus atom and the chain length of the alkyl/alkoxy substituents. Using the two previously determined structures and that of a new crystal structure obtained with the other (S(P))-phosphonate enantiomer [C(11)Y(4)(-)], we constructed models of phosphonate inhibitors fitting into the active site crevices of DGL and HGL. All inhibitors with a chain length of fewer than 12 carbon atoms were found to be completely buried in the catalytic crevice, whereas longer alkyl/alkoxy chains were found to point out of the cavity. The main stereospecific determinant explaining the stronger inhibition of the S(P) enantiomers is the presence of a hydrogen bond involving the catalytic histidine as found in the DGL-C(11)Y(4)(-) complex. On the basis of these results, we have built a model of the first tetrahedral intermediate corresponding to the tristearoyl-lipase complex. The triglyceride molecule completely fills the active site crevice of DGL, in contrast with what is observed with other lipases such as pancreatic lipases which have a shallower and narrower active site. For substrate hydrolysis, the supply of water molecules to the active site might be achieved through a lateral channel identified in the protein core.

Measurements and mechanisms of localized aqueous corrosion in aluminum-lithium alloys

NASA Technical Reports Server (NTRS)

Buchheit, Rudolph G., Jr.; Stoner, Glenn E.

1990-01-01

Like most heat treatable aluminum alloys, localized corrosion and stress corrosion of Al-Li-Cu alloys is strongly dependent on the nature and distribution of second phase particles. To develop a mechanistic understanding of the role of localized corrosion in the stress corrosion process, bulk samples of T(sub 1) (Al2CuLi) and a range of Al-Cu-Fe impurity phases were prepared for electrochemical experiments. Potentiodynamic polarization and galvanic couple experiments were performed in standard 0.6 M NaCl and in simulated crevice solutions to assess corrosion behavior of these particles with respect to the alpha-Al matrix. A comparison of time to failure versus applied potential using a constant load, smooth bar SCC test technique in Cl(-), Cl(-)/CrO4(2-), and Cl(-)/CO3(2-) environments shows that rapid failures are to be expected when applied potentials are more positive than the breakaway potential (E sub br) of T(sub 1) (crack tip) but less than E(sub br) of alpha-Al (crack walls). It is shown that this criterion is not satisfied in aerated Cl(-) solutions. Accordingly, SCC resistance is good. This criterion is satisfied, however, in an alkaline isolated fissure exposed to a CO2 containing atmosphere. Rapid failure induced by these fissures was recently termed preexposure embrittlement. Anodic polarization shows that the corrosion behavior of T(sub 1) is relatively unaffected in alkaline CO3(2-) environments but the alpha-Al phase is rapidly passivated. X ray diffraction of crevice walls from artificial crevices suggests that passivation of alpha-Al occurs as hydrotalcite-type compound (LiAl2(OH)6)2(+) - CO3(2-) - nH2O.

Determination of the Corrosive Conditions Present within Aircraft Lap-Splice Joints

NASA Technical Reports Server (NTRS)

Lewis, Karen S.; Kelly, Robert G.; Piascik, Robert S.

1999-01-01

The complexity of airframe structure lends itself to damage resulting from crevice corrosion. Fuselage lap-splice joints are a particularly important structural detail in this regard because of the difficulty associated with detection and measurement of corrosion in these occluded regions. The objective of this work is to develop a laboratory corrosion test protocol to identify the chemistry to which lap joints are exposed and to develop a model of the corrosion within the joints. A protocol for collecting and identifying the chemistry of airframe crevice corrosion has been developed. Capillary electrophoresis (CE) is used to identify the ionic species contained in corrosion product samples removed from fuselage lap splice joints. CE analysis has been performed on over sixty corrosion product samples removed from both civilian and military aircraft. Over twenty different ions have been detected. Measurements of pH of wetted corroded surfaces indicated an alkaline occluded solution. After determining the species present and their relative concentrations, the resultant solution was reproduced in bulk and electrochemical tests were performed to determine the corrosion rate. Electrochemical analyses of the behavior of AA2024-T3 in these solutions gave corrosion rates of up to 250 microns per year (10 mpy). Additional tests have determined the relative importance of each of the detected ions in model solutions used for future predictive tests. The statistically significant ions have been used to create a second generation solution. Laboratory studies have also included exposure tests involving artificial lap joints exposed to various simulated bulk and crevice environments. The extent and morphology of the attack in artificial lap joints has been compared to studies of corroded samples from actual aircraft. Other effects, such as temperature and potential, as well as the impact of the environment on fatigue crack growth have also been studied.

MetaGenomic Assembly by Merging (MeGAMerge)

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

Scholz Chien-Chi Lo, Matthew B.

2015-08-03

"MetaGenomic Assembly by Merging" (MeGAMerge)Is a novel method of merging of multiple genomic assembly or long read data sources for assembly by use of internal trimming/filtering of data, followed by use of two 3rd party tools to merge data by overlap based assembly.

Process for producing fine and ultrafine filament superconductor wire

DOEpatents

Kanithi, H.C.

1992-02-18

A process for producing a superconductor wire made up of a large number of round monofilament rods is provided for, comprising assembling a multiplicity of round monofilaments inside each of a multiplicity of thin wall hexagonal tubes and then assembling a number of said thin wall hexagonal tubes within an extrusion can and subsequently consolidating, extruding and drawing the entire assembly down to the desired wire size. 8 figs.

Process for producing fine and ultrafine filament superconductor wire

DOEpatents

Kanithi, Hem C.

1992-01-01

A process for producing a superconductor wire made up of a large number of round monofilament rods is provided for, comprising assembling a multiplicity of round monofilaments inside each of a multiplicity of thin wall hexagonal tubes and then assembling a number of said thin wall hexagonal tubes within an extrusion can and subsequently consolidating, extruding and drawing the entire assembly down to the desired wire size.

POST-APPLICATION EXPOSURE POTENTIAL TO PESTICIDES IN THE RESIDENTIAL ENVIRONMENT

EPA Science Inventory

A study to investigate the temporal and spatial distributions of pesticides applied by homeowners and commercial applicators for indoor crack and crevice treatments was initiated by the U.S. EPA in 1999. In participating households, pre- and post-application samples of indoor ...

40 CFR 180.530 - 2,2-Dimethyl-1,3-benzodioxol-4-ol methylcarbamate; tolerances for residues.

Code of Federal Regulations, 2010 CFR

2010-07-01

... used in spot and/or crack and crevice treatments in animal feed handling establishments, including feed... insecticide 2,2-dimethyl-1,3-benzodioxol-4-yl methylcarbamate may be safely used in spot and/or crack and...

Elastomer-induced crevice corrosion and stress corrosion cracking of stainless steel heat exchanger plates in sour amine service

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

Hay, M.G.; Baron, J.J.; Moffat, T.A.

1996-08-01

Types S31600 and S31254 stainless steel heat exchanger plates have suffered crevice corrosion and stress corrosion cracking under gaskets in rich amine service in a sour gas plant. The gasket material, ethylene-propylene-diene monomer (EPDM), has been used successfully for many years at other sour gas plants. Laboratory testing has duplicated the corrosion observed and shown that the mechanism is synergistic sulfide-halide attack. The use of a bromine plus chlorine-activated curing system for the EPDM rubber gaskets provided the necessary halides. Laboratory testing identified some nickel-based superalloys which were resistant to this corrosion and also demonstrated that essentially halogen-free, peroxide-cured EPDMmore » gaskets do not cause attack of S31600 or S31254. The heat exchanger packs were replaced with S31600 plates and peroxide-cured EPDM gaskets having a specified total halogen concentration of 200 ppm maximum. Field operating experience has been excellent.« less

Fretting crevice corrosion of stainless steel stem-CoCr femoral head connections: comparisons of materials, initial moisture, and offset length.

PubMed

Gilbert, Jeremy L; Mehta, Manav; Pinder, Bryan

2009-01-01

Modular tapers continue to be used in a wide variety of orthopedic implants. In this study, stainless steel (ASTM F-1568) femoral hip stems combined with Co-Cr-Mo alloy heads (SS/CoCr) were tested in an in vitro fretting corrosion test set-up to assess the propensity for mechanically assisted corrosion. Three different aspects of the modular design were evaluated in this study: (1) material combination compared to CoCr/CoCr, (2) wet versus dry assembly for SS/CoCr couples, and (3) 0- and 6-mm head offset for SS/CoCr couples. Fretting corrosion tests over a range of cyclic loads up to 3300 N were performed, and continuous cyclic loading at 3300 N for 1 M cycles were performed on each group (n = 5). Fretting micromotion was measured as a function of cyclic load on select couples to detect the nature and extent of motion present. The results showed that SS/CoCr couples were more susceptible to fretting corrosion than CoCr/CoCr couples, that dry assembly does not prevent fretting corrosion from taking place but raises the onset load, and that 6-mm offset heads had higher visual evidence of fretting damage but showed mixed statistical results in terms of onset loads and OCP shifts and currents compared to the 0-mm offset samples. Current and voltage excursions over 1 million cycles tended to diminish towards their unloaded control levels but did not fully recover until cyclic loading ceased. Micromotion measurements indicated fretting motions in the range of 10-25 microm where 0-mm heads tended to piston on the trunion, while 6 mm heads tended to rock. (c) 2008 Wiley Periodicals, Inc.

A pipeline for the de novo assembly of the Themira biloba (Sepsidae: Diptera) transcriptome using a multiple k-mer length approach.

PubMed

Melicher, Dacotah; Torson, Alex S; Dworkin, Ian; Bowsher, Julia H

2014-03-12

The Sepsidae family of flies is a model for investigating how sexual selection shapes courtship and sexual dimorphism in a comparative framework. However, like many non-model systems, there are few molecular resources available. Large-scale sequencing and assembly have not been performed in any sepsid, and the lack of a closely related genome makes investigation of gene expression challenging. Our goal was to develop an automated pipeline for de novo transcriptome assembly, and to use that pipeline to assemble and analyze the transcriptome of the sepsid Themira biloba. Our bioinformatics pipeline uses cloud computing services to assemble and analyze the transcriptome with off-site data management, processing, and backup. It uses a multiple k-mer length approach combined with a second meta-assembly to extend transcripts and recover more bases of transcript sequences than standard single k-mer assembly. We used 454 sequencing to generate 1.48 million reads from cDNA generated from embryo, larva, and pupae of T. biloba and assembled a transcriptome consisting of 24,495 contigs. Annotation identified 16,705 transcripts, including those involved in embryogenesis and limb patterning. We assembled transcriptomes from an additional three non-model organisms to demonstrate that our pipeline assembled a higher-quality transcriptome than single k-mer approaches across multiple species. The pipeline we have developed for assembly and analysis increases contig length, recovers unique transcripts, and assembles more base pairs than other methods through the use of a meta-assembly. The T. biloba transcriptome is a critical resource for performing large-scale RNA-Seq investigations of gene expression patterns, and is the first transcriptome sequenced in this Dipteran family.

Seamless tiled display system

NASA Technical Reports Server (NTRS)

Dubin, Matthew B. (Inventor); Larson, Brent D. (Inventor); Kolosowsky, Aleksandra (Inventor)

2006-01-01

A modular and scalable seamless tiled display apparatus includes multiple display devices, a screen, and multiple lens assemblies. Each display device is subdivided into multiple sections, and each section is configured to display a sectional image. One of the lens assemblies is optically coupled to each of the sections of each of the display devices to project the sectional image displayed on that section onto the screen. The multiple lens assemblies are configured to merge the projected sectional images to form a single tiled image. The projected sectional images may be merged on the screen by magnifying and shifting the images in an appropriate manner. The magnification and shifting of these images eliminates any visual effect on the tiled display that may result from dead-band regions defined between each pair of adjacent sections on each display device, and due to gaps between multiple display devices.

Applying Uncertainty Analysis to a Risk Assessment for the Pesticide Permethrin

EPA Science Inventory

We discuss the application of methods of uncertainty analysis from our previous poster to the problem of a risk assessment for exposure to the food-use pesticide permethrin resulting from residential pesticide crack and crevice application. Exposures are simulated by the SHEDS (S...

Spatial variability in community composition on a granite breakwater versus natural rocky shores: lack of microhabitats suppresses intertidal biodiversity.

PubMed

Aguilera, Moisés A; Broitman, Bernardo R; Thiel, Martin

2014-10-15

Strong differences have been observed between the assemblages on artificial reefs and on natural hard-bottom habitats worldwide, but little is known about the mechanisms that cause contrasting biodiversity patterns. We examined the influence of spatial attributes in relation to both biogenic and topographic microhabitats, in the distribution and composition of intertidal species on both artificial and natural reefs. We found higher small-scale spatial heterogeneity on the natural reef compared with the study breakwater. Species richness and diversity were associated with a higher availability of crevices, rock pools and mussels in natural habitats. Spatial distribution of certain grazers corresponded well with the spatial structure of microhabitats. In contrast, the lack of microhabitats on the breakwater resulted in the absence of several grazers reflected in lower species richness. Biogenic and topographic microhabitats can have interactive effects providing niche opportunities for multiple species, explaining differences in species diversity between artificial versus natural reefs. Copyright © 2014 Elsevier Ltd. All rights reserved.

Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies

PubMed Central

Denton, James F.; Lugo-Martinez, Jose; Tucker, Abraham E.; Schrider, Daniel R.; Warren, Wesley C.; Hahn, Matthew W.

2014-01-01

Current sequencing methods produce large amounts of data, but genome assemblies based on these data are often woefully incomplete. These incomplete and error-filled assemblies result in many annotation errors, especially in the number of genes present in a genome. In this paper we investigate the magnitude of the problem, both in terms of total gene number and the number of copies of genes in specific families. To do this, we compare multiple draft assemblies against higher-quality versions of the same genomes, using several new assemblies of the chicken genome based on both traditional and next-generation sequencing technologies, as well as published draft assemblies of chimpanzee. We find that upwards of 40% of all gene families are inferred to have the wrong number of genes in draft assemblies, and that these incorrect assemblies both add and subtract genes. Using simulated genome assemblies of Drosophila melanogaster, we find that the major cause of increased gene numbers in draft genomes is the fragmentation of genes onto multiple individual contigs. Finally, we demonstrate the usefulness of RNA-Seq in improving the gene annotation of draft assemblies, largely by connecting genes that have been fragmented in the assembly process. PMID:25474019

Extensive error in the number of genes inferred from draft genome assemblies.

PubMed

Denton, James F; Lugo-Martinez, Jose; Tucker, Abraham E; Schrider, Daniel R; Warren, Wesley C; Hahn, Matthew W

2014-12-01

Current sequencing methods produce large amounts of data, but genome assemblies based on these data are often woefully incomplete. These incomplete and error-filled assemblies result in many annotation errors, especially in the number of genes present in a genome. In this paper we investigate the magnitude of the problem, both in terms of total gene number and the number of copies of genes in specific families. To do this, we compare multiple draft assemblies against higher-quality versions of the same genomes, using several new assemblies of the chicken genome based on both traditional and next-generation sequencing technologies, as well as published draft assemblies of chimpanzee. We find that upwards of 40% of all gene families are inferred to have the wrong number of genes in draft assemblies, and that these incorrect assemblies both add and subtract genes. Using simulated genome assemblies of Drosophila melanogaster, we find that the major cause of increased gene numbers in draft genomes is the fragmentation of genes onto multiple individual contigs. Finally, we demonstrate the usefulness of RNA-Seq in improving the gene annotation of draft assemblies, largely by connecting genes that have been fragmented in the assembly process.

76 FR 31471 - Ethylene Glycol; Exemption From the Requirement of a Tolerance

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-01

... production (NAICS code 112). Food manufacturing (NAICS code 311). Pesticide manufacturing (NAICS code 32532..., submitted a petition to EPA under the Federal Food, Drug, and Cosmetic Act (FFDCA), requesting an... residual, and crack and crevice sprays in and around food and nonfood areas of residential and...

Nonequilibrium Synthesis of Highly Porous Single-Crystalline Oxide Nanostructures

DOE PAGES

Lee, Dongkyu; Gao, Xiang; Fan, Lisha; ...

2017-01-20

A novel synthesis route to the formation of vertically aligned single–crystalline oxide nanostructures is found by precisely controlling the nonequilibrium pulsed laser deposition process. Here, the columnar nanostructures with deep crevices offering a large surface area are generated owing to the diffusion limited geometric shadowing effect.

Multiple and configurable optical logic systems based on layered double hydroxides and chromophore assemblies.

PubMed

Shi, Wenying; Fu, Yi; Li, Zhixiong; Wei, Min

2015-01-14

Multiple and configurable fluorescence logic gates were fabricated via self-assembly of layered double hydroxides and various chromophores. These logic gates were operated by observation of different emissions with the same excitation wavelength, which achieve YES, NOT, AND, INH and INHIBIT logic operations, respectively.

Fresh Fuel Measurements With the Differential Die-Away Self-Interrogation Instrument

NASA Astrophysics Data System (ADS)

Trahan, Alexis C.; Belian, Anthony P.; Swinhoe, Martyn T.; Menlove, Howard O.; Flaska, Marek; Pozzi, Sara A.

2017-07-01

The purpose of the Next Generation Safeguards Initiative (NGSI)-Spent Fuel (SF) Project is to strengthen the technical toolkit of safeguards inspectors and/or other interested parties. The NGSI-SF team is working to achieve the following technical goals more easily and efficiently than in the past using nondestructive assay measurements of spent fuel assemblies: 1) verify the initial enrichment, burnup, and cooling time of facility declaration; 2) detect the diversion or replacement of pins; 3) estimate the plutonium mass; 4) estimate decay heat; and 5) determine the reactivity of spent fuel assemblies. The differential die-away self-interrogation (DDSI) instrument is one instrument that was assessed for years regarding its feasibility for robust, timely verification of spent fuel assemblies. The instrument was recently built and was tested using fresh fuel assemblies in a variety of configurations, including varying enrichment, neutron absorber content, and symmetry. The early die-away method, a multiplication determination method developed in simulation space, was successfully tested on the fresh fuel assembly data and determined multiplication with a root-mean-square (RMS) error of 2.9%. The experimental results were compared with MCNP simulations of the instrument as well. Low multiplication assemblies had agreement with an average RMS error of 0.2% in the singles count rate (i.e., total neutrons detected per second) and 3.4% in the doubles count rates (i.e., neutrons detected in coincidence per second). High-multiplication assemblies had agreement with an average RMS error of 4.1% in the singles and 13.3% in the doubles count rates.

Fresh Fuel Measurements With the Differential Die-Away Self-Interrogation Instrument

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

Trahan, Alexis C.; Belian, Anthony P.; Swinhoe, Martyn T.

The purpose of the Next Generation Safeguards Initiative (NGSI)-Spent Fuel (SF) Project is to strengthen the technical toolkit of safeguards inspectors and/or other interested parties. Thus the NGSI-SF team is working to achieve the following technical goals more easily and efficiently than in the past using nondestructive assay measurements of spent fuel assemblies: 1) verify the initial enrichment, burnup, and cooling time of facility declaration; 2) detect the diversion or replacement of pins; 3) estimate the plutonium mass; 4) estimate decay heat; and 5) determine the reactivity of spent fuel assemblies. The differential die-away self-interrogation (DDSI) instrument is one instrumentmore » that was assessed for years regarding its feasibility for robust, timely verification of spent fuel assemblies. The instrument was recently built and was tested using fresh fuel assemblies in a variety of configurations, including varying enrichment, neutron absorber content, and symmetry. The early die-away method, a multiplication determination method developed in simulation space, was successfully tested on the fresh fuel assembly data and determined multiplication with a root-mean-square (RMS) error of 2.9%. The experimental results were compared with MCNP simulations of the instrument as well. Low multiplication assemblies had agreement with an average RMS error of 0.2% in the singles count rate (i.e., total neutrons detected per second) and 3.4% in the doubles count rates (i.e., neutrons detected in coincidence per second). High-multiplication assemblies had agreement with an average RMS error of 4.1% in the singles and 13.3% in the doubles count rates.« less

Fresh Fuel Measurements With the Differential Die-Away Self-Interrogation Instrument

DOE PAGES

Trahan, Alexis C.; Belian, Anthony P.; Swinhoe, Martyn T.; ...

2017-01-05

The purpose of the Next Generation Safeguards Initiative (NGSI)-Spent Fuel (SF) Project is to strengthen the technical toolkit of safeguards inspectors and/or other interested parties. Thus the NGSI-SF team is working to achieve the following technical goals more easily and efficiently than in the past using nondestructive assay measurements of spent fuel assemblies: 1) verify the initial enrichment, burnup, and cooling time of facility declaration; 2) detect the diversion or replacement of pins; 3) estimate the plutonium mass; 4) estimate decay heat; and 5) determine the reactivity of spent fuel assemblies. The differential die-away self-interrogation (DDSI) instrument is one instrumentmore » that was assessed for years regarding its feasibility for robust, timely verification of spent fuel assemblies. The instrument was recently built and was tested using fresh fuel assemblies in a variety of configurations, including varying enrichment, neutron absorber content, and symmetry. The early die-away method, a multiplication determination method developed in simulation space, was successfully tested on the fresh fuel assembly data and determined multiplication with a root-mean-square (RMS) error of 2.9%. The experimental results were compared with MCNP simulations of the instrument as well. Low multiplication assemblies had agreement with an average RMS error of 0.2% in the singles count rate (i.e., total neutrons detected per second) and 3.4% in the doubles count rates (i.e., neutrons detected in coincidence per second). High-multiplication assemblies had agreement with an average RMS error of 4.1% in the singles and 13.3% in the doubles count rates.« less

Four-port gas separation membrane module assembly

DOEpatents

Wynn, Nicholas P.; Fulton, Donald A.; Lokhandwala, Kaaeid A.; Kaschemekat, Jurgen

2010-07-20

A gas-separation membrane assembly, and a gas-separation process using the assembly. The assembly incorporates multiple gas-separation membranes in an array within a single vessel or housing, and is equipped with two permeate ports, enabling permeate gas to be withdrawn from both ends of the membrane module permeate pipes.

A comparative evaluation of genome assembly reconciliation tools.

PubMed

Alhakami, Hind; Mirebrahim, Hamid; Lonardi, Stefano

2017-05-18

The majority of eukaryotic genomes are unfinished due to the algorithmic challenges of assembling them. A variety of assembly and scaffolding tools are available, but it is not always obvious which tool or parameters to use for a specific genome size and complexity. It is, therefore, common practice to produce multiple assemblies using different assemblers and parameters, then select the best one for public release. A more compelling approach would allow one to merge multiple assemblies with the intent of producing a higher quality consensus assembly, which is the objective of assembly reconciliation. Several assembly reconciliation tools have been proposed in the literature, but their strengths and weaknesses have never been compared on a common dataset. We fill this need with this work, in which we report on an extensive comparative evaluation of several tools. Specifically, we evaluate contiguity, correctness, coverage, and the duplication ratio of the merged assembly compared to the individual assemblies provided as input. None of the tools we tested consistently improved the quality of the input GAGE and synthetic assemblies. Our experiments show an increase in contiguity in the consensus assembly when the original assemblies already have high quality. In terms of correctness, the quality of the results depends on the specific tool, as well as on the quality and the ranking of the input assemblies. In general, the number of misassemblies ranges from being comparable to the best of the input assembly to being comparable to the worst of the input assembly.

Liquid-liquid interfacial nanoparticle assemblies

DOEpatents

Emrick, Todd S [South Deerfield, MA; Russell, Thomas P [Amherst, MA; Dinsmore, Anthony [Amherst, MA; Skaff, Habib [Amherst, MA; Lin, Yao [Amherst, MA

2008-12-30

Self-assembly of nanoparticles at the interface between two fluids, and methods to control such self-assembly process, e.g., the surface density of particles assembling at the interface; to utilize the assembled nanoparticles and their ligands in fabrication of capsules, where the elastic properties of the capsules can be varied from soft to tough; to develop capsules with well-defined porosities for ultimate use as delivery systems; and to develop chemistries whereby multiple ligands or ligands with multiple functionalities can be attached to the nanoparticles to promote the interfacial segregation and assembly of the nanoparticles. Certain embodiments use cadmium selenide (CdSe) nanoparticles, since the photoluminescence of the particles provides a convenient means by which the spatial location and organization of the particles can be probed. However, the systems and methodologies presented here are general and can, with suitable modification of the chemistries, be adapted to any type of nanoparticle.

Multiple assembly chaperones govern biogenesis of the proteasome regulatory particle base.

PubMed

Funakoshi, Minoru; Tomko, Robert J; Kobayashi, Hideki; Hochstrasser, Mark

2009-05-29

The central protease of eukaryotes, the 26S proteasome, has a 20S proteolytic core particle (CP) and an attached 19S regulatory particle (RP). The RP is further subdivided into lid and base subcomplexes. Little is known about RP assembly. Here, we show that four conserved assembly factors govern biogenesis of the yeast RP base. Nas2 forms a complex with the Rpt4 and Rpt5 ATPases and enhances 26S proteasome formation in vivo and in vitro. Other RP subcomplexes contain Hsm3, which is related to mammalian proteasome subunit S5b. Hsm3 also contributes to base assembly. Larger Hsm3-containing complexes include two additional proteins, Nas6 and Rpn14, which function as assembly chaperones as well. Specific deletion combinations affecting these four factors cause severe perturbations to RP assembly. Our results demonstrate that proteasomal RP biogenesis requires multiple, functionally overlapping chaperones and suggest a model in which subunits form specific subcomplexes that then assemble into the base.

A light-trapping strategy for nanocrystalline silicon thin-film solar cells using three-dimensionally assembled nanoparticle structures.

PubMed

Ha, Kyungyeon; Jang, Eunseok; Jang, Segeun; Lee, Jong-Kwon; Jang, Min Seok; Choi, Hoseop; Cho, Jun-Sik; Choi, Mansoo

2016-02-05

We report three-dimensionally assembled nanoparticle structures inducing multiple plasmon resonances for broadband light harvesting in nanocrystalline silicon (nc-Si:H) thin-film solar cells. A three-dimensional multiscale (3DM) assembly of nanoparticles generated using a multi-pin spark discharge method has been accomplished over a large area under atmospheric conditions via ion-assisted aerosol lithography. The multiscale features of the sophisticated 3DM structures exhibit surface plasmon resonances at multiple frequencies, which increase light scattering and absorption efficiency over a wide spectral range from 350-1100 nm. The multiple plasmon resonances, together with the antireflection functionality arising from the conformally deposited top surface of the 3D solar cell, lead to a 22% and an 11% improvement in power conversion efficiency of the nc-Si:H thin-film solar cells compared to flat cells and cells employing nanoparticle clusters, respectively. Finite-difference time-domain simulations were also carried out to confirm that the improved device performance mainly originates from the multiple plasmon resonances generated from three-dimensionally assembled nanoparticle structures.

Multiple filters affect tree species assembly in mid-latitude forest communities.

PubMed

Kubota, Y; Kusumoto, B; Shiono, T; Ulrich, W

2018-05-01

Species assembly patterns of local communities are shaped by the balance between multiple abiotic/biotic filters and dispersal that both select individuals from species pools at the regional scale. Knowledge regarding functional assembly can provide insight into the relative importance of the deterministic and stochastic processes that shape species assembly. We evaluated the hierarchical roles of the α niche and β niches by analyzing the influence of environmental filtering relative to functional traits on geographical patterns of tree species assembly in mid-latitude forests. Using forest plot datasets, we examined the α niche traits (leaf and wood traits) and β niche properties (cold/drought tolerance) of tree species, and tested non-randomness (clustering/over-dispersion) of trait assembly based on null models that assumed two types of species pools related to biogeographical regions. For most plots, species assembly patterns fell within the range of random expectation. However, particularly for cold/drought tolerance-related β niche properties, deviation from randomness was frequently found; non-random clustering was predominant in higher latitudes with harsh climates. Our findings demonstrate that both randomness and non-randomness in trait assembly emerged as a result of the α and β niches, although we suggest the potential role of dispersal processes and/or species equalization through trait similarities in generating the prevalence of randomness. Clustering of β niche traits along latitudinal climatic gradients provides clear evidence of species sorting by filtering particular traits. Our results reveal that multiple filters through functional niches and stochastic processes jointly shape geographical patterns of species assembly across mid-latitude forests.

Cell-assembly coding in several memory processes.

PubMed

Sakurai, Y

1998-01-01

The present paper discusses why the cell assembly, i.e., an ensemble population of neurons with flexible functional connections, is a tenable view of the basic code for information processes in the brain. The main properties indicating the reality of cell-assembly coding are neurons overlaps among different assemblies and connection dynamics within and among the assemblies. The former can be detected as multiple functions of individual neurons in processing different kinds of information. Individual neurons appear to be involved in multiple information processes. The latter can be detected as changes of functional synaptic connections in processing different kinds of information. Correlations of activity among some of the recorded neurons appear to change in multiple information processes. Recent experiments have compared several different memory processes (tasks) and detected these two main properties, indicating cell-assembly coding of memory in the working brain. The first experiment compared different types of processing of identical stimuli, i.e., working memory and reference memory of auditory stimuli. The second experiment compared identical processes of different types of stimuli, i.e., discriminations of simple auditory, simple visual, and configural auditory-visual stimuli. The third experiment compared identical processes of different types of stimuli with or without temporal processing of stimuli, i.e., discriminations of elemental auditory, configural auditory-visual, and sequential auditory-visual stimuli. Some possible features of the cell-assembly coding, especially "dual coding" by individual neurons and cell assemblies, are discussed for future experimental approaches. Copyright 1998 Academic Press.

Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes.

PubMed

Olson, Nathan D; Treangen, Todd J; Hill, Christopher M; Cepeda-Espinoza, Victoria; Ghurye, Jay; Koren, Sergey; Pop, Mihai

2017-08-07

Metagenomic samples are snapshots of complex ecosystems at work. They comprise hundreds of known and unknown species, contain multiple strain variants and vary greatly within and across environments. Many microbes found in microbial communities are not easily grown in culture making their DNA sequence our only clue into their evolutionary history and biological function. Metagenomic assembly is a computational process aimed at reconstructing genes and genomes from metagenomic mixtures. Current methods have made significant strides in reconstructing DNA segments comprising operons, tandem gene arrays and syntenic blocks. Shorter, higher-throughput sequencing technologies have become the de facto standard in the field. Sequencers are now able to generate billions of short reads in only a few days. Multiple metagenomic assembly strategies, pipelines and assemblers have appeared in recent years. Owing to the inherent complexity of metagenome assembly, regardless of the assembly algorithm and sequencing method, metagenome assemblies contain errors. Recent developments in assembly validation tools have played a pivotal role in improving metagenomics assemblers. Here, we survey recent progress in the field of metagenomic assembly, provide an overview of key approaches for genomic and metagenomic assembly validation and demonstrate the insights that can be derived from assemblies through the use of assembly validation strategies. We also discuss the potential for impact of long-read technologies in metagenomics. We conclude with a discussion of future challenges and opportunities in the field of metagenomic assembly and validation. © The Author 2017. Published by Oxford University Press.

83. Photographic copy of historic photo, December 16, 1929 (original ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

83. Photographic copy of historic photo, December 16, 1929 (original print filed in Record Group 115, National Archives, Washington, D.C.). OWYHEE DAM-LOOKING DOWNSTREAM FROM UPPER COFFERDAM (POINT #15) SHOWING CREVICE AND KEYWAY CUTOFF; ALSO CABLEWAY CONTROL HOUSE AND ENTRANCE ADIT. - Owyhee Dam, Across Owyhee River, Nyssa, Malheur County, OR

THE DISTRIBUTION OF CHLORPYRIFOS FOLLOWING A CRACK AND CREVICE TYPE APPLICAITON IN THE U.S. EPA INDOOR AIR QUALITY (IAQ) TEST HOUSE

EPA Science Inventory

Pesticides found in homes may result from indoor applications to control household pests or by translocation from outdoor sources. Pesticides disperse according to their physical properties and other factors such as human activity, residential air exchange, temperature and humi...

THE SPATIAL AND TEMPORAL DISTRIBUTION OF CHLORPYRIFOS IN THE U.S. EPA INDOOR AIR QUALITY (IAQ) TEST HOUSE FOLLOWING CRACK AND CREVICE TYPE APPLICATIONS

EPA Science Inventory

Pesticides found in homes may result from indoor applications to control household pests or by translocation from outdoor sources. Pesticides disperse according to their physical properties and other factors such as human activity, air exchange, temperature and humidity. Insect...

Effect of temperature on the passivation behavior of steel rebar

NASA Astrophysics Data System (ADS)

Chen, Shan-meng; Cao, Bei; Wu, Yin-shun; Ma, Ke

2014-05-01

Steel rebar normally forms an oxide or rusty skin before it is embedded into concrete and the passivation properties of this skin will be heavily influenced by temperature. To study the effect of temperature on the passivation properties of steel rebar under different surface conditions, we conducted scanning electron microscopy (SEM) observations and electrochemical measurements, such as measurements of the free corrosion potential and polarization curves of HPB235 steel rebar. These measurements identified three kinds of surfaces: polished, oxide skin, and rusty skin. Our results show that the passivation properties of all the surface types decrease with the increase of temperature. Temperature has the greatest effect on the rusty-skin rebar and least effect on the polished steel rebar, because of cracks and crevices on the mill scale on the steel rebar's surface. The rusty-skin rebar exhibits the highest corrosion rate because crevice corrosion can accelerate the corrosion of the steel rebar, particularly at high temperature. The results also indicate that the threshold temperatures of passivation for the oxide-skin rebar and the rusty-skin rebar are 37°C and 20°C, respectively.

Results from Alloy 600 And Alloy 690 Caustic SCC Model Boiler Tests

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

Miller, Frederick D.; Thomas, Larry E.

2009-08-03

A versatile model boiler test methodology was developed and used to compare caustic stress corrosion cracking (SCC) of mill annealed Alloy 600 and thermally treated Alloy 690. The model boiler included simulated crevice devices that efficiently and consistently concentrated Na2CO3, resulting in volatilization of CO2 with the steam and concentration of NaOH at the tube surfaces. The test methodology also included variation in tube stress, either produced by the primary to secondary side pressure differential, or by a novel method that reproducibly yields a higher stress condition on the tube. The significant effect of residual stress on tube SCC wasmore » also considered. SCC of both Alloy 600 and Alloy 690 were evaluated as a function of temperature and stress. Analytical transmission electron microscopy (ATEM) evaluations of the cracks and the grain boundaries ahead of the cracks were performed, providing insight into the SCC mechanism. This model boiler test methodology may be applicable to a range of bulkwater secondary chemistries that concentrate to produce aggressive crevice environments.« less

Effect of pH on Structural Changes in Perch Hemoglobin that Can Alter Redox Stability and Heme Affinity

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

Richards, Mark P.; Aranda, IV, Roman; He, Cai

2010-01-07

pH can be manipulated to alter the oxidative stability of fish-based foods during storage. X-ray diffraction was used to investigate the ability of reduced pH to cause structural changes in fish hemoglobins that lead to enhanced oxidative degradation. Decreasing pH from 8.0 to 6.3 and 5.7 created a large channel for solvent entry into the heme crevice of perch hemoglobin beta chains. The proton-induced opening of this channel occurred between site CD3 and the heme-6-propionate. Solvent entry into the heme crevice can enhance metHb formation and hemin loss, processes that accelerate lipid oxidation. Reduced pH also decreased the distance betweenmore » Ile at E11 in one of the alpha chains and the ligand above the heme iron atom. This sterically displaces O{sub 2} and protonated O{sub 2} which increases metHb formation. These studies demonstrate that pH reduction causes structural changes in perch hemoglobin which increase oxidative degradation of the heme pigment.« less

Electrostatic field of the large fragment of Escherichia coli DNA polymerase I.

PubMed

Warwicker, J; Ollis, D; Richards, F M; Steitz, T A

1985-12-05

The electrostatic field of the large fragment of Escherichia coli DNA polymerase I (Klenow fragment) has been calculated by the finite difference procedure on a 2 A grid. The potential field is substantially negative at physiological pH (reflecting the net negative charge at this pH). The largest regions of positive potential are in the deep crevice of the C-terminal domain, which is the proposed binding site for the DNA substrate. Within the crevice, the electrostatic potential has a partly helical form. If the DNA is positioned to fulfil stereochemical requirements, then the positive potential generally follows the major groove and (to a lesser extent) the negative potential is in the minor groove. Such an arrangement could stabilize DNA configurations related by screw symmetry. The histidine residues of the Klenow fragment give the positive field of the groove a sensitivity to relatively small pH changes around neutrality. We suggest that the histidine residues could change their ionization states in response to DNA binding, and that this effect could contribute to the protein-DNA binding energy.

Task allocation among multiple intelligent robots

NASA Technical Reports Server (NTRS)

Gasser, L.; Bekey, G.

1987-01-01

Researchers describe the design of a decentralized mechanism for allocating assembly tasks in a multiple robot assembly workstation. Currently, the approach focuses on distributed allocation to explore its feasibility and its potential for adaptability to changing circumstances, rather than for optimizing throughput. Individual greedy robots make their own local allocation decisions using both dynamic allocation policies which propagate through a network of allocation goals, and local static and dynamic constraints describing which robots are elibible for which assembly tasks. Global coherence is achieved by proper weighting of allocation pressures propagating through the assembly plan. Deadlock avoidance and synchronization is achieved using periodic reassessments of local allocation decisions, ageing of allocation goals, and short-term allocation locks on goals.

Supramolecular Differentiation for Construction of Anisotropic Fullerene Nanostructures by Time-Programmed Control of Interfacial Growth.

PubMed

Bairi, Partha; Minami, Kosuke; Hill, Jonathan P; Nakanishi, Waka; Shrestha, Lok Kumar; Liu, Chao; Harano, Koji; Nakamura, Eiichi; Ariga, Katsuhiko

2016-09-27

Supramolecular assembly can be used to construct a wide variety of ordered structures by exploiting the cumulative effects of multiple noncovalent interactions. However, the construction of anisotropic nanostructures remains subject to some limitations. Here, we demonstrate the preparation of anisotropic fullerene-based nanostructures by supramolecular differentiation, which is the programmed control of multiple assembly strategies. We have carefully combined interfacial assembly and local phase separation phenomena. Two fullerene derivatives, PhH and C12H, were together formed into self-assembled anisotropic nanostructures by using this approach. This technique is applicable for the construction of anisotropic nanostructures without requiring complex molecular design or complicated methodology.

Unique nucleotide sequence-guided assembly of repetitive DNA parts for synthetic biology applications

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

Torella, JP; Lienert, F; Boehm, CR

2014-08-07

Recombination-based DNA construction methods, such as Gibson assembly, have made it possible to easily and simultaneously assemble multiple DNA parts, and they hold promise for the development and optimization of metabolic pathways and functional genetic circuits. Over time, however, these pathways and circuits have become more complex, and the increasing need for standardization and insulation of genetic parts has resulted in sequence redundancies-for example, repeated terminator and insulator sequences-that complicate recombination-based assembly. We and others have recently developed DNA assembly methods, which we refer to collectively as unique nucleotide sequence (UNS)-guided assembly, in which individual DNA parts are flanked withmore » UNSs to facilitate the ordered, recombination-based assembly of repetitive sequences. Here we present a detailed protocol for UNS-guided assembly that enables researchers to convert multiple DNA parts into sequenced, correctly assembled constructs, or into high-quality combinatorial libraries in only 2-3 d. If the DNA parts must be generated from scratch, an additional 2-5 d are necessary. This protocol requires no specialized equipment and can easily be implemented by a student with experience in basic cloning techniques.« less

Unique nucleotide sequence (UNS)-guided assembly of repetitive DNA parts for synthetic biology applications

PubMed Central

Torella, Joseph P.; Lienert, Florian; Boehm, Christian R.; Chen, Jan-Hung; Way, Jeffrey C.; Silver, Pamela A.

2016-01-01

Recombination-based DNA construction methods, such as Gibson assembly, have made it possible to easily and simultaneously assemble multiple DNA parts and hold promise for the development and optimization of metabolic pathways and functional genetic circuits. Over time, however, these pathways and circuits have become more complex, and the increasing need for standardization and insulation of genetic parts has resulted in sequence redundancies — for example repeated terminator and insulator sequences — that complicate recombination-based assembly. We and others have recently developed DNA assembly methods that we refer to collectively as unique nucleotide sequence (UNS)-guided assembly, in which individual DNA parts are flanked with UNSs to facilitate the ordered, recombination-based assembly of repetitive sequences. Here we present a detailed protocol for UNS-guided assembly that enables researchers to convert multiple DNA parts into sequenced, correctly-assembled constructs, or into high-quality combinatorial libraries in only 2–3 days. If the DNA parts must be generated from scratch, an additional 2–5 days are necessary. This protocol requires no specialized equipment and can easily be implemented by a student with experience in basic cloning techniques. PMID:25101822

A Multiple Objective Test Assembly Approach for Exposure Control Problems in Computerized Adaptive Testing

ERIC Educational Resources Information Center

Veldkamp, Bernard P.; Verschoor, Angela J.; Eggen, Theo J. H. M.

2010-01-01

Overexposure and underexposure of items in the bank are serious problems in operational computerized adaptive testing (CAT) systems. These exposure problems might result in item compromise, or point at a waste of investments. The exposure control problem can be viewed as a test assembly problem with multiple objectives. Information in the test has…

Dynamics of the His79-heme alkaline transition of yeast iso-1-cytochrome c probed by conformationally gated electron transfer with Co(II)bis(terpyridine).

PubMed

Cherney, Melisa M; Junior, Carolyn C; Bergquist, Bryan B; Bowler, Bruce E

2013-08-28

Alkaline conformers of cytochrome c may be involved in both its electron transport and apoptotic functions. We use cobalt(II)bis(terpyridine), Co(terpy)2(2+), as a reagent for conformationally gated electron-transfer (gated ET) experiments to study the alkaline conformational transition of K79H variants of yeast iso-1-cytochrome c expressed in Escherichia coli , WT*K79H, with alanine at position 72 and Saccharomyces cerevisiae , yK79H, with trimethyllysine (Tml) at position 72. Co(terpy)2(2+) is well-suited to the 100 ms to 1 s time scale of the His79-mediated alkaline conformational transition of these variants. Reduction of the His79-heme alkaline conformer by Co(terpy)2(2+) occurs primarily by gated ET, which involves conversion to the native state followed by reduction, with a small fraction of the His79-heme alkaline conformer directly reduced by Co(terpy)2(2+). The gated ET experiments show that the mechanism of formation of the His79-heme alkaline conformer involves only two ionizable groups. In previous work, we showed that the mechanism of the His73-mediated alkaline conformational transition requires three ionizable groups. Thus, the mechanism of heme crevice opening depends upon the position of the ligand mediating the process. The microscopic rate constants provided by gated ET studies show that mutation of Tml72 (yK79H variant) in the heme crevice loop to Ala72 (WT*K79H variant) affects the dynamics of heme crevice opening through a small destabilization of both the native conformer and the transition state relative to the His79-heme alkaline conformer. Previous pH jump data had indicated that the Tml72→Ala mutation primarily stabilized the transition state for the His79-mediated alkaline conformational transition.

Structure–function characterization of three human antibodies targeting the vaccinia virus adhesion molecule D8

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

Matho, Michael H.; Schlossman, Andrew; Gilchuk, Iuliia M.

Vaccinia virus (VACV) envelope protein D8 is one of three glycosaminoglycan adhesion molecules and binds to the linear polysaccharide chondroitin sulfate (CS). D8 is also a target for neutralizing antibody responses that are elicited by the smallpox vaccine, which has enabled the first eradication of a human viral pathogen and is a useful model for studying antibody responses. However, to date, VACV epitopes targeted by human antibodies have not been characterized at atomic resolution. Here in this paper, we characterized the binding properties of several human anti-D8 antibodies and determined the crystal structures of three VACV-mAb variants, VACV-66, VACV-138, andmore » VACV-304, separately bound to D8. Although all these antibodies bound D8 with high affinity and were moderately neutralizing in the presence of complement, VACV-138 and VACV-304 also fully blocked D8 binding to CS-A, the low affinity ligand for D8. VACV-138 also abrogated D8 binding to the high-affinity ligand CS-E, but we observed residual CS-E binding was observed in the presence of VACV-304. Analysis of the VACV-138– and VACV-304–binding sites along the CS-binding crevice of D8, combined with different efficiencies of blocking D8 adhesion to CS-A and CS-E allowed us to propose that D8 has a high- and low-affinity CS-binding region within its central crevice. The crevice is amenable to protein engineering to further enhance both specificity and affinity of binding to CS-E. Finally, a wild-type D8 tetramer specifically bound to structures within the developing glomeruli of the kidney, which express CS-E. We propose that through structure-based protein engineering, an improved D8 tetramer could be used as a potential diagnostic tool to detect expression of CS-E, which is a possible biomarker for ovarian cancer.« less

Structure–function characterization of three human antibodies targeting the vaccinia virus adhesion molecule D8

DOE PAGES

Matho, Michael H.; Schlossman, Andrew; Gilchuk, Iuliia M.; ...

2017-11-09

Vaccinia virus (VACV) envelope protein D8 is one of three glycosaminoglycan adhesion molecules and binds to the linear polysaccharide chondroitin sulfate (CS). D8 is also a target for neutralizing antibody responses that are elicited by the smallpox vaccine, which has enabled the first eradication of a human viral pathogen and is a useful model for studying antibody responses. However, to date, VACV epitopes targeted by human antibodies have not been characterized at atomic resolution. Here in this paper, we characterized the binding properties of several human anti-D8 antibodies and determined the crystal structures of three VACV-mAb variants, VACV-66, VACV-138, andmore » VACV-304, separately bound to D8. Although all these antibodies bound D8 with high affinity and were moderately neutralizing in the presence of complement, VACV-138 and VACV-304 also fully blocked D8 binding to CS-A, the low affinity ligand for D8. VACV-138 also abrogated D8 binding to the high-affinity ligand CS-E, but we observed residual CS-E binding was observed in the presence of VACV-304. Analysis of the VACV-138– and VACV-304–binding sites along the CS-binding crevice of D8, combined with different efficiencies of blocking D8 adhesion to CS-A and CS-E allowed us to propose that D8 has a high- and low-affinity CS-binding region within its central crevice. The crevice is amenable to protein engineering to further enhance both specificity and affinity of binding to CS-E. Finally, a wild-type D8 tetramer specifically bound to structures within the developing glomeruli of the kidney, which express CS-E. We propose that through structure-based protein engineering, an improved D8 tetramer could be used as a potential diagnostic tool to detect expression of CS-E, which is a possible biomarker for ovarian cancer.« less

Dynamics of the His79-heme Alkaline Transition of Yeast Iso-1-cytochrome c Probed by Conformationally-gated Electron Transfer with Co(II)bis(terpyridine)†

PubMed Central

Cherney, Melisa M.; Junior, Carolyn C.; Bergquist, Bryan B.; Bowler, Bruce E.

2013-01-01

Alkaline conformers of cytochrome c may be involved in both its electron transport and apoptotic functions. We use cobalt(II)bis(terpyridine), Co(terpy)22+, as a reagent for conformationally-gated electron transfer (gated ET) experiments to study the alkaline conformational transition of K79H variants of yeast iso-1-cytochrome c expressed in Escherichia coli, WT*K79H, with alanine at position 72, and Saccharomyces cerevisiae, yK79H, with trimethyllysine (Tml) at position 72. Co(terpy)22+ is well-suited to the 100 ms to 1 s time scale of the His79-mediated alkaline conformational transition of these variants. Reduction of the His79-heme alkaline conformer by Co(terpy)22+ occurs primarily by gated ET, which involves conversion to the native state followed by reduction, with a small fraction of the His79- heme alkaline conformer directly reduced by Co(terpy)22+. The gated ET experiments show that the mechanism of formation of the His79-heme alkaline conformer involves only two ionizable groups. In previous work, we showed that the mechanism of the His73-mediated alkaline conformational transition requires three ionizable groups. Thus, the mechanism of heme crevice opening depends upon the position of the ligand mediating the process. The microscopic rate constants provided by gated ET studies show that mutation of Tml72 (yK79H variant) in the heme crevice loop to Ala72 (WT*K79H variant) affects the dynamics of heme crevice opening through a small destabilization of both the native conformer and the transition state relative to the His79-heme alkaline conformer. Previous pH jump data had indicated that the Tml72→Ala mutation primarily stabilized the transition state for the His79-mediated alkaline conformational transition. PMID:23899348

Interspecific Competition for Shelters in Territorial and Gregarious Intertidal Grazers: Consequences for Individual Behaviour

PubMed Central

Aguilera, Moisés A.; Navarrete, Sergio A.

2012-01-01

Experiments have shown that interspecific interactions within consumer guilds can alter patterns of distribution, abundance and size of species. Plastic behavioural responses can be modulated by agonistic interactions. In many cases, consumers compete for space and shelters, and these interactions change the manner in which they exploit food. This study investigates the consequences of competition in the spatial and temporal organization of behaviour of intertidal grazers, which share algal resources and the use of rock crevices while resting, but exhibit different body sizes, spatial behaviour and foraging modes. We evaluate interaction strength between small gregarious Siphonaria lessoni and the larger territorial keyhole limpet Fissurella crassa and between S. lessoni and the medium-size gregarious chiton Chiton granosus. Using field manipulations and artificial arenas in the laboratory, we tested whether the use of crevices, micro-spatial distribution and activity are modified by the density of conspecifics and the presence of heterospecifics. Our results show that small-scale spatial segregation observed in the field between S. lessoni and C. granosus result from species-specific differences in habitat use. In turn, we found evidence that spatial segregation between F. crassa and S. lessoni results from highly asymmetric interference competition in the use of shelters. The presence of F. crassa reduced the use of crevices and growth rates of S. lessoni. Effects on growth rates are assumed to result from exposure to harsh environmental conditions rather than food limitation. Thus, neither gregarious behaviour nor differences in activity were sufficient to prevent competition with the larger grazer. Our study illustrates the importance of competition for shelters, which results in behavioural changes of the smaller-sized species, and how these plastic responses can translate into differences in growth rates. Use of shelters can thus be modulated by environmental conditions in a species-specific as well as an interactive manner within consumers’ guilds. PMID:23049980

Neutron Detector Signal Processing to Calculate the Effective Neutron Multiplication Factor of Subcritical Assemblies

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

Talamo, Alberto; Gohar, Yousry

2016-06-01

This report describes different methodologies to calculate the effective neutron multiplication factor of subcritical assemblies by processing the neutron detector signals using MATLAB scripts. The subcritical assembly can be driven either by a spontaneous fission neutron source (e.g. californium) or by a neutron source generated from the interactions of accelerated particles with target materials. In the latter case, when the particle accelerator operates in a pulsed mode, the signals are typically stored into two files. One file contains the time when neutron reactions occur and the other contains the times when the neutron pulses start. In both files, the timemore » is given by an integer representing the number of time bins since the start of the counting. These signal files are used to construct the neutron count distribution from a single neutron pulse. The built-in functions of MATLAB are used to calculate the effective neutron multiplication factor through the application of the prompt decay fitting or the area method to the neutron count distribution. If the subcritical assembly is driven by a spontaneous fission neutron source, then the effective multiplication factor can be evaluated either using the prompt neutron decay constant obtained from Rossi or Feynman distributions or the Modified Source Multiplication (MSM) method.« less

Peptide-directed self-assembly of functionalized polymeric nanoparticles. Part II: effects of nanoparticle composition on assembly behavior and multiple drug loading ability.

PubMed

Xiang, Xu; Ding, Xiaochu; Moser, Trevor; Gao, Qi; Shokuhfar, Tolou; Heiden, Patricia A

2015-04-01

Peptide-functionalized polymeric nanoparticles were designed and self-assembled into continuous nanoparticle fibers and three-dimensional scaffolds via ionic complementary peptide interaction. Different nanoparticle compositions can be designed to be appropriate for each desired drug, so that the release of each drug is individually controlled and the simultaneous sustainable release of multiple drugs is achieved in a single scaffold. A self-assembled scaffold membrane was incubated with NIH3T3 fibroblast cells in a culture dish that demonstrated non-toxicity and non-inhibition on cell proliferation. This type of nanoparticle scaffold combines the advantages of peptide self-assembly and the versatility of polymeric nanoparticle controlled release systems for tissue engineering. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

GRAbB: Selective Assembly of Genomic Regions, a New Niche for Genomic Research

PubMed Central

Zhang, Hao; van Diepeningen, Anne D.; van der Lee, Theo A. J.; Waalwijk, Cees; de Hoog, G. Sybren

2016-01-01

GRAbB (Genomic Region Assembly by Baiting) is a new program that is dedicated to assemble specific genomic regions from NGS data. This approach is especially useful when dealing with multi copy regions, such as mitochondrial genome and the rDNA repeat region, parts of the genome that are often neglected or poorly assembled, although they contain interesting information from phylogenetic or epidemiologic perspectives, but also single copy regions can be assembled. The program is capable of targeting multiple regions within a single run. Furthermore, GRAbB can be used to extract specific loci from NGS data, based on homology, like sequences that are used for barcoding. To make the assembly specific, a known part of the region, such as the sequence of a PCR amplicon or a homologous sequence from a related species must be specified. By assembling only the region of interest, the assembly process is computationally much less demanding and may lead to assemblies of better quality. In this study the different applications and functionalities of the program are demonstrated such as: exhaustive assembly (rDNA region and mitochondrial genome), extracting homologous regions or genes (IGS, RPB1, RPB2 and TEF1a), as well as extracting multiple regions within a single run. The program is also compared with MITObim, which is meant for the exhaustive assembly of a single target based on a similar query sequence. GRAbB is shown to be more efficient than MITObim in terms of speed, memory and disk usage. The other functionalities (handling multiple targets simultaneously and extracting homologous regions) of the new program are not matched by other programs. The program is available with explanatory documentation at https://github.com/b-brankovics/grabb. GRAbB has been tested on Ubuntu (12.04 and 14.04), Fedora (23), CentOS (7.1.1503) and Mac OS X (10.7). Furthermore, GRAbB is available as a docker repository: brankovics/grabb (https://hub.docker.com/r/brankovics/grabb/). PMID:27308864

GRAbB: Selective Assembly of Genomic Regions, a New Niche for Genomic Research.

PubMed

Brankovics, Balázs; Zhang, Hao; van Diepeningen, Anne D; van der Lee, Theo A J; Waalwijk, Cees; de Hoog, G Sybren

2016-06-01

GRAbB (Genomic Region Assembly by Baiting) is a new program that is dedicated to assemble specific genomic regions from NGS data. This approach is especially useful when dealing with multi copy regions, such as mitochondrial genome and the rDNA repeat region, parts of the genome that are often neglected or poorly assembled, although they contain interesting information from phylogenetic or epidemiologic perspectives, but also single copy regions can be assembled. The program is capable of targeting multiple regions within a single run. Furthermore, GRAbB can be used to extract specific loci from NGS data, based on homology, like sequences that are used for barcoding. To make the assembly specific, a known part of the region, such as the sequence of a PCR amplicon or a homologous sequence from a related species must be specified. By assembling only the region of interest, the assembly process is computationally much less demanding and may lead to assemblies of better quality. In this study the different applications and functionalities of the program are demonstrated such as: exhaustive assembly (rDNA region and mitochondrial genome), extracting homologous regions or genes (IGS, RPB1, RPB2 and TEF1a), as well as extracting multiple regions within a single run. The program is also compared with MITObim, which is meant for the exhaustive assembly of a single target based on a similar query sequence. GRAbB is shown to be more efficient than MITObim in terms of speed, memory and disk usage. The other functionalities (handling multiple targets simultaneously and extracting homologous regions) of the new program are not matched by other programs. The program is available with explanatory documentation at https://github.com/b-brankovics/grabb. GRAbB has been tested on Ubuntu (12.04 and 14.04), Fedora (23), CentOS (7.1.1503) and Mac OS X (10.7). Furthermore, GRAbB is available as a docker repository: brankovics/grabb (https://hub.docker.com/r/brankovics/grabb/).

An improved genome assembly uncovers prolific tandem repeats in Atlantic cod.

PubMed

Tørresen, Ole K; Star, Bastiaan; Jentoft, Sissel; Reinar, William B; Grove, Harald; Miller, Jason R; Walenz, Brian P; Knight, James; Ekholm, Jenny M; Peluso, Paul; Edvardsen, Rolf B; Tooming-Klunderud, Ave; Skage, Morten; Lien, Sigbjørn; Jakobsen, Kjetill S; Nederbragt, Alexander J

2017-01-18

The first Atlantic cod (Gadus morhua) genome assembly published in 2011 was one of the early genome assemblies exclusively based on high-throughput 454 pyrosequencing. Since then, rapid advances in sequencing technologies have led to a multitude of assemblies generated for complex genomes, although many of these are of a fragmented nature with a significant fraction of bases in gaps. The development of long-read sequencing and improved software now enable the generation of more contiguous genome assemblies. By combining data from Illumina, 454 and the longer PacBio sequencing technologies, as well as integrating the results of multiple assembly programs, we have created a substantially improved version of the Atlantic cod genome assembly. The sequence contiguity of this assembly is increased fifty-fold and the proportion of gap-bases has been reduced fifteen-fold. Compared to other vertebrates, the assembly contains an unusual high density of tandem repeats (TRs). Indeed, retrospective analyses reveal that gaps in the first genome assembly were largely associated with these TRs. We show that 21% of the TRs across the assembly, 19% in the promoter regions and 12% in the coding sequences are heterozygous in the sequenced individual. The inclusion of PacBio reads combined with the use of multiple assembly programs drastically improved the Atlantic cod genome assembly by successfully resolving long TRs. The high frequency of heterozygous TRs within or in the vicinity of genes in the genome indicate a considerable standing genomic variation in Atlantic cod populations, which is likely of evolutionary importance.

In-Space Assembly Capability Assessment for Potential Human Exploration and Science Applications

NASA Technical Reports Server (NTRS)

Jefferies, Sharon A.; Jones, Christopher A.; Arney, Dale C.; Stillwagen, Frederic H.; Chai, Patrick R.; Hutchinson, Craig D.; Stafford, Matthew A.; Moses, Robert W.; Dempsey, James A.; Rodgers, Erica M.;

Host-regulated Hepatitis B Virus Capsid Assembly in a Mammalian Cell-free System.

PubMed

Liu, Kuancheng; Hu, Jianming

2018-04-20

The hepatitis B virus (HBV) is an important global human pathogen and represents a major cause of hepatitis, liver cirrhosis and liver cancer. The HBV capsid is composed of multiple copies of a single viral protein, the capsid or core protein (HBc), plays multiple roles in the viral life cycle, and has emerged recently as a major target for developing antiviral therapies against HBV infection. Although several systems have been developed to study HBV capsid assembly, including heterologous overexpression systems like bacteria and insect cells, in vitro assembly using purified protein, and mammalian cell culture systems, the requirement for non-physiological concentrations of HBc and salts and the difficulty in manipulating host regulators of assembly presents major limitations for detailed studies on capsid assembly under physiologically relevant conditions. We have recently developed a mammalian cell-free system based on the rabbit reticulocyte lysate (RRL), in which HBc is expressed at physiological concentrations and assembles into capsids under near-physiological conditions. This system has already revealed HBc assembly requirements that are not anticipated based on previous assembly systems. Furthermore, capsid assembly in this system is regulated by endogenous host factors that can be readily manipulated. Here we present a detailed protocol for this cell-free capsid assembly system, including an illustration on how to manipulate host factors that regulate assembly.

Biology of bats in Douglas-fir forests.

Treesearch

Robin E. Christy; Stephen D. West

1993-01-01

Twelve species of bats occur in Douglas-fir forests of the Pacific Northwest, of which nine are known to roost in tree cavities, bark crevices, or foliage, and several are closely associated with old-growth forests. Thus bat populations may be detrimentally affected by forest management practices involving the removal of large, old trees and snags. We review the life...

Working the Crevices: Granting Students Authority in Authoritarian Schools

ERIC Educational Resources Information Center

Goodman, Joan F.; Hoagland, Jessica; Pierre-Toussaint, Nadel; Rodriguez, Celeste; Sanabria, Christina

2011-01-01

Schools are beset with a serious "alienation gap" between teachers and students that is no less a problem than the "achievement gap." Increasing student voice is thought to be one means to fill the gap, for it activates agency and thereby decreases passivity. The extent of agency ranges from attentive adult listening to strong student leadership.…

Method of preparing gas tags for identification of single and multiple failures of nuclear reactor fuel assemblies

DOEpatents

McCormick, Norman J.

1976-01-01

For use in the identification of failed fuel assemblies in a nuclear reactor, the ratios of the tag gas isotopic concentrations are located on curved surfaces to enable the ratios corresponding to failure of a single fuel assembly to be distinguished from those formed from any combination of two or more failed assemblies.

MIDAS: A Modular DNA Assembly System for Synthetic Biology.

PubMed

van Dolleweerd, Craig J; Kessans, Sarah A; Van de Bittner, Kyle C; Bustamante, Leyla Y; Bundela, Rudranuj; Scott, Barry; Nicholson, Matthew J; Parker, Emily J

2018-04-20

A modular and hierarchical DNA assembly platform for synthetic biology based on Golden Gate (Type IIS restriction enzyme) cloning is described. This enabling technology, termed MIDAS (for Modular Idempotent DNA Assembly System), can be used to precisely assemble multiple DNA fragments in a single reaction using a standardized assembly design. It can be used to build genes from libraries of sequence-verified, reusable parts and to assemble multiple genes in a single vector, with full user control over gene order and orientation, as well as control of the direction of growth (polarity) of the multigene assembly, a feature that allows genes to be nested between other genes or genetic elements. We describe the detailed design and use of MIDAS, exemplified by the reconstruction, in the filamentous fungus Penicillium paxilli, of the metabolic pathway for production of paspaline and paxilline, key intermediates in the biosynthesis of a range of indole diterpenes-a class of secondary metabolites produced by several species of filamentous fungi. MIDAS was used to efficiently assemble a 25.2 kb plasmid from 21 different modules (seven genes, each composed of three basic parts). By using a parts library-based system for construction of complex assemblies, and a unique set of vectors, MIDAS can provide a flexible route to assembling tailored combinations of genes and other genetic elements, thereby supporting synthetic biology applications in a wide range of expression hosts.

Multi-Robot Assembly Strategies and Metrics.

PubMed

Marvel, Jeremy A; Bostelman, Roger; Falco, Joe

2018-02-01

We present a survey of multi-robot assembly applications and methods and describe trends and general insights into the multi-robot assembly problem for industrial applications. We focus on fixtureless assembly strategies featuring two or more robotic systems. Such robotic systems include industrial robot arms, dexterous robotic hands, and autonomous mobile platforms, such as automated guided vehicles. In this survey, we identify the types of assemblies that are enabled by utilizing multiple robots, the algorithms that synchronize the motions of the robots to complete the assembly operations, and the metrics used to assess the quality and performance of the assemblies.

Multi-Robot Assembly Strategies and Metrics

PubMed Central

MARVEL, JEREMY A.; BOSTELMAN, ROGER; FALCO, JOE

2018-01-01

We present a survey of multi-robot assembly applications and methods and describe trends and general insights into the multi-robot assembly problem for industrial applications. We focus on fixtureless assembly strategies featuring two or more robotic systems. Such robotic systems include industrial robot arms, dexterous robotic hands, and autonomous mobile platforms, such as automated guided vehicles. In this survey, we identify the types of assemblies that are enabled by utilizing multiple robots, the algorithms that synchronize the motions of the robots to complete the assembly operations, and the metrics used to assess the quality and performance of the assemblies. PMID:29497234

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

Bae, Brian; Nayak, Dhananjaya; Ray, Ananya

RNA polymerase inhibitors like the CBR class that target the enzyme’s complex catalytic center are attractive leads for new antimicrobials. The catalysis by RNA polymerase involves multiple rearrangements of bridge helix, trigger loop, and active-center side chains that isomerize the triphosphate of bound NTP and two Mg 2+ ions from a preinsertion state to a reactive configuration. CBR inhibitors target a crevice between the N-terminal portion of the bridge helix and a surrounding cap region within which the bridge helix is thought to rearrange during the nucleotide addition cycle. Here, we report crystal structures of CBR inhibitor/Escherichia coli RNA polymerasemore » complexes as well as biochemical tests that establish two distinct effects of the inhibitors on the RNA polymerase catalytic site. One effect involves inhibition of trigger-loop folding via the F loop in the cap, which affects both nucleotide addition and hydrolysis of 3'-terminal dinucleotides in certain backtracked complexes. The second effect is trigger-loop independent, affects only nucleotide addition and pyrophosphorolysis, and may involve inhibition of bridge-helix movements that facilitate reactive triphosphate alignment.« less

Darwin Assembly: fast, efficient, multi-site bespoke mutagenesis

PubMed Central

Cozens, Christopher

2018-01-01

Abstract Engineering proteins for designer functions and biotechnological applications almost invariably requires (or at least benefits from) multiple mutations to non-contiguous residues. Several methods for multiple site-directed mutagenesis exist, but there remains a need for fast and simple methods to efficiently introduce such mutations – particularly for generating large, high quality libraries for directed evolution. Here, we present Darwin Assembly, which can deliver high quality libraries of >108 transformants, targeting multiple (>10) distal sites with minimal wild-type contamination (<0.25% of total population) and which takes a single working day from purified plasmid to library transformation. We demonstrate its efficacy with whole gene codon reassignment of chloramphenicol acetyl transferase, mutating 19 codons in a single reaction in KOD DNA polymerase and generating high quality, multiple-site libraries in T7 RNA polymerase and Tgo DNA polymerase. Darwin Assembly uses commercially available enzymes, can be readily automated, and offers a cost-effective route to highly complex and customizable library generation. PMID:29409059

Status of ash (Fraxinus spp.) species in Alabama, Arkansas, Mississippi, and Louisiana, 2013

Treesearch

S.N. Oswalt

2015-01-01

The emerald ash borer (EAB; Agrilus planipennis) is an introduced Asian beetle species that was first detected in trees in the Fraxinus (ash) genus in the United States in 2002. Female EAB beetles lay between 40 to 70 eggs in cracks, crevices, and beneath bark flakes. The eggs hatch within about 2 weeks, larvae bore through the...

ATLAS 60’ Fording Study

DTIC Science & Technology

1992-03-03

crack. Carbon steel stress cracks in the presence of sodium hydroxide (" caustic embrittlement"), whereas austenitic stainless steels stress crack in...transmission life. - Outboard planetary axle design reduces stresses on differential, drive shafts and axle shaft U-joints. . Enclosed oil disc brakes on... Stress Corrosion Crevice Pitting Erosion Corrosion Uniform Corrosion Intergranular Selective Leaching Page 19 Caterpflar Inc. ATLAS Fording Study Q The

Office of Naval Research Overview of Corrosion S&T Program

DTIC Science & Technology

2010-12-02

a carbon induced passivity for LTCSS treated austenitic stainless steels - Low temp. allows interstitial C diffusion, but not substitutional...paraequilibrium carburization mechanism(s) that lead to the enhanced corrosion resistance seaw ater crevice corrosion on 316 Stainless Steel LTC...Treated 316 untreated LTC process TTT diagram LTCSS Surface Modification: • Carbon concentrations > 12 at. % in 316 stainless steel while maintaining

Structural variability and species diversity of a dwarf Caribbean dry forest

Treesearch

E. Medina; E. Cuevas; S. Molina; A.E. Lugo; O. Ramos

2010-01-01

Low stature woody vegetation of the south-west coast of Puerto Rico grows on a rocky calcareous substrate where plants can only root in holes, cracks, and crevices accumulating water and sediments that allow seed germination and seedling development. Being in a coastal location these communities are influenced by steady onshore winds, high solar radiation, and salt...

Coordinated vigilance provides evidence for direct reciprocity in coral reef fishes.

PubMed

Brandl, Simon J; Bellwood, David R

2015-09-25

Reciprocity is frequently assumed to require complex cognitive abilities. Therefore, it has been argued that reciprocity may be restricted to animals that can meet these demands. Here, we provide evidence for the potential presence of direct reciprocity in teleost fishes. We demonstrate that in pairs of coral reef rabbitfishes (f. Siganidae), one fish frequently assumes an upright vigilance position in the water column, while the partner forages in small crevices in the reef substratum. Both behaviours are strongly coordinated and partners regularly alternate their positions, resulting in a balanced distribution of foraging activity. Compared to solitary individuals, fishes in pairs exhibit longer vigilance bouts, suggesting that the help provided to the partner is costly. In turn, fishes in pairs take more consecutive bites and penetrate deeper into crevices than solitary individuals, suggesting that the safety provided by a vigilant partner may outweigh initial costs by increasing foraging efficiency. Thus, the described system appears to meet all of the requirements for direct reciprocity. We argue that the nature of rabbitfish pairs provides favourable conditions for the establishment of direct reciprocity, as continuous interaction with the same partner, simultaneous needs, interdependence, and communication relax the cognitive demands of reciprocal cooperation.

Using Aerogel-Based Insulation Material To Prevent Foam Loss on the Liquid-Hydrogen Intertank

NASA Technical Reports Server (NTRS)

2008-01-01

Uninsulated areas on cryogenic propellant tanks and feedlines cause moisture in the air to condense or ice to form. Flange joints, bracket supports, expansion bellows, and other cavities are uninsulated by design. These areas cannot be sealed because conventional thermal insulation materials would restrict mechanical articulations. Aerogel-based thermal insulation systems are able to seal critical locations such as the liquid-oxygen (LO2) feedline bellows. A new thermal insulation system was also necessary between the intertank wall, flange, and the liquid-hydrogen (LH2) tank dome, where there is a cavity (or crevice) with an exposed 20-K surface. When nitrogen gas is used for purging within the intertank volume, it condenses on this cold surface. Some solid nitrogen may also form on the colder side of the crevice. Voids or discontinuities within the foam can pressurize and cause areas of foam to weaken and break off, reducing thermal efficiency and creating potentially dangerous debris. To prevent this foam loss, we developed a thermal insulation system using bulk-fill aerogel material and demonstrated it with a one-tenth-scale model of the LH2 intertank flange area

Experimental tooth pain elevates substance P and matrix metalloproteinase-8 levels in human gingival crevice fluid.

PubMed

Avellán, Nina-Li; Sorsa, Timo; Tervahartiala, Taina; Forster, Clemens; Kemppainen, Pentti

2008-02-01

Tooth pain can induce a neurogenic inflammatory reaction in gingiva in association with local elevations of matrix metalloproteinase (MMP)-8, which is considered the major tissue destructive protease in gingival crevice fluid (GCF). The pro-inflammatory neuropeptides released by sensory nerves coordinate the activities of the immuno-effector cells and may influence the secretion of MMP-8. With this background, we studied whether experimental tooth pain can trigger changes in GCF levels of the neuropeptide substance P (SP) and MMP-8. The GCF SP levels of stimulated and non-stimulated teeth were analyzed for SP using a competitive enzyme immunoassay (EIA). The GCF MMP-8 levels were determined by quantitative immunofluorometric assay (IFMA). Painful stimulation of the upper central incisor caused significant elevations in GCF SP and MMP-8 levels of the stimulated tooth. At the same time, the GCF SP and MMP-8 levels of non-stimulated control teeth were unchanged. These data indicate that experimental tooth pain can induce local elevations of SP and MMP-8 levels in GCF simultaneously. This supports the possibility of a local neurogenic spread of inflammatory reactions from intrapulpal to surrounding periodontal tissues.

Methanation assembly using multiple reactors

DOEpatents

Jahnke, Fred C.; Parab, Sanjay C.

2007-07-24

A methanation assembly for use with a water supply and a gas supply containing gas to be methanated in which a reactor assembly has a plurality of methanation reactors each for methanating gas input to the assembly and a gas delivery and cooling assembly adapted to deliver gas from the gas supply to each of said methanation reactors and to combine water from the water supply with the output of each methanation reactor being conveyed to a next methanation reactor and carry the mixture to such next methanation reactor.

PAVE: program for assembling and viewing ESTs.

PubMed

Soderlund, Carol; Johnson, Eric; Bomhoff, Matthew; Descour, Anne

2009-08-26

New sequencing technologies are rapidly emerging. Many laboratories are simultaneously working with the traditional Sanger ESTs and experimenting with ESTs generated by the 454 Life Science sequencers. Though Sanger ESTs have been used to generate contigs for many years, no program takes full advantage of the 5' and 3' mate-pair information, hence, many tentative transcripts are assembled into two separate contigs. The new 454 technology has the benefit of high-throughput expression profiling, but introduces time and space problems for assembling large contigs. The PAVE (Program for Assembling and Viewing ESTs) assembler takes advantage of the 5' and 3' mate-pair information by requiring that the mate-pairs be assembled into the same contig and joined by n's if the two sub-contigs do not overlap. It handles the depth of 454 data sets by "burying" similar ESTs during assembly, which retains the expression level information while circumventing time and space problems. PAVE uses MegaBLAST for the clustering step and CAP3 for assembly, however it assembles incrementally to enforce the mate-pair constraint, bury ESTs, and reduce incorrect joins and splits. The PAVE data management system uses a MySQL database to store multiple libraries of ESTs along with their metadata; the management system allows multiple assemblies with variations on libraries and parameters. Analysis routines provide standard annotation for the contigs including a measure of differentially expressed genes across the libraries. A Java viewer program is provided for display and analysis of the results. Our results clearly show the benefit of using the PAVE assembler to explicitly use mate-pair information and bury ESTs for large contigs. The PAVE assembler provides a software package for assembling Sanger and/or 454 ESTs. The assembly software, data management software, Java viewer and user's guide are freely available.

Interplay between Short- and Long-Term Plasticity in Cell-Assembly Formation

PubMed Central

Hiratani, Naoki; Fukai, Tomoki

2014-01-01

Various hippocampal and neocortical synapses of mammalian brain show both short-term plasticity and long-term plasticity, which are considered to underlie learning and memory by the brain. According to Hebb’s postulate, synaptic plasticity encodes memory traces of past experiences into cell assemblies in cortical circuits. However, it remains unclear how the various forms of long-term and short-term synaptic plasticity cooperatively create and reorganize such cell assemblies. Here, we investigate the mechanism in which the three forms of synaptic plasticity known in cortical circuits, i.e., spike-timing-dependent plasticity (STDP), short-term depression (STD) and homeostatic plasticity, cooperatively generate, retain and reorganize cell assemblies in a recurrent neuronal network model. We show that multiple cell assemblies generated by external stimuli can survive noisy spontaneous network activity for an adequate range of the strength of STD. Furthermore, our model predicts that a symmetric temporal window of STDP, such as observed in dopaminergic modulations on hippocampal neurons, is crucial for the retention and integration of multiple cell assemblies. These results may have implications for the understanding of cortical memory processes. PMID:25007209

Measuring spent fuel assembly multiplication in borated water with a passive neutron albedo reactivity instrument

NASA Astrophysics Data System (ADS)

Tobin, Stephen J.; Peura, Pauli; Bélanger-Champagne, Camille; Moring, Mikael; Dendooven, Peter; Honkamaa, Tapani

2018-07-01

The performance of a passive neutron albedo reactivity (PNAR) instrument to measure neutron multiplication of spent nuclear fuel in borated water is investigated as part of an integrated non-destructive assay safeguards system. To measure the PNAR Ratio, which is proportional to the neutron multiplication, the total neutron count rate is measured in high- and low-multiplying environments by the PNAR instrument. The integrated system also contains a load cell and a passive gamma emission tomograph, and as such meets all the recommendations of the IAEA's recent ASTOR Experts Group report. A virtual spent fuel library for VVER-440 fuel was used in conjunction with MCNP simulations of the PNAR instrument to estimate the measurement uncertainties from (1) variation in the water boron content, (2) assembly positioning in the detector and (3) counting statistics. The estimated aggregate measurement uncertainty on the PNAR Ratio measurement is 0.008, to put this uncertainty in context, the difference in the PNAR Ratio between a fully irradiated assembly and this same assembly when fissile isotopes only absorb neutrons, but do not emit neutrons, is 0.106, a 13-sigma effect. The 1-sigma variation of 0.008 in the PNAR Ratio is estimated to correspond to a 3.2 GWd/tU change in assembly burnup.

Self-assembly behaviours of peptide-drug conjugates: influence of multiple factors on aggregate morphology and potential self-assembly mechanism

NASA Astrophysics Data System (ADS)

Fan, Qin; Ji, Yujie; Wang, Jingjing; Wu, Li; Li, Weidong; Chen, Rui; Chen, Zhipeng

2018-04-01

Peptide-drug conjugates (PDCs) as self-assembly prodrugs have the unique and specific features to build one-component nanomedicines. Supramolecular structure based on PDCs could form various morphologies ranging from nanotube, nanofibre, nanobelt to hydrogel. However, the assembly process of PDCs is too complex to predict or control. Herein, we investigated the effects of extrinsic factors on assembly morphology and the possible formation of nanostructures based on PDCs. To this end, we designed a PDC consisting of hydrophobic drug (S)-ketoprofen (Ket) and valine-glutamic acid dimeric repeats peptide (L-VEVE) to study their assembly behaviour. Our results showed that the critical assembly concentration of Ket-L-VEVE was 0.32 mM in water to form various nanostructures which experienced from micelle, nanorod, nanofibre to nanoribbon. The morphology was influenced by multiple factors including molecular design, assembly time, pH and hydrogen bond inhibitor. On the basis of experimental results, we speculated the possible assembly mechanism of Ket-L-VEVE. The π-π stacking interaction between Ket molecules could serve as an anchor, and hydrogen bonded-induced β-sheets and hydrophilic/hydrophobic balance between L-VEVE peptide play structure-directing role in forming filament-like or nanoribbon morphology. This work provides a new sight to rationally design and precisely control the nanostructure of PDCs based on aromatic fragment.

Mussel-inspired nano-building block assemblies for mimicking extracellular matrix microenvironments with multiple functions.

PubMed

Wang, Zhenming; Jia, Zhanrong; Jiang, Yanan; Li, Pengfei; Han, Lu; Lu, Xiong; Ren, Fuzeng; Wang, Kefeng; Yuan, Huiping

2017-08-03

The assembly of nano-building blocks is an effective way to produce artificial extracellular matrix microenvironments with hierarchical micro/nano structures. However, it is hard to assemble different types of nano-building blocks, to form composite coatings with multiple functions, by traditional layer-by-layer (LbL) self-assembly methods. Inspired by the mussel adhesion mechanism, we developed polydopamine (PDA)-decorated bovine serum albumin microspheres (BSA-MS) and nano-hydroxyapatite (nano-HA), and assembled them to form bioactive coatings with micro/nano structures encapsulating bone morphogenetic protein-2 (BMP-2). First, PDA-decorated nano-HA (nano-pHA) was obtained by oxidative polymerization of dopamine on nano-HA. Second, BMP-2-encapsulated BSA microspheres were prepared through desolvation, and then were also decorated by PDA (pBSA-MS). Finally, the nano-pHA and pBSA-MS were assembled using the adhesive properties of PDA. Bone marrow stromal cell cultures and in vivo implantation, showed that the pHA/pBSA (BMP-2) coatings can promote cell adhesion, proliferation, and benefited for osteoinductivity. PDA decoration was also applied to assemble various functional nanoparticles, such as nano-HA, polystyrene, and Fe 3 O 4 nanoparticles. In summary, this study provides a novel strategy for the assembly of biofunctional nano-building blocks, which surpasses traditional LbL self-assembly of polyelectrolytes, and can find broad applications in bioactive agents delivery or multi-functional coatings.

Self-assembly behaviours of peptide-drug conjugates: influence of multiple factors on aggregate morphology and potential self-assembly mechanism.

PubMed

Fan, Qin; Ji, Yujie; Wang, Jingjing; Wu, Li; Li, Weidong; Chen, Rui; Chen, Zhipeng

2018-04-01

Peptide-drug conjugates (PDCs) as self-assembly prodrugs have the unique and specific features to build one-component nanomedicines. Supramolecular structure based on PDCs could form various morphologies ranging from nanotube, nanofibre, nanobelt to hydrogel. However, the assembly process of PDCs is too complex to predict or control. Herein, we investigated the effects of extrinsic factors on assembly morphology and the possible formation of nanostructures based on PDCs. To this end, we designed a PDC consisting of hydrophobic drug ( S )-ketoprofen (Ket) and valine-glutamic acid dimeric repeats peptide (L-VEVE) to study their assembly behaviour. Our results showed that the critical assembly concentration of Ket-L-VEVE was 0.32 mM in water to form various nanostructures which experienced from micelle, nanorod, nanofibre to nanoribbon. The morphology was influenced by multiple factors including molecular design, assembly time, pH and hydrogen bond inhibitor. On the basis of experimental results, we speculated the possible assembly mechanism of Ket-L-VEVE. The π-π stacking interaction between Ket molecules could serve as an anchor, and hydrogen bonded-induced β-sheets and hydrophilic/hydrophobic balance between L-VEVE peptide play structure-directing role in forming filament-like or nanoribbon morphology. This work provides a new sight to rationally design and precisely control the nanostructure of PDCs based on aromatic fragment.

Space assembly fixtures and aids

NASA Technical Reports Server (NTRS)

Bloom, K. A.; Lillenas, A. N.

1980-01-01

Concepts and requirements for assembly fixtures and aids necessary for the assembly and maintenance of spare platforms were studied. Emphasis was placed on erectable and deployable type structures with the shuttle orbiter as the assembly base. Both single and multiple orbiter flight cases for the platform assembly were considered. Applicable space platform assembly studies were reviewed to provide a data base for establishing the assembly fixture and aids design requirements, assembly constraints, and the development of representative design concepts. Conclusions indicated that fixture requirements will vary with platform size. Larger platforms will require translation relative to the orbiter RMS working volume. The installation of platform payloads and subsystems (e.g., utility distribution) must also be considered in the specification of assembly fixtures and aids.

Multiple electrokinetic actuators for feedback control of colloidal crystal size.

PubMed

Juárez, Jaime J; Mathai, Pramod P; Liddle, J Alexander; Bevan, Michael A

2012-10-21

We report a feedback control method to precisely target the number of colloidal particles in quasi-2D ensembles and their subsequent assembly into crystals in a quadrupole electrode. Our approach relies on tracking the number of particles within a quadrupole electrode, which is used in a real-time feedback control algorithm to dynamically actuate competing electrokinetic transport mechanisms. Particles are removed from the quadrupole using DC-field mediated electrophoretic-electroosmotic transport, while high-frequency AC-field mediated dielectrophoretic transport is used to concentrate and assemble colloidal crystals. Our results show successful control of the size of crystals containing 20 to 250 colloidal particles with less than 10% error. Assembled crystals are characterized by their radius of gyration, crystallinity, and number of edge particles, and demonstrate the expected size-dependent properties. Our findings demonstrate successful ensemble feedback control of the assembly of different sized colloidal crystals using multiple actuators, which has broad implications for control over nano- and micro- scale assembly processes involving colloidal components.

Separating homeologs by phasing in the tetraploid wheat transcriptome.

PubMed

Krasileva, Ksenia V; Buffalo, Vince; Bailey, Paul; Pearce, Stephen; Ayling, Sarah; Tabbita, Facundo; Soria, Marcelo; Wang, Shichen; Akhunov, Eduard; Uauy, Cristobal; Dubcovsky, Jorge

2013-06-25

The high level of identity among duplicated homoeologous genomes in tetraploid pasta wheat presents substantial challenges for de novo transcriptome assembly. To solve this problem, we develop a specialized bioinformatics workflow that optimizes transcriptome assembly and separation of merged homoeologs. To evaluate our strategy, we sequence and assemble the transcriptome of one of the diploid ancestors of pasta wheat, and compare both assemblies with a benchmark set of 13,472 full-length, non-redundant bread wheat cDNAs. A total of 489 million 100 bp paired-end reads from tetraploid wheat assemble in 140,118 contigs, including 96% of the benchmark cDNAs. We used a comparative genomics approach to annotate 66,633 open reading frames. The multiple k-mer assembly strategy increases the proportion of cDNAs assembled full-length in a single contig by 22% relative to the best single k-mer size. Homoeologs are separated using a post-assembly pipeline that includes polymorphism identification, phasing of SNPs, read sorting, and re-assembly of phased reads. Using a reference set of genes, we determine that 98.7% of SNPs analyzed are correctly separated by phasing. Our study shows that de novo transcriptome assembly of tetraploid wheat benefit from multiple k-mer assembly strategies more than diploid wheat. Our results also demonstrate that phasing approaches originally designed for heterozygous diploid organisms can be used to separate the close homoeologous genomes of tetraploid wheat. The predicted tetraploid wheat proteome and gene models provide a valuable tool for the wheat research community and for those interested in comparative genomic studies.

Separating homeologs by phasing in the tetraploid wheat transcriptome

PubMed Central

2013-01-01

Background The high level of identity among duplicated homoeologous genomes in tetraploid pasta wheat presents substantial challenges for de novo transcriptome assembly. To solve this problem, we develop a specialized bioinformatics workflow that optimizes transcriptome assembly and separation of merged homoeologs. To evaluate our strategy, we sequence and assemble the transcriptome of one of the diploid ancestors of pasta wheat, and compare both assemblies with a benchmark set of 13,472 full-length, non-redundant bread wheat cDNAs. Results A total of 489 million 100 bp paired-end reads from tetraploid wheat assemble in 140,118 contigs, including 96% of the benchmark cDNAs. We used a comparative genomics approach to annotate 66,633 open reading frames. The multiple k-mer assembly strategy increases the proportion of cDNAs assembled full-length in a single contig by 22% relative to the best single k-mer size. Homoeologs are separated using a post-assembly pipeline that includes polymorphism identification, phasing of SNPs, read sorting, and re-assembly of phased reads. Using a reference set of genes, we determine that 98.7% of SNPs analyzed are correctly separated by phasing. Conclusions Our study shows that de novo transcriptome assembly of tetraploid wheat benefit from multiple k-mer assembly strategies more than diploid wheat. Our results also demonstrate that phasing approaches originally designed for heterozygous diploid organisms can be used to separate the close homoeologous genomes of tetraploid wheat. The predicted tetraploid wheat proteome and gene models provide a valuable tool for the wheat research community and for those interested in comparative genomic studies. PMID:23800085

Gradated assembly of multiple proteins into supramolecular nanomaterials

NASA Astrophysics Data System (ADS)

Hudalla, Gregory A.; Sun, Tao; Gasiorowski, Joshua Z.; Han, Huifang; Tian, Ye F.; Chong, Anita S.; Collier, Joel H.

2014-08-01

Biomaterials exhibiting precise ratios of different bioactive protein components are critical for applications ranging from vaccines to regenerative medicine, but their design is often hindered by limited choices and cross-reactivity of protein conjugation chemistries. Here, we describe a strategy for inducing multiple different expressed proteins of choice to assemble into nanofibres and gels with exceptional compositional control. The strategy employs ‘βTail’ tags, which allow for good protein expression in bacteriological cultures, yet can be induced to co-assemble into nanomaterials when mixed with additional β-sheet fibrillizing peptides. Multiple different βTail fusion proteins could be inserted into peptide nanofibres alone or in combination at predictable, smoothly gradated concentrations, providing a simple yet versatile route to install precise combinations of proteins into nanomaterials. The technology is illustrated by achieving precisely targeted hues using mixtures of fluorescent proteins, by creating nanofibres bearing enzymatic activity, and by adjusting antigenic dominance in vaccines.

Two men with multiple disabilities carry out an assembly work activity with the support of a technology system.

PubMed

Lancioni, Giulio E; Singh, Nirbhay N; O'Reilly, Mark F; Green, Vanessa A; Oliva, Doretta; Campodonico, Francesca

2013-10-01

To assess whether two persons with multiple disabilities could learn a work activity (i.e., assembling trolley wheels) with the support of a technology system. After an initial baseline, the study compared the effects of intervention sessions relying on the technology system (which called the participants to the different workstations and provided feedback and final stimulation) with the effects of intervention sessions carried out without technology. The two types of intervention sessions were conducted according to an alternating treatments design. Eventually, only intervention sessions relying on the technology system were used. Both participants managed to assemble wheels independently during intervention sessions relying on the technology system while they failed during sessions without the system. Their performance was strengthened during the final part of the study, in which only sessions with the system occurred. Technology may be critical in helping persons with multiple disabilities manage multi-step work activities.

40 CFR 1060.102 - What permeation emission control requirements apply for fuel lines?

Code of Federal Regulations, 2011 CFR

2011-07-01

... assemblies as aggregated systems that include multiple sections of fuel line with connectors and fittings. For example, you may certify fuel lines for portable marine fuel tanks as assemblies of fuel hose, primer bulbs, and self-sealing end connections. The length of such an assembly must not be longer than a...

40 CFR 1060.102 - What permeation emission control requirements apply for fuel lines?

Code of Federal Regulations, 2010 CFR

2010-07-01

... assemblies as aggregated systems that include multiple sections of fuel line with connectors and fittings. For example, you may certify fuel lines for portable marine fuel tanks as assemblies of fuel hose, primer bulbs, and self-sealing end connections. The length of such an assembly must not be longer than a...

One-step formation of multiple Pickering emulsions stabilized by self-assembled poly(dodecyl acrylate-co-acrylic acid) nanoparticles.

PubMed

Zhu, Ye; Sun, Jianhua; Yi, Chenglin; Wei, Wei; Liu, Xiaoya

2016-09-13

In this study, a one-step generation of stable multiple Pickering emulsions using pH-responsive polymeric nanoparticles as the only emulsifier was reported. The polymeric nanoparticles were self-assembled from an amphiphilic random copolymer poly(dodecyl acrylate-co-acrylic acid) (PDAA), and the effect of the copolymer content on the size and morphology of PDAA nanoparticles was determined by dynamic light scattering (DLS) and transmission electron microscopy (TEM). The emulsification study of PDAA nanoparticles revealed that multiple Pickering emulsions could be generated through a one-step phase inversion process by using PDAA nanoparticles as the stabilizer. Moreover, the emulsification performance of PDAA nanoparticles at different pH values demonstrated that multiple emulsions with long-time stability could only be stabilized by PDAA nanoparticles at pH 5.5, indicating that the surface wettability of PDAA nanoparticles plays a crucial role in determining the type and stability of the prepared Pickering emulsions. Additionally, the polarity of oil does not affect the emulsification performance of PDAA nanoparticles, and a wide range of oils could be used as the oil phase to prepare multiple emulsions. These results demonstrated that multiple Pickering emulsions could be generated via the one-step emulsification process using self-assembled polymeric nanoparticles as the stabilizer, and the prepared multiple emulsions have promising potential to be applied in the cosmetic, medical, and food industries.

Planar multi-electrode array sensor for localized electrochemical corrosion detection

DOEpatents

Tormoen, Garth William; Brossia, Christopher Sean

2014-01-07

A planarized type of coupled multi-electrode corrosion sensing device. Electrode pads are fabricated on a thin backing, such as a thin film. Each pad has an associated electrical lead for connection to auxiliary electronic circuitry, which may include a resistor associated with each electrical pad. The design permits the device to be easily placed in small crevices or under coatings such as paint.

Corrosion Fatigue

DTIC Science & Technology

1981-10-01

particularly under conditions of cathodic polarization. Sul- fate ion , while less damaging under free corrosion conditions, is equally aggressive at...Editing and Reproduction Ltd Harford 11ouse, 7-9 Charlotte St, London, WIP 1HD I I - PREFACE Failure by fatigue and degradation by corrosion continue to...of halide ions . In the unstressed state, this degrada- tion may be manifested by localized corrosion such as pitting, crevice corrosion or ex

Grand Marais Harbor, Cook County, Minnesota, Operation and Maintenance Activities, Environment Assessment Report.

DTIC Science & Technology

1974-12-01

34 - . .. .. . . . . . . -.. 2.523 In rocky crevices along the shore walls there are a variety of sedges, rushes, grasses, mosses, lichens ...our dre~tinn anid d!’aonal planu ~ for 1rand ’N r~ls Hxariors ihe a1tcrrat.v.e deacrit’,ed In’ tti..i; le.tter ealicatn. dipoa plans for l𔃺tii pollato-4

Multi-Scale Investigation of the Formation and Breakdown of Passive Films on Carbon Steel Rebar in Concrete

NASA Astrophysics Data System (ADS)

Ghods, Pouria

The multi-scale investigation presented in this thesis was carried out to understand better the mechanisms of passivation and chloride-induced depassivation of carbon steel reinforcement in concrete. The study consisted of electrochemical experiments (electrochemical impedance spectroscopy, linear polarization resistance, free corrosion potential, anodic polarization), microscopic examinations (scanning electron microscopy, transmission electron microscopy, selected area diffraction, convergent beam electron diffraction), numerical modeling (finite element method), and spectroscopic studies (x-ray photoelectron, energy dispersed x-ray, electron energy loss). Electrochemical and microscopic studies showed that the composition of the pore solution and the surface conditions of the rebar affect the passivity and depassivation of carbon steel in concrete. It was demonstrated that crevices between mill scale and steel may become potential sites for depassivation and pit nucleation. The numerical investigation that was carried out to test this hypothesis confirmed that the ratio of chloride to hydroxide concentrations, Cl-/OH-, in crevices increased to levels higher than that of the bulk pore solution, making crevices more vulnerable to depassivation. Therefore, it was concluded that the variability associated with reported chloride thresholds might be attributed, at least in part, to the variability in mill scale properties resulting from the variability in manufacturing. The nano-scale microscopic and spectroscopic studies indicated the formation of 4-10 nm-thick passive oxide films on carbon steel in simulated concrete pore solutions, and these films consisted of two layers separated with an indistinct border. The inner layer was mainly composed of protective Fe2+-rich oxides that are in epitaxial relationship with the underlying steel surface; while the outer layer mostly consisted of (possibly porous) Fe3+-rich oxides, through which chlorides can penetrate. It was proposed that, in the presence of chlorides, Fe+2-rich oxides in the inner layer transform into Fe+3-rich oxides and potentially become un-protective. Although how this transformation occurs is still subject of future research, there are evidences showing that the process most likely leads to the formation of local anodic and cathodic sites on the steel surface.

[In vitro anti-Trichomonas vaginalis effects of a mixture of dihydroartemisinin and metronidazole].

PubMed

Tang, Zi-Hao; Liu, Ke-Yue; Mei, Jun; Gao, Xing-Zheng

2010-12-30

To observe the effect of a mixture of dihydroartemisinin and metronidazole on ultrastructure of Trichomonas vaginalis trophozoites in vitro for exploring trichomonacidal mechanism of the drug mixture. The trophozoites were cultivated with liver extract solution medium that contained 2.5 x 10(6) parasites/ml. There were dihydroartemisinin 0.5 mg/ml and metronidazole 0.002 mg/ml in the experimental tubes of the drug mixture group. Groups of control (without drug), dihydroartemisinin (1 mg/ml) and metronidazole (5 mg/ml) were established and performed in the same experimental conditions. The parasites were observed by scanning and transmission electron microscopes after having treated with the drugs at 37 degrees for 3.5-5 h. Under scanning electron microscope, the cell membrane of T. vaginalis treated only with dihydroartemisinin for 35 h was damaged, part of pellicle peeled off. Although the surface of the trophozoites treated only with metronidazole for 5 h showed many small bubbles and hollows, the cell membrane looked integral. However, surface of the parasite exposed to the drug mixture for 3.5-4.2 h showed deep folds and cracks, the cell membrane was damaged and even peeled off. When the cell ruptured, the nucleus, axostyle, pelta and hydrogenosomes were exposed, and the cytoplasm spilled out. Transmission electron microscopy showed that the membrane system of the trophozoites treated only with dihydroartemisinin for 3.5 h was damaged considerably. The cytoplasm of damaged parasite spilled out. The cytoplasm of the parasite treated only with metronidazole for 3.5-5 h was damaged seriously. Vacuoles and crevices were visible in the cytoplasm. The cell membrane and the content of the parasites treated with the drug mixture for 3.5-4.5 h were damaged seriously. There were some vacuoles and crevices, dilated endoplasmic reticulum, injured and deformed hydrogenosomes in the cytoplasm. The cell organelles mostly disappeared. Crevices also existed in the nucleus. The nuclear membrane fractured and even disappeared. The acting targets of dihydroartemisinin and metronidazole to T. vaginalis trophozoite were different, and a combination of the two drugs shows stronger effect in killing the parasites.

A complex of cardiac cytochrome c1 and cytochrome c.

PubMed

Chiang, Y L; Kaminsky, L S; King, T E

1976-01-10

The interactions of cytochrome c1 and cytochrome c from bovine cardiac mitochondria were investigated. Cytochrome c1 and cytochrome c formed a 1:1 molecular complex in aqueous solutions of low ionic strength. The complex was stable to Sephadex G-75 chromatography. The formation and stability of the complex were independent of the oxidation state of the cytochrome components as far as those reactions studied were concerned. The complex was dissociated in solutions of ionic strength higher than 0.07 or pH exceeding 10 and only partially dissociated in 8 M urea. No complexation occurred when cytochrome c was acetylated on 64% of its lysine residues or photooxidized on its 2 methionine residues. Complexes with molecular ratios of less than 1:1 (i.e. more cytochrome c) were obtained when polymerized cytochrome c, or cytochrome c with all lysine residues guanidinated, or a "1-65 heme peptide" from cyanogen bromide cleavage of cytochrome c was used. These results were interpreted to imply that the complex was predominantly maintained by ionic interactions probably involving some of the lysine residues of cytochrome c but with major stabilization dependent on the native conformations of both cytochromes. The reduced complex was autooxidizable with biphasic kinetics with first order rate constants of 6 X 10(-5) and 5 X U0(-5) s-1 but did not react with carbon monoxide. The complex reacted with cyanide and was reduced by ascorbate at about 32% and 40% respectively, of the rates of reaction with cytochrome c alone. The complex was less photoreducible than cytochrome c1 alone. The complex exhibited remarkably different circular dichroic behavior from that of the summation of cytochrome c1 plus cytochrome c. We concluded that when cytochromes c1 and c interacted they underwent dramatic conformational changes resulting in weakening of their heme crevices. All results available would indicate that in the complex cytochrome c1 was bound at the entrance to the heme crevice of cytochrome c on the methionine-80 side of the heme crevice.

Multiple pure tone elimination strut assembly. [air breathing engines

NASA Technical Reports Server (NTRS)

Burcham, F. W. (Inventor)

1981-01-01

An acoustic noise elimination assembly is disclosed which has a capability for disrupting the continuity of fields of sound pressures forwardly projected from fans or rotors of a type commonly found in the fan or compressor first stage for air-breathing engines, when operating at tip speeds in the supersonic range. The assembly includes a tubular cowl defining a duct for delivering an air stream axially into the intake for a jet engine. A sound barrier, defined by a number of intersecting flat plates or struts has a line of intersection coincident with a longitudinal axis of the tubular cowl, which serves to disrupt the continuity of rotating fields of multiple pure tonal components of noise.

Self-aligning hydraulic piston assembly for tensile testing of ceramic

DOEpatents

Liu, Kenneth C.

1987-01-01

The present invention is directed to a self-aligning grip housing assembly that can transmit an uniaxial load to a tensil specimen without introducing bending stresses into the specimen. Disposed inside said grip housing assembly are a multiplicity of supporting pistons connected to a common source of pressurized oil that carry equal shares of the load applied to the specimen irregardless whether there is initial misalignment between the specimen load column assembly and housing axis.

Self-aligning hydraulic piston assembly for tensile testing of ceramic

DOEpatents

Liu, K.C.

1987-08-18

The present invention is directed to a self-aligning grip housing assembly that can transmit an uniaxial load to a tensile specimen without introducing bending stresses into the specimen. Disposed inside said grip housing assembly are a multiplicity of supporting pistons connected to a common source of pressurized oil that carry equal shares of the load applied to the specimen regardless whether there is initial misalignment between the specimen load column assembly and housing axis. 4 figs.

Membrane Assembly during the Infection Cycle of the Giant Mimivirus

PubMed Central

Mutsafi, Yael; Shimoni, Eyal; Shimon, Amir; Minsky, Abraham

2013-01-01

Although extensively studied, the structure, cellular origin and assembly mechanism of internal membranes during viral infection remain unclear. By combining diverse imaging techniques, including the novel Scanning-Transmission Electron Microscopy tomography, we elucidate the structural stages of membrane biogenesis during the assembly of the giant DNA virus Mimivirus. We show that this elaborate multistage process occurs at a well-defined zone localized at the periphery of large viral factories that are generated in the host cytoplasm. Membrane biogenesis is initiated by fusion of multiple vesicles, ∼70 nm in diameter, that apparently derive from the host ER network and enable continuous supply of lipid components to the membrane-assembly zone. The resulting multivesicular bodies subsequently rupture to form large open single-layered membrane sheets from which viral membranes are generated. Membrane generation is accompanied by the assembly of icosahedral viral capsids in a process involving the hypothetical major capsid protein L425 that acts as a scaffolding protein. The assembly model proposed here reveals how multiple Mimivirus progeny can be continuously and efficiently generated and underscores the similarity between the infection cycles of Mimivirus and Vaccinia virus. Moreover, the membrane biogenesis process indicated by our findings provides new insights into the pathways that might mediate assembly of internal viral membranes in general. PMID:23737745

Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop

PubMed Central

Hatakeyama, Masaomi; Aluri, Sirisha; Balachadran, Mathi Thumilan; Sivarajan, Sajeevan Radha; Patrignani, Andrea; Grüter, Simon; Poveda, Lucy; Shimizu-Inatsugi, Rie; Baeten, John; Francoijs, Kees-Jan; Nataraja, Karaba N; Reddy, Yellodu A Nanja; Phadnis, Shamprasad; Ravikumar, Ramapura L; Schlapbach, Ralph; Sreeman, Sheshshayee M; Shimizu, Kentaro K

2018-01-01

Abstract Finger millet (Eleusine coracana (L.) Gaertn) is an important crop for food security because of its tolerance to drought, which is expected to be exacerbated by global climate changes. Nevertheless, it is often classified as an orphan/underutilized crop because of the paucity of scientific attention. Among several small millets, finger millet is considered as an excellent source of essential nutrient elements, such as iron and zinc; hence, it has potential as an alternate coarse cereal. However, high-quality genome sequence data of finger millet are currently not available. One of the major problems encountered in the genome assembly of this species was its polyploidy, which hampers genome assembly compared with a diploid genome. To overcome this problem, we sequenced its genome using diverse technologies with sufficient coverage and assembled it via a novel multiple hybrid assembly workflow that combines next-generation with single-molecule sequencing, followed by whole-genome optical mapping using the Bionano Irys® system. The total number of scaffolds was 1,897 with an N50 length >2.6 Mb and detection of 96% of the universal single-copy orthologs. The majority of the homeologs were assembled separately. This indicates that the proposed workflow is applicable to the assembly of other allotetraploid genomes. PMID:28985356

Multiple pump housing

DOEpatents

Donoho, II, Michael R.; Elliott; Christopher M.

2010-03-23

A fluid delivery system includes a first pump having a first drive assembly, a second pump having a second drive assembly, and a pump housing. At least a portion of each of the first and second pumps are located in the housing.

Aerial cooperative transporting and assembling control using multiple quadrotor-manipulator systems

NASA Astrophysics Data System (ADS)

Qi, Yuhua; Wang, Jianan; Shan, Jiayuan

2018-02-01

In this paper, a fully distributed control scheme for aerial cooperative transporting and assembling is proposed using multiple quadrotor-manipulator systems with each quadrotor equipped with a robotic manipulator. First, the kinematic and dynamic models of a quadrotor with multi-Degree of Freedom (DOF) robotic manipulator are established together using Euler-Lagrange equations. Based on the aggregated dynamic model, the control scheme consisting of position controller, attitude controller and manipulator controller is presented. Regarding cooperative transporting and assembling, multiple quadrotor-manipulator systems should be able to form a desired formation without collision among quadrotors from any initial position. The desired formation is achieved by the distributed position controller and attitude controller, while the collision avoidance is guaranteed by an artificial potential function method. Then, the transporting and assembling tasks request the manipulators to reach the desired angles cooperatively, which is achieved by the distributed manipulator controller. The overall stability of the closed-loop system is proven by a Lyapunov method and Matrosov's theorem. In the end, the proposed control scheme is simplified for the real application and then validated by two formation flying missions of four quadrotors with 2-DOF manipulators.

Identification of optimum sequencing depth especially for de novo genome assembly of small genomes using next generation sequencing data.

PubMed

Desai, Aarti; Marwah, Veer Singh; Yadav, Akshay; Jha, Vineet; Dhaygude, Kishor; Bangar, Ujwala; Kulkarni, Vivek; Jere, Abhay

2013-01-01

Next Generation Sequencing (NGS) is a disruptive technology that has found widespread acceptance in the life sciences research community. The high throughput and low cost of sequencing has encouraged researchers to undertake ambitious genomic projects, especially in de novo genome sequencing. Currently, NGS systems generate sequence data as short reads and de novo genome assembly using these short reads is computationally very intensive. Due to lower cost of sequencing and higher throughput, NGS systems now provide the ability to sequence genomes at high depth. However, currently no report is available highlighting the impact of high sequence depth on genome assembly using real data sets and multiple assembly algorithms. Recently, some studies have evaluated the impact of sequence coverage, error rate and average read length on genome assembly using multiple assembly algorithms, however, these evaluations were performed using simulated datasets. One limitation of using simulated datasets is that variables such as error rates, read length and coverage which are known to impact genome assembly are carefully controlled. Hence, this study was undertaken to identify the minimum depth of sequencing required for de novo assembly for different sized genomes using graph based assembly algorithms and real datasets. Illumina reads for E.coli (4.6 MB) S.kudriavzevii (11.18 MB) and C.elegans (100 MB) were assembled using SOAPdenovo, Velvet, ABySS, Meraculous and IDBA-UD. Our analysis shows that 50X is the optimum read depth for assembling these genomes using all assemblers except Meraculous which requires 100X read depth. Moreover, our analysis shows that de novo assembly from 50X read data requires only 6-40 GB RAM depending on the genome size and assembly algorithm used. We believe that this information can be extremely valuable for researchers in designing experiments and multiplexing which will enable optimum utilization of sequencing as well as analysis resources.

Rapid Assembly of DNA via Ligase Cycling Reaction (LCR).

PubMed

Chandran, Sunil

2017-01-01

The assembly of multiple DNA parts into a larger DNA construct is a requirement in most synthetic biology laboratories. Here we describe a method for the efficient, high-throughput, assembly of DNA utilizing the ligase chain reaction (LCR). The LCR method utilizes non-overlapping DNA parts that are ligated together with the guidance of bridging oligos. Using this method, we have successfully assembled up to 20 DNA parts in a single reaction or DNA constructs up to 26 kb in size.

Scarless assembly of unphosphorylated DNA fragments with a simplified DATEL method.

PubMed

Ding, Wenwen; Weng, Huanjiao; Jin, Peng; Du, Guocheng; Chen, Jian; Kang, Zhen

2017-05-04

Efficient assembly of multiple DNA fragments is a pivotal technology for synthetic biology. A scarless and sequence-independent DNA assembly method (DATEL) using thermal exonucleases has been developed recently. Here, we present a simplified DATEL (sDATEL) for efficient assembly of unphosphorylated DNA fragments with low cost. The sDATEL method is only dependent on Taq DNA polymerase and Taq DNA ligase. After optimizing the committed parameters of the reaction system such as pH and the concentration of Mg 2+ and NAD+, the assembly efficiency was increased by 32-fold. To further improve the assembly capacity, the number of thermal cycles was optimized, resulting in successful assembly 4 unphosphorylated DNA fragments with an accuracy of 75%. sDATEL could be a desirable method for routine manual and automated assembly.

Mechanical Rope and Cable

DTIC Science & Technology

1975-04-01

seawater. The principal effect of crevices on the corrosion of zinc- or aluminum - coated or uncoated steel rope is to entrap corrosive liquids and...visual inspection of the rope surface. j 5. The effect of stresses, such as tensile, bending, torsion , and comn- pression, upon rope in service is not...questionable A value. d. The effect of stresses, such as tensile, bending, torsion , and compressive contact, on rope is not understood well. 2

Truncated Dual-Cap Nucleation Site Development

NASA Technical Reports Server (NTRS)

Matson, Douglas M.; Sander, Paul J.

2012-01-01

During heterogeneous nucleation within a metastable mushy-zone, several geometries for nucleation site development must be considered. Traditional spherical dual cap and crevice models are compared to a truncated dual cap to determine the activation energy and critical cluster growth kinetics in ternary Fe-Cr-Ni steel alloys. Results of activation energy results indicate that nucleation is more probable at grain boundaries within the solid than at the solid-liquid interface.

METHOD OF IMPROVING CORROSION RESISTANCE OF ZIRCONIUM

DOEpatents

Shannon, D.W.

1961-03-28

An improved intermediate rinse for zirconium counteracts an anomalous deposit that often results in crevices and outof-the-way places when ordinary water is used to rinse away a strong fluoride etching solution designed to promote passivation of the metal. The intermediate rinse, which is used after the etching solution and before the water, is characterized by a complexing agent for fluoride ions such as aluminum or zirconium nitrates or chlorides.

Linear shaped charge

DOEpatents

Peterson, David; Stofleth, Jerome H.; Saul, Venner W.

2017-07-11

Linear shaped charges are described herein. In a general embodiment, the linear shaped charge has an explosive with an elongated arrowhead-shaped profile. The linear shaped charge also has and an elongated v-shaped liner that is inset into a recess of the explosive. Another linear shaped charge includes an explosive that is shaped as a star-shaped prism. Liners are inset into crevices of the explosive, where the explosive acts as a tamper.

AutoAssemblyD: a graphical user interface system for several genome assemblers.

PubMed

Veras, Adonney Allan de Oliveira; de Sá, Pablo Henrique Caracciolo Gomes; Azevedo, Vasco; Silva, Artur; Ramos, Rommel Thiago Jucá

2013-01-01

Next-generation sequencing technologies have increased the amount of biological data generated. Thus, bioinformatics has become important because new methods and algorithms are necessary to manipulate and process such data. However, certain challenges have emerged, such as genome assembly using short reads and high-throughput platforms. In this context, several algorithms have been developed, such as Velvet, Abyss, Euler-SR, Mira, Edna, Maq, SHRiMP, Newbler, ALLPATHS, Bowtie and BWA. However, most such assemblers do not have a graphical interface, which makes their use difficult for users without computing experience given the complexity of the assembler syntax. Thus, to make the operation of such assemblers accessible to users without a computing background, we developed AutoAssemblyD, which is a graphical tool for genome assembly submission and remote management by multiple assemblers through XML templates. AssemblyD is freely available at https://sourceforge.net/projects/autoassemblyd. It requires Sun jdk 6 or higher.

Can gingival crevicular blood be relied upon for assessment of blood glucose level?

PubMed

Dwivedi, Shivani; Verma, Sharmila J; Shah, Monali; Jain, Kapil

2014-11-01

Diabetes mellitus (DM) is undiagnosed in approximately half of the patients actually suffering from the disease. In addition, the prevalence of DM is more than twice as high as in patients with periodontitis when compared to periodontally healthy subjects. Thus, a high number of patients with periodontitis may have undiagnosed DM. The purpose of the present study was to evaluate whether blood oozing from a gingival crevice during routine periodontal examination can be used for determining glucose levels. Observational cross-sectional studies were carried out in 75 patients (43 males and 32 females) with chronic periodontitis who were divided into two groups: Group I and Group II, respectively. Blood oozing from the gingival crevices of anterior teeth following periodontal probing was collected with the stick of glucose self-monitoring device, and the blood glucose levels were measured. At the same time, finger-prick blood was taken for glucometric analysis and subsequent readings were recorded. The patient's blood glucose values ranged from 74 to 256 mg/dl. The comparison between gingival crevicular blood and finger-prick blood showed a very strong correlation, with a t value of 3.97 (at P value = 0.001). The data from this study has shown that GCB collected during diagnostic periodontal examination can be an excellent source of blood for glucometric analysis.

Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism.

PubMed

Graham, Emily B; Crump, Alex R; Resch, Charles T; Fansler, Sarah; Arntzen, Evan; Kennedy, David W; Fredrickson, Jim K; Stegen, James C

2016-01-01

Community assembly processes generate shifts in species abundances that influence ecosystem cycling of carbon and nutrients, yet our understanding of assembly remains largely separate from ecosystem-level functioning. Here, we investigate relationships between assembly and changes in microbial metabolism across space and time in hyporheic microbial communities. We pair sampling of two habitat types (i.e., attached and planktonic) through seasonal and sub-hourly hydrologic fluctuation with null modeling and temporally explicit multivariate statistics. We demonstrate that multiple selective pressures-imposed by sediment and porewater physicochemistry-integrate to generate changes in microbial community composition at distinct timescales among habitat types. These changes in composition are reflective of contrasting associations of Betaproteobacteria and Thaumarchaeota with ecological selection and with seasonal changes in microbial metabolism. We present a conceptual model based on our results in which metabolism increases when oscillating selective pressures oppose temporally stable selective pressures. Our conceptual model is pertinent to both macrobial and microbial systems experiencing multiple selective pressures and presents an avenue for assimilating community assembly processes into predictions of ecosystem-level functioning.

A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies.

PubMed

Utturkar, Sagar M; Klingeman, Dawn M; Hurt, Richard A; Brown, Steven D

2017-01-01

This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations. Our hypothesis that strong secondary DNA structures blocked DNA polymerases and contributed to gap sequences was not accepted. PacBio assemblies had few limitations overall and gaps were explained as cumulative effect of lower than average sequence coverage and repetitive sequences at contig termini. An important aspect of the present study is the compilation of biological features that interfered with assembly and included active transposons, multiple plasmid sequences, phage DNA integration, and large sequence duplication. Our targeted genome finishing approach and systematic evaluation of the unassembled DNA will be useful for others looking to close, finish, and polish microbial genome sequences.

Self-Organization in Coordination-Driven Self-Assembly

PubMed Central

Northrop, Brian H.; Zheng, Yao-Rong; Chi, Ki-Whan; Stang, Peter J.

2009-01-01

Conspectus Self-assembly allows for the preparation of highly complex molecular and supramolecular systems from relatively simple starting materials. Typically, self-assembled supramolecules are constructed by combining complementary pairs of two highly symmetric molecular components, thus limiting the chances of forming unwanted side products. Combining asymmetric molecular components or multiple complementary sets of molecules in one complex mixture can produce myriad different ordered and disordered supramolecular assemblies. Alternatively, spontaneous self-organization phenomena can promote the formation of specific product(s) out of a collection of multiple possibilities. Self-organization processes are common throughout much of nature and are especially common in biological systems. Recently, researchers have studied self-organized self-assembly in purely synthetic systems. This Account describes our investigations of self-organization in the coordination-driven self-assembly of platinum(II)-based metallosupramolecules. The modularity of the coordination-driven approach to self-assembly has allowed us to systematically study a wide variety of different factors that can control the extent of supramolecular self-organization. In particular, we have evaluated the effects of the symmetry and polarity of ambidentate donor subunits, differences in geometrical parameters (e.g. the size, angularity, and dimensionality) of Pt(II)-based acceptors and organic donors, the influence of temperature and solvent, and the effects of intermolecular steric interactions and hydrophobic interactions on self-organization. Our studies have shown that the extent of self-organization in the coordination-driven self-assembly of both 2D polygons and 3D polyhedra ranges from no organization (a statistical mixture of multiple products), to amplified organization (wherein a particular product or products are favored over others), and all the way to the absolute self-organization of discrete supramolecular assemblies. In many cases, inputs such as dipolar interactions, steric interactions, and differences in the geometric parameters of subunits—used either alone or as multiple factors simultaneously—can achieve absolute self-organization of discrete supramolecules. We have also observed instances where self-organization is not absolute and varies in its deviation from statistical results. Steric interactions are particularly useful control factors for driving such amplified self-organization because they can be subtly tuned through small structural variations. Having the ability to fully understand and control the self-organization of complex mixtures into specific synthetic supramolecules can provide a better understanding of analogous processes in biological systems. Furthermore, self-organization may allow for the facile synthesis of complex multifunctional, multicomponent systems from simply mixing a collection of much simpler, judiciously designed individual molecular components. PMID:19555073

Crystal Structure of the Core Region of Hantavirus Nucleocapsid Protein Reveals the Mechanism for Ribonucleoprotein Complex Formation

PubMed Central

Guo, Yu; Wang, Wenming; Sun, Yuna; Ma, Chao; Wang, Xu; Wang, Xin; Liu, Pi; Shen, Shu; Li, Baobin; Lin, Jianping; Deng, Fei

2015-01-01

ABSTRACT Hantaviruses, which belong to the genus Hantavirus in the family Bunyaviridae, infect mammals, including humans, causing either hemorrhagic fever with renal syndrome (HFRS) or hantavirus cardiopulmonary syndrome (HCPS) in humans with high mortality. Hantavirus encodes a nucleocapsid protein (NP) to encapsidate the genome and form a ribonucleoprotein complex (RNP) together with viral polymerase. Here, we report the crystal structure of the core domains of NP (NPcore) encoded by Sin Nombre virus (SNV) and Andes virus (ANDV), which are two representative members that cause HCPS in the New World. The constructs of SNV and ANDV NPcore exclude the N- and C-terminal portions of full polypeptide to obtain stable proteins for crystallographic study. The structure features an N lobe and a C lobe to clamp RNA-binding crevice and exhibits two protruding extensions in both lobes. The positively charged residues located in the RNA-binding crevice play a key role in RNA binding and virus replication. We further demonstrated that the C-terminal helix and the linker region connecting the N-terminal coiled-coil domain and NPcore are essential for hantavirus NP oligomerization through contacts made with two adjacent protomers. Moreover, electron microscopy (EM) visualization of native RNPs extracted from the virions revealed that a monomer-sized NP-RNA complex is the building block of viral RNP. This work provides insight into the formation of hantavirus RNP and provides an understanding of the evolutionary connections that exist among bunyaviruses. IMPORTANCE Hantaviruses are distributed across a wide and increasing range of host reservoirs throughout the world. In particular, hantaviruses can be transmitted via aerosols of rodent excreta to humans or from human to human and cause HFRS and HCPS, with mortalities of 15% and 50%, respectively. Hantavirus is therefore listed as a category C pathogen. Hantavirus encodes an NP that plays essential roles both in RNP formation and in multiple biological functions. NP is also the exclusive target for the serological diagnoses. This work reveals the structure of hantavirus NP, furthering the knowledge of hantavirus RNP formation, revealing the relationship between hantavirus NP and serological specificity and raising the potential for the development of new diagnosis and therapeutics targeting hantavirus infection. PMID:26559827

Crystal Structure of the Core Region of Hantavirus Nucleocapsid Protein Reveals the Mechanism for Ribonucleoprotein Complex Formation.

PubMed

Guo, Yu; Wang, Wenming; Sun, Yuna; Ma, Chao; Wang, Xu; Wang, Xin; Liu, Pi; Shen, Shu; Li, Baobin; Lin, Jianping; Deng, Fei; Wang, Hualin; Lou, Zhiyong

2016-01-15

Hantaviruses, which belong to the genus Hantavirus in the family Bunyaviridae, infect mammals, including humans, causing either hemorrhagic fever with renal syndrome (HFRS) or hantavirus cardiopulmonary syndrome (HCPS) in humans with high mortality. Hantavirus encodes a nucleocapsid protein (NP) to encapsidate the genome and form a ribonucleoprotein complex (RNP) together with viral polymerase. Here, we report the crystal structure of the core domains of NP (NPcore) encoded by Sin Nombre virus (SNV) and Andes virus (ANDV), which are two representative members that cause HCPS in the New World. The constructs of SNV and ANDV NPcore exclude the N- and C-terminal portions of full polypeptide to obtain stable proteins for crystallographic study. The structure features an N lobe and a C lobe to clamp RNA-binding crevice and exhibits two protruding extensions in both lobes. The positively charged residues located in the RNA-binding crevice play a key role in RNA binding and virus replication. We further demonstrated that the C-terminal helix and the linker region connecting the N-terminal coiled-coil domain and NPcore are essential for hantavirus NP oligomerization through contacts made with two adjacent protomers. Moreover, electron microscopy (EM) visualization of native RNPs extracted from the virions revealed that a monomer-sized NP-RNA complex is the building block of viral RNP. This work provides insight into the formation of hantavirus RNP and provides an understanding of the evolutionary connections that exist among bunyaviruses. Hantaviruses are distributed across a wide and increasing range of host reservoirs throughout the world. In particular, hantaviruses can be transmitted via aerosols of rodent excreta to humans or from human to human and cause HFRS and HCPS, with mortalities of 15% and 50%, respectively. Hantavirus is therefore listed as a category C pathogen. Hantavirus encodes an NP that plays essential roles both in RNP formation and in multiple biological functions. NP is also the exclusive target for the serological diagnoses. This work reveals the structure of hantavirus NP, furthering the knowledge of hantavirus RNP formation, revealing the relationship between hantavirus NP and serological specificity and raising the potential for the development of new diagnosis and therapeutics targeting hantavirus infection. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Stoichiometric Control of Multiple Different Tectons in Coordination-Driven Self-assembly

PubMed Central

Lee, Junseong; Ghosh, Koushik; Stang, Peter J.

2009-01-01

We present a general strategy for the synthesis of stable, multi-component fused polygon complexes where coordination-driven self-assembly allows for single supramolecular species can be formed from multi-component self-assembly and the shape of the obtained polygons can be controlled by simply changing the ratio of individual components. The compounds are characterized by Multinuclear NMR, ESI Mass spectrometry. PMID:19663439

Multiple Approaches to the Investigation of Cell Assembly in Memory Research-Present and Future.

PubMed

Sakurai, Yoshio; Osako, Yuma; Tanisumi, Yuta; Ishihara, Eriko; Hirokawa, Junya; Manabe, Hiroyuki

2018-01-01

In this review article we focus on research methodologies for detecting the actual activity of cell assemblies, which are populations of functionally connected neurons that encode information in the brain. We introduce and discuss traditional and novel experimental methods and those currently in development and briefly discuss their advantages and disadvantages for the detection of cell-assembly activity. First, we introduce the electrophysiological method, i.e., multineuronal recording, and review former and recent examples of studies showing models of dynamic coding by cell assemblies in behaving rodents and monkeys. We also discuss how the firing correlation of two neurons reflects the firing synchrony among the numerous surrounding neurons that constitute cell assemblies. Second, we review the recent outstanding studies that used the novel method of optogenetics to show causal relationships between cell-assembly activity and behavioral change. Third, we review the most recently developed method of live-cell imaging, which facilitates the simultaneous observation of firings of a large number of neurons in behaving rodents. Currently, all these available methods have both advantages and disadvantages, and no single measurement method can directly and precisely detect the actual activity of cell assemblies. The best strategy is to combine the available methods and utilize each of their advantages with the technique of operant conditioning of multiple-task behaviors in animals and, if necessary, with brain-machine interface technology to verify the accuracy of neural information detected as cell-assembly activity.

Self-Assembly through Noncovalent Preorganization of Reactants: Explaining the Formation of a Polyfluoroxometalate.

PubMed

Schreiber, Roy E; Avram, Liat; Neumann, Ronny

2018-01-09

High-order elementary reactions in homogeneous solutions involving more than two molecules are statistically improbable and very slow to proceed. They are not generally considered in classical transition-state or collision theories. Yet, rather selective, high-yield product formation is common in self-assembly processes that require many reaction steps. On the basis of recent observations of crystallization as well as reactions in dense phases, it is shown that self-assembly can occur by preorganization of reactants in a noncovalent supramolecular assembly, whereby directing forces can lead to an apparent one-step transformation of multiple reactants. A simple and general kinetic model for multiple reactant transformation in a dense phase that can account for many-bodied transformations was developed. Furthermore, the self-assembly of polyfluoroxometalate anion [H 2 F 6 NaW 18 O 56 ] 7- from simple tungstate Na 2 WO 2 F 4 was demonstrated by using 2D 19 F- 19 F NOESY, 2D 19 F- 19 F COSY NMR spectroscopy, a new 2D 19 F{ 183 W} NMR technique, as well as ESI-MS and diffusion NMR spectroscopy, and the crucial involvement of a supramolecular assembly was found. The deterministic kinetic reaction model explains the reaction in a dense phase and supports the suggested self-assembly mechanism. Reactions in dense phases may be of general importance in understanding other self-assembly reactions. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Consensus generation and variant detection by Celera Assembler.

PubMed

Denisov, Gennady; Walenz, Brian; Halpern, Aaron L; Miller, Jason; Axelrod, Nelson; Levy, Samuel; Sutton, Granger

2008-04-15

We present an algorithm to identify allelic variation given a Whole Genome Shotgun (WGS) assembly of haploid sequences, and to produce a set of haploid consensus sequences rather than a single consensus sequence. Existing WGS assemblers take a column-by-column approach to consensus generation, and produce a single consensus sequence which can be inconsistent with the underlying haploid alleles, and inconsistent with any of the aligned sequence reads. Our new algorithm uses a dynamic windowing approach. It detects alleles by simultaneously processing the portions of aligned reads spanning a region of sequence variation, assigns reads to their respective alleles, phases adjacent variant alleles and generates a consensus sequence corresponding to each confirmed allele. This algorithm was used to produce the first diploid genome sequence of an individual human. It can also be applied to assemblies of multiple diploid individuals and hybrid assemblies of multiple haploid organisms. Being applied to the individual human genome assembly, the new algorithm detects exactly two confirmed alleles and reports two consensus sequences in 98.98% of the total number 2,033311 detected regions of sequence variation. In 33,269 out of 460,373 detected regions of size >1 bp, it fixes the constructed errors of a mosaic haploid representation of a diploid locus as produced by the original Celera Assembler consensus algorithm. Using an optimized procedure calibrated against 1 506 344 known SNPs, it detects 438 814 new heterozygous SNPs with false positive rate 12%. The open source code is available at: http://wgs-assembler.cvs.sourceforge.net/wgs-assembler/

Single-Molecule Studies of Actin Assembly and Disassembly Factors

PubMed Central

Smith, Benjamin A.; Gelles, Jeff; Goode, Bruce L.

2014-01-01

The actin cytoskeleton is very dynamic and highly regulated by multiple associated proteins in vivo. Understanding how this system of proteins functions in the processes of actin network assembly and disassembly requires methods to dissect the mechanisms of activity of individual factors and of multiple factors acting in concert. The advent of single-filament and single-molecule fluorescence imaging methods has provided a powerful new approach to discovering actin-regulatory activities and obtaining direct, quantitative insights into the pathways of molecular interactions that regulate actin network architecture and dynamics. Here we describe techniques for acquisition and analysis of single-molecule data, applied to the novel challenges of studying the filament assembly and disassembly activities of actin-associated proteins in vitro. We discuss the advantages of single-molecule analysis in directly visualizing the order of molecular events, measuring the kinetic rates of filament binding and dissociation, and studying the coordination among multiple factors. The methods described here complement traditional biochemical approaches in elucidating actin-regulatory mechanisms in reconstituted filamentous networks. PMID:24630103

Phosphotyrosine-mediated LAT assembly on membranes drives kinetic bifurcation in recruitment dynamics of the Ras activator SOS

DOE PAGES

Huang, William Y. C.; Yan, Qingrong; Lin, Wan-Chen; ...

2016-07-01

The assembly of cell surface receptors with downstream signaling molecules is a commonly occurring theme in multiple signaling systems. However, little is known about how these assemblies modulate reaction kinetics and the ultimate propagation of signals. Here, we reconstitute phosphotyrosine-mediated assembly of extended linker for the activation of T cells (LAT):growth factor receptor-bound protein 2 (Grb2):Son of Sevenless (SOS) networks, derived from the T-cell receptor signaling system, on supported membranes. Single-molecule dwell time distributions reveal two, well-differentiated kinetic species for both Grb2 and SOS on the LAT assemblies. The majority fraction of membrane-recruited Grb2 and SOS both exhibit fast kineticsmore » and single exponential dwell time distributions, with average dwell times of hundreds of milliseconds. The minor fraction exhibits much slower kinetics, extending the dwell times to tens of seconds. Considering this result in the context of the multistep process by which the Ras GEF (guanine nucleotide exchange factor) activity of SOS is activated indicates that kinetic stabilization from the LAT assembly may be important. This kinetic proofreading effect would additionally serve as a stochastic noise filter by reducing the relative probability of spontaneous SOS activation in the absence of receptor triggering. In conclusion, the generality of receptor-mediated assembly suggests that such effects may play a role in multiple receptor proximal signaling processes.« less

Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop.

PubMed

Hatakeyama, Masaomi; Aluri, Sirisha; Balachadran, Mathi Thumilan; Sivarajan, Sajeevan Radha; Patrignani, Andrea; Grüter, Simon; Poveda, Lucy; Shimizu-Inatsugi, Rie; Baeten, John; Francoijs, Kees-Jan; Nataraja, Karaba N; Reddy, Yellodu A Nanja; Phadnis, Shamprasad; Ravikumar, Ramapura L; Schlapbach, Ralph; Sreeman, Sheshshayee M; Shimizu, Kentaro K

2017-09-05

Finger millet (Eleusine coracana (L.) Gaertn) is an important crop for food security because of its tolerance to drought, which is expected to be exacerbated by global climate changes. Nevertheless, it is often classified as an orphan/underutilized crop because of the paucity of scientific attention. Among several small millets, finger millet is considered as an excellent source of essential nutrient elements, such as iron and zinc; hence, it has potential as an alternate coarse cereal. However, high-quality genome sequence data of finger millet are currently not available. One of the major problems encountered in the genome assembly of this species was its polyploidy, which hampers genome assembly compared with a diploid genome. To overcome this problem, we sequenced its genome using diverse technologies with sufficient coverage and assembled it via a novel multiple hybrid assembly workflow that combines next-generation with single-molecule sequencing, followed by whole-genome optical mapping using the Bionano Irys® system. The total number of scaffolds was 1,897 with an N50 length >2.6 Mb and detection of 96% of the universal single-copy orthologs. The majority of the homeologs were assembled separately. This indicates that the proposed workflow is applicable to the assembly of other allotetraploid genomes. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

High precision optomechanical assembly using threads as mechanical reference

NASA Astrophysics Data System (ADS)

Lamontagne, Frédéric; Desnoyers, Nichola; Bergeron, Guy; Cantin, Mario

2016-09-01

A convenient method to assemble optomechanical components is to use threaded interface. For example, lenses are often secured inside barrels using threaded rings. In other cases, multiple optical sub-assemblies such as lens barrels can be threaded to each other. Threads have the advantage to provide a simple assembly method, to be easy to manufacture, and to offer a compact mechanical design. On the other hand, threads are not considered to provide accurate centering between parts because of the assembly clearance between the inner and outer threads. For that reason, threads are often used in conjunction with precision cylindrical surfaces to limit the radial clearance between the parts to be centered. Therefore, tight manufacturing tolerances are needed on these pilot diameters, which affect the cost of the optical assembly. This paper presents a new optomechanical approach that uses threads as mechanical reference. This innovative method relies on geometric principles to auto-center parts to each other with a very low centering error that is usually less than 5 μm. The method allows to auto-center an optical group in a main barrel, to perform an axial adjustment of an optical group inside a main barrel, and to perform stacking of multiple barrels. In conjunction with the lens auto-centering method that also used threads as a mechanical reference, this novel solution opens new possibilities to realize a variety of different high precision optomechanical assemblies at lower cost.

Phosphotyrosine-mediated LAT assembly on membranes drives kinetic bifurcation in recruitment dynamics of the Ras activator SOS

PubMed Central

Huang, William Y. C.; Yan, Qingrong; Lin, Wan-Chen; Chung, Jean K.; Hansen, Scott D.; Christensen, Sune M.; Tu, Hsiung-Lin; Kuriyan, John; Groves, Jay T.

2016-01-01

The assembly of cell surface receptors with downstream signaling molecules is a commonly occurring theme in multiple signaling systems. However, little is known about how these assemblies modulate reaction kinetics and the ultimate propagation of signals. Here, we reconstitute phosphotyrosine-mediated assembly of extended linker for the activation of T cells (LAT):growth factor receptor-bound protein 2 (Grb2):Son of Sevenless (SOS) networks, derived from the T-cell receptor signaling system, on supported membranes. Single-molecule dwell time distributions reveal two, well-differentiated kinetic species for both Grb2 and SOS on the LAT assemblies. The majority fraction of membrane-recruited Grb2 and SOS both exhibit fast kinetics and single exponential dwell time distributions, with average dwell times of hundreds of milliseconds. The minor fraction exhibits much slower kinetics, extending the dwell times to tens of seconds. Considering this result in the context of the multistep process by which the Ras GEF (guanine nucleotide exchange factor) activity of SOS is activated indicates that kinetic stabilization from the LAT assembly may be important. This kinetic proofreading effect would additionally serve as a stochastic noise filter by reducing the relative probability of spontaneous SOS activation in the absence of receptor triggering. The generality of receptor-mediated assembly suggests that such effects may play a role in multiple receptor proximal signaling processes. PMID:27370798

Phosphotyrosine-mediated LAT assembly on membranes drives kinetic bifurcation in recruitment dynamics of the Ras activator SOS.

PubMed

Huang, William Y C; Yan, Qingrong; Lin, Wan-Chen; Chung, Jean K; Hansen, Scott D; Christensen, Sune M; Tu, Hsiung-Lin; Kuriyan, John; Groves, Jay T

2016-07-19

The assembly of cell surface receptors with downstream signaling molecules is a commonly occurring theme in multiple signaling systems. However, little is known about how these assemblies modulate reaction kinetics and the ultimate propagation of signals. Here, we reconstitute phosphotyrosine-mediated assembly of extended linker for the activation of T cells (LAT):growth factor receptor-bound protein 2 (Grb2):Son of Sevenless (SOS) networks, derived from the T-cell receptor signaling system, on supported membranes. Single-molecule dwell time distributions reveal two, well-differentiated kinetic species for both Grb2 and SOS on the LAT assemblies. The majority fraction of membrane-recruited Grb2 and SOS both exhibit fast kinetics and single exponential dwell time distributions, with average dwell times of hundreds of milliseconds. The minor fraction exhibits much slower kinetics, extending the dwell times to tens of seconds. Considering this result in the context of the multistep process by which the Ras GEF (guanine nucleotide exchange factor) activity of SOS is activated indicates that kinetic stabilization from the LAT assembly may be important. This kinetic proofreading effect would additionally serve as a stochastic noise filter by reducing the relative probability of spontaneous SOS activation in the absence of receptor triggering. The generality of receptor-mediated assembly suggests that such effects may play a role in multiple receptor proximal signaling processes.

Peroxisome Biogenesis Disorders: Biological, Clinical and Pathophysiological Perspectives

ERIC Educational Resources Information Center

Braverman, Nancy E.; D'Agostino, Maria Daniela; MacLean, Gillian E.

2013-01-01

The peroxisome biogenesis disorders (PBD) are a heterogeneous group of autosomal recessive disorders in which peroxisome assembly is impaired, leading to multiple peroxisome enzyme deficiencies, complex developmental sequelae and progressive disabilities. Mammalian peroxisome assembly involves the protein products of 16 "PEX" genes;…

STRATEGIES OF MARINE DINOFLAGELLATE SURVIVAL AND SOME RULES OF ASSEMBLY. (R829368)

EPA Science Inventory

Dinoflagellate ecology is based on multiple adaptive strategies and species having diverse habitat preferences. Nine types of mixing-irradiance-nutrient habitats selecting for specific marine dinoflagellate life-form types are recognised, with five rules of assembly proposed t...

Recurrence of Mexican long-tongued bats (Choeronycteris mexicana) at historical sites in Arizona and New Mexico

USGS Publications Warehouse

Cryan, P.M.; Bogan, M.A.

2003-01-01

The Mexican long-tongued bat (Choeronycteris mexicana) is a nectar-eating species that seasonally inhabits the southwestern United States. Since 1906, fewer than 1500 individuals of C. mexicana have been documented throughout the range of the species. We conducted a field survey in Arizona and New Mexico during summer 1999 to check historically occupied areas for recurrence of C. mexicana. We observed C. mexicana occupying a majority (75%, n = 18) of visited sites. Multiple individuals were observed at many sites, including young-of-year. Choeronycteris mexicana roosted in lighted areas close to entrances within mine adits, abandoned buildings, wide rock crevices, and caves. All occupied sites were in Madrean evergreen woodlands or semidesert grasslands where species of Agave were present. Most sites were located near a water source and, with the exception of a single site, near areas of riparian vegetation. Sites at which we did not encounter C. mexicana were frequently disturbed, difficult to search, or historically occupied by single individuals. Based on the relatively high rate of bat recurrence, we do not believe that populations of C. mexicana in the region have declined dramatically over the past several decades.

Observations of territorial breeding common ravens caching eggs of greater sage-grouse

USGS Publications Warehouse

Howe, Kristy B.; Coates, Peter S.

2015-01-01

Previous investigations using continuous video monitoring of greater sage-grouse Centrocercus urophasianus nests have unambiguously identified common ravens Corvus corax as an important egg predator within the western United States. The quantity of greater sage-grouse eggs an individual common raven consumes during the nesting period and the extent to which common ravens actively hunt greater sage-grouse nests are largely unknown. However, some evidence suggests that territorial breeding common ravens, rather than nonbreeding transients, are most likely responsible for nest depredations. We describe greater sage-grouse egg depredation observations obtained opportunistically from three common raven nests located in Idaho and Nevada where depredated greater sage-grouse eggs were found at or in the immediate vicinity of the nest site, including the caching of eggs in nearby rock crevices. We opportunistically monitored these nests by counting and removing depredated eggs and shell fragments from the nest sites during each visit to determine the extent to which the common raven pairs preyed on greater sage-grouse eggs. To our knowledge, our observations represent the first evidence that breeding, territorial pairs of common ravens cache greater sage-grouse eggs and are capable of depredating multiple greater sage-grouse nests.

A multi-stimuli responive, self-assembling, boronic acid dipeptide

DOE PAGES

Jones, Brad Howard; Martinez, Alina Marissa; Wheeler, Jill S.; ...

2015-08-11

Modification of the dipeptide of phenylalanine, FF, with a boronic acid (BA) functionality imparts unique aqueous self-assembly behavior that responds to multiple stimuli. Changes in pH and ionic strength are used to trigger hydrogelation via the formation of nanoribbon networks. Thus, we show for the first time that the binding of polyols to the BA functionality can modulate a peptide between its assembled and disassembled states.

Corrosion and fatigue of surgical implants

NASA Technical Reports Server (NTRS)

Lisagor, W. B.

1975-01-01

Implants for the treatment of femoral fractures, mechanisms leading to the failure or degradation of such structures, and current perspectives on surgical implants are discussed. Under the first heading, general usage, materials and procedures, environmental conditions, and laboratory analyses of implants after service are considered. Corrosion, crevice corrosion, stress corrosion cracking, intergranular corrosion, pitting corrosion, fatigue, and corrosion fatigue are the principal degradation mechanisms described. The need for improvement in the reliability of implants is emphasized.

[Developmental radicular groove as a cause of endodontic failure].

PubMed

Fabra Campos, H; Millet Part, J

1989-01-01

A clinical case of apical injury on an upper lateral incisor with endodontical and surgical failures in its treatment is presented. Extraction of the incisor and its study at the stereoscopic microscope showed the existence of a developmental groove running from the cingulum to the end of the root, establishing a communication between the crevice and the apical part of the tooth. Bacterial infection through the groove could provide an explanation for treatment failure.

Crevice Corrosion Behavior of 45 Molybdenum-Containing Stainless Steels in Seawater.

DTIC Science & Technology

1981-12-01

Armco, Avesta Jernverks, Cabot, Carpenter Technology, Crucible, Eastern, Firth-Brown, Huntington, Jessup, Langley Alloys, and Uddeholm. 16...Department of Energy, Report ANL/OTEC-BCM-022. 7. Wallen, B., and M. Liljas, " Avesta 254 SMO - A New, High Molybdenum Stainless Steel," presented at NKM8...1977).; 11. Wallen, B., " Avesta 254 SMO - A Stainless Steel for Seawater Service," presented at the Advanced Stainless Steels for Turbine Condensors

Rapid heterogeneous assembly of multiple magma reservoirs prior to Yellowstone supereruptions.

PubMed

Wotzlaw, Jörn-Frederik; Bindeman, Ilya N; Stern, Richard A; D'Abzac, Francois-Xavier; Schaltegger, Urs

2015-09-10

Large-volume caldera-forming eruptions of silicic magmas are an important feature of continental volcanism. The timescales and mechanisms of assembly of the magma reservoirs that feed such eruptions as well as the durations and physical conditions of upper-crustal storage remain highly debated topics in volcanology. Here we explore a comprehensive data set of isotopic (O, Hf) and chemical proxies in precisely U-Pb dated zircon crystals from all caldera-forming eruptions of Yellowstone supervolcano. Analysed zircons record rapid assembly of multiple magma reservoirs by repeated injections of isotopically heterogeneous magma batches and short pre-eruption storage times of 10(3) to 10(4) years. Decoupled oxygen-hafnium isotope systematics suggest a complex source for these magmas involving variable amounts of differentiated mantle-derived melt, Archean crust and hydrothermally altered shallow-crustal rocks. These data demonstrate that complex magma reservoirs with multiple sub-chambers are a common feature of rift- and hotspot related supervolcanoes. The short duration of reservoir assembly documents rapid crustal remelting and two to three orders of magnitude higher magma production rates beneath Yellowstone compared to continental arc volcanoes. The short pre-eruption storage times further suggest that the detection of voluminous reservoirs of eruptible magma beneath active supervolcanoes may only be possible prior to an impending eruption.

Rapid heterogeneous assembly of multiple magma reservoirs prior to Yellowstone supereruptions

PubMed Central

Wotzlaw, Jörn-Frederik; Bindeman, Ilya N.; Stern, Richard A.; D’Abzac, Francois-Xavier; Schaltegger, Urs

2015-01-01

Large-volume caldera-forming eruptions of silicic magmas are an important feature of continental volcanism. The timescales and mechanisms of assembly of the magma reservoirs that feed such eruptions as well as the durations and physical conditions of upper-crustal storage remain highly debated topics in volcanology. Here we explore a comprehensive data set of isotopic (O, Hf) and chemical proxies in precisely U-Pb dated zircon crystals from all caldera-forming eruptions of Yellowstone supervolcano. Analysed zircons record rapid assembly of multiple magma reservoirs by repeated injections of isotopically heterogeneous magma batches and short pre-eruption storage times of 103 to 104 years. Decoupled oxygen-hafnium isotope systematics suggest a complex source for these magmas involving variable amounts of differentiated mantle-derived melt, Archean crust and hydrothermally altered shallow-crustal rocks. These data demonstrate that complex magma reservoirs with multiple sub-chambers are a common feature of rift- and hotspot related supervolcanoes. The short duration of reservoir assembly documents rapid crustal remelting and two to three orders of magnitude higher magma production rates beneath Yellowstone compared to continental arc volcanoes. The short pre-eruption storage times further suggest that the detection of voluminous reservoirs of eruptible magma beneath active supervolcanoes may only be possible prior to an impending eruption. PMID:26356304

Extension arm for mobile travelers suit case

DOEpatents

Byington, Gerald A.

1999-01-01

The invention is an apparatus for adjusting a luggage handle in relation to a luggage frame utilized to transport luggage by a traveler. The handle is connected to two extendable and retractable slide tube assemblies, the assemblies allow for the telescoping of the luggage handle to multiple positions in relation to a pair of fixed frame tubes connected to a luggage shell with wheels, to accommodate the height and personal stride of traveler. The luggage handle incorporates triggering buttons that allow ambidextrous and single-handed control of the height of the handle and slide tube assembly in relation to the luggage. The handle and slide tube assembly are connected by interior filaments to pulleys and filaments within two concentric light-weight slide tubes, which are inserted respectively into two fixed frame tubes, to allow a multitude of positions for the slide tubes to lock into the fixed frame tubes. The apparatus can be pushed or pulled by the traveler, and the support shell can accommodate multiple pieces of luggage.

A modular platform for one-step assembly of multi-component membrane systems by fusion of charged proteoliposomes

NASA Astrophysics Data System (ADS)

Ishmukhametov, Robert R.; Russell, Aidan N.; Berry, Richard M.

2016-10-01

An important goal in synthetic biology is the assembly of biomimetic cell-like structures, which combine multiple biological components in synthetic lipid vesicles. A key limiting assembly step is the incorporation of membrane proteins into the lipid bilayer of the vesicles. Here we present a simple method for delivery of membrane proteins into a lipid bilayer within 5 min. Fusogenic proteoliposomes, containing charged lipids and membrane proteins, fuse with oppositely charged bilayers, with no requirement for detergent or fusion-promoting proteins, and deliver large, fragile membrane protein complexes into the target bilayers. We demonstrate the feasibility of our method by assembling a minimal electron transport chain capable of adenosine triphosphate (ATP) synthesis, combining Escherichia coli F1Fo ATP-synthase and the primary proton pump bo3-oxidase, into synthetic lipid vesicles with sizes ranging from 100 nm to ~10 μm. This provides a platform for the combination of multiple sets of membrane protein complexes into cell-like artificial structures.

Whole transcriptome analysis using next-generation sequencing of model species Setaria viridis to support C4 photosynthesis research.

PubMed

Xu, Jiajia; Li, Yuanyuan; Ma, Xiuling; Ding, Jianfeng; Wang, Kai; Wang, Sisi; Tian, Ye; Zhang, Hui; Zhu, Xin-Guang

2013-09-01

Setaria viridis is an emerging model species for genetic studies of C4 photosynthesis. Many basic molecular resources need to be developed to support for this species. In this paper, we performed a comprehensive transcriptome analysis from multiple developmental stages and tissues of S. viridis using next-generation sequencing technologies. Sequencing of the transcriptome from multiple tissues across three developmental stages (seed germination, vegetative growth, and reproduction) yielded a total of 71 million single end 100 bp long reads. Reference-based assembly using Setaria italica genome as a reference generated 42,754 transcripts. De novo assembly generated 60,751 transcripts. In addition, 9,576 and 7,056 potential simple sequence repeats (SSRs) covering S. viridis genome were identified when using the reference based assembled transcripts and the de novo assembled transcripts, respectively. This identified transcripts and SSR provided by this study can be used for both reverse and forward genetic studies based on S. viridis.

Robust and efficient overset grid assembly for partitioned unstructured meshes

NASA Astrophysics Data System (ADS)

Roget, Beatrice; Sitaraman, Jayanarayanan

2014-03-01

This paper presents a method to perform efficient and automated Overset Grid Assembly (OGA) on a system of overlapping unstructured meshes in a parallel computing environment where all meshes are partitioned into multiple mesh-blocks and processed on multiple cores. The main task of the overset grid assembler is to identify, in parallel, among all points in the overlapping mesh system, at which points the flow solution should be computed (field points), interpolated (receptor points), or ignored (hole points). Point containment search or donor search, an algorithm to efficiently determine the cell that contains a given point, is the core procedure necessary for accomplishing this task. Donor search is particularly challenging for partitioned unstructured meshes because of the complex irregular boundaries that are often created during partitioning.

Development of a modularized two-step (M2S) chromosome integration technique for integration of multiple transcription units in Saccharomyces cerevisiae.

PubMed

Li, Siwei; Ding, Wentao; Zhang, Xueli; Jiang, Huifeng; Bi, Changhao

2016-01-01

Saccharomyces cerevisiae has already been used for heterologous production of fuel chemicals and valuable natural products. The establishment of complicated heterologous biosynthetic pathways in S. cerevisiae became the research focus of Synthetic Biology and Metabolic Engineering. Thus, simple and efficient genomic integration techniques of large number of transcription units are demanded urgently. An efficient DNA assembly and chromosomal integration method was created by combining homologous recombination (HR) in S. cerevisiae and Golden Gate DNA assembly method, designated as modularized two-step (M2S) technique. Two major assembly steps are performed consecutively to integrate multiple transcription units simultaneously. In Step 1, Modularized scaffold containing a head-to-head promoter module and a pair of terminators was assembled with two genes. Thus, two transcription units were assembled with Golden Gate method into one scaffold in one reaction. In Step 2, the two transcription units were mixed with modules of selective markers and integration sites and transformed into S. cerevisiae for assembly and integration. In both steps, universal primers were designed for identification of correct clones. Establishment of a functional β-carotene biosynthetic pathway in S. cerevisiae within 5 days demonstrated high efficiency of this method, and a 10-transcriptional-unit pathway integration illustrated the capacity of this method. Modular design of transcription units and integration elements simplified assembly and integration procedure, and eliminated frequent designing and synthesis of DNA fragments in previous methods. Also, by assembling most parts in Step 1 in vitro, the number of DNA cassettes for homologous integration in Step 2 was significantly reduced. Thus, high assembly efficiency, high integration capacity, and low error rate were achieved.

Self-assembled single-crystal silicon circuits on plastic

PubMed Central

Stauth, Sean A.; Parviz, Babak A.

2006-01-01

We demonstrate the use of self-assembly for the integration of freestanding micrometer-scale components, including single-crystal, silicon field-effect transistors (FETs) and diffusion resistors, onto flexible plastic substrates. Preferential self-assembly of multiple microcomponent types onto a common platform is achieved through complementary shape recognition and aided by capillary, fluidic, and gravitational forces. We outline a microfabrication process that yields single-crystal, silicon FETs in a freestanding, powder-like collection for use with self-assembly. Demonstrations of self-assembled FETs on plastic include logic inverters and measured electron mobility of 592 cm2/V-s. Finally, we extend the self-assembly process to substrates each containing 10,000 binding sites and realize 97% self-assembly yield within 25 min for 100-μm-sized elements. High-yield self-assembly of micrometer-scale functional devices as outlined here provides a powerful approach for production of macroelectronic systems. PMID:16968780

Stoichiometric control of multiple different tectons in coordination-driven self-assembly: preparation of fused metallacyclic polygons.

PubMed

Lee, Junseong; Ghosh, Koushik; Stang, Peter J

2009-09-02

We present a general strategy for the synthesis of stable, multicomponent fused polygon complexes in which coordination-driven self-assembly allows for single supramolecular species to be formed from multicomponent self-assembly and the shape of the obtained polygons can be controlled simply by changing the ratio of individual components. The compounds have been characterized by multinuclear NMR spectroscopy and electrospray ionization mass spectrometry.

A parallel algorithm for generation and assembly of finite element stiffness and mass matrices

NASA Technical Reports Server (NTRS)

Storaasli, O. O.; Carmona, E. A.; Nguyen, D. T.; Baddourah, M. A.

1991-01-01

A new algorithm is proposed for parallel generation and assembly of the finite element stiffness and mass matrices. The proposed assembly algorithm is based on a node-by-node approach rather than the more conventional element-by-element approach. The new algorithm's generality and computation speed-up when using multiple processors are demonstrated for several practical applications on multi-processor Cray Y-MP and Cray 2 supercomputers.

A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies

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

Utturkar, Sagar M.; Klingeman, Dawn M.; Hurt, Jr., Richard A.

This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations. Our hypothesis that strong secondary DNA structures blocked DNA polymerases and contributed to gap sequences was not accepted.more » PacBio assemblies had few limitations overall and gaps were explained as cumulative effect of lower than average sequence coverage and repetitive sequences at contig termini. An important aspect of the present study is the compilation of biological features that interfered with assembly and included active transposons, multiple plasmid sequences, phage DNA integration, and large sequence duplication. Furthermore, our targeted genome finishing approach and systematic evaluation of the unassembled DNA will be useful for others looking to close, finish, and polish microbial genome sequences.« less

Should We Stop Developing Heuristics and Only Rely on Mixed Integer Programming Solvers in Automated Test Assembly? A Rejoinder to van der Linden and Li (2016).

PubMed

Chen, Pei-Hua

2017-05-01

This rejoinder responds to the commentary by van der Linden and Li entiled "Comment on Three-Element Item Selection Procedures for Multiple Forms Assembly: An Item Matching Approach" on the article "Three-Element Item Selection Procedures for Multiple Forms Assembly: An Item Matching Approach" by Chen. Van der Linden and Li made a strong statement calling for the cessation of test assembly heuristics development, and instead encouraged embracing mixed integer programming (MIP). This article points out the nondeterministic polynomial (NP)-hard nature of MIP problems and how solutions found using heuristics could be useful in an MIP context. Although van der Linden and Li provided several practical examples of test assembly supporting their view, the examples ignore the cases in which a slight change of constraints or item pool data might mean it would not be possible to obtain solutions as quickly as before. The article illustrates the use of heuristic solutions to improve both the performance of MIP solvers and the quality of solutions. Additional responses to the commentary by van der Linden and Li are included.

A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies

DOE PAGES

Utturkar, Sagar M.; Klingeman, Dawn M.; Hurt, Jr., Richard A.; ...

2017-07-18

This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations. Our hypothesis that strong secondary DNA structures blocked DNA polymerases and contributed to gap sequences was not accepted.more » PacBio assemblies had few limitations overall and gaps were explained as cumulative effect of lower than average sequence coverage and repetitive sequences at contig termini. An important aspect of the present study is the compilation of biological features that interfered with assembly and included active transposons, multiple plasmid sequences, phage DNA integration, and large sequence duplication. Furthermore, our targeted genome finishing approach and systematic evaluation of the unassembled DNA will be useful for others looking to close, finish, and polish microbial genome sequences.« less

A Case Study into Microbial Genome Assembly Gap Sequences and Finishing Strategies

PubMed Central

Utturkar, Sagar M.; Klingeman, Dawn M.; Hurt, Richard A.; Brown, Steven D.

2017-01-01

This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations. Our hypothesis that strong secondary DNA structures blocked DNA polymerases and contributed to gap sequences was not accepted. PacBio assemblies had few limitations overall and gaps were explained as cumulative effect of lower than average sequence coverage and repetitive sequences at contig termini. An important aspect of the present study is the compilation of biological features that interfered with assembly and included active transposons, multiple plasmid sequences, phage DNA integration, and large sequence duplication. Our targeted genome finishing approach and systematic evaluation of the unassembled DNA will be useful for others looking to close, finish, and polish microbial genome sequences. PMID:28769883

Three-dimensional interstitial space mediates predator foraging success in different spatial arrangements.

PubMed

Hesterberg, Stephen G; Duckett, C Cole; Salewski, Elizabeth A; Bell, Susan S

2017-04-01

Identifying and quantifying the relevant properties of habitat structure that mediate predator-prey interactions remains a persistent challenge. Most previous studies investigate effects of structural density on trophic interactions and typically quantify refuge quality using one or two-dimensional metrics. Few consider spatial arrangement of components (i.e., orientation and shape) and often neglect to measure the total three-dimensional (3D) space available as refuge. This study tests whether the three-dimensionality of interstitial space, an attribute produced by the spatial arrangement of oyster (Crassostrea virginica) shells, impacts the foraging success of nektonic predators (primary blue crab, Callinectes sapidus) on mud crab prey (Eurypanopeus depressus) in field and mesocosm experiments. Interstices of 3D-printed shell mimics were manipulated by changing either their orientation (angle) or internal shape (crevice or channel). In both field and mesocosm experiments, under conditions of constant structural density, predator foraging success was influenced by 3D aspects of interstitial space. Proportional survivorship of tethered mud crabs differed significantly as 3D interstitial space varied by orientation, displaying decreasing prey survivorship as angle of orientation increased (0° = 0.76, 22.5° = 0.13, 45° = 0.0). Tethered prey survivorship was high when 3D interstitial space of mimics was modified by internal shape (crevice survivorship = 0.89, channel survivorship = 0.96) and these values did not differ significantly. In mesocosms, foraging success of blue crabs varied with 3D interstitial space as mean proportional survivorship (± SE) of mud crabs was significantly lower in 45° (0.27 ± 0.06) vs. 0° (0.86 ± 0.04) orientations and for crevice (0.52 ± 0.11) vs. channel shapes (0.95 ± 0.02). These results suggest that 3D aspects of interstitial space, which have direct relevance to refuge quality, can strongly influence foraging success in our oyster reef habitat. Our findings highlight the importance of spatial arrangement in mediating consumptive pathways in hard-structured habitats and demonstrate how quantifying the three-dimensionality of living space captures aspects of habitat structure that have been missing from previous empirical studies of trophic interactions and structural complexity. © 2017 by the Ecological Society of America.

Comparison of multiple gene assembly methods for metabolic engineering

Treesearch

Chenfeng Lu; Karen Mansoorabadi; Thomas Jeffries

2007-01-01

A universal, rapid DNA assembly method for efficient multigene plasmid construction is important for biological research and for optimizing gene expression in industrial microbes. Three different approaches to achieve this goal were evaluated. These included creating long complementary extensions using a uracil-DNA glycosylase technique, overlap extension polymerase...

Structures of ribonucleoprotein particle modification enzymes

PubMed Central

Liang, Bo; Li, Hong

2016-01-01

Small nucleolar and Cajal body ribonucleoprotein particles (RNPs) are required for the maturation of ribosomes and spliceosomes. They consist of small nucleolar RNA or Cajal body RNA combined with partner proteins and represent the most complex RNA modification enzymes. Recent advances in structure and function studies have revealed detailed information regarding ribonucleoprotein assembly and substrate binding. These enzymes form intertwined RNA–protein assemblies that facilitate reversible binding of the large ribosomal RNA or small nuclear RNA. These revelations explain the specificity among the components in enzyme assembly and substrate modification. The multiple conformations of individual components and those of complete RNPs suggest a dynamic assembly process and justify the requirement of many assembly factors in vivo. PMID:21108865

Passive Films, Surface Structure and Stress Corrosion and Crevice Corrosion Susceptibility.

DTIC Science & Technology

1980-08-01

with pure titanium ( 4 ], it is of interest to pursue the effects on titanium -palladium alloys, to evaluate their susceptibility to stress corrosion...cracking due to hydrogen embrittlement with the field ion microscope, and to compare the results with those previously obtained with pure titanium [ 4 ...characterized as 99.99+ percent pure, and was used in the previous field ion microscopy study of titanium [ 4 ], where it was found that strain annealing titanium

Effect of chlorides on solution corrosivity of methyldiethanolamine (MDEA) solutions

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

Rooney, P.C.; Bacon, T.R.; DuPart, M.S.

1997-08-01

Solution corrosivity of MDEA/water solutions containing added HCl or NaCl have been measured by weight loss coupons at 250 F and by linear polarization resistance (LPR) at 208 F using carbon steel, 304SS, 316SS and 410SS. General corrosion as well as pitting or crevice corrosion tendencies were recorded for each species. Based on these results, recommendations are made for chlorides in MDEA that minimizes corrosion in gas treating operations.

Passive Films, Surface Structure and Stress Corrosion and Crevice Corrosion Susceptibility.

DTIC Science & Technology

1983-11-01

thiadiazole ( DMTDA ), when dispersed in the coating were observed to delay the onset of delamifnation. Catechol was found to be an ineffective inhibitor. A...similar beneficial effect was noted with a two-layer system employing a zinc chromate primer. However, when 8-HQ and DMTDA were applied by an anodic...shows the ellipsometric responses for the iron/acrylic system with DMTDA dispersed in the coating. The pre-puncture signals suggest changes in surface

Seawater Corrosion of Fasteners in Various Structural Materials

DTIC Science & Technology

1976-04-01

17 - 4PH stainless steel. The seven bolt materials were: 2024 aluminum, anodized ASTM grade 5 steel, 304 and 316 stainless steels, A286 stain- less...performed well in titanium structures. Use of MP35N, A286, and 304 stainless steel fasteners for constantly immersed 17 - 4PH stainless steel structures...would have been satisfactory only if sealant was not used and if protection had been provided to the 17 - 4PH to minimize crevice corrosion. Additional

Predation cues rather than resource availability promote cryptic behaviour in a habitat-forming sea urchin.

PubMed

Spyksma, Arie J P; Taylor, Richard B; Shears, Nick T

2017-03-01

It is well known that predators often influence the foraging behaviour of prey through the so-called "fear effect". However, it is also possible that predators could change prey behaviour indirectly by altering the prey's food supply through a trophic cascade. The predator-sea urchin-kelp trophic cascade is widely assumed to be driven by the removal of sea urchins by predators, but changes in sea urchin behaviour in response to predators or increased food availability could also play an important role. We tested whether increased crevice occupancy by herbivorous sea urchins in the presence of abundant predatory fishes and lobsters is a response to the increased risk of predation, or an indirect response to higher kelp abundances. Inside two New Zealand marine reserves with abundant predators and kelp, individuals of the sea urchin Evechinus chloroticus were rarer and remained cryptic (i.e. found in crevices) to larger sizes than on adjacent fished coasts where predators and kelp are rare. In a mesocosm experiment, cryptic behaviour was induced by simulated predation (the addition of crushed conspecifics), but the addition of food in the form of drift kelp did not induce cryptic behaviour. These findings demonstrate that the 'fear' of predators is more important than food availability in promoting sea urchin cryptic behaviour and suggest that both density- and behaviourally mediated interactions are important in the predator-sea urchin-kelp trophic cascade.

Stereo imaging and cytocompatibility of a model dental implant surface formed by direct laser fabrication.

PubMed

Mangano, Carlo; Raspanti, Mario; Traini, Tonino; Piattelli, Adriano; Sammons, Rachel

2009-03-01

Direct laser fabrication (DLF) allows solids with complex geometry to be produced by sintering metal powder particles in a focused laser beam. In this study, 10 Ti6Al4V alloy model dental root implants were obtained by DLF, and surface characterization was carried out using stereo scanning electron microscopy to produce 3D reconstructions. The surfaces were extremely irregular, with approximately 100 microm deep, narrow intercommunicating crevices, shallow depressions and deep, rounded pits of widely variable shape and size, showing ample scope for interlocking with the host bone. Roughness parameters were as follows: R(t), 360.8 microm; R(z), 358.4 microm; R(a), 67.4 microm; and R(q), 78.0 microm. Disc specimens produced by DLF with an identically prepared surface were used for biocompatibility studies with rat calvarial osteoblasts: After 9 days, cells had attached and spread on the DLF surface, spanning across the crevices, and voids. Cell density was similar to that on a commercial rough microtextured surface but lower than on commercial smooth machined and smooth-textured grit-blasted, acid-etched surfaces. Human fibrin clot extension on the DLF surface was slightly improved by inorganic acid etching to increase the microroughness. With further refinements, DLF could be an economical means of manufacturing implants from titanium alloys. (c) 2008 Wiley Periodicals, Inc.

Geochemical evidence for hydroclimatic variability over the last 2460 years from Crevice Lake in Yellowstone National Park, USA

USGS Publications Warehouse

Stevens, L.R.; Dean, W.E.

2008-01-01

A 2460-year-long hydroclimatic record for Crevice Lake, Yellowstone National Park, Montana was constructed from the ??18O values of endogenic carbonates. The ??18O record is compared to the Palmer Hydrologic Drought Index (PHDI) and Pacific Decadal Oscillation (PDO) indices, as well as inferred discharge of the Yellowstone River. During the last century, high ??18O values coincide with drought conditions and the warm phase of the PDO index. Low ??18O values coincide with wet years and a negative PDO index. Comparison of tree-ring inferred discharge of the Yellowstone River with the ??18O record over the last 300 years indicates that periods of high discharge (i.e., wet winters with significant snow pack) correspond with low ??18O values. Extrapolating this relationship we infer wet winters and high river discharge for the periods of 1090-1030, 970-870, 670-620, and 500-430 cal years BP. The wet intervals at 670 and 500 cal BP are synchronous with similar events in Banff, Canada and Walker Lake, Nevada. The wet intervals at 970 and 670 cal BP overlap with wet intervals at Walker Lake and major drought events identified in the western Great Basin. These results suggest that the northern border of Yellowstone National Park straddles the boundary between Northern Rocky Mountains and Great Basin climate regimes. ?? 2007 Elsevier Ltd and INQUA.

Consequences of volcanic ash deposition on the locomotor performance of the Phymaturus spectabilis lizard from Patagonia, Argentina.

PubMed

Cabezas-Cartes, Facundo; Kubisch, Erika Leticia; Ibargüengoytía, Nora Ruth

2014-03-01

The locomotor performance of lizards depends on their morphological and physiological adaptations to the habitat. However, when the habitat changes dramatically, for example, by a volcanic eruption, the performance of lizards may be affected. We registered the vegetation cover, the surface covered by ash, the presence of crevices suitable for Phymaturus and the rocks slopes to analyze the effects of ash accumulation produced by the eruption of Puyehue-Cordon Caulle volcanic complex on microhabitat use and availability of the Phymaturus spectabilis lizard. In addition, we studied the effect of ashes and slope on the locomotor performance of P. spectabilis by registering the maximum speed in sprint runs and long runs under four different treatments (cork and on the level, ashes and on the level, cork and slope, and ashes and slope). P. spectabilis selected microhabitats unvegetated, with crevices and steep slopes. Regarding locomotor performance, the speed of lizards was negatively affected by the presence of ash only in sprint runs on the level and in long runs with slope. The slope had a negative impact on the speed in all the treatments. These results show that the presence of volcanic ashes in the substrate might have affected the locomotor performance of the lizards, especially in long runs, and hence, the interaction of individuals with the environment, that is, escaping from predators and social behavior. © 2013 Wiley Periodicals, Inc.

Micro-topography mediates interactions between corals, algae, and herbivorous fishes on coral reefs

NASA Astrophysics Data System (ADS)

Brandl, S. J.; Hoey, A. S.; Bellwood, D. R.

2014-06-01

Processes occurring during the early life stages of corals are important for the replenishment of coral assemblages and the resilience of coral reefs. However, the factors influencing early life stages of corals are not well understood, and the role of micro-topographic complexity for habitat associations of juvenile corals is largely unexplored. This study investigated the microhabitat distribution patterns of early life stages of corals and a potential macroalgal competitor ( Turbinaria ornata) across two reef zones (reef crest and outer reef flat) on Lizard Island, Great Barrier Reef. In both reef zones, both corals and T. ornata were significantly more abundant in concealed microhabitats than in semi-concealed or open microhabitats (GLMM: P < 0.001). The prevalence of juvenile corals and T. ornata within concealed environments suggests that they might be effective refuges from grazing by herbivorous fishes. The density of juvenile corals was positively related, and density of T. ornata negatively related to the abundance of two groups of herbivorous fishes, pairing rabbitfishes, and surgeonfishes in the genus Zebrasoma (BEST ENV-BIO: r s = 0.72, P < 0.01), which feed in concealed microhabitats. This correlative evidence suggests that crevices may be important for early life stages of both coral and macroalgae, and that a specific suite of crevice-feeding fishes may influence benthic community dynamics in these microhabitats.

Technological capabilities of surface layers formation on implant made of Ti-6Al-4V ELI alloy.

PubMed

Kiel-Jamrozik, Marta; Szewczenko, Janusz; Basiaga, Marcin; Nowińska, Katarzyna

2015-01-01

The aim of the presented research was to find a combination of surface modification methods of implants made of the Ti-6Al-4V ELI alloy, that lead to formation of effective barrier for metallic ions that may infiltrate into solution. To this end, the following tests were carried out: roughness measurement, the voltamperometric tests (potentiodynamic and potentiostatic), and the ion infiltration test. The electropolishing process resulted in the lowering of surface roughness in comparison with mechanical treatment of the surface layer. The anodization process and steam sterilization increased corrosion resistance regardless of the mechanical treatment or electropolishing. The crevice corrosion tests revealed that independent of the modification method applied, the Ti-6Al-4V ELI alloy has excellent crevice corrosion resistance. The smallest quantity of ions infiltrated to the solution was observed for surface modification consisting in the mechanical treatment and anodization with the potential of 97 V. Electric parameters deter- mined during studies were the basis for effectiveness estimation of particular surface treatment methods. The research has shown that the anodization process significantly influences the pitting corrosion resistance of the Ti-6Al-4V ELI alloy independent of the previous surface treatment methods (mechanical and electrochemical). The surface layer after such modification is a protective barrier for metallic ions infiltrated to solution and protects titanium alloy against corrosive environment influence.

Emitter and absorber assembly for multiple self-dual operation and directional transparency

NASA Astrophysics Data System (ADS)

Kalozoumis, P. A.; Morfonios, C. V.; Kodaxis, G.; Diakonos, F. K.; Schmelcher, P.

2017-03-01

We demonstrate how to systematically design wave scattering systems with simultaneous coherent perfect absorbing and lasing operation at multiple and prescribed frequencies. The approach is based on the recursive assembly of non-Hermitian emitter and absorber units into self-dual emitter-absorber trimers at different composition levels, exploiting the simple structure of the corresponding transfer matrices. In particular, lifting the restriction to parity-time-symmetric setups enables the realization of emitter and absorber action at distinct frequencies and provides flexibility with respect to the choice of realistic parameters. We further show how the same assembled scatterers can be rearranged to produce unidirectional and bidirectional transparency at the selected frequencies. With the design procedure being generically applicable to wave scattering in single-channel settings, we demonstrate it with concrete examples of photonic multilayer setups.

Engineering at SLAC: Designing and constructing experimental devices for the Stanford Synchrotron Radiation Lightsource - Final Paper

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

Djang, Austin

2015-08-22

Thanks to the versatility of the beam lines at SSRL, research there is varied and benefits multiple fields. Each experiment requires a particular set of experiment equipment, which in turns requires its own particular assembly. As such, new engineering challenges arise from each new experiment. My role as an engineering intern has been to help solve these challenges, by designing and assembling experimental devices. My first project was to design a heated sample holder, which will be used to investigate the effect of temperature on a sample's x-ray diffraction pattern. My second project was to help set up an imagingmore » test, which involved designing a cooled grating holder and assembling multiple positioning stages. My third project was designing a 3D-printed pencil holder for the SSRL workstations.« less

Robot Serviced Space Facility

NASA Technical Reports Server (NTRS)

Purves, Lloyd R. (Inventor)

1992-01-01

A robot serviced space facility includes multiple modules which are identical in physical structure, but selectively differing in function. and purpose. Each module includes multiple like attachment points which are identically placed on each module so as to permit interconnection with immediately adjacent modules. Connection is made through like outwardly extending flange assemblies having identical male and female configurations for interconnecting to and locking to a complementary side of another flange. Multiple rows of interconnected modules permit force, fluid, data and power transfer to be accomplished by redundant circuit paths. Redundant modules of critical subsystems are included. Redundancy of modules and of interconnections results in a space complex with any module being removable upon demand, either for module replacement or facility reconfiguration. without eliminating any vital functions of the complex. Module replacement and facility assembly or reconfiguration are accomplished by a computer controlled articulated walker type robotic manipulator arm assembly having two identical end-effectors in the form of male configurations which are identical to those on module flanges and which interconnect to female configurations on other flanges. The robotic arm assembly moves along a connected set or modules by successively disconnecting, moving and reconnecting alternate ends of itself to a succession of flanges in a walking type maneuver. To transport a module, the robot keeps the transported module attached to one of its end-effectors and uses another flange male configuration of the attached module as a substitute end-effector during walking.

Cognitive Processes in the Production of Multiple-Goal Messages: Evidence from the Temporal Characteristics of Speech.

ERIC Educational Resources Information Center

Greene, John O.; And Others

1993-01-01

Finds that the increased cognitive load accompanying multiple-goal messages arises from demands on time and processing capacity associated with assembling incompatible message features and that multiple-goal messages are characterized by heavier demand on processing capacity associated with maintaining more complex message-relevant specifications…

29 CFR 1926.753 - Hoisting and rigging.

Code of Federal Regulations, 2010 CFR

2010-07-01

... lift rigging procedure. (1) A multiple lift shall only be performed if the following criteria are met: (i) A multiple lift rigging assembly is used; (ii) A maximum of five members are hoisted per lift... multiple lift have been trained in these procedures in accordance with § 1926.761(c)(1). (v) No crane is...

Wireline system for multiple direct push tool usage

DOEpatents

Bratton, Wesley L.; Farrington, Stephen P.; Shinn, II, James D.; Nolet, Darren C.

2003-11-11

A tool latching and retrieval system allows the deployment and retrieval of a variety of direct push subsurface characterization tools through an embedded rod string during a single penetration without requiring withdrawal of the string from the ground. This enables the in situ interchange of different tools, as well as the rapid retrieval of soil core samples from multiple depths during a single direct push penetration. The system includes specialized rods that make up the rod string, a tool housing which is integral to the rod string, a lock assembly, and several tools which mate to the lock assembly.

Simple method for assembly of CRISPR synergistic activation mediator gRNA expression array.

PubMed

Vad-Nielsen, Johan; Nielsen, Anders Lade; Luo, Yonglun

2018-05-20

When studying complex interconnected regulatory networks, effective methods for simultaneously manipulating multiple genes expression are paramount. Previously, we have developed a simple method for generation of an all-in-one CRISPR gRNA expression array. We here present a Golden Gate Assembly-based system of synergistic activation mediator (SAM) compatible CRISPR/dCas9 gRNA expression array for the simultaneous activation of multiple genes. Using this system, we demonstrated the simultaneous activation of the transcription factors, TWIST, SNAIL, SLUG, and ZEB1 a human breast cancer cell line. Copyright © 2018 Elsevier B.V. All rights reserved.

Unknown Aspects of Self-Assembly of PbS Microscale Superstructures

PubMed Central

Querejeta-Fernández, Ana; Hernández-Garrido, Juan C.; Yang, Hengxi; Zhou, Yunlong; Varela, Aurea; Parras, Marina; Calvino-Gámez, José J.; González-Calbet, Jose M.; Green, Peter F.; Kotov, Nicholas A.

2012-01-01

A lot of interesting and sophisticated examples of nanoparticle (NP) self-assembly (SA) are known. From both fundamental and technological standpoints this field requires advancements in three principle directions: a) understanding the mechanism and driving forces of three-dimensional (3D) SA with both nano- and micro-levels of organization; b) understanding of disassembly/deconstruction processes; and c) finding synthetic methods of assembly into continuous superstructures without insulating barriers. From this perspective, we investigated the formation of well-known star-like PbS superstructures and found a number of previously unknown or overlooked aspects that can advance the knowledge of NP self-assembly in these three directions. The primary one is that the formation of large seemingly monocrystalline PbS superstructures with multiple levels of octahedral symmetry can be explained only by SA of small octahedral NPs. We found five distinct periods in the formation PbS hyperbranched stars: 1) nucleation of early PbS NPs with an average diameter of 31 nm; 2) assembly into 100–500 nm octahedral mesocrystals; 3) assembly into 1000–2500 nm hyperbranched stars; 4) assembly and ionic recrystallization into six-arm rods accompanied by disappearance of fine nanoscale structure; 5) deconstruction into rods and cubooctahedral NPs. The switches in assembly patterns between the periods occur due to variable dominance of pattern–determining forces that include vander Waals and electrostatic (charge-charge, dipole-dipole, and polarization) interactions. The superstructure deconstruction is triggered by chemical changes in the deep eutectic solvent (DES) used as the media. PbS superstructures can be excellent models for fundamental studies of nanoscale organization and SA manufacturing of (opto)electronics and energy harvesting devices which require organization of PbS components at multiple scales. PMID:22515512

Unknown aspects of self-assembly of PbS microscale superstructures.

PubMed

Querejeta-Fernández, Ana; Hernández-Garrido, Juan C; Yang, Hengxi; Zhou, Yunlong; Varela, Aurea; Parras, Marina; Calvino-Gámez, José J; González-Calbet, Jose M; Green, Peter F; Kotov, Nicholas A

2012-05-22

A lot of interesting and sophisticated examples of nanoparticle (NP) self-assembly (SA) are known. From both fundamental and technological standpoints, this field requires advancements in three principle directions: (a) understanding the mechanism and driving forces of three-dimensional (3D) SA with both nano- and microlevels of organization; (b) understanding disassembly/deconstruction processes; and (c) finding synthetic methods of assembly into continuous superstructures without insulating barriers. From this perspective, we investigated the formation of well-known star-like PbS superstructures and found a number of previously unknown or overlooked aspects that can advance the knowledge of NP self-assembly in these three directions. The primary one is that the formation of large seemingly monocrystalline PbS superstructures with multiple levels of octahedral symmetry can be explained only by SA of small octahedral NPs. We found five distinct periods in the formation PbS hyperbranched stars: (1) nucleation of early PbS NPs with an average diameter of 31 nm; (2) assembly into 100-500 nm octahedral mesocrystals; (3) assembly into 1000-2500 nm hyperbranched stars; (4) assembly and ionic recrystallization into six-arm rods accompanied by disappearance of fine nanoscale structure; (5) deconstruction into rods and cuboctahedral NPs. The switches in assembly patterns between the periods occur due to variable dominance of pattern-determining forces that include van der Waals and electrostatic (charge-charge, dipole-dipole, and polarization) interactions. The superstructure deconstruction is triggered by chemical changes in the deep eutectic solvent (DES) used as the media. PbS superstructures can be excellent models for fundamental studies of nanoscale organization and SA manufacturing of (opto)electronics and energy-harvesting devices which require organization of PbS components at multiple scales.

An active locking mechanism for assembling 3D micro structures

NASA Astrophysics Data System (ADS)

Zhang, Ping; Mayyas, Mohammad; Lee, Woo Ho; Popa, Dan; Shiakolas, Panos; Stephanou, Harry; Chiao, J. C.

2007-01-01

Microassembly is an enabling technology to build 3D microsystems consisting of microparts made of different materials and processes. Multiple microparts can be connected together to construct complicated in-plane and out-of-plane microsystems by using compliant mechanical structures such as micro hinges and snap fasteners. This paper presents design, fabrication, and assembly of an active locking mechanism that provides mechanical and electrical interconnections between mating microparts. The active locking mechanism is composed of thermally actuated Chevron beams and sockets. Assembly by means of an active locking mechanism offers more flexibility in designing microgrippers as it reduces or minimizes mating force, which is one of the main reasons causing fractures in a microgripper during microassembly operation. Microgrippers, microparts, and active locking mechanisms were fabricated on a silicon substrate using the deep reactive ion etching (DRIE) processes with 100-um thick silicon on insulator (SOI) wafers. A precision robotic assembly platform with a dual microscope vision system was used to automate the manipulation and assembly processes of microparts. The assembly sequence includes (1) tether breaking and picking up of a micropart by using an electrothermally actuated microgripper, (2) opening of a socket area for zero-force insertion, (3) a series of translation and rotation of a mating micropart to align it onto the socket, (4) insertion of a micropart into the socket, and (5) deactivation and releasing of locking fingers. As a result, the micropart was held vertically to the substrate and locked by the compliance of Chevron beams. Microparts were successfully assembled using the active locking mechanism and the measured normal angle was 89.2°. This active locking mechanism provides mechanical and electrical interconnections, and it can potentially be used to implement a reconfigurable microrobot that requires complex assembly of multiple links and joints.

Active control of complex, multicomponent self-assembly processes

NASA Astrophysics Data System (ADS)

Schulman, Rebecca

The kinetics of many complex biological self-assembly processes such as cytoskeletal assembly are precisely controlled by cells. Spatiotemporal control over rates of filament nucleation, growth and disassembly determine how self-assembly occurs and how the assembled form changes over time. These reaction rates can be manipulated by changing the concentrations of the components needed for assembly by activating or deactivating them. I will describe how we can use these principles to design driven self-assembly processes in which we assemble and disassemble multiple types of components to create micron-scale networks of semiflexible filaments assembled from DNA. The same set of primitive components can be assembled into many different, structures depending on the concentrations of different components and how designed, DNA-based chemical reaction networks manipulate these concentrations over time. These chemical reaction networks can in turn interpret environmental stimuli to direct complex, multistage response. Such a system is a laboratory for understanding complex active material behaviors, such as metamorphosis, self-healing or adaptation to the environment that are ubiquitous in biological systems but difficult to quantitatively characterize or engineer.

SKYLAB (SL)-3 - EXPERIMENT HARDWARE

NASA Image and Video Library

1973-11-08

S74-19675 (1974) --- Medium close-up view of the M512 materials processing equipment storage assembly and the M518 electric furnace in the Multiple Docking Adapter (MDA), one of the primary elements of the Skylab space station. The assembly holds equipment designed to explore space manufacturing capability in a weightless state. Photo credit: NASA

Assembly of microparticles by optical trapping with a photonic crystal nanocavity

NASA Astrophysics Data System (ADS)

Renaut, C.; Dellinger, J.; Cluzel, B.; Honegger, T.; Peyrade, D.; Picard, E.; de Fornel, F.; Hadji, E.

2012-03-01

In this work, we report the auto-assembly experiments of micrometer sized particles by optical trapping in the evanescent field of a photonic crystal nanocavity. The nanocavity is inserted inside an optofluidic cell designed to enable the real time control of the nanoresonator transmittance as well as the real time visualization of the particles motion in the vicinity of the nanocavity. It is demonstrated that the optical trap above the cavity enables the assembly of multiple particles in respect of different stable conformations.

Automated assembly of oligosaccharides containing multiple cis-glycosidic linkages

NASA Astrophysics Data System (ADS)

Hahm, Heung Sik; Hurevich, Mattan; Seeberger, Peter H.

2016-09-01

Automated glycan assembly (AGA) has advanced from a concept to a commercial technology that rapidly provides access to diverse oligosaccharide chains as long as 30-mers. To date, AGA was mainly employed to incorporate trans-glycosidic linkages, where C2 participating protecting groups ensure stereoselective couplings. Stereocontrol during the installation of cis-glycosidic linkages cannot rely on C2-participation and anomeric mixtures are typically formed. Here, we demonstrate that oligosaccharides containing multiple cis-glycosidic linkages can be prepared efficiently by AGA using monosaccharide building blocks equipped with remote participating protecting groups. The concept is illustrated by the automated syntheses of biologically relevant oligosaccharides bearing various cis-galactosidic and cis-glucosidic linkages. This work provides further proof that AGA facilitates the synthesis of complex oligosaccharides with multiple cis-linkages and other biologically important oligosaccharides.

Nonmedially assembled F-actin cables incorporate into the actomyosin ring in fission yeast

PubMed Central

Huang, Junqi; Huang, Yinyi; Yu, Haochen; Subramanian, Dhivya; Padmanabhan, Anup; Thadani, Rahul; Tao, Yaqiong; Tang, Xie; Wedlich-Soldner, Roland

2012-01-01

In many eukaryotes, cytokinesis requires the assembly and constriction of an actomyosin-based contractile ring. Despite the central role of this ring in cytokinesis, the mechanism of F-actin assembly and accumulation in the ring is not fully understood. In this paper, we investigate the mechanism of F-actin assembly during cytokinesis in Schizosaccharomyces pombe using lifeact as a probe to monitor actin dynamics. Previous work has shown that F-actin in the actomyosin ring is assembled de novo at the division site. Surprisingly, we find that a significant fraction of F-actin in the ring was recruited from formin-Cdc12p nucleated long actin cables that were generated at multiple nonmedial locations and incorporated into the ring by a combination of myosin II and myosin V activities. Our results, together with findings in animal cells, suggest that de novo F-actin assembly at the division site and directed transport of F-actin cables assembled elsewhere can contribute to ring assembly. PMID:23185032

Recent advances in sequence assembly: principles and applications.

PubMed

Chen, Qingfeng; Lan, Chaowang; Zhao, Liang; Wang, Jianxin; Chen, Baoshan; Chen, Yi-Ping Phoebe

2017-11-01

The application of advanced sequencing technologies and the rapid growth of various sequence data have led to increasing interest in DNA sequence assembly. However, repeats and polymorphism occur frequently in genomes, and each of these has different impacts on assembly. Further, many new applications for sequencing, such as metagenomics regarding multiple species, have emerged in recent years. These not only give rise to higher complexity but also prevent short-read assembly in an efficient way. This article reviews the theoretical foundations that underlie current mapping-based assembly and de novo-based assembly, and highlights the key issues and feasible solutions that need to be considered. It focuses on how individual processes, such as optimal k-mer determination and error correction in assembly, rely on intelligent strategies or high-performance computation. We also survey primary algorithms/software and offer a discussion on the emerging challenges in assembly. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Optimal use of human and machine resources for Space Station assembly operations

NASA Technical Reports Server (NTRS)

Parrish, Joseph C.

1988-01-01

This paper investigates the issues involved in determining the best mix of human and machine resources for assembly of the Space Station. It presents the current Station assembly sequence, along with descriptions of the available assembly resources. A number of methodologies for optimizing the human/machine tradeoff problem have been developed, but the Space Station assembly offers some unique issues that have not yet been addressed. These include a strong constraint on available EVA time for early flights and a phased deployment of assembly resources over time. A methodology for incorporating the previously developed decision methods to the special case of the Space Station is presented. This methodology emphasizes an application of multiple qualitative and quantitative techniques, including simulation and decision analysis, for producing an objective, robust solution to the tradeoff problem.

An analytical investigation of NO sub x control techniques for methanol fueled spark ignition engines

NASA Technical Reports Server (NTRS)

Browning, L. H.; Argenbright, L. A.

1983-01-01

A thermokinetic SI engine simulation was used to study the effects of simple nitrogen oxide control techniques on performance and emissions of a methanol fueled engine. As part of this simulation, a ring crevice storage model was formulated to predict UBF emissions. The study included spark retard, two methods of compression ratio increase and EGR. The study concludes that use of EGR in high turbulence, high compression engines will both maximize power and thermal efficiency while minimizing harmful exhaust pollutants.

Attachment Levels and Crevicular Depths at the Distal of Mandibular Second Molars Following Removal of Adjacent Third Molars.

DTIC Science & Technology

1981-02-01

attachment by determining the distance between the bottom of the crevice and the cemento -enamel junction prior to surgery were unsuccessful, but they were...measuring from the tips of the distolingual and distobuccal cusps and the midpoint of the distal marginal ridge (the cemento -enamel junction could not be...The cemento -enamel junction, usually used as a refer- ence point for determining attachment level, could not be visualized on the distal of the

Ultrasound-induced inertial cavitation from gas-stabilizing nanoparticles.

PubMed

Kwan, J J; Graham, S; Myers, R; Carlisle, R; Stride, E; Coussios, C C

2015-08-01

The understanding of cavitation from nanoparticles has been hindered by the inability to control nanobubble size. We present a method to manufacture nanoparticles with a tunable single hemispherical depression (nanocups) of mean diameter 90, 260, or 650 nm entrapping a nanobubble. A modified Rayleigh-Plesset crevice model predicts the inertial cavitation threshold as a function of cavity size and frequency, and is verified experimentally. The ability to tune cavitation nanonuclei and predict their behavior will be useful for applications ranging from cancer therapy to ultrasonic cleaning.

Cavitation Inception Scale Effects. 1. Nuclei Distributions in Natural Waters. 2. Cavitation Inception in a Turbulent Shear Flow.

DTIC Science & Technology

1987-05-01

ratio of specific heats for the gas and an adiabatic bubble pressure- volume relation has been assumed (Plesset & Prosperetti 1977). When viscosity...pressure because of surface tension at the gas -liquid interface , so the gas is stabilized in the crevice and will not dissolve into the liquid. The concave... interface toward the gas is estab- lished by the hydrophobic nature of the particle, and results in surface tension acting to oppose the liquid

Nanomechanical testing system

DOEpatents

Vodnick, David James; Dwivedi, Arpit; Keranen, Lucas Paul; Okerlund, Michael David; Schmitz, Roger William; Warren, Oden Lee; Young, Christopher David

2014-07-08

An automated testing system includes systems and methods to facilitate inline production testing of samples at a micro (multiple microns) or less scale with a mechanical testing instrument. In an example, the system includes a probe changing assembly for coupling and decoupling a probe of the instrument. The probe changing assembly includes a probe change unit configured to grasp one of a plurality of probes in a probe magazine and couple one of the probes with an instrument probe receptacle. An actuator is coupled with the probe change unit, and the actuator is configured to move and align the probe change unit with the probe magazine and the instrument probe receptacle. In another example, the automated testing system includes a multiple degree of freedom stage for aligning a sample testing location with the instrument. The stage includes a sample stage and a stage actuator assembly including translational and rotational actuators.

Nanomechanical testing system

DOEpatents

Vodnick, David James; Dwivedi, Arpit; Keranen, Lucas Paul; Okerlund, Michael David; Schmitz, Roger William; Warren, Oden Lee; Young, Christopher David

2015-01-27

An automated testing system includes systems and methods to facilitate inline production testing of samples at a micro (multiple microns) or less scale with a mechanical testing instrument. In an example, the system includes a probe changing assembly for coupling and decoupling a probe of the instrument. The probe changing assembly includes a probe change unit configured to grasp one of a plurality of probes in a probe magazine and couple one of the probes with an instrument probe receptacle. An actuator is coupled with the probe change unit, and the actuator is configured to move and align the probe change unit with the probe magazine and the instrument probe receptacle. In another example, the automated testing system includes a multiple degree of freedom stage for aligning a sample testing location with the instrument. The stage includes a sample stage and a stage actuator assembly including translational and rotational actuators.

Nanomechanical testing system

DOEpatents

Vodnick, David James; Dwivedi, Arpit; Keranen, Lucas Paul; Okerlund, Michael David; Schmitz, Roger William; Warren, Oden Lee; Young, Christopher David

2015-02-24

An automated testing system includes systems and methods to facilitate inline production testing of samples at a micro (multiple microns) or less scale with a mechanical testing instrument. In an example, the system includes a probe changing assembly for coupling and decoupling a probe of the instrument. The probe changing assembly includes a probe change unit configured to grasp one of a plurality of probes in a probe magazine and couple one of the probes with an instrument probe receptacle. An actuator is coupled with the probe change unit, and the actuator is configured to move and align the probe change unit with the probe magazine and the instrument probe receptacle. In another example, the automated testing system includes a multiple degree of freedom stage for aligning a sample testing location with the instrument. The stage includes a sample stage and a stage actuator assembly including translational and rotational actuators.

Cryogenic Optical Performance of a Light-weight Mirror Assembly for Future Space Astronomical Telescopes: Optical Test Results and Thermal Optical Model

NASA Technical Reports Server (NTRS)

Eng, Ron; Arnold, William; Baker, Markus A.; Bevan, Ryan M.; Carpenter, James R.; Effinger, Michael R.; Gaddy, Darrell E.; Goode, Brian K.; Kegley, Jeffrey R.; Hogue, William D.;

Histidine Kinase-Mediated Production and Autoassembly of Porphyromonas gingivalis Fimbriae▿ †

PubMed Central

Nishikawa, Kiyoshi; Duncan, Margaret J.

2010-01-01

Porphyromonas gingivalis, a Gram-negative oral anaerobe, is strongly associated with chronic adult periodontitis, and it utilizes FimA fimbriae to persistently colonize and evade host defenses in the periodontal crevice. The FimA-related gene cluster (the fim gene cluster) is positively regulated by the FimS-FimR two-component system. In this study, comparative analyses between fimbriate type strain ATCC 33277 and fimbria-deficient strain W83 revealed differences in their fimS loci, which encode FimS histidine kinase. Using a reciprocal gene exchange system, we established that FimS from W83 is malfunctional. Complementation analysis with chimeric fimS constructs revealed that W83 FimS has a defective kinase domain due to a truncated conserved G3 box motif that provides an ATP-binding pocket. The introduction of the functional fimS from 33277 restored the production, but not polymerization, of endogenous FimA subunits in W83. Further analyses with a fimA-exchanged W83 isogenic strain showed that even the fimbria-deficient W83 retains the ability to polymerize FimA from 33277, indicating the assembly of mature FimA by a primary structure-dependent mechanism. It also was shown that the substantial expression of 33277-type FimA fimbriae in the W83 derivative requires the introduction and expression of the functional 33277 fimS. These findings indicate that FimSR is the unique and universal regulatory system that activates the fim gene cluster in a fimA genotype-independent manner. PMID:20118268

Allosteric Control of Icosahedral Capsid Assembly

PubMed Central

Lazaro, Guillermo R.

2017-01-01

During the lifecycle of a virus, viral proteins and other components self-assemble to form an ordered protein shell called a capsid. This assembly process is subject to multiple competing constraints, including the need to form a thermostable shell while avoiding kinetic traps. It has been proposed that viral assembly satisfies these constraints through allosteric regulation, including the interconversion of capsid proteins among conformations with different propensities for assembly. In this article we use computational and theoretical modeling to explore how such allostery affects the assembly of icosahedral shells. We simulate assembly under a wide range of protein concentrations, protein binding affinities, and two different mechanisms of allosteric control. We find that, above a threshold strength of allosteric control, assembly becomes robust over a broad range of subunit binding affinities and concentrations, allowing the formation of highly thermostable capsids. Our results suggest that allostery can significantly shift the range of protein binding affinities that lead to successful assembly, and thus should be accounted for in models that are used to estimate interaction parameters from experimental data. PMID:27117092

Ionic self-assembly for functional hierarchical nanostructured materials.

PubMed

Faul, Charl F J

2014-12-16

CONSPECTUS: The challenge of constructing soft functional materials over multiple length scales can be addressed by a number of different routes based on the principles of self-assembly, with the judicious use of various noncovalent interactions providing the tools to control such self-assembly processes. It is within the context of this challenge that we have extensively explored the use of an important approach for materials construction over the past decade: exploiting electrostatic interactions in our ionic self-assembly (ISA) method. In this approach, cooperative assembly of carefully chosen charged surfactants and oppositely charged building blocks (or tectons) provides a facile noncovalent route for the rational design and production of functional nanostructured materials. Generally, our research efforts have developed with an initial focus on establishing rules for the construction of novel noncovalent liquid-crystalline (LC) materials. We found that the use of double-tailed surfactant species (especially branched double-tailed surfactants) led to the facile formation of thermotropic (and, in certain cases, lyotropic) phases, as demonstrated by extensive temperature-dependent X-ray and light microscopy investigations. From this core area of activity, research expanded to cover issues beyond simple construction of anisotropic materials, turning to the challenge of inclusion and exploitation of switchable functionality. The use of photoactive azobenzene-containing ISA materials afforded opportunities to exploit both photo-orientation and surface relief grating formation. The preparation of these anisotropic LC materials was of interest, as the aim was the facile production of disposable and low-cost optical components for display applications and data storage. However, the prohibitive cost of the photo-orientation processes hampered further exploitation of these materials. We also expanded our activities to explore ISA of biologically relevant tectons, specifically deoxyguanosine monophosphate. This approach proved, in combination with block copolymer (BCP) self-assembly, very fruitful for the construction of complex and hierarchical functional materials across multiple length scales. Molecular frustration and incommensurability, which played a major role in structure formation in combination with nucleotide assembly, have now become important tools to tune supramolecular structure formation. These concepts, that is, the use of BCP assembly and incommensurability, in combination with metal-containing polymeric materials, have provided access to novel supramolecular morphologies and, more importantly, design rules to prepare such constructs. These design rules are now also being applied to the assembly of electroactive oligo(aniline)-based materials for the preparation of highly ordered functional soft materials, and present an opportunity for materials development for applications in energy storage. In this Account, we therefore discuss investigations into (i) the inclusion and preparation of supramolecular photoactive and electroactive materials; (ii) the exploitation and control over multiple noncovalent interactions to fine-tune function, internal structure, and long-range order and (iii) exploration of construction over multiple length scales by combination of ISA with well-known BCP self-assembly. Combination of ISA with tuning of volume fractions, mutual compatibility, and molecular frustration now provides a versatile tool kit to construct complex and hierarchical functional materials in a facile noncovalent way. A direct challenge for future ISA activities would certainly be the construction of functional mesoscale objects. However, within a broader scientific context, the challenge would be to exploit this powerful assembly tool for application in areas of research with societal impact, for example, energy storage and generation. The hope is that this Account will provide a platform for such future research activities and opportunities.

Neutron Collar Evolution and Fresh PWR Assembly Measurements with a New Fast Neutron Passive Collar

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

Menlove, Howard Olsen; Geist, William H.; Root, Margaret A.

The passive neutron collar approach removes the effect of poison rods when using a 1mm Gd liner. This project sets out to solve the following challenges: BWR fuel assemblies have less mass and less neutron multiplication than PWR; and effective removal of cosmic ray spallation neutron bursts needed via QC tests.

Reference quality assembly of the 3.5 Gb genome of Capsicum annuum form a single linked-read library

USDA-ARS?s Scientific Manuscript database

Linked-Read sequencing technology has recently been employed successfully for de novo assembly of multiple human genomes, however the utility of this technology for complex plant genomes is unproven. We evaluated the technology for this purpose by sequencing the 3.5 gigabase (Gb) diploid pepper (Cap...

Developing Form Assembly Specifications for Exams with Multiple Choice and Constructed Response Items: Balancing Reliability and Validity Concerns

ERIC Educational Resources Information Center

Hendrickson, Amy; Patterson, Brian; Ewing, Maureen

2010-01-01

The psychometric considerations and challenges associated with including constructed response items on tests are discussed along with how these issues affect the form assembly specifications for mixed-format exams. Reliability and validity, security and fairness, pretesting, content and skills coverage, test length and timing, weights, statistical…

Multidimensional Test Assembly Based on Lagrangian Relaxation Techniques. Research Report 98-08.

ERIC Educational Resources Information Center

Veldkamp, Bernard P.

In this paper, a mathematical programming approach is presented for the assembly of ability tests measuring multiple traits. The values of the variance functions of the estimators of the traits are minimized, while test specifications are met. The approach is based on Lagrangian relaxation techniques and provides good results for the two…

Multiple Assembly Rules Drive the Co-occurrence of Orthopteran and Plant Species in Grasslands: Combining Network, Functional and Phylogenetic Approaches

PubMed Central

Fournier, Bertrand; Mouly, Arnaud; Gillet, François

2016-01-01

Understanding the factors underlying the co-occurrence of multiple species remains a challenge in ecology. Biotic interactions, environmental filtering and neutral processes are among the main mechanisms evoked to explain species co-occurrence. However, they are most often studied separately or even considered as mutually exclusive. This likely hampers a more global understanding of species assembly. Here, we investigate the general hypothesis that the structure of co-occurrence networks results from multiple assembly rules and its potential implications for grassland ecosystems. We surveyed orthopteran and plant communities in 48 permanent grasslands of the French Jura Mountains and gathered functional and phylogenetic data for all species. We constructed a network of plant and orthopteran species co-occurrences and verified whether its structure was modular or nested. We investigated the role of all species in the structure of the network (modularity and nestedness). We also investigated the assembly rules driving the structure of the plant-orthopteran co-occurrence network by using null models on species functional traits, phylogenetic relatedness and environmental conditions. We finally compared our results to abundance-based approaches. We found that the plant-orthopteran co-occurrence network had a modular organization. Community assembly rules differed among modules for plants while interactions with plants best explained the distribution of orthopterans into modules. Few species had a disproportionately high positive contribution to this modular organization and are likely to have a key importance to modulate future changes. The impact of agricultural practices was restricted to some modules (3 out of 5) suggesting that shifts in agricultural practices might not impact the entire plant-orthopteran co-occurrence network. These findings support our hypothesis that multiple assembly rules drive the modular structure of the plant-orthopteran network. This modular structure is likely to play a key role in the response of grassland ecosystems to future changes by limiting the impact of changes in agricultural practices such as intensification to some modules leaving species from other modules poorly impacted. The next step is to understand the importance of this modular structure for the long-term maintenance of grassland ecosystem structure and functions as well as to develop tools to integrate network structure into models to improve their capacity to predict future changes. PMID:27582754

Potentiodynamic polarization study of the in vitro corrosion behavior of 3 high-palladium alloys and a gold-palladium alloy in 5 media.

PubMed

Sun, Desheng; Monaghan, Peter; Brantley, William A; Johnston, William M

2002-01-01

Corrosion of cast alloy restorations may lead to their failure or adversely affect their biocompatibility. Although some documentation of the corrosion behavior of the high-palladium dental alloys exists, questions remain about their corrosion resistance and mechanisms. This study compared the in vitro corrosion characteristics of 3 high-palladium alloys and 1 gold-palladium alloy in simulated body fluid and oral environments. Two Pd-Cu-Ga alloys and 1 Pd-Ga alloy were selected; an Au-Pd alloy served as the control. The corrosion behavior for the as-cast and simulated porcelain-firing (heat-treated) conditions of each alloy (N = 5) was evaluated in 0.9% NaCl, 0.09% NaCl, and Fusayama solutions. Heat-treated specimens of each alloy (N = 5) were also tested in N(2)-deaerated 0.09% NaCl and Fusayama solutions (pH 4). After immersion in the electrolyte for 24 hours, the open-circuit potential (OCP) was measured, and linear polarization was performed from -20 mV to +20 mV (vs. OCP) at a scanning rate of 0.125 mV/s. Cyclic polarization was performed from -300 mV to +1000 mV and back to -300 mV (vs. OCP) at a scanning rate of 1 mV/s. Data were evaluated with analysis of variance and the Ryan-Einot-Gabriel-Welsch multiple-range test (alpha=.05). The OCP of each alloy varied with the condition (as-cast or heat-treated) and electrolyte used. Corrosion resistance was similar for the 4 alloys tested. For cyclic polarization, all alloys showed active-passive or spontaneous passive behavior in nearly all electrolytes. During some reverse scans, the 3 high-palladium alloys displayed 3 or 5 anodic peaks. No positive hysteresis was observed for any of the alloy/electrolyte combinations evaluated. The corrosion resistances of the 3 high-palladium alloys in simulated body fluid and oral environments were comparable to that of the gold-palladium alloy. The similar corrosion resistance for the 3 high-palladium alloys was attributed to their high noble metal content and theorized stable structure at the submicron level. Selective corrosion of different phases and elements, surface enrichment of palladium, and adsorption of species are possible corrosion mechanisms. The cyclic polarization results suggest that none of the 4 alloys would be prone to pitting or crevice corrosion under in vivo conditions, but crevice conditions should nonetheless be avoided for these alloys in the oral environment.

PLLA-PHB fiber membranes obtained by solvent-free electrospinning for short-time drug delivery.

PubMed

Cao, K; Liu, Y; Olkhov, A A; Siracusa, V; Iordanskii, A L

2018-02-01

Fibers of poly(L-lactic acid) (PLLA)/polyhydroxybutyrate (PHB) with different concentrations of the drug dipyridamole (DPD) were prepared using solvent-free melt electrospinning to obtain a polymeric drug delivery system. The electrospun fibers were morphologically, structurally, thermally, and dynamically characterized. Crazes that resemble lotus root crevices were interestingly observed in the 7:3 PLLA/PHB fibers with 1% DPD. The crystallinity of PLLA slightly decreased as PHB was incorporated, and the addition of DPD significantly reduced the melting temperature of the composite. The interactions between PLLA and PHB mainly occurred at a proportion of 7:3, and drug encapsulation in the fibers was verified. The kinetic profiles of drug release demonstrated the predominant multiple patterns involving a diffusional stage in the short-term mode of release and kinetic process related to the hydrolysis of the biopolymers. Furthermore, the dynamic behavior of the polymer molecules was evaluated based on the segmental mobility using probe electron spin resonance spectroscopy. The segmental mobility in the amorphous fraction of PLLA decreased with increasing PLLA content. The 9:1 PLLA/PHB system was more resistant to polymer hydrolysis than to the 7:3 system and the rate of diffusion transport was approximately two times higher for the 7:3 PLLA/PHB fibers than for the 9:1 PLLA/PHB fibers.

The Prevalence and Control of Bacillus and Related Spore-Forming Bacteria in the Dairy Industry.

PubMed

Gopal, Nidhi; Hill, Colin; Ross, Paul R; Beresford, Tom P; Fenelon, Mark A; Cotter, Paul D

2015-01-01

Milk produced in udder cells is sterile but due to its high nutrient content, it can be a good growth substrate for contaminating bacteria. The quality of milk is monitored via somatic cell counts and total bacterial counts, with prescribed regulatory limits to ensure quality and safety. Bacterial contaminants can cause disease, or spoilage of milk and its secondary products. Aerobic spore-forming bacteria, such as those from the genera Sporosarcina, Paenisporosarcina, Brevibacillus, Paenibacillus, Geobacillus and Bacillus, are a particular concern in this regard as they are able to survive industrial pasteurization and form biofilms within pipes and stainless steel equipment. These single or multiple-species biofilms become a reservoir of spoilage microorganisms and a cycle of contamination can be initiated. Indeed, previous studies have highlighted that these microorganisms are highly prevalent in dead ends, corners, cracks, crevices, gaskets, valves and the joints of stainless steel equipment used in the dairy manufacturing plants. Hence, adequate monitoring and control measures are essential to prevent spoilage and ensure consumer safety. Common controlling approaches include specific cleaning-in-place processes, chemical and biological biocides and other novel methods. In this review, we highlight the problems caused by these microorganisms, and discuss issues relating to their prevalence, monitoring thereof and control with respect to the dairy industry.

The Prevalence and Control of Bacillus and Related Spore-Forming Bacteria in the Dairy Industry

PubMed Central

Gopal, Nidhi; Hill, Colin; Ross, Paul R.; Beresford, Tom P.; Fenelon, Mark A.; Cotter, Paul D.

2015-01-01

Milk produced in udder cells is sterile but due to its high nutrient content, it can be a good growth substrate for contaminating bacteria. The quality of milk is monitored via somatic cell counts and total bacterial counts, with prescribed regulatory limits to ensure quality and safety. Bacterial contaminants can cause disease, or spoilage of milk and its secondary products. Aerobic spore-forming bacteria, such as those from the genera Sporosarcina, Paenisporosarcina, Brevibacillus, Paenibacillus, Geobacillus and Bacillus, are a particular concern in this regard as they are able to survive industrial pasteurization and form biofilms within pipes and stainless steel equipment. These single or multiple-species biofilms become a reservoir of spoilage microorganisms and a cycle of contamination can be initiated. Indeed, previous studies have highlighted that these microorganisms are highly prevalent in dead ends, corners, cracks, crevices, gaskets, valves and the joints of stainless steel equipment used in the dairy manufacturing plants. Hence, adequate monitoring and control measures are essential to prevent spoilage and ensure consumer safety. Common controlling approaches include specific cleaning-in-place processes, chemical and biological biocides and other novel methods. In this review, we highlight the problems caused by these microorganisms, and discuss issues relating to their prevalence, monitoring thereof and control with respect to the dairy industry. PMID:26733963

Micro-Masonry: Construction of 3D Structures by Mesoscale Self-Assembly

PubMed Central

Fernandez, Javier G.; Khademhosseini, Ali

2010-01-01

A general method for construction of three dimensional structures by directed assembly of microscale polymeric sub-units is presented. Shape-controlled microgels are directed to assemble into different shapes by limiting their movement onto a molded substrate. The capillary forces, resulting from the presence of a liquid polymer, assemble the microgels in close contact with the rest of the units and with the free surface, the latter imposing the final geometry of the resulting construct. The result is a freestanding structure composed of one or multiple layers of sub-units assembled in a tightly packed conformation. The applicability of the technique for the construction of scaffolds with cell-laden sub-units is demonstrated. In addition, scaffolds formed by the sequential aggregation of sub-units are produced. PMID:20440697

SynTrack: DNA Assembly Workflow Management (SynTrack) v2.0.1

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

MENG, XIANWEI; SIMIRENKO, LISA

2016-12-01

SynTrack is a dynamic, workflow-driven data management system that tracks the DNA build process: Management of the hierarchical relationships of the DNA fragments; Monitoring of process tasks for the assembly of multiple DNA fragments into final constructs; Creations of vendor order forms with selectable building blocks. Organizing plate layouts barcodes for vendor/pcr/fusion/chewback/bioassay/glycerol/master plate maps (default/condensed); Creating or updating Pre-Assembly/Assembly process workflows with selected building blocks; Generating Echo pooling instructions based on plate maps; Tracking of building block orders, received and final assembled for delivering; Bulk updating of colony or PCR amplification information, fusion PCR and chewback results; Updating with QA/QCmore » outcome with .csv & .xlsx template files; Re-work assembly workflow enabled before and after sequencing validation; and Tracking of plate/well data changes and status updates and reporting of master plate status with QC outcomes.« less

Modular anode assemblies and methods of using the same for electrochemical reduction

DOEpatents

Wiedmeyer, Stanley G; Barnes, Laurel A; Williamson, Mark A; Willit, James L

2015-02-17

Modular anode assemblies are used in electrolytic oxide reduction systems for scalable reduced metal production via electrolysis. Assemblies include a channel frame connected to several anode rods extending into an electrolyte. An electrical system powers the rods while being insulated from the channel frame. A cooling system removes heat from anode rods and the electrical system. An anode guard attaches to the channel frame to prevent accidental electrocution or damage during handling or repositioning. Each anode rod may be divided into upper and lower sections to permit easy repair and swapping out of lower sections. The modular assemblies may have standardized components to permit placement at multiple points within a reducing system. Example methods may operate an electrolytic oxide reduction system by positioning the modular anode assemblies in the reduction system and applying electrical power to the plurality of anode assemblies.

RPA binds histone H3-H4 and functions in DNA replication-coupled nucleosome assembly.

PubMed

Liu, Shaofeng; Xu, Zhiyun; Leng, He; Zheng, Pu; Yang, Jiayi; Chen, Kaifu; Feng, Jianxun; Li, Qing

2017-01-27

DNA replication-coupled nucleosome assembly is essential to maintain genome integrity and retain epigenetic information. Multiple involved histone chaperones have been identified, but how nucleosome assembly is coupled to DNA replication remains elusive. Here we show that replication protein A (RPA), an essential replisome component that binds single-stranded DNA, has a role in replication-coupled nucleosome assembly. RPA directly binds free H3-H4. Assays using a synthetic sequence that mimics freshly unwound single-stranded DNA at replication fork showed that RPA promotes DNA-(H3-H4) complex formation immediately adjacent to double-stranded DNA. Further, an RPA mutant defective in H3-H4 binding exhibited attenuated nucleosome assembly on nascent chromatin. Thus, we propose that RPA functions as a platform for targeting histone deposition to replication fork, through which RPA couples nucleosome assembly with ongoing DNA replication. Copyright © 2017, American Association for the Advancement of Science.

Core protein cleavage by signal peptide peptidase is required for hepatitis C virus-like particle assembly

PubMed Central

Ait-Goughoulte, Malika; Hourioux, Christophe; Patient, Romuald; Trassard, Sylvie; Brand, Denys; Roingeard, Philippe

2006-01-01

SUMMARY Hepatitis C virus (HCV) core protein, expressed with a Semliki forest virus (SFV) replicon, self-assembles into HCV-like particles (HCV-LP) at the endoplasmic reticulum (ER) membrane, providing an opportunity to study HCV assembly and morphogenesis by electron microscopy. We used this model to investigate whether the processing of the HCV core protein by the signal peptide peptidase (SPP) is required for the HCV-LP assembly. We designed several mutants as there are conflicting reports concerning the cleavage of mutant proteins by SPP. Production of the only core mutant protein that escaped SPP processing led to the formation of multiple layers of electron-dense ER membrane, with no evidence of HCV-LP assembly. Our data shed light on the HCV core residues involved in SPP cleavage and suggest that this cleavage is essential for HCV assembly. PMID:16528035

Application of the Modular Automated Reconfigurable Assembly System (MARAS) concept to adaptable vision gauging and parts feeding

NASA Technical Reports Server (NTRS)

By, Andre Bernard; Caron, Ken; Rothenberg, Michael; Sales, Vic

1994-01-01

This paper presents the first phase results of a collaborative effort between university researchers and a flexible assembly systems integrator to implement a comprehensive modular approach to flexible assembly automation. This approach, named MARAS (Modular Automated Reconfigurable Assembly System), has been structured to support multiple levels of modularity in terms of both physical components and system control functions. The initial focus of the MARAS development has been on parts gauging and feeding operations for cylinder lock assembly. This phase is nearing completion and has resulted in the development of a highly configurable system for vision gauging functions on a wide range of small components (2 mm to 100 mm in size). The reconfigurable concepts implemented in this adaptive Vision Gauging Module (VGM) are now being extended to applicable aspects of the singulating, selecting, and orienting functions required for the flexible feeding of similar mechanical components and assemblies.

Film riding seals for rotary machines

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

Bidkar, Rahul Anil; Sarawate, Neelesh Nandkumar; Wolfe, Christopher Edward

A seal assembly for a rotary machine is provided. The seal assembly includes multiple sealing device segments disposed circumferentially intermediate to a stationary housing and a rotor. Each of the segments includes a shoe plate with a forward-shoe section and an aft-shoe section having one or more labyrinth teeth therebetween facing the rotor. The sealing device includes a stator interface element having a groove or slot for allowing disposal of a spline seal for preventing segment leakages. The sealing device segment also includes multiple bellow springs or flexures connected to the shoe plate and to the stator interface element. Further,more » the sealing device segments include a secondary seal integrated with the stator interface element at one end and positioned about the multiple bellow springs or flexures and the shoe plate at the other end.« less

The formation of floor-fractured craters in Xanthe Terra

NASA Astrophysics Data System (ADS)

Sato, Hiroyuki; Kurita, Kei; Baratoux, David

2010-05-01

Floor-fractured craters (FFC) are a peculiar form of degradation of impact craters defined by the presence of crevice networks and mesas affecting crater floors. They are preferentially distributed near chaotic terrains and outflow channels. The scope of this paper is to present a detailed systematic analysis of FFC at Xanthe Terra. FFC morphologies in this region are classified into five types making a picture of different stages of the same degradation process. FFC are geographically intermixed with un-fractured normal craters (non-FFC). Young craters are less prone to show this type of degradation, as suggested by fresh ejecta layer with preserved crater floor. Size distributions of FFC and non-FFC indicate that larger craters are preferentially fractured. Careful examinations of the crater floor elevations reveal that the crevices often extend deeper than the original crater cavity. Furthermore, an onset depth for the formation of FFC is evidenced from the difference of spatial distributions between FFC and non-FFC. Roof-collapsed depressions observed in the same region have been also documented and their characteristics suggest the removal of subsurface material at depth from about 1200 to 4000 m. These observations taken together suggest a subsurface zone of volume deficit at depth from 1 to 2 km down to several kilometers responsible for FFC formation. Then a scenario of FFC formations is presented in the context of groundwater discharge events at the late Hesperian. This scenario involves two key processes, Earth fissuring and piping erosion, known to occur with rapid groundwater migrations on Earth.

Revised methods for estimating potential reentry exposure associated with indoor crack and crevice and perimeter application.

PubMed

Driver, Jeffrey H; Ross, John H; Pandian, Muhilan; Selim, Sami; Sharp, Janice K

2013-01-01

Surface deposition of insecticides applied as indoor residential foggers, baseboard or perimeter sprays, spot sprays, and crack-and-crevice (C&C) sprays represent pathways of unintentional, postapplication exposure for children and adults. Estimation of the magnitude of this exposure following an application event is associated with uncertainty due to many factors, including (1) surface residue deposition and distribution, (2) access to and the nature of contact with treated surfaces based on time-activity patterns of residents, and (3) the role of residue removal mechanisms such as cleaning treated surfaces, pesticide degradation or redistribution, and hand washing and bathing following contact. A comparative spatial deposition study was conducted involving broadcast, perimeter, and C&C application methods. Residues measured using a spatial grid of deposition dosimeters on floor surfaces demonstrated significantly lower residue concentrations in readily accessible areas following C&C and perimeter applications, versus broadcast treatment. Analyses of other monitoring studies support this finding. The implications of these findings are discussed for both screening-level and higher tier probabilistic postapplication, residential exposure assessment. The U.S. Environmental Protection Agency (EPA) current guidance on interpretation of deposition following C&C application is supported by data in this study and others that indicate a ratio of 10:1 for deposition for broadcast versus C&C application. However, the perimeter deposition data are quite similar to C&C deposition and do not support a 70/30 default relative to broadcast recommended by the U.S. EPA (2012).

Root Cause Investigation of Lead-Free Solder Joint Interfacial Failures After Multiple Reflows

NASA Astrophysics Data System (ADS)

Li, Yan; Hatch, Olen; Liu, Pilin; Goyal, Deepak

2017-03-01

Solder joint interconnects in three-dimensional (3D) packages with package stacking configurations typically must undergo multiple reflow cycles during the assembly process. In this work, interfacial open joint failures between the bulk solder and the intermetallic compound (IMC) layer were found in Sn-Ag-Cu (SAC) solder joints connecting a small package to a large package after multiple reflow reliability tests. Systematic progressive 3D x-ray computed tomography experiments were performed on both incoming and assembled parts to reveal the initiation and evolution of the open failures in the same solder joints before and after the reliability tests. Characterization studies, including focused ion beam cross-sections, scanning electron microscopy, and energy-dispersive x-ray spectroscopy, were conducted to determine the correlation between IMC phase transformation and failure initiation in the solder joints. A comprehensive failure mechanism, along with solution paths for the solder joint interfacial failures after multiple reflow cycles, is discussed in detail.

Elucidating energy and electron transfer dynamics within molecular assemblies for solar energy conversion

NASA Astrophysics Data System (ADS)

Morseth, Zachary Aaron

The use of sunlight to make chemical fuels (i.e. solar fuels) is an attractive approach in the quest to develop sustainable energy sources. Using nature as a guide, assemblies for artificial photosynthesis will need to perform multiple functions. They will need to be able to harvest light across a broad region of the solar spectrum, transport excited-state energy to charge-separation sites, and then transport and store redox equivalents for use in the catalytic reactions that produce chemical fuels. This multifunctional behavior will require the assimilation of multiple components into a single macromolecular system. A wide variety of different architectures including porphyrin arrays, peptides, dendrimers, and polymers have been explored, with each design posing unique challenges. Polymer assemblies are attractive due to their relative ease of production and facile synthetic modification. However, their disordered nature gives rise to stochastic dynamics not present in more ordered assemblies. The rational design of assemblies requires a detailed understanding of the energy and electron transfer events that follow light absorption, which can occur on timescales ranging from femtoseconds to hundreds of microseconds, necessitating the use of sophisticated techniques. We have used a combination of time-resolved absorption and emission spectroscopies with observation times that span nine orders of magnitude to follow the excited-state evolution within single-site and polymer-based molecular assemblies. We complement experimental observations with electronic structure calculations, molecular dynamics simulations, and kinetic modeling to develop a microscopic view of these dynamics. This thesis provides an overview of work on single-site molecular assemblies and polymers decorated with pendant chromophores, both in solution and on surfaces. This work was made possible through extensive collaboration with Dr. Kirk Schanze's and Dr. John Reynolds' research groups who synthesized the samples for study.

Optimizing Hybrid de Novo Transcriptome Assembly and Extending Genomic Resources for Giant Freshwater Prawns (Macrobrachium rosenbergii): The Identification of Genes and Markers Associated with Reproduction.

PubMed

Jung, Hyungtaek; Yoon, Byung-Ha; Kim, Woo-Jin; Kim, Dong-Wook; Hurwood, David A; Lyons, Russell E; Salin, Krishna R; Kim, Heui-Soo; Baek, Ilseon; Chand, Vincent; Mather, Peter B

2016-05-07

The giant freshwater prawn, Macrobrachium rosenbergii, a sexually dimorphic decapod crustacean is currently the world's most economically important cultured freshwater crustacean species. Despite its economic importance, there is currently a lack of genomic resources available for this species, and this has limited exploration of the molecular mechanisms that control the M. rosenbergii sex-differentiation system more widely in freshwater prawns. Here, we present the first hybrid transcriptome from M. rosenbergii applying RNA-Seq technologies directed at identifying genes that have potential functional roles in reproductive-related traits. A total of 13,733,210 combined raw reads (1720 Mbp) were obtained from Ion-Torrent PGM and 454 FLX. Bioinformatic analyses based on three state-of-the-art assemblers, the CLC Genomic Workbench, Trans-ABySS, and Trinity, that use single and multiple k-mer methods respectively, were used to analyse the data. The influence of multiple k-mers on assembly performance was assessed to gain insight into transcriptome assembly from short reads. After optimisation, de novo assembly resulted in 44,407 contigs with a mean length of 437 bp, and the assembled transcripts were further functionally annotated to detect single nucleotide polymorphisms and simple sequence repeat motifs. Gene expression analysis was also used to compare expression patterns from ovary and testis tissue libraries to identify genes with potential roles in reproduction and sex differentiation. The large transcript set assembled here represents the most comprehensive set of transcriptomic resources ever developed for reproduction traits in M. rosenbergii, and the large number of genetic markers predicted should constitute an invaluable resource for future genetic research studies on M. rosenbergii and can be applied more widely on other freshwater prawn species in the genus Macrobrachium.

Optimizing Hybrid de Novo Transcriptome Assembly and Extending Genomic Resources for Giant Freshwater Prawns (Macrobrachium rosenbergii): The Identification of Genes and Markers Associated with Reproduction

PubMed Central

Jung, Hyungtaek; Yoon, Byung-Ha; Kim, Woo-Jin; Kim, Dong-Wook; Hurwood, David A.; Lyons, Russell E.; Salin, Krishna R.; Kim, Heui-Soo; Baek, Ilseon; Chand, Vincent; Mather, Peter B.

2016-01-01

The giant freshwater prawn, Macrobrachium rosenbergii, a sexually dimorphic decapod crustacean is currently the world’s most economically important cultured freshwater crustacean species. Despite its economic importance, there is currently a lack of genomic resources available for this species, and this has limited exploration of the molecular mechanisms that control the M. rosenbergii sex-differentiation system more widely in freshwater prawns. Here, we present the first hybrid transcriptome from M. rosenbergii applying RNA-Seq technologies directed at identifying genes that have potential functional roles in reproductive-related traits. A total of 13,733,210 combined raw reads (1720 Mbp) were obtained from Ion-Torrent PGM and 454 FLX. Bioinformatic analyses based on three state-of-the-art assemblers, the CLC Genomic Workbench, Trans-ABySS, and Trinity, that use single and multiple k-mer methods respectively, were used to analyse the data. The influence of multiple k-mers on assembly performance was assessed to gain insight into transcriptome assembly from short reads. After optimisation, de novo assembly resulted in 44,407 contigs with a mean length of 437 bp, and the assembled transcripts were further functionally annotated to detect single nucleotide polymorphisms and simple sequence repeat motifs. Gene expression analysis was also used to compare expression patterns from ovary and testis tissue libraries to identify genes with potential roles in reproduction and sex differentiation. The large transcript set assembled here represents the most comprehensive set of transcriptomic resources ever developed for reproduction traits in M. rosenbergii, and the large number of genetic markers predicted should constitute an invaluable resource for future genetic research studies on M. rosenbergii and can be applied more widely on other freshwater prawn species in the genus Macrobrachium. PMID:27164098

Advanced composite applications for sub-micron biologically derived microstructures

NASA Technical Reports Server (NTRS)

Schnur, J. M.; Price, R. R.; Schoen, P. E.; Bonanventura, Joseph; Kirkpatrick, Douglas

1991-01-01

A major thrust of advanced material development is in the area of self-assembled ultra-fine particulate based composites (micro-composites). The application of biologically derived, self-assembled microstructures to form advanced composite materials is discussed. Hollow 0.5 micron diameter cylindrical shaped microcylinders self-assemble from diacetylenic lipids. These microstructures have a multiplicity of potential applications in the material sciences. Exploratory development is proceeding in application areas such as controlled release for drug delivery, wound repair, and biofouling as well as composites for electronic and magnetic applications, and high power microwave cathodes.

Construction and engineering of large biochemical pathways via DNA assembler

PubMed Central

Shao, Zengyi; Zhao, Huimin

2015-01-01

Summary DNA assembler enables rapid construction and engineering of biochemical pathways in a one-step fashion by exploitation of the in vivo homologous recombination mechanism in Saccharomyces cerevisiae. It has many applications in pathway engineering, metabolic engineering, combinatorial biology, and synthetic biology. Here we use two examples including the zeaxanthin biosynthetic pathway and the aureothin biosynthetic gene cluster to describe the key steps in the construction of pathways containing multiple genes using the DNA assembler approach. Methods for construct design, pathway assembly, pathway confirmation, and functional analysis are shown. The protocol for fine genetic modifications such as site-directed mutagenesis for engineering the aureothin gene cluster is also illustrated. PMID:23996442

Scaffold Free Bio-orthogonal Assembly of 3-Dimensional Cardiac Tissue via Cell Surface Engineering

NASA Astrophysics Data System (ADS)

Rogozhnikov, Dmitry; O'Brien, Paul J.; Elahipanah, Sina; Yousaf, Muhammad N.

2016-12-01

There has been tremendous interest in constructing in vitro cardiac tissue for a range of fundamental studies of cardiac development and disease and as a commercial system to evaluate therapeutic drug discovery prioritization and toxicity. Although there has been progress towards studying 2-dimensional cardiac function in vitro, there remain challenging obstacles to generate rapid and efficient scaffold-free 3-dimensional multiple cell type co-culture cardiac tissue models. Herein, we develop a programmed rapid self-assembly strategy to induce specific and stable cell-cell contacts among multiple cell types found in heart tissue to generate 3D tissues through cell-surface engineering based on liposome delivery and fusion to display bio-orthogonal functional groups from cell membranes. We generate, for the first time, a scaffold free and stable self assembled 3 cell line co-culture 3D cardiac tissue model by assembling cardiomyocytes, endothelial cells and cardiac fibroblast cells via a rapid inter-cell click ligation process. We compare and analyze the function of the 3D cardiac tissue chips with 2D co-culture monolayers by assessing cardiac specific markers, electromechanical cell coupling, beating rates and evaluating drug toxicity.

Distinct self-interaction domains promote Multi Sex Combs accumulation in and formation of the Drosophila histone locus body

PubMed Central

Terzo, Esteban A.; Lyons, Shawn M.; Poulton, John S.; Temple, Brenda R. S.; Marzluff, William F.; Duronio, Robert J.

2015-01-01

Nuclear bodies (NBs) are structures that concentrate proteins, RNAs, and ribonucleoproteins that perform functions essential to gene expression. How NBs assemble is not well understood. We studied the Drosophila histone locus body (HLB), a NB that concentrates factors required for histone mRNA biosynthesis at the replication-dependent histone gene locus. We coupled biochemical analysis with confocal imaging of both fixed and live tissues to demonstrate that the Drosophila Multi Sex Combs (Mxc) protein contains multiple domains necessary for HLB assembly. An important feature of this assembly process is the self-interaction of Mxc via two conserved N-terminal domains: a LisH domain and a novel self-interaction facilitator (SIF) domain immediately downstream of the LisH domain. Molecular modeling suggests that the LisH and SIF domains directly interact, and mutation of either the LisH or the SIF domain severely impairs Mxc function in vivo, resulting in reduced histone mRNA accumulation. A region of Mxc between amino acids 721 and 1481 is also necessary for HLB assembly independent of the LisH and SIF domains. Finally, the C-terminal 195 amino acids of Mxc are required for recruiting FLASH, an essential histone mRNA-processing factor, to the HLB. We conclude that multiple domains of the Mxc protein promote HLB assembly in order to concentrate factors required for histone mRNA biosynthesis. PMID:25694448

Complete Taiwanese Macaque (Macaca cyclopis) Mitochondrial Genome: Reference-Assisted de novo Assembly with Multiple k-mer Strategy.

PubMed

Huang, Yu-Feng; Midha, Mohit; Chen, Tzu-Han; Wang, Yu-Tai; Smith, David Glenn; Pei, Kurtis Jai-Chyi; Chiu, Kuo Ping

2015-01-01

The Taiwanese (Formosan) macaque (Macaca cyclopis) is the only nonhuman primate endemic to Taiwan. This primate species is valuable for evolutionary studies and as subjects in medical research. However, only partial fragments of the mitochondrial genome (mitogenome) of this primate species have been sequenced, not mentioning its nuclear genome. We employed next-generation sequencing to generate 2 x 90 bp paired-end reads, followed by reference-assisted de novo assembly with multiple k-mer strategy to characterize the M. cyclopis mitogenome. We compared the assembled mitogenome with that of other macaque species for phylogenetic analysis. Our results show that, the M. cyclopis mitogenome consists of 16,563 nucleotides encoding for 13 protein-coding genes, 2 ribosomal RNAs and 22 transfer RNAs. Phylogenetic analysis indicates that M. cyclopis is most closely related to M. mulatta lasiota (Chinese rhesus macaque), supporting the notion of Asia-continental origin of M. cyclopis proposed in previous studies based on partial mitochondrial sequences. Our work presents a novel approach for assembling a mitogenome that utilizes the capabilities of de novo genome assembly with assistance of a reference genome. The availability of the complete Taiwanese macaque mitogenome will facilitate the study of primate evolution and the characterization of genetic variations for the potential usage of this species as a non-human primate model for medical research.

Self-assembled nanolaminate coatings (SV)

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

Fan, H.

2012-03-01

Sandia National Laboratories (Sandia) and Lockheed Martin Aeronautics (LM Aero) are collaborating to develop affordable, self-assembled, nanocomposite coatings and associated fabrication processes that will be tailored to Lockheed Martin product requirements. The purpose of this project is to develop a family of self-assembled coatings with properties tailored to specific performance requirements, such as antireflective (AR) optics, using Sandia-developed self-assembled techniques. The project met its objectives by development of a simple and economic self-assembly processes to fabricate multifunctional coatings. Specifically, materials, functionalization methods, and associated coating processes for single layer and multiple layers coatings have been developed to accomplish high reflectivemore » coatings, hydrophobic coatings, and anti-reflective coatings. Associated modeling and simulations have been developed to guide the coating designs for optimum optical performance. The accomplishments result in significant advantages of reduced costs, increased manufacturing freedom/producibility, improved logistics, and the incorporation of new technology solutions not possible with conventional technologies. These self-assembled coatings with tailored properties will significantly address LMC's needs and give LMC a significant competitive lead in new engineered materials. This work complements SNL's LDRD and BES programs aimed at developing multifunctional nanomaterials for microelectronics and optics as well as structure/property investigations of self-assembled nanomaterials. In addition, this project will provide SNL with new opportunities to develop and apply self-assembled nanocomposite optical coatings for use in the wavelength ranges of 3-5 and 8-12 micrometers, ranges of vital importance to military-based sensors and weapons. The SANC technologies will be applied to multiple programs within the LM Company including the F-35, F-22, ADP (Future Strike Bomber, UAV, UCAV, etc.). The SANC technologies will establish LMA and related US manufacturing capability for commercial and military applications therefore reducing reliance on off-shore development and production of related critical technologies. If these technologies are successfully licensed, production of these coatings in manufactory will create significant technical employment opportunities.« less

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy.

PubMed

Loquet, Antoine; Tolchard, James; Berbon, Melanie; Martinez, Denis; Habenstein, Birgit

2017-09-17

Supramolecular protein assemblies play fundamental roles in biological processes ranging from host-pathogen interaction, viral infection to the propagation of neurodegenerative disorders. Such assemblies consist in multiple protein subunits organized in a non-covalent way to form large macromolecular objects that can execute a variety of cellular functions or cause detrimental consequences. Atomic insights into the assembly mechanisms and the functioning of those macromolecular assemblies remain often scarce since their inherent insolubility and non-crystallinity often drastically reduces the quality of the data obtained from most techniques used in structural biology, such as X-ray crystallography and solution Nuclear Magnetic Resonance (NMR). We here present magic-angle spinning solid-state NMR spectroscopy (SSNMR) as a powerful method to investigate structures of macromolecular assemblies at atomic resolution. SSNMR can reveal atomic details on the assembled complex without size and solubility limitations. The protocol presented here describes the essential steps from the production of 13 C/ 15 N isotope-labeled macromolecular protein assemblies to the acquisition of standard SSNMR spectra and their analysis and interpretation. As an example, we show the pipeline of a SSNMR structural analysis of a filamentous protein assembly.

Directed self-assembly of block copolymer films on atomically-thin graphene chemical patterns

DOE PAGES

Chang, Tzu-Hsuan; Xiong, Shisheng; Jacobberger, Robert M.; ...

2016-08-16

Directed self-assembly of block copolymers is a scalable method to fabricate well-ordered patterns over the wafer scale with feature sizes below the resolution of conventional lithography. Typically, lithographically-defined prepatterns with varying chemical contrast are used to rationally guide the assembly of block copolymers. The directed self-assembly to obtain accurate registration and alignment is largely influenced by the assembly kinetics. Furthermore, a considerably broad processing window is favored for industrial manufacturing. Using an atomically-thin layer of graphene on germanium, after two simple processing steps, we create a novel chemical pattern to direct the assembly of polystyreneblock-poly(methyl methacrylate). Faster assembly kinetics aremore » observed on graphene/germanium chemical patterns than on conventional chemical patterns based on polymer mats and brushes. This new chemical pattern allows for assembly on a wide range of guiding periods and along designed 90° bending structures. We also achieve density multiplication by a factor of 10, greatly enhancing the pattern resolution. Lastly, the rapid assembly kinetics, minimal topography, and broad processing window demonstrate the advantages of inorganic chemical patterns composed of hard surfaces.« less

Nondestructive Assay Data Integration with the SKB-50 Assemblies - FY16 Update

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

Tobin, Stephen Joseph; Fugate, Michael Lynn; Trellue, Holly Renee

2016-10-28

A project to research the application of non-destructive assay (NDA) techniques for spent fuel assemblies is underway at the Central Interim Storage Facility for Spent Nuclear Fuel (for which the Swedish acronym is Clab) in Oskarshamn, Sweden. The research goals of this project contain both safeguards and non-safeguards interests. These nondestructive assay (NDA) technologies are designed to strengthen the technical toolkit of safeguard inspectors and others to determine the following technical goals more accurately; Verify initial enrichment, burnup, and cooling time of facility declaration for spent fuel assemblies; Detect replaced or missing pins from a given spent fuel assembly tomore » confirm its integrity; and Estimate plutonium mass and related plutonium and uranium fissile mass parameters in spent fuel assemblies. Estimate heat content, and measure reactivity (multiplication).« less

Flexture plate motion-transfer mechanism, beam-splitter assembly, and interferometer incorporating the same

DOEpatents

Carangelo, R.M.; Dettori, M.D.; Grigely, L.J.; Murray, T.C.; Solomon, P.R.; Dine, C.P. Van; Wright, D.D.

1996-01-23

A multiplicity of one-piece flexure plates are assembled in pairs to provide a support system on which a retroreflector may be mounted for reciprocal motion. Combined with balance bodies, the flexure plates provide a support system having portions that are dynamically and statically balanced with one another, irrespective of orientation, so as to thereby immunize the unit against extraneous forces. The motion transfer assembly is especially adapted for use to support a moving retroreflector in a two-arm interferometer that may further include a beamsplitter assembly constructed from a one-piece, integrally formed body, the body having convergent, optically flat planar surfaces of specular reflectance, and means for adjustably mounting a beamsplitter therein. The spectrometer is of modular construction, and employs an integrated clocking sub-assembly as well as a light-weight voice-coil motor. 15 figs.

Flexture plate motion-transfer mechanism, beam-splitter assembly, and interferometer incorporating the same

DOEpatents

Carangelo, Robert M.; Dettori, Mark D.; Grigely, Lawrence J.; Murray, Terence C.; Solomon, Peter R.; Van Dine, C. Peter; Wright, David D.

1996-01-01

A multiplicity of one-piece flexure plates are assembled in pairs to provide a support system on which a retroreflector may be mounted for reciprocal motion. Combined with balance bodies, the flexure plates provide a support system having portions that are dynamically and statically balanced with one another, irrespective of orientation, so as to thereby immunize the unit against extraneous forces. The motion transfer assembly is especially adapted for use to support a moving retroreflector in a two-arm interferometer that may further include a beamsplitter assembly constructed from a one-piece, integrally formed body, the body having convergent, optically flat planar surfaces of specular reflectance, and means for adjustably mounting a beamsplitter therein. The spectrometer is of modular construction, and employs an integrated clocking sub-assembly as well as a light-weight voice-coil motor.

Multiplexed mRNA Sensing and Combinatorial-Targeted Drug Delivery Using DNA-Gold Nanoparticle Dimers.

PubMed

Kyriazi, Maria-Eleni; Giust, Davide; El-Sagheer, Afaf H; Lackie, Peter M; Muskens, Otto L; Brown, Tom; Kanaras, Antonios G

2018-04-24

The design of nanoparticulate systems which can perform multiple synergistic functions in cells with high specificity and selectivity is of great importance in applications. Here we combine recent advances in DNA-gold nanoparticle self-assembly and sensing to develop gold nanoparticle dimers that are able to perform multiplexed synergistic functions within a cellular environment. These dimers can sense two mRNA targets and simultaneously or independently deliver one or two DNA-intercalating anticancer drugs (doxorubicin and mitoxantrone) in live cells. Our study focuses on the design of sophisticated nanoparticle assemblies with multiple and synergistic functions that have the potential to advance sensing and drug delivery in cells.

Golden Gate Assembly of CRISPR gRNA expression array for simultaneously targeting multiple genes.

PubMed

Vad-Nielsen, Johan; Lin, Lin; Bolund, Lars; Nielsen, Anders Lade; Luo, Yonglun

2016-11-01

The engineered CRISPR/Cas9 technology has developed as the most efficient and broadly used genome editing tool. However, simultaneously targeting multiple genes (or genomic loci) in the same individual cells using CRISPR/Cas9 remain one technical challenge. In this article, we have developed a Golden Gate Assembly method for the generation of CRISPR gRNA expression arrays, thus enabling simultaneous gene targeting. Using this method, the generation of CRISPR gRNA expression array can be accomplished in 2 weeks, and contains up to 30 gRNA expression cassettes. We demonstrated in the study that simultaneously targeting 10 genomic loci or simultaneously inhibition of multiple endogenous genes could be achieved using the multiplexed gRNA expression array vector in human cells. The complete set of plasmids is available through the non-profit plasmid repository Addgene.

Improved block copolymer domain dispersity on chemical patterns via homopolymer-blending and molecular transfer printing

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

Liu, Guoliang; Nealey, Paul F.

Herein we have investigated the domain width distributions of block copolymers and their ternary blends after directed assembly on chemically patterned surfaces with and without density multiplication. On chemical patterns with density multiplication, the width of the interpolated block copolymer domains was bimodal. Once blended with the corresponding homopolymers, the block copolymers exhibited unimodal distributions of domain width due to the redistribution of homopolymers in the block copolymer domains. When the block copolymers were blended with hydroxyl-terminated homopolymers, the homopolymers with functional end-groups healed the chemical patterns and facilitated the formation of nanostructures with further improved domain width distributions. Lastly,more » it is demonstrated that the block copolymers achieved the most improved domain width distributions when directed to assemble without density multiplication on one-to-one chemical patterns generated by molecular transfer printing.« less

Data Visualization for ESM and ELINT: Visualizing 3D and Hyper Dimensional Data

DTIC Science & Technology

2011-06-01

technique to present multiple 2D views was devised by D. Asimov . He assembled multiple two dimensional scatter plot views of the hyper dimensional...Viewing Multidimensional Data”, D. Asimov , DIAM Journal on Scientific and Statistical Computing, vol.61, pp.128-143, 1985. [2] “High-Dimensional

Research on the Improvements of the Assembly Areas, Evacuation Routes, and Shelters against Multiple Disasters

NASA Astrophysics Data System (ADS)

Jin, S.; Lee, Y. M.; Jeong, S. Y.; Hong, S. J.

2016-12-01

The considerable casualties were resulted at the tsunami shelters during the Great East Japan Tsunami on 11 March 2011. The one of the important lessons learned from the Great East Japan Tsunami and the Fukushima NPP accidents provided the nuclear power plant emergency plan should consider the natural disaster. However, most of cases, the nuclear emergency preparedness strategies have not incorporated the natural disaster management plan. In this study, we reviewed the safety of the assembly areas, evacuation routes, and shelters of some nuclear emergency planning zone using the new tsunami hazard mapping results through the characteristic inundation analysis. As the result of this study, the improvements can be achieved by considering both natural and nuclear disaster to set up the assembly areas, evacuation routes, and shelters against the multiple disasters. Also, The most important protective measures can be achieved by integrating and linking the emergency preparedness strategy both natural disasters and nuclear disaster in the future.

DIANA: A multi-phase, multi-component hydrodynamic model for the analysis of severe accidents in heavy water reactors with multiple-tube assemblies

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

Tentner, A.M.

1994-03-01

A detailed hydrodynamic fuel relocation model has been developed for the analysis of severe accidents in Heavy Water Reactors with multiple-tube Assemblies. This model describes the Fuel Disruption and Relocation inside a nuclear fuel assembly and is designated by the acronym DIANA. DIANA solves the transient hydrodynamic equations for all the moving materials in the core and treats all the relevant flow regimes. The numerical solution techniques and some of the physical models included in DIANA have been developed taking advantage of the extensive experience accumulated in the development and validation of the LEVITATE (1) fuel relocation model of SAS4Amore » [2, 3]. The model is designed to handle the fuel and cladding relocation in both voided and partially voided channels. It is able to treat a wide range of thermal/ hydraulic/neutronic conditions and the presence of various flow regimes at different axial locations within the same hydrodynamic channel.« less

Influence of Chloride Ion and Temperature on the Corrosion Behavior of Ni-Fe-Cr Alloy 028

NASA Astrophysics Data System (ADS)

Zhang, L. N.; Dong, J. X.; Szpunar, J. A.; Zhang, M. C.; Basu, R.

Recently, the working condition of tubing systems used in oil and natural gas industries are severer than before with the increasing exploitation of acidic gas fields. The corrosion problems induced from the corrosive environment with chloride ion medium and high temperature have been much more concerned. The presence of chloride ion can accelerate the dissolution of metals. The corrosion performance is also sensitive to the operating temperature. Classic localized corrosions such as the pitting or the crevice type due to environmental temperature and chloride ion.

Feeding behaviour: hydrothermal vent crabs feast on sea 'snow'.

PubMed

Jeng, M-S; Ng, N K; Ng, P K L

2004-12-23

The crab Xenograpsus testudinatus lives at enormously high densities around the sulphur-rich hydrothermal vents found in shallow waters off Taiwan, even though this acidic environment is low in nutrients. Here we show that these crabs swarm out of their crevices at slack water and feed on the vast numbers of zooplankton that are killed by the vents' sulphurous plumes, and that rain down like marine 'snow'. This opportunistic feeding behaviour explains how the crabs are able to survive in the adverse toxic environment of these shallow hydrothermal vents.

Enhancement Of Water-Jet Stripping Of Foam

NASA Technical Reports Server (NTRS)

Cosby, Steven A.; Shockney, Charles H.; Bates, Keith E.; Shalala, John P.; Daniels, Larry S.

1995-01-01

Improved robotic high-pressure-water-jet system strips foam insulation from parts without removing adjacent coating materials like paints, primers, and sealants. Even injects water into crevices and blind holes to clean out foam, without harming adjacent areas. Eliminates both cost of full stripping and recoating and problem of disposing of toxic solutions used in preparation for coating. Developed for postflight refurbishing of aft skirts of booster rockets. System includes six-axis robot provided with special end effector and specially written control software, called Aftfoam. Adaptable to cleaning and stripping in other industrial settings.

Nonequilibrium Self-Assembly of π-Conjugated Oligopeptides in Solution.

PubMed

Li, Bo; Li, Songsong; Zhou, Yuecheng; Ardoña, Herdeline Ann M; Valverde, Lawrence R; Wilson, William L; Tovar, John D; Schroeder, Charles M

2017-02-01

Supramolecular assembly is a powerful method that can be used to generate materials with well-defined structures across multiple length scales. Supramolecular assemblies consisting of biopolymer-synthetic polymer subunits are specifically known to exhibit exceptional structural and functional diversity as well as programmable control of noncovalent interactions through hydrogen bonding in biopolymer subunits. Despite recent progress, there is a need to control and quantitatively understand assembly under nonequilibrium conditions. In this work, we study the nonequilibrium self-assembly of π-conjugated synthetic oligopeptides using a combination of experiments and analytical modeling. By isolating an aqueous peptide solution droplet within an immiscible organic layer, the rate of peptide assembly in the aqueous solution can be controlled by tuning the transport rate of acid that is used to trigger assembly. Using this approach, peptides are guided to assemble under reaction-dominated and diffusion-dominated conditions, with results showing a transition from a diffusion-limited reaction front to spatially homogeneous assembly as the transport rate of acid decreases. Interestingly, our results show that the morphology of self-assembled peptide fibers is controlled by the assembly kinetics such that increasingly homogeneous structures of self-assembled synthetic oligopeptides were generally obtained using slower rates of assembly. We further developed an analytical reaction-diffusion model to describe oligopeptide assembly, and experimental results are compared to the reaction-diffusion model across a range of parameters. Overall, this work highlights the importance of molecular self-assembly under nonequilibrium conditions, specifically showing that oligopeptide assembly is governed by a delicate balance between reaction kinetics and transport processes.

Item Selection for the Development of Parallel Forms from an IRT-Based Seed Test Using a Sampling and Classification Approach

ERIC Educational Resources Information Center

Chen, Pei-Hua; Chang, Hua-Hua; Wu, Haiyan

2012-01-01

Two sampling-and-classification-based procedures were developed for automated test assembly: the Cell Only and the Cell and Cube methods. A simulation study based on a 540-item bank was conducted to compare the performance of the procedures with the performance of a mixed-integer programming (MIP) method for assembling multiple parallel test…

Coverage induced structural transformations of tetracene on Ag(110)

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

Takasugi, Kazushiro; Yokoyama, Takashi, E-mail: tyoko@yokohama-cu.ac.jp

2016-03-14

Self-assembly of tetracene on an anisotropic surface of Ag(110) has been investigated using scanning tunneling microscopy and low-energy electron diffraction. We observe multistage structural transformations of the self-assembled tetracene on Ag(110) as a function of molecular coverages, which are accompanied by the changes in molecular orientations. They are analyzed by a balance between multiple molecule-molecule and anisotropic substrate-molecule interactions.

Color from hierarchy: Diverse optical properties of micron-sized spherical colloidal assemblies.

PubMed

Vogel, Nicolas; Utech, Stefanie; England, Grant T; Shirman, Tanya; Phillips, Katherine R; Koay, Natalie; Burgess, Ian B; Kolle, Mathias; Weitz, David A; Aizenberg, Joanna

2015-09-01

Materials in nature are characterized by structural order over multiple length scales have evolved for maximum performance and multifunctionality, and are often produced by self-assembly processes. A striking example of this design principle is structural coloration, where interference, diffraction, and absorption effects result in vivid colors. Mimicking this emergence of complex effects from simple building blocks is a key challenge for man-made materials. Here, we show that a simple confined self-assembly process leads to a complex hierarchical geometry that displays a variety of optical effects. Colloidal crystallization in an emulsion droplet creates micron-sized superstructures, termed photonic balls. The curvature imposed by the emulsion droplet leads to frustrated crystallization. We observe spherical colloidal crystals with ordered, crystalline layers and a disordered core. This geometry produces multiple optical effects. The ordered layers give rise to structural color from Bragg diffraction with limited angular dependence and unusual transmission due to the curved nature of the individual crystals. The disordered core contributes nonresonant scattering that induces a macroscopically whitish appearance, which we mitigate by incorporating absorbing gold nanoparticles that suppress scattering and macroscopically purify the color. With increasing size of the constituent colloidal particles, grating diffraction effects dominate, which result from order along the crystal's curved surface and induce a vivid polychromatic appearance. The control of multiple optical effects induced by the hierarchical morphology in photonic balls paves the way to use them as building blocks for complex optical assemblies--potentially as more efficient mimics of structural color as it occurs in nature.

Surface mediated assembly of small, metastable gold nanoclusters

NASA Astrophysics Data System (ADS)

Pettibone, John M.; Osborn, William A.; Rykaczewski, Konrad; Talin, A. Alec; Bonevich, John E.; Hudgens, Jeffrey W.; Allendorf, Mark D.

2013-06-01

The unique properties of metallic nanoclusters are attractive for numerous commercial and industrial applications but are generally less stable than nanocrystals. Thus, developing methodologies for stabilizing nanoclusters and retaining their enhanced functionality is of great interest. We report the assembly of PPh3-protected Au9 clusters from a heterogeneous mixture into films consisting of sub 3 nm nanocluster assemblies. The depositing nanoclusters are metastable in solution, but the resulting nanocluster assemblies are stabilized indefinitely in air or fresh solvent. The films exhibit distinct structure from Au nanoparticles observed by X-ray diffraction, and film dissolution data support the preservation of small nanoclusters. UV-Vis spectroscopy, electrospray ionization mass spectrometry, X-ray photoelectron spectroscopy and electron microscopy are used to elucidate information regarding the nanocluster formation and assembly mechanism. Preferential deposition of nanocluster assemblies can be achieved on multiple substrates, including polymer, Cr, Si, SiO2, SiNx, and metal-organic frameworks (MOFs). Unlike other vapor phase coating processes, nanocluster assembly on the MIL-68(In) MOF crystal is capable of preferentially coating the external surface and stabilizing the crystal structure in hydrothermal conditions, which should enhance their storage, separation and delivery capabilities.The unique properties of metallic nanoclusters are attractive for numerous commercial and industrial applications but are generally less stable than nanocrystals. Thus, developing methodologies for stabilizing nanoclusters and retaining their enhanced functionality is of great interest. We report the assembly of PPh3-protected Au9 clusters from a heterogeneous mixture into films consisting of sub 3 nm nanocluster assemblies. The depositing nanoclusters are metastable in solution, but the resulting nanocluster assemblies are stabilized indefinitely in air or fresh solvent. The films exhibit distinct structure from Au nanoparticles observed by X-ray diffraction, and film dissolution data support the preservation of small nanoclusters. UV-Vis spectroscopy, electrospray ionization mass spectrometry, X-ray photoelectron spectroscopy and electron microscopy are used to elucidate information regarding the nanocluster formation and assembly mechanism. Preferential deposition of nanocluster assemblies can be achieved on multiple substrates, including polymer, Cr, Si, SiO2, SiNx, and metal-organic frameworks (MOFs). Unlike other vapor phase coating processes, nanocluster assembly on the MIL-68(In) MOF crystal is capable of preferentially coating the external surface and stabilizing the crystal structure in hydrothermal conditions, which should enhance their storage, separation and delivery capabilities. Electronic supplementary information (ESI) available: Further details on stored plating solution preparation, film characterization, solution processing, MOF crystal FIB reconstruction and stability are available. See DOI: 10.1039/c3nr01708g

One-pot DNA construction for synthetic biology: the Modular Overlap-Directed Assembly with Linkers (MODAL) strategy

PubMed Central

Casini, Arturo; MacDonald, James T.; Jonghe, Joachim De; Christodoulou, Georgia; Freemont, Paul S.; Baldwin, Geoff S.; Ellis, Tom

2014-01-01

Overlap-directed DNA assembly methods allow multiple DNA parts to be assembled together in one reaction. These methods, which rely on sequence homology between the ends of DNA parts, have become widely adopted in synthetic biology, despite being incompatible with a key principle of engineering: modularity. To answer this, we present MODAL: a Modular Overlap-Directed Assembly with Linkers strategy that brings modularity to overlap-directed methods, allowing assembly of an initial set of DNA parts into a variety of arrangements in one-pot reactions. MODAL is accompanied by a custom software tool that designs overlap linkers to guide assembly, allowing parts to be assembled in any specified order and orientation. The in silico design of synthetic orthogonal overlapping junctions allows for much greater efficiency in DNA assembly for a variety of different methods compared with using non-designed sequence. In tests with three different assembly technologies, the MODAL strategy gives assembly of both yeast and bacterial plasmids, composed of up to five DNA parts in the kilobase range with efficiencies of between 75 and 100%. It also seamlessly allows mutagenesis to be performed on any specified DNA parts during the process, allowing the one-step creation of construct libraries valuable for synthetic biology applications. PMID:24153110

Assembling the Streptococcus thermophilus clustered regularly interspaced short palindromic repeats (CRISPR) array for multiplex DNA targeting.

PubMed

Guo, Lijun; Xu, Kun; Liu, Zhiyuan; Zhang, Cunfang; Xin, Ying; Zhang, Zhiying

2015-06-01

In addition to the advantages of scalable, affordable, and easy to engineer, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) technology is superior for multiplex targeting, which is laborious and inconvenient when achieved by cloning multiple gRNA expressing cassettes. Here, we report a simple CRISPR array assembling method which will facilitate multiplex targeting usage. First, the Streptococcus thermophilus CRISPR3/Cas locus was cloned. Second, different CRISPR arrays were assembled with different crRNA spacers. Transformation assays using different Escherichia coli strains demonstrated efficient plasmid DNA targeting, and we achieved targeting efficiency up to 95% with an assembled CRISPR array with three crRNA spacers. Copyright © 2015 Elsevier Inc. All rights reserved.

Outpost Assembly Using the ATHLETE Mobility System

NASA Technical Reports Server (NTRS)

Howe, A. Scott; Wilcox, Brian

2016-01-01

A planetary surface outpost will likely consist of elements delivered on multiple manifests, that will need to be assembled from a scattering of landings. Using the All-Terrain Hex-Limbed Extra-Terrestrial Explorer (ATHLETE) limbed robotic mobility system, the outpost site can be prepared in advance through leveling, paving, and in-situ structures. ATHLETE will be able to carry pressurized and non-pressurized payloads overland from the lander descent stage to the outpost location, and perform precision docking and assembly of components. In addition, spent descent stages can be carried to assembly locations to form elevated decks for external work platforms above the planet surface. This paper discusses several concepts that have been studied for possible inclusion in the NASA Evolvable Mars Campaign human exploration mission scenarios.

Functional connectivity of task context representations in prefrontal nodes of the multiple demand network.

PubMed

Stiers, Peter; Goulas, Alexandros

2018-06-01

A subset of regions in the lateral and medial prefrontal cortex and the anterior insula increase their activity level whenever a cognitive task becomes more demanding, regardless of the specific nature of this demand. During execution of a task, these areas and the surrounding cortex temporally encode aspects of the task context in spatially distributed patterns of activity. It is not clear whether these patterns reflect underlying anatomical subnetworks that still exist when task execution has finished. We use fMRI in 12 participants performing alternating blocks of three cognitive tasks to address this question. A first data set is used to define multiple demand regions in each participant. A second dataset from the same participants is used to determine multiple demand voxel assemblies with a preference for one task over the others. We then show that these voxels remain functionally coupled during execution of non-preferred tasks and that they exhibit stronger functional connectivity during rest. This indicates that the assemblies of task preference sharing voxels reflect patterns of underlying anatomical connections. Moreover, we show that voxels preferring the same task have more similar whole brain functional connectivity profiles that are consistent across participants. This suggests that voxel assemblies differ in patterns of input-output connections, most likely reflecting task demand-specific information exchange.

Efficient generation of complete sequences of MDR-encoding plasmids by rapid assembly of MinION barcoding sequencing data.

PubMed

Li, Ruichao; Xie, Miaomiao; Dong, Ning; Lin, Dachuan; Yang, Xuemei; Wong, Marcus Ho Yin; Chan, Edward Wai-Chi; Chen, Sheng

2018-03-01

Multidrug resistance (MDR)-encoding plasmids are considered major molecular vehicles responsible for transmission of antibiotic resistance genes among bacteria of the same or different species. Delineating the complete sequences of such plasmids could provide valuable insight into the evolution and transmission mechanisms underlying bacterial antibiotic resistance development. However, due to the presence of multiple repeats of mobile elements, complete sequencing of MDR plasmids remains technically complicated, expensive, and time-consuming. Here, we demonstrate a rapid and efficient approach to obtaining multiple MDR plasmid sequences through the use of the MinION nanopore sequencing platform, which is incorporated in a portable device. By assembling the long sequencing reads generated by a single MinION run according to a rapid barcoding sequencing protocol, we obtained the complete sequences of 20 plasmids harbored by multiple bacterial strains. Importantly, single long reads covering a plasmid end-to-end were recorded, indicating that de novo assembly may be unnecessary if the single reads exhibit high accuracy. This workflow represents a convenient and cost-effective approach for systematic assessment of MDR plasmids responsible for treatment failure of bacterial infections, offering the opportunity to perform detailed molecular epidemiological studies to probe the evolutionary and transmission mechanisms of MDR-encoding elements.

CASMO5/TSUNAMI-3D spent nuclear fuel reactivity uncertainty analysis

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

Ferrer, R.; Rhodes, J.; Smith, K.

2012-07-01

The CASMO5 lattice physics code is used in conjunction with the TSUNAMI-3D sequence in ORNL's SCALE 6 code system to estimate the uncertainties in hot-to-cold reactivity changes due to cross-section uncertainty for PWR assemblies at various burnup points. The goal of the analysis is to establish the multiplication factor uncertainty similarity between various fuel assemblies at different conditions in a quantifiable manner and to obtain a bound on the hot-to-cold reactivity uncertainty over the various assembly types and burnup attributed to fundamental cross-section data uncertainty. (authors)

Comparing highly ordered monolayers of nanoparticles fabricated using electrophoretic deposition: Cobalt ferrite nanoparticles versus iron oxide nanoparticles

DOE PAGES

Dickerson, James H.; Krejci, Alex J.; Garcia, Adriana -Mendoza; ...

2015-08-01

Ordered assemblies of nanoparticles remain challenging to fabricate, yet could open the door to many potential applications of nanomaterials. Here, we demonstrate that locally ordered arrays of nanoparticles, using electrophoretic deposition, can be extended to produce long-range order among the constituents. Voronoi tessellations along with multiple statistical analyses show dramatic increases in order compared with previously reported assemblies formed through electric field-assisted assembly. As a result, based on subsequent physical measurements of the nanoparticles and the deposition system, the underlying mechanisms that generate increased order are inferred.

Method of producing silicon. [gas phase reactor multiple injector liquid feed system

NASA Technical Reports Server (NTRS)

Wolf, C. B.; Meyer, T. N. (Inventor)

1980-01-01

A liquid reactant injector assembly suited for the injection of liquid reactant into a high temperature metal reductant vapor and carrier gas stream for the production of metal is presented. The assembly is especially adapted for the continuous production of high purity silicon by the reduction of SiCl4 with sodium. The assembly includes a refractory-lined, hollow metal shell having ten equally-spaced, concentric, radially directed ports provided in the shell and wall. A hydraulic, atomizing type spray nozzle is mounted in each of the ports recessed from the inner wall surface.

Multicomponent self-assembly as a tool to harness new properties from peptides and proteins in material design.

PubMed

Okesola, Babatunde O; Mata, Alvaro

2018-05-21

Nature is enriched with a wide variety of complex, synergistic, and highly functional protein-based multicomponent assemblies. As such, nature has served as a source of inspiration for using multicomponent self-assembly as a platform to create highly ordered, complex, and dynamic protein and peptide-based nanostructures. Such an assembly system relies on the initial interaction of distinct individual building blocks leading to the formation of a complex that subsequently assembles into supramolecular architectures. This approach not only serves as a powerful platform for gaining insight into how proteins co-assemble in nature but also offers huge opportunities to harness new properties not inherent in the individual building blocks. In the past decades, various multicomponent self-assembly strategies have been used to extract synergistic properties from proteins and peptides. This review highlights the updates in the field of multicomponent self-assembly of proteins and peptides and summarizes various strategies, including covalent conjugation, ligand-receptor interactions, templated/directed assembly and non-specific co-assembly, for driving the self-assembly of multiple proteins and peptide-based building blocks into functional materials. In particular, we focus on peptide- or protein-containing multicomponent systems that, upon self-assembly, enable the emergence of new properties or phenomena. The ultimate goal of this review is to highlight the importance of multicomponent self-assembly in protein and peptide engineering, and to advocate its growth in the fields of materials science and nanotechnology.

Protein cage assembly across multiple length scales.

PubMed

Aumiller, William M; Uchida, Masaki; Douglas, Trevor

2018-05-21

Within the materials science community, proteins with cage-like architectures are being developed as versatile nanoscale platforms for use in protein nanotechnology. Much effort has been focused on the functionalization of protein cages with biological and non-biological moieties to bring about new properties of not only individual protein cages, but collective bulk-scale assemblies of protein cages. In this review, we report on the current understanding of protein cage assembly, both of the cages themselves from individual subunits, and the assembly of the individual protein cages into higher order structures. We start by discussing the key properties of natural protein cages (for example: size, shape and structure) followed by a review of some of the mechanisms of protein cage assembly and the factors that influence it. We then explore the current approaches for functionalizing protein cages, on the interior or exterior surfaces of the capsids. Lastly, we explore the emerging area of higher order assemblies created from individual protein cages and their potential for new and exciting collective properties.

De novo Assembly of the Burying Beetle Nicrophorus orbicollis (Coleoptera: Silphidae) Transcriptome Across Developmental Stages with Identification of Key Immune Transcripts

PubMed Central

Won, Harim I.; Schulze, Thomas T.; Clement, Emalie J.; Watson, Gabrielle F.; Watson, Sean M.; Warner, Rosalie C.; Ramler, Elizabeth A. M.; Witte, Elias J.; Schoenbeck, Mark A.; Rauter, Claudia M.; Davis, Paul H.

2018-01-01

Burying beetles (Nicrophorus spp.) are among the relatively few insects that provide parental care while not belonging to the eusocial insects such as ants or bees. This behavior incurs energy costs as evidenced by immune deficits and shorter life-spans in reproducing beetles. In the absence of an assembled transcriptome, relatively little is known concerning the molecular biology of these beetles. This work details the assembly and analysis of the Nicrophorus orbicollis transcriptome at multiple developmental stages. RNA-Seq reads were obtained by next-generation sequencing and the transcriptome was assembled using the Trinity assembler. Validation of the assembly was performed by functional characterization using Gene Ontology (GO), Eukaryotic Orthologous Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Differential expression analysis highlights developmental stage-specific expression patterns, and immunity-related transcripts are discussed. The data presented provides a valuable molecular resource to aid further investigation into immunocompetence throughout this organism's sexual development. PMID:29707046

Subtle balance of tropoelastin molecular shape and flexibility regulates dynamics and hierarchical assembly.

PubMed

Yeo, Giselle C; Tarakanova, Anna; Baldock, Clair; Wise, Steven G; Buehler, Markus J; Weiss, Anthony S

2016-02-01

The assembly of the tropoelastin monomer into elastin is vital for conferring elasticity on blood vessels, skin, and lungs. Tropoelastin has dual needs for flexibility and structure in self-assembly. We explore the structure-dynamics-function interplay, consider the duality of molecular order and disorder, and identify equally significant functional contributions by local and global structures. To study these organizational stratifications, we perturb a key hinge region by expressing an exon that is universally spliced out in human tropoelastins. We find a herniated nanostructure with a displaced C terminus and explain by molecular modeling that flexible helices are replaced with substantial β sheets. We see atypical higher-order cross-linking and inefficient assembly into discontinuous, thick elastic fibers. We explain this dysfunction by correlating local and global structural effects with changes in the molecule's assembly dynamics. This work has general implications for our understanding of elastomeric proteins, which balance disordered regions with defined structural modules at multiple scales for functional assembly.

Nuclear reactor power for a space-based radar. SP-100 project

NASA Technical Reports Server (NTRS)

Bloomfield, Harvey; Heller, Jack; Jaffe, Leonard; Beatty, Richard; Bhandari, Pradeep; Chow, Edwin; Deininger, William; Ewell, Richard; Fujita, Toshio; Grossman, Merlin

1986-01-01

A space-based radar mission and spacecraft, using a 300 kWe nuclear reactor power system, has been examined, with emphasis on aspects affecting the power system. The radar antenna is a horizontal planar array, 32 X 64 m. The orbit is at 61 deg, 1088 km. The mass of the antenna with support structure is 42,000 kg; of the nuclear reactor power system, 8,300 kg; of the whole spacecraft about 51,000 kg, necessitating multiple launches and orbital assembly. The assembly orbit is at 57 deg, 400 km, high enough to provide the orbital lifetime needed for orbital assembly. The selected scenario uses six Shuttle launches to bring the spacecraft and a Centaur G upper-stage vehicle to assembly orbit. After assembly, the Centaur places the spacecraft in operational orbit, where it is deployed on radio command, the power system started, and the spacecraft becomes operational. Electric propulsion is an alternative and allows deployment in assembly orbit, but introduces a question of nuclear safety.

Perispeckles are major assembly sites for the exon junction core complex

PubMed Central

Daguenet, Elisabeth; Baguet, Aurélie; Degot, Sébastien; Schmidt, Ute; Alpy, Fabien; Wendling, Corinne; Spiegelhalter, Coralie; Kessler, Pascal; Rio, Marie-Christine; Le Hir, Hervé; Bertrand, Edouard; Tomasetto, Catherine

2012-01-01

The exon junction complex (EJC) is loaded onto mRNAs as a consequence of splicing and regulates multiple posttranscriptional events. MLN51, Magoh, Y14, and eIF4A3 form a highly stable EJC core, but where this tetrameric complex is assembled in the cell remains unclear. Here we show that EJC factors are enriched in domains that we term perispeckles and are visible as doughnuts around nuclear speckles. Fluorescence resonance energy transfer analyses and EJC assembly mutants show that perispeckles do not store free subunits, but instead are enriched for assembled cores. At the ultrastructural level, perispeckles are distinct from interchromatin granule clusters that may function as storage sites for splicing factors and intermingle with perichromatin fibrils, where nascent RNAs and active RNA Pol II are present. These results support a model in which perispeckles are major assembly sites for the tetrameric EJC core. This subnuclear territory thus represents an intermediate region important for mRNA maturation, between transcription sites and splicing factor reservoirs and assembly sites. PMID:22419818

Cloning Should Be Simple: Escherichia coli DH5α-Mediated Assembly of Multiple DNA Fragments with Short End Homologies

PubMed Central

Richardson, Ruth E.; Suzuki, Yo

2015-01-01

Numerous DNA assembly technologies exist for generating plasmids for biological studies. Many procedures require complex in vitro or in vivo assembly reactions followed by plasmid propagation in recombination-impaired Escherichia coli strains such as DH5α, which are optimal for stable amplification of the DNA materials. Here we show that despite its utility as a cloning strain, DH5α retains sufficient recombinase activity to assemble up to six double-stranded DNA fragments ranging in size from 150 bp to at least 7 kb into plasmids in vivo. This process also requires surprisingly small amounts of DNA, potentially obviating the need for upstream assembly processes associated with most common applications of DNA assembly. We demonstrate the application of this process in cloning of various DNA fragments including synthetic genes, preparation of knockout constructs, and incorporation of guide RNA sequences in constructs for clustered regularly interspaced short palindromic repeats (CRISPR) genome editing. This consolidated process for assembly and amplification in a widely available strain of E. coli may enable productivity gain across disciplines involving recombinant DNA work. PMID:26348330

Understanding the complex needs of automotive training at final assembly lines.

PubMed

Hermawati, Setia; Lawson, Glyn; D'Cruz, Mirabelle; Arlt, Frank; Apold, Judith; Andersson, Lina; Lövgren, Maria Gink; Malmsköld, Lennart

2015-01-01

Automobile final assembly operators must be highly skilled to succeed in a low automation environment where multiple variants must be assembled in quick succession. This paper presents formal user studies conducted at OPEL and VOLVO Group to identify assembly training needs and a subset of requirements; and to explore potential features of a hypothetical game-based virtual training system. Stakeholder analysis, timeline analysis, link analysis, Hierarchical Task Analysis and thematic content analysis were used to analyse the results of interviews with various stakeholders (17 and 28 participants at OPEL and VOLVO, respectively). The results show that there is a strong case for the implementation of virtual training for assembly tasks. However, it was also revealed that stakeholders would prefer to use a virtual training to complement, rather than replace, training on pre-series vehicles. Copyright © 2014 Elsevier Ltd and The Ergonomics Society. All rights reserved.

Grinding assembly, grinding apparatus, weld joint defect repair system, and methods

DOEpatents

Larsen, Eric D.; Watkins, Arthur D.; Bitsoi, Rodney J.; Pace, David P.

2005-09-27

A grinding assembly for grinding a weld joint of a workpiece includes a grinder apparatus, a grinder apparatus includes a grinding wheel configured to grind the weld joint, a member configured to receive the grinding wheel, the member being configured to be removably attached to the grinder apparatus, and a sensor assembly configured to detect a contact between the grinding wheel and the workpiece. The grinding assembly also includes a processing circuitry in communication with the grinder apparatus and configured to control operations of the grinder apparatus, the processing circuitry configured to receive weld defect information of the weld joint from an inspection assembly to create a contour grinding profile to grind the weld joint in a predetermined shape based on the received weld defect information, and a manipulator having an end configured to carry the grinder apparatus, the manipulator further configured to operate in multiple dimensions.

MetaQUAST: evaluation of metagenome assemblies.

PubMed

Mikheenko, Alla; Saveliev, Vladislav; Gurevich, Alexey

2016-04-01

During the past years we have witnessed the rapid development of new metagenome assembly methods. Although there are many benchmark utilities designed for single-genome assemblies, there is no well-recognized evaluation and comparison tool for metagenomic-specific analogues. In this article, we present MetaQUAST, a modification of QUAST, the state-of-the-art tool for genome assembly evaluation based on alignment of contigs to a reference. MetaQUAST addresses such metagenome datasets features as (i) unknown species content by detecting and downloading reference sequences, (ii) huge diversity by giving comprehensive reports for multiple genomes and (iii) presence of highly relative species by detecting chimeric contigs. We demonstrate MetaQUAST performance by comparing several leading assemblers on one simulated and two real datasets. http://bioinf.spbau.ru/metaquast aleksey.gurevich@spbu.ru Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Natural supramolecular building blocks: from virus coat proteins to viral nanoparticles.

PubMed

Liu, Zhi; Qiao, Jing; Niu, Zhongwei; Wang, Qian

2012-09-21

Viruses belong to a fascinating class of natural supramolecular structures, composed of multiple copies of coat proteins (CPs) that assemble into different shapes with a variety of sizes from tens to hundreds of nanometres. Because of their advantages including simple/economic production, well-defined structural features, unique shapes and sizes, genetic programmability and robust chemistries, recently viruses and virus-like nanoparticles (VLPs) have been used widely in biomedical applications and materials synthesis. In this critical review, we highlight recent advances in the use of virus coat proteins (VCPs) and viral nanoparticles (VNPs) as building blocks in self-assembly studies and materials development. We first discuss the self-assembly of VCPs into VLPs, which can efficiently incorporate a variety of different materials as cores inside the viral protein shells. Then, the self-assembly of VNPs at surfaces or interfaces is summarized. Finally, we discuss the co-assembly of VNPs with different functional materials (178 references).

Genetically encoded photochemical covalent crosslinking within the Hcp-1 self-assembling bacterial secretion machinery.

PubMed

Antonczak, Alicja K; Milholland, Kedric; Tippmann, Eric M

2018-05-01

The target protein, Hcp1, was first described as part of the bacterial Type VI secretion system from Pseudomonas aeruginosa. The protein first self-assembles into a hexamer and then the hexamers further stack into a nanotubular structure. Hcp1 monomers were targeted for mutagenesis with two widely used photoactivatable amino acids: para-benzoyl phenylalanine or para-azidophenylalanine. The ability of these amino acids to form covalent adducts within the Hcp1 self-assembled system was investigated. Multiple residues, putatively of equal distance between the monomer-monomer interface were targeted. The efficiency of each amino acid to covalently link self-assembled hexamers was determined. The results demonstrate the choice and role of genetically encoded tools applied to complicated biological processes such as self-assembly and also suggested some structural dynamics of the Hcp-1 protein not obvious from crystallographic structures.

Self-assembling choline mimicks with enhanced binding affinities to C-LytA protein

PubMed Central

Shi, Yang; Zhou, Hao; Zhang, Xiaoli; Wang, Jingyu; Long, Jiafu; Yang, Zhimou; Ding, Dan

2014-01-01

Streptococcus pneumoniae (pneumococcus) causes multiple illnesses in humans. Exploration of effective inhibitors with multivalent attachment sites for choline-binding modules is of great importance to reduce the pneumococcal virulence. In this work, we successfully developed two self-assembling choline mimicks, Ada-GFFYKKK' and Nap-GFFYKKK', which have the abilities to self-assemble into nanoparticles and nanofibers, respectively, yielding multivalent architectures. Additionally, the best characterized choline-binding module, C-terminal moiety of the pneumococcal cell-wall amidase LytA (C-LytA) was also produced with high purity. The self-assembling Ada-GFFYKKK' and Nap-GFFYKKK' show strong interactions with C-LytA, which possess much higher association constant values to the choline-binding modules as compared to the individual peptide Fmoc-K'. This study thus provides a self-assembly approach to yield inhibitors that are very promising for reducing the pneumococcal virulence. PMID:25315737

Optical assembly of microsnap-fits fabricated by two-photon polymerization

NASA Astrophysics Data System (ADS)

Köhler, Jannis; Kutlu, Yunus; Zyla, Gordon; Ksouri, Sarah I.; Esen, Cemal; Gurevich, Evgeny L.; Ostendorf, Andreas

2017-10-01

To respond to current demands of nano- and microtechnologies, e.g., miniaturization and integration, different bottom-up strategies have been developed. These strategies are based on picking, placing, and assembly of multiple components to produce microsystems with desired features. This paper covers the fabrication of arbitrary-shaped microcomponents by two-photon polymerization and the trapping, moving, and aligning of these structures by the use of a holographic optical tweezer. The main focus is on the assembly technique based on a cantilever microsnap-fit. More precisely, mechanical properties are characterized by optical forces and a suitable geometry of the snap-fit is designed. As a result of these investigations, a fast and simple assembly technique is developed. Furthermore, disassembly is provided by an optimized design. These findings suggest that the microsnap-fit is suitable for the assembly of miniaturized systems and could broaden the application opportunities of bottom-up strategies.

Evaluation and validation of de novo and hybrid assembly techniques to derive high quality genome sequences

DOE PAGES

Utturkar, Sagar M.; Klingeman, Dawn Marie; Land, Miriam L.; ...

2014-06-14

Our motivation with this work was to assess the potential of different types of sequence data combined with de novo and hybrid assembly approaches to improve existing draft genome sequences. Our results show Illumina, 454 and PacBio sequencing technologies were used to generate de novo and hybrid genome assemblies for four different bacteria, which were assessed for quality using summary statistics (e.g. number of contigs, N50) and in silico evaluation tools. Differences in predictions of multiple copies of rDNA operons for each respective bacterium were evaluated by PCR and Sanger sequencing, and then the validated results were applied as anmore » additional criterion to rank assemblies. In general, assemblies using longer PacBio reads were better able to resolve repetitive regions. In this study, the combination of Illumina and PacBio sequence data assembled through the ALLPATHS-LG algorithm gave the best summary statistics and most accurate rDNA operon number predictions. This study will aid others looking to improve existing draft genome assemblies. As to availability and implementation–all assembly tools except CLC Genomics Workbench are freely available under GNU General Public License.« less

Flow-oriented dynamic assembly algorithm in TCP over OBS networks

NASA Astrophysics Data System (ADS)

Peng, Shuping; Li, Zhengbin; He, Yongqi; Xu, Anshi

2008-11-01

OBS is envisioned as a promising infrastructure for the next generation optical network, and TCP is likely to be the dominant transport protocol in the next generation network. Therefore, it is necessary to evaluate the performance of TCP over OBS networks. The assembly at the ingress edge nodes will impact the network performance. There have been several Fixed Assembly Period (FAP) algorithms proposed. However, the assembly period in FAP is fixed, and it can not be adjusted according to the network condition. Moreover, in FAP, the packets from different TCP sources are assembled into one burst. In that case, if such a burst is dropped, the TCP windows of the corresponding sources will shrink and the throughput will be reduced. In this paper, we introduced a flow-oriented Dynamic Assembly Period (DAP) algorithm for TCP over OBS networks. Through comparing the previous and current burst lengths, DAP can track the variation of TCP window, and update the assembly period dynamically for the next assembly. The performance of DAP is evaluated over a single TCP connection and multiple connections, respectively. The simulation results show that DAP performs better than FAP at almost the whole range of burst dropping probability.

Multiplication and Presence of Shielding Material from Time-Correlated Pulse-Height Measurements of Subcritical Plutonium Assemblies

DOE PAGES

Monterial, Mateusz; Marleau, Peter; Paff, Marc; ...

2017-01-20

Here, we present the results from the first measurements of the Time-Correlated Pulse-Height (TCPH) distributions from 4.5 kg sphere of α-phase weapons-grade plutonium metal in five configurations: bare, reflected by 1.27 cm and 2.54 cm of tungsten, and 2.54 cm and 7.62 cm of polyethylene. A new method for characterizing source multiplication and shielding configuration is also demonstrated. The method relies on solving for the underlying fission chain timing distribution that drives the spreading of the measured TCPH distribution. We found that a gamma distribution fits the fission chain timing distribution well and that the fit parameters correlate with bothmore » multiplication (rate parameter) and shielding material types (shape parameter). The source-to-detector distance was another free parameter that we were able to optimize, and proved to be the most well constrained parameter. MCNPX-PoliMi simulations were used to complement the measurements and help illustrate trends in these parameters and their relation to multiplication and the amount and type of material coupled to the subcritical assembly.« less

Multiplication and Presence of Shielding Material from Time-Correlated Pulse-Height Measurements of Subcritical Plutonium Assemblies

NASA Astrophysics Data System (ADS)

Monterial, Mateusz; Marleau, Peter; Paff, Marc; Clarke, Shaun; Pozzi, Sara

2017-04-01

We present the results from the first measurements of the Time-Correlated Pulse-Height (TCPH) distributions from 4.5 kg sphere of α-phase weapons-grade plutonium metal in five configurations: bare, reflected by 1.27 cm and 2.54 cm of tungsten, and 2.54 cm and 7.62 cm of polyethylene. A new method for characterizing source multiplication and shielding configuration is also demonstrated. The method relies on solving for the underlying fission chain timing distribution that drives the spreading of the measured TCPH distribution. We found that a gamma distribution fits the fission chain timing distribution well and that the fit parameters correlate with both multiplication (rate parameter) and shielding material types (shape parameter). The source-to-detector distance was another free parameter that we were able to optimize, and proved to be the most well constrained parameter. MCNPX-PoliMi simulations were used to complement the measurements and help illustrate trends in these parameters and their relation to multiplication and the amount and type of material coupled to the subcritical assembly.

Constructing Cost-Effective Crystal Structures with Table Tennis Balls and Tape That Allows Students to Assemble and Model Multiple Unit Cells

ERIC Educational Resources Information Center

Elsworth, Catherine; Li, Barbara T. Y.; Ten, Abilio

2017-01-01

In this letter we present an innovative and cost-effective method of constructing crystal structures using Dual Lock fastening adhesive tape with table tennis (ping pong) balls. The use of these fasteners allows the balls to be easily assembled into layers to model various crystal structures and unit cells and then completely disassembled again.…

Effect of mixed alloy combinations on fretting corrosion performance of spinal screw and rod implants.

PubMed

Mali, Sachin A; Singh, Vaneet; Gilbert, Jeremy L

2017-07-01

Spinal implants are made from a variety of materials to meet the unique mechanical demands of each application. However, the medical device community has raised concern about mixing dissimilar metals in an implant because of fear of inducing corrosion. There is a lack of systematic studies on the effects of mixing metals on performance of spinal implants, especially in fretting corrosion conditions. Hence, the goal was to determine whether mixing stainless steel (SS316L), titanium alloy (Ti6Al4V) and cobalt chromium (CoCrMo) alloy components in a spinal implant leads to any increased risk of corrosion degradation. Spinal constructs consisting of single assembly screw-connector-rod components were tested using a novel short-term cyclic fretting corrosion test method. A total of 17 alloy component combinations (comprised of SS316L, Ti6Al4V-anodized and CoCrMo alloy for rod, screws and connectors) were tested under three anatomic orientations. Spinal constructs having all SS316L were most susceptible to fretting-initiated crevice corrosion attack and showed higher average fretting currents (∼25 - 30 µA), whereas constructs containing all Ti6Al4V components were less susceptible to fretting corrosion with average fretting currents in the range of 1 - 6 µA. Mixed groups showed evidence of fretting corrosion but they were not as severe as all SS316L group. SEM results showed evidence of severe corrosion attack in constructs having SS316L components. There also did not appear to be any galvanic effects of combining alloys together. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 105B: 1169-1177, 2017. © 2016 Wiley Periodicals, Inc.

A Modular Plasmid Assembly Kit for Multigene Expression, Gene Silencing and Silencing Rescue in Plants

PubMed Central

Binder, Andreas; Lambert, Jayne; Morbitzer, Robert; Popp, Claudia; Ott, Thomas; Lahaye, Thomas; Parniske, Martin

2014-01-01

The Golden Gate (GG) modular assembly approach offers a standardized, inexpensive and reliable way to ligate multiple DNA fragments in a pre-defined order in a single-tube reaction. We developed a GG based toolkit for the flexible construction of binary plasmids for transgene expression in plants. Starting from a common set of modules, such as promoters, protein tags and transcribed regions of interest, synthetic genes are assembled, which can be further combined to multigene constructs. As an example, we created T-DNA constructs encoding multiple fluorescent proteins targeted to distinct cellular compartments (nucleus, cytosol, plastids) and demonstrated simultaneous expression of all genes in Nicotiana benthamiana, Lotus japonicus and Arabidopsis thaliana. We assembled an RNA interference (RNAi) module for the construction of intron-spliced hairpin RNA constructs and demonstrated silencing of GFP in N. benthamiana. By combination of the silencing construct together with a codon adapted rescue construct into one vector, our system facilitates genetic complementation and thus confirmation of the causative gene responsible for a given RNAi phenotype. As proof of principle, we silenced a destabilized GFP gene (dGFP) and restored GFP fluorescence by expression of a recoded version of dGFP, which was not targeted by the silencing construct. PMID:24551083

Design of Revolute Joints for In-Mold Assembly Using Insert Molding.

PubMed

Ananthanarayanan, Arvind; Ehrlich, Leicester; Desai, Jaydev P; Gupta, Satyandra K

2011-12-01

Creating highly articulated miniature structures requires assembling a large number of small parts. This is a very challenging task and increases cost of mechanical assemblies. Insert molding presents the possibility of creating a highly articulated structure in a single molding step. This can be accomplished by placing multiple metallic bearings in the mold and injecting plastic on top of them. In theory, this idea can generate a multi degree of freedom structures in just one processing step without requiring any post molding assembly operations. However, the polymer material has a tendency to shrink on top of the metal bearings and hence jam the joints. Hence, until now insert molding has not been used to create articulated structures. This paper presents a theoretical model for estimating the extent of joint jamming that occurs due to the shrinkage of the polymer on top of the metal bearings. The level of joint jamming is seen as the effective torque needed to overcome the friction in the revolute joints formed by insert molding. We then use this model to select the optimum design parameters which can be used to fabricate functional, highly articulating assemblies while meeting manufacturing constraints. Our analysis shows that the strength of weld-lines formed during the in-mold assembly process play a significant role in determining the minimum joint dimensions necessary for fabricating functional revolute joints. We have used the models and methods described in this paper to successfully fabricate the structure for a minimally invasive medical robot prototype with potential applications in neurosurgery. To the best of our knowledge, this is the first demonstration of building an articulated structure with multiple degrees of freedom using insert molding.

ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species.

PubMed

Zeng, Victor; Extavour, Cassandra G

2012-01-01

The increased throughput and decreased cost of next-generation sequencing (NGS) have shifted the bottleneck genomic research from sequencing to annotation, analysis and accessibility. This is particularly challenging for research communities working on organisms that lack the basic infrastructure of a sequenced genome, or an efficient way to utilize whatever sequence data may be available. Here we present a new database, the Assembled Searchable Giant Arthropod Read Database (ASGARD). This database is a repository and search engine for transcriptomic data from arthropods that are of high interest to multiple research communities but currently lack sequenced genomes. We demonstrate the functionality and utility of ASGARD using de novo assembled transcriptomes from the milkweed bug Oncopeltus fasciatus, the cricket Gryllus bimaculatus and the amphipod crustacean Parhyale hawaiensis. We have annotated these transcriptomes to assign putative orthology, coding region determination, protein domain identification and Gene Ontology (GO) term annotation to all possible assembly products. ASGARD allows users to search all assemblies by orthology annotation, GO term annotation or Basic Local Alignment Search Tool. User-friendly features of ASGARD include search term auto-completion suggestions based on database content, the ability to download assembly product sequences in FASTA format, direct links to NCBI data for predicted orthologs and graphical representation of the location of protein domains and matches to similar sequences from the NCBI non-redundant database. ASGARD will be a useful repository for transcriptome data from future NGS studies on these and other emerging model arthropods, regardless of sequencing platform, assembly or annotation status. This database thus provides easy, one-stop access to multi-species annotated transcriptome information. We anticipate that this database will be useful for members of multiple research communities, including developmental biology, physiology, evolutionary biology, ecology, comparative genomics and phylogenomics. Database URL: asgard.rc.fas.harvard.edu.

Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set.

PubMed

Damas, Joana; O'Connor, Rebecca; Farré, Marta; Lenis, Vasileios Panagiotis E; Martell, Henry J; Mandawala, Anjali; Fowler, Katie; Joseph, Sunitha; Swain, Martin T; Griffin, Darren K; Larkin, Denis M

2017-05-01

Most recent initiatives to sequence and assemble new species' genomes de novo fail to achieve the ultimate endpoint to produce contigs, each representing one whole chromosome. Even the best-assembled genomes (using contemporary technologies) consist of subchromosomal-sized scaffolds. To circumvent this problem, we developed a novel approach that combines computational algorithms to merge scaffolds into chromosomal fragments, PCR-based scaffold verification, and physical mapping to chromosomes. Multigenome-alignment-guided probe selection led to the development of a set of universal avian BAC clones that permit rapid anchoring of multiple scaffolds to chromosomes on all avian genomes. As proof of principle, we assembled genomes of the pigeon ( Columbia livia ) and peregrine falcon ( Falco peregrinus ) to chromosome levels comparable, in continuity, to avian reference genomes. Both species are of interest for breeding, cultural, food, and/or environmental reasons. Pigeon has a typical avian karyotype (2n = 80), while falcon (2n = 50) is highly rearranged compared to the avian ancestor. By using chromosome breakpoint data, we established that avian interchromosomal breakpoints appear in the regions of low density of conserved noncoding elements (CNEs) and that the chromosomal fission sites are further limited to long CNE "deserts." This corresponds with fission being the rarest type of rearrangement in avian genome evolution. High-throughput multiple hybridization and rapid capture strategies using the current BAC set provide the basis for assembling numerous avian (and possibly other reptilian) species, while the overall strategy for scaffold assembly and mapping provides the basis for an approach that (provided metaphases can be generated) could be applied to any animal genome. © 2017 Damas et al.; Published by Cold Spring Harbor Laboratory Press.

Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set

PubMed Central

O'Connor, Rebecca; Lenis, Vasileios Panagiotis E.; Martell, Henry J.; Mandawala, Anjali; Fowler, Katie; Joseph, Sunitha; Swain, Martin T.; Griffin, Darren K.; Larkin, Denis M.

2017-01-01

Most recent initiatives to sequence and assemble new species’ genomes de novo fail to achieve the ultimate endpoint to produce contigs, each representing one whole chromosome. Even the best-assembled genomes (using contemporary technologies) consist of subchromosomal-sized scaffolds. To circumvent this problem, we developed a novel approach that combines computational algorithms to merge scaffolds into chromosomal fragments, PCR-based scaffold verification, and physical mapping to chromosomes. Multigenome-alignment-guided probe selection led to the development of a set of universal avian BAC clones that permit rapid anchoring of multiple scaffolds to chromosomes on all avian genomes. As proof of principle, we assembled genomes of the pigeon (Columbia livia) and peregrine falcon (Falco peregrinus) to chromosome levels comparable, in continuity, to avian reference genomes. Both species are of interest for breeding, cultural, food, and/or environmental reasons. Pigeon has a typical avian karyotype (2n = 80), while falcon (2n = 50) is highly rearranged compared to the avian ancestor. By using chromosome breakpoint data, we established that avian interchromosomal breakpoints appear in the regions of low density of conserved noncoding elements (CNEs) and that the chromosomal fission sites are further limited to long CNE “deserts.” This corresponds with fission being the rarest type of rearrangement in avian genome evolution. High-throughput multiple hybridization and rapid capture strategies using the current BAC set provide the basis for assembling numerous avian (and possibly other reptilian) species, while the overall strategy for scaffold assembly and mapping provides the basis for an approach that (provided metaphases can be generated) could be applied to any animal genome. PMID:27903645

Production of intergranular attack of alloy 600, alloy 690, and alloy 800 tubing in tubesheet crevices: Topical report

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

Scott, D.B.; Glaves, C.L.,

1987-07-01

Three model boilers, manufactured to simulate full-size tube sheet crevices, were tested with various secondary side environments. The first was faulted with organics representative of the decomposition of humic acid. The second was faulted with sodium carbonate and sodium hydroxide, while the third was faulted with sodium sulfate and sodium hydroxide. Each model contained seven tubes, which included Alloy 600 in the mill-annealed (MA) and thermally-treated (TT) conditions and Alloy 690 in the thermally-treated condition. Two models contained Alloy 800 tubes in the mill-annealed condition and one had Alloy 800 in the mill-annealed/cold-worked/glass-bead-peened condition. Two different sizes of tubesheet crevicesmore » were used in all model boilers. In the organics-faulted boiler, tubes of Alloy 600MA, Alloy 690TT and Alloy 800MA experienced no significant intergranular attack (IGA); however, the Alloy 600TT had intergranular attack (IGA) three to four grains deep. The carbonate-caustic faulted boiler experienced throughwall stress corrosion cracking (SCC) in all tubes of Alloy 600 MA and Alloy 800 MA. Eddy current indications were present in Alloy 690TT, Alloy 600TT and Alloy 800 in the mill-annealed/cold worked/glass-bead-peened condition. Metallographic examination of tubes from the third model boiler, faulted with sodium sulfate and caustic, revealed IGA in the mill-annealed Alloy 600 tubes. The IGA was more extensive in an Alloy 600 tube annealed at 1700/sup 0/F than an Alloy 600 tube annealed at 1875/sup 0/F.« less

Corrosion resistance characteristics of a Ti-6Al-4V alloy scaffold that is fabricated by electron beam melting and selective laser melting for implantation in vivo.

PubMed

Zhao, Bingjing; Wang, Hong; Qiao, Ning; Wang, Chao; Hu, Min

2017-01-01

The purpose of this study is to determine the corrosion resistance of Ti-6Al-4V alloy fabricated with electron beam melting and selective laser melting for implantation in vivo. Ti-6Al-4V alloy specimens were fabricated with electron beam melting (EBM) and selective laser melting (SLM). A wrought form of Ti-6Al-4V alloy was used as a control. Surface morphology observation, component analysis, corrosion resistance experimental results, electrochemical impedance spectroscopy, crevice corrosion resistance experimental results, immersion test and metal ions precipitation analysis were processed, respectively. The thermal stability of EBM specimen was the worst, based on the result of open circuit potential (OCP) result. The result of electrochemical impedance spectroscopy indicated that the corrosion resistance of the SLM specimen was the best under the low electric potential. The result of potentiodynamic polarization suggested that the corrosion resistance of the SLM specimen was the best under the low electric potential (<1.5V) and EBM specimen was the best under the high electric potential (>1.5V).The crevice corrosion resistance of the EBM specimen was the best. The corrosion resistance of SLM specimen was the best, based on the result of immersion test. The content of Ti, Al and V ions of EBM, SLM and wrought specimens was very low. In general, the scaffolds that were fabricated with EBM and SLM had good corrosion resistance, and were suitable for implantation in vivo. Copyright © 2016 Elsevier B.V. All rights reserved.

Analysis of in vivo corrosion of 316L stainless steel posterior thoracolumbar plate systems: a retrieval study.

PubMed

Majid, Kamran; Crowder, Terence; Baker, Erin; Baker, Kevin; Koueiter, Denise; Shields, Edward; Herkowitz, Harry N

2011-12-01

One hundred eighteen patients retrieved 316L stainless steel thoracolumbar plates, of 3 different designs, used for fusion in 60 patients were examined for evidence of corrosion. A medical record review and statistical analysis were also carried out. This study aims to identify types of corrosion and examine preferential metal ion release and the possibility of statistical correlation to clinical effects. Earlier studies have found that stainless steel spine devices showed evidence of mild-to-severe corrosion; fretting and crevice corrosion were the most commonly reported types. Studies have also shown the toxicity of metal ions released from stainless steel corrosion and how the ions may adversely affect bone formation and/or induce granulomatous foreign body responses. The retrieved plates were visually inspected and graded based on the degree of corrosion. The plates were then analyzed with optical microscopy, scanning electron microscopy, and energy dispersive x-ray spectroscopy. A retrospective medical record review was performed and statistical analysis was carried out to determine any correlations between experimental findings and patient data. More than 70% of the plates exhibited some degree of corrosion. Both fretting and crevice corrosion mechanisms were observed, primarily at the screw plate interface. Energy dispersive x-ray spectroscopy analysis indicated reductions in nickel content in corroded areas, suggestive of nickel ion release to the surrounding biological environment. The incidence and severity of corrosion was significantly correlated with the design of the implant. Stainless steel thoracolumbar plates show a high incidence of corrosion, with statistical dependence on device design.

Botulinum neurotoxin B recognizes its protein receptor with high affinity and specificity.

PubMed

Jin, Rongsheng; Rummel, Andreas; Binz, Thomas; Brunger, Axel T

2006-12-21

Botulinum neurotoxins (BoNTs) are produced by Clostridium botulinum and cause the neuroparalytic syndrome of botulism. With a lethal dose of 1 ng kg(-1), they pose a biological hazard to humans and a serious potential bioweapon threat. BoNTs bind with high specificity at neuromuscular junctions and they impair exocytosis of synaptic vesicles containing acetylcholine through specific proteolysis of SNAREs (soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptors), which constitute part of the synaptic vesicle fusion machinery. The molecular details of the toxin-cell recognition have been elusive. Here we report the structure of a BoNT in complex with its protein receptor: the receptor-binding domain of botulinum neurotoxin serotype B (BoNT/B) bound to the luminal domain of synaptotagmin II, determined at 2.15 A resolution. On binding, a helix is induced in the luminal domain which binds to a saddle-shaped crevice on a distal tip of BoNT/B. This crevice is adjacent to the non-overlapping ganglioside-binding site of BoNT/B. Synaptotagmin II interacts with BoNT/B with nanomolar affinity, at both neutral and acidic endosomal pH. Biochemical and neuronal ex vivo studies of structure-based mutations indicate high specificity and affinity of the interaction, and high selectivity of BoNT/B among synaptotagmin I and II isoforms. Synergistic binding of both synaptotagmin and ganglioside imposes geometric restrictions on the initiation of BoNT/B translocation after endocytosis. Our results provide the basis for the rational development of preventive vaccines or inhibitors against these neurotoxins.

Electrochemical, Polarization, and Crevice Corrosion Testing of Nitinol 60, A Supplement to the ECLSS Sustaining Materials Compatibility Study

NASA Technical Reports Server (NTRS)

Lee, R. E.

2016-01-01

In earlier trials, electrochemical test results were presented for six noble metals evaluated in test solutions representative of waste liquids processed in the Environmental Control and Life Support System (ECLSS) aboard the International Space Station (ISS). Subsequently, a seventh metal, Nitinol 60, was added for evaluation and subjected to the same test routines, data analysis, and theoretical methodologies. The previous six test metals included three titanium grades, (commercially pure, 6Al-4V alloy and 6Al-4V low interstitial alloy), two nickel-chromium alloys (Inconel(RegisteredTrademark) 625 and Hastelloy(RegisteredTrademark) C276), and one high-tier stainless steel (Cronidur(RegisteredTrademark) 30). The three titanium alloys gave the best results of all the metals, indicating superior corrosive nobility and galvanic protection properties. For this current effort, the results have clearly shown that Nitinol 60 is almost as noble as titanium, being very corrosion-resistant and galvanically compatible with the other six metals electrochemically and during long-term exposure. is also quite noble as it is very corrosion resistant and galvanically compatible with the other six metals from both an electrochemical perspective and long-term crevice corrosion scenario. This was clearly demonstrated utilizing the same techniques for linear, Tafel and cyclic polarization, and galvanic coupling of the metal candidate as was done for the previous study. The high nobility and low corrosion susceptibility for Nitinol 60 appear to be intermediate to the nickel/chromium alloys and the titanium metals with indications that are more reflective of the titanium metals in terms of general corrosion and pitting behavior.

Entropic depletion in colloidal suspensions and polymer liquids: Role of nanoparticle surface topography

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

Banerjee, Debapriya; Yang, Jian; Schweizer, Kenneth S.

2015-01-01

Here, we employ a hybrid Monte Carlo plus integral equation theory approach to study how dense fluids of small nanoparticles or polymer chains mediate entropic depletion interactions between topographically rough particles where all interaction potentials are hard core repulsion. The corrugated particle surfaces are composed of densely packed beads which present variable degrees of controlled topographic roughness and free volume associated with their geometric crevices. This pure entropy problem is characterized by competing ideal translational and (favorable and unfavorable) excess entropic contributions. Surface roughness generically reduces particle depletion aggregation relative to the smooth hard sphere case. However, the competition betweenmore » ideal and excess packing entropy effects in the bulk, near the particle surface and in the crevices, results in a non-monotonic variation of the particle-monomer packing correlation function as a function of the two dimensionless length scale ratios that quantify the effective surface roughness. As a result, the inter-particle potential of mean force (PMF), second virial coefficient, and spinodal miscibility volume fraction vary non-monotonically with the surface bead to monomer diameter and particle core to surface bead diameter ratios. A miscibility window is predicted corresponding to an optimum degree of surface roughness that completely destroys depletion attraction resulting in a repulsive PMF. Variation of the (dense) matrix packing fraction can enhance or suppress particle miscibility depending upon the amount of surface roughness. Connecting the monomers into polymer chains destabilizes the system via enhanced contact depletion attraction, but the non-monotonic variations with surface roughness metrics persist.« less

A modular assembling platform for manufacturing of microsystems by optical tweezers

NASA Astrophysics Data System (ADS)

Ksouri, Sarah Isabelle; Aumann, Andreas; Ghadiri, Reza; Prüfer, Michael; Baer, Sebastian; Ostendorf, Andreas

2013-09-01

Due to the increased complexity in terms of materials and geometries for microsystems new assembling techniques are required. Assembling techniques from the semiconductor industry are often very specific and cannot fulfill all specifications in more complex microsystems. Therefore, holographic optical tweezers are applied to manipulate structures in micrometer range with highest flexibility and precision. As is well known non-spherical assemblies can be trapped and controlled by laser light and assembled with an additional light modulator application, where the incident laser beam is rearranged into flexible light patterns in order to generate multiple spots. The complementary building blocks are generated by a two-photon-polymerization process. The possibilities of manufacturing arbitrary microstructures and the potential of optical tweezers lead to the idea of combining manufacturing techniques with manipulation processes to "microrobotic" processes. This work presents the manipulation of generated complex microstructures with optical tools as well as a storage solution for 2PP assemblies. A sample holder has been developed for the manual feeding of 2PP building blocks. Furthermore, a modular assembling platform has been constructed for an `all-in-one' 2PP manufacturing process as a dedicated storage system. The long-term objective is the automation process of feeding and storage of several different 2PP micro-assemblies to realize an automated assembly process.

A Versatile Microfluidic Device for Automating Synthetic Biology.

PubMed

Shih, Steve C C; Goyal, Garima; Kim, Peter W; Koutsoubelis, Nicolas; Keasling, Jay D; Adams, Paul D; Hillson, Nathan J; Singh, Anup K

2015-10-16

New microbes are being engineered that contain the genetic circuitry, metabolic pathways, and other cellular functions required for a wide range of applications such as producing biofuels, biobased chemicals, and pharmaceuticals. Although currently available tools are useful in improving the synthetic biology process, further improvements in physical automation would help to lower the barrier of entry into this field. We present an innovative microfluidic platform for assembling DNA fragments with 10× lower volumes (compared to that of current microfluidic platforms) and with integrated region-specific temperature control and on-chip transformation. Integration of these steps minimizes the loss of reagents and products compared to that with conventional methods, which require multiple pipetting steps. For assembling DNA fragments, we implemented three commonly used DNA assembly protocols on our microfluidic device: Golden Gate assembly, Gibson assembly, and yeast assembly (i.e., TAR cloning, DNA Assembler). We demonstrate the utility of these methods by assembling two combinatorial libraries of 16 plasmids each. Each DNA plasmid is transformed into Escherichia coli or Saccharomyces cerevisiae using on-chip electroporation and further sequenced to verify the assembly. We anticipate that this platform will enable new research that can integrate this automated microfluidic platform to generate large combinatorial libraries of plasmids and will help to expedite the overall synthetic biology process.

Photocontrolled reversible self-assembly of dodecamer nitrilase.

PubMed

Yu, Qiao; Wang, Yong; Zhao, Shengyun; Ren, Yuhong

2017-01-01

Naturally photoswitchable proteins act as a powerful tool for the spatial and temporal control of biological processes by inducing the formation of a photodimerizer. In this study, a method for the precise and reversible inducible self-assembly of dodecamer nitrilase in vivo (in Escherichia coli ) and in vitro (in a cell-free solution) was developed by means of the photoswitch-improved light-inducible dimer (iLID) system which could induce protein-protein dimerization. Nitrilase was fused with the photoswitch protein AsLOV2-SsrA to achieve the photocontrolled self-assembly of dodecamer nitrilase. The fusion protein self-assembled into a supramolecular assembly when illuminated at 470 nm. Scanning electron microscopy showed that the assembly formed a circular sheet structure. Self-assembly was also induced by light in E. coli . Dynamic light scattering and turbidity assay experiments showed that the assemblies formed within a few seconds under 470-nm light and completely disassembled within 5 min in the dark. Assembly and disassembly could be maintained for at least five cycles. Both in vitro and in vivo, the assemblies retained 90% of the initial activity of nitrilase and could be reused at least four times in vitro with 90% activity. An efficient method was developed for the photocontrolled assembly and disassembly of dodecamer nitrilase and for scaffold-free reversible self-assembly of multiple oligomeric enzymes in vivo and in vitro, providing new ideas and methods for immobilization of enzyme without carrier.

Swamp Works- Multiple Projects

NASA Technical Reports Server (NTRS)

Carelli, Jonathan M.; Schuler, Jason M.; Chandler, Meredith L.

2013-01-01

My Surface Systems internship over the summer 2013 session covered a broad range of projects that utilized multiple fields of engineering and technology. This internship included a project to create a command center for a 120 ton regolith bin, for the design and assembly of a blast shield to add further protection for the Surface Systems engineers, for the design and assembly of a portable four monitor hyper wall strip that could extend as large as needed, research and programming a nano drill that could be utilized on a next generation robot or rover, and social media tasks including the making of videos, posting to social networking websites and creation of a new outreach program to help spread the word about the Swamp Works laboratory.

Sputter-deposited fuel cell membranes and electrodes

NASA Technical Reports Server (NTRS)

Narayanan, Sekharipuram R. (Inventor); Jeffries-Nakamura, Barbara (Inventor); Chun, William (Inventor); Ruiz, Ron P. (Inventor); Valdez, Thomas I. (Inventor)

2001-01-01

A method for preparing a membrane for use in a fuel cell membrane electrode assembly includes the steps of providing an electrolyte membrane, and sputter-depositing a catalyst onto the electrolyte membrane. The sputter-deposited catalyst may be applied to multiple sides of the electrolyte membrane. A method for forming an electrode for use in a fuel cell membrane electrode assembly includes the steps of obtaining a catalyst, obtaining a backing, and sputter-depositing the catalyst onto the backing. The membranes and electrodes are useful for assembling fuel cells that include an anode electrode, a cathode electrode, a fuel supply, and an electrolyte membrane, wherein the electrolyte membrane includes a sputter-deposited catalyst, and the sputter-deposited catalyst is effective for sustaining a voltage across a membrane electrode assembly in the fuel cell.

Jam proof closure assembly for lidded pressure vessels

DOEpatents

Cioletti, Olisse C.

1992-01-01

An expendable closure assembly is provided for use (in multiple units) with a lockable pressure vessel cover along its rim, such as of an autoclave. This assembly is suited to variable compressive contact and locking with the vessel lid sealing gasket. The closure assembly consists of a thick walled sleeve insert for retention in the under bores fabricated in the cover periphery and the sleeve is provided with internal threading only. A snap serves as a retainer on the underside of the sleeve, locking it into an under bore retention channel. Finally, a standard elongate externally threaded bolt is sized for mating cooperation with the so positioned sleeve, whereby the location of the bolt shaft in the cover bore hole determines its compressive contact on the underlying gasket.

Versatile microrobotics using simple modular subunits

NASA Astrophysics Data System (ADS)

Cheang, U. Kei; Meshkati, Farshad; Kim, Hoyeon; Lee, Kyoungwoo; Fu, Henry Chien; Kim, Min Jun

2016-07-01

The realization of reconfigurable modular microrobots could aid drug delivery and microsurgery by allowing a single system to navigate diverse environments and perform multiple tasks. So far, microrobotic systems are limited by insufficient versatility; for instance, helical shapes commonly used for magnetic swimmers cannot effectively assemble and disassemble into different size and shapes. Here by using microswimmers with simple geometries constructed of spherical particles, we show how magnetohydrodynamics can be used to assemble and disassemble modular microrobots with different physical characteristics. We develop a mechanistic physical model that we use to improve assembly strategies. Furthermore, we experimentally demonstrate the feasibility of dynamically changing the physical properties of microswimmers through assembly and disassembly in a controlled fluidic environment. Finally, we show that different configurations have different swimming properties by examining swimming speed dependence on configuration size.

Versatile microrobotics using simple modular subunits

PubMed Central

Cheang, U Kei; Meshkati, Farshad; Kim, Hoyeon; Lee, Kyoungwoo; Fu, Henry Chien; Kim, Min Jun

2016-01-01

The realization of reconfigurable modular microrobots could aid drug delivery and microsurgery by allowing a single system to navigate diverse environments and perform multiple tasks. So far, microrobotic systems are limited by insufficient versatility; for instance, helical shapes commonly used for magnetic swimmers cannot effectively assemble and disassemble into different size and shapes. Here by using microswimmers with simple geometries constructed of spherical particles, we show how magnetohydrodynamics can be used to assemble and disassemble modular microrobots with different physical characteristics. We develop a mechanistic physical model that we use to improve assembly strategies. Furthermore, we experimentally demonstrate the feasibility of dynamically changing the physical properties of microswimmers through assembly and disassembly in a controlled fluidic environment. Finally, we show that different configurations have different swimming properties by examining swimming speed dependence on configuration size. PMID:27464852

Characterizing subcritical assemblies with time of flight fixed by energy estimation distributions

NASA Astrophysics Data System (ADS)

Monterial, Mateusz; Marleau, Peter; Pozzi, Sara

2018-04-01

We present the Time of Flight Fixed by Energy Estimation (TOFFEE) as a measure of the fission chain dynamics in subcritical assemblies. TOFFEE is the time between correlated gamma rays and neutrons, subtracted by the estimated travel time of the incident neutron from its proton recoil. The measured subcritical assembly was the BeRP ball, a 4.482 kg sphere of α-phase weapons grade plutonium metal, which came in five configurations: bare, 0.5, 1, and 1.5 in iron, and 1 in nickel closed fitting shell reflectors. We extend the measurement with MCNPX-PoliMi simulations of shells ranging up to 6 inches in thickness, and two new reflector materials: aluminum and tungsten. We also simulated the BeRP ball with different masses ranging from 1 to 8 kg. A two-region and single-region point kinetics models were used to model the behavior of the positive side of the TOFFEE distribution from 0 to 100 ns. The single region model of the bare cases gave positive linear correlations between estimated and expected neutron decay constants and leakage multiplications. The two-region model provided a way to estimate neutron multiplication for the reflected cases, which correlated positively with expected multiplication, but the nature of the correlation (sub or superlinear) changed between material types. Finally, we found that the areal density of the reflector shells had a linear correlation with the integral of the two-region model fit. Therefore, we expect that with knowledge of reflector composition, one could determine the shell thickness, or vice versa. Furthermore, up to a certain amount and thickness of the reflector, the two-region model provides a way of distinguishing bare and reflected plutonium assemblies.

Micromorphology of two prehistoric ritual burials from Yemen, and considerations on methodological aspects of sampling the burial matrix - work in progress

NASA Astrophysics Data System (ADS)

Usai, Maria-Raimonda; Brothwell, Don; Buckley, Stephen; Ai-Thour, Kalid; Canti, Matthew

2010-05-01

Introduction In the central area of Yemen, two burial sites placed high in the crevices of vertical cliff face of Cretaceous sandstone (Tawilah Group) provided evidence of human remains and yielded burial soils. Radiocarbon dating indicated c.2500-2900 years BP for the burials. In other local comparable sites the deep horizontal crevices yielded Bronze Age human remains, in exceptional state of preservation Questions: What was the nature of the burial matrix? Are other human influences superimposed on the soils derived from it? Is it simply decomposed crevice rock, scraped together at the time of burial, or the result of a more complex burial practice? Such questions are also relevant to a variety of other burials of different periods and world regions. Methods Seven matrix samples from Cliff Burials (A) Talan (Layers 4,10,12,14,18,20 and 22, from top to bottom) and (B) Shiban Kawkaban (Layer 1 and 9) were analysed with micromorphology, supplemented by SEM microprobe, X-ray diffraction, gas chromatography/mass spectrometry. Results Cliff Burial Site Talan. The presence of cholesterol was confirmed in the lower sample. The second layer contained darker earth with fibrous plant material. A hard calcareous upper capping contrasted with the other levels of matrix, and it displayed a highly birefingent material with a significant component of uric acid. The other levels had variable organic content and plant inclusions, and possibly pollen. In Layer 10, aromatic acids indicative of balsam and sugar markers suggested plant gum. Cholesterol was the major sterol in Layers 10 and 22, but whilst in Layer 10 its oxidation products were present and cholestanol was abundant as normally in soils, it was only a minor component of Layer 22 where, rather, a significant amount of coprostanol indicated faecal input, and cholesterol oxidation products were absent. Cliff Burial Site Shiban Kawkaban. Although no stratification was visible to the naked eye, variation was observed at a micromorphological level. Layer 1 included mineral, bone, plant and soil-like fragments, with leaf and woody tissue, including vascular parts and seeds. Layer 9 included plant tissue, hair, seeds and some fly puparia. Comments Layering of the burial matrix in the Yemeni burials was unexpected and the burial matrix in one case was very clearly not the result of natural soil forming processes within the rock crevice. In Burial Site A the hard upper capping contained uric acid-rich deposits embedding organic tissue. This sample could possibly represent an intentional ‘plaster layer' including plant, hair and seed fragments. The abundant cholesterol confirms an animal/human origin within the matrix of Layers 10 and 22, and the stanol and bile acid distributions unequivocally confirm a human origin, despite the lack of any physical human remains. Microprobe analysis indicated that the hard cup of Burial 1 contained K, Si, Al, Cu, Mg, S, Fe and Na with amounts fluctuating relatively to depth. No special significance can be placed on the differences. This study calls attention to a neglected aspect of burial archaeology: grave infillings can no longer be assumed to be simply the return of material removed for the burial, but may be influenced by other factors. Through micromorphology, decomposed wood, shroud or other textiles or skins and hair can be detected and, if local rituals influenced the way materials were returned into the grave, then this also deserves investigation. A new ERC-funded project (Title: "Interred with their bones", acronym: "InterArChive") tackles these issues (please see separate poster). Acknowledgments We thank Allan Hall, Brendan Keely, Trevor Dransfield, Andrea Vacca and Cagliari University

Microgravity

NASA Image and Video Library

2000-12-15

NASA is looking to biological techniques that are millions of years old to help it develop new materials and technologies for the 21st century. Sponsored by NASA, Jeffrey Brinker of the University of New Mexico is studying how multiple elements can assemble themselves into a composite material that is clear, tough, and impermeable. His research is based on the model of how an abalone builds the nacre, also called mother-of-pearl, inside its shell. Strong thin coatings, or lamellae, in Brinker's research are formed when objects are dip-coated. Evaporation drives the self-assembly of molecular aggregates (micelles) of surfactant, soluble silica, and organic monomers and their further self-organization into layered organic and inorganic assemblies.

Multilayer checkpoints for microRNA authenticity during RISC assembly.

PubMed

Kawamata, Tomoko; Yoda, Mayuko; Tomari, Yukihide

2011-09-01

MicroRNAs (miRNAs) function through the RNA-induced silencing complex (RISC), which contains an Argonaute (Ago) protein at the core. RISC assembly follows a two-step pathway: miRNA/miRNA* duplex loading into Ago, and separation of the two strands within Ago. Here we show that the 5' phosphate of the miRNA strand is essential for duplex loading into Ago, whereas the preferred 5' nucleotide of the miRNA strand and the base-pairing status in the seed region and the middle of the 3' region function as additive anchors to Ago. Consequently, the miRNA authenticity is inspected at multiple steps during RISC assembly.

Competing Thermodynamic and Dynamic Factors Select Molecular Assemblies on a Gold Surface

NASA Astrophysics Data System (ADS)

Haxton, Thomas K.; Zhou, Hui; Tamblyn, Isaac; Eom, Daejin; Hu, Zonghai; Neaton, Jeffrey B.; Heinz, Tony F.; Whitelam, Stephen

2013-12-01

Controlling the self-assembly of surface-adsorbed molecules into nanostructures requires understanding physical mechanisms that act across multiple length and time scales. By combining scanning tunneling microscopy with hierarchical ab initio and statistical mechanical modeling of 1,4-substituted benzenediamine (BDA) molecules adsorbed on a gold (111) surface, we demonstrate that apparently simple nanostructures are selected by a subtle competition of thermodynamics and dynamics. Of the collection of possible BDA nanostructures mechanically stabilized by hydrogen bonding, the interplay of intermolecular forces, surface modulation, and assembly dynamics select at low temperature a particular subset: low free energy oriented linear chains of monomers and high free energy branched chains.

An application of a zero-inflated lifetime distribution with multiple and incomplete data sources

DOE PAGES

Hamada, M. S.; Margevicius, K. J.

2016-02-11

In this study, we analyze data sampled from a population of parts in which an associated anomaly can occur at assembly or after assembly. Using a zero-inflated lifetime distribution to fit left-censored and right-censored data as well data from a supplementary sample, we make predictions about the proportion of the population with anomalies today and in the future. Goodness-of-fit is also addressed.

Artificial intelligence approach to planning the robotic assembly of large tetrahedral truss structures

NASA Technical Reports Server (NTRS)

Homemdemello, Luiz S.

1992-01-01

An assembly planner for tetrahedral truss structures is presented. To overcome the difficulties due to the large number of parts, the planner exploits the simplicity and uniformity of the shapes of the parts and the regularity of their interconnection. The planning automation is based on the computational formalism known as production system. The global data base consists of a hexagonal grid representation of the truss structure. This representation captures the regularity of tetrahedral truss structures and their multiple hierarchies. It maps into quadratic grids and can be implemented in a computer by using a two-dimensional array data structure. By maintaining the multiple hierarchies explicitly in the model, the choice of a particular hierarchy is only made when needed, thus allowing a more informed decision. Furthermore, testing the preconditions of the production rules is simple because the patterned way in which the struts are interconnected is incorporated into the topology of the hexagonal grid. A directed graph representation of assembly sequences allows the use of both graph search and backtracking control strategies.

Molybdenum-99 production calculation analysis of SAMOP reactor based on thorium nitrate fuel

NASA Astrophysics Data System (ADS)

Syarip; Togatorop, E.; Yassar

2018-03-01

SAMOP (Subcritical Assembly for Molybdenum-99 Production) has the potential to use thorium as fuel to produce 99Mo after modifying the design, but the production performance has not been discovered yet. A study needs to be done to obtain the correlation between 99Mo production with the mixed fuel composition of uranium and with SAMOP power on the modified SAMOP design. The study aims to obtain the production of 99Mo based thorium nitrate fuel on SAMOP’s modified designs. Monte Carlo N-Particle eXtended (MCNPX) is required to simulate the operation of the assembly by varying the composition of the uranium-thorium nitrate mixed fuel, geometry and power fraction on the SAMOP modified designs. The burnup command on the MCNPX is used to confirm the 99Mo production result. The assembly is simulated to operate for 6 days with subcritical neutron multiplication factor (keff = 0.97-0.99). The neutron multiplication factor of the modified design (keff) is 0.97, the activity obtained from 99Mo is 18.58 Ci at 1 kW power operation.

Characterisation of minimalist co-assembled fluorenylmethyloxycarbonyl self-assembling peptide systems for presentation of multiple bioactive peptides.

PubMed

Horgan, Conor C; Rodriguez, Alexandra L; Li, Rui; Bruggeman, Kiara F; Stupka, Nicole; Raynes, Jared K; Day, Li; White, John W; Williams, Richard J; Nisbet, David R

2016-07-01

The nanofibrillar structures that underpin self-assembling peptide (SAP) hydrogels offer great potential for the development of finely tuned cellular microenvironments suitable for tissue engineering. However, biofunctionalisation without disruption of the assembly remains a key issue. SAPS present the peptide sequence within their structure, and studies to date have typically focused on including a single biological motif, resulting in chemically and biologically homogenous scaffolds. This limits the utility of these systems, as they cannot effectively mimic the complexity of the multicomponent extracellular matrix (ECM). In this work, we demonstrate the first successful co-assembly of two biologically active SAPs to form a coassembled scaffold of distinct two-component nanofibrils, and demonstrate that this approach is more bioactive than either of the individual systems alone. Here, we use two bioinspired SAPs from two key ECM proteins: Fmoc-FRGDF containing the RGD sequence from fibronectin and Fmoc-DIKVAV containing the IKVAV sequence from laminin. Our results demonstrate that these SAPs are able to co-assemble to form stable hybrid nanofibres containing dual epitopes. Comparison of the co-assembled SAP system to the individual SAP hydrogels and to a mixed system (composed of the two hydrogels mixed together post-assembly) demonstrates its superior stable, transparent, shear-thinning hydrogels at biological pH, ideal characteristics for tissue engineering applications. Importantly, we show that only the coassembled hydrogel is able to induce in vitro multinucleate myotube formation with C2C12 cells. This work illustrates the importance of tissue engineering scaffold functionalisation and the need to develop increasingly advanced multicomponent systems for effective ECM mimicry. Successful control of stem cell fate in tissue engineering applications requires the use of sophisticated scaffolds that deliver biological signals to guide growth and differentiation. The complexity of such processes necessitates the presentation of multiple signals in order to effectively mimic the native extracellular matrix (ECM). Here, we establish the use of two biofunctional, minimalist self-assembling peptides (SAPs) to construct the first co-assembled SAP scaffold. Our work characterises this construct, demonstrating that the physical, chemical, and biological properties of the peptides are maintained during the co-assembly process. Importantly, the coassembled system demonstrates superior biological performance relative to the individual SAPs, highlighting the importance of complex ECM mimicry. This work has important implications for future tissue engineering studies. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Software Architecture for a Virtual Environment for Nano Scale Assembly (VENSA).

PubMed

Lee, Yong-Gu; Lyons, Kevin W; Feng, Shaw C

2004-01-01

A Virtual Environment (VE) uses multiple computer-generated media to let a user experience situations that are temporally and spatially prohibiting. The information flow between the user and the VE is bidirectional and the user can influence the environment. The software development of a VE requires orchestrating multiple peripherals and computers in a synchronized way in real time. Although a multitude of useful software components for VEs exists, many of these are packaged within a complex framework and can not be used separately. In this paper, an architecture is presented which is designed to let multiple frameworks work together while being shielded from the application program. This architecture, which is called the Virtual Environment for Nano Scale Assembly (VENSA), has been constructed for interfacing with an optical tweezers instrument for nanotechnology development. However, this approach can be generalized for most virtual environments. Through the use of VENSA, the programmer can rely on existing solutions and concentrate more on the application software design.

Community assembly rules affect the diversity of expanding communities.

PubMed

Peng, Zechen; Zhou, Shurong

2014-11-01

Despite centuries of interest in species range limits, few studies have taken a whole community into consideration. Actually, multiple species may simultaneously respond to environmental changes, for example, global warming, leading a series of dynamical communities toward the advancing front. We investigated multiple species range expansions through the analysis of a two-species dispersion model and simulations of multiple species assemblages regulated by neutral and fecundity-survival trade-offs (FSTs), respectively, and found that species assemblages regulated by different mechanisms would initiate different expanding patterns in geographic ranges in response to environmental changes. The neutral model generally predicts a higher biodiversity near the core of an expanding range, and a lower community similarity compared with a FST model. Without considering the evolution of life history traits, an assortment of the reproduction ability happens at the advancing front under FSTs at the expense of a higher death rate or lower competitive ability. These results emphasize the importance of community assembly rules to the biodiversity maintenance of range expanding communities.

Software Architecture for a Virtual Environment for Nano Scale Assembly (VENSA)

PubMed Central

Lee, Yong-Gu; Lyons, Kevin W.; Feng, Shaw C.

2004-01-01

A Virtual Environment (VE) uses multiple computer-generated media to let a user experience situations that are temporally and spatially prohibiting. The information flow between the user and the VE is bidirectional and the user can influence the environment. The software development of a VE requires orchestrating multiple peripherals and computers in a synchronized way in real time. Although a multitude of useful software components for VEs exists, many of these are packaged within a complex framework and can not be used separately. In this paper, an architecture is presented which is designed to let multiple frameworks work together while being shielded from the application program. This architecture, which is called the Virtual Environment for Nano Scale Assembly (VENSA), has been constructed for interfacing with an optical tweezers instrument for nanotechnology development. However, this approach can be generalized for most virtual environments. Through the use of VENSA, the programmer can rely on existing solutions and concentrate more on the application software design. PMID:27366610

The Role of Passive Film Growth Kinetics and Properties in Stress Corrosion and Crevice Corrosion Susceptibility

DTIC Science & Technology

1975-10-01

Kleinzack-Mathieu Cl. Mertens, J. Meunier, Cl. Vanlengenhaghe, L. de Munck, L. Laureys , L. N. Nellmans, and M . Warzu, Corrosion Science, 3, 239 (1963). 10) H...312O448 DEPARTMENT OF COMMERCE 11. CoMfact/Grat No. WASHINGTON. D.C. 20234 M 1 mRO36-082 12. Spoasoring Organizstion N~me and Complete Address (Street...Ill. Undw Swnay Dr. 111"y Alu-Juhws. AsnluaM ScWaty fr Salome and T0e@* M /WY NATIONAL UMAU OF STANDAWS. Ernest Ambler. Acting Dimwt PART I (To be

Selectable-Tip Corrosion-Testing Electrochemical Cell

NASA Technical Reports Server (NTRS)

Lomness, Janice; Hintze, Paul

2008-01-01

The figure depicts aspects of an electrochemical cell for pitting- corrosion tests of material specimens. The cell is designed to generate a region of corrosion having a pit diameter determined by the diameter of a selectable tip. The average depth of corrosion is controlled by controlling the total electric charge passing through the cell in a test. The cell is also designed to produce minimal artifacts associated with crevice corrosion. There are three selectable tips, having diameters of 0.1 in. (0.254 cm), 0.3 in. (0.762 cm), and 0.6 in. (1.524 cm), respectively.

Performance and combustion characteristics of direct-injection stratified-charge rotary engines

NASA Technical Reports Server (NTRS)

Nguyen, Hung Lee

1987-01-01

Computer simulations of the direct-injection stratified-charge (DISC) Wankel engine have been used to calculate heat release rates and performance and efficiency characteristics of the 1007R engine. Engine pressure data have been used in a heat release analysis to study the effects of heat transfer, leakage, and crevice flows. Predicted engine performance data are compared with experimental test data over a range of engine speeds and loads. An examination of methods to improve the performance of the Wankel engine with faster combustion, reduced leakage, higher compression ratio, and turbocharging is presented.

Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly

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

Torella, JP; Boehm, CR; Lienert, F

2013-12-28

In vitro recombination methods have enabled one-step construction of large DNA sequences from multiple parts. Although synthetic biological circuits can in principle be assembled in the same fashion, they typically contain repeated sequence elements such as standard promoters and terminators that interfere with homologous recombination. Here we use a computational approach to design synthetic, biologically inactive unique nucleotide sequences (UNSes) that facilitate accurate ordered assembly. Importantly, our designed UNSes make it possible to assemble parts with repeated terminator and insulator sequences, and thereby create insulated functional genetic circuits in bacteria and mammalian cells. Using UNS-guided assembly to construct repeating promoter-gene-terminatormore » parts, we systematically varied gene expression to optimize production of a deoxychromoviridans biosynthetic pathway in Escherichia coli. We then used this system to construct complex eukaryotic AND-logic gates for genomic integration into embryonic stem cells. Construction was performed by using a standardized series of UNS-bearing BioBrick-compatible vectors, which enable modular assembly and facilitate reuse of individual parts. UNS-guided isothermal assembly is broadly applicable to the construction and optimization of genetic circuits and particularly those requiring tight insulation, such as complex biosynthetic pathways, sensors, counters and logic gates.« less

Surface mediated assembly of small, metastable gold nanoclusters.

PubMed

Pettibone, John M; Osborn, William A; Rykaczewski, Konrad; Talin, A Alec; Bonevich, John E; Hudgens, Jeffrey W; Allendorf, Mark D

2013-07-21

The unique properties of metallic nanoclusters are attractive for numerous commercial and industrial applications but are generally less stable than nanocrystals. Thus, developing methodologies for stabilizing nanoclusters and retaining their enhanced functionality is of great interest. We report the assembly of PPh3-protected Au9 clusters from a heterogeneous mixture into films consisting of sub 3 nm nanocluster assemblies. The depositing nanoclusters are metastable in solution, but the resulting nanocluster assemblies are stabilized indefinitely in air or fresh solvent. The films exhibit distinct structure from Au nanoparticles observed by X-ray diffraction, and film dissolution data support the preservation of small nanoclusters. UV-Vis spectroscopy, electrospray ionization mass spectrometry, X-ray photoelectron spectroscopy and electron microscopy are used to elucidate information regarding the nanocluster formation and assembly mechanism. Preferential deposition of nanocluster assemblies can be achieved on multiple substrates, including polymer, Cr, Si, SiO2, SiNx, and metal-organic frameworks (MOFs). Unlike other vapor phase coating processes, nanocluster assembly on the MIL-68(In) MOF crystal is capable of preferentially coating the external surface and stabilizing the crystal structure in hydrothermal conditions, which should enhance their storage, separation and delivery capabilities.

Ligand-Receptor Interaction Modulates the Energy Landscape of Enzyme-Instructed Self-Assembly of Small Molecules.

PubMed

Haburcak, Richard; Shi, Junfeng; Du, Xuewen; Yuan, Dan; Xu, Bing

2016-11-30

The concurrence of enzymatic reaction and ligand-receptor interactions is common for proteins, but rare for small molecules and has yet to be explored. Here we show that ligand-receptor interaction modulates the morphology of molecular assemblies formed by enzyme-instructed assembly of small molecules. While the absence of ligand-receptor interaction allows enzymatic dephosphorylation of a precursor to generate the hydrogelator that self-assembles to form long nanofibers, the presence of the ligand-receptor interaction biases the pathway to form precipitous aggregates containing short nanofibers. While the hydrogelators self-assemble to form nanofibers or nanoribbons that are unable to bind with the ligand (i.e., vancomycin), the addition of surfactant breaks up the assemblies to restore the ligand-receptor interaction. In addition, an excess amount of the ligands can disrupt the nanofibers and result in the precipitates. As the first example of the use of ligand-receptor interaction to modulate the kinetics of enzymatic self-assembly, this work not only provides a solution to evaluate the interaction between aggregates and target molecules but also offers new insight for understanding the emergent behavior of sophisticated molecular systems having multiple and parallel processes.

Selective self-assembly of adenine-silver nanoparticles forms rings resembling the size of cells

NASA Astrophysics Data System (ADS)

Choi, Sungmoon; Park, Soonyoung; Yang, Seon-Ah; Jeong, Yujin; Yu, Junhua

2015-12-01

Self-assembly has played critical roles in the construction of functional nanomaterials. However, the structure of the macroscale multicomponent materials built by the self-assembly of nanoscale building blocks is hard to predict due to multiple intermolecular interactions of great complexity. Evaporation of solvents is usually an important approach to induce kinetically stable assemblies of building blocks with a large-scale specific arrangement. During such a deweting process, we tried to monitor the possible interactions between silver nanoparticles and nucleobases at a larger scale by epifluorescence microscopy, thanks to the doping of silver nanoparticles with luminescent silver nanodots. ssDNA oligomer-stabilized silver nanoparticles and adenine self-assemble to form ring-like compartments similar to the size of modern cells. However, the silver ions only dismantle the self-assembly of adenine. The rings are thermodynamically stable as the drying process only enrich the nanoparticles-nucleobase mixture to a concentration that activates the self-assembly. The permeable membrane-like edge of the ring is composed of adenine filaments glued together by silver nanoparticles. Interestingly, chemicals are partially confined and accumulated inside the ring, suggesting that this might be used as a microreactor to speed up chemical reactions during a dewetting process.

Cloning should be simple: Escherichia coli DH5α-mediated assembly of multiple DNA fragments with short end homologies

DOE PAGES

Kostylev, Maxim; Otwell, Anne E.; Richardson, Ruth E.; ...

2015-09-08

Numerous DNA assembly technologies exist for generating plasmids for biological studies. Many procedures require complex in vitro or in vivo assembly reactions followed by plasmid propagation in recombination-impaired Escherichia coli strains such as DH5α, which are optimal for stable amplification of the DNA materials. Here we show that despite its utility as a cloning strain, DH5α retains sufficient recombinase activity to assemble up to six doublestranded DNA fragments ranging in size from 150 bp to at least 7 kb into plasmids in vivo. This process also requires surprisingly small amounts of DNA, potentially obviating the need for upstream assembly processesmore » associated with most common applications of DNA assembly. In addition, we demonstrate the application of this process in cloning of various DNA fragments including synthetic genes, preparation of knockout constructs, and incorporation of guide RNA sequences in constructs for clustered regularly interspaced short palindromic repeats (CRISPR) genome editing. This consolidated process for assembly and amplification in a widely available strain of E. coli may enable productivity gain across disciplines involving recombinant DNA work.« less

Cloning should be simple: Escherichia coli DH5α-mediated assembly of multiple DNA fragments with short end homologies

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

Kostylev, Maxim; Otwell, Anne E.; Richardson, Ruth E.

Numerous DNA assembly technologies exist for generating plasmids for biological studies. Many procedures require complex in vitro or in vivo assembly reactions followed by plasmid propagation in recombination-impaired Escherichia coli strains such as DH5α, which are optimal for stable amplification of the DNA materials. Here we show that despite its utility as a cloning strain, DH5α retains sufficient recombinase activity to assemble up to six doublestranded DNA fragments ranging in size from 150 bp to at least 7 kb into plasmids in vivo. This process also requires surprisingly small amounts of DNA, potentially obviating the need for upstream assembly processesmore » associated with most common applications of DNA assembly. In addition, we demonstrate the application of this process in cloning of various DNA fragments including synthetic genes, preparation of knockout constructs, and incorporation of guide RNA sequences in constructs for clustered regularly interspaced short palindromic repeats (CRISPR) genome editing. This consolidated process for assembly and amplification in a widely available strain of E. coli may enable productivity gain across disciplines involving recombinant DNA work.« less

Proteins from Multiple Metabolic Pathways Associate with Starch Biosynthetic Enzymes in High Molecular Weight Complexes: A Model for Regulation of Carbon Allocation in Maize Amyloplasts1[C][W][OA

PubMed Central

Hennen-Bierwagen, Tracie A.; Lin, Qiaohui; Grimaud, Florent; Planchot, Véronique; Keeling, Peter L.; James, Martha G.; Myers, Alan M.

2009-01-01

Starch biosynthetic enzymes from maize (Zea mays) and wheat (Triticum aestivum) amyloplasts exist in cell extracts in high molecular weight complexes; however, the nature of those assemblies remains to be defined. This study tested the interdependence of the maize enzymes starch synthase IIa (SSIIa), SSIII, starch branching enzyme IIb (SBEIIb), and SBEIIa for assembly into multisubunit complexes. Mutations that eliminated any one of those proteins also prevented the others from assembling into a high molecular mass form of approximately 670 kD, so that SSIII, SSIIa, SBEIIa, and SBEIIb most likely all exist together in the same complex. SSIIa, SBEIIb, and SBEIIa, but not SSIII, were also interdependent for assembly into a complex of approximately 300 kD. SSIII, SSIIa, SBEIIa, and SBEIIb copurified through successive chromatography steps, and SBEIIa, SBEIIb, and SSIIa coimmunoprecipitated with SSIII in a phosphorylation-dependent manner. SBEIIa and SBEIIb also were retained on an affinity column bearing a specific conserved fragment of SSIII located outside of the SS catalytic domain. Additional proteins that copurified with SSIII in multiple biochemical methods included the two known isoforms of pyruvate orthophosphate dikinase (PPDK), large and small subunits of ADP-glucose pyrophosphorylase, and the sucrose synthase isoform SUS-SH1. PPDK and SUS-SH1 required SSIII, SSIIa, SBEIIa, and SBEIIb for assembly into the 670-kD complex. These complexes may function in global regulation of carbon partitioning between metabolic pathways in developing seeds. PMID:19168640

Sequencing and assembly of the 22-gb loblolly pine genome.

PubMed

Zimin, Aleksey; Stevens, Kristian A; Crepeau, Marc W; Holtz-Morris, Ann; Koriabine, Maxim; Marçais, Guillaume; Puiu, Daniela; Roberts, Michael; Wegrzyn, Jill L; de Jong, Pieter J; Neale, David B; Salzberg, Steven L; Yorke, James A; Langley, Charles H

2014-03-01

Conifers are the predominant gymnosperm. The size and complexity of their genomes has presented formidable technical challenges for whole-genome shotgun sequencing and assembly. We employed novel strategies that allowed us to determine the loblolly pine (Pinus taeda) reference genome sequence, the largest genome assembled to date. Most of the sequence data were derived from whole-genome shotgun sequencing of a single megagametophyte, the haploid tissue of a single pine seed. Although that constrained the quantity of available DNA, the resulting haploid sequence data were well-suited for assembly. The haploid sequence was augmented with multiple linking long-fragment mate pair libraries from the parental diploid DNA. For the longest fragments, we used novel fosmid DiTag libraries. Sequences from the linking libraries that did not match the megagametophyte were identified and removed. Assembly of the sequence data were aided by condensing the enormous number of paired-end reads into a much smaller set of longer "super-reads," rendering subsequent assembly with an overlap-based assembly algorithm computationally feasible. To further improve the contiguity and biological utility of the genome sequence, additional scaffolding methods utilizing independent genome and transcriptome assemblies were implemented. The combination of these strategies resulted in a draft genome sequence of 20.15 billion bases, with an N50 scaffold size of 66.9 kbp.

SAGE: String-overlap Assembly of GEnomes.

PubMed

Ilie, Lucian; Haider, Bahlul; Molnar, Michael; Solis-Oba, Roberto

2014-09-15

De novo genome assembly of next-generation sequencing data is one of the most important current problems in bioinformatics, essential in many biological applications. In spite of significant amount of work in this area, better solutions are still very much needed. We present a new program, SAGE, for de novo genome assembly. As opposed to most assemblers, which are de Bruijn graph based, SAGE uses the string-overlap graph. SAGE builds upon great existing work on string-overlap graph and maximum likelihood assembly, bringing an important number of new ideas, such as the efficient computation of the transitive reduction of the string overlap graph, the use of (generalized) edge multiplicity statistics for more accurate estimation of read copy counts, and the improved use of mate pairs and min-cost flow for supporting edge merging. The assemblies produced by SAGE for several short and medium-size genomes compared favourably with those of existing leading assemblers. SAGE benefits from innovations in almost every aspect of the assembly process: error correction of input reads, string-overlap graph construction, read copy counts estimation, overlap graph analysis and reduction, contig extraction, and scaffolding. We hope that these new ideas will help advance the current state-of-the-art in an essential area of research in genomics.

The C. elegans RSA complex localizes protein phosphatase 2A to centrosomes and regulates mitotic spindle assembly.

PubMed

Schlaitz, Anne-Lore; Srayko, Martin; Dammermann, Alexander; Quintin, Sophie; Wielsch, Natalie; MacLeod, Ian; de Robillard, Quentin; Zinke, Andrea; Yates, John R; Müller-Reichert, Thomas; Shevchenko, Andrei; Oegema, Karen; Hyman, Anthony A

2007-01-12

Microtubule behavior changes during the cell cycle and during spindle assembly. However, it remains unclear how these changes are regulated and coordinated. We describe a complex that targets the Protein Phosphatase 2A holoenzyme (PP2A) to centrosomes in C. elegans embryos. This complex includes Regulator of Spindle Assembly 1 (RSA-1), a targeting subunit for PP2A, and RSA-2, a protein that binds and recruits RSA-1 to centrosomes. In contrast to the multiple functions of the PP2A catalytic subunit, RSA-1 and RSA-2 are specifically required for microtubule outgrowth from centrosomes and for spindle assembly. The centrosomally localized RSA-PP2A complex mediates these functions in part by regulating two critical mitotic effectors: the microtubule destabilizer KLP-7 and the C. elegans regulator of spindle assembly TPXL-1. By regulating a subset of PP2A functions at the centrosome, the RSA complex could therefore provide a means of coordinating microtubule outgrowth from centrosomes and kinetochore microtubule stability during mitotic spindle assembly.

Launch and Assembly Reliability Analysis for Mars Human Space Exploration Missions

NASA Technical Reports Server (NTRS)

Cates, Grant R.; Stromgren, Chel; Cirillo, William M.; Goodliff, Kandyce E.

2013-01-01

NASA s long-range goal is focused upon human exploration of Mars. Missions to Mars will require campaigns of multiple launches to assemble Mars Transfer Vehicles in Earth orbit. Launch campaigns are subject to delays, launch vehicles can fail to place their payloads into the required orbit, and spacecraft may fail during the assembly process or while loitering prior to the Trans-Mars Injection (TMI) burn. Additionally, missions to Mars have constrained departure windows lasting approximately sixty days that repeat approximately every two years. Ensuring high reliability of launching and assembling all required elements in time to support the TMI window will be a key enabler to mission success. This paper describes an integrated methodology for analyzing and improving the reliability of the launch and assembly campaign phase. A discrete event simulation involves several pertinent risk factors including, but not limited to: manufacturing completion; transportation; ground processing; launch countdown; ascent; rendezvous and docking, assembly, and orbital operations leading up to TMI. The model accommodates varying numbers of launches, including the potential for spare launches. Having a spare launch capability provides significant improvement to mission success.

Internal combustion engine for natural gas compressor operation

DOEpatents

Hagen, Christopher L.; Babbitt, Guy; Turner, Christopher; Echter, Nick; Weyer-Geigel, Kristina

2016-04-19

This application concerns systems and methods for compressing natural gas with an internal combustion engine. In a representative embodiment, a system for compressing a gas comprises a reciprocating internal combustion engine including at least one piston-cylinder assembly comprising a piston configured to travel in a cylinder and to compress gas in the cylinder in multiple compression stages. The system can further comprise a first pressure tank in fluid communication with the piston-cylinder assembly to receive compressed gas from the piston-cylinder assembly until the first pressure tank reaches a predetermined pressure, and a second pressure tank in fluid communication with the piston-cylinder assembly and the first pressure tank. The second pressure tank can be configured to receive compressed gas from the piston-cylinder assembly until the second pressure tank reaches a predetermined pressure. When the first and second pressure tanks have reached the predetermined pressures, the first pressure tank can be configured to supply gas to the piston-cylinder assembly, and the piston can be configured to compress the gas supplied by the first pressure tank such that the compressed gas flows into the second pressure tank.

Metagenome assembly through clustering of next-generation sequencing data using protein sequences.

PubMed

Sim, Mikang; Kim, Jaebum

2015-02-01

The study of environmental microbial communities, called metagenomics, has gained a lot of attention because of the recent advances in next-generation sequencing (NGS) technologies. Microbes play a critical role in changing their environments, and the mode of their effect can be solved by investigating metagenomes. However, the difficulty of metagenomes, such as the combination of multiple microbes and different species abundance, makes metagenome assembly tasks more challenging. In this paper, we developed a new metagenome assembly method by utilizing protein sequences, in addition to the NGS read sequences. Our method (i) builds read clusters by using mapping information against available protein sequences, and (ii) creates contig sequences by finding consensus sequences through probabilistic choices from the read clusters. By using simulated NGS read sequences from real microbial genome sequences, we evaluated our method in comparison with four existing assembly programs. We found that our method could generate relatively long and accurate metagenome assemblies, indicating that the idea of using protein sequences, as a guide for the assembly, is promising. Copyright © 2015 Elsevier B.V. All rights reserved.

Ebola virus VP35 blocks stress granule assembly.

PubMed

Le Sage, Valerie; Cinti, Alessandro; McCarthy, Stephen; Amorim, Raquel; Rao, Shringar; Daino, Gian Luca; Tramontano, Enzo; Branch, Donald R; Mouland, Andrew J

2017-02-01

Stress granules (SGs) are dynamic cytoplasmic aggregates of translationally silenced mRNAs that assemble in response to environmental stress. SGs appear to play an important role in antiviral innate immunity and many viruses have evolved to block or subvert SGs components for their own benefit. Here, we demonstrate that intracellular Ebola virus (EBOV) replication and transcription-competent virus like particles (trVLP) infection does not lead to SG assembly but leads to a blockade to Arsenite-induced SG assembly. Moreover we show that EBOV VP35 represses the assembly of canonical and non-canonical SGs induced by a variety of pharmacological stresses. This SG blockade requires, at least in part, the C-terminal domain of VP35. Furthermore, results from our co-immunoprecipitation studies indicate that VP35 interacts with multiple SG components, including G3BP1, eIF3 and eEF2 through a stress- and RNA-independent mechanism. These data suggest a novel function for EBOV VP35 in the repression of SG assembly. Copyright © 2016 Elsevier Inc. All rights reserved.

The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum.

PubMed

Zimin, Aleksey V; Puiu, Daniela; Hall, Richard; Kingan, Sarah; Clavijo, Bernardo J; Salzberg, Steven L

2017-11-01

Common bread wheat, Triticum aestivum, has one of the most complex genomes known to science, with 6 copies of each chromosome, enormous numbers of near-identical sequences scattered throughout, and an overall haploid size of more than 15 billion bases. Multiple past attempts to assemble the genome have produced assemblies that were well short of the estimated genome size. Here we report the first near-complete assembly of T. aestivum, using deep sequencing coverage from a combination of short Illumina reads and very long Pacific Biosciences reads. The final assembly contains 15 344 693 583 bases and has a weighted average (N50) contig size of 232 659 bases. This represents by far the most complete and contiguous assembly of the wheat genome to date, providing a strong foundation for future genetic studies of this important food crop. We also report how we used the recently published genome of Aegilops tauschii, the diploid ancestor of the wheat D genome, to identify 4 179 762 575 bp of T. aestivum that correspond to its D genome components. © The Author 2017. Published by Oxford University Press.

Arabidopsis ARGONAUTE7 selects miR390 through multiple checkpoints during RISC assembly.

PubMed

Endo, Yayoi; Iwakawa, Hiro-oki; Tomari, Yukihide

2013-07-01

Plant ARGONAUTE7 (AGO7) assembles RNA-induced silencing complex (RISC) specifically with miR390 and regulates the auxin-signalling pathway via production of TAS3 trans-acting siRNAs (tasiRNAs). However, how AGO7 discerns miR390 among other miRNAs remains unclear. Here, we show that the 5' adenosine of miR390 and the central region of miR390/miR390* duplex are critical for the specific interaction with AGO7. Furthermore, despite the existence of mismatches in the seed and central regions of the duplex, cleavage of the miR390* strand is required for maturation of AGO7-RISC. These findings suggest that AGO7 uses multiple checkpoints to select miR390, thereby circumventing promiscuous tasiRNA production.

Rational Design of High-Number dsDNA Fragments Based on Thermodynamics for the Construction of Full-Length Genes in a Single Reaction.

PubMed

Birla, Bhagyashree S; Chou, Hui-Hsien

2015-01-01

Gene synthesis is frequently used in modern molecular biology research either to create novel genes or to obtain natural genes when the synthesis approach is more flexible and reliable than cloning. DNA chemical synthesis has limits on both its length and yield, thus full-length genes have to be hierarchically constructed from synthesized DNA fragments. Gibson Assembly and its derivatives are the simplest methods to assemble multiple double-stranded DNA fragments. Currently, up to 12 dsDNA fragments can be assembled at once with Gibson Assembly according to its vendor. In practice, the number of dsDNA fragments that can be assembled in a single reaction are much lower. We have developed a rational design method for gene construction that allows high-number dsDNA fragments to be assembled into full-length genes in a single reaction. Using this new design method and a modified version of the Gibson Assembly protocol, we have assembled 3 different genes from up to 45 dsDNA fragments at once. Our design method uses the thermodynamic analysis software Picky that identifies all unique junctions in a gene where consecutive DNA fragments are specifically made to connect to each other. Our novel method is generally applicable to most gene sequences, and can improve both the efficiency and cost of gene assembly.

A Theoretical and Experimental Study of DNA Self-assembly

NASA Astrophysics Data System (ADS)

Chandran, Harish

The control of matter and phenomena at the nanoscale is fast becoming one of the most important challenges of the 21st century with wide-ranging applications from energy and health care to computing and material science. Conventional top-down approaches to nanotechnology, having served us well for long, are reaching their inherent limitations. Meanwhile, bottom-up methods such as self-assembly are emerging as viable alternatives for nanoscale fabrication and manipulation. A particularly successful bottom up technique is DNA self-assembly where a set of carefully designed DNA strands form a nanoscale object as a consequence of specific, local interactions among the different components, without external direction. The final product of the self-assembly process might be a static nanostructure or a dynamic nanodevice that performs a specific function. Over the past two decades, DNA self-assembly has produced stunning nanoscale objects such as 2D and 3D lattices, polyhedra and addressable arbitrary shaped substrates, and a myriad of nanoscale devices such as molecular tweezers, computational circuits, biosensors and molecular assembly lines. In this dissertation we study multiple problems in the theory, simulations and experiments of DNA self-assembly. We extend the Turing-universal mathematical framework of self-assembly known as the Tile Assembly Model by incorporating randomization during the assembly process. This allows us to reduce the tile complexity of linear assemblies. We develop multiple techniques to build linear assemblies of expected length N using far fewer tile types than previously possible. We abstract the fundamental properties of DNA and develop a biochemical system, which we call meta-DNA, based entirely on strands of DNA as the only component molecule. We further develop various enzyme-free protocols to manipulate meta-DNA systems and provide strand level details along with abstract notations for these mechanisms. We simulate DNA circuits by providing detailed designs for local molecular computations that involve spatially contiguous molecules arranged on addressable substrates via enzyme-free DNA hybridization reaction cascades. We use the Visual DSD simulation software in conjunction with localized reaction rates obtained from biophysical modeling to create chemical reaction networks of localized hybridization circuits that are then model checked using the PRISM model checking software. We develop a DNA detection system employing the triggered self-assembly of a novel DNA dendritic nanostructure. Detection begins when a specific, single-stranded target DNA strand triggers a hybridization chain reaction between two distinct DNA hairpins. Each hairpin opens and hybridizes up to two copies of the other, and hence each layer of the growing dendritic nanostructure can in principle accommodate an exponentially increasing number of cognate molecules, generating a nanostructure with high molecular weight. We build linear activatable assemblies employing a novel protection/deprotection strategy to strictly enforce the direction of tiling assembly growth to ensure the robustness of the assembly process. Our system consists of two tiles that can form a linear co-polymer. These tiles, which are initially protected such that they do not react with each other, can be activated to form linear co-polymers via the use of a strand displacing enzyme.

Stackable Form-Factor Peripheral Component Interconnect Device and Assembly

NASA Technical Reports Server (NTRS)

Somervill, Kevin M. (Inventor); Ng, Tak-kwong (Inventor); Torres-Pomales, Wilfredo (Inventor); Malekpour, Mahyar R. (Inventor)

2013-01-01

A stackable form-factor Peripheral Component Interconnect (PCI) device can be configured as a host controller or a master/target for use on a PCI assembly. PCI device may comprise a multiple-input switch coupled to a PCI bus, a multiplexor coupled to the switch, and a reconfigurable device coupled to one of the switch and multiplexor. The PCI device is configured to support functionality from power-up, and either control function or add-in card function.

Layer-by-layer-assembled healable antifouling films.

PubMed

Chen, Dongdong; Wu, Mingda; Li, Bochao; Ren, Kefeng; Cheng, Zhongkai; Ji, Jian; Li, Yang; Sun, Junqi

2015-10-21

Healable antifouling films are fabricated by the exponential layer-by-layer assembly of PEGylated branched poly(ethylenimine) and hyaluronic acid followed by post-crosslinking. The antifouling function originates from the grafted PEG and the extremely soft nature of the films. The rapid and multiple healing of damaged antifouling functions caused by cuts and scratches can be readily achieved by immersing the films in normal saline solution. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multiple lead seal assembly for a liquid-metal-cooled fast-breeder nuclear reactor

DOEpatents

Hutter, Ernest; Pardini, John A.

1977-03-15

A reusable multiple lead seal assembly provides leak-free passage of stainless-steel-clad instrument leads through the cover on the primary tank of a liquid-metal-cooled fast-breeder nuclear reactor. The seal isolates radioactive argon cover gas and sodium vapor within the primary tank from the exterior atmosphere and permits reuse of the assembly and the stainless-steel-clad instrument leads. Leads are placed in flutes in a seal body, and a seal shell is then placed around the seal body. Circumferential channels in the body and inner surface of the shell are contiguous and together form a conduit which intersects each of the flutes, placing them in communication with a port through the wall of the seal shell. Liquid silicone rubber sealant is injected into the flutes through the port and conduit; the sealant fills the space in the flutes not occupied by the leads themselves and dries to a rubbery hardness. A nut, threaded onto a portion of the seal body not covered by the seal shell, jacks the body out of the shell and shears the sealant without damage to the body, shell, or leads. The leads may then be removed from the body. The sheared sealant is cleaned from the body, leads, and shell and the assembly may then be reused with the same or different leads.

Method of reducing multipole content in a conductor assembly during manufacture

DOEpatents

Meinke, Rainer [Melbourne, FL

2011-08-09

A method for manufacture of a conductor assembly. The assembly is of the type which, when conducting current, generates a magnetic field or in which, in the presence of a changing magnetic field, a voltage is induced. In an example embodiment one or more first coil rows are formed. The assembly has multiple coil rows about an axis with outer coil rows formed about inner coil rows. A determination is made of deviations from specifications associated with the formed one or more first coil rows. One or more deviations correspond to a magnitude of a multipole field component which departs from a field specification. Based on the deviations, one or more wiring patterns are generated for one or more second coil rows to be formed about the one or more first coil rows. The one or more second coil rows are formed in the assembly. The magnitude of each multipole field component that departs from the field specification is offset.

Platform technology for scalable assembly of instantaneously functional mosaic tissues

PubMed Central

Zhang, Boyang; Montgomery, Miles; Davenport-Huyer, Locke; Korolj, Anastasia; Radisic, Milica

2015-01-01

Engineering mature tissues requires a guided assembly of cells into organized three-dimensional (3D) structures with multiple cell types. Guidance is usually achieved by microtopographical scaffold cues or by cell-gel compaction. The assembly of individual units into functional 3D tissues is often time-consuming, relying on cell ingrowth and matrix remodeling, whereas disassembly requires an invasive method that includes either matrix dissolution or mechanical cutting. We invented Tissue-Velcro, a bio-scaffold with a microfabricated hook and loop system. The assembly of Tissue-Velcro preserved the guided cell alignment realized by the topographical features in the 2D scaffold mesh and allowed for the instant establishment of coculture conditions by spatially defined stacking of cardiac cell layers or through endothelial cell coating. The assembled cardiac 3D tissue constructs were immediately functional as measured by their ability to contract in response to electrical field stimulation. Facile, on-demand tissue disassembly was demonstrated while preserving the structure, physical integrity, and beating function of individual layers. PMID:26601234

Method of reducing multipole content in a conductor assembly during manufacture

DOEpatents

Meinke, Rainer

2013-08-20

A method for manufacture of a conductor assembly. The assembly is of the type which, when conducting current, generates a magnetic field or in which, in the presence of a changing magnetic field, a voltage is induced. In an example embodiment one or more first coil rows are formed. The assembly has multiple coil rows about an axis with outer coil rows formed about inner coil rows. A determination is made of deviations from specifications associated with the formed one or more first coil rows. One or more deviations correspond to a magnitude of a multipole field component which departs from a field specification. Based on the deviations, one or more wiring patterns are generated for one or more second coil rows to be formed about the one or more first coil rows. The one or more second coil rows are formed in the assembly. The magnitude of each multipole field component that departs from the field specification is offset.

Endocytosis-dependent coordination of multiple actin regulators is required for wound healing

PubMed Central

Matsubayashi, Yutaka; Coulson-Gilmer, Camilla

2015-01-01

The ability to heal wounds efficiently is essential for life. After wounding of an epithelium, the cells bordering the wound form dynamic actin protrusions and/or a contractile actomyosin cable, and these actin structures drive wound closure. Despite their importance in wound healing, the molecular mechanisms that regulate the assembly of these actin structures at wound edges are not well understood. In this paper, using Drosophila melanogaster embryos, we demonstrate that Diaphanous, SCAR, and WASp play distinct but overlapping roles in regulating actin assembly during wound healing. Moreover, we show that endocytosis is essential for wound edge actin assembly and wound closure. We identify adherens junctions (AJs) as a key target of endocytosis during wound healing and propose that endocytic remodeling of AJs is required to form “signaling centers” along the wound edge that control actin assembly. We conclude that coordination of actin assembly, AJ remodeling, and membrane traffic is required for the construction of a motile leading edge during wound healing. PMID:26216900

Programming Hierarchical Self-Assembly of Patchy Particles into Colloidal Crystals via Colloidal Molecules.

PubMed

Morphew, Daniel; Shaw, James; Avins, Christopher; Chakrabarti, Dwaipayan

2018-03-27

Colloidal self-assembly is a promising bottom-up route to a wide variety of three-dimensional structures, from clusters to crystals. Programming hierarchical self-assembly of colloidal building blocks, which can give rise to structures ordered at multiple levels to rival biological complexity, poses a multiscale design problem. Here we explore a generic design principle that exploits a hierarchy of interaction strengths and employ this design principle in computer simulations to demonstrate the hierarchical self-assembly of triblock patchy colloidal particles into two distinct colloidal crystals. We obtain cubic diamond and body-centered cubic crystals via distinct clusters of uniform size and shape, namely, tetrahedra and octahedra, respectively. Such a conceptual design framework has the potential to reliably encode hierarchical self-assembly of colloidal particles into a high level of sophistication. Moreover, the design framework underpins a bottom-up route to cubic diamond colloidal crystals, which have remained elusive despite being much sought after for their attractive photonic applications.

Multilayer block copolymer meshes by orthogonal self-assembly

PubMed Central

Tavakkoli K. G., Amir; Nicaise, Samuel M.; Gadelrab, Karim R.; Alexander-Katz, Alfredo; Ross, Caroline A.; Berggren, Karl K.

2016-01-01

Continued scaling-down of lithographic-pattern feature sizes has brought templated self-assembly of block copolymers (BCPs) into the forefront of nanofabrication research. Technologies now exist that facilitate significant control over otherwise unorganized assembly of BCP microdomains to form both long-range and locally complex monolayer patterns. In contrast, the extension of this control into multilayers or 3D structures of BCP microdomains remains limited, despite the possible technological applications in next-generation devices. Here, we develop and analyse an orthogonal self-assembly method in which multiple layers of distinct-molecular-weight BCPs naturally produce nanomesh structures of cylindrical microdomains without requiring layer-by-layer alignment or high-resolution lithographic templating. The mechanisms for orthogonal self-assembly are investigated with both experiment and simulation, and we determine that the control over height and chemical preference of templates are critical process parameters. The method is employed to produce nanomeshes with the shapes of circles and Y-intersections, and is extended to produce three layers of orthogonally oriented cylinders. PMID:26796218

Self-assembly and transformation of hybrid nano-objects and nanostructures under equilibrium and non-equilibrium conditions

NASA Astrophysics Data System (ADS)

Mann, Stephen

2009-10-01

Understanding how chemically derived processes control the construction and organization of matter across extended and multiple length scales is of growing interest in many areas of materials research. Here we review present equilibrium and non-equilibrium self-assembly approaches to the synthetic construction of discrete hybrid (inorganic-organic) nano-objects and higher-level nanostructured networks. We examine a range of synthetic modalities under equilibrium conditions that give rise to integrative self-assembly (supramolecular wrapping, nanoscale incarceration and nanostructure templating) or higher-order self-assembly (programmed/directed aggregation). We contrast these strategies with processes of transformative self-assembly that use self-organizing media, reaction-diffusion systems and coupled mesophases to produce higher-level hybrid structures under non-equilibrium conditions. Key elements of the constructional codes associated with these processes are identified with regard to existing theoretical knowledge, and presented as a heuristic guideline for the rational design of hybrid nano-objects and nanomaterials.

BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts.

PubMed

Yang, Kun; Stracquadanio, Giovanni; Luo, Jingchuan; Boeke, Jef D; Bader, Joel S

2016-03-15

Combinatorial assembly of DNA elements is an efficient method for building large-scale synthetic pathways from standardized, reusable components. These methods are particularly useful because they enable assembly of multiple DNA fragments in one reaction, at the cost of requiring that each fragment satisfies design constraints. We developed BioPartsBuilder as a biologist-friendly web tool to design biological parts that are compatible with DNA combinatorial assembly methods, such as Golden Gate and related methods. It retrieves biological sequences, enforces compliance with assembly design standards and provides a fabrication plan for each fragment. BioPartsBuilder is accessible at http://public.biopartsbuilder.org and an Amazon Web Services image is available from the AWS Market Place (AMI ID: ami-508acf38). Source code is released under the MIT license, and available for download at https://github.com/baderzone/biopartsbuilder joel.bader@jhu.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

An investigation of Hebbian phase sequences as assembly graphs

PubMed Central

Almeida-Filho, Daniel G.; Lopes-dos-Santos, Vitor; Vasconcelos, Nivaldo A. P.; Miranda, José G. V.; Tort, Adriano B. L.; Ribeiro, Sidarta

2014-01-01

Hebb proposed that synapses between neurons that fire synchronously are strengthened, forming cell assemblies and phase sequences. The former, on a shorter scale, are ensembles of synchronized cells that function transiently as a closed processing system; the latter, on a larger scale, correspond to the sequential activation of cell assemblies able to represent percepts and behaviors. Nowadays, the recording of large neuronal populations allows for the detection of multiple cell assemblies. Within Hebb's theory, the next logical step is the analysis of phase sequences. Here we detected phase sequences as consecutive assembly activation patterns, and then analyzed their graph attributes in relation to behavior. We investigated action potentials recorded from the adult rat hippocampus and neocortex before, during and after novel object exploration (experimental periods). Within assembly graphs, each assembly corresponded to a node, and each edge corresponded to the temporal sequence of consecutive node activations. The sum of all assembly activations was proportional to firing rates, but the activity of individual assemblies was not. Assembly repertoire was stable across experimental periods, suggesting that novel experience does not create new assemblies in the adult rat. Assembly graph attributes, on the other hand, varied significantly across behavioral states and experimental periods, and were separable enough to correctly classify experimental periods (Naïve Bayes classifier; maximum AUROCs ranging from 0.55 to 0.99) and behavioral states (waking, slow wave sleep, and rapid eye movement sleep; maximum AUROCs ranging from 0.64 to 0.98). Our findings agree with Hebb's view that assemblies correspond to primitive building blocks of representation, nearly unchanged in the adult, while phase sequences are labile across behavioral states and change after novel experience. The results are compatible with a role for phase sequences in behavior and cognition. PMID:24782715

The Autographa californica Multiple Nucleopolyhedrovirus ac83 Gene Contains a cis-Acting Element That Is Essential for Nucleocapsid Assembly.

PubMed

Huang, Zhihong; Pan, Mengjia; Zhu, Silei; Zhang, Hao; Wu, Wenbi; Yuan, Meijin; Yang, Kai

2017-03-01

Baculoviridae is a family of insect-specific viruses that have a circular double-stranded DNA genome packaged within a rod-shaped capsid. The mechanism of baculovirus nucleocapsid assembly remains unclear. Previous studies have shown that deletion of the ac83 gene of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) blocks viral nucleocapsid assembly. Interestingly, the ac83 -encoded protein Ac83 is not a component of the nucleocapsid, implying a particular role for ac83 in nucleocapsid assembly that may be independent of its protein product. To examine this possibility, Ac83 synthesis was disrupted by insertion of a chloramphenicol resistance gene into its coding sequence or by deleting its promoter and translation start codon. Both mutants produced progeny viruses normally, indicating that the Ac83 protein is not required for nucleocapsid assembly. Subsequently, complementation assays showed that the production of progeny viruses required the presence of ac83 in the AcMNPV genome instead of its presence in trans Therefore, we reasoned that ac83 is involved in nucleocapsid assembly via an internal cis -acting element, which we named the nucleocapsid assembly-essential element (NAE). The NAE was identified to lie within nucleotides 1651 to 1850 of ac83 and had 8 conserved A/T-rich regions. Sequences homologous to the NAE were found only in alphabaculoviruses and have a conserved positional relationship with another essential cis -acting element that was recently identified. The identification of the NAE may help to connect the data of viral cis -acting elements and related proteins in the baculovirus nucleocapsid assembly, which is important for elucidating DNA-protein interaction events during this process. IMPORTANCE Virus nucleocapsid assembly usually requires specific cis -acting elements in the viral genome for various processes, such as the selection of the viral genome from the cellular nucleic acids, the cleavage of concatemeric viral genome replication intermediates, and the encapsidation of the viral genome into procapsids. In linear DNA viruses, such elements generally locate at the ends of the viral genome; however, most of these elements remain unidentified in circular DNA viruses (including baculovirus) due to their circular genomic conformation. Here, we identified a nucleocapsid assembly-essential element in the AcMNPV (the archetype of baculovirus) genome. This finding provides an important reference for studies of nucleocapsid assembly-related elements in baculoviruses and other circular DNA viruses. Moreover, as most of the previous studies of baculovirus nucleocapsid assembly have been focused on viral proteins, our study provides a novel entry point to investigate this mechanism via cis -acting elements in the viral genome. Copyright © 2017 American Society for Microbiology.

Simultaneous detection of multiple DNA targets by integrating dual-color graphene quantum dot nanoprobes and carbon nanotubes.

PubMed

Qian, Zhaosheng; Shan, Xiaoyue; Chai, Lujing; Chen, Jianrong; Feng, Hui

2014-12-01

Simultaneous detection of multiple DNA targets was achieved based on a biocompatible graphene quantum dots (GQDs) and carbon nanotubes (CNTs) platform through spontaneous assembly between dual-color GQD-based probes and CNTs and subsequently self-recognition between DNA probes and targets. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Progress Toward Overset-Grid Moving Body Capability for USM3D Unstructured Flow Solver

NASA Technical Reports Server (NTRS)

Pandyna, Mohagna J.; Frink, Neal T.; Noack, Ralph W.

2005-01-01

A static and dynamic Chimera overset-grid capability is added to an established NASA tetrahedral unstructured parallel Navier-Stokes flow solver, USM3D. Modifications to the solver primarily consist of a few strategic calls to the Donor interpolation Receptor Transaction library (DiRTlib) to facilitate communication of solution information between various grids. The assembly of multiple overlapping grids into a single-zone composite grid is performed by the Structured, Unstructured and Generalized Grid AssembleR (SUGGAR) code. Several test cases are presented to verify the implementation, assess overset-grid solution accuracy and convergence relative to single-grid solutions, and demonstrate the prescribed relative grid motion capability.

Cryogenic Optical Performance of a Lightweighted Mirror Assembly for Future Space Astronomical Telescopes: Correlating Optical Test Results and Thermal Optical Model

NASA Technical Reports Server (NTRS)

Eng, Ron; Arnold, William R.; Baker, Marcus A.; Bevan, Ryan M.; Burdick, Gregory; Effinger, Michael R.; Gaddy, Darrell E.; Goode, Brian K.; Hanson, Craig; Hogue, William D.;

Supramolecular catalysis beyond enzyme mimics.

PubMed

Meeuwissen, Jurjen; Reek, Joost N H

2010-08-01

Supramolecular catalysis - the assembly of catalyst species by harnessing multiple weak intramolecular interactions - has, until recently, been dominated by enzyme-inspired approaches. Such approaches often attempt to create an enzyme-like 'active site' and have concentrated on reactions similar to those catalysed by enzymes themselves. Here, we discuss the application of supramolecular assembly to the more traditional transition metal catalysis and to small-molecule organocatalysis. The modularity of self-assembled multicomponent catalysts means that a relatively small pool of catalyst components can provide rapid access to a large number of catalysts that can be evaluated for industrially relevant reactions. In addition, we discuss how catalyst-substrate interactions can be tailored to direct substrates along particular reaction paths and selectivities.

Ancient techniques for new materials

NASA Technical Reports Server (NTRS)

2000-01-01

NASA is looking to biological techniques that are millions of years old to help it develop new materials and technologies for the 21st century. Sponsored by NASA, Jeffrey Brinker of the University of New Mexico is studying how multiple elements can assemble themselves into a composite material that is clear, tough, and impermeable. His research is based on the model of how an abalone builds the nacre, also called mother-of-pearl, inside its shell. Strong thin coatings, or lamellae, in Brinker's research are formed when objects are dip-coated. Evaporation drives the self-assembly of molecular aggregates (micelles) of surfactant, soluble silica, and organic monomers and their further self-organization into layered organic and inorganic assemblies.

Multilayer checkpoints for microRNA authenticity during RISC assembly

PubMed Central

Kawamata, Tomoko; Yoda, Mayuko; Tomari, Yukihide

2011-01-01

MicroRNAs (miRNAs) function through the RNA-induced silencing complex (RISC), which contains an Argonaute (Ago) protein at the core. RISC assembly follows a two-step pathway: miRNA/miRNA* duplex loading into Ago, and separation of the two strands within Ago. Here we show that the 5′ phosphate of the miRNA strand is essential for duplex loading into Ago, whereas the preferred 5′ nucleotide of the miRNA strand and the base-pairing status in the seed region and the middle of the 3′ region function as additive anchors to Ago. Consequently, the miRNA authenticity is inspected at multiple steps during RISC assembly. PMID:21738221

Synthesis of Polyheteroaromatic Compounds via Rhodium-Catalyzed Multiple C-H Bond Activation and Oxidative Annulation.

PubMed

Peng, Shiyong; Liu, Suna; Zhang, Sai; Cao, Shengyu; Sun, Jiangtao

2015-10-16

Polyheteroaromatic compounds are potential optoelectronic conjugated materials due to their electro- and photochemical properties. Transition-metal-catalyzed multiple C-H activation and sequential oxidative annulation allows rapidly assembling of those compounds from readily available starting materials. A rhodium-catalyzed cascade oxidative annulation of β-enamino esters or 4-aminocoumarins with internal alkynes is described to access those compounds, featuring multiple C-H/N-H bond cleavages and sequential C-C/C-N bond formations in one pot.

Multiple Site-Directed and Saturation Mutagenesis by the Patch Cloning Method.

PubMed

Taniguchi, Naohiro; Murakami, Hiroshi

2017-01-01

Constructing protein-coding genes with desired mutations is a basic step for protein engineering. Herein, we describe a multiple site-directed and saturation mutagenesis method, termed MUPAC. This method has been used to introduce multiple site-directed mutations in the green fluorescent protein gene and in the moloney murine leukemia virus reverse transcriptase gene. Moreover, this method was also successfully used to introduce randomized codons at five desired positions in the green fluorescent protein gene, and for simple DNA assembly for cloning.

Crystal structure of the human cytosolic sialidase Neu2. Evidence for the dynamic nature of substrate recognition.

PubMed

Chavas, Leonard M G; Tringali, Cristina; Fusi, Paola; Venerando, Bruno; Tettamanti, Guido; Kato, Ryuichi; Monti, Eugenio; Wakatsuki, Soichi

2005-01-07

Gangliosides play key roles in cell differentiation, cell-cell interactions, and transmembrane signaling. Sialidases hydrolyze sialic acids to produce asialo compounds, which is the first step of degradation processes of glycoproteins and gangliosides. Sialidase involvement has been implicated in some lysosomal storage disorders such as sialidosis and galactosialidosis. Neu2 is a recently identified human cytosolic sialidase. Here we report the first high resolution x-ray structures of mammalian sialidase, human Neu2, in its apo form and in complex with an inhibitor, 2-deoxy-2,3-dehydro-N-acetylneuraminic acid (DANA). The structure shows the canonical six-blade beta-propeller observed in viral and bacterial sialidases with its active site in a shallow crevice. In the complex structure, the inhibitor lies in the catalytic crevice surrounded by ten amino acids. In particular, the arginine triad, conserved among sialidases, aids in the proper positioning of the carboxylate group of DANA within the active site region. The tyrosine residue, Tyr(334), conserved among mammalian and bacterial sialidases as well as in viral neuraminidases, facilitates the enzymatic reaction by stabilizing a putative carbonium ion in the transition state. The loops containing Glu(111) and the catalytic aspartate Asp(46) are disordered in the apo form but upon binding of DANA become ordered to adopt two short alpha-helices to cover the inhibitor, illustrating the dynamic nature of substrate recognition. The N-acetyl and glycerol moieties of DANA are recognized by Neu2 residues not shared by bacterial sialidases and viral neuraminidases, which can be regarded as a key structural difference for potential drug design against bacteria, influenza, and other viruses.

Biological responses of Crested and Least auklets to volcanic destruction of nesting habitat in the Aleutian Islands, Alaska

USGS Publications Warehouse

Drew, Gary S.; Piatt, John F.; Williams, Jeffrey C.

2018-01-01

Crested Auklets (Aethia cristatella) and Least Auklets (A. pusilla) are crevice-nesting birds that breed in large mixed colonies at relatively few sites in the Aleutian Island archipelago, Bering Sea, Gulf of Alaska, and Sea of Okhotsk. Many of these colonies are located on active volcanic islands. The eruption of Kasatochi volcano, in the central Aleutians, on August 7, 2008, completely buried all crevice-nesting seabird habitat on the island. This provided an opportunity to examine the response of a large, mixed auklet colony to a major geological disturbance. Time-lapse imagery of nesting habitat indicated that both species returned to the largest pre-eruption colony site for several years, but subsequently abandoned it within 5 yr after the eruption. In 2010, a rockfall site in a cove north of the old colony site began to accumulate talus, and groups of auklets were observed using the site in 2011. Use of the new colony appeared to coincide with the abandonment of the old colony site by both species, though surface counts suggested that Least Auklets shifted to the new colony sooner than Crested Auklets. At-sea surveys of seabirds before and after the eruption indicated that both Crested and Least auklets shifted their at-sea distributions from the waters around Kasatochi Island to nearby Koniuji Island. In combination, at-sea counts and colony time-lapse imagery indicated that Crested and Least auklets using Kasatochi responded to the volcanic disturbance and complete loss of nesting habitat at the main colony on Kasatochi with dispersal either to newly created habitat on Kasatochi or to an alternate colony on a nearby island.

In situ nano- to microscopic imaging and growth mechanism of electrochemical dissolution (e.g., corrosion) of a confined metal surface

PubMed Central

Merola, C.; Cheng, H.-W.; Schwenzfeier, K.; Kristiansen, K.; Chen, Y.-J.; Dobbs, H. A.; Valtiner, M.

2017-01-01

Reactivity in confinement is central to a wide range of applications and systems, yet it is notoriously difficult to probe reactions in confined spaces in real time. Using a modified electrochemical surface forces apparatus (EC-SFA) on confined metallic surfaces, we observe in situ nano- to microscale dissolution and pit formation (qualitatively similar to previous observation on nonmetallic surfaces, e.g., silica) in well-defined geometries in environments relevant to corrosion processes. We follow “crevice corrosion” processes in real time in different pH-neutral NaCl solutions and applied surface potentials of nickel (vs. Ag|AgCl electrode in solution) for the mica–nickel confined interface of total area ∼0.03 mm2. The initial corrosion proceeds as self-catalyzed pitting, visualized by the sudden appearance of circular pits with uniform diameters of 6–7 μm and depth ∼2–3 nm. At concentrations above 10 mM NaCl, pitting is initiated at the outer rim of the confined zone, while below 10 mM NaCl, pitting is initiated inside the confined zone. We compare statistical analysis of growth kinetics and shape evolution of individual nanoscale deep pits with estimates from macroscopic experiments to study initial pit growth and propagation. Our data and experimental techniques reveal a mechanism that suggests initial corrosion results in formation of an aggressive interfacial electrolyte that rapidly accelerates pitting, similar to crack initiation and propagation within the confined area. These results support a general mechanism for nanoscale material degradation and dissolution (e.g., crevice corrosion) of polycrystalline nonnoble metals, alloys, and inorganic materials within confined interfaces. PMID:28827338

Comparative skull anatomy of terrestrial and crevice-dwelling Trachylepis skinks (Squamata: Scincidae) with a survey of resources in scincid cranial osteology.

PubMed

Paluh, Daniel J; Bauer, Aaron M

2017-01-01

Skinks account for more than 25% of all lizard species; however, representatives of fewer than a quarter of all species have been characterized osteologically. All but a few of the available cranial descriptions concentrate solely on characters that can be seen externally on the intact skull. Mabuyid skinks of the genus Trachylepis are the dominant, fully limbed skinks in Sub-Saharan Africa, and nearly all species have the same generalized body plan. Although a few rock crevice-dwelling species possess slight body depression, extreme dorsoventral depression is observed only in Trachylepis laevis. We investigated the detailed skull anatomy of three Trachylepis skinks (T. laevis, T. sulcata, and T. gonwouoi, a recently described species allied to T. affinis) using high-resolution X-ray micro-computed tomography. Our goals were to review the scincid cranial osteology literature in a phylogenetic context, provide a detailed anatomical atlas for the mabuyid lineage, and investigate the morphological adaptations of the highly modified T. laevis. Our results demonstrate that there is significant morphological variation between these three taxa, including the loss and fusion of structures, as well as changes in the shape, scale, and relationship between individual elements. Trachylepis laevis possesses several osteological modifications that have produced a reducton in head depth that are likely functional consequences of extreme rupicolous habits, including a flat skull roof, many strongly recumbent elements, and a depressed neurocranium.We hypothesize these modifications may correspond to descreased bite force and increased capabilities of cranial kinesis. Our study is the first element-by-element description of a skink using computed tomography technology.

Basking and torpor in a rock-dwelling desert marsupial: survival strategies in a resource-poor environment.

PubMed

Geiser, Fritz; Pavey, Chris R

2007-11-01

Australian deserts are characterized by unpredictability, low primary productivity, and high temperature fluctuations. Despite these adverse conditions the diversity of small insectivorous marsupials of the family Dasyuridae is surprisingly high. We quantified the thermal biology of the dasyurid Pseudantechinus madonnellensis (body mass approximately 30 g) in the wild to gain some understanding of whether the success of dasyurids in the arid zone may be related to some extent to their use of energy conservation strategies. In winter, most free-ranging Pseudantechinus frequently (58.3% of 131 animal days) entered daily torpor after midnight (mean 0157 hours) in rock crevices when outside ambient temperatures (T (a)) were low. Most animals remained torpid until the next morning when they moved while still torpid from rock crevices to sun-exposed basking sites. We visually observed basking during rewarming from torpor (mean commencement at 0943 hours) at body temperatures (T (b)) as low as 19.3 degrees C when radiant heat was high and T (a) was rising. Basking continued for the rest of the day. Torpor use was not strongly correlated with T (a), but the temporal organization of daily torpor and activity were apparently linked to the thermal characteristics of basking sites. Our study suggests that by frequently employing daily torpor and basking and by appropriately coordinating their thermal biology with that of specific locations in their environment, Pseudantechinus can reduce daily energy expenditure and thus can live and reproduce in a challenging environment. It is likely that the success of other small dasyurids and perhaps many other small mammals living in deserts is linked to employment of torpor and basking for energy conservation.

Total reflection X-ray fluorescence analysis of oral fluids of women affected by osteoporosis and osteopenia

NASA Astrophysics Data System (ADS)

Sánchez, Héctor Jorge; Valentinuzzi, María Cecilia; Grenón, Miram; Abraham, José

2008-12-01

Osteoporosis is a disease characterized by low bone mass and microarchitectural deterioration of bone tissue, leading to bone fragility and an increased susceptibility to fractures; the early stage of decreased bone density is called osteopenia. More than 200 million people are affected and about 50% of post-menopausic women are expected to develop the disease. Osteoporosis, osteopenia and periodontal disease have in common several risk factors, being hyperthyroidism and smoking habits the most important ones. There is scarce information in the literature about the association between periodontal disease and osteoporosis and/or osteopenia. Some works suggest that osteoporotic women are susceptible to a higher loss of periodontal insertion, alveolar bones, and teeth. Thirty adult post-menopausic women were studied; some of them were healthy (control group) and the rest of them were undergoing some stage of osteoporosis or osteopenia. All the subjects were healthy, non-smokers, not having dental implants, and with communitarian periodontal index higher than 1(CPI > 1). Samples of saliva and gingival crevice fluid were extracted with calibrated micro-capillaries and deposited on Si reflectors. Known amounts of Ga were added to the samples in order to act as internal standard for quantification by the total reflection x-ray fluorescence technique. Experimental concentrations of several elements (P, S, Cl, K, Ca, Cr, Fe, NI, Cu, and Zn) were determined. The concentration of some elements in saliva showed different behavior as compared to gingival crevice fluid. Some critical elements of bone composition, such as Ca and Zn, present very distinguishable behavior. Improvements in the statistics are required for a better assessment of a routine method and to establish some correlation with periodontal disease. TXRF seems to be a promising method to evaluate the evolution of osteoporosis.

Multi-locus DNA sequence data reveal a history of deep cryptic vicariance and habitat-driven convergence in the desert night lizard Xantusia vigilis species complex (Squamata: Xantusiidae).

PubMed

Leavitt, Dean H; Bezy, Robert L; Crandall, Keith A; Sites, Jack W

2007-11-01

The lizard genus Xantusia of southwestern North America has received recent attention in relation to delimiting species. Using more than 500 lizards from 156 localities, we further test hypothesized species boundaries and clarify phylogeographical patterns, particularly in regions of potential secondary contact. We sequenced the entire mitochondrial cytochrome b gene for every lizard in the study, plus a second mitochondrial DNA (mtDNA) region and two nuclear introns for subsets of the total sample. Phylogenetic analyses of the mtDNA recover a well-resolved, novel hypothesis for species in the Xantusia vigilis complex. The nuclear DNA (nDNA) data provide independent support for the recognition of X. arizonae, X. bezyi and X. wigginsi. Differences between the respective mtDNA and nDNA topologies result from either the effects of lineage sorting or ancient introgression. Nuclear data confirm the inference that some populations of X. vigilis in northwestern Arizona converged on rock-crevice-dwelling morphology and are not X. arizonae with an introgressed X. vigilis mtDNA genome. The historical independence of ancient cryptic lineages of Xantusia in southern California is also corroborated, though limited introgression is detected. Our proposed biogeographical scenario indicates that diversification of this group was driven by vicariance beginning in the late Miocene. Additionally, Pleistocene climatical changes influenced Xantusia distribution, and the now inhospitable Colorado Desert previously supported night lizard presence. The current taxonomy of the group likely underestimates species diversity within the group, and our results collectively show that while convergence on the rock-crevice-dwelling morphology is one hallmark of Xantusia evolution, morphological stasis is paradoxically another.

Mapping the membrane-aqueous border for the voltage-sensing domain of a potassium channel.

PubMed

Neale, Edward J; Rong, Honglin; Cockcroft, Christopher J; Sivaprasadarao, Asipu

2007-12-28

Voltage-sensing domains (VSDs) play diverse roles in biology. As integral components, they can detect changes in the membrane potential of a cell and couple these changes to activity of ion channels and enzymes. As independent proteins, homologues of the VSD can function as voltage-dependent proton channels. To sense voltage changes, the positively charged fourth transmembrane segment, S4, must move across the energetically unfavorable hydrophobic core of the bilayer, which presents a barrier to movement of both charged species and protons. To reduce the barrier to S4 movement, it has been suggested that aqueous crevices may penetrate the protein, reducing the extent of total movement. To investigate this hypothesis in a system containing fully functional channels in a native environment with an intact membrane potential, we have determined the contour of the membrane-aqueous border of the VSD of KvAP in Escherichia coli by examining the chemical accessibility of introduced cysteines. The results revealed the contour of the membrane-aqueous border of the VSD in its activated conformation. The water-inaccessible regions of S1 and S2 correspond to the standard width of the membrane bilayer (~28 A), but those of S3 and S4 are considerably shorter (> or = 40%), consistent with aqueous crevices pervading both the extracellular and intracellular ends. One face of S3b and the entire S3a were water-accessible, reducing the water-inaccessible region of S3 to just 10 residues, significantly shorter than for S4. The results suggest a key role for S3 in reducing the distance S4 needs to move to elicit gating.

Comparative skull anatomy of terrestrial and crevice-dwelling Trachylepis skinks (Squamata: Scincidae) with a survey of resources in scincid cranial osteology

PubMed Central

Bauer, Aaron M.

2017-01-01

Skinks account for more than 25% of all lizard species; however, representatives of fewer than a quarter of all species have been characterized osteologically. All but a few of the available cranial descriptions concentrate solely on characters that can be seen externally on the intact skull. Mabuyid skinks of the genus Trachylepis are the dominant, fully limbed skinks in Sub-Saharan Africa, and nearly all species have the same generalized body plan. Although a few rock crevice-dwelling species possess slight body depression, extreme dorsoventral depression is observed only in Trachylepis laevis. We investigated the detailed skull anatomy of three Trachylepis skinks (T. laevis, T. sulcata, and T. gonwouoi, a recently described species allied to T. affinis) using high-resolution X-ray micro-computed tomography. Our goals were to review the scincid cranial osteology literature in a phylogenetic context, provide a detailed anatomical atlas for the mabuyid lineage, and investigate the morphological adaptations of the highly modified T. laevis. Our results demonstrate that there is significant morphological variation between these three taxa, including the loss and fusion of structures, as well as changes in the shape, scale, and relationship between individual elements. Trachylepis laevis possesses several osteological modifications that have produced a reducton in head depth that are likely functional consequences of extreme rupicolous habits, including a flat skull roof, many strongly recumbent elements, and a depressed neurocranium.We hypothesize these modifications may correspond to descreased bite force and increased capabilities of cranial kinesis. Our study is the first element-by-element description of a skink using computed tomography technology. PMID:28902864

The distribution of chlorpyrifos following a crack and crevice type application in the US EPA Indoor Air Quality Research House

NASA Astrophysics Data System (ADS)

Stout, D. M.; Mason, M. A.

A study was conducted in the US EPA Indoor Air Quality (IAQ) Research House to determine the spatial and temporal distribution of chlorpyrifos following a professional crack and crevice application in the kitchen. Following the application, measurements were made in the kitchen, den and master bedroom over 21 days. Airborne concentrations were collected using both polyurethane foam (PUF) and the OSHA versatile sampler composed of XAD and PUF media located in tandem. Measured airborne concentrations were similar for the two samplers and were higher in the three rooms following the application. The highest measured concentrations were reached during the initial 24-h following application; concentrations subsequently declined over the 21-day study period to levels slightly above background. Spatial and temporal distributions onto surfaces were measured using 10-cm 2 rayon deposition coupons located on the floor. Sections were cut from existing carpet to determine the total extractable residues. Chlorpyrifos was measured from all matrixes in the kitchen, den and bedroom and the data shows the transport of airborne residues from the point of application to remote locations in the house. The findings are compared and discussed relative to another study conducted in which total release aerosols containing chlorpyrifos were activated in the IAQ research house and the resulting distributions evaluated. For both studies dose estimates were constructed for the exposure pathways using the Stochastic Human Exposure and Dose Estimation Model for pesticides. The United States Environmental Protection Agency has been mandated to examine children's exposure to environmental pollutants such as pesticides. This research specifically reduces uncertainties associated with estimating children's potential exposures to residentially applied pesticides and provides inputs to further evaluate and validate residential exposure models which might be used to reduce exposures and perform risk assessments.

Insight into the binding modes of Lassa nucleoprotein complexed with ssRNA by molecular dynamic simulations and free energy calculations.

PubMed

Zhang, Ying; Chen, Hang; Han, Ju-Guang

2015-01-01

Lassa virus (LASV), an arenavirus known to be responsible for a severe hemorrhagic fever, causes thousands of deaths annually and there is no effective vaccine for it so far. The nucleoprotein (NP) of LASV plays an essential role in the replication and transcription of the viral genome. Recent research shows that viral RNA binds in a deep crevice located within the N-terminal domain of NP and suggests a gating mechanism in which NP transforms from a "closed" position to an "open" position to bind RNA. To characterize the molecular mechanisms of how RNA binds to N-terminal domain of NP, two molecular dynamic (MD) simulations of RNA-binding structure and RNA-free structure have been performed. The simulation results show that an important helix α6 interacts with RNA in the "open" conformation, while helix α6 rotates toward the binding crevice and reduces the space of RNA-binding pocket in the "closed" conformation; it appears that helix α6 would clash with RNA while NP is in a "closed" state. In addition, to characterize the role of residues involved in the binding of RNA, the MD simulations of the double-mutant (W164A/F176A) and the single-mutant (G243P) RNA-binding NP complexes have been performed. Our MD simulations and molecular mechanics-generalized born surface area (MM-GBSA) energy calculations exhibit that the three mutant residues increase the binding affinity. Furthermore, we infer that the defect of the replication and transcription of viral genome is possibly due to the change of structural integrity rather than the reduction of RNA-binding affinity.

High-Resolution Structure of a Self-Assembly-Competent Form of a Hydrophobic Peptide Captured in a Soluble [beta]-Sheet Scaffold

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

Makabe, Koki; Biancalana, Matthew; Yan, Shude

2010-02-08

{beta}-Rich self-assembly is a major structural class of polypeptides, but still little is known about its atomic structures and biophysical properties. Major impediments for structural and biophysical studies of peptide self-assemblies include their insolubility and heterogeneous composition. We have developed a model system, termed peptide self-assembly mimic (PSAM), based on the single-layer {beta}-sheet of Borrelia outer surface protein A. PSAM allows for the capture of a defined number of self-assembly-like peptide repeats within a water-soluble protein, making structural and energetic studies possible. In this work, we extend our PSAM approach to a highly hydrophobic peptide sequence. We show that amore » penta-Ile peptide (Ile{sub 5}), which is insoluble and forms {beta}-rich self-assemblies in aqueous solution, can be captured within the PSAM scaffold in a form capable of self-assembly. The 1.1-{angstrom} crystal structure revealed that the Ile{sub 5} stretch forms a highly regular {beta}-strand within this flat {beta}-sheet. Self-assembly models built with multiple copies of the crystal structure of the Ile5 peptide segment showed no steric conflict, indicating that this conformation represents an assembly-competent form. The PSAM retained high conformational stability, suggesting that the flat {beta}-strand of the Ile{sub 5} stretch primed for self-assembly is a low-energy conformation of the Ile{sub 5} stretch and rationalizing its high propensity for self-assembly. The ability of the PSAM to 'solubilize' an otherwise insoluble peptide stretch suggests the potential of the PSAM approach to the characterization of self-assembling peptides.« less

Multiple chiral topological states in liquid crystals from unstructured light beams

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

Loussert, Charles; Brasselet, Etienne, E-mail: e.brasselet@loma.u-bordeaux1.fr

2014-02-03

It is shown experimentally that unstructured light beams can generate a wealth of distinct metastable defect structures in thin films of chiral liquid crystals. Various kinds of individual chiral topological states are obtained as well as dimers and trimers, which correspond to the entanglement of several topological unit cells. Self-assembled nested assemblies of several metastable particle-like topological states can also be formed. Finally, we propose and experimentally demonstrate an opto-electrical approach to generate tailor-made architectures.

Turn Basin Construction

NASA Image and Video Library

2017-06-30

Across from the Vehicle Assembly Building at NASA's Kennedy Space Center in Florida, cement trucks stand by to support a construction project to upgrade the turn basin wharf. The work includes driving multiple precast concrete piles to a depth of about 70 feet to accommodate arrival of the core stage for the agency's Space Launch System (SLS) rocket. When the stage for NASA's SLS departs the Michoud Assembly Facility in New Orleans, it will be shipped by the agency's modified barge to the Launch Complex 39 turn basin.

Turn Basin Construction

NASA Image and Video Library

2017-06-30

Across from the Vehicle Assembly Building at NASA's Kennedy Space Center in Florida, cement is poured as part of a construction project to upgrade the turn basin wharf. The work includes driving multiple precast concrete piles to a depth of about 70 feet to accommodate arrival of the core stage for the agency's Space Launch System (SLS) rocket. When the stage for NASA's SLS departs the Michoud Assembly Facility in New Orleans, it will be shipped by the agency's modified barge to the Launch Complex 39 turn basin.

Insert metering plates for gas turbine nozzles

DOEpatents

Burdgick, Steven S.; Itzel, Gary; Chopra, Sanjay; Abuaf, Nesim; Correia, Victor H.

2004-05-11

The invention comprises a metering plate which is assembled to an impingement insert for use in the nozzle of a gas turbine. The metering plate can have one or more metering holes and is used to balance the cooling flow within the nozzle. A metering plate with multiple holes reduces static pressure variations which result from the cooling airflow through the metering plate. The metering plate can be assembled to the insert before or after the insert is inserted into the nozzle.

Fibre Optic Connections And Method For Using Same

DOEpatents

Chan, Benson; Cohen, Mitchell S.; Fortier, Paul F.; Freitag, Ladd W.; Hall, Richard R.; Johnson, Glen W.; Lin, How Tzu; Sherman, John H.

2004-03-30

A package is described that couples a twelve channel wide fiber optic cable to a twelve channel Vertical Cavity Surface Emitting Laser (VCSEL) transmitter and a multiple channel Perpendicularly Aligned Integrated Die (PAID) receiver. The package allows for reduction in the height of the assembly package by vertically orienting certain dies parallel to the fiber optic cable and horizontally orienting certain other dies. The assembly allows the vertically oriented optoelectronic dies to be perpendicularly attached to the horizontally oriented laminate via a flexible circuit.

SKYLAB (SL) PRIME CREW - BLDG. 5 - JSC

NASA Image and Video Library

1973-03-20

S73-20759 (1 March 1973) --- Astronaut Charles Conrad Jr., commander of the first manned Skylab mission, takes items from the M512 materials processing equipment storage assembly during Skylab training at Johnson Space Center. Conrad is standing in the Multiple Docking Adapter (MDA) trainer in the JSC Mission Simulation and Training Facility. The assembly holds equipment designed to explore space manufacturing capability in a weightless state. Conrad is holding one of the experiment parts in his left hand. Photo credit: NASA

Enzyme-free Detection of Hydrogen Peroxide from Cerium Oxide Nanoparticles Immobilized on Poly(4-vinylpyridine) Self-Assembled Monolayers

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

Gaynor, James D.; Karakoti, Ajay S.; Inerbaev, Talgat

2013-05-02

A single layer of oxygen-deficient cerium oxide nanoparticles (CNPs) are immobilized on microscopic glass slide using poly(4-vinylpyridine) (PVP) self-assembled monolayers (SAMs). A specific colorimetric property of CNPs when reacted with hydrogen peroxide allows for the direct, single-step peroxide detection which can be used in medical diagnosis and explosives detection. Multiple PVP-CNP immobilized layers improve sensitivity of detection and the sensor can be regenerated for reuse.

Programming function into mechanical forms by directed assembly of silk bulk materials

PubMed Central

Patel, Nereus; Duggan, Thomas; Perotto, Giovanni; Shirman, Elijah; Li, Chunmei; Kaplan, David L.; Omenetto, Fiorenzo G.

2017-01-01

We report simple, water-based fabrication methods based on protein self-assembly to generate 3D silk fibroin bulk materials that can be easily hybridized with water-soluble molecules to obtain multiple solid formats with predesigned functions. Controlling self-assembly leads to robust, machinable formats that exhibit thermoplastic behavior consenting material reshaping at the nanoscale, microscale, and macroscale. We illustrate the versatility of the approach by realizing demonstrator devices where large silk monoliths can be generated, polished, and reshaped into functional mechanical components that can be nanopatterned, embed optical function, heated on demand in response to infrared light, or can visualize mechanical failure through colorimetric chemistries embedded in the assembled (bulk) protein matrix. Finally, we show an enzyme-loaded solid mechanical part, illustrating the ability to incorporate biological function within the bulk material with possible utility for sustained release in robust, programmably shapeable mechanical formats. PMID:28028213

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

Meinke, Rainer

A method for manufacture of a conductor assembly. The assembly is of the type which, when conducting current, generates a magnetic field or in which, in the presence of a changing magnetic field, a voltage is induced. In an example embodiment one or more first coil rows are formed. The assembly has multiple coil rows about an axis with outer coil rows formed about inner coil rows. A determination is made of deviations from specifications associated with the formed one or more first coil rows. One or more deviations correspond to a magnitude of a multipole field component which departsmore » from a field specification. Based on the deviations, one or more wiring patterns are generated for one or more second coil rows to be formed about the one or more first coil rows. The one or more second coil rows are formed in the assembly. The magnitude of each multipole field component that departs from the field specification is offset.« less

Sequentially Programmable and Cellularly Selective Assembly of Fluorescent Polymerized Vesicles for Monitoring Cell Apoptosis

PubMed Central

Peng, Shu; Pan, Yu‐Chen; Wang, Yaling; Xu, Zhe; Chen, Chao

2017-01-01

Abstract The introduction of controlled self‐assembly into living organisms opens up desired biomedical applications in wide areas including bioimaging/assays, drug delivery, and tissue engineering. Besides the enzyme‐activated examples reported before, controlled self‐assembly under integrated stimuli, especially in the form of sequential input, is unprecedented and ultimately challenging. This study reports a programmable self‐assembling strategy in living cells under sequentially integrated control of both endogenous and exogenous stimuli. Fluorescent polymerized vesicles are constructed by using cholinesterase conversion followed by photopolymerization and thermochromism. Furthermore, as a proof‐of‐principle application, the cell apoptosis involved in the overexpression of cholinesterase in virtue of the generated fluorescence is monitored, showing potential in screening apoptosis‐inducing drugs. The approach exhibits multiple advantages for bioimaging in living cells, including specificity to cholinesterase, red emission, wash free, high signal‐to‐noise ratio. PMID:29201625

Sequentially Programmable and Cellularly Selective Assembly of Fluorescent Polymerized Vesicles for Monitoring Cell Apoptosis.

PubMed

Peng, Shu; Pan, Yu-Chen; Wang, Yaling; Xu, Zhe; Chen, Chao; Ding, Dan; Wang, Yongjian; Guo, Dong-Sheng

2017-11-01

The introduction of controlled self-assembly into living organisms opens up desired biomedical applications in wide areas including bioimaging/assays, drug delivery, and tissue engineering. Besides the enzyme-activated examples reported before, controlled self-assembly under integrated stimuli, especially in the form of sequential input, is unprecedented and ultimately challenging. This study reports a programmable self-assembling strategy in living cells under sequentially integrated control of both endogenous and exogenous stimuli. Fluorescent polymerized vesicles are constructed by using cholinesterase conversion followed by photopolymerization and thermochromism. Furthermore, as a proof-of-principle application, the cell apoptosis involved in the overexpression of cholinesterase in virtue of the generated fluorescence is monitored, showing potential in screening apoptosis-inducing drugs. The approach exhibits multiple advantages for bioimaging in living cells, including specificity to cholinesterase, red emission, wash free, high signal-to-noise ratio.

Role of Chromatin assembly factor 1 in DNA replication of Plasmodium falciparum.

PubMed

Gupta, Mohit Kumar; Agarawal, Meetu; Banu, Khadija; Reddy, K Sony; Gaur, Deepak; Dhar, Suman Kumar

2018-01-01

Nucleosome assembly in P. falciparum could be the key process in maintaining its genomic integrity as DNA replicates more than once per cell cycle during several stages of its life cycle. Here, we report the functional characterization of P. falciparum chromatin assembly factor 1 (CAF1), which interacts with several proteins namely PfCAF2, Histones, PfHP1 and others. Consistent with the above findings, we demonstrate the presence of PfCAF1 at the telomeric repeat regions, central and subtelomeric var genes of multiple var gene family along with PfHP1. Further, we report the upregulation of PfCAF1 after treatment with genotoxic agents like MMS and HU. Together, these findings establish role of PfCAF1 in heterochromatin maintenance and as histone chaperone in nucleosome assembly and DNA damage repair. Copyright © 2017 Elsevier Inc. All rights reserved.

Modular Self-Assembly of Protein Cage Lattices for Multistep Catalysis

DOE PAGES

Uchida, Masaki; McCoy, Kimberly; Fukuto, Masafumi; ...

2017-11-13

The assembly of individual molecules into hierarchical structures is a promising strategy for developing three-dimensional materials with properties arising from interaction between the individual building blocks. Virus capsids are elegant examples of biomolecular nanostructures, which are themselves hierarchically assembled from a limited number of protein subunits. Here, we demonstrate the bio-inspired modular construction of materials with two levels of hierarchy: the formation of catalytically active individual virus-like particles (VLPs) through directed self-assembly of capsid subunits with enzyme encapsulation, and the assembly of these VLP building blocks into three-dimensional arrays. The structure of the assembled arrays was successfully altered from anmore » amorphous aggregate to an ordered structure, with a face-centered cubic lattice, by modifying the exterior surface of the VLP without changing its overall morphology, to modulate interparticle interactions. The assembly behavior and resultant lattice structure was a consequence of interparticle interaction between exterior surfaces of individual particles and thus independent of the enzyme cargos encapsulated within the VLPs. These superlattice materials, composed of two populations of enzyme-packaged VLP modules, retained the coupled catalytic activity in a two-step reaction for isobutanol synthesis. As a result, this study demonstrates a significant step toward the bottom-up fabrication of functional superlattice materials using a self-assembly process across multiple length scales and exhibits properties and function that arise from the interaction between individual building blocks.« less

Modular Self-Assembly of Protein Cage Lattices for Multistep Catalysis

PubMed Central

Uchida, Masaki; McCoy, Kimberly; Fukuto, Masafumi; Yang, Lin; Yoshimura, Hideyuki; Miettinen, Heini M.; LaFrance, Ben; Patterson, Dustin P.; Schwarz, Benjamin; Karty, Jonathan A.; Prevelige, Peter E.; Lee, Byeongdu; Douglas, Trevor

2018-01-01

The assembly of individual molecules into hierarchical structures is a promising strategy for developing three-dimensional materials with properties arising from interaction between the individual building blocks. Virus capsids are elegant examples of biomolecular nanostructures, which are themselves hierarchically assembled from a limited number of protein subunits. Here we demonstrate the bio-inspired modular construction of materials with two levels of hierarchy; the formation of catalytically active individual virus-like particles (VLPs) through directed self-assembly of capsid subunits with enzyme encapsulation, and the assembly of these VLP building blocks into three-dimensional arrays. The structure of the assembled arrays was successfully altered from an amorphous aggregate to an ordered structure, with a face-centered cubic lattice, by modifying the exterior surface of the VLP without changing its overall morphology, to modulate interparticle interactions. The assembly behavior and resultant lattice structure was a consequence of interparticle interaction between exterior surfaces of individual particles, and thus independent of the enzyme cargos encapsulated within the VLPs. These superlattice materials, composed of two populations of enzyme packaged VLP modules, retained the coupled catalytic activity in a two-step reaction for isobutanol synthesis. This study demonstrates a significant step toward the bottom-up fabrication of functional superlattice materials using a self-assembly process across multiple length scales, and exhibits properties and function that arise from the interaction between individual building blocks. PMID:29131580

Modular Self-Assembly of Protein Cage Lattices for Multistep Catalysis

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

Uchida, Masaki; McCoy, Kimberly; Fukuto, Masafumi

The assembly of individual molecules into hierarchical structures is a promising strategy for developing three-dimensional materials with properties arising from interaction between the individual building blocks. Virus capsids are elegant examples of biomolecular nanostructures, which are themselves hierarchically assembled from a limited number of protein subunits. Here, we demonstrate the bio-inspired modular construction of materials with two levels of hierarchy: the formation of catalytically active individual virus-like particles (VLPs) through directed self-assembly of capsid subunits with enzyme encapsulation, and the assembly of these VLP building blocks into three-dimensional arrays. The structure of the assembled arrays was successfully altered from anmore » amorphous aggregate to an ordered structure, with a face-centered cubic lattice, by modifying the exterior surface of the VLP without changing its overall morphology, to modulate interparticle interactions. The assembly behavior and resultant lattice structure was a consequence of interparticle interaction between exterior surfaces of individual particles and thus independent of the enzyme cargos encapsulated within the VLPs. These superlattice materials, composed of two populations of enzyme-packaged VLP modules, retained the coupled catalytic activity in a two-step reaction for isobutanol synthesis. As a result, this study demonstrates a significant step toward the bottom-up fabrication of functional superlattice materials using a self-assembly process across multiple length scales and exhibits properties and function that arise from the interaction between individual building blocks.« less

Arabidopsis ARGONAUTE7 selects miR390 through multiple checkpoints during RISC assembly

PubMed Central

Endo, Yayoi; Iwakawa, Hiro-oki; Tomari, Yukihide

2013-01-01

Plant ARGONAUTE7 (AGO7) assembles RNA-induced silencing complex (RISC) specifically with miR390 and regulates the auxin-signalling pathway via production of TAS3 trans-acting siRNAs (tasiRNAs). However, how AGO7 discerns miR390 among other miRNAs remains unclear. Here, we show that the 5′ adenosine of miR390 and the central region of miR390/miR390* duplex are critical for the specific interaction with AGO7. Furthermore, despite the existence of mismatches in the seed and central regions of the duplex, cleavage of the miR390* strand is required for maturation of AGO7–RISC. These findings suggest that AGO7 uses multiple checkpoints to select miR390, thereby circumventing promiscuous tasiRNA production. PMID:23732541

Pressure actuated film riding seals for turbo machinery

DOEpatents

Bidkar, Rahul Anil; Thatte, Azam Mihir; Gibson, Nathan Evan McCurdy; Giametta, Andrew Paul

2015-08-25

A seal assembly for a rotary machine is provided. The seal assembly includes multiple sealing device segments disposed circumferentially intermediate to a stationary housing and a rotor. Each of the sealing device segments includes a stator interface element, a shoe plate having an extended portion having one or more labyrinth teeth facing the rotor and a load bearing portion, wherein the shoe plate is configured to generate an aerodynamic force between the shoe plate and the rotor. The sealing device segment further includes a secondary seal configured to be in contact with the stator interface element at a radially outer end and configured to be in contact with an elevated nose section of the extended portion of the shoe plate on a radially inner end; and multiple flexible elements attached to the shoe plate and to the stator interface element.

Assembly of micro/nanomaterials into complex, three-dimensional architectures by compressive buckling

NASA Astrophysics Data System (ADS)

Xu, Sheng; Yan, Zheng; Jang, Kyung-In; Huang, Wen; Fu, Haoran; Kim, Jeonghyun; Wei, Zijun; Flavin, Matthew; McCracken, Joselle; Wang, Renhan; Badea, Adina; Liu, Yuhao; Xiao, Dongqing; Zhou, Guoyan; Lee, Jungwoo; Chung, Ha Uk; Cheng, Huanyu; Ren, Wen; Banks, Anthony; Li, Xiuling; Paik, Ungyu; Nuzzo, Ralph G.; Huang, Yonggang; Zhang, Yihui; Rogers, John A.

2015-01-01

Complex three-dimensional (3D) structures in biology (e.g., cytoskeletal webs, neural circuits, and vasculature networks) form naturally to provide essential functions in even the most basic forms of life. Compelling opportunities exist for analogous 3D architectures in human-made devices, but design options are constrained by existing capabilities in materials growth and assembly. We report routes to previously inaccessible classes of 3D constructs in advanced materials, including device-grade silicon. The schemes involve geometric transformation of 2D micro/nanostructures into extended 3D layouts by compressive buckling. Demonstrations include experimental and theoretical studies of more than 40 representative geometries, from single and multiple helices, toroids, and conical spirals to structures that resemble spherical baskets, cuboid cages, starbursts, flowers, scaffolds, fences, and frameworks, each with single- and/or multiple-level configurations.

The interaction of DiaA and DnaA regulates the replication cycle in E. coli by directly promoting ATP–DnaA-specific initiation complexes

PubMed Central

Keyamura, Kenji; Fujikawa, Norie; Ishida, Takuma; Ozaki, Shogo; Su’etsugu, Masayuki; Fujimitsu, Kazuyuki; Kagawa, Wataru; Yokoyama, Shigeyuki; Kurumizaka, Hitoshi; Katayama, Tsutomu

2007-01-01

Escherichia coli DiaA is a DnaA-binding protein that is required for the timely initiation of chromosomal replication during the cell cycle. In this study, we determined the crystal structure of DiaA at 1.8 Å resolution. DiaA forms a homotetramer consisting of a symmetrical pair of homodimers. Mutational analysis revealed that the DnaA-binding activity and formation of homotetramers are required for the stimulation of initiation by DiaA. DiaA tetramers can bind multiple DnaA molecules simultaneously. DiaA stimulated the assembly of multiple DnaA molecules on oriC, conformational changes in ATP–DnaA-specific initiation complexes, and unwinding of oriC duplex DNA. The mutant DiaA proteins are defective in these stimulations. DiaA associated also with ADP–DnaA, and stimulated the assembly of inactive ADP–DnaA–oriC complexes. Specific residues in the putative phosphosugar-binding motif of DiaA were required for the stimulation of initiation and formation of ATP–DnaA-specific–oriC complexes. Our data indicate that DiaA regulates initiation by a novel mechanism, in which DiaA tetramers most likely bind to multiple DnaA molecules and stimulate the assembly of specific ATP–DnaA–oriC complexes. These results suggest an essential role for DiaA in the promotion of replication initiation in a cell cycle coordinated manner. PMID:17699754

Selective self-assembly of adenine-silver nanoparticles forms rings resembling the size of cells

PubMed Central

Choi, Sungmoon; Park, Soonyoung; Yang, Seon-Ah; Jeong, Yujin; Yu, Junhua

2015-01-01

Self-assembly has played critical roles in the construction of functional nanomaterials. However, the structure of the macroscale multicomponent materials built by the self-assembly of nanoscale building blocks is hard to predict due to multiple intermolecular interactions of great complexity. Evaporation of solvents is usually an important approach to induce kinetically stable assemblies of building blocks with a large-scale specific arrangement. During such a deweting process, we tried to monitor the possible interactions between silver nanoparticles and nucleobases at a larger scale by epifluorescence microscopy, thanks to the doping of silver nanoparticles with luminescent silver nanodots. ssDNA oligomer-stabilized silver nanoparticles and adenine self-assemble to form ring-like compartments similar to the size of modern cells. However, the silver ions only dismantle the self-assembly of adenine. The rings are thermodynamically stable as the drying process only enrich the nanoparticles-nucleobase mixture to a concentration that activates the self-assembly. The permeable membrane-like edge of the ring is composed of adenine filaments glued together by silver nanoparticles. Interestingly, chemicals are partially confined and accumulated inside the ring, suggesting that this might be used as a microreactor to speed up chemical reactions during a dewetting process. PMID:26643504

Distinct self-interaction domains promote Multi Sex Combs accumulation in and formation of the Drosophila histone locus body.

PubMed

Terzo, Esteban A; Lyons, Shawn M; Poulton, John S; Temple, Brenda R S; Marzluff, William F; Duronio, Robert J

2015-04-15

Nuclear bodies (NBs) are structures that concentrate proteins, RNAs, and ribonucleoproteins that perform functions essential to gene expression. How NBs assemble is not well understood. We studied the Drosophila histone locus body (HLB), a NB that concentrates factors required for histone mRNA biosynthesis at the replication-dependent histone gene locus. We coupled biochemical analysis with confocal imaging of both fixed and live tissues to demonstrate that the Drosophila Multi Sex Combs (Mxc) protein contains multiple domains necessary for HLB assembly. An important feature of this assembly process is the self-interaction of Mxc via two conserved N-terminal domains: a LisH domain and a novel self-interaction facilitator (SIF) domain immediately downstream of the LisH domain. Molecular modeling suggests that the LisH and SIF domains directly interact, and mutation of either the LisH or the SIF domain severely impairs Mxc function in vivo, resulting in reduced histone mRNA accumulation. A region of Mxc between amino acids 721 and 1481 is also necessary for HLB assembly independent of the LisH and SIF domains. Finally, the C-terminal 195 amino acids of Mxc are required for recruiting FLASH, an essential histone mRNA-processing factor, to the HLB. We conclude that multiple domains of the Mxc protein promote HLB assembly in order to concentrate factors required for histone mRNA biosynthesis. © 2015 Terzo et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Development and validation of an rDNA operon based primer walking strategy applicable to de novo bacterial genome finishing

PubMed Central

Eastman, Alexander W.; Yuan, Ze-Chun

2015-01-01

Advances in sequencing technology have drastically increased the depth and feasibility of bacterial genome sequencing. However, little information is available that details the specific techniques and procedures employed during genome sequencing despite the large numbers of published genomes. Shotgun approaches employed by second-generation sequencing platforms has necessitated the development of robust bioinformatics tools for in silico assembly, and complete assembly is limited by the presence of repetitive DNA sequences and multi-copy operons. Typically, re-sequencing with multiple platforms and laborious, targeted Sanger sequencing are employed to finish a draft bacterial genome. Here we describe a novel strategy based on the identification and targeted sequencing of repetitive rDNA operons to expedite bacterial genome assembly and finishing. Our strategy was validated by finishing the genome of Paenibacillus polymyxa strain CR1, a bacterium with potential in sustainable agriculture and bio-based processes. An analysis of the 38 contigs contained in the P. polymyxa strain CR1 draft genome revealed 12 repetitive rDNA operons with varied intragenic and flanking regions of variable length, unanimously located at contig boundaries and within contig gaps. These highly similar but not identical rDNA operons were experimentally verified and sequenced simultaneously with multiple, specially designed primer sets. This approach also identified and corrected significant sequence rearrangement generated during the initial in silico assembly of sequencing reads. Our approach reduces the required effort associated with blind primer walking for contig assembly, increasing both the speed and feasibility of genome finishing. Our study further reinforces the notion that repetitive DNA elements are major limiting factors for genome finishing. Moreover, we provided a step-by-step workflow for genome finishing, which may guide future bacterial genome finishing projects. PMID:25653642

Information Compression, Multiple Alignment, and the Representation and Processing of Knowledge in the Brain.

PubMed

Wolff, J Gerard

2016-01-01

The SP theory of intelligence , with its realization in the SP computer model , aims to simplify and integrate observations and concepts across artificial intelligence, mainstream computing, mathematics, and human perception and cognition, with information compression as a unifying theme. This paper describes how abstract structures and processes in the theory may be realized in terms of neurons, their interconnections, and the transmission of signals between neurons. This part of the SP theory- SP-neural -is a tentative and partial model for the representation and processing of knowledge in the brain. Empirical support for the SP theory-outlined in the paper-provides indirect support for SP-neural. In the abstract part of the SP theory (SP-abstract), all kinds of knowledge are represented with patterns , where a pattern is an array of atomic symbols in one or two dimensions. In SP-neural, the concept of a "pattern" is realized as an array of neurons called a pattern assembly , similar to Hebb's concept of a "cell assembly" but with important differences. Central to the processing of information in SP-abstract is information compression via the matching and unification of patterns (ICMUP) and, more specifically, information compression via the powerful concept of multiple alignment , borrowed and adapted from bioinformatics. Processes such as pattern recognition, reasoning and problem solving are achieved via the building of multiple alignments, while unsupervised learning is achieved by creating patterns from sensory information and also by creating patterns from multiple alignments in which there is a partial match between one pattern and another. It is envisaged that, in SP-neural, short-lived neural structures equivalent to multiple alignments will be created via an inter-play of excitatory and inhibitory neural signals. It is also envisaged that unsupervised learning will be achieved by the creation of pattern assemblies from sensory information and from the neural equivalents of multiple alignments, much as in the non-neural SP theory-and significantly different from the "Hebbian" kinds of learning which are widely used in the kinds of artificial neural network that are popular in computer science. The paper discusses several associated issues, with relevant empirical evidence.

j5 v2.8.4

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

Hillson, Nathan

j5 automates and optimizes the design of the molecular biological process of cloning/constructing DNA. j5 enables users to benefit from (combinatorial) multi-part scar-less SLIC, Gibson, CPEC, Golden Gate assembly, or variants thereof, for which automation software does not currently exist, without the intense labor currently associated with the process. j5 inputs a list of the DNA sequences to be assembled, along with a Genbank, FASTA, jbei-seq, or SBOL v1.1 format sequence file for each DNA source. Given the list of DNA sequences to be assembled, j5 first determines the cost-minimizing assembly strategy for each part (direct synthesis, PCR/SOE, or oligo-embedding),more » designs DNA oligos with Primer3, adds flanking homology sequences (SLIC, Gibson, and CPEC; optimized with Primer3 for CPEC) or optimized overhang sequences (Golden Gate) to the oligos and direct synthesis pieces, and utilizes BLAST to check against oligo mis-priming and assembly piece incompatibility events. After identifying DNA oligos that are already contained within a local collection for reuse, the program estimates the total cost of direct synthesis and new oligos to be ordered. In the instance that j5 identifies putative assembly piece incompatibilities (multiple pieces with high flanking sequence homology), the program suggests hierarchical subassemblies where possible. The program outputs a comma-separated value (CSV) file, viewable via Excel or other spreadsheet software, that contains assembly design information (such as the PCR/SOE reactions to perform, their anticipated sizes and sequences, etc.) as well as a properly annotated genbank file containing the sequence resulting from the assembly, and appends the local oligo library with the oligos to be ordered j5 condenses multiple independent assembly projects into 96-well format for high-throughput liquid-handling robotics platforms, and generates configuration files for the PR-PR biology-friendly robot programming language. j5 thus provides a new way to design DNA assembly procedures much more productively and efficiently, not only in terms of time, but also in terms of cost. To a large extent, however, j5 does not allow people to do something that could not be done before by hand given enough time and effort. An exception to this is that, since the very act of using j5 to design the DNA assembly process standardizes the experimental details and workflow, j5 enables a single person to concurrently perform the independent DNA construction tasks of an entire group of researchers. Currently, this is not readily possible, since separate researchers employ disparate design strategies and workflows, and furthermore, their designs and workflows are very infrequently fully captured in an electronic format which is conducive to automation.« less

SERS-barcoded colloidal gold NP assemblies as imaging agents for use in biodiagnostics

NASA Astrophysics Data System (ADS)

Dey, Priyanka; Olds, William; Blakey, Idriss; Thurecht, Kristofer J.; Izake, Emad L.; Fredericks, Peter M.

2014-03-01

There is a growing need for new biodiagnostics that combine high throughput with enhanced spatial resolution and sensitivity. Gold nanoparticle (NP) assemblies with sub-10 nm particle spacing have the benefits of improving detection sensitivity via Surface enhanced Raman scattering (SERS) and being of potential use in biomedicine due to their colloidal stability. A promising and versatile approach to form solution-stable NP assemblies involves the use of multi-branched molecular linkers which allows tailoring of the assembly size, hot-spot density and interparticle distance. We have shown that linkers with multiple anchoring end-groups can be successfully employed as a linker to assemble gold NPs into dimers, linear NP chains and clustered NP assemblies. These NP assemblies with diameters of 30-120 nm are stable in solution and perform better as SERS substrates compared with single gold NPs, due to an increased hot-spot density. Thus, tailored gold NP assemblies are potential candidates for use as biomedical imaging agents. We observed that the hot-spot density and in-turn the SERS enhancement is a function of the linker polymer concentration and polymer architecture. New deep Raman techniques like Spatially Offset Raman Spectroscopy (SORS) have emerged that allow detection from beneath diffusely scattering opaque materials, including biological media such as animal tissue. We have been able to demonstrate that the gold NP assemblies could be detected from within both proteinaceous and high lipid containing animal tissue by employing a SORS technique with a backscattered geometry.

Measure Guideline: Water Management at Tub and Shower Assemblies

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

Dickson, B.

2011-12-01

Due to the high concentrations of water and the consequential risk of water damage to the home's structure a comprehensive water management system is imperative to protect the building assemblies underlying the finish surround of tub and shower areas. This guide shows how to install fundamental waterproofing strategies to prevent water related issues at shower and tub areas. When conducting a total gut rehab of a structure or constructing a new home, best practice installation and detailing for effective waterproofing are critically important at bathtub and shower assemblies. Water management issues in a structure may go unrecognized for long periods,more » so that when they are finally observed, the damage from long-term water exposure is extensive. A gut rehab is often undertaken when a home has experienced a natural disaster or when the homeowners are interested in converting an old, high-energy-use building into a high-quality, efficient structure that meets or exceeds one of the national energy standards, such as ENERGY STAR or LEED for homes. During a gut rehab, bath areas need to be replaced with diligent attention to detail. Employing effective water management practices in the installation and detailing of tub and shower assemblies will minimize or eliminate water issues within the building cavities and on the finished surfaces. A residential tub-and-shower surround or shower-stall assembly is designed to handle a high volume of water - 2.5 gallons per minute, with multiple baths occurring during a typical day. Transitions between dissimilar materials and connections between multiple planes must be installed with care to avoid creating a pathway for water to enter the building assemblies. Due to the high volume of water and the consequential risk of water damage to the home's structure, a comprehensive water management system is imperative to protect the building assemblies underlying the finish surround of tub and shower areas. At each stage of construction, successive trades must take care not to create a defect nor to compound or cover up a previous trade's defect. Covering a defect hides the inevitable point of failure and may even exacerbate the situation.« less

Dynamics of HIV-1 Assembly and Release

PubMed Central

Ivanchenko, Sergey; Godinez, William J.; Lampe, Marko; Kräusslich, Hans-Georg; Eils, Roland; Rohr, Karl; Bräuchle, Christoph; Müller, Barbara; Lamb, Don C.

2009-01-01

Assembly and release of human immunodeficiency virus (HIV) occur at the plasma membrane of infected cells and are driven by the Gag polyprotein. Previous studies analyzed viral morphogenesis using biochemical methods and static images, while dynamic and kinetic information has been lacking until very recently. Using a combination of wide-field and total internal reflection fluorescence microscopy, we have investigated the assembly and release of fluorescently labeled HIV-1 at the plasma membrane of living cells with high time resolution. Gag assembled into discrete clusters corresponding to single virions. Formation of multiple particles from the same site was rarely observed. Using a photoconvertible fluorescent protein fused to Gag, we determined that assembly was nucleated preferentially by Gag molecules that had recently attached to the plasma membrane or arrived directly from the cytosol. Both membrane-bound and cytosol derived Gag polyproteins contributed to the growing bud. After their initial appearance, assembly sites accumulated at the plasma membrane of individual cells over 1–2 hours. Assembly kinetics were rapid: the number of Gag molecules at a budding site increased, following a saturating exponential with a rate constant of ∼5×10−3 s−1, corresponding to 8–9 min for 90% completion of assembly for a single virion. Release of extracellular particles was observed at ∼1,500±700 s after the onset of assembly. The ability of the virus to recruit components of the cellular ESCRT machinery or to undergo proteolytic maturation, or the absence of Vpu did not significantly alter the assembly kinetics. PMID:19893629

Autographa californica multiple nucleopolyhedrovirus ac53 plays a role in nucleocapsid assembly

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

Liu Chao; Li Zhaofei; Wu Wenbi

2008-12-05

Autographa californica multiple nucleopolyhedrovirus (AcMNPV) orf53 (ac53) is a highly conserved gene existing in all sequenced Lepidoptera and Hymenoptera baculoviruses, but its function remains unknown. To investigate its role in the baculovirus life cycle, an ac53 deletion virus (vAc{sup ac53KO-PH-GFP}) was generated through homologous recombination in Escherichia coli. Fluorescence and light microscopy and titration analysis revealed that vAc{sup ac53KO-PH-GFP} could not produce infectious budded virus in infected Sf9 cells. Real-time PCR demonstrated that the ac53 deletion did not affect the levels of viral DNA replication. Electron microscopy showed that many lucent tubular shells devoid of the nucleoprotein core are presentmore » in the virogenic stroma and ring zone, indicating that the ac53 knockout affected nucleocapsid assembly. With a recombinant virus expressing an Ac53-GFP fusion protein, we observed that Ac53 was distributed within the cytoplasm and nucleus at 24 h post-infection, but afterwards accumulated predominantly near the nucleus-cytoplasm boundary. These data demonstrate that ac53 is involved in nucleocapsid assembly and is an essential gene for virus production.« less

Using droplet-on-demand based printing to guide self-assembly in a peptide-protein based bioink

NASA Astrophysics Data System (ADS)

Hedegaard, Clara; Collin, Estelle; Redondo-Gomez, Carlos; Nguyen, Luong T. H.; Ng, Kee Woei; Castrejon-Pita, Alfonso A.; Castrejon-Pita, J. Rafael; Mata, Alvaro

2017-11-01

Tissue engineering aims to capture details of the extracellular matrix (ECM) that stimulate tissue regeneration. Advanced biofabrication techniques have enabled structural complexity, however they are restricted by the choice of material due to stringent printing requirements, leading to a lack of nanoscale control and molecular versatility. In this project, we exploit the dynamics of droplet fluid interactions combined with the co-assembly of peptide amphiphiles (PAs) with biomolecules/proteins to develop a new approach to droplet-based biofabrication. A custom-made droplet generator was developed and used to controllably dispense droplets of PA into a protein solution resulting in gel formation within milliseconds. Taking advantage of the interfacial and inertial forces during the droplet/liquid interaction, it is possible to control the co-assembly kinetics, to give rise to aligned or disordered nanofibers, hydrogel structures of different geometries and sizes, surface topographies, and higher-ordered structures made from multiple hydrogels. The process allows multiple cell types to be spatially distributed on the outside or embedded within the ECM mimetic scaffolds, whilst exhibiting high cell viability (>88%). ERC Starting Grant (STROFUNSCAFF), FP7-PEOPLE-2013-CIG Biomorph and the Royal Society.

Orthogonal combinatorial mutagenesis: a codon-level combinatorial mutagenesis method useful for low multiplicity and amino acid-scanning protocols

PubMed Central

Gaytán, Paul; Yáñez, Jorge; Sánchez, Filiberto; Soberón, Xavier

2001-01-01

We describe here a method to generate combinatorial libraries of oligonucleotides mutated at the codon-level, with control of the mutagenesis rate so as to create predictable binomial distributions of mutants. The method allows enrichment of the libraries with single, double or larger multiplicity of amino acid replacements by appropriate choice of the mutagenesis rate, depending on the concentration of synthetic precursors. The method makes use of two sets of deoxynucleoside-phosphoramidites bearing orthogonal protecting groups [4,4′-dimethoxytrityl (DMT) and 9-fluorenylmethoxycarbonyl (Fmoc)] in the 5′ hydroxyl. These phosphoramidites are divergently combined during automated synthesis in such a way that wild-type codons are assembled with commercial DMT-deoxynucleoside-methyl-phosphoramidites while mutant codons are assembled with Fmoc-deoxynucleoside-methyl-phosphoramidites in an NNG/C fashion in a single synthesis column. This method is easily automated and suitable for low mutagenesis rates and large windows, such as those required for directed evolution and alanine scanning. Through the assembly of three oligonucleotide libraries at different mutagenesis rates, followed by cloning at the polylinker region of plasmid pUC18 and sequencing of 129 clones, we concluded that the method performs essentially as intended. PMID:11160911

Observation of layered antiferromagnetism in self-assembled parallel NiSi nanowire arrays on Si(110) by spin-polarized scanning tunneling spectromicroscopy

NASA Astrophysics Data System (ADS)

Hong, Ie-Hong; Hsu, Hsin-Zan

2018-03-01

The layered antiferromagnetism of parallel nanowire (NW) arrays self-assembled on Si(110) have been observed at room temperature by direct imaging of both the topographies and magnetic domains using spin-polarized scanning tunneling microscopy/spectroscopy (SP-STM/STS). The topographic STM images reveal that the self-assembled unidirectional and parallel NiSi NWs grow into the Si(110) substrate along the [\\bar{1}10] direction (i.e. the endotaxial growth) and exhibit multiple-layer growth. The spatially-resolved SP-STS maps show that these parallel NiSi NWs of different heights produce two opposite magnetic domains, depending on the heights of either even or odd layers in the layer stack of the NiSi NWs. This layer-wise antiferromagnetic structure can be attributed to an antiferromagnetic interlayer exchange coupling between the adjacent layers in the multiple-layer NiSi NW with a B2 (CsCl-type) crystal structure. Such an endotaxial heterostructure of parallel magnetic NiSi NW arrays with a layered antiferromagnetic ordering in Si(110) provides a new and important perspective for the development of novel Si-based spintronic nanodevices.

TIMMDC1/C3orf1 functions as a membrane-embedded mitochondrial complex I assembly factor through association with the MCIA complex.

PubMed

Guarani, Virginia; Paulo, Joao; Zhai, Bo; Huttlin, Edward L; Gygi, Steven P; Harper, J Wade

2014-03-01

Complex I (CI) of the electron transport chain, a large membrane-embedded NADH dehydrogenase, couples electron transfer to the release of protons into the mitochondrial inner membrane space to promote ATP production through ATP synthase. In addition to being a central conduit for ATP production, CI activity has been linked to neurodegenerative disorders, including Parkinson's disease. CI is built in a stepwise fashion through the actions of several assembly factors. We employed interaction proteomics to interrogate the molecular associations of 15 core subunits and assembly factors previously linked to human CI deficiency, resulting in a network of 101 proteins and 335 interactions (edges). TIMMDC1, a predicted 4-pass membrane protein, reciprocally associated with multiple members of the MCIA CI assembly factor complex and core CI subunits and was localized in the mitochondrial inner membrane, and its depletion resulted in reduced CI activity and cellular respiration. Quantitative proteomics demonstrated a role for TIMMDC1 in assembly of membrane-embedded and soluble arms of the complex. This study defines a new membrane-embedded CI assembly factor and provides a resource for further analysis of CI biology.

Self-assembly concepts for multicompartment nanostructures

NASA Astrophysics Data System (ADS)

Gröschel, André H.; Müller, Axel H. E.

2015-07-01

Compartmentalization is ubiquitous to many biological and artificial systems, be it for the separate storage of incompatible matter or to isolate transport processes. Advancements in the synthesis of sequential block copolymers offer a variety of tools to replicate natural design principles with tailor-made soft matter for the precise spatial separation of functionalities on multiple length scales. Here, we review recent trends in the self-assembly of amphiphilic block copolymers to multicompartment nanostructures (MCNs) under (semi-)dilute conditions, with special emphasis on ABC triblock terpolymers. The intrinsic immiscibility of connected blocks induces short-range repulsion into discrete nano-domains stabilized by a third, soluble block or molecular additive. Polymer blocks can be synthesized from an arsenal of functional monomers directing self-assembly through packing frustration or response to various fields. The mobility in solution further allows the manipulation of self-assembly processes into specific directions by clever choice of environmental conditions. This review focuses on practical concepts that direct self-assembly into predictable nanostructures, while narrowing particle dispersity with respect to size, shape and internal morphology. The growing understanding of underlying self-assembly mechanisms expands the number of experimental concepts providing the means to target and manipulate progressively complex superstructures.

Facile route to versatile nanoplatforms for drug delivery by one-pot self-assembly.

PubMed

Zhou, Xing; Che, Ling; Wei, Yanling; Dou, Yin; Chen, Sha; He, Hongmei; Gong, Hao; Li, Xiaohui; Zhang, Jianxiang

2014-06-01

There is still unmet demand for developing powerful approaches to produce polymeric nanoplatforms with versatile functions and broad applications, which are essential for the successful bench-to-bedside translation of polymeric nanotherapeutics developed in the laboratory. We have discovered a facile, convenient, cost-effective and easily scalable one-pot strategy to assemble various lipophilic therapeutics bearing carboxyl groups into nanomedicines, through which highly effective cargo loading and nanoparticle formation can be achieved simultaneously. Besides dramatically improving water solubility, the assembled nanopharmaceuticals showed significantly higher bioavailability and much better therapeutic activity. These one-pot assemblies may also serve as nanocontainers to effectively accommodate other highly hydrophobic drugs such as paclitaxel (PTX). PTX nanomedicines thus formulated display strikingly enhanced in vitro antitumor activity and can reverse the multidrug resistance of tumor cells to PTX therapy. The special surface chemistry offers these assembled entities the additional capability of efficiently packaging and efficaciously transfecting plasmid DNA, with a transfection efficiency markedly higher than that of commonly used positive controls. Consequently, this one-pot assembly approach provides a facile route to multifunctional nanoplatforms for simultaneous delivery of multiple therapeutics with improved therapeutic significance. Copyright © 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Hunting behavior of a marine mammal beneath the antarctic fast Ice

PubMed

Davis; Fuiman; Williams; Collier; Hagey; Kanatous; Kohin; Horning

1999-02-12

The hunting behavior of a marine mammal was studied beneath the Antarctic fast ice with an animal-borne video system and data recorder. Weddell seals stalked large Antarctic cod and the smaller subice fish Pagothenia borchgrevinki, often with the under-ice surface for backlighting, which implies that vision is important for hunting. They approached to within centimeters of cod without startling the fish. Seals flushed P. borchgrevinki by blowing air into subice crevices or pursued them into the platelet ice. These observations highlight the broad range of insights that are possible with simultaneous recordings of video, audio, three-dimensional dive paths, and locomotor effort.

Method and apparatus for remote tube crevice detection by current and voltage probe resistance measurement

DOEpatents

Kikta, Thomas J.; Mitchell, Ronald D.

1992-01-01

A method and apparatus for determining the extent of contact between an electrically conducting tube and an electrically conductive tubesheet surrounding the tube, based upon the electrical resistance of the tube and tubesheet. A constant current source is applied to the interior of the electrically conducting tube by probes and a voltmeter is connected between other probes to measure the voltage at the point of current injection, which is inversely proportional to the amount of contact between the tube and tubesheet. Namely, the higher the voltage measured by the voltmeter, the less contact between the tube and tubesheet.

Method and apparatus for remote tube crevice detection by current and voltage probe resistance measurement

DOEpatents

Kikta, T.J.; Mitchell, R.D.

1992-11-24

A method and apparatus for determining the extent of contact between an electrically conducting tube and an electrically conductive tubesheet surrounding the tube, based upon the electrical resistance of the tube and tubesheet. A constant current source is applied to the interior of the electrically conducting tube by probes and a voltmeter is connected between other probes to measure the voltage at the point of current injection, which is inversely proportional to the amount of contact between the tube and tubesheet. Namely, the higher the voltage measured by the voltmeter, the less contact between the tube and tubesheet. 4 figs.

The design of superhydrophobic stainless steel surfaces by controlling nanostructures: A key parameter to reduce the implantation of pathogenic bacteria.

PubMed

Bruzaud, Jérôme; Tarrade, Jeanne; Celia, Elena; Darmanin, Thierry; Taffin de Givenchy, Elisabeth; Guittard, Frédéric; Herry, Jean-Marie; Guilbaud, Morgan; Bellon-Fontaine, Marie-Noëlle

2017-04-01

Reducing bacterial adhesion on substrates is fundamental for various industries. In this work, new superhydrophobic surfaces are created by electrodeposition of hydrophobic polymers (PEDOT-F 4 or PEDOT-H 8 ) on stainless steel with controlled topographical features, especially at a nano-scale. Results show that anti-bioadhesive and anti-biofilm properties require the control of the surface topographical features, and should be associated with a low adhesion of water onto the surface (Cassie-Baxter state) with limited crevice features at the scale of bacterial cells (nano-scale structures). Copyright © 2016. Published by Elsevier B.V.

ECLSS Sustaining Metal Materials Compatibility Final Report, Electrochemical and Crevice Corrosion Test Results

NASA Technical Reports Server (NTRS)

Lee, R. E.

2015-01-01

Electrochemical test results are presented for six noble metals evaluated in two acidic test solutions which are representative of waste liquids processed in the Environmental Control and Life Support System (ECLSS) aboard the International Space Station (ISS). The two test solutions consisted of fresh waste liquid which had been modified with a proposed or alternate pretreatment formulation and its associated brine concentrate. The six test metals included three titanium grades, (Commercially Pure, 6Al-4V alloy and 6Al-4V Low Interstitial alloy), two nickel-chromium alloys (Inconel® 625 and Hastelloy® C276), and one high tier stainless steel (Cronidur® 30).