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Sample records for 60-mer probes reveals

  1. Multi-stringency wash of partially hybridized 60-mer probes reveals that the stringency along the probe decreases with distance from the microarray surface

    PubMed Central

    Poulsen, Lena; Søe, Martin Jensen; Snakenborg, Detlef; Møller, Lisbeth Birk; Dufva, Martin

    2008-01-01

    Here, we describe a multi-parametric study of DNA hybridization to probes with 20–70% G + C content. Probes were designed towards 71 different sites/mutations in the phenylalanine hydroxylase gene. Seven probe lengths, three spacer lengths and six stringencies were systematically varied. The three spacer lengths were obtained by placing the gene-specific sequence in discrete steps along the 60-mer probes. The study was performed using Agilent 8 × 15 000 probes custom-made arrays and a home-built array washer providing different stringencies to each of the eight sub-arrays on the slides. Investigation of hybridization signals, specificity and dissociation curves indicated that probes close to the surface were influenced by an additional stringency provided by the microarray surface. Consistent with this, probes close to the surface required 4 × SSC, while probes placed away from the surface required 0.35 × SSC wash buffers in order to give accurate genotyping results. Multiple step dissociation was frequently observed for probes placed furthest away from surface, but not for probes placed proximal to the surface, which is consistent with the hypothesis that there is different stringency along the 60-mer. The results have impact on design of probes for genotyping, gene expression and comparative genome hybridization analysis. PMID:18805905

  2. Saturn Probe: Revealing Solar System Origins

    NASA Astrophysics Data System (ADS)

    Spilker, T. R.

    2015-12-01

    Comparative studies of the gas giant and ice giant planets are needed to reliably discriminate among competing theories of the origin and evolution of giant planets and the solar system, but we lack critical measurements. A Saturn atmospheric entry probe mission would fill a vital part of that gap, allowing comparative studies of Jupiter and Saturn, providing the basis for later comparisons with the ice giants Uranus and Neptune, and informing studies of extrasolar planetary systems now being characterized. The Galileo Probe mission provided the first in situ studies of Jupiter's atmosphere. Similar measurements at Saturn, Uranus and Neptune would provide an important comparative planetology context for the Galileo results. Cassini's "Proximal Orbits" in 2017 will reveal Saturn's internal structure to complement the Juno mission's similar measurements at Jupiter. A Saturn entry probe, complementing the Galileo Probe investigations at Jupiter, would complete a solid basis for improved understanding of both Jupiter and Saturn, an important stepping stone to understanding Uranus and Neptune and solar system formation and evolution. The 2012 Decadal Survey ("DS") added Saturn Probe science objectives to NASA's New Frontiers Program: highest-priority Tier 1 objectives any New Frontiers implementation must achieve, and Tier 2, high priority but lower than Tier 1. A DS mission concept study using extremely conservative assumptions concluded that a Saturn Probe project could fit within New Frontiers resource constraints, giving a PI confidence that they could pursue some Tier 2 objectives, customizing for the proper balance of science return, science team composition, procured or contributed instruments, etc. Contributed instruments could significantly enhance the payload and the science team for greater science return. They also provide international collaboration opportunities, with science benefits well demonstrated by missions such as Cassini-Huygens and Rosetta.

  3. DNA-based digital tension probes reveal integrin forces during early cell adhesion

    PubMed Central

    Zhang, Yun; Ge, Chenghao; Zhu, Cheng; Salaita, Khalid

    2014-01-01

    Mechanical stimuli profoundly alter cell fate, yet the mechanisms underlying mechanotransduction remain obscure due to a lack of methods for molecular force imaging. Here, to address this need, we develop a new class of molecular tension probes that function as a switch to generate a 20–30-fold increase in fluorescence upon experiencing a threshold piconewton force. The probes employ immobilized DNA-hairpins with tunable force response thresholds, ligands, and fluorescence reporters. Quantitative imaging reveals that integrin tension is highly dynamic and increases with an increasing integrin density during adhesion formation. Mixtures of fluorophore-encoded probes show integrin mechanical preference for cyclized-RGD over linear-RGD peptides. Multiplexed probes with variable guanine-cytosine content within their hairpins reveal integrin preference for the more stable probes at the leading tip of growing adhesions near the cell edge. DNA-based tension probes are among the most sensitive optical force reporters to date, overcoming the force and spatial-resolution limitations of traction force microscopy. PMID:25342432

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

    PubMed Central

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

    2014-01-01

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

  5. Automated design of probes for rRNA-targeted fluorescence in situ hybridization reveals the advantages of using dual probes for accurate identification.

    PubMed

    Wright, Erik S; Yilmaz, L Safak; Corcoran, Andrew M; Ökten, Hatice E; Noguera, Daniel R

    2014-08-01

    Fluorescence in situ hybridization (FISH) is a common technique for identifying cells in their natural environment and is often used to complement next-generation sequencing approaches as an integral part of the full-cycle rRNA approach. A major challenge in FISH is the design of oligonucleotide probes with high sensitivity and specificity to their target group. The rapidly expanding number of rRNA sequences has increased awareness of the number of potential nontargets for every FISH probe, making the design of new FISH probes challenging using traditional methods. In this study, we conducted a systematic analysis of published probes that revealed that many have insufficient coverage or specificity for their intended target group. Therefore, we developed an improved thermodynamic model of FISH that can be applied at any taxonomic level, used the model to systematically design probes for all recognized genera of bacteria and archaea, and identified potential cross-hybridizations for the selected probes. This analysis resulted in high-specificity probes for 35.6% of the genera when a single probe was used in the absence of competitor probes and for 60.9% when up to two competitor probes were used. Requiring the hybridization of two independent probes for positive identification further increased specificity. In this case, we could design highly specific probe sets for up to 68.5% of the genera without the use of competitor probes and 87.7% when up to two competitor probes were used. The probes designed in this study, as well as tools for designing new probes, are available online (http://DECIPHER.cee.wisc.edu). PMID:24928876

  6. Solvatochromic Nile Red probes with FRET quencher reveal lipid order heterogeneity in living and apoptotic cells.

    PubMed

    Kreder, Rémy; Pyrshev, Kyrylo A; Darwich, Zeinab; Kucherak, Oleksandr A; Mély, Yves; Klymchenko, Andrey S

    2015-06-19

    Detecting and imaging lipid microdomains (rafts) in cell membranes remain a challenge despite intensive research in the field. Two types of fluorescent probes are used for this purpose: one specifically labels a given phase (liquid ordered, Lo, or liquid disordered, Ld), while the other, being environment-sensitive (solvatochromic), stains the two phases in different emission colors. Here, we combined the two approaches by designing a phase-sensitive probe of the Ld phase and a quencher of the Ld phase. The former is an analogue of the recently developed Nile Red-based probe NR12S, bearing a bulky hydrophobic chain (bNR10S), while the latter is based on Black Hole Quencher-2 designed as bNR10S (bQ10S). Fluorescence spectroscopy of large unilamellar vesicles and microscopy of giant vesicles showed that the bNR10S probe can partition specifically into the Ld phase, while bQ10S can specifically quench the NR12S probe in the Ld phase so that only its fraction in the Lo phase remains fluorescent. Thus, the toolkit of two probes with quencher can specifically target Ld and Lo phases and identify their lipid order from the emission color. Application of this toolkit in living cells (HeLa, CHO, and 293T cell lines) revealed heterogeneity in the cell plasma membranes, observed as distinct probe environments close to the Lo and Ld phases of model membranes. In HeLa cells undergoing apoptosis, our toolkit showed the formation of separate domains of the Ld-like phase in the form of blebs. The developed tools open new possibilities in lipid raft research. PMID:25710589

  7. Ideal probe single-molecule experiments reveal the intrinsic dynamic heterogeneity of a supercooled liquid

    PubMed Central

    Paeng, Keewook; Park, Heungman; Hoang, Dat Tien; Kaufman, Laura J.

    2015-01-01

    The concept of dynamic heterogeneity and the picture of the supercooled liquid as a mosaic of environments with distinct dynamics that interchange in time have been invoked to explain the nonexponential relaxations measured in these systems. The spatial extent and temporal persistence of these regions of distinct dynamics have remained challenging to identify. Here, single-molecule fluorescence measurements using a probe similar in size and mobility to the host o-terphenyl unambiguously reveal exponential relaxations distributed in time and space and directly demonstrate ergodicity of the system down to the glass transition temperature. In the temperature range probed, at least 200 times the structural relaxation time of the host is required to recover ensemble-averaged relaxation at every spatial region in the system. PMID:25825739

  8. A filtering method to reveal crystalline patterns from atom probe microscopy desorption maps

    PubMed Central

    Yao, Lan

    2016-01-01

    A filtering method to reveal the crystallographic information present in Atom Probe Microscopy (APM) data is presented. The method filters atoms based on the time difference between their evaporation and the evaporation of the previous atom. Since this time difference correlates with the location and the local structure of the evaporating atoms on the surface, it can be used to reveal any crystallographic information contained within APM data. The demonstration of this method is illustrated on: • A pure Al specimen for which crystallographic poles are clearly visible on the desorption patterns easily indexed. • Three Fe-15at.% Cr datasets where crystallographic patterns are less obvious and require this filtering method. PMID:27104149

  9. The elastase-PK101 structure: Mechanism of an ultrasensitive activity-based probe revealed

    SciTech Connect

    Lechtenberg, Bernhard C.; Robinson, Howard R.; Kasperkiewicz, Paulina; Drag, Marcin; Riedl, Stefan J.

    2015-01-22

    Human neutrophil elastase (HNE) plays a central role in neutrophil host defense, but its broad specificity makes HNE a difficult target for both inhibitor and probe development. Recently, we identified the unnatural amino acid containing activity-based probe PK101, which exhibits astounding sensitivity and selectivity for HNE, yet completely lacks mechanistic explanation for its unique characteristics. Here, we present the crystal structure of the HNE-PK101 complex which not only reveals the basis for PK101 ultrasensitivity but also uncovers so far unrecognized HNE features. Strikingly, the Nle(O-Bzl) function in the P4 position of PK101 reveals and leverages an “exo-pocket” on HNE as a critical factor for selectivity. Furthermore, the PK101 P3 position harbors a methionine dioxide function, which mimics a post-translationally oxidized methionine residue and forms a critical hydrogen bond to the backbone amide of Gly219 of HNE. Gly219 resides in a Gly–Gly motif that is unique to HNE, yet compulsory for this interaction. Consequently, this feature enables HNE to accommodate substrates that have undergone methionine oxidation, which constitutes a hallmark post-translational modification of neutrophil signaling.

  10. The elastase-PK101 structure: Mechanism of an ultrasensitive activity-based probe revealed

    DOE PAGESBeta

    Lechtenberg, Bernhard C.; Robinson, Howard R.; Kasperkiewicz, Paulina; Drag, Marcin; Riedl, Stefan J.

    2015-01-22

    Human neutrophil elastase (HNE) plays a central role in neutrophil host defense, but its broad specificity makes HNE a difficult target for both inhibitor and probe development. Recently, we identified the unnatural amino acid containing activity-based probe PK101, which exhibits astounding sensitivity and selectivity for HNE, yet completely lacks mechanistic explanation for its unique characteristics. Here, we present the crystal structure of the HNE-PK101 complex which not only reveals the basis for PK101 ultrasensitivity but also uncovers so far unrecognized HNE features. Strikingly, the Nle(O-Bzl) function in the P4 position of PK101 reveals and leverages an “exo-pocket” on HNE asmore » a critical factor for selectivity. Furthermore, the PK101 P3 position harbors a methionine dioxide function, which mimics a post-translationally oxidized methionine residue and forms a critical hydrogen bond to the backbone amide of Gly219 of HNE. Gly219 resides in a Gly–Gly motif that is unique to HNE, yet compulsory for this interaction. Consequently, this feature enables HNE to accommodate substrates that have undergone methionine oxidation, which constitutes a hallmark post-translational modification of neutrophil signaling.« less

  11. Complementary probes reveal that phosphatidylserine is required for the proper transbilayer distribution of cholesterol.

    PubMed

    Maekawa, Masashi; Fairn, Gregory D

    2015-04-01

    Cholesterol is an essential component of metazoan cellular membranes and it helps to maintain the structural integrity and fluidity of the plasma membrane. Here, we developed a cholesterol biosensor, termed D4H, based on the fourth domain of Clostridium perfringens theta-toxin, which recognizes cholesterol in the cytosolic leaflet of the plasma membrane and organelles. The D4H probe disassociates from the plasma membrane upon cholesterol extraction and after perturbations in cellular cholesterol trafficking. When used in combination with a recombinant version of the biosensor, we show that plasmalemmal phosphatidylserine is essential for retaining cholesterol in the cytosolic leaflet of the plasma membrane. In vitro experiments reveal that 1-stearoy-2-oleoyl phosphatidylserine can induce phase separation in cholesterol-containing lipid bilayers and shield cholesterol from cholesterol oxidase. Finally, the altered transbilayer distribution of cholesterol causes flotillin-1 to relocalize to endocytic organelles. This probe should be useful in the future to study pools of cholesterol in the cytosolic leaflet of the plasma membrane and organelles. PMID:25663704

  12. Cellular heterogeneity profiling by hyaluronan probes reveals an invasive but slow-growing breast tumor subset

    PubMed Central

    Veiseh, Mandana; Kwon, Daniel H.; Borowsky, Alexander D.; Tolg, Cornelia; Leong, Hon S.; Lewis, John D.; Turley, Eva A.; Bissell, Mina J.

    2014-01-01

    Tumor heterogeneity confounds cancer diagnosis and the outcome of therapy, necessitating analysis of tumor cell subsets within the tumor mass. Elevated expression of hyaluronan (HA) and HA receptors, receptor for HA-mediated motility (RHAMM)/HA-mediated motility receptor and cluster designation 44 (CD44), in breast tumors correlates with poor outcome. We hypothesized that a probe for detecting HA–HA receptor interactions may reveal breast cancer (BCa) cell heterogeneity relevant to tumor progression. A fluorescent HA (F-HA) probe containing a mixture of polymer sizes typical of tumor microenvironments (10–480 kDa), multiplexed profiling, and flow cytometry were used to monitor HA binding to BCa cell lines of different molecular subtypes. Formulae were developed to quantify binding heterogeneity and to measure invasion in vivo. Two subsets exhibiting differential binding (HA−/low vs. HAhigh) were isolated and characterized for morphology, growth, and invasion in culture and as xenografts in vivo. F-HA–binding amounts and degree of heterogeneity varied with BCa subtype, were highest in the malignant basal-like cell lines, and decreased upon reversion to a nonmalignant phenotype. Binding amounts correlated with CD44 and RHAMM displayed but binding heterogeneity appeared to arise from a differential ability of HA receptor-positive subpopulations to interact with F-HA. HAhigh subpopulations exhibited significantly higher local invasion and lung micrometastases but, unexpectedly, lower proliferation than either unsorted parental cells or the HA−/low subpopulation. Querying F-HA binding to aggressive tumor cells reveals a previously undetected form of heterogeneity that predicts invasive/metastatic behavior and that may aid both early identification of cancer patients susceptible to metastasis, and detection/therapy of invasive BCa subpopulations. PMID:24733940

  13. Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities

    PubMed Central

    Marlow, Jeffrey J.; Skennerton, Connor T.; Li, Zhou; Chourey, Karuna; Hettich, Robert L.; Pan, Chongle; Orphan, Victoria J.

    2016-01-01

    Marine methane seep habitats represent an important control on the global flux of methane. Nucleotide-based meta-omics studies outline community-wide metabolic potential, but expression patterns of environmentally relevant proteins are poorly characterized. Proteomic stable isotope probing (proteomic SIP) provides additional information by characterizing phylogenetically specific, functionally relevant activity in mixed microbial communities, offering enhanced detection through system-wide product integration. Here we applied proteomic SIP to 15NH4+ and CH4 amended seep sediment microcosms in an attempt to track protein synthesis of slow-growing, low-energy microbial systems. Across all samples, 3495 unique proteins were identified, 11% of which were 15N-labeled. Consistent with the dominant anaerobic oxidation of methane (AOM) activity commonly observed in anoxic seep sediments, proteins associated with sulfate reduction and reverse methanogenesis—including the ANME-2 associated methylenetetrahydromethanopterin reductase (Mer)—were all observed to be actively synthesized (15N-enriched). Conversely, proteins affiliated with putative aerobic sulfur-oxidizing epsilon- and gammaproteobacteria showed a marked decrease over time in our anoxic sediment incubations. The abundance and phylogenetic range of 15N-enriched methyl-coenzyme M reductase (Mcr) orthologs, many of which exhibited novel post-translational modifications, suggests that seep sediments provide niches for multiple organisms performing analogous metabolisms. In addition, 26 proteins of unknown function were consistently detected and actively expressed under conditions supporting AOM, suggesting that they play important roles in methane seep ecosystems. Stable isotope probing in environmental proteomics experiments provides a mechanism to determine protein durability and evaluate lineage-specific responses in complex microbial communities placed under environmentally relevant conditions. Our work here

  14. Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities.

    PubMed

    Marlow, Jeffrey J; Skennerton, Connor T; Li, Zhou; Chourey, Karuna; Hettich, Robert L; Pan, Chongle; Orphan, Victoria J

    2016-01-01

    Marine methane seep habitats represent an important control on the global flux of methane. Nucleotide-based meta-omics studies outline community-wide metabolic potential, but expression patterns of environmentally relevant proteins are poorly characterized. Proteomic stable isotope probing (proteomic SIP) provides additional information by characterizing phylogenetically specific, functionally relevant activity in mixed microbial communities, offering enhanced detection through system-wide product integration. Here we applied proteomic SIP to (15)[Formula: see text] and CH4 amended seep sediment microcosms in an attempt to track protein synthesis of slow-growing, low-energy microbial systems. Across all samples, 3495 unique proteins were identified, 11% of which were (15)N-labeled. Consistent with the dominant anaerobic oxidation of methane (AOM) activity commonly observed in anoxic seep sediments, proteins associated with sulfate reduction and reverse methanogenesis-including the ANME-2 associated methylenetetrahydromethanopterin reductase (Mer)-were all observed to be actively synthesized ((15)N-enriched). Conversely, proteins affiliated with putative aerobic sulfur-oxidizing epsilon- and gammaproteobacteria showed a marked decrease over time in our anoxic sediment incubations. The abundance and phylogenetic range of (15)N-enriched methyl-coenzyme M reductase (Mcr) orthologs, many of which exhibited novel post-translational modifications, suggests that seep sediments provide niches for multiple organisms performing analogous metabolisms. In addition, 26 proteins of unknown function were consistently detected and actively expressed under conditions supporting AOM, suggesting that they play important roles in methane seep ecosystems. Stable isotope probing in environmental proteomics experiments provides a mechanism to determine protein durability and evaluate lineage-specific responses in complex microbial communities placed under environmentally relevant

  15. Polyketide Intermediate Mimics as Probes for Revealing Cryptic Stereochemistry of Ketoreductase Domains

    PubMed Central

    2015-01-01

    Among natural product families, polyketides have shown the most promise for combinatorial biosynthesis of natural product-like libraries. Though recent research in the area has provided many mechanistic revelations, a basic-level understanding of kinetic and substrate tolerability is still needed before the full potential of combinatorial biosynthesis can be realized. We have developed a novel set of chemical probes for the study of ketoreductase domains of polyketide synthases. This chemical tool-based approach was validated using the ketoreductase of pikromycin module 2 (PikKR2) as a model system. Triketide substrate mimics 12 and 13 were designed to increase stability (incorporating a nonhydrolyzable thioether linkage) and minimize nonessential functionality (truncating the phosphopantetheinyl arm). PikKR2 reduction product identities as well as steady-state kinetic parameters were determined by a combination of LC-MS/MS analysis of synthetic standards and a NADPH consumption assay. The d-hydroxyl product is consistent with bioinformatic analysis and results from a complementary biochemical and molecular biological approach. When compared to widely employed substrates in previous studies, diketide 63 and trans-decalone 64, substrates 12 and 13 showed 2–10 fold lower KM values (2.4 ± 0.8 and 7.8 ± 2.7 mM, respectively), indicating molecular recognition of intermediate-like substrates. Due to an abundance of the nonreducable enol-tautomer, the kcat values were attenuated by as much as 15–336 fold relative to known substrates. This study reveals the high stereoselectivity of PikKR2 in the face of gross substrate permutation, highlighting the utility of a chemical probe-based approach in the study of polyketide ketoreductases. PMID:25299319

  16. Polyketide intermediate mimics as probes for revealing cryptic stereochemistry of ketoreductase domains.

    PubMed

    Li, Yang; Fiers, William D; Bernard, Steffen M; Smith, Janet L; Aldrich, Courtney C; Fecik, Robert A

    2014-12-19

    Among natural product families, polyketides have shown the most promise for combinatorial biosynthesis of natural product-like libraries. Though recent research in the area has provided many mechanistic revelations, a basic-level understanding of kinetic and substrate tolerability is still needed before the full potential of combinatorial biosynthesis can be realized. We have developed a novel set of chemical probes for the study of ketoreductase domains of polyketide synthases. This chemical tool-based approach was validated using the ketoreductase of pikromycin module 2 (PikKR2) as a model system. Triketide substrate mimics 12 and 13 were designed to increase stability (incorporating a nonhydrolyzable thioether linkage) and minimize nonessential functionality (truncating the phosphopantetheinyl arm). PikKR2 reduction product identities as well as steady-state kinetic parameters were determined by a combination of LC-MS/MS analysis of synthetic standards and a NADPH consumption assay. The d-hydroxyl product is consistent with bioinformatic analysis and results from a complementary biochemical and molecular biological approach. When compared to widely employed substrates in previous studies, diketide 63 and trans-decalone 64, substrates 12 and 13 showed 2-10 fold lower K(M) values (2.4 ± 0.8 and 7.8 ± 2.7 mM, respectively), indicating molecular recognition of intermediate-like substrates. Due to an abundance of the nonreducable enol-tautomer, the k(cat) values were attenuated by as much as 15-336 fold relative to known substrates. This study reveals the high stereoselectivity of PikKR2 in the face of gross substrate permutation, highlighting the utility of a chemical probe-based approach in the study of polyketide ketoreductases. PMID:25299319

  17. Lineage-specific molecular probing reveals novel diversity and ecological partitioning of haplosporidians

    PubMed Central

    Hartikainen, Hanna; Ashford, Oliver S; Berney, Cédric; Okamura, Beth; Feist, Stephen W; Baker-Austin, Craig; Stentiford, Grant D; Bass, David

    2014-01-01

    Haplosporidians are rhizarian parasites of mostly marine invertebrates. They include the causative agents of diseases of commercially important molluscs, including MSX disease in oysters. Despite their importance for food security, their diversity and distributions are poorly known. We used a combination of group-specific PCR primers to probe environmental DNA samples from planktonic and benthic environments in Europe, South Africa and Panama. This revealed several highly distinct novel clades, novel lineages within known clades and seasonal (spring vs autumn) and habitat-related (brackish vs littoral) variation in assemblage composition. High frequencies of haplosporidian lineages in the water column provide the first evidence for life cycles involving planktonic hosts, host-free stages or both. The general absence of haplosporidian lineages from all large online sequence data sets emphasises the importance of lineage-specific approaches for studying these highly divergent and diverse lineages. Combined with host-based field surveys, environmental sampling for pathogens will enhance future detection of known and novel pathogens and the assessment of disease risk. PMID:23966100

  18. A toxin-based probe reveals cytoplasmic exposure of Golgi sphingomyelin.

    PubMed

    Bakrac, Biserka; Kladnik, Ales; Macek, Peter; McHaffie, Gavin; Werner, Andreas; Lakey, Jeremy H; Anderluh, Gregor

    2010-07-16

    Although sphingomyelin is an important cellular lipid, its subcellular distribution is not precisely known. Here we use a sea anemone cytolysin, equinatoxin II (EqtII), which specifically binds sphingomyelin, as a new marker to detect cellular sphingomyelin. A purified fusion protein composed of EqtII and green fluorescent protein (EqtII-GFP) binds to the SM rich apical membrane of Madin-Darby canine kidney (MDCK) II cells when added exogenously, but not to the SM-free basolateral membrane. When expressed intracellularly within MDCK II cells, EqtII-GFP colocalizes with markers for Golgi apparatus and not with those for nucleus, mitochondria, endoplasmic reticulum or plasma membrane. Colocalization with the Golgi apparatus was confirmed by also using NIH 3T3 fibroblasts. Moreover, EqtII-GFP was enriched in cis-Golgi compartments isolated by gradient ultracentrifugation. The data reveal that EqtII-GFP is a sensitive probe for membrane sphingomyelin, which provides new information on cytosolic exposure, essential to understand its diverse physiological roles. PMID:20463009

  19. Tertiary network in mammalian mitochondrial tRNAAsp revealed by solution probing and phylogeny

    PubMed Central

    Messmer, Marie; Pütz, Joern; Suzuki, Takeo; Suzuki, Tsutomu; Sauter, Claude; Sissler, Marie; Catherine, Florentz

    2009-01-01

    Primary and secondary structures of mammalian mitochondrial (mt) tRNAs are divergent from canonical tRNA structures due to highly skewed nucleotide content and large size variability of D- and T-loops. The nonconservation of nucleotides involved in the expected network of tertiary interactions calls into question the rules governing a functional L-shaped three-dimensional (3D) structure. Here, we report the solution structure of human mt-tRNAAsp in its native post-transcriptionally modified form and as an in vitro transcript. Probing performed with nuclease S1, ribonuclease V1, dimethylsulfate, diethylpyrocarbonate and lead, revealed several secondary structures for the in vitro transcribed mt-tRNAAsp including predominantly the cloverleaf. On the contrary, the native tRNAAsp folds into a single cloverleaf structure, highlighting the contribution of the four newly identified post-transcriptional modifications to correct folding. Reactivities of nucleotides and phosphodiester bonds in the native tRNA favor existence of a full set of six classical tertiary interactions between the D-domain and the variable region, forming the core of the 3D structure. Reactivities of D- and T-loop nucleotides support an absence of interactions between these domains. According to multiple sequence alignments and search for conservation of Leontis–Westhof interactions, the tertiary network core building rules apply to all tRNAAsp from mammalian mitochondria. PMID:19767615

  20. Magnetization measurements reveal the local shear stiffness of hydrogels probed by ferromagnetic nanorods

    NASA Astrophysics Data System (ADS)

    Bender, P.; Tschöpe, A.; Birringer, R.

    2014-12-01

    The local mechanical coupling of ferromagnetic nanorods in hydrogels was characterized by magnetization measurements. Nickel nanorods were synthesized by the AAO-template method and embedded in gelatine hydrogels with mechanically soft or hard matrix properties determined by the gelatine weight fraction. By applying a homogeneous magnetic field during gelation the nanorods were aligned along the field resulting in uniaxially textured ferrogels. The magnetization curves of the soft ferrogel exhibited not only important similarities but also characteristic differences as compared to the hard ferrogel. The hystereses measured in a field parallel to the texture axis were almost identical for both samples indicating effective coupling of the nanorods with the polymer network. By contrast, measurements in a magnetic field perpendicular to the texture axis revealed a much higher initial susceptibility of the soft as compared to the hard ferrogel. This difference was attributed to the additional rotation of the nanorods allowed by the reduced shear modulus in the soft ferrogel matrix. Two methods for data analysis were presented which enabled us to determine the shear modulus of the gelatine matrix which was interpreted as a local rather than macroscopic quantity in consideration of the nanoscale of the probe particles.

  1. Deformation-induced trace element redistribution in zircon revealed using atom probe tomography

    PubMed Central

    Piazolo, Sandra; La Fontaine, Alexandre; Trimby, Patrick; Harley, Simon; Yang, Limei; Armstrong, Richard; Cairney, Julie M.

    2016-01-01

    Trace elements diffuse negligible distances through the pristine crystal lattice in minerals: this is a fundamental assumption when using them to decipher geological processes. For example, the reliable use of the mineral zircon (ZrSiO4) as a U-Th-Pb geochronometer and trace element monitor requires minimal radiogenic isotope and trace element mobility. Here, using atom probe tomography, we document the effects of crystal–plastic deformation on atomic-scale elemental distributions in zircon revealing sub-micrometre-scale mechanisms of trace element mobility. Dislocations that move through the lattice accumulate U and other trace elements. Pipe diffusion along dislocation arrays connected to a chemical or structural sink results in continuous removal of selected elements (for example, Pb), even after deformation has ceased. However, in disconnected dislocations, trace elements remain locked. Our findings have important implications for the use of zircon as a geochronometer, and highlight the importance of deformation on trace element redistribution in minerals and engineering materials. PMID:26868040

  2. Deformation-induced trace element redistribution in zircon revealed using atom probe tomography.

    PubMed

    Piazolo, Sandra; La Fontaine, Alexandre; Trimby, Patrick; Harley, Simon; Yang, Limei; Armstrong, Richard; Cairney, Julie M

    2016-01-01

    Trace elements diffuse negligible distances through the pristine crystal lattice in minerals: this is a fundamental assumption when using them to decipher geological processes. For example, the reliable use of the mineral zircon (ZrSiO4) as a U-Th-Pb geochronometer and trace element monitor requires minimal radiogenic isotope and trace element mobility. Here, using atom probe tomography, we document the effects of crystal-plastic deformation on atomic-scale elemental distributions in zircon revealing sub-micrometre-scale mechanisms of trace element mobility. Dislocations that move through the lattice accumulate U and other trace elements. Pipe diffusion along dislocation arrays connected to a chemical or structural sink results in continuous removal of selected elements (for example, Pb), even after deformation has ceased. However, in disconnected dislocations, trace elements remain locked. Our findings have important implications for the use of zircon as a geochronometer, and highlight the importance of deformation on trace element redistribution in minerals and engineering materials. PMID:26868040

  3. Deformation-induced trace element redistribution in zircon revealed using atom probe tomography

    NASA Astrophysics Data System (ADS)

    Piazolo, Sandra; La Fontaine, Alexandre; Trimby, Patrick; Harley, Simon; Yang, Limei; Armstrong, Richard; Cairney, Julie M.

    2016-02-01

    Trace elements diffuse negligible distances through the pristine crystal lattice in minerals: this is a fundamental assumption when using them to decipher geological processes. For example, the reliable use of the mineral zircon (ZrSiO4) as a U-Th-Pb geochronometer and trace element monitor requires minimal radiogenic isotope and trace element mobility. Here, using atom probe tomography, we document the effects of crystal-plastic deformation on atomic-scale elemental distributions in zircon revealing sub-micrometre-scale mechanisms of trace element mobility. Dislocations that move through the lattice accumulate U and other trace elements. Pipe diffusion along dislocation arrays connected to a chemical or structural sink results in continuous removal of selected elements (for example, Pb), even after deformation has ceased. However, in disconnected dislocations, trace elements remain locked. Our findings have important implications for the use of zircon as a geochronometer, and highlight the importance of deformation on trace element redistribution in minerals and engineering materials.

  4. Revealing Nucleic Acid Mutations Using Förster Resonance Energy Transfer-Based Probes.

    PubMed

    Junager, Nina P L; Kongsted, Jacob; Astakhova, Kira

    2016-01-01

    Nucleic acid mutations are of tremendous importance in modern clinical work, biotechnology and in fundamental studies of nucleic acids. Therefore, rapid, cost-effective and reliable detection of mutations is an object of extensive research. Today, Förster resonance energy transfer (FRET) probes are among the most often used tools for the detection of nucleic acids and in particular, for the detection of mutations. However, multiple parameters must be taken into account in order to create efficient FRET probes that are sensitive to nucleic acid mutations. In this review; we focus on the design principles for such probes and available computational methods that allow for their rational design. Applications of advanced, rationally designed FRET probes range from new insights into cellular heterogeneity to gaining new knowledge of nucleic acid structures directly in living cells. PMID:27472344

  5. A Metabolic Probe-Enabled Strategy Reveals Uptake and Protein Targets of Polyunsaturated Aldehydes in the Diatom Phaeodactylum tricornutum

    PubMed Central

    Wolfram, Stefanie; Wielsch, Natalie; Hupfer, Yvonne; Mönch, Bettina; Lu-Walther, Hui-Wen; Heintzmann, Rainer; Werz, Oliver; Svatoš, Aleš; Pohnert, Georg

    2015-01-01

    Diatoms are unicellular algae of crucial importance as they belong to the main primary producers in aquatic ecosystems. Several diatom species produce polyunsaturated aldehydes (PUAs) that have been made responsible for chemically mediated interactions in the plankton. PUA-effects include chemical defense by reducing the reproductive success of grazing copepods, allelochemical activity by interfering with the growth of competing phytoplankton and cell to cell signaling. We applied a PUA-derived molecular probe, based on the biologically highly active 2,4-decadienal, with the aim to reveal protein targets of PUAs and affected metabolic pathways. By using fluorescence microscopy, we observed a substantial uptake of the PUA probe into cells of the diatom Phaeodactylum tricornutum in comparison to the uptake of a structurally closely related control probe based on a saturated aldehyde. The specific uptake motivated a chemoproteomic approach to generate a qualitative inventory of proteins covalently targeted by the α,β,γ,δ-unsaturated aldehyde structure element. Activity-based protein profiling revealed selective covalent modification of target proteins by the PUA probe. Analysis of the labeled proteins gave insights into putative affected molecular functions and biological processes such as photosynthesis including ATP generation and catalytic activity in the Calvin cycle or the pentose phosphate pathway. The mechanism of action of PUAs involves covalent reactions with proteins that may result in protein dysfunction and interference of involved pathways. PMID:26496085

  6. A Metabolic Probe-Enabled Strategy Reveals Uptake and Protein Targets of Polyunsaturated Aldehydes in the Diatom Phaeodactylum tricornutum.

    PubMed

    Wolfram, Stefanie; Wielsch, Natalie; Hupfer, Yvonne; Mönch, Bettina; Lu-Walther, Hui-Wen; Heintzmann, Rainer; Werz, Oliver; Svatoš, Aleš; Pohnert, Georg

    2015-01-01

    Diatoms are unicellular algae of crucial importance as they belong to the main primary producers in aquatic ecosystems. Several diatom species produce polyunsaturated aldehydes (PUAs) that have been made responsible for chemically mediated interactions in the plankton. PUA-effects include chemical defense by reducing the reproductive success of grazing copepods, allelochemical activity by interfering with the growth of competing phytoplankton and cell to cell signaling. We applied a PUA-derived molecular probe, based on the biologically highly active 2,4-decadienal, with the aim to reveal protein targets of PUAs and affected metabolic pathways. By using fluorescence microscopy, we observed a substantial uptake of the PUA probe into cells of the diatom Phaeodactylum tricornutum in comparison to the uptake of a structurally closely related control probe based on a saturated aldehyde. The specific uptake motivated a chemoproteomic approach to generate a qualitative inventory of proteins covalently targeted by the α,β,γ,δ-unsaturated aldehyde structure element. Activity-based protein profiling revealed selective covalent modification of target proteins by the PUA probe. Analysis of the labeled proteins gave insights into putative affected molecular functions and biological processes such as photosynthesis including ATP generation and catalytic activity in the Calvin cycle or the pentose phosphate pathway. The mechanism of action of PUAs involves covalent reactions with proteins that may result in protein dysfunction and interference of involved pathways. PMID:26496085

  7. Molecular Probe Dynamics Reveals Suppression of Ice-Like Regions in Strongly Confined Supercooled Water

    PubMed Central

    Banerjee, Debamalya; Bhat, Shrivalli N.; Bhat, Subray V.; Leporini, Dino

    2012-01-01

    The structure of the hydrogen bond network is a key element for understanding water's thermodynamic and kinetic anomalies. While ambient water is strongly believed to be a uniform, continuous hydrogen-bonded liquid, there is growing consensus that supercooled water is better described in terms of distinct domains with either a low-density ice-like structure or a high-density disordered one. We evidenced two distinct rotational mobilities of probe molecules in interstitial supercooled water of polycrystalline ice [Banerjee D, et al. (2009) ESR evidence for 2 coexisting liquid phases in deeply supercooled bulk water. Proc Natl Acad Sci USA 106: 11448–11453]. Here we show that, by increasing the confinement of interstitial water, the mobility of probe molecules, surprisingly, increases. We argue that loose confinement allows the presence of ice-like regions in supercooled water, whereas a tighter confinement yields the suppression of this ordered fraction and leads to higher fluidity. Compelling evidence of the presence of ice-like regions is provided by the probe orientational entropy barrier which is set, through hydrogen bonding, by the configuration of the surrounding water molecules and yields a direct measure of the configurational entropy of the same. We find that, under loose confinement of supercooled water, the entropy barrier surmounted by the slower probe fraction exceeds that of equilibrium water by the melting entropy of ice, whereas no increase of the barrier is observed under stronger confinement. The lower limit of metastability of supercooled water is discussed. PMID:23049747

  8. Site-Specific DNA Structural and Dynamic Features Revealed by Nucleotide-Independent Nitroxide Probes

    SciTech Connect

    Popova, Anna; Kalai, Tamas; Hideg, Kalman; Qin, Peter Z.

    2009-09-15

    In site-directed spin labeling, a covalently attached nitroxide probe containing a chemically inert unpaired electron is utilized to obtain information on the local environment of the parent macromolecule. Studies presented here examine the feasibility of probing local DNA structural and dynamic features using a class of nitroxide probes that are linked to chemically substituted phosphorothioate positions at the DNA backbone. Two members of this family, designated as R5 and R5a, were attached to eight different sites of a dodecameric DNA duplex without severely perturbing the native B-form conformation. Measured X-band electron paramagnetic resonance (EPR) spectra, which report on nitroxide rotational motions, were found to vary depending on the location of the label (e.g., duplex center vs termini) and the surrounding DNA sequence. This indicates that R5 and R5a can provide information on the DNA local environment at the level of an individual nucleotide. As these probes can be attached to arbitrary nucleotides within a nucleic acid sequence, they may provide a means to “scan” a given DNA molecule in order to interrogate its local structural and dynamic features.

  9. Complex structural dynamics of nanocatalysts revealed in Operando conditions by correlated imaging and spectroscopy probes.

    PubMed

    Li, Y; Zakharov, D; Zhao, S; Tappero, R; Jung, U; Elsen, A; Baumann, Ph; Nuzzo, R G; Stach, E A; Frenkel, A I

    2015-01-01

    Understanding how heterogeneous catalysts change size, shape and structure during chemical reactions is limited by the paucity of methods for studying catalytic ensembles in working state, that is, in operando conditions. Here by a correlated use of synchrotron X-ray absorption spectroscopy and scanning transmission electron microscopy in operando conditions, we quantitatively describe the complex structural dynamics of supported Pt catalysts exhibited during an exemplary catalytic reaction-ethylene hydrogenation. This work exploits a microfabricated catalytic reactor compatible with both probes. The results demonstrate dynamic transformations of the ensemble of Pt clusters that spans a broad size range throughout changing reaction conditions. This method is generalizable to quantitative operando studies of complex systems using a wide variety of X-ray and electron-based experimental probes. PMID:26119246

  10. Complex structural dynamics of nanocatalysts revealed in Operando conditions by correlated imaging and spectroscopy probes

    NASA Astrophysics Data System (ADS)

    Li, Y.; Zakharov, D.; Zhao, S.; Tappero, R.; Jung, U.; Elsen, A.; Baumann, Ph.; Nuzzo, R. G.; Stach, E. A.; Frenkel, A. I.

    2015-06-01

    Understanding how heterogeneous catalysts change size, shape and structure during chemical reactions is limited by the paucity of methods for studying catalytic ensembles in working state, that is, in operando conditions. Here by a correlated use of synchrotron X-ray absorption spectroscopy and scanning transmission electron microscopy in operando conditions, we quantitatively describe the complex structural dynamics of supported Pt catalysts exhibited during an exemplary catalytic reaction--ethylene hydrogenation. This work exploits a microfabricated catalytic reactor compatible with both probes. The results demonstrate dynamic transformations of the ensemble of Pt clusters that spans a broad size range throughout changing reaction conditions. This method is generalizable to quantitative operando studies of complex systems using a wide variety of X-ray and electron-based experimental probes.

  11. Complex structural dynamics of nanocatalysts revealed in Operando conditions by correlated imaging and spectroscopy probes

    SciTech Connect

    Li, Y.; Zakharov, D.; Zhao, S.; Tappero, R.; Jung, U.; Elsen, A.; Baumann, Ph.; Nuzzo, R. G.; Stach, E. A.; Frenkel, A. I.

    2015-06-29

    Understanding how heterogeneous catalysts change size, shape and structure during chemical reactions is limited by the paucity of methods for studying catalytic ensembles in working state, that is, in operando conditions. Here by a correlated use of synchrotron X-ray absorption spectroscopy and scanning transmission electron microscopy in operando conditions, we quantitatively describe the complex structural dynamics of supported Pt catalysts exhibited during an exemplary catalytic reaction—ethylene hydrogenation. This work exploits a microfabricated catalytic reactor compatible with both probes. The results demonstrate dynamic transformations of the ensemble of Pt clusters that spans a broad size range throughout changing reaction conditions. Lastly, this method is generalizable to quantitative operando studies of complex systems using a wide variety of X-ray and electron-based experimental probes.

  12. In Situ X-Ray Probing Reveals Fingerprints of Surface Platinum Oxide

    SciTech Connect

    Friebel, Daniel

    2011-08-24

    In situ x-ray absorption spectroscopy (XAS) at the Pt L{sub 3} edge is a useful probe for Pt-O interactions at polymer electrolyte membrane fuel cell (PEMFC) cathodes. We show that XAS using the high energy resolution fluorescence detection (HERFD) mode, applied to a well-defined monolayer Pt/Rh(111) sample where the bulk penetrating hard x-rays probe only surface Pt atoms, provides a unique sensitivity to structure and chemical bonding at the Pt-electrolyte interface. Ab initio multiple-scattering calculations using the FEFF8 code and complementary extended x-ray absorption fine structure (EXAFS) results indicate that the commonly observed large increase of the white-line at high electrochemical potentials on PEMFC cathodes originates from platinum oxide formation, whereas previously proposed chemisorbed oxygen-containing species merely give rise to subtle spectral changes.

  13. Complex structural dynamics of nanocatalysts revealed in Operando conditions by correlated imaging and spectroscopy probes

    DOE PAGESBeta

    Li, Y.; Zakharov, D.; Zhao, S.; Tappero, R.; Jung, U.; Elsen, A.; Baumann, Ph.; Nuzzo, R. G.; Stach, E. A.; Frenkel, A. I.

    2015-06-29

    Understanding how heterogeneous catalysts change size, shape and structure during chemical reactions is limited by the paucity of methods for studying catalytic ensembles in working state, that is, in operando conditions. Here by a correlated use of synchrotron X-ray absorption spectroscopy and scanning transmission electron microscopy in operando conditions, we quantitatively describe the complex structural dynamics of supported Pt catalysts exhibited during an exemplary catalytic reaction—ethylene hydrogenation. This work exploits a microfabricated catalytic reactor compatible with both probes. The results demonstrate dynamic transformations of the ensemble of Pt clusters that spans a broad size range throughout changing reaction conditions. Lastly,more » this method is generalizable to quantitative operando studies of complex systems using a wide variety of X-ray and electron-based experimental probes.« less

  14. Complex structural dynamics of nanocatalysts revealed in Operando conditions by correlated imaging and spectroscopy probes

    PubMed Central

    Li, Y.; Zakharov, D.; Zhao, S.; Tappero, R.; Jung, U.; Elsen, A.; Baumann, Ph.; Nuzzo, R.G.; Stach, E.A.; Frenkel, A.I.

    2015-01-01

    Understanding how heterogeneous catalysts change size, shape and structure during chemical reactions is limited by the paucity of methods for studying catalytic ensembles in working state, that is, in operando conditions. Here by a correlated use of synchrotron X-ray absorption spectroscopy and scanning transmission electron microscopy in operando conditions, we quantitatively describe the complex structural dynamics of supported Pt catalysts exhibited during an exemplary catalytic reaction—ethylene hydrogenation. This work exploits a microfabricated catalytic reactor compatible with both probes. The results demonstrate dynamic transformations of the ensemble of Pt clusters that spans a broad size range throughout changing reaction conditions. This method is generalizable to quantitative operando studies of complex systems using a wide variety of X-ray and electron-based experimental probes. PMID:26119246

  15. Atom probe tomographic mapping directly reveals the atomic distribution of phosphorus in resin embedded ferritin

    DOE PAGESBeta

    Perea, Daniel E.; Liu, Jia; Bartrand, Jonah A. G.; Dicken, Quinten G.; Thevuthasan, Suntharampillai Theva; Browning, Nigel D.; Evans, James E.

    2016-02-29

    In this study, we report the atomic-scale analysis of biological interfaces using atom probe tomography. Embedding the protein ferritin in an organic polymer resin lacking nitrogen provided chemical contrast to visualize atomic distributions and distinguish organic-organic and organic-inorganic interfaces. The sample preparation method can be directly extended to further enhance the study of biological, organic and inorganic nanomaterials relevant to health, energy or the environment.

  16. Properties of polyethylene glycol/cyclodextrin hydrogels revealed by spin probes and spin labelling methods.

    PubMed

    Ionita, Gabriela; Ariciu, Ana Maria; Turcu, Ioana Maria; Chechik, Victor

    2014-03-21

    The properties of a gel consisting of a covalent network formed by the reaction of isocyanate end-capped polyethylene glycol (PEG) with β-cyclodextrin, were investigated by EPR spectroscopy. Spin-labelled cyclodextrin was incorporated into the cross-link points of the gel and at the chain ends. The dynamics of the gel fibres as reported by the spin label, was found to be sensitive to the H-bonding ability of the solvent, density of cross-links and temperature. Addition of spin probes (e.g., TEMPO and adamantane-TEMPO) to the unlabelled gel made it possible to characterise the solvent pools in the gel. While TEMPO was uniformly distributed throughout the solvent pools, the adamantane derivative was located at the gel fibre-solvent pool interface; these two probes thus reported on the different locations in the solvent pools. At low temperature, the gels were shown to prevent ice crystallisation in the solvent pools resulting in the formation of supercooled water. Both probes showed that the water froze at ca. 250 K, thus suggesting that the properties of the supercooled water are uniform across the solvent pools. PMID:24651650

  17. Vibrational energy flow in photoactive yellow protein revealed by infrared pump-visible probe spectroscopy.

    PubMed

    Nakamura, Ryosuke; Hamada, Norio

    2015-05-14

    Vibrational energy flow in the electronic ground state of photoactive yellow protein (PYP) is studied by ultrafast infrared (IR) pump-visible probe spectroscopy. Vibrational modes of the chromophore and the surrounding protein are excited with a femtosecond IR pump pulse, and the subsequent vibrational dynamics in the chromophore are selectively probed with a visible probe pulse through changes in the absorption spectrum of the chromophore. We thus obtain the vibrational energy flow with four characteristic time constants. The vibrational excitation with an IR pulse at 1340, 1420, 1500, or 1670 cm(-1) results in ultrafast intramolecular vibrational redistribution (IVR) with a time constant of 0.2 ps. The vibrational modes excited through the IVR process relax to the initial ground state with a time constant of 6-8 ps in parallel with vibrational cooling with a time constant of 14 ps. In addition, upon excitation with an IR pulse at 1670 cm(-1), we observe the energy flow from the protein backbone to the chromophore that occurs with a time constant of 4.2 ps. PMID:25896223

  18. A caspase active site probe reveals high fractional inhibition needed to block DNA fragmentation.

    PubMed

    Méthot, Nathalie; Vaillancourt, John P; Huang, JingQi; Colucci, John; Han, Yongxin; Ménard, Stéphane; Zamboni, Robert; Toulmond, Sylvie; Nicholson, Donald W; Roy, Sophie

    2004-07-01

    Apoptotic markers consist of either caspase substrate cleavage products or phenotypic changes that manifest themselves as a consequence of caspase-mediated substrate cleavage. We have shown recently that pharmacological inhibitors of caspase activity prevent the appearance of two such apoptotic manifestations, alphaII-spectrin cleavage and DNA fragmentation, but that blockade of the latter required a significantly higher concentration of inhibitor. We investigated this phenomenon through the use of a novel radiolabeled caspase inhibitor, [(125)I]M808, which acts as a caspase active site probe. [(125)I]M808 bound to active caspases irreversibly and with high sensitivity in apoptotic cell extracts, in tissue extracts from several commonly used animal models of cellular injury, and in living cells. Moreover, [(125)I]M808 detected active caspases in septic mice when injected intravenously. Using this caspase probe, an active site occupancy assay was developed and used to measure the fractional inhibition required to block apoptosis-induced DNA fragmentation. In thymocytes, occupancy of up to 40% of caspase active sites had no effect on DNA fragmentation, whereas inhibition of half of the DNA cleaving activity required between 65 and 75% of active site occupancy. These results suggest that a high and persistent fractional inhibition will be required for successful caspase inhibition-based therapies. PMID:15067000

  19. Benzene Probes in Molecular Dynamics Simulations Reveal Novel Binding Sites for Ligand Design.

    PubMed

    Tan, Yaw Sing; Reeks, Judith; Brown, Christopher J; Thean, Dawn; Ferrer Gago, Fernando Jose; Yuen, Tsz Ying; Goh, Eunice Tze Leng; Lee, Xue Er Cheryl; Jennings, Claire E; Joseph, Thomas L; Lakshminarayanan, Rajamani; Lane, David P; Noble, Martin E M; Verma, Chandra S

    2016-09-01

    Protein flexibility poses a major challenge in binding site identification. Several computational pocket detection methods that utilize small-molecule probes in molecular dynamics (MD) simulations have been developed to address this issue. Although they have proven hugely successful at reproducing experimental structural data, their ability to predict new binding sites that are yet to be identified and characterized has not been demonstrated. Here, we report the use of benzenes as probe molecules in ligand-mapping MD (LMMD) simulations to predict the existence of two novel binding sites on the surface of the oncoprotein MDM2. One of them was serendipitously confirmed by biophysical assays and X-ray crystallography to be important for the binding of a new family of hydrocarbon stapled peptides that were specifically designed to target the other putative site. These results highlight the predictive power of LMMD and suggest that predictions derived from LMMD simulations can serve as a reliable basis for the identification of novel ligand binding sites in structure-based drug design. PMID:27532490

  20. Recombinant Probes Reveal Dynamic Localization of CaMKIIα within Somata of Cortical Neurons

    PubMed Central

    Mora, Rudy J.; Roberts, Richard W.

    2013-01-01

    In response to NMDA receptor stimulation, CaMKIIα moves rapidly from a diffuse distribution within the shafts of neuronal dendrites to a clustered postsynaptic distribution. However, less is known about CaMKIIα localization and trafficking within neuronal somata. Here we use a novel recombinant probe capable of labeling endogenous CaMKIIα in living rat neurons to examine its localization and trafficking within the somata of cortical neurons. This probe, which was generated using an mRNA display selection, binds to endogenous CaMKIIα at high affinity and specificity following expression in rat cortical neurons in culture. In ∼45% of quiescent cortical neurons, labeled clusters of CaMKIIα 1–4 μm in diameter were present. Upon exposure to glutamate and glycine, CaMKIIα clusters disappeared in a Ca2+-dependent manner within seconds. Moreover, minutes after the removal of glutamate and glycine, the clusters returned to their original configuration. The clusters, which also appear in cortical neurons in sections taken from mouse brains, contain actin and disperse upon exposure to cytochalasin D, an actin depolymerizer. In conclusion, within the soma, CaMKII localizes and traffics in a manner that is distinct from its localization and trafficking within the dendrites. PMID:24005308

  1. Fractal Nature of Metallic and Insulating Domain Configurations in a VO2 Thin Film Revealed by Kelvin Probe Force Microscopy

    PubMed Central

    Sohn, Ahrum; Kanki, Teruo; Sakai, Kotaro; Tanaka, Hidekazu; Kim, Dong-Wook

    2015-01-01

    We investigated the surface work function (WS) and its spatial distribution for epitaxial VO2/TiO2 thin films using Kelvin probe force microscopy (KPFM). Nearly grain-boundary-free samples allowed observation of metallic and insulating domains with distinct WS values, throughout the metal–insulator transition. The metallic fraction, estimated from WS maps, describes the evolution of the resistance based on a two-dimensional percolation model. The KPFM measurements also revealed the fractal nature of the domain configuration. PMID:25982229

  2. Atom Probe Tomographic Mapping Directly Reveals the Atomic Distribution of Phosphorus in Resin Embedded Ferritin

    PubMed Central

    Perea, Daniel E.; Liu, Jia; Bartrand, Jonah; Dicken, Quinten; Thevuthasan, S. Theva; Browning, Nigel D.; Evans, James E.

    2016-01-01

    Here we report the atomic-scale analysis of biological interfaces within the ferritin protein using atom probe tomography that is facilitated by an advanced specimen preparation approach. Embedding ferritin in an organic polymer resin lacking nitrogen provided chemical contrast to visualise atomic distributions and distinguish the inorganic-organic interface of the ferrihydrite mineral core and protein shell, as well as the organic-organic interface between the ferritin protein shell and embedding resin. In addition, we definitively show the atomic-scale distribution of phosphorus as being at the surface of the ferrihydrite mineral with the distribution of sodium mapped within the protein shell environment with an enhanced distribution at the mineral/protein interface. The sample preparation method is robust and can be directly extended to further enhance the study of biological, organic and inorganic nanomaterials relevant to health, energy or the environment. PMID:26924804

  3. Peptide Probes Reveal a Hydrophobic Steric Ratchet in the Anthrax Toxin Protective Antigen Translocase.

    PubMed

    Colby, Jennifer M; Krantz, Bryan A

    2015-11-01

    Anthrax toxin is a tripartite virulence factor produced by Bacillus anthracis during infection. Under acidic endosomal pH conditions, the toxin's protective antigen (PA) component forms a transmembrane channel in host cells. The PA channel then translocates its two enzyme components, lethal factor and edema factor, into the host cytosol under the proton motive force. Protein translocation under a proton motive force is catalyzed by a series of nonspecific polypeptide binding sites, called clamps. A 10-residue guest/host peptide model system, KKKKKXXSXX, was used to functionally probe polypeptide-clamp interactions within wild-type PA channels. The guest residues were Thr, Ala, Leu, Phe, Tyr, and Trp. In steady-state translocation experiments, the channel blocked most tightly with peptides that had increasing amounts of nonpolar surface area. Cooperative peptide binding was observed in the Trp-containing peptide sequence but not the other tested sequences. Trp substitutions into a flexible, uncharged linker between the lethal factor amino-terminal domain and diphtheria toxin A chain expedited translocation. Therefore, peptide-clamp sites in translocase channels can sense large steric features (like tryptophan) in peptides, and while these steric interactions may make a peptide translocate poorly, in the context of folded domains, they can make the protein translocate more rapidly presumably via a hydrophobic steric ratchet mechanism. PMID:26363343

  4. Combining structure probing data on RNA mutants with evolutionary information reveals RNA-binding interfaces

    PubMed Central

    Reinharz, Vladimir; Ponty, Yann; Waldispühl, Jérôme

    2016-01-01

    Systematic structure probing experiments (e.g. SHAPE) of RNA mutants such as the mutate-and-map (MaM) protocol give us a direct access into the genetic robustness of ncRNA structures. Comparative studies of homologous sequences provide a distinct, yet complementary, approach to analyze structural and functional properties of non-coding RNAs. In this paper, we introduce a formal framework to combine the biochemical signal collected from MaM experiments, with the evolutionary information available in multiple sequence alignments. We apply neutral theory principles to detect complex long-range dependencies between nucleotides of a single stranded RNA, and implement these ideas into a software called aRNhAck. We illustrate the biological significance of this signal and show that the nucleotides networks calculated with aRNhAck are correlated with nucleotides located in RNA–RNA, RNA–protein, RNA–DNA and RNA–ligand interfaces. aRNhAck is freely available at http://csb.cs.mcgill.ca/arnhack. PMID:27095200

  5. Micron-sized structure in a thin glycerol film revealed by fluorescent probes.

    PubMed

    Xia, Ted; Xiao, Liantuan; Orrit, Michel

    2009-12-01

    We report on micrometer-sized structures in supercooled glycerol observed by imaging fluorescent probes at the temperatures close to, but above, the glass transition temperature (190 K). Two distinct heterogeneous patterns of the fluorescence intensity were detected, depending on how fast the sample was cooled down. In a slowly cooled sample, we observed a Swiss cheese-like pattern in which many micrometer-sized dark spots were nucleated in a bright background. A quickly cooled sample resulted in a spinodal decomposition pattern where many bright island-like features on micrometer scale were dispersed in a dark matrix. Similar patterns were seen earlier in triphenyl phosphite, another molecular liquid, which shows solid-like behavior at temperatures above its glass transition. Once the heterogeneous patterns are formed in the glycerol, they can persist for days, unless the samples are heated above 260 K for more than 10 h. Such heterogeneous patterns are ascribed to differential dye distributions in the glycerol film, pointing to long-lived and micrometer-scale density fluctuations in supercooled glycerol. The observation of such heterogeneity may provide additional understanding on how supercooled glycerol behaves before it turns into a glass. PMID:19929008

  6. Combining structure probing data on RNA mutants with evolutionary information reveals RNA-binding interfaces.

    PubMed

    Reinharz, Vladimir; Ponty, Yann; Waldispühl, Jérôme

    2016-06-20

    Systematic structure probing experiments (e.g. SHAPE) of RNA mutants such as the mutate-and-map (MaM) protocol give us a direct access into the genetic robustness of ncRNA structures. Comparative studies of homologous sequences provide a distinct, yet complementary, approach to analyze structural and functional properties of non-coding RNAs. In this paper, we introduce a formal framework to combine the biochemical signal collected from MaM experiments, with the evolutionary information available in multiple sequence alignments. We apply neutral theory principles to detect complex long-range dependencies between nucleotides of a single stranded RNA, and implement these ideas into a software called aRNhAck We illustrate the biological significance of this signal and show that the nucleotides networks calculated with aRNhAck are correlated with nucleotides located in RNA-RNA, RNA-protein, RNA-DNA and RNA-ligand interfaces. aRNhAck is freely available at http://csb.cs.mcgill.ca/arnhack. PMID:27095200

  7. Generic affinities among crocodilians as revealed by DNA fingerprinting with a Bkm-derived probe.

    PubMed Central

    Aggarwal, R K; Majumdar, K C; Lang, J W; Singh, L

    1994-01-01

    Genetic fingerprint profiles have been successfully used for establishing biological relationships, in linkage analysis, and in studies of population structure but have not so far been used for ascertaining phylogenetic relationships among related groups of species and genera. This is largely because these profiles are thought to evolve too rapidly to be informative over large time intervals. However, we show here that among the Crocodilia, whose phylogeny is a debated issue, these profiles can provide phylogenetically useful information. By using the probe Bkm-2(8), DNA fingerprints with distinct bands distributed in the size range 0.5-23.0 kb were obtained for individuals of 18 species belonging to seven of the eight genera of crocodilians. These genetic profiles showed individual-, species-, and restriction enzyme-specific patterns. In addition, striking differences were observed in the copy number of Bkm-related sequences in genomes of different crocodilian species. The qualitative data from DNA fingerprint profiles, and quantitative data on copy number variation in Bkm-related sequences, suggest that these genera belong to two distinct groups, one of which includes Alligator, Paleosuchus, and Caiman; the other includes Crocodylus, Osteolaemus, Tomistoma, and Gavialis. A close relationship between Tomistoma and Gavialis is also suggested by these results. Images PMID:7937999

  8. Probing HIV-1 membrane liquid order by Laurdan staining reveals producer cell-dependent differences.

    PubMed

    Lorizate, Maier; Brügger, Britta; Akiyama, Hisashi; Glass, Bärbel; Müller, Barbara; Anderluh, Gregor; Wieland, Felix T; Kräusslich, Hans-Georg

    2009-08-14

    Viruses acquire their envelope by budding from a host cell membrane, but viral lipid composition may differ from that of the budding membrane. We have previously reported that the HIV-1 membrane is highly enriched in cholesterol, sphingolipids, and other raft lipids, suggesting that the virus may bud from pre-existing or virus-induced lipid rafts. Here, we employed the environmentally sensitive fluorescent dye Laurdan to study the membrane lateral structure of HIV-1 derived from different cell lines. Differences in viral membrane order detected by Laurdan staining were shown by mass spectrometry to be due to differences in lipid composition. Isogenic viruses from two different cell lines were both strongly enriched in raft lipids and displayed a liquid-ordered membrane, but these effects were significantly more pronounced for HIV-1 from the T-cell line MT-4 compared with virus from 293T cells. Host-dependent differences in the lipidomes predominantly affected the ratio of sphingomyelins (including dihydrosphingomyelin) to phosphatidylcholine, whereas cholesterol contents were similar. Accordingly, treatment of infectious HIV-1 with the sphingomyelin-binding toxins Equinatoxin-II or lysenin showed differential inhibition of infectivity. Liposomes consisting of lipids that had been extracted from viral particles exhibited slightly less liquid order than the respective viral membranes, which is likely to be due to absence of membrane proteins and to loss of lipid asymmetry. Synthetic liposomes consisting of a quaternary lipid mixture emulating the viral lipids showed a liquid order similar to liposomes derived from virion lipids. Thus, Laurdan staining represents a rapid and quantitative method to probe viral membrane liquid order and may prove useful in the search for lipid active drugs. PMID:19553682

  9. Probing HIV-1 Membrane Liquid Order by Laurdan Staining Reveals Producer Cell-dependent Differences*

    PubMed Central

    Lorizate, Maier; Brügger, Britta; Akiyama, Hisashi; Glass, Bärbel; Müller, Barbara; Anderluh, Gregor; Wieland, Felix T.; Kräusslich, Hans-Georg

    2009-01-01

    Viruses acquire their envelope by budding from a host cell membrane, but viral lipid composition may differ from that of the budding membrane. We have previously reported that the HIV-1 membrane is highly enriched in cholesterol, sphingolipids, and other raft lipids, suggesting that the virus may bud from pre-existing or virus-induced lipid rafts. Here, we employed the environmentally sensitive fluorescent dye Laurdan to study the membrane lateral structure of HIV-1 derived from different cell lines. Differences in viral membrane order detected by Laurdan staining were shown by mass spectrometry to be due to differences in lipid composition. Isogenic viruses from two different cell lines were both strongly enriched in raft lipids and displayed a liquid-ordered membrane, but these effects were significantly more pronounced for HIV-1 from the T-cell line MT-4 compared with virus from 293T cells. Host-dependent differences in the lipidomes predominantly affected the ratio of sphingomyelins (including dihydrosphingomyelin) to phosphatidylcholine, whereas cholesterol contents were similar. Accordingly, treatment of infectious HIV-1 with the sphingomyelin-binding toxins Equinatoxin-II or lysenin showed differential inhibition of infectivity. Liposomes consisting of lipids that had been extracted from viral particles exhibited slightly less liquid order than the respective viral membranes, which is likely to be due to absence of membrane proteins and to loss of lipid asymmetry. Synthetic liposomes consisting of a quaternary lipid mixture emulating the viral lipids showed a liquid order similar to liposomes derived from virion lipids. Thus, Laurdan staining represents a rapid and quantitative method to probe viral membrane liquid order and may prove useful in the search for lipid active drugs. PMID:19553682

  10. The Role of ULF Waves in Ring Current and Radiation Belt Dynamics as Revealed by NASA's Van Allen Probes

    NASA Astrophysics Data System (ADS)

    Claudepierre, S. G.; Mann, I. R.; Takahashi, K.; Toffoletto, F. R.; Wiltberger, M. J.; O'Brien, T. P., III; Fennell, J. F.

    2015-12-01

    NASA's Van Allen Probes have been on orbit since late-August 2012, precessing through all local times over the first two years of the mission, returning high-quality wave and particle observations in the near-Earth space environment. The Probes reveal radiation belt and ring current dynamics with unrivaled accuracy and resolution, providing unambiguous evidence of resonant wave-particle interactions in the inner magnetosphere (e.g., L<7). It is well known that a class of such wave-particle interactions, namely ultra-low frequency (ULF; ~1-10 mHz) wave interactions, contribute to the radial transport of electrons and protons in this region and thus, the large-scale, global morphology of the radiation belts. We focus our investigations on observations of drift-resonance with shock-induced ULF waves, drift-resonance with localized, monochromatic ULF waves, and ULF fluctuations related to nightside particle injections. We also discuss recent advances in the modeling of ULF waves and the challenges that lie ahead.

  11. High Resolution Dopant Profiles Revealed by Atom Probe Tomography and STEM-EBIC for CdTe Based Solar Cells

    SciTech Connect

    Poplawsky, Jonathan D.; Li, Chen; Paudel, Naba; Guo, Wei; Yan, Yanfa; Pennycook, Stephen J.

    2016-01-01

    Segregated elements and their diffusion profiles within grain boundaries and interfaces resulting from post deposition heat treatments are revealed using atom probe tomography (APT), scanning transmission electron microscopy (STEM), and electron beam induced current (EBIC) techniques. The results demonstrate how these techniques complement each other to provide conclusive evidence for locations of space charge regions and mechanisms that create them at the nanoscale. Most importantly, a Cl dopant profile that extends ~5 nm into CdTe grains interfacing the CdS is shown using APT and STEM synergy, which has been shown to push the pn-junction into the CdTe layer indicative of a homojunction (revealed by STEM EBIC). In addition, Cu and Cl concentrations within grain boundaries within several nms and µms from the CdS/CdTe interface are compared, Na segregation of <0.1% is detected, and S variations of ~1–3% are witnessed between CdTe grains close to the CdS/CdTe interface. The segregation and diffusion of these elements directly impacts on the material properties, such as band gap energy and n/p type properties. Optimization of the interfacial and grain boundary doping will lead to higher efficiency solar cells.

  12. High Resolution Dopant Profiles Revealed by Atom Probe Tomography and STEM-EBIC for CdTe Based Solar Cells

    DOE PAGESBeta

    Poplawsky, Jonathan D.; Li, Chen; Paudel, Naba; Guo, Wei; Yan, Yanfa; Pennycook, Stephen J.

    2016-01-01

    Segregated elements and their diffusion profiles within grain boundaries and interfaces resulting from post deposition heat treatments are revealed using atom probe tomography (APT), scanning transmission electron microscopy (STEM), and electron beam induced current (EBIC) techniques. The results demonstrate how these techniques complement each other to provide conclusive evidence for locations of space charge regions and mechanisms that create them at the nanoscale. Most importantly, a Cl dopant profile that extends ~5 nm into CdTe grains interfacing the CdS is shown using APT and STEM synergy, which has been shown to push the pn-junction into the CdTe layer indicative ofmore » a homojunction (revealed by STEM EBIC). In addition, Cu and Cl concentrations within grain boundaries within several nms and µms from the CdS/CdTe interface are compared, Na segregation of <0.1% is detected, and S variations of ~1–3% are witnessed between CdTe grains close to the CdS/CdTe interface. The segregation and diffusion of these elements directly impacts on the material properties, such as band gap energy and n/p type properties. Optimization of the interfacial and grain boundary doping will lead to higher efficiency solar cells.« less

  13. Stable-isotope probing and metagenomics reveal predation by protozoa drives E. coli removal in slow sand filters

    PubMed Central

    Haig, Sarah-Jane; Schirmer, Melanie; D'Amore, Rosalinda; Gibbs, Joseph; Davies, Robert L; Collins, Gavin; Quince, Christopher

    2015-01-01

    Stable-isotope probing and metagenomics were applied to study samples taken from laboratory-scale slow sand filters 0.5, 1, 2, 3 and 4 h after challenging with 13C-labelled Escherichia coli to determine the mechanisms and organisms responsible for coliform removal. Before spiking, the filters had been continuously operated for 7 weeks using water from the River Kelvin, Glasgow as their influent source. Direct counts and quantitative PCR assays revealed a clear predator–prey response between protozoa and E. coli. The importance of top-down trophic-interactions was confirmed by metagenomic analysis, identifying several protozoan and viral species connected to E. coli attrition, with protozoan grazing responsible for the majority of the removal. In addition to top-down mechanisms, indirect mechanisms, such as algal reactive oxygen species-induced lysis, and mutualistic interactions between algae and fungi, were also associated with coliform removal. The findings significantly further our understanding of the processes and trophic interactions underpinning E. coli removal. This study provides an example for similar studies, and the opportunity to better understand, manage and enhance E. coli removal by allowing the creation of more complex trophic interaction models. PMID:25279786

  14. Ultrafast pump-probe microscopy reveals the mechanism of selective fs laser structuring of transparent thin films for maskless micropatterning

    NASA Astrophysics Data System (ADS)

    Rapp, Stephan; Rosenberger, Janosch; Domke, Matthias; Heise, Gerhard; Huber, Heinz P.; Schmidt, Michael

    2014-01-01

    Maskless patterning of biocompatible Ta2O5/Pt/glass sensor chips can be realized by ultra-short laser pulse ablation. At a fluence of 0.2 J/cm2, the thin Ta2O5 film is selectively lifted-off by indirectly-induced ablation at laser wavelenghts where the Ta2O5 is transparent and the Pt absorbing. This enables precise and very fast structuring. Here, 660 fs laser pulses at a center wavelength of 1053 nm are applied. The driving physical effects of this ablation mechanism are revealed by pump-probe microscopy. This technique allows the observation of the whole ablation process ranging temporally from femtoseconds to microseconds. An ultrafast heat-expansion in the absorbing Pt, initiating a shock-wave to the Ta2O5 within the first 10 ps, bulges the Ta2O5 film after some nanoseconds. Bulging velocities of 750 m/s are determined corresponding to an extreme acceleration of about 1010 g. Exceeding the stress limit in the Ta2O5 causes film disintegration after 50 ns. A model, describing essential reaction steps, is developed. This model is also applicable to other industrial important layer systems, where thin transparent films have to be removed.

  15. Pronounced Surface Band Bending of Thin-Film Silicon Revealed by Modeling Core Levels Probed with Hard X-rays.

    PubMed

    Wippler, David; Wilks, Regan G; Pieters, Bart E; van Albada, Sacha J; Gerlach, Dominic; Hüpkes, Jürgen; Bär, Marcus; Rau, Uwe

    2016-07-13

    Enhancing the probing depth of photoemission studies by using hard X-rays allows the investigation of buried interfaces of real-world device structures. However, it also requires the consideration of photoelectron-signal attenuation when evaluating surface effects. Here, we employ a computational model incorporating surface band bending and exponential photoelectron-signal attenuation to model depth-dependent spectral changes of Si 1s and Si 2s core level lines. The data were acquired from hydrogenated boron-doped microcrystalline thin-film silicon, which is applied in silicon-based solar cells. The core level spectra, measured by hard X-ray photoelectron spectroscopy using different excitation energies, reveal the presence of a 0.29 nm thick surface oxide layer. In the silicon film a downward surface band bending of eVbb = -0.65 eV over ∼6 nm obtained via inverse modeling explains the observed core level shifts and line broadening. Moreover, the computational model allows the extraction of the "real" Si 1s and Si 2s bulk core level binding energies as 1839.13 and 150.39 eV, and their natural Lorentzian line widths as 496 and 859 meV, respectively. These values significantly differ from those directly extracted from the measured spectra. Because band bending usually occurs at material surfaces we highly recommend the detailed consideration of signal integration over depth for quantitative statements from depth-dependent measurements. PMID:27294978

  16. The key microorganisms for anaerobic degradation of pentachlorophenol in paddy soil as revealed by stable isotope probing.

    PubMed

    Tong, Hui; Liu, Chengshuai; Li, Fangbai; Luo, Chunling; Chen, Manjia; Hu, Min

    2015-11-15

    Pentachlorophenol (PCP) is a common residual persistent pesticide in paddy soil and has resulted in harmful effect on soil ecosystem. The anaerobic microbial transformation of PCP, therefore, has been received much attentions, especially the functional microbial communities for the reductive transformation. However, the key functional microorganisms for PCP mineralization in the paddy soil still remain unknown. In this work, DNA-based stable isotope probing (SIP) was applied to explore the key microorganisms responsible for PCP mineralization in paddy soil. The SIP results indicated that the dominant bacteria responsible for PCP biodegradation belonged to the genus Dechloromonas of the class β-Proteobacteria. In addition, the increased production of (13)CH4 and (13)CO2 indicated that the addition of lactate enhanced the rate of biodegradation and mineralization of PCP. Two archaea classified as the genera of Methanosaeta and Methanocella of class Methanobacteria were enriched in the heavy fraction when with lactate, whereas no archaea was detected in the absence of lactate. These findings provide direct evidence for the species of bacteria and archaea responsible for anaerobic PCP or its breakdown products mineralization and reveal a new insight into the microorganisms linked with PCP degradation in paddy soil. PMID:26073380

  17. Stable isotope probing reveals the importance of Comamonas and Pseudomonadaceae in RDX degradation in samples from a Navy detonation site.

    PubMed

    Jayamani, Indumathy; Cupples, Alison M

    2015-07-01

    This study investigated the microorganisms involved in hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) degradation from a detonation area at a Navy base. Using Illumina sequencing, microbial communities were compared between the initial sample, samples following RDX degradation, and controls not amended with RDX to determine which phylotypes increased in abundance following RDX degradation. The effect of glucose on these communities was also examined. In addition, stable isotope probing (SIP) using labeled ((13)C3, (15)N3-ring) RDX was performed. Illumina sequencing revealed that several phylotypes were more abundant following RDX degradation compared to the initial soil and the no-RDX controls. For the glucose-amended samples, this trend was strong for an unclassified Pseudomonadaceae phylotype and for Comamonas. Without glucose, Acinetobacter exhibited the greatest increase following RDX degradation compared to the initial soil and no-RDX controls. Rhodococcus, a known RDX degrader, also increased in abundance following RDX degradation. For the SIP study, unclassified Pseudomonadaceae was the most abundant phylotype in the heavy fractions in both the presence and absence of glucose. In the glucose-amended heavy fractions, the 16S ribosomal RNA (rRNA) genes of Comamonas and Anaeromxyobacter were also present. Without glucose, the heavy fractions also contained the 16S rRNA genes of Azohydromonas and Rhodococcus. However, all four phylotypes were present at a much lower level compared to unclassified Pseudomonadaceae. Overall, these data indicate that unclassified Pseudomonadaceae was primarily responsible for label uptake in both treatments. This study indicates, for the first time, the importance of Comamonas for RDX removal. PMID:25721530

  18. Accumulation of Polyunsaturated Aldehydes in the Gonads of the Copepod Acartia tonsa Revealed by Tailored Fluorescent Probes

    PubMed Central

    Wolfram, Stefanie; Nejstgaard, Jens C.; Pohnert, Georg

    2014-01-01

    Polyunsaturated aldehydes (PUAs) are released by several diatom species during predation. Besides other attributed activities, these oxylipins can interfere with the reproduction of copepods, important predators of diatoms. While intensive research has been carried out to document the effects of PUAs on copepod reproduction, little is known about the underlying mechanistic aspects of PUA action. Especially PUA uptake and accumulation in copepods has not been addressed to date. To investigate how PUAs are taken up and interfere with the reproduction in copepods we developed a fluorescent probe containing the α,β,γ,δ-unsaturated aldehyde structure element that is essential for the activity of PUAs as well as a set of control probes. We developed incubation and monitoring procedures for adult females of the calanoid copepod Acartia tonsa and show that the PUA derived fluorescent molecular probe selectively accumulates in the gonads of this copepod. In contrast, a saturated aldehyde derived probe of an inactive parent molecule was enriched in the lipid sac. This leads to a model for PUAs' teratogenic mode of action involving accumulation and covalent interaction with nucleophilic moieties in the copepod reproductive tissue. The teratogenic effect of PUAs can therefore be explained by a selective targeting of the molecules into the reproductive tissue of the herbivores, while more lipophilic but otherwise strongly related structures end up in lipid bodies. PMID:25383890

  19. Accumulation of polyunsaturated aldehydes in the gonads of the copepod Acartia tonsa revealed by tailored fluorescent probes.

    PubMed

    Wolfram, Stefanie; Nejstgaard, Jens C; Pohnert, Georg

    2014-01-01

    Polyunsaturated aldehydes (PUAs) are released by several diatom species during predation. Besides other attributed activities, these oxylipins can interfere with the reproduction of copepods, important predators of diatoms. While intensive research has been carried out to document the effects of PUAs on copepod reproduction, little is known about the underlying mechanistic aspects of PUA action. Especially PUA uptake and accumulation in copepods has not been addressed to date. To investigate how PUAs are taken up and interfere with the reproduction in copepods we developed a fluorescent probe containing the α,β,γ,δ-unsaturated aldehyde structure element that is essential for the activity of PUAs as well as a set of control probes. We developed incubation and monitoring procedures for adult females of the calanoid copepod Acartia tonsa and show that the PUA derived fluorescent molecular probe selectively accumulates in the gonads of this copepod. In contrast, a saturated aldehyde derived probe of an inactive parent molecule was enriched in the lipid sac. This leads to a model for PUAs' teratogenic mode of action involving accumulation and covalent interaction with nucleophilic moieties in the copepod reproductive tissue. The teratogenic effect of PUAs can therefore be explained by a selective targeting of the molecules into the reproductive tissue of the herbivores, while more lipophilic but otherwise strongly related structures end up in lipid bodies. PMID:25383890

  20. The preferential growth of branched GDGT source microorganisms under aerobic conditions in peat revealed by stable isotope probing experiments

    NASA Astrophysics Data System (ADS)

    Huguet, Arnaud; Meador, Travis B.; Laggoun-Défarge, Fatima; Könneke, Martin; Derenne, Sylvie; Hinrichs, Kai-Uwe

    2016-04-01

    Branched glycerol dialkyl glycerol tetraether (brGDGTs) membrane lipids are widely distributed in aquatic and terrestrial environments and are being increasingly used as temperature proxies. Nevertheless, little is known regarding the microorganisms that produce these lipids, which are found in especially high abundance in the anaerobic horizons of peat bogs. We initiated stable isotope probing incubations of peat samples from a Sphagnum-dominated peatland (Jura Mountains, France) to measure the incorporation of (D)-D2O and 13C-labeled dissolved inorganic carbon (DIC) into brGDGTs, and thus gauge the activity, growth, and turnover times of their source organisms. Peat samples were collected from two adjacent sites with contrasting humidity levels (hereafter called "fen" and "bog" sites). For each site, samples from the surficial aerobic layer (acrotelm) and deeper anaerobic layer (catotelm) were collected and were incubated under both anaerobic and aerobic conditions for the acrotelm samples and only anaerobic conditions for the catotelm. The incubations were performed at 12 ° C, consistent with the mean summer air temperature at the sampling site. After two months of incubation, there was no incorporation of 13C label in brGDGTs for samples incubated under either aerobic or anaerobic conditions, showing that brGDGT-producing bacteria are heterotrophic microorganisms, as previously observed in organo-mineral soils (Weijers et al., 2011). Similarly, little to no deuterium incorporation was observed for brGDGTs isolated from anaerobically-incubated deep samples. In contrast, in the aerobic incubations of acrotelm samples from bog and fen, the weighted average δD of brGDGT core lipids (CLs) increased by up to 3332‰ and 933‰ after two months, respectively, indicating that fresh brGDGT CLs were biosynthesized at the peat surface. D incorporation into brGDGT CLs converted to production rates ranging from 30-106 ng cm‑3y‑1 in the aerobic acrotelm from bog and

  1. Microsurgery-aided in-situ force probing reveals extensibility and viscoelastic properties of individual stress fibers

    PubMed Central

    Labouesse, Céline; Gabella, Chiara; Meister, Jean-Jacques; Vianay, Benoît; Verkhovsky, Alexander B.

    2016-01-01

    Actin-myosin filament bundles (stress fibers) are critical for tension generation and cell shape, but their mechanical properties are difficult to access. Here we propose a novel approach to probe individual peripheral stress fibers in living cells through a microsurgically generated opening in the cytoplasm. By applying large deformations with a soft cantilever we were able to fully characterize the mechanical response of the fibers and evaluate their tension, extensibility, elastic and viscous properties. PMID:27025817

  2. Distinct Length Scales in the VO{sub 2} Metal–Insulator Transition Revealed by Bi-chromatic Optical Probing

    SciTech Connect

    Wang, Lei; Novikova, Irina B.; Klopf, John M.; Madaras, Scott E.; Williams, Gwyn P.; Madaras, Eric; Lu, Liwei; Wolf, Stuart A.; Lukaszew, Rosa A.

    2014-01-01

    Upon a heating-induced metal–instulator transition (MIT) in VO{sub 2}, microscopic metallic VO{sub 2} puddles nucleate and coarsen within the insulating matrix. This coexistence of the two phases across the transition spans distinct length scales as their relative domain sizes change. Far-field optical probing is applied to follow the dynamic evolution of the highly correlated metallic domains as the MIT progresses.

  3. FRET ratiometric probes reveal the chiral-sensitive cysteine-dependent H2S production and regulation in living cells

    NASA Astrophysics Data System (ADS)

    Wei, Lv; Yi, Long; Song, Fanbo; Wei, Chao; Wang, Bai-Fan; Xi, Zhen

    2014-04-01

    Hydrogen sulfide (H2S) is an endogenously produced gaseous signalling molecule with multiple biological functions. In order to visualize and quantify the endogenous in situ production of H2S in living cells, here we developed two new sulphide ratiometric probes (SR400 and SR550) based on fluorescence resonance energy transfer (FRET) strategy for live capture of H2S. The FRET-based probes show excellent selectivity toward H2S in a high thiol background under physiological buffer. The probe can be used to in situ visualize cysteine-dependent H2S production in a chiral-sensitive manner in living cells. The ratiometric imaging studies indicated that D-Cys induces more H2S production than that of L-Cys in mitochondria of human embryonic kidney 293 cells (HEK293). The cysteine mimics propargylglycine (PPG) has also been found to inhibit the cysteine-dependent endogenous H2S production in a chiral-sensitive manner in living cells. D-PPG inhibited D-Cys-dependent H2S production more efficiently than L-PPG, while, L-PPG inhibited L-Cys-dependent H2S production more efficiently than D-PPG. Our bioimaging studies support Kimura's discovery of H2S production from D-cysteine in mammalian cells and further highlight the potential of D-cysteine and its derivatives as an alternative strategy for classical H2S-releasing drugs.

  4. Combined probes of X-ray scattering and optical spectroscopy reveal how global conformational change is temporally and spatially linked to local structural perturbation in photoactive yellow protein.

    PubMed

    Kim, Tae Wu; Yang, Cheolhee; Kim, Youngmin; Kim, Jong Goo; Kim, Jeongho; Jung, Yang Ouk; Jun, Sunhong; Lee, Sang Jin; Park, Sungjun; Kosheleva, Irina; Henning, Robert; van Thor, Jasper J; Ihee, Hyotcherl

    2016-03-23

    Real-time probing of structural transitions of a photoactive protein is challenging owing to the lack of a universal time-resolved technique that can probe the changes in both global conformation and light-absorbing chromophores of the protein. In this work, we combine time-resolved X-ray solution scattering (TRXSS) and transient absorption (TA) spectroscopy to investigate how the global conformational changes involved in the photoinduced signal transduction of photoactive yellow protein (PYP) is temporally and spatially related to the local structural change around the light-absorbing chromophore. In particular, we examine the role of internal proton transfer in developing a signaling state of PYP by employing its E46Q mutant (E46Q-PYP), where the internal proton transfer is inhibited by the replacement of a proton donor. The comparison of TRXSS and TA spectroscopy data directly reveals that the global conformational change of the protein, which is probed by TRXSS, is temporally delayed by tens of microseconds from the local structural change of the chromophore, which is probed by TA spectroscopy. The molecular shape of the signaling state reconstructed from the TRXSS curves directly visualizes the three-dimensional conformations of protein intermediates and reveals that the smaller structural change in E46Q-PYP than in wild-type PYP suggested by previous studies is manifested in terms of much smaller protrusion, confirming that the signaling state of E46Q-PYP is only partially developed compared with that of wild-type PYP. This finding provides direct evidence of how the environmental change in the vicinity of the chromophore alters the conformational change of the entire protein matrix. PMID:26960811

  5. Te inclusion-induced electrical field perturbation in CdZnTe single crystals revealed by Kelvin probe force microscopy.

    PubMed

    Gu, Yaxu; Jie, Wanqi; Li, Linglong; Xu, Yadong; Yang, Yaodong; Ren, Jie; Zha, Gangqiang; Wang, Tao; Xu, Lingyan; He, Yihui; Xi, Shouzhi

    2016-09-01

    To understand the effects of tellurium (Te) inclusions on the device performance of CdZnTe radiation detectors, the perturbation of the electrical field in and around Te inclusions was studied in CdZnTe single crystals via Kelvin probe force microscopy (KPFM). Te inclusions were proved to act as lower potential centers with respect to surrounding CdZnTe matrix. Based on the KPFM results, the energy band diagram at the Te/CdZnTe interface was established, and the bias-dependent effects of Te inclusion on carrier transportation is discussed. PMID:27376976

  6. Selective activation of SHP2 activity by cisplatin revealed by a novel chemical probe-based assay

    SciTech Connect

    Kuo, Chun-Chen; Chu, Chi-Yuan; Lin, Jing-Jer; Lo, Lee-Chiang

    2010-01-01

    Src homology-2 (SH2) domain-containing phosphatase 2 (SHP2) is known to participate in several different signaling pathways to mediate cell growth, survival, migration, and differentiation. However, due to the lack of proper analytical tools, it is unclear whether the phosphatase activity of SHP2 is activated in most studies. We have previously developed an activity-based probe LCL2 that formed covalent linkage with catalytically active protein tyrosine phosphatases (PTPs). Here, by combining LCL2 with a SHP2 specific antibody, we established an assay system that enables the direct monitoring of SHP2 activity upon cisplatin treatment of cancer cells. The protocol is advantageous over conventional colorimetric or in-gel PTP assays as it is specific and does not require the use of radioisotope reagents. Using this assay, we found SHP2 activity was selectively activated by cisplatin. Moreover, the activation of SHP2 appeared to be specific for cisplatin as other DNA damage agents failed to activate the activity. Although the role of SHP2 activation by cisplatin treatments is still unclear to us, our results provide the first direct evidence for the activation of SHP2 during cisplatin treatments. More importantly, the concept of using activity-based probe in conjunction with target-specific antibodies could be extended to other enzyme classes.

  7. Non-hydrolyzable Diubiquitin Probes Reveal Linkage-Specific Reactivity of Deubiquitylating Enzymes Mediated by S2 Pockets

    PubMed Central

    Flierman, Dennis; van der Heden van Noort, Gerbrand J.; Ekkebus, Reggy; Geurink, Paul P.; Mevissen, Tycho E.T.; Hospenthal, Manuela K.; Komander, David; Ovaa, Huib

    2016-01-01

    Summary Ubiquitin chains are important post-translational modifications that control a large number of cellular processes. Chains can be formed via different linkages, which determines the type of signal they convey. Deubiquitylating enzymes (DUBs) regulate ubiquitylation status by trimming or removing chains from attached proteins. DUBs can contain several ubiquitin-binding pockets, which confer specificity toward differently linked chains. Most tools for monitoring DUB specificity target binding pockets on opposing sides of the active site; however, some DUBs contain additional pockets. Therefore, reagents targeting additional pockets are essential to fully understand linkage specificity. We report the development of active site-directed probes and fluorogenic substrates, based on non-hydrolyzable diubiquitin, that are equipped with a C-terminal warhead or a fluorogenic activity reporter moiety. We demonstrate that various DUBs in lysates display differential reactivity toward differently linked diubiquitin probes, as exemplified by the proteasome-associated DUB USP14. In addition, OTUD2 and OTUD3 show remarkable linkage-specific reactivity with our diubiquitin-based reagents. PMID:27066941

  8. The short-lived signaling state of the photoactive yellow protein photoreceptor revealed by combined structural probes.

    PubMed

    Ramachandran, Pradeep L; Lovett, Janet E; Carl, Patrick J; Cammarata, Marco; Lee, Jae Hyuk; Jung, Yang Ouk; Ihee, Hyotcherl; Timmel, Christiane R; van Thor, Jasper J

    2011-06-22

    The signaling state of the photoactive yellow protein (PYP) photoreceptor is transiently developed via isomerization of its blue-light-absorbing chromophore. The associated structural rearrangements have large amplitude but, due to its transient nature and chemical exchange reactions that complicate NMR detection, its accurate three-dimensional structure in solution has been elusive. Here we report on direct structural observation of the transient signaling state by combining double electron electron resonance spectroscopy (DEER), NMR, and time-resolved pump-probe X-ray solution scattering (TR-SAXS/WAXS). Measurement of distance distributions for doubly spin-labeled photoreceptor constructs using DEER spectroscopy suggests that the signaling state is well ordered and shows that interspin-label distances change reversibly up to 19 Å upon illumination. The SAXS/WAXS difference signal for the signaling state relative to the ground state indicates the transient formation of an ordered and rearranged conformation, which has an increased radius of gyration, an increased maximum dimension, and a reduced excluded volume. Dynamical annealing calculations using the DEER derived long-range distance restraints in combination with short-range distance information from (1)H-(15)N HSQC perturbation spectroscopy give strong indication for a rearrangement that places part of the N-terminal domain in contact with the exposed chromophore binding cleft while the terminal residues extend away from the core. Time-resolved global structural information from pump-probe TR-SAXS/WAXS data supports this conformation and allows subsequent structural refinement that includes the combined energy terms from DEER, NMR, and SAXS/WAXS together. The resulting ensemble simultaneously satisfies all restraints, and the inclusion of TR-SAXS/WAXS effectively reduces the uncertainty arising from the possible spin-label orientations. The observations are essentially compatible with reduced folding of the

  9. Nonradiative Decay Dynamics of METHYL-4-HYDROXYCINNAMATE and its Monohydrated Complex Revealed by Picosecond Pump-Probe Spectroscopy

    NASA Astrophysics Data System (ADS)

    Ebata, T.; Shimada, D.; Kusaka, R.; Inokuchi, Y.; Ehara, M.

    2012-06-01

    The lifetimes of methyl 4-hydroxycinnamate (OMpCA) and its mono-hydrated complex (OMpCA-H_2O) in the S_1 state have been measured by picosecond pump-probe spectroscopy in a supersonic beam. For OMpCA, the lifetime of the S_1 - S_0 origin is 8 - 9 ps. On the other hand, the lifetime of OMpCA-H_2O complex at the origin is 930 ps, which is 100 times longer than that. Furthermore, in the complex the S_1 lifetime shows rapid decrease at an energy of 200 cm-1 above the origin and becomes as short as 9 ps at 500 cm-1. Theoretical calculations with symmetry-adapted cluster-configuration interaction (SAC-CI) method suggest that in OMpCA, the trans - cis isomerization occurs smoothly without a barrier on the S_1surface, while in OMpCA-H_2O complex, there exists a barrier along the isomerization coordinate. The calculated barrier height of OMpCA-H_2O is in good agreement with that estimated from the lifetime measurements.

  10. Subcellular integrities in Chroococcidiopsis sp. CCMEE 029 survivors after prolonged desiccation revealed by molecular probes and genome stability assays.

    PubMed

    Billi, Daniela

    2009-01-01

    Desiccation-tolerant cells must either protect their cellular components from desiccation-induced damage and/or repair it upon rewetting. Subcellular damage to the anhydrobiotic cyanobacterium Chroococcidiopsis sp. CCMEE 029 stored in the desiccated state for 4 years was evaluated at the single-cell level using fluorescent DNA strand breakage labelling, membrane integrity and potential related molecular probes, oxidant-sensing fluorochrome and redox dye. Covalent modifications of dried genomes were assessed by testing their suitability as PCR template. Results suggest that desiccation survivors avoid/and or limit genome fragmentation and genome covalent modifications, preserve intact plasma membranes and phycobiliprotein autofluorescence, exhibit spatially-reduced ROS accumulation and dehydrogenase activity upon rewetting. Damaged cells undergo genome fragmentation, loss of plasma membrane potential and integrity, phycobiliprotein bleaching, whole-cell ROS accumulation and lack respiratory activity upon rewetting. The co-occurrence of live and dead cells within dried aggregates of Chroococcidiopsis confirms that desiccation resistance is not a simple process and that subtle modifications to the cellular milieu are required to dry without dying. It rises also intriguing questions about the triggers of dead cells in response to drying. The capability of desiccation survivors to avoid and/or reduce subcellular damage, shows that protection mechanisms are relevant in the desiccation tolerance of this cyanobacterium. PMID:18931823

  11. Survival of free-living Acholeplasma in aerated pig manure slurry revealed by 13C-labeled bacterial biomass probing

    PubMed Central

    Hanajima, Dai; Aoyagi, Tomo; Hori, Tomoyuki

    2015-01-01

    Many studies have been performed on microbial community succession and/or predominant taxa during the composting process; however, the ecophysiological roles of microorganisms are not well understood because microbial community structures are highly diverse and dynamic. Bacteria are the most important contributors to the organic-waste decomposition process, while decayed bacterial cells can serve as readily digested substrates for other microbial populations. In this study, we investigated the active bacterial species responsible for the assimilation of dead bacterial cells and their components in aerated pig manure slurry by using 13C-labeled bacterial biomass probing. After 3 days of forced aeration, 13C-labeled and unlabeled dead Escherichia coli cell suspensions were added to the slurry. The suspensions contained 13C-labeled and unlabeled bacterial cell components, possibly including the cell wall and membrane, as well as intracellular materials. RNA extracted from each slurry sample 2 h after addition of E. coli suspension was density-resolved by isopycnic centrifugation and analyzed by terminal restriction fragment length polymorphism, followed by cloning and sequencing of bacterial 16S rRNA genes. In the heavy isotopically labeled RNA fraction, the predominant 13C-assimilating population was identified as belonging to the genus Acholeplasma, which was not detected in control heavy RNA. Acholeplasma spp. have limited biosynthetic capabilities and possess a wide variety of transporters, resulting in their metabolic dependence on external carbon and energy sources. The prevalence of Acholeplasma spp. was further confirmed in aerated pig manure slurry from four different pig farms by pyrosequencing of 16S rRNA genes; their relative abundance was ∼4.4%. Free-living Acholeplasma spp. had a competitive advantage for utilizing dead bacterial cells and their components more rapidly relative to other microbial populations, thus allowing the survival and prevalence

  12. Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo.

    PubMed

    Rouskin, Silvi; Zubradt, Meghan; Washietl, Stefan; Kellis, Manolis; Weissman, Jonathan S

    2014-01-30

    RNA has a dual role as an informational molecule and a direct effector of biological tasks. The latter function is enabled by RNA's ability to adopt complex secondary and tertiary folds and thus has motivated extensive computational and experimental efforts for determining RNA structures. Existing approaches for evaluating RNA structure have been largely limited to in vitro systems, yet the thermodynamic forces which drive RNA folding in vitro may not be sufficient to predict stable RNA structures in vivo. Indeed, the presence of RNA-binding proteins and ATP-dependent helicases can influence which structures are present inside cells. Here we present an approach for globally monitoring RNA structure in native conditions in vivo with single-nucleotide precision. This method is based on in vivo modification with dimethyl sulphate (DMS), which reacts with unpaired adenine and cytosine residues, followed by deep sequencing to monitor modifications. Our data from yeast and mammalian cells are in excellent agreement with known messenger RNA structures and with the high-resolution crystal structure of the Saccharomyces cerevisiae ribosome. Comparison between in vivo and in vitro data reveals that in rapidly dividing cells there are vastly fewer structured mRNA regions in vivo than in vitro. Even thermostable RNA structures are often denatured in cells, highlighting the importance of cellular processes in regulating RNA structure. Indeed, analysis of mRNA structure under ATP-depleted conditions in yeast shows that energy-dependent processes strongly contribute to the predominantly unfolded state of mRNAs inside cells. Our studies broadly enable the functional analysis of physiological RNA structures and reveal that, in contrast to the Anfinsen view of protein folding whereby the structure formed is the most thermodynamically favourable, thermodynamics have an incomplete role in determining mRNA structure in vivo. PMID:24336214

  13. Comet-FISH with strand-specific probes reveals transcription-coupled repair of 8-oxoGuanine in human cells

    PubMed Central

    Guo, Jia; Hanawalt, Philip C.; Spivak, Graciela

    2013-01-01

    Oxidized bases in DNA have been implicated in cancer, aging and neurodegenerative disease. We have developed an approach combining single-cell gel electrophoresis (comet) with fluorescence in situ hybridization (FISH) that enables the comparative quantification of low, physiologically relevant levels of DNA lesions in the respective strands of defined nucleotide sequences and in the genome overall. We have synthesized single-stranded probes targeting the termini of DNA segments of interest using a polymerase chain reaction-based method. These probes facilitate detection of damage at the single-molecule level, as the lesions are converted to DNA strand breaks by lesion-specific endonucleases or glycosylases. To validate our method, we have documented transcription-coupled repair of cyclobutane pyrimidine dimers in the ataxia telangiectasia-mutated (ATM) gene in human fibroblasts irradiated with 254 nm ultraviolet at 0.1 J/m2, a dose ∼100-fold lower than those typically used. The high specificity and sensitivity of our approach revealed that 7,8-dihydro-8-oxoguanine (8-oxoG) at an incidence of approximately three lesions per megabase is preferentially repaired in the transcribed strand of the ATM gene. We have also demonstrated that the hOGG1, XPA, CSB and UVSSA proteins, as well as actively elongating RNA polymerase II, are required for this process, suggesting cross-talk between DNA repair pathways. PMID:23775797

  14. Comet-FISH with strand-specific probes reveals transcription-coupled repair of 8-oxoGuanine in human cells.

    PubMed

    Guo, Jia; Hanawalt, Philip C; Spivak, Graciela

    2013-09-01

    Oxidized bases in DNA have been implicated in cancer, aging and neurodegenerative disease. We have developed an approach combining single-cell gel electrophoresis (comet) with fluorescence in situ hybridization (FISH) that enables the comparative quantification of low, physiologically relevant levels of DNA lesions in the respective strands of defined nucleotide sequences and in the genome overall. We have synthesized single-stranded probes targeting the termini of DNA segments of interest using a polymerase chain reaction-based method. These probes facilitate detection of damage at the single-molecule level, as the lesions are converted to DNA strand breaks by lesion-specific endonucleases or glycosylases. To validate our method, we have documented transcription-coupled repair of cyclobutane pyrimidine dimers in the ataxia telangiectasia-mutated (ATM) gene in human fibroblasts irradiated with 254 nm ultraviolet at 0.1 J/m2, a dose ∼100-fold lower than those typically used. The high specificity and sensitivity of our approach revealed that 7,8-dihydro-8-oxoguanine (8-oxoG) at an incidence of approximately three lesions per megabase is preferentially repaired in the transcribed strand of the ATM gene. We have also demonstrated that the hOGG1, XPA, CSB and UVSSA proteins, as well as actively elongating RNA polymerase II, are required for this process, suggesting cross-talk between DNA repair pathways. PMID:23775797

  15. Irreversible adsorption-driven assembly of nanoparticles at fluid interfaces revealed by a dynamic surface tension probe.

    PubMed

    Bizmark, Navid; Ioannidis, Marios A; Henneke, Dale E

    2014-01-28

    Adsorption-driven self-assembly of nanoparticles at fluid interfaces is a promising bottom-up approach for the preparation of advanced functional materials and devices. Full realization of its potential requires quantitative understanding of the parameters controlling the self-assembly, the structure of nanoparticles at the interface, the barrier properties of the assembly, and the rate of particle attachment. We argue that models of dynamic surface or interfacial tension (DST) appropriate for molecular species break down when the adsorption energy greatly exceeds the mean energy of thermal fluctuations and validate alternative models extending the application of generalized random sequential adsorption theory to nanoparticle adsorption at fluid interfaces. Using a model colloidal system of hydrophobic, charge-stabilized ethyl cellulose nanoparticles at neutral pH, we demonstrate the potential of DST measurements to reveal information on the energy of adsorption, the adsorption rate constant, and the energy of particle-interface interaction at different degrees of nanoparticle coverage of the interface. These findings have significant implications for the quantitative description of nanoparticle adsorption at fluid interfaces. PMID:24397479

  16. SinoProbe-02: Integrated experiment of deep-exploring techniques to reveal the interior structure beneath the Chinese continent (Invited)

    NASA Astrophysics Data System (ADS)

    Gao, R.; Lu, Z.; Wang, H.; Li, W.; Zeng, L.

    2010-12-01

    SinoProbe is a new five year program (2008-2012) funded by the Chinese government. Its primary objectives are (1) to explore the interior structure and geodynamic processes beneath the Chinese continent, (2) to reveal the tectonic evolution of continent, and (3) to provide new scientific data and information for the exploration of new resources at depth. SinoProbe-02 is one of the key projects essential for fulfilling the primary objectives of SinoProbe. In this project, we will apply techniques including deep seismic reflection profiling (CMP), deep seismic sounding (DSS), broadband seismic observation (BB), magnetotelluric sounding (MT), and other methods to determine the physical properties and in turn to image the structure and composition of the crust and mantle of the Chinese continent. In conjunction with high resolution geologic field mapping and observation, these data will be integrated to extend the near surface structures down to significant deeper levels, to address the key mechanisms for the deformation of the crust at different levels, to provide scientific information for exploration of energy and mineral resources at depth, to tackle important problems of the tectonic evolution of continental crust and mantle, and finally to shed new insights on the mechanisms for large earthquake, volcanism, and other catastrophic events. To achieve the major objectives of the SinoProbe-2, experiments with different techniques will be deployed along four major cross-section lines that traverse key orogenic belts and sedimentary basins. These include the Himalaya-Karakoram-Tibet (HKT) profile, South China Profile (SCP), North China Profile (NCP), and Northeast China Profile (NECP), respectively. By the end of year 2010, our team has completed ~1900 km long seismic experiments which include 300 km of HKT, 500 km of SCP, 500 km of NCP, and 600 km of NECP, respectively. These new data reveal several important features of the structure of continental lithosphere. In

  17. DNA stable-isotope probing of oil sands tailings pond enrichment cultures reveals different key players for toluene degradation under methanogenic and sulfidogenic conditions.

    PubMed

    Laban, Nidal Abu; Dao, Anh; Foght, Julia

    2015-05-01

    Oil sands tailings ponds are anaerobic repositories of fluid wastes produced by extraction of bitumen from oil sands ores. Diverse indigenous microbiota biodegrade hydrocarbons (including toluene) in situ, producing methane, carbon dioxide and/or hydrogen sulfide, depending on electron acceptor availability. Stable-isotope probing of cultures enriched from tailings associated specific taxa and functional genes to (13)C6- and (12)C7-toluene degradation under methanogenic and sulfate-reducing conditions. Total DNA was subjected to isopycnic ultracentrifugation followed by gradient fraction analysis using terminal restriction fragment length polymorphism (T-RFLP) and construction of 16S rRNA, benzylsuccinate synthase (bssA) and dissimilatory sulfite reductase (dsrB) gene clone libraries. T-RFLP analysis plus sequencing and in silico digestion of cloned taxonomic and functional genes revealed that Clostridiales, particularly Desulfosporosinus (136 bp T-RF) contained bssA genes and were key toluene degraders during methanogenesis dominated by Methanosaeta. Deltaproteobacterial Desulfobulbaceae (157 bp T-RF) became dominant under sulfidogenic conditions, likely because the Desulfosporosinus T-RF 136 apparently lacks dsrB and therefore, unlike its close relatives, is presumed incapable of dissimilatory sulfate reduction. We infer incomplete oxidation of toluene by Desulfosporosinus in syntrophic association with Methanosaeta under methanogenic conditions, and complete toluene oxidation by Desulfobulbaceae during sulfate reduction. PMID:25873466

  18. Differences in the neurochemical and behavioural profiles of lisdexamfetamine methylphenidate and modafinil revealed by simultaneous dual-probe microdialysis and locomotor activity measurements in freely-moving rats.

    PubMed

    Rowley, Helen L; Kulkarni, Rajiv S; Gosden, Jane; Brammer, Richard J; Hackett, David; Heal, David J

    2014-03-01

    Lisdexamfetamine dimesylate is a novel prodrug approved in North America, Europe and Brazil for treating attention deficit hyperactivity disorder (ADHD). It undergoes rate-limited hydrolysis by red blood cells to yield d-amphetamine. Following our previous work comparing lisdexamfetamine with d-amphetamine, the neurochemical and behavioural profiles of lisdexamfetamine, methylphenidate and modafinil were compared by dual-probe microdialysis in the prefrontal cortex (PFC) and striatum of conscious rats with simultaneous locomotor activity measurement. We employed pharmacologically equivalent doses of all compounds and those that spanned the therapeutically relevant and psychostimulant range. Lisdexamfetamine (0.5, 1.5, 4.5 mg/kg d-amphetamine base, per os (po)), methylphenidate (3, 10, 30 mg/kg base, po) and modafinil (100, 300, 600 mg/kg base, po) increased efflux of dopamine and noradrenaline in PFC, and dopamine in striatum. Only lisdexamfetamine increased 5-hydroxytryptamine (5-HT) efflux in PFC and striatum. Lisdexamfetamine had larger and more sustained effects on catecholaminergic neurotransmission than methylphenidate or modafinil. Linear correlations were observed between striatal dopamine efflux and locomotor activity for lisdexamfetamine and methylphenidate, but not modafinil. Regression slopes revealed greater increases in extracellular dopamine could be elicited without producing locomotor activation by lisdexamfetamine than methylphenidate. These results are consistent with clinical findings showing that lisdexamfetamine is an effective ADHD medication with prolonged duration of action and good separation between its therapeutic actions and stimulant side-effects. PMID:24327450

  19. Field-Based Stable Isotope Probing Reveals the Identities of Benzoic Acid-Metabolizing Microorganisms and Their In Situ Growth in Agricultural Soil▿

    PubMed Central

    Pumphrey, Graham M.; Madsen, Eugene L.

    2008-01-01

    We used a combination of stable isotope probing (SIP), gas chromatography-mass spectrometry-based respiration, isolation/cultivation, and quantitative PCR procedures to discover the identity and in situ growth of soil microorganisms that metabolize benzoic acid. We added [13C]benzoic acid or [12C]benzoic acid (100 μg) once, four times, or five times at 2-day intervals to agricultural field plots. After monitoring 13CO2 evolution from the benzoic acid-dosed soil, field soils were harvested and used for nucleic acid extraction and for cultivation of benzoate-degrading bacteria. Exposure of soil to benzoate increased the number of culturable benzoate degraders compared to unamended soil, and exposure to benzoate shifted the dominant culturable benzoate degraders from Pseudomonas species to Burkholderia species. Isopycnic separation of heavy [13C]DNA from the unlabeled fraction allowed terminal restriction fragment length polymorphism (T-RFLP) analyses to confirm that distinct 16S rRNA genes were localized in the heavy fraction. Phylogenetic analysis of sequenced 16S rRNA genes revealed a predominance (15 of 58 clones) of Burkholderia species in the heavy fraction. Burkholderia sp. strain EBA09 shared 99.5% 16S rRNA sequence similarity with a group of clones representing the dominant RFLP pattern, and the T-RFLP fragment for strain EBA09 and a clone from that cluster matched the fragment enriched in the [13C]DNA fraction. Growth of the population represented by EBA09 during the field-dosing experiment was demonstrated by using most-probable-number-PCR and primers targeting EBA09 and the closely related species Burkholderia hospita. Thus, the target population identified by SIP not only actively metabolized benzoic acid but reproduced in the field upon the addition of the substrate. PMID:18469130

  20. Long-term nitrogen fertilization of paddy soil shifts iron-reducing microbial community revealed by RNA-(13)C-acetate probing coupled with pyrosequencing.

    PubMed

    Ding, Long-Jun; Su, Jian-Qiang; Xu, Hui-Juan; Jia, Zhong-Jun; Zhu, Yong-Guan

    2015-03-01

    Iron reduction is an important biogeochemical process in paddy soils, yet little is known about the microbial coupling between nitrogen and iron reduction. Here, we investigated the shift of acetate-metabolizing iron-reducers under long-term nitrogen fertilization using (13)C-acetate-based ribosomal RNA (rRNA)-stable isotope probing (SIP) and pyrosequencing in an incubation experiment, and the shift of putative iron-reducers in original field samples were investigated by 16S rRNA gene-based pyrosequencing. During SIP incubations, in the presence of iron(III) oxyhydroxides, more iron(II) formation and less methane production were detected in nitrogen-fertilized (N) compared with non-fertilized (NF) soil. In (13)C-rRNA from microcosms amended with ferrihydrite (FER), Geobacter spp. were the important active iron-reducers in both soils, and labeled to a greater extent in N (31% of the bacterial classified sequences) than NF soils (11%). Pyrosequencing of the total 16S rRNA transcripts from microcosms at the whole community level further revealed hitherto unknown metabolisms of potential FER reduction by microorganisms including Pseudomonas and Solibacillus spp. in N soil, Dechloromonas, Clostridium, Bacillus and Solibacillus spp. in NF soil. Goethite (GOE) amendment stimulated Geobacter spp. to a lesser extent in both soils compared with FER treatment. Pseudomonas spp. in the N soil and Clostridium spp. in the NF soil may also be involved in GOE reduction. Pyrosequencing results from field samples showed that Geobacter spp. were the most abundant putative iron-reducers in both soils, and significantly stimulated by long-term nitrogen fertilization. Overall, for the first time, we demonstrate that long-term nitrogen fertilization promotes iron(III) reduction and modulates iron-reducing bacterial community in paddy soils. PMID:25171335

  1. Revealing the ionization ability of binding site I of human serum albumin using 2-(2'-hydroxyphenyl)benzoxazole as a pH sensitive probe.

    PubMed

    Abou-Zied, Osama K

    2012-02-28

    The ability of site I of human serum albumin (HSA) to bind medium sized molecules is important for the distribution, metabolism, and efficacy of many drugs. Herein, we show that this binding site has the ionization ability that may alter the drug structure during the process of its delivery. We reveal this ability by employing 2-(2'-hydroxyphenyl)benzoxazole (HBO) as a pH sensitive probe. Binding of HBO in site I is studied here at physiological pH 7.2 using steady-state and lifetime spectroscopic measurements, molecular docking and molecular dynamics (MD) simulation methods. The complex photophysics of HBO and the unique fluorescence signature of its anionic form indicate that, upon binding with HSA, the molecule exists in equilibrium between the anionic and the syn-keto forms. The position of HBO inside the binding site was determined experimentally by measuring the fluorescence quenching of W214, the sole tryptophan residue in HSA. The ionization degree of HBO inside the binding site was estimated to be close to the ionization degree of HBO in an aqueous solution of pH 10. This was concluded by comparing the fluorescence behavior of bound HBO to that of HBO in different solvents and in aqueous solutions of different pH values. Molecular docking and MD simulations show that HBO binds in site I close to W214, confirming the experimental results, and pinpoint the dominant role of hydrophobic interactions in the binding site. The formation of the anionic form is proposed to be due to through-space interaction between the OH group of HBO and both R222 and I290 with a binding mode similar to that of warfarin in site I. Comparison of the results with those of HBO mixed with key amino acids in solution indicates the importance of through-space interaction in the formation of the anion, similar to enzymatic reactions. PMID:22267206

  2. Growth, Survival, and Death of Bacteria and Fungi Following Wet-up of Seasonally Dried Soil Revealed by Heavy Water Stable Isotope Probing

    NASA Astrophysics Data System (ADS)

    Blazewicz, S.; Nuccio, E. E.; Lim, H.; Schwartz, E.; Brodie, E.; Firestone, M.

    2013-12-01

    The rapid increase in microbial activity that occurs when a dry soil is rewetted has been well documented and is of great interest due to implications of changing precipitation patterns on soil C dynamics. Several studies have shown minor net changes in microbial population diversity or abundance following wet-up, but the gross population dynamics of bacteria and fungi resulting from soil wet-up are virtually unknown due to the technical difficulties associated with such measurements. Here we applied DNA stable isotope probing with H218O coupled with quantitative PCR and high throughput sequencing of bacterial 16S rRNA genes to characterize taxonomic composition of bacteria and to describe new growth, survival, and mortality of bacteria and fungi following the rewetting of a seasonally dried California annual grassland soil. Total microbial abundance revealed little change throughout the 7-day post-wet incubation, but there was substantial turnover of both bacterial and fungal populations (49 and 52% respectively). New growth was linear between 24 and 168 hours for both bacteria and fungi with average growth rates of 2.3 x 108 bacterial 16S rRNA gene copies gdw-1 h-1 and 4.3 x 107 fungal ITS copies gdw-1 h-1. While bacteria and fungi differed in their mortality and survival characteristics during the 7-day incubation, mortality that occurred within the first 3 hours was similar with 25 and 27% of bacterial and fungal gene copies disappearing from the pre-wet community, respectively. The rapid disappearance of gene copies indicates that cell death, occurring either during the extreme dry down period (preceding 5 months) or during the rapid change in water-potential due to wet-up, generates a significant pool of available C that likely contributes to the large pulse in CO2 associated with wet-up. Sequential bacterial growth patterns observed at the phylum and order levels suggest that an ecologically coherent response was observable at coarse taxonomic levels with

  3. New Degenerate Cytophaga-Flexibacter-Bacteroides-Specific 16S Ribosomal DNA-Targeted Oligonucleotide Probes Reveal High Bacterial Diversity in River Taff Epilithon

    PubMed Central

    O’Sullivan, Louise A.; Weightman, Andrew J.; Fry, John C.

    2002-01-01

    River microbial communities play an important role in global nutrient cycles, and aggregated bacteria such as those in epilithic biofilms may be major contributors. In this study the bacterial diversity of River Taff epilithon in South Wales was investigated. A 16S ribosomal DNA (rDNA) clone library was constructed and analyzed by partial sequencing of 76 of 347 clones and hybridization with taxon-specific probes. The epilithon was found to be very diverse, with an estimated 59.6% of the bacterial populations not accounted for by these clones. Members of the Cytophaga-Flexibacter-Bacteroides division (CFBs) were most abundant in the library, representing 25% of clones, followed by members of the α subdivision of the division Proteobacteria (α-Proteobacteria), γ-Proteobacteria, gram-positive bacteria, Cyanobacteria, β-Proteobacteria, δ-Proteobacteria, and the Prosthecobacter group. This study concentrated on the epilithic CFB populations, and a new set of degenerate 16S rDNA probes was developed to enhance their detection, namely, CFB560, CFB562, and CFB376. The commonly used probe CF319a/b may frequently lead to the underestimation of CFB populations in environmental studies, because it does not fully detect members of the division. CFB560 had exact matches to 95.6% of CFBs listed in the Ribosomal Database Project (release 8.0) small-subunit phylogenetic trees, compared to 60% for CF319a/b. The CFB probes detected 66 of 347 epilithon TAF clones, and 60 of these were partially sequenced. They affiliated with the RDP-designated groups Cytophaga, Sphingobacterium, Lewinella, and Cytophaga aurantiaca. CFB560 and CF319a/b detected 94% (62 of 66) and 48.5% (32 of 66) of clones, respectively, and therefore CFB560 is recommended for future use. Probe design in this study illustrated that multiple degenerate positions can greatly increase target range without adversely effecting specificity or experimental performance. PMID:11772628

  4. Probe assembly

    SciTech Connect

    Avera, C.J.

    1981-01-06

    A hand-held probe assembly, suitable for monitoring a radioactive fibrinogen tracer, is disclosed comprising a substantially cylindrically shaped probe handle having an open end. The probe handle is adapted to be interconnected with electrical circuitry for monitoring radioactivity that is sensed or detected by the probe assembly. Mounted within the probe handle is a probe body assembly that includes a cylindrically shaped probe body inserted through the open end of the probe handle. The probe body includes a photomultiplier tube that is electrically connected with a male connector positioned at the rearward end of the probe body. Mounted at the opposite end of the probe body is a probe head which supports an optical coupler therewithin. The probe head is interconnected with a probe cap which supports a detecting crystal. The probe body assembly, which consists of the probe body, the probe head, and the probe cap is supported within the probe handle by means of a pair of compressible o-rings which permit the probe assembly to be freely rotatable, preferably through 360*, within the probe handle and removable therefrom without requiring any disassembly.

  5. Work Function Modification in P3HT H/J Aggregate Nanostructures Revealed by Kelvin Probe Force Microscopy and Photoluminescence Imaging.

    PubMed

    Baghgar, Mina; Barnes, Michael D

    2015-07-28

    We show that surface electronic properties of poly-3-hexylthiophene (P3HT) crystalline nanofibers as probed by Kelvin probe force microscopy (KPFM) depends sensitively on the degree of polymer packing order and dominant coupling type (e.g., H- or J-aggregate) as signaled by absorption or photoluminescence spectroscopy. Nominal HOMO energies between high molecular weight (J-aggregate) nanofibers and low-molecular weight (H-aggregate) nanofibers differ by ≈160 meV. This is consistent with shifts expected from H-type charge-transfer (CT) interactions that lower HOMO energies according to registration between thiophene moieties on adjacent polymer chains. These results show how KPFM combined with wavelength-resolved photoluminescence imaging can be used to extract information on "dark" (CT) interactions in polymer assemblies. PMID:26095304

  6. A 1.6-Mb contig of yeast artificial chromosomes around the human factor VIII gene reveals three regions homologous to probes for the DXS115 locus and two for the DXYS64 locus.

    PubMed Central

    Freije, D; Schlessinger, D

    1992-01-01

    Two yeast artificial chromosome (YAC) libraries were screened for probes in Xq28, around the gene for coagulation factor VIII (F8). A set of 30 YACs were recovered and assembled into a contig spanning at least 1.6 Mb from the DXYS64 locus to the glucose 6-phosphate dehydrogenase gene (G6PD). Overlaps among the YACs were determined by several fingerprinting techniques and by additional probes generated from YAC inserts by using Alu-vector or ligation-mediated PCR. Analysis of more than 30 probes and sequence-tagged sites (STSs) made from the region revealed the presence of several homologous genomic segments. For example, a probe for the DXYS64 locus, which maps less than 500 kb 5' of F8, detects a similar but not identical locus between F8 and G6PD. Also, a probe for the DXS115 locus detects at least three identical copies in this region, one in intron 22 of F8 and at least two more, which are upstream of the 5' end of the gene. Comparisons of genomic and YAC DNA suggest that the multiple loci are not created artifactually during cloning but reflect the structure of uncloned human DNA. On the basis of these data, the most likely order for the loci analyzed is tel-DXYS61-DXYS64-(DXS115-3-DXS115-2)-5'F8-(D XS115-1)-3'F8-G6PD. Images Figure 2 Figure 3 Figure 4 Figure 5 PMID:1609806

  7. Tethered Hsp90 Inhibitors Carrying Optical or Radioiodinated Probes Reveal Selective Internalization of Ectopic Hsp90 in Malignant Breast Tumor Cells

    PubMed Central

    Barrott, Jared J.; Hughes, Philip F.; Osada, Takuya; Yang, Xiao-Yi; Hartman, Zachary C.; Loiselle, David R.; Spector, Neil L.; Neckers, Len; Rajaram, Narasimhan; Hu, Fangyao; Ramanujam, Nimmi; Vaidyanathan, Ganesan; Zalutsky, Michael R.; Lyerly, H. Kim; Haystead, Timothy A.

    2013-01-01

    Summary Hsp90 inhibitors have demonstrated unusual selectivity for tumor cells despite its ubiquitous expression. This phenomenon has remained unexplained but could be influenced by ectopically expressed Hsp90 in tumors. We have synthesized novel Hsp90 inhibitors that can carry optical or radioiodinated probes via a PEG tether. We show that these tethered inhibitors selectively recognize cells expressing ectopic Hsp90 and become internalized. The internalization process is blocked by Hsp90 antibodies, suggesting that active cycling of the protein is occurring at the plasma membrane. In mice, we show exquisite accumulation of the fluor-tethered versions within breast tumors at very sensitive levels. Cell-based assays with the radiolabeled version showed picomolar detection in cells that express ectopic Hsp90. Our findings show that fluor-tethered or radiolabeled inhibitors targeting ectopic Hsp90 can be used to detect breast cancer malignancies through non-invasive imaging. PMID:24035283

  8. Ground state and low-energy magnetic dynamics in the frustrated magnet CoAl2O4 as revealed by local spin probes

    NASA Astrophysics Data System (ADS)

    Iakovleva, M.; Vavilova, E.; Grafe, H.-J.; Zimmermann, S.; Alfonsov, A.; Luetkens, H.; Klauss, H.-H.; Maljuk, A.; Wurmehl, S.; Büchner, B.; Kataev, V.

    2015-04-01

    We report a combined experimental study of magnetic properties of a single crystal of the frustrated diamond lattice antiferromagnet CoAl2O4 with Co2+ electron spin resonance, 27Al nuclear magnetic resonance, and muon spin rotation/relaxation techniques. With our local probes, we show that the frustration of spin interactions and the Co/Al site disorder strongly affect the spin dynamics. The experimental results evidence inhomogeneous and slow magnetic fluctuations and the occurrence of short-range electron spin correlations far above a characteristic temperature T*=8 K at which the spin system turns into in a quasistatic state. Our data indicate that this spin order is likely short range and unconventional with spin fluctuations persistent even at T ≪T* . The results of three spectroscopy techniques highlight a nontrivial role of structural disorder for the magnetism of a frustrated diamond spin lattice at the proximity to the critical point.

  9. Terahertz dielectric response of photoexcited carriers in Si revealed via single-shot optical-pump and terahertz-probe spectroscopy

    SciTech Connect

    Minami, Yasuo; Horiuchi, Kohei; Masuda, Kaisei; Takeda, Jun; Katayama, Ikufumi

    2015-10-26

    We have demonstrated accurate observations of terahertz (THz) dielectric response due to photoexcited carriers in a Si plate via single-shot optical-pump and THz-probe spectroscopy. In contrast to conventional THz time-domain spectroscopy, this spectroscopic technique allows single-shot detection of the THz response of materials at a given delay time between the pump and THz pulses, thereby sufficiently extending the time interval between the pump pulses. As a result, we can accurately measure the dielectric properties of materials, while avoiding artifacts in the response caused by the accumulation of long-lived photoexcited carriers. Using our single-shot scheme, the transmittance of a Si plate was measured in the range of 0.5–2.5 THz with different pump fluences. Based on a Drude model analysis, the optically induced complex dielectric constant, plasma frequency, and damping rate in the THz region were quantitatively evaluated.

  10. Local Magnetoelectric Effect in La-Doped BiFeO3 Multiferroic Thin Films Revealed by Magnetic-Field-Assisted Scanning Probe Microscopy.

    PubMed

    Pan, Dan-Feng; Zhou, Ming-Xiu; Lu, Zeng-Xing; Zhang, Hao; Liu, Jun-Ming; Wang, Guang-Hou; Wan, Jian-Guo

    2016-12-01

    Multiferroic La-doped BiFeO3 thin films have been prepared by a sol-gel plus spin-coating process, and the local magnetoelectric coupling effect has been investigated by the magnetic-field-assisted scanning probe microscopy connected with a ferroelectric analyzer. The local ferroelectric polarization response to external magnetic fields is observed and a so-called optimized magnetic field of ~40 Oe is obtained, at which the ferroelectric polarization reaches the maximum. Moreover, we carry out the magnetic-field-dependent surface conductivity measurements and illustrate the origin of local magnetoresistance in the La-doped BiFeO3 thin films, which is closely related to the local ferroelectric polarization response to external magnetic fields. This work not only provides a useful technique to characterize the local magnetoelectric coupling for a wide range of multiferroic materials but also is significant for deeply understanding the local multiferroic behaviors in the BiFeO3-based systems. PMID:27356565

  11. Influence of Salmonella enterica Serovar Typhimurium ssrB on Colonization of Eastern Oysters (Crassostrea virginica) as Revealed by a Promoter Probe Screen

    PubMed Central

    Cox, Clayton E.; Wright, Anita C.; McClelland, Michael

    2015-01-01

    Although Salmonella has been isolated from 7.4 to 8.6% of domestic raw oysters, representing a significant risk for food-borne illness, little is known about the factors that influence their initial colonization by Salmonella. This study tested the hypothesis that specific regulatory changes enable a portion of the invading Salmonella population to colonize oysters. An in vivo promoter probe library screen identified 19 unique regions as regulated during colonization. The mutants in the nearest corresponding downstream genes were tested for colonization defects in oysters. Only one mutation, in ssrB, resulted in a significantly reduced ability to colonize oysters compared to that of wild-type Salmonella. Because ssrB regulates Salmonella pathogenicity island 2 (SPI-2)-dependent infections in vertebrate macrophages, the possibility that ssrB mediated colonization of oyster hemocytes in a similar manner was examined. However, no difference in hemocyte colonization was observed. The complementary hypothesis that signal exchange between Salmonella and the oyster's native microbial community aids colonization was also tested. Signals that triggered responses in quorum sensing (QS) reporters were shown to be produced by oyster-associated bacteria and present in oyster tissue. However, no evidence for signal exchange was observed in vivo. The sdiA reporter responded to salinity, suggesting that SdiA may also have a role in environmental sensing. Overall, this study suggests the initial colonization of live oysters by Salmonella is controlled by a limited number of regulators, including ssrB. PMID:26497459

  12. Bacteria capable of degrading anthracene, phenanthrene, and fluoranthene as revealed by DNA based stable-isotope probing in a forest soil.

    PubMed

    Song, Mengke; Jiang, Longfei; Zhang, Dayi; Luo, Chunling; Wang, Yan; Yu, Zhiqiang; Yin, Hua; Zhang, Gan

    2016-05-01

    Information on microorganisms possessing the ability to metabolize different polycyclic aromatic hydrocarbons (PAHs) in complex environments helps in understanding PAHs behavior in natural environment and developing bioremediation strategies. In the present study, stable-isotope probing (SIP) was applied to investigate degraders of PAHs in a forest soil with the addition of individually (13)C-labeled phenanthrene, anthracene, and fluoranthene. Three distinct phylotypes were identified as the active phenanthrene-, anthracene- and fluoranthene-degrading bacteria. The putative phenanthrene degraders were classified as belonging to the genus Sphingomona. For anthracene, bacteria of the genus Rhodanobacter were the putative degraders, and in the microcosm amended with fluoranthene, the putative degraders were identified as belonging to the phylum Acidobacteria. Our results from DNA-SIP are the first to directly link Rhodanobacter- and Acidobacteria-related bacteria with anthracene and fluoranthene degradation, respectively. The results also illustrate the specificity and diversity of three- and four-ring PAHs degraders in forest soil, contributes to our understanding on natural PAHs biodegradation processes, and also proves the feasibility and practicality of DNA-based SIP for linking functions with identity especially uncultured microorganisms in complex microbial biota. PMID:26808242

  13. Local Magnetoelectric Effect in La-Doped BiFeO3 Multiferroic Thin Films Revealed by Magnetic-Field-Assisted Scanning Probe Microscopy

    NASA Astrophysics Data System (ADS)

    Pan, Dan-Feng; Zhou, Ming-Xiu; Lu, Zeng-Xing; Zhang, Hao; Liu, Jun-Ming; Wang, Guang-Hou; Wan, Jian-Guo

    2016-06-01

    Multiferroic La-doped BiFeO3 thin films have been prepared by a sol-gel plus spin-coating process, and the local magnetoelectric coupling effect has been investigated by the magnetic-field-assisted scanning probe microscopy connected with a ferroelectric analyzer. The local ferroelectric polarization response to external magnetic fields is observed and a so-called optimized magnetic field of ~40 Oe is obtained, at which the ferroelectric polarization reaches the maximum. Moreover, we carry out the magnetic-field-dependent surface conductivity measurements and illustrate the origin of local magnetoresistance in the La-doped BiFeO3 thin films, which is closely related to the local ferroelectric polarization response to external magnetic fields. This work not only provides a useful technique to characterize the local magnetoelectric coupling for a wide range of multiferroic materials but also is significant for deeply understanding the local multiferroic behaviors in the BiFeO3-based systems.

  14. Inhomogeneous distribution of manganese atoms in ferromagnetic ZnSnAs{sub 2}:Mn thin films on InP revealed by three-dimensional atom probe investigation

    SciTech Connect

    Uchitomi, Naotaka Inoue, Hiroaki; Kato, Takahiro; Toyota, Hideyuki; Uchida, Hiroshi

    2015-05-07

    Atomic-scale Mn distributions in ferromagnetic ZnSnAs{sub 2}:Mn thin films grown on InP substrates have been studied by applying three-dimensional atom probe (3DAP) microscopy. It is found that Mn atoms in cross-sectional 3DAP maps show the presence of inhomogeneities in Mn distribution, which is characteristic patterns of a spinoidal decomposition phase with slightly high and low concentration regions. The high Mn concentration regions are expected to be coherently clustered MnAs in the zinc-blende structure, resulting in the formation of Mn-As random connecting patterns. The origin of room-temperature ferromagnetism in ZnSnAs{sub 2}:Mn on InP can be well explained by the formation of atomic-scale magnetic clustering by spinoidal decomposition without breaking the continuity of the zinc-blende structure, which has been suggested by previous theoretical works. The lattice-matching between magnetic epi-layers and substrates should be one of the most important factors to avoid the formation of secondary hexagonal MnAs phase precipitates in preparing ferromagnetic semiconductor thin films.

  15. Copper binding to chicken and human prion protein amylodogenic regions: differences and similarities revealed by Ni2+ as a diamagnetic probe.

    PubMed

    Valensin, Daniela; Gajda, Karolina; Gralka, Ewa; Valensin, Gianni; Kamysz, Wojciech; Kozlowski, Henryk

    2010-01-01

    Both human (h) and chicken (Ch) prion proteins (PrP) bind copper ions within the so called "tandem repeat" N-terminal region. Outside this region, hPrP possesses two additional copper binding sites, localized at His-96 and His-111 in the so called "amylodogenic" or neurotoxic region (residues 91-126). Also ChPrP possesses a similar region (ChPrP(105-140)) containing two His (His-110 and His-124) and an identical hydrophobic tail of 15 amino acids rich in Ala and Gly. The copper binding abilities within such region of ChPrP were investigated by NMR, CD and potentiometry using Ni(2+) as diamagnetic probe. The formation of diamagnetic metal complexes allowed to monitor the chemical shift and signal intensity variations and to determine the structural and kinetic features of the His-110 and His-124 metal binding sites. Finally a comparison between the hPrP and ChPrP metal binding abilities was performed. We found that the two prion proteins exhibited different copper and nickel preferences with the favoured metal binding sites localized at opposite His: His-110 for ChPrP, and His-111 for hPrP. PMID:19883942

  16. Lectin histochemistry reveals SNA as a prognostic carbohydrate-dependent probe for invasive ductal carcinoma of the breast: a clinicopathological and immunohistochemical auxiliary tool

    PubMed Central

    dos-Santos, Petra B; Zanetti, Juliana S; Vieira-de-Mello, Gabriela S; Rêgo, Moacyr BM; A, Alfredo Ribeiro-Silva; Beltrão, Eduardo Isidoro Carneiro

    2014-01-01

    Increased sialylation and β1,6-branched oligosaccharides has been associated with a variety of structural changes in cell surface carbohydrates, most notably in tumorigenesis. Lectins are defined as proteins that preferentially recognize and bind carbohydrate complexes protruding from glycolipids and glycoproteins. This interaction with carbohydrates can be as specific as the interaction between antigen and antibody. Due to this type of interaction lectins have been used as experimental auxiliary tools in histopathological diagnosis of cancer. This study was designed to evaluate the differential expression of sialic acids and β1,6-N-acetylglucosaminyltransferase V (MGAT5) in invasive (IDC) and in situ (DCIS) ductal carcinoma of the breast and its possible application as prognostic biomarkers. A possible transition between pre-malign and malign lesions was evaluated using DCIS samples. Biopsies were analyzed regarding the expression of MUC1, p53, Ki-67, estrogen receptor, progesterone receptor, HER-2 and MGAT5. α2,6-linked sialic acids residues recognized by SNA lectin was overexpressed in 33.3% of IDC samples and it was related with Ki-67 (p=0.042), PR (p=0.029), lymphnodes status (p=0.017) and death (p=0.011). Regarding survival analysis SNA was the only lectin able to correlate with specific-disease survival and disease-free survival (p=0.024 and p=0.041, respectively), besides, it presents itself as an independent variable by Cox Regression analysis (p= 0.004). Comparing IDC and DCIS cases, only SNA showed different staining pattern (p=0.034). The presence of sialic acids on tumor cell surface can be an indicative of poor prognosis and our study provides further evidence that SNA lectin can be used as a prognostic probe in IDC and DCIS patients. PMID:24966944

  17. Crustal structure and Moho geometry of the northeastern Tibetan plateau as revealed by SinoProbe-02 deep seismic-reflection profiling

    NASA Astrophysics Data System (ADS)

    Wang, Haiyan; Gao, Rui; Zeng, Lingsen; Kuang, Zhaoyang; Xue, Aimin; Li, Wenhui; Xiong, Xiaosong; Huang, Weiyi

    2014-12-01

    Underthrusting of India below Eurasia has resulted in the formation of the Himalayan and the Qinghai-Tibet Plateau. Distributed deformation coupled with block translation and rotation has generated the Qilian Shan thrust belt and a series of east- and northwest-striking strike-slip faults across northeastern Tibet. Because these structures lie in a transition zone between the high plateau region to the south and the lowlands of the North China craton in the north, determining their deep-crustal and upper-mantle structures has important implications for unraveling the mechanism of Tibetan plateau formation. In this paper, we present new results from the SinoProbe-02 deep seismic reflection project across the eastern part of the Qilian Shan and the southern margin of the Alxa block. Interpretation of the reflection profile obtained from this study is based on constraints from surface geology and detailed geometric analysis of structural relationships among key reflectors in the crust and the upper mantle. Our results indicate that the upper crust of the eastern Qilian Shan is characterized by fault-bend folds and duplex systems involving Phanerozoic strata that may have resulted from early Paleozoic collisional tectonics and Cenozoic intra-continental deformation. Locally, half-graben structures hosting Cretaceous strata are also present. The active structures in the region are dominated by left-slip Haiyuan and Tianjian fault systems marking the northern margin of the Tibetan plateau. The strike-slip structures have variable dips and dip directions and sole into a common décollement with a depth of 40-45 km. Because the two faults do not cut and offset the Moho below, the active crustal and mantle deformation in the northeastern Tibet must be decoupled.

  18. High Resolution DNA Stable Isotope Probing Reveals that Root Exudate Addition to Soil Changes the Identity of the Microbes that Degrade Cellulose but not the Rate of Degradation

    NASA Astrophysics Data System (ADS)

    Campbell, A.; Pepe-Ranney, C. P.; Nguyen, A. V. T.; Buckley, D. H.

    2015-12-01

    Plant roots release compounds, such as root exudates, which can alter soil organic matter (SOM) decomposition and have large impacts on soil carbon (C) retention. The changes in SOM turnover resulting from the addition of organic and/or inorganic substrates are termed 'priming effects'. In this study we examine the effects of root exudates on the priming of cellulose added as particulate organic matter. We amended soil microcosms with 13C-cellulose in the presence or absence of artificial root exudate additions and incubated over time for 45 days. Soils receiving the root exudate (RE) were given either one large dose or multiple, small doses of RE. In each treatment we tracked operational taxonomic units (OTUs) assimilating 13C from cellulose (herein, known as a 'responder') over time using DNA stable isotope probing coupled with next generation sequencing. In all treatments the same amount of cellulose-13C was respired indicating the addition of RE did not result in the priming of cellulose decomposition. However, cellulose responders were different depending on treatment and time of sampling (days 14, 28 and 45). We identified a total of 10,361 OTUs, of which there were 369 cellulose responders in the cellulose only treatment, 273 in the repeated, small dose RE treatment, and 358 in the RE single, large dose treatment. Most of the cellulose responders found in all treatments belonged to phyla Bacteroidetes, Planctomycetes, Proteobacteria, Verrucomicrobia, and Chloroflexi. The response time of phyla varies; for instance, more OTUs in Bacteroidetes were observed on day 14 and diminish with each subsequent sampling time. On the other hand, OTUs in Verrucomicrobia increased in response over time. Our study shows no priming effect resulting from the addition of root exudates, although the identity of the microbial mediators of cellulose decomposition varies in each treatment.

  19. Spectrophotometric probe

    DOEpatents

    Prather, W.S.; O'Rourke, P.E.

    1994-08-02

    A support structure is described bearing at least one probe for making spectrophotometric measurements of a fluid using a source of light and a spectrophotometer. The probe includes a housing with two optical fibers and a planoconvex lens. A sleeve bearing a mirror surrounds the housing. The lens is separated from the mirror by a fixed distance, defining an interior space for receiving a volume of the fluid sample. A plurality of throughholes extending through the sleeve communicate between the sample volume and the exterior of the probe, all but one hole bearing a screen. A protective jacket surrounds the probe. A hollow conduit bearing a tube is formed in the wall of the probe for venting any air in the interior space when fluid enters. The probe is held at an acute angle so the optic fibers carrying the light to and from the probe are not bent severely on emergence from the probe. 3 figs.

  20. Spectrophotometric probe

    DOEpatents

    Prather, William S.; O'Rourke, Patrick E.

    1994-01-01

    A support structure bearing at least one probe for making spectrophotometric measurements of a fluid using a source of light and a spectrophotometer. The probe includes a housing with two optical fibers and a planoconvex lens. A sleeve bearing a mirror surrounds the housing. The lens is separated from the mirror by a fixed distance, defining an interior space for receiving a volume of the fluid sample. A plurality of throughholes extending through the sleeve communicate between the sample volume and the exterior of the probe, all but one hole bearing a screen. A protective jacket surrounds the probe. A hollow conduit bearing a tube is formed in the wall of the probe for venting any air in the interior space when fluid enters. The probe is held at an acute angle so the optic fibers carrying the light to and from the probe are not bent severely on emergence from the probe.

  1. Complexities of bloom dynamics in the toxic dinoflagellate Alexandrium fundyense revealed through DNA measurements by imaging flow cytometry coupled with species-specific rRNA probes

    PubMed Central

    Brosnahan, Michael L.; Farzan, Shahla; Keafer, Bruce A.; Sosik, Heidi M.; Olson, Robert J.; Anderson, Donald M.

    2013-01-01

    Measurements of the DNA content of different protist populations can shed light on a variety of processes, including cell division, sex, prey ingestion, and parasite invasion. Here, we modified an Imaging FlowCytobot (IFCB), a custom-built flow cytometer that records images of microplankton, to measure the DNA content of large dinoflagellates and other high-DNA content species. The IFCB was also configured to measure fluorescence from Cy3-labeled rRNA probes, aiding the identification of Alexandrium fundyense (syn. A. tamarense Group I), a photosynthetic dinoflagellate that causes paralytic shellfish poisoning (PSP). The modified IFCB was used to analyze samples from the development, peak and termination phases of an inshore A. fundyense bloom (Salt Pond, Eastham, MA USA), and from a rare A. fundyense ‘red tide’ that occurred in the western Gulf of Maine, offshore of Portsmouth, NH (USA). Diploid or G2 phase (‘2C’) A. fundyense cells were frequently enriched at the near-surface, suggesting an important role for aggregation at the air-sea interface during sexual events. Also, our analysis showed that large proportions of A. fundyense cells in both the Salt Pond and red tide blooms were planozygotes during bloom decline, highlighting the importance of sexual fusion to bloom termination. At Salt Pond, bloom decline also coincided with a dramatic rise in infections by the parasite genus Amoebophrya. The samples that were most heavily infected contained many large cells with higher DNA-associated fluorescence than 2C vegetative cells, but these cells’ nuclei were also frequently consumed by Amoebophrya trophonts. Neither large cell size nor increased DNA-associated fluorescence could be replicated by infecting an A. fundyense culture of vegetative cells. Therefore we attribute these characteristics of the large Salt Pond cells to planozygote maturation rather than Amoebophrya infection, though an interaction between infection and planozygote maturation may

  2. Complexities of bloom dynamics in the toxic dinoflagellate Alexandrium fundyense revealed through DNA measurements by imaging flow cytometry coupled with species-specific rRNA probes.

    PubMed

    Brosnahan, Michael L; Farzan, Shahla; Keafer, Bruce A; Sosik, Heidi M; Olson, Robert J; Anderson, Donald M

    2014-05-01

    Measurements of the DNA content of different protist populations can shed light on a variety of processes, including cell division, sex, prey ingestion, and parasite invasion. Here, we modified an Imaging FlowCytobot (IFCB), a custom-built flow cytometer that records images of microplankton, to measure the DNA content of large dinoflagellates and other high-DNA content species. The IFCB was also configured to measure fluorescence from Cy3-labeled rRNA probes, aiding the identification of Alexandrium fundyense (syn. A. tamarense Group I), a photosynthetic dinoflagellate that causes paralytic shellfish poisoning (PSP). The modified IFCB was used to analyze samples from the development, peak and termination phases of an inshore A. fundyense bloom (Salt Pond, Eastham, MA USA), and from a rare A. fundyense 'red tide' that occurred in the western Gulf of Maine, offshore of Portsmouth, NH (USA). Diploid or G2 phase ('2C') A. fundyense cells were frequently enriched at the near-surface, suggesting an important role for aggregation at the air-sea interface during sexual events. Also, our analysis showed that large proportions of A. fundyense cells in both the Salt Pond and red tide blooms were planozygotes during bloom decline, highlighting the importance of sexual fusion to bloom termination. At Salt Pond, bloom decline also coincided with a dramatic rise in infections by the parasite genus Amoebophrya. The samples that were most heavily infected contained many large cells with higher DNA-associated fluorescence than 2C vegetative cells, but these cells' nuclei were also frequently consumed by Amoebophrya trophonts. Neither large cell size nor increased DNA-associated fluorescence could be replicated by infecting an A. fundyense culture of vegetative cells. Therefore we attribute these characteristics of the large Salt Pond cells to planozygote maturation rather than Amoebophrya infection, though an interaction between infection and planozygote maturation may also have

  3. Complexities of bloom dynamics in the toxic dinoflagellate Alexandrium fundyense revealed through DNA measurements by imaging flow cytometry coupled with species-specific rRNA probes

    NASA Astrophysics Data System (ADS)

    Brosnahan, Michael L.; Farzan, Shahla; Keafer, Bruce A.; Sosik, Heidi M.; Olson, Robert J.; Anderson, Donald M.

    2014-05-01

    Measurements of the DNA content of different protist populations can shed light on a variety of processes, including cell division, sex, prey ingestion, and parasite invasion. Here, we modified an Imaging FlowCytobot (IFCB), a custom-built flow cytometer that records images of microplankton, to measure the DNA content of large dinoflagellates and other high-DNA content species. The IFCB was also configured to measure fluorescence from Cy3-labeled rRNA probes, aiding the identification of Alexandrium fundyense (syn. A. tamarense Group I), a photosynthetic dinoflagellate that causes paralytic shellfish poisoning (PSP). The modified IFCB was used to analyze samples from the development, peak and termination phases of an inshore A. fundyense bloom (Salt Pond, Eastham, MA, USA), and from a rare A. fundyense ‘red tide’ that occurred in the western Gulf of Maine, offshore of Portsmouth, NH (USA). Diploid or G2 phase (‘2C’) A. fundyense cells were frequently enriched at the near-surface, suggesting an important role for aggregation at the air-sea interface during sexual events. Also, our analysis showed that large proportions of A. fundyense cells in both the Salt Pond and red tide blooms were planozygotes during bloom decline, highlighting the importance of sexual fusion to bloom termination. At Salt Pond, bloom decline also coincided with a dramatic rise in infections by the parasite genus Amoebophrya. The samples that were most heavily infected contained many large cells with higher DNA-associated fluorescence than 2C vegetative cells, but these cells' nuclei were also frequently consumed by Amoebophrya trophonts. Neither large cell size nor increased DNA-associated fluorescence could be replicated by infecting an A. fundyense culture of vegetative cells. Therefore, we attribute these characteristics of the large Salt Pond cells to planozygote maturation rather than Amoebophrya infection, though an interaction between infection and planozygote maturation may

  4. Mutations in the leader region of ribosomal RNA operons cause structurally defective 30 S ribosomes as revealed by in vivo structural probing.

    PubMed

    Balzer, M; Wagner, R

    1998-02-27

    The biogenesis of functional ribosomes is regulated in a very complex manner, involving different proteins and RNA molecules. RNAs are not only essential components of both ribosomal subunits but also transiently interacting factors during particle formation. In eukaryotes snoRNAs act as molecular chaperones to assist maturation, modification and assembly. In a very similar way highly conserved leader sequences of bacterial rRNA operons are involved in the correct formation of 30 S ribosomal subunits. Certain mutations in the rRNA leader region cause severe growth defects due to malfunction of ribosomes which are assembled from such transcription units. To understand how the leader sequences act to facilitate the formation of the correct 30 S subunits we performed in vivo chemical probing to assess structural differences between ribosomes assembled either from rRNA transcribed from wild-type operons or from operons which contain mutations in the rRNA leader region. Cells transformed with plasmids containing the respective rRNA operons were reacted with dimethylsulphate (DMS). Ribosomes were isolated by sucrose gradient centrifugation and modified nucleotides within the 16 S rRNA were identified by primer extension reaction. Structural differences between ribosomes from wild-type and mutant rRNA operons occur in several clusters within the 16 S rRNA secondary structure. The most prominent differences are located in the central domain including the universally conserved pseudoknot structure which connects the 5', the central and the 3' domain of 16 S rRNA. Two other clusters with structural differences fall in the 5' domain where the leader had been shown to interact with mature 16 S rRNA and within the ribosomal protein S4 binding site. The other differences in structure are located in sites which are also known as sites for the action of several antibiotics. The data explain the functional defects of ribosomes from rRNA operons with leader mutations and help to

  5. Daily Rhythms in the Cyanobacterium Synechococcus elongatus Probed by High-resolution Mass Spectrometry–based Proteomics Reveals a Small Defined Set of Cyclic Proteins*

    PubMed Central

    Guerreiro, Ana C. L.; Benevento, Marco; Lehmann, Robert; van Breukelen, Bas; Post, Harm; Giansanti, Piero; Maarten Altelaar, A. F.; Axmann, Ilka M.; Heck, Albert J. R.

    2014-01-01

    Circadian rhythms are self-sustained and adjustable cycles, typically entrained with light/dark and/or temperature cycles. These rhythms are present in animals, plants, fungi, and several bacteria. The central mechanism behind these “pacemakers” and the connection to the circadian regulated pathways are still poorly understood. The circadian rhythm of the cyanobacterium Synechococcus elongatus PCC 7942 (S. elongatus) is highly robust and controlled by only three proteins, KaiA, KaiB, and KaiC. This central clock system has been extensively studied functionally and structurally and can be reconstituted in vitro. These characteristics, together with a relatively small genome (2.7 Mbp), make S. elongatus an ideal model system for the study of circadian rhythms. Different approaches have been used to reveal the influence of the central S. elongatus clock on rhythmic gene expression, rhythmic mRNA abundance, rhythmic DNA topology changes, and cell division. However, a global analysis of its proteome dynamics has not been reported yet. To uncover the variation in protein abundances during 48 h under light and dark cycles (12:12 h), we used quantitative proteomics, with TMT 6-plex isobaric labeling. We queried the S. elongatus proteome at 10 different time points spanning a single 24-h period, leading to 20 time points over the full 48-h period. Employing multidimensional separation and high-resolution mass spectrometry, we were able to find evidence for a total of 82% of the S. elongatus proteome. Of the 1537 proteins quantified over the time course of the experiment, only 77 underwent significant cyclic variations. Interestingly, our data provide evidence for in- and out-of-phase correlation between mRNA and protein levels for a set of specific genes and proteins. As a range of cyclic proteins are functionally not well annotated, this work provides a resource for further studies to explore the role of these proteins in the cyanobacterial circadian rhythm. PMID

  6. Optical probe

    DOEpatents

    Hencken, Kenneth; Flower, William L.

    1999-01-01

    A compact optical probe is disclosed particularly useful for analysis of emissions in industrial environments. The instant invention provides a geometry for optically-based measurements that allows all optical components (source, detector, rely optics, etc.) to be located in proximity to one another. The geometry of the probe disclosed herein provides a means for making optical measurements in environments where it is difficult and/or expensive to gain access to the vicinity of a flow stream to be measured. Significantly, the lens geometry of the optical probe allows the analysis location within a flow stream being monitored to be moved while maintaining optical alignment of all components even when the optical probe is focused on a plurality of different analysis points within the flow stream.

  7. Conductivity Probe

    NASA Technical Reports Server (NTRS)

    2008-01-01

    The Thermal and Electrical Conductivity Probe (TECP) for NASA's Phoenix Mars Lander took measurements in Martian soil and in the air.

    The needles on the end of the instrument were inserted into the Martian soil, allowing TECP to measure the propagation of both thermal and electrical energy. TECP also measured the humidity in the surrounding air.

    The needles on the probe are 15 millimeters (0.6 inch) long.

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  8. Pollution Probe.

    ERIC Educational Resources Information Center

    Chant, Donald A.

    This book is written as a statement of concern about pollution by members of Pollution Probe, a citizens' anti-pollution group in Canada. Its purpose is to create public awareness and pressure for the eventual solution to pollution problems. The need for effective government policies to control the population explosion, conserve natural resources,…

  9. Displacement Compensation of Temperature Probe Data

    NASA Technical Reports Server (NTRS)

    Welch, Christopher S.; Hubert, James A.; Barber, Patrick G.

    1996-01-01

    Analysis of temperature data from a probe in a vertical Bridgman furnace growing germanium crystals revealed a displacement of the temperature profile due to conduction error. A theoretical analysis shows that the displacement compensation is independent of local temperature gradient. A displacement compensation value should become a standard characteristic of temperature probes used for temperature profile measurements.

  10. Formative Assessment Probes: To Hypothesize or Not

    ERIC Educational Resources Information Center

    Keeley, Page

    2010-01-01

    Formative assessment probes are used not only to uncover the ideas students bring to their learning, they can also be used to reveal teachers' common misconceptions. Consider a process widely used in inquiry science--developing hypotheses. In this article, the author features the probe "Is It a Hypothesis?", which serves as an example of how…

  11. Hydrodynamic ultrasonic probe

    DOEpatents

    Day, Robert A.; Conti, Armond E.

    1980-01-01

    An improved probe for in-service ultrasonic inspection of long lengths of a workpiece, such as small diameter tubing from the interior. The improved probe utilizes a conventional transducer or transducers configured to inspect the tubing for flaws and/or wall thickness variations. The probe utilizes a hydraulic technique, in place of the conventional mechanical guides or bushings, which allows the probe to move rectilinearly or rotationally while preventing cocking thereof in the tube and provides damping vibration of the probe. The probe thus has lower friction and higher inspection speed than presently known probes.

  12. A Comparative pO2 Probe and [18F]-Fluoro-Azomycinarabino-Furanoside ([18F]FAZA) PET Study Reveals Anesthesia-Induced Impairment of Oxygenation and Perfusion in Tumor and Muscle

    PubMed Central

    Mahling, Moritz; Fuchs, Kerstin; Thaiss, Wolfgang M.; Maier, Florian C.; Feger, Martina; Bukala, Daniel; Harant, Maren; Eichner, Martin; Reutershan, Jörg; Lang, Florian; Reischl, Gerald; Pichler, Bernd J.; Kneilling, Manfred

    2015-01-01

    Tumor hypoxia can be identified by [18F]FAZA positron emission tomography, or invasively using oxygen probes. The impact of anesthetics on tumor hypoxia remains controversial. The aim of this comprehensive study was to investigate the impact of isoflurane and ketamine/xylazine anesthesia on [18F]FAZA uptake and partial oxygen pressure (pO2) in carcinoma and muscle tissue of air- and oxygen-breathing mice. Methods CT26 colon carcinoma-bearing mice were anesthetized with isoflurane (IF) or ketamine/xylazine (KX) while breathing air or oxygen (O2). We performed 10 min static PET scans 1 h, 2 h and 3 h after [18F]FAZA injection and calculated the [18F]FAZA-uptake and tumor-to-muscle ratios (T/M). In another experimental group, we placed a pO2 probe in the tumor as well as in the gastrocnemius muscle to measure the pO2 and perfusion. Results Ketamine/xylazine-anesthetized mice yielded up to 3.5-fold higher T/M-ratios compared to their isoflurane-anesthetized littermates 1 h, 2 h and 3 h after [18F]FAZA injection regardless of whether the mice breathed air or oxygen (3 h, KX-air: 7.1 vs. IF-air: 1.8, p = 0.0001, KX-O2: 4.4 vs. IF-O2: 1.4, p < 0.0001). The enhanced T/M-ratios in ketamine/xylazine-anesthetized mice were mainly caused by an increased [18F]FAZA uptake in the carcinomas. Invasive pO2 probe measurements yielded enhanced intra-tumoral pO2 values in air- and oxygen-breathing ketamine/xylazine-anesthetized mice compared to isoflurane-anesthetized mice (KX-air: 1.01 mmHg, IF-air: 0.45 mmHg; KX-O2 9.73 mmHg, IF-O2: 6.25 mmHg). Muscle oxygenation was significantly higher in air-breathing isoflurane-anesthetized (56.9 mmHg) than in ketamine/xylazine-anesthetized mice (33.8 mmHg, p = 0.0003). Conclusion [18F]FAZA tumor uptake was highest in ketamine/xylazine-anesthetized mice regardless of whether the mice breathed air or oxygen. The generally lower [18F]FAZA whole-body uptake in isoflurane-anesthetized mice could be due to the higher muscle pO2-values in these mice

  13. Revisiting Mitochondrial pH with an Improved Algorithm for Calibration of the Ratiometric 5(6)-carboxy-SNARF-1 Probe Reveals Anticooperative Reaction with H+ Ions and Warrants Further Studies of Organellar pH

    PubMed Central

    Żurawik, Tomasz Michał; Pomorski, Adam; Belczyk-Ciesielska, Agnieszka; Goch, Grażyna; Niedźwiedzka, Katarzyna; Kucharczyk, Róża; Krężel, Artur; Bal, Wojciech

    2016-01-01

    Fluorescence measurements of pH and other analytes in the cell rely on accurate calibrations, but these have routinely used algorithms that inadequately describe the properties of indicators. Here, we have established a more accurate method for calibrating and analyzing data obtained using the ratiometric probe 5(6)-carboxy-SNARF-1. We tested the implications of novel approach to measurements of pH in yeast mitochondria, a compartment containing a small number of free H+ ions. Our findings demonstrate that 5(6)-carboxy-SNARF-1 interacts with H+ ions inside the mitochondria in an anticooperative manner (Hill coefficient n of 0.5) and the apparent pH inside the mitochondria is ~0.5 unit lower than had been generally assumed. This result, at odds with the current consensus on the mechanism of energy generation in the mitochondria, is in better agreement with theoretical considerations and warrants further studies of organellar pH. PMID:27557123

  14. Revisiting Mitochondrial pH with an Improved Algorithm for Calibration of the Ratiometric 5(6)-carboxy-SNARF-1 Probe Reveals Anticooperative Reaction with H+ Ions and Warrants Further Studies of Organellar pH.

    PubMed

    Żurawik, Tomasz Michał; Pomorski, Adam; Belczyk-Ciesielska, Agnieszka; Goch, Grażyna; Niedźwiedzka, Katarzyna; Kucharczyk, Róża; Krężel, Artur; Bal, Wojciech

    2016-01-01

    Fluorescence measurements of pH and other analytes in the cell rely on accurate calibrations, but these have routinely used algorithms that inadequately describe the properties of indicators. Here, we have established a more accurate method for calibrating and analyzing data obtained using the ratiometric probe 5(6)-carboxy-SNARF-1. We tested the implications of novel approach to measurements of pH in yeast mitochondria, a compartment containing a small number of free H+ ions. Our findings demonstrate that 5(6)-carboxy-SNARF-1 interacts with H+ ions inside the mitochondria in an anticooperative manner (Hill coefficient n of 0.5) and the apparent pH inside the mitochondria is ~0.5 unit lower than had been generally assumed. This result, at odds with the current consensus on the mechanism of energy generation in the mitochondria, is in better agreement with theoretical considerations and warrants further studies of organellar pH. PMID:27557123

  15. Microarray reveals complement components are regulated in the serum-deprived rat retinal ganglion cell line

    PubMed Central

    Khalyfa, Abdelnaby; Chlon, Timothy; Qiang, He; Agarwal, Neeraj

    2007-01-01

    Purpose Glaucoma is a progressive eye disease that leads to blindness due to loss of retinal ganglion cells (RGCs). There are difficulties in using primary cultures of purified RGC to study this pathophysiology. RGC-5, a transformed not RGC line, expresses several markers characteristic of the RGCs. The aim of this study was to generate a genome-wide gene expression of RGC-5 following serum deprivation and to identify candidate genes that may be involved in the signal transduction pathways. Methods Apoptosis in the transformed rat RGC-5 was induced by serum deprivation for 0, 8, 24, 48, and 96 h. Briefly, 400 ng of RNA from each sample was reverse transcribed and labeled with Cy3 dye. Fragmented fluorescent cRNA was mixed with hybridization buffer and incubated at 60 °C for 16 h. Labeled cRNA was hybridized to Rat Genome Oligonucleotide Arrays. These arrays contain 22,775 transcripts with one oligonucleotide per transcript (60-mer). Gene expression from scanned images was quantified and analyzed using ArrayVision software. Reproducibility among triplicate arrays was determined by ANOVA statistical analysis. Significant differences in gene expression between apoptotic and nonapoptotic cells were determined based on p-values. Results Of the 22,775 transcripts present on the arrays (Agilent rat genome, 60-mer), 713 (8 h), 1,967 (24 h), 1,011 (48 h), and 1,161 (96 h) were differentially expressed relative to the 0 h time point (p-values <0.05). Twenty-three transcripts were common to 8, 24, 48, and 96 h and 130 transcripts were common to the 24, 48, and 96 h time points. The two most highly upregulated genes were Fdft1 and Lgals3 (8 h), C3 and Fcgrt (24 h), C and Lcn2 (48 h), and Mgp and C3 (96 h). A subset of the differentially expressed genes identified in microarray data (Ftl1, C3, C1s, Neu1, Polr2g, Acadm, Nupr1, Gch, Dia1, DNase1, Tgfb2, and Cyr61) were validated using quantitative real time polymerase chain reaction (QRT-PCR). Here we show that complement factor

  16. EDITORIAL: Probing the nanoworld Probing the nanoworld

    NASA Astrophysics Data System (ADS)

    Miles, Mervyn

    2009-10-01

    In nanotechnology, it is the unique properties arising from nanometre-scale structures that lead not only to their technological importance but also to a better understanding of the underlying science. Over the last twenty years, material properties at the nanoscale have been dominated by the properties of carbon in the form of the C60 molecule, single- and multi-wall carbon nanotubes, nanodiamonds, and recently graphene. During this period, research published in the journal Nanotechnology has revealed the amazing mechanical properties of such materials as well as their remarkable electronic properties with the promise of new devices. Furthermore, nanoparticles, nanotubes, nanorods, and nanowires from metals and dielectrics have been characterized for their electronic, mechanical, optical, chemical and catalytic properties. Scanning probe microscopy (SPM) has become the main characterization technique and atomic force microscopy (AFM) the most frequently used SPM. Over the past twenty years, SPM techniques that were previously experimental in nature have become routine. At the same time, investigations using AFM continue to yield impressive results that demonstrate the great potential of this powerful imaging tool, particularly in close to physiological conditions. In this special issue a collaboration of researchers in Europe report the use of AFM to provide high-resolution topographical images of individual carbon nanotubes immobilized on various biological membranes, including a nuclear membrane for the first time (Lamprecht C et al 2009 Nanotechnology 20 434001). Other SPM developments such as high-speed AFM appear to be making a transition from specialist laboratories to the mainstream, and perhaps the same may be said for non-contact AFM. Looking to the future, characterisation techniques involving SPM and spectroscopy, such as tip-enhanced Raman spectroscopy, could emerge as everyday methods. In all these advanced techniques, routinely available probes will

  17. NeuroMEMS: Neural Probe Microtechnologies

    PubMed Central

    HajjHassan, Mohamad; Chodavarapu, Vamsy; Musallam, Sam

    2008-01-01

    Neural probe technologies have already had a significant positive effect on our understanding of the brain by revealing the functioning of networks of biological neurons. Probes are implanted in different areas of the brain to record and/or stimulate specific sites in the brain. Neural probes are currently used in many clinical settings for diagnosis of brain diseases such as seizers, epilepsy, migraine, Alzheimer's, and dementia. We find these devices assisting paralyzed patients by allowing them to operate computers or robots using their neural activity. In recent years, probe technologies were assisted by rapid advancements in microfabrication and microelectronic technologies and thus are enabling highly functional and robust neural probes which are opening new and exciting avenues in neural sciences and brain machine interfaces. With a wide variety of probes that have been designed, fabricated, and tested to date, this review aims to provide an overview of the advances and recent progress in the microfabrication techniques of neural probes. In addition, we aim to highlight the challenges faced in developing and implementing ultra-long multi-site recording probes that are needed to monitor neural activity from deeper regions in the brain. Finally, we review techniques that can improve the biocompatibility of the neural probes to minimize the immune response and encourage neural growth around the electrodes for long term implantation studies.

  18. Galileo Probe Battery System

    NASA Technical Reports Server (NTRS)

    Dagarin, B. P.; Taenaka, R. K.; Stofel, E. J.

    1997-01-01

    The conclusions of the Galileo probe battery system are: the battery performance met mission requirements with margin; extensive ground-based and flight tests of batteries prior to probe separation from orbiter provided good prediction of actual entry performance at Jupiter; and the Li-SO2 battery was an important choice for the probe's main power.

  19. Heat pipe cooled probe

    NASA Technical Reports Server (NTRS)

    Camarda, C. J. (Inventor); Couch, L. M.

    1984-01-01

    The basic heat pipe principle is employed to provide a self-contained passively cooled probe that may be placed into a high temperature environment. The probe consists of an evaporator region of a heat pipe and a sensing instrument. Heat is absorbed as the working fluid evaporates in the probe. The vapor is transported to the vapor space of the condenser region. Heat is dissipated from the condenser region and fins causing condensation of the working fluid, which returns to the probe by gravity and the capillary action of the wick. Working fluid, wick and condenser configurations and structure materials can be selected to maintain the probe within an acceptable temperature range.

  20. Ultrafast scanning probe microscopy

    DOEpatents

    Weiss, Shimon; Chemla, Daniel S.; Ogletree, D. Frank; Botkin, David

    1995-01-01

    An ultrafast scanning probe microscopy method for achieving subpicosecond-temporal resolution and submicron-spatial resolution of an observation sample. In one embodiment of the present claimed invention, a single short optical pulse is generated and is split into first and second pulses. One of the pulses is delayed using variable time delay means. The first pulse is then directed at an observation sample located proximate to the probe of a scanning probe microscope. The scanning probe microscope produces probe-sample signals indicative of the response of the probe to characteristics of the sample. The second pulse is used to modulate the probe of the scanning probe microscope. The time delay between the first and second pulses is then varied. The probe-sample response signal is recorded at each of the various time delays created between the first and second pulses. The probe-sample response signal is then plotted as a function of time delay to produce a cross-correlation of the probe sample response. In so doing, the present invention provides simultaneous subpicosecond-temporal resolution and submicron-spatial resolution of the sample.

  1. Traversing probe system

    DOEpatents

    Mashburn, Douglas N.; Stevens, Richard H.; Woodall, Harold C.

    1977-01-01

    This invention comprises a rotatable annular probe-positioner which carries at least one radially disposed sensing probe, such as a Pitot tube having a right-angled tip. The positioner can be coaxially and rotatably mounted within a compressor casing or the like and then actuated to orient the sensing probe as required to make measurements at selected stations in the annulus between the positioner and compressor casing. The positioner can be actuated to (a) selectively move the probe along its own axis, (b) adjust the yaw angle of the right-angled probe tip, and (c) revolve the probe about the axis common to the positioner and casing. A cam plate engages a cam-follower portion of the probe and normally rotates with the positioner. The positioner includes a first-motor-driven ring gear which effects slidable movement of the probe by rotating the positioner at a time when an external pneumatic cylinder is actuated to engage the cam plate and hold it stationary. When the pneumatic cylinder is not actuated, this ring gear can be driven to revolve the positioner and thus the probe to a desired circumferential location about the above-mentioned common axis. A second motor-driven ring gear included in the positioner can be driven to rotate the probe about its axis, thus adjusting the yaw angle of the probe tip. The positioner can be used in highly corrosive atmosphere, such as gaseous uranium hexafluoride.

  2. Ultrafast scanning probe microscopy

    DOEpatents

    Weiss, S.; Chemla, D.S.; Ogletree, D.F.; Botkin, D.

    1995-05-16

    An ultrafast scanning probe microscopy method is described for achieving subpicosecond-temporal resolution and submicron-spatial resolution of an observation sample. In one embodiment of the present claimed invention, a single short optical pulse is generated and is split into first and second pulses. One of the pulses is delayed using variable time delay means. The first pulse is then directed at an observation sample located proximate to the probe of a scanning probe microscope. The scanning probe microscope produces probe-sample signals indicative of the response of the probe to characteristics of the sample. The second pulse is used to modulate the probe of the scanning probe microscope. The time delay between the first and second pulses is then varied. The probe-sample response signal is recorded at each of the various time delays created between the first and second pulses. The probe-sample response signal is then plotted as a function of time delay to produce a cross-correlation of the probe sample response. In so doing, the present invention provides simultaneous subpicosecond-temporal resolution and submicron-spatial resolution of the sample. 6 Figs.

  3. Electrical resistivity probes

    DOEpatents

    Lee, Ki Ha; Becker, Alex; Faybishenko, Boris A.; Solbau, Ray D.

    2003-10-21

    A miniaturized electrical resistivity (ER) probe based on a known current-voltage (I-V) electrode structure, the Wenner array, is designed for local (point) measurement. A pair of voltage measuring electrodes are positioned between a pair of current carrying electrodes. The electrodes are typically about 1 cm long, separated by 1 cm, so the probe is only about 1 inch long. The electrodes are mounted to a rigid tube with electrical wires in the tube and a sand bag may be placed around the electrodes to protect the electrodes. The probes can be positioned in a borehole or on the surface. The electrodes make contact with the surrounding medium. In a dual mode system, individual probes of a plurality of spaced probes can be used to measure local resistance, i.e. point measurements, but the system can select different probes to make interval measurements between probes and between boreholes.

  4. Functional probes for scanning probe microscopy

    NASA Astrophysics Data System (ADS)

    Hasegawa, Yukio; Akiyama, Kotone; Hamada, Masayuki; Eguchi, Toyoaki; An, Toshu; Fujikawa, Yasunori; Sakurai, Toshio

    2008-03-01

    Inspite of importance of the probe in scanning probe microscopy (SPM), little attention was paid for the SPM probes for most of the measurements of SPM. We developed sharp metal-tip cantilevers with a typical curvature radius better than 5nm using focused ion beam (FIB) suitable for Kelvin probe force microscopy (KFM)^1. We obtained atomically resolved KFM images with an energy resolution less than 3meV with the probe^2. We also developed a glass-coated tungsten tip for synchrotron radiation-scanning tunneling microscopy with the FIB method^3 and obtained elementally resolved images in a resolution less than 20nm^4. We are now developing a precise atomic force microscope (AFM) lithography^5 with the FIB-milled tip attached to a quartz tuning fork controlled by noncontact AFM. We will present recent results of our AFM lithography, such as an Au line with a width of 20˜30 nm and characters drawn with Au nano dots on a Si surface. 1 K. Akiyama et al., RSI 76, 033705 (2005) 2 T. Eguchi, K. Akiyama et al., PRL 93, 266102 (2004) 3 K. Akiyama et al., RSI 76, 083711 (2005) 4 T. Eguchi, K. Akiyama et al., APL 89, 243119 (2006) 5 K. Akiyama et al., JP 61, 22 (2007).

  5. Periodontal probing: a review.

    PubMed

    Al Shayeb, Kwthar Nassar A; Turner, Wendy; Gillam, David G

    2014-08-01

    Periodontal probes are the main instruments that are used to assess the status of the periodontium, either for screening purposes or to evaluate periodontal changes throughout the treatment process. With increased knowledge and understanding of periodontal disease, the probes have evolved from a unidimensional manual shape into a more sophisticated computerised instrument. This is due to the need to increase the accuracy and reproducibility of readings and to improve efficiency (time, effort, money). Each probe has characteristic features that makes it unique and, in some cases, specific and limited to use. The aim of this paper is to present a brief introduction to periodontal disease and the methodology of measuring it, followed by probing limitations. The paper will also discuss the methodology of reducing probing error, examiner calibration and probing reproducibility. PMID:25198634

  6. High temperature probe

    DOEpatents

    Swan, Raymond A.

    1994-01-01

    A high temperature probe for sampling, for example, smokestack fumes, and is able to withstand temperatures of 3000.degree. F. The probe is constructed so as to prevent leakage via the seal by placing the seal inside the water jacket whereby the seal is not exposed to high temperature, which destroys the seal. The sample inlet of the probe is also provided with cooling fins about the area of the seal to provide additional cooling to prevent the seal from being destroyed. Also, a heated jacket is provided for maintaining the temperature of the gas being tested as it passes through the probe. The probe includes pressure sensing means for determining the flow velocity of an efficient being sampled. In addition, thermocouples are located in various places on the probe to monitor the temperature of the gas passing there through.

  7. Chemical Address Tags of Fluorescent Bioimaging Probes

    PubMed Central

    Shedden, Kerby; Rosania, Gus R.

    2010-01-01

    Chemical address tags can be defined as specific structural features shared by a set of bioimaging probes having a predictable influence on cell-associated visual signals obtained from these probes. Here, using a large image dataset acquired with a high content screening instrument, machine vision and cheminformatics analysis have been applied to reveal chemical address tags. With a combinatorial library of fluorescent molecules, fluorescence signal intensity, spectral, and spatial features characterizing each one of the probes' visual signals were extracted from images acquired with the three different excitation and emission channels of the imaging instrument. With multivariate regression, the additive contribution from each one of the different building blocks of the bioimaging probes towards each measured, cell-associated image-based feature was calculated. In this manner, variations in the chemical features of the molecules were associated with the resulting staining patterns, facilitating quantitative, objective analysis of chemical address tags. Hierarchical clustering and paired image-cheminformatics analysis revealed key structure-property relationships amongst many building blocks of the fluorescent molecules. The results point to different chemical modifications of the bioimaging probes that can exert similar (or different) effects on the probes' visual signals. Inspection of the clustered structures suggests intramolecular charge migration or partial charge distribution as potential mechanistic determinants of chemical address tag behavior. PMID:20104576

  8. Titan Probe navigation analysis

    NASA Technical Reports Server (NTRS)

    Vijayaraghavan, A.; Wood, L. J.

    1986-01-01

    In the proposed Cassini mission, a combined Saturn Orbiter/Titan Probe spacecraft will be launched from the Space Shuttle to arrive at Saturn around 2002, by means of a delta-VEGA trajectory. After Saturn-orbit insertion and a pericrone raise maneuver, the probe will be released to enter the Titan atmosphere and impact onto its surface. During its descent phase and impact onto Titan, the probe will maintain radio contact with the orbiter. Since the Titan-probe experimental phase lasts for only about four hours, probe-orbiter geometry and probe-delivery accuracy are critical to successful completion of this part of the mission. From a preliminary navigation analysis for probe delivery accuracy, it seems feasible to deliver the probe within 50 km (1-sigma value) of the desired aim-point in the Titan B-plane. The covariance study, however, clearly indicates the need for optical data, in addition to radio metric data. A Monte Carlo study indicates that a Delta-V capability of 98 m/sec for trajectory correction maneuvers will be sufficient to cover 99 percent of all contingencies during the segment from Saturn-orbit insertion to Titan-probe release.

  9. Radio frequency-compensated Langmuir probe with auxiliary double probes

    SciTech Connect

    Oh, Se-Jin; Oh, Seung-Ju; Chung, Chin-Wook

    2010-09-15

    A radio frequency (rf) compensation design using auxiliary double probes connected in parallel with a main measurement probe was developed for Langmuir probe diagnostics. This probe structure can reduce the sheath impedance of the main probe. In our probe design, the sheath capacitance of the probe can be increased and its sheath resistance can be decreased with increasing dc bias differential voltage between the auxiliary double probes. The I-V characteristic curve and electron energy distribution functions measured by our probe system had sufficient rf compensation performance in inductively coupled plasmas.

  10. Radio frequency-compensated Langmuir probe with auxiliary double probes.

    PubMed

    Oh, Se-Jin; Oh, Seung-Ju; Chung, Chin-Wook

    2010-09-01

    A radio frequency (rf) compensation design using auxiliary double probes connected in parallel with a main measurement probe was developed for Langmuir probe diagnostics. This probe structure can reduce the sheath impedance of the main probe. In our probe design, the sheath capacitance of the probe can be increased and its sheath resistance can be decreased with increasing dc bias differential voltage between the auxiliary double probes. The I-V characteristic curve and electron energy distribution functions measured by our probe system had sufficient rf compensation performance in inductively coupled plasmas. PMID:20886976

  11. Single molecule probes of membrane structure: orientation of BODIPY probes in DPPC as a function of probe structure.

    PubMed

    Armendariz, Kevin P; Huckabay, Heath A; Livanec, Philip W; Dunn, Robert C

    2012-03-21

    Single molecule fluorescence measurements have recently been used to probe the orientation of fluorescent lipid analogs doped into lipid films at trace levels. Using defocused polarized total internal reflection fluorescence microscopy (PTIRF-M), these studies have shown that fluorophore orientation responds to changes in membrane surface pressure and composition, providing a molecular level marker of membrane structure. Here we extend those studies by characterizing the single molecule orientations of six related BODIPY probes doped into monolayers of DPPC. Langmuir-Blodgett monolayers transferred at various surface pressures are used to compare the response from fluorescent lipid analogs in which the location of the BODIPY probe is varied along the length of the acyl chain. For each BODIPY probe location along the chain, comparisons are made between analogs containing phosphocholine and smaller fatty acid headgroups. Together these studies show a general propensity of the BODIPY analogs to insert into membranes with the BODIPY probe aligned along the acyl chains or looped back to interact with the headgroups. For all BODIPY probes studied, a bimodal orientation distribution is observed which is sensitive to surface pressure, with the population of BODIPY probes aligned along the acyl chains increasing with elevated surface pressure. Trends in the single molecule orientations for the six analogs reveal a configuration where optimal placement of the BODIPY probe within the acyl chain maximizes its sensitivity to the surrounding membrane structure. These results are discussed in terms of balancing the effects of headgroup association with acyl chain length in designing the optimal placement of the BODIPY probe. PMID:22322157

  12. Formative Assessment Probes

    ERIC Educational Resources Information Center

    Eberle, Francis; Keeley, Page

    2008-01-01

    Formative assessment probes can be effective tools to help teachers build a bridge between students' initial ideas and scientific ones. In this article, the authors describe how using two formative assessment probes can help teachers determine the extent to which students make similar connections between developing a concept of matter and a…

  13. Magnetically driven filament probe.

    PubMed

    Schmid, A; Herrmann, A; Rohde, V; Maraschek, M; Müller, H W

    2007-05-01

    A radially movable probe has been developed for studies of filamentary transport in ASDEX Upgrade during edge localized modes (ELMs) by means of Langmuir tips and magnetic pickup coils. The probe is permanently installed at the low field side in the ASDEX Upgrade vacuum vessel and is not subject to limitations in probe size, as, for example, probes on a shared manipulator are. The probe is moved by a magnetic drive, which allows for easy installation in the vessel, and has moderate machine requirements, as it will only require an electric feedthrough and an external power supply. The drive gives a linear motion with a radial range of 5 cm within 50 ms, where range and velocity can be largely scaled according to experimental requirements. The probe has been installed in the outer midplane of the ASDEX Upgrade vessel, where ELM filaments are expected to have their maximum amplitude. Filaments are coherent substructures within an ELM, carrying a fraction of the ELM released energy towards the wall. The new probe allows to measure the structure of these filaments, in particular, parameters such as filament rotation (by time delay measurements) and size (by peak width analysis). Activating the drive moves the probe from a safe position behind the limiter to a position in front of the limiters, i.e., exposes the Langmuir pins to the scrape-off layer plasma. PMID:17552815

  14. PDV Probe Alignment Technique

    SciTech Connect

    Whitworth, T L; May, C M; Strand, O T

    2007-10-26

    This alignment technique was developed while performing heterodyne velocimetry measurements at LLNL. There are a few minor items needed, such as a white card with aperture in center, visible alignment laser, IR back reflection meter, and a microscope to view the bridge surface. The work was performed on KCP flyers that were 6 and 8 mils wide. The probes used were Oz Optics manufactured with focal distances of 42mm and 26mm. Both probes provide a spot size of approximately 80?m at 1550nm. The 42mm probes were specified to provide an internal back reflection of -35 to -40dB, and the probe back reflections were measured to be -37dB and -33dB. The 26mm probes were specified as -30dB and both measured -30.5dB. The probe is initially aligned normal to the flyer/bridge surface. This provides a very high return signal, up to -2dB, due to the bridge reflectivity. A white card with a hole in the center as an aperture can be used to check the reflected beam position relative to the probe and launch beam, and the alignment laser spot centered on the bridge, see Figure 1 and Figure 2. The IR back reflection meter is used to measure the dB return from the probe and surface, and a white card or similar object is inserted between the probe and surface to block surface reflection. It may take several iterations between the visible alignment laser and the IR back reflection meter to complete this alignment procedure. Once aligned normal to the surface, the probe should be tilted to position the visible alignment beam as shown in Figure 3, and the flyer should be translated in the X and Y axis to reposition the alignment beam onto the flyer as shown in Figure 4. This tilting of the probe minimizes the amount of light from the bridge reflection into the fiber within the probe while maintaining the alignment as near normal to the flyer surface as possible. When the back reflection is measured after the tilt adjustment, the level should be about -3dB to -6dB higher than the probes

  15. Revealing Rembrandt

    PubMed Central

    Parker, Andrew J.

    2014-01-01

    The power and significance of artwork in shaping human cognition is self-evident. The starting point for our empirical investigations is the view that the task of neuroscience is to integrate itself with other forms of knowledge, rather than to seek to supplant them. In our recent work, we examined a particular aspect of the appreciation of artwork using present-day functional magnetic resonance imaging (fMRI). Our results emphasized the continuity between viewing artwork and other human cognitive activities. We also showed that appreciation of a particular aspect of artwork, namely authenticity, depends upon the co-ordinated activity between the brain regions involved in multiple decision making and those responsible for processing visual information. The findings about brain function probably have no specific consequences for understanding how people respond to the art of Rembrandt in comparison with their response to other artworks. However, the use of images of Rembrandt's portraits, his most intimate and personal works, clearly had a significant impact upon our viewers, even though they have been spatially confined to the interior of an MRI scanner at the time of viewing. Neuroscientific studies of humans viewing artwork have the capacity to reveal the diversity of human cognitive responses that may be induced by external advice or context as people view artwork in a variety of frameworks and settings. PMID:24795552

  16. Circumferential pressure probe

    NASA Technical Reports Server (NTRS)

    Holmes, Harlan K. (Inventor); Moore, Thomas C. (Inventor); Fantl, Andrew J. (Inventor)

    1989-01-01

    A probe for measuring circumferential pressure inside a body cavity is disclosed. In the preferred embodiment, a urodynamic pressure measurement probe for evaluating human urinary sphincter function is disclosed. Along the length of the probe are disposed a multiplicity of deformable wall sensors which typically comprise support tube sections with flexible side wall areas. These are arranged along the length of the probe in two areas, one just proximal to the tip for the sensing of fluid pressure inside the bladder, and five in the sensing section which is positioned within the urethra at the point at which the urinary sphincter constricts to control the flow of urine. The remainder of the length of the probe comprises multiple rigid support tube sections interspersed with flexible support tube sections in the form of bellows to provide flexibility.

  17. Formative Assessment Probes: Representing Microscopic Life

    ERIC Educational Resources Information Center

    Keeley, Page

    2011-01-01

    This column focuses on promoting learning through assessment. The author discusses the formative assessment probe "Pond Water," which reveals how elementary children will often apply what they know about animal structures to newly discovered microscopic organisms, connecting their knowledge of the familiar to the unfamiliar through…

  18. Pioneer Jupiter orbiter probe mission 1980, probe description

    NASA Technical Reports Server (NTRS)

    Defrees, R. E.

    1974-01-01

    The adaptation of the Saturn-Uranus Atmospheric Entry Probe (SUAEP) to a Jupiter entry probe is summarized. This report is extracted from a comprehensive study of Jovian missions, atmospheric model definitions and probe subsystem alternatives.

  19. Revealing Mercury

    NASA Astrophysics Data System (ADS)

    Prockter, L. M.; Solomon, S. C.; Head, J. W.; Watters, T. R.; Murchie, S. L.; Robinson, M. S.; Chapman, C. R.; McNutt, R. L.

    2009-04-01

    The MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) spacecraft, developed under NASA's Discovery Program, launched in August 2004. En route to insertion into orbit about Mercury in 2011, MESSENGER flies by Mercury three times. The first and second of these encounters were accomplished in January and October of 2008. These flybys viewed portions of Mercury's surface that were not observed by Mariner 10 during its reconnaissance of somewhat less than half of the planet in 1974-1975. All MESSENGER instruments operated during each flyby and returned a wealth of new data. Many of the new observations were focused on the planet's geology, including monochrome imaging at resolutions as high as 100 m/pixel, multispectral imaging in 11 filters at resolutions as high as 500 m/pixel, laser altimetry tracks extending over several thousands of kilometers, and high-resolution spectral measurements of several types of terrain. Here we present an overview of the first inferences on the global geology of Mercury from the MESSENGER observations. Whereas evidence for volcanism was equivocal from Mariner 10 data, the new MESSENGER images and altimetry provide compelling evidence that volcanism was widespread and protracted on Mercury. Color imaging reveals three common spectral units on the surface: a higher-reflectance, relatively red material occurring as a distinct class of smooth plains, typically with distinct embayment relationships interpreted to indicate volcanic emplacement; a lower-reflectance, relatively blue material typically excavated by impact craters and therefore inferred to be more common at depth; and a spectrally intermediate terrain that constitutes much of the uppermost crust. Three more minor spectral units are also seen: fresh crater ejecta, reddish material associated with rimless depressions interpreted to be volcanic centers, and high-reflectance deposits seen in some crater floors. Preliminary measurements of crater size

  20. A FRET-based probe with a chemically deactivatable quencher.

    PubMed

    Leriche, Geoffray; Budin, Ghyslain; Darwich, Zeinab; Weltin, Denis; Mély, Yves; Klymchenko, Andrey S; Wagner, Alain

    2012-03-28

    A new concept of a chemically deactivatable quencher is proposed for a FRET-based probe that turns-on its fluorescence by either an enzymatic cleavage or a chemical reagent (sodium dithionite). This concept allowed us to quantify the caspase-3 cleavage activity in solution and to reveal unreacted probes in cell experiments. PMID:22327268

  1. ALEX neutral beam probe

    SciTech Connect

    Pourrezaei, K.

    1982-01-01

    A neutral beam probe capable of measuring plasma space potential in a fully 3-dimensional magnetic field geometry has been developed. This neutral beam was successfully used to measure an arc target plasma contained within the ALEX baseball magnetic coil. A computer simulation of the experiment was performed to refine the experimental design and to develop a numerical model for scaling the ALEX neutral beam probe to other cases of fully 3-dimensional magnetic field. Based on this scaling a 30 to 50 keV neutral cesium beam probe capable of measuring space potential in the thermal barrier region of TMX Upgrade was designed.

  2. Foldable polymers as probes

    DOEpatents

    Li, Alexander D. Q.; Wang, Wei

    2007-07-03

    Disclosed herein are novel probes, which can be used to detect and identify target molecules of interest in a sample. The disclosed probes can be used to monitor conformational changes induced by molecular recognition events in addition to providing signaling the presence and/or identity of a target molecule. Methods, including solid phase synthesis techniques, for making probe molecules that exhibit changes in their optical properties upon target molecule binding are described in the disclosure. Also disclosed herein are novel chromophore moieties, which have tailored fluorescent emission spectra.

  3. Foldable polymers as probes

    DOEpatents

    Li, Alexander D. Q.; Wang, Wei

    2009-07-07

    Disclosed herein are novel probes, which can be used to detect and identify target molecules of interest in a sample. The disclosed probes can be used to monitor conformational changes induced by molecular recognition events in addition to providing signaling the presence and/or identity of a target molecule. Methods, including solid phase synthesis techniques, for making probe molecules that exhibit changes in their optical properties upon target molecule binding are described in the disclosure. Also disclosed herein are novel chromophore moieties, which have tailored fluorescent emission spectra.

  4. Chemical sensing flow probe

    DOEpatents

    Laguna, George R.; Peter, Frank J.; Butler, Michael A.

    1999-01-01

    A new chemical probe determines the properties of an analyte using the light absorption of the products of a reagent/analyte reaction. The probe places a small reaction volume in contact with a large analyte volume. Analyte diffuses into the reaction volume. Reagent is selectively supplied to the reaction volume. The light absorption of the reaction in the reaction volume indicates properties of the original analyte. The probe is suitable for repeated use in remote or hostile environments. It does not require physical sampling of the analyte or result in significant regent contamination of the analyte reservoir.

  5. Chemical sensing flow probe

    DOEpatents

    Laguna, G.R.; Peter, F.J.; Butler, M.A.

    1999-02-16

    A new chemical probe determines the properties of an analyte using the light absorption of the products of a reagent/analyte reaction. The probe places a small reaction volume in contact with a large analyte volume. Analyte diffuses into the reaction volume. Reagent is selectively supplied to the reaction volume. The light absorption of the reaction in the reaction volume indicates properties of the original analyte. The probe is suitable for repeated use in remote or hostile environments. It does not require physical sampling of the analyte or result in significant regent contamination of the analyte reservoir. 7 figs.

  6. Focus: DNA probes

    SciTech Connect

    Not Available

    1986-11-01

    Progress in the development of DNA probes for the identification and quantitation of specific genetic sequences in biological samples is reviewed. Current research efforts in the development of DNA probes for the diagnosis of a wide variety of bacterial, viral, and other infectious diseases, such as herpes simplex and cytomegalovirus, and inherited genetic diseases such as cystic fibrosis and sickle cell anemia are discussed. Progress in development of DNA probe assays for cancer diagnosis, detection of Salmonella food poisoning, tissue typing (detection of histocompatibility antigens), mutagen screening, and animal diseases, among other applications is included.

  7. BEAM CONTROL PROBE

    DOEpatents

    Chesterman, A.W.

    1959-03-17

    A probe is described for intercepting a desired portion of a beam of charged particles and for indicating the spatial disposition of the beam. The disclosed probe assembly includes a pair of pivotally mounted vanes moveable into a single plane with adjacent edges joining and a calibrated mechanical arrangement for pivoting the vancs apart. When the probe is disposed in the path of a charged particle beam, the vanes may be adjusted according to the beam current received in each vane to ascertain the dimension of the beam.

  8. Crater Floor Fractures: Probes Into Habitable Martian Environments

    NASA Astrophysics Data System (ADS)

    Thomas, R. J.; Hynek, B. M.

    2016-05-01

    Geologic and spectral analysis of martian impact craters reveals the potential for floor-fractures with a aqueous/volcanic genesis to probe into both ancient surface and Hesperian-aged deep habitable environments.

  9. Functional Probes for Scanning Probe Microscopy

    NASA Astrophysics Data System (ADS)

    Akiyama, Kotone; Eguchi, Toyoaki; An, Toshu; Fujikawa, Yasunori; Hasegawa, Yukio; Sakurai, Toshio

    2007-03-01

    For superior performance of scanning probe microscopy, we are working to fabricate functional probes. For Kelvin probe force microscopy, we fabricated a metal-tip cantilever by attaching a thin metal wire to a regular Si cantilever and milling it by focused ion beam (FIB)^1. By using the W tip with a curvature radius of 3.5 nm, we obtained the potential profile of Ge/Si(105) surface in atomic resolution with the energy resolution better than 3 meV^2. For synchrotron-radiation-light-irradiated scanning tunneling microscopy which aims at atomically resolved elemental analysis, we fabricated a glass-coated W tip using FIB^3. It is found that the glass coating blocks the unwanted secondary electrons, which come from large area of the sample, by a factor of 40 with respect to the case no coating. Using the tip to detect the electrons emitted just below the tip, we obtained element specific images with a spatial resolution better than 20 nm under the photo irradiation whose energy is just above the adsorption edge of the element^4. 1 K. Akiyama et al., RSI 76, 033705 (2005) 2 T. Eguchi, K. Akiyama et al., PRL 93, 266102 (2004) 3 K. Akiyama et al., RSI 76, 083711 (2005) 4 T. Eguchi, K. Akiyama et al., APL, in press

  10. Technology for Entry Probes

    NASA Technical Reports Server (NTRS)

    Cutts, James A.; Arnold, James; Venkatapathy, Ethiraj; Kolawa, Elizabeth; Munk, Michelle; Wercinski, Paul; Laub, Bernard

    2005-01-01

    A viewgraph describing technologies for entry probes is presented. The topics include: 1) Entry Phase; 2) Descent Phase; 3) Long duration atmospheric observations; 4) Survivability at high temperatures; and 5) Summary.

  11. An Ultrasonographic Periodontal Probe

    NASA Astrophysics Data System (ADS)

    Bertoncini, C. A.; Hinders, M. K.

    2010-02-01

    Periodontal disease, commonly known as gum disease, affects millions of people. The current method of detecting periodontal pocket depth is painful, invasive, and inaccurate. As an alternative to manual probing, an ultrasonographic periodontal probe is being developed to use ultrasound echo waveforms to measure periodontal pocket depth, which is the main measure of periodontal disease. Wavelet transforms and pattern classification techniques are implemented in artificial intelligence routines that can automatically detect pocket depth. The main pattern classification technique used here, called a binary classification algorithm, compares test objects with only two possible pocket depth measurements at a time and relies on dimensionality reduction for the final determination. This method correctly identifies up to 90% of the ultrasonographic probe measurements within the manual probe's tolerance.

  12. Dexamethasone Coated Neural Probes Elicit Attenuated Inflammatory Response and Neuronal Loss Compared to Uncoated Neural Probes

    PubMed Central

    Zhong, Yinghui; Bellamkonda, Ravi V.

    2007-01-01

    Glial scar formation around implanted silicon neural probes compromises their ability to facilitate long-term recordings. One approach to modulate the tissue reaction around implanted probes in the brain is to develop probe coatings that locally release antiinflammatory drugs. In this study, we developed a nitrocellulose-based coating for the local delivery of the anti-inflammatory drug dexamethasone (DEX). Silicon neural probes with and without nitrocellulose-DEX coatings were implanted into rat brains, and inflammatory response was evaluated 1 week and 4 weeks post implantation. DEX coatings significantly reduced the reactivity of microglia and macrophages one week post implantation as evidenced by ED1 immunostaining. CS56 staining demonstrated that DEX treatment significantly reduced chondroitin sulfate proteoglycan (CSPG) expression one week post implantation. Both at one week and at four week time points, GFAP staining for reactive astrocytes and neurofilament (NF) staining revealed that local DEX treatment significantly attenuated astroglial response and reduced neuronal loss in the vicinity of the probes. Weak ED1, neurocan, and NG2 positive signal was detected four weeks post implantation for both coated and uncoated probes, suggesting a stabilization of the inflammatory response over time in this implant model. In conclusion, this study demonstrates that the nitrocellulose-DEX coating can effectively attenuate the inflammatory response to the implanted neural probes, and reduce neuronal loss in the vicinity of the coated probes. Thus anti-inflammatory probe coatings may represent a promising approach to attenuate astroglial scar and reduce neural loss around implanted neural probes. PMID:17376408

  13. Reflections on Electric Probes

    NASA Astrophysics Data System (ADS)

    Braithwaite, Nicholas

    2007-10-01

    One of the more immediate temptations for an experimental plasma physicist is to insert some kind of refractory, conducting material into a plasma, as a simple means of probing its charge composition. Irvine Langmuir tried it in the 1920s and was one of the first to develop an electrical probe method in his early work on electrical discharge plasmas. There are now numerous variations on the theme including planar, cylindrical and spherical geometry with single, double and triple probes. There are also probes that resonate, propagate and reciprocate. Some probes are electrostatic and others are electromagnetic; some are effectively wireless; most absorb but some emit. All types can be used in steady and transient plasmas, while special schemes have been devised for RF plasmas, using passive and active compensation. Magnetised plasmas pose further challenges. Each configuration is accompanied by assumptions that constrain both their applicability and the analytical methods that translate the measured currents and voltages variously into charge densities, space potentials, particle fluxes, energy distributions and measures of collisionality. This talk will take a broad look at the options and opportunities for electric probes, principally in the environment of non-equilibrium plasma.

  14. Ultrafast optical pump-probe spectroscopy is used to reveal the coexistence of coupled antiferromagnetic (AFM)/ferroelectric (FE) and ferromagnetic (FM) orders in multiferroic TbMnO3 films, which can guide researchers in creating new kinds of multiferroic materials.

    SciTech Connect

    Qi, Jingbo; Zhu, Jianxin; Trugman, Stuart A.; Taylor, Antoinette; Jia, Quanxi; Prasankumar, Rohit

    2012-07-06

    , experimental techniques capable of dynamically unraveling the interplay between these degrees of freedom on an ultrafast timescale are needed. Here, we use ultrafast optical pump-probe spectroscopy to reveal coexisting coupled magnetic orders in epitaxial TMO thin films grown on (001)-STO, which were not observed in previous work. Our temperature (T)-dependent transient differential reflectivity ({Delta}R/R) measurements show clear signatures of sinusoidal AFM, spiral AFM (FE) and FM phases developing as the film thickness changes. We carry out first-principle density functional theory (DFT) calculations to explain the coupling between AFM/FE and FM orders. These results reveal that the coupling between different magnetic orders observed in our multiferroic TMO thin films may offer greater control of functionality as compared to bulk single crystal multiferroics.

  15. Model for resonant plasma probe.

    SciTech Connect

    Warne, Larry Kevin; Johnson, William Arthur; Hebner, Gregory Albert; Jorgenson, Roy E.; Coats, Rebecca Sue

    2007-04-01

    This report constructs simple circuit models for a hairpin shaped resonant plasma probe. Effects of the plasma sheath region surrounding the wires making up the probe are determined. Electromagnetic simulations of the probe are compared to the circuit model results. The perturbing effects of the disc cavity in which the probe operates are also found.

  16. Probing from Both Sides: Reshaping the Graphene Landscape via Face-to-Face Dual-Probe Microscopy

    PubMed Central

    2013-01-01

    In two-dimensional samples, all atoms are at the surface and thereby exposed for probing and manipulation by physical or chemical means from both sides. Here, we show that we can access the same point on both surfaces of a few-layer graphene membrane simultaneously, using a dual-probe scanning tunneling microscopy (STM) setup. At the closest point, the two probes are separated only by the thickness of the graphene membrane. This allows us for the first time to directly measure the deformations induced by one STM probe on a free-standing membrane with an independent second probe. We reveal different regimes of stability of few-layer graphene and show how the STM probes can be used as tools to shape the membrane in a controlled manner. Our work opens new avenues for the study of mechanical and electronic properties of two-dimensional materials. PMID:23547751

  17. Convective heat flow probe

    DOEpatents

    Dunn, J.C.; Hardee, H.C.; Striker, R.P.

    1984-01-09

    A convective heat flow probe device is provided which measures heat flow and fluid flow magnitude in the formation surrounding a borehole. The probe comprises an elongate housing adapted to be lowered down into the borehole; a plurality of heaters extending along the probe for heating the formation surrounding the borehole; a plurality of temperature sensors arranged around the periphery of the probe for measuring the temperature of the surrounding formation after heating thereof by the heater elements. The temperature sensors and heater elements are mounted in a plurality of separate heater pads which are supported by the housing and which are adapted to be radially expanded into firm engagement with the walls of the borehole. The heat supplied by the heater elements and the temperatures measured by the temperature sensors are monitored and used in providing the desired measurements. The outer peripheral surfaces of the heater pads are configured as segments of a cylinder and form a full cylinder when taken together. A plurality of temperature sensors are located on each pad so as to extend along the length and across the width thereof, with a heating element being located in each pad beneath the temperature sensors. An expansion mechanism driven by a clamping motor provides expansion and retraction of the heater pads and expandable packet-type seals are provided along the probe above and below the heater pads.

  18. Convective heat flow probe

    DOEpatents

    Dunn, James C.; Hardee, Harry C.; Striker, Richard P.

    1985-01-01

    A convective heat flow probe device is provided which measures heat flow and fluid flow magnitude in the formation surrounding a borehole. The probe comprises an elongate housing adapted to be lowered down into the borehole; a plurality of heaters extending along the probe for heating the formation surrounding the borehole; a plurality of temperature sensors arranged around the periphery of the probe for measuring the temperature of the surrounding formation after heating thereof by the heater elements. The temperature sensors and heater elements are mounted in a plurality of separate heater pads which are supported by the housing and which are adapted to be radially expanded into firm engagement with the walls of the borehole. The heat supplied by the heater elements and the temperatures measured by the temperature sensors are monitored and used in providing the desired measurements. The outer peripheral surfaces of the heater pads are configured as segments of a cylinder and form a full cylinder when taken together. A plurality of temperature sensors are located on each pad so as to extend along the length and across the width thereof, with a heating element being located in each pad beneath the temperature sensors. An expansion mechanism driven by a clamping motor provides expansion and retraction of the heater pads and expandable packer-type seals are provided along the probe above and below the heater pads.

  19. Surgical force detection probe

    NASA Technical Reports Server (NTRS)

    Tcheng, Ping; Roberts, Paul; Scott, Charles; Prass, Richard

    1991-01-01

    The development progress of a precision electro-mechanical instrument which allows the detection and documentation of the forces and moment applied to human tissue during surgery (under actual operation room conditions), is reported. The pen-shaped prototype probe which measures 1/2 inch in diameter and 7 inches in length was fabricated using an aerodynamic balance. The aerodynamic balance, a standard wind tunnel force and moment sensing transducer, measures the forces and the moments transmitted through the surgeon's hand to the human tissue during surgery. The prototype probe which was fabricated as a development tool was tested successfully. The final version of the surgical force detection probe will be designed based on additional laboratory tests in order to establish the full scale loads. It is expected that the final product will require a simplified aerodynamic balance with two or three force components and one moment component with lighter full scale loads. A signal conditioner was fabricated to process and display the outputs from the prototype probe. This unit will be interfaced with a PC-based data system to provide automatic data acquisition, data processing, and graphics display. The expected overall accuracy of the probe is better than one percent full scale.

  20. Pressure measuring probe

    NASA Technical Reports Server (NTRS)

    Ashby, George C., Jr. (Inventor)

    1988-01-01

    The invention is a probe for measuring changes in pressure in a high velocity fluid stream over and adjacent to the surface of an object. The probe is formed of an exterior housing having a closed pressure chamber in which a piezoelectric pressure transducer is mounted. An open connector tube having a probe tip passes a portion of the fluid stream into the closed pressure chamber; any change of pressure within, which requires a settling-time to appear in the closed pressure chamber, is inversely proportional to the cross-sectional area of the connector tube. A cooling chamber formed around the pressure chamber is connected to a source of cooling fluid by means of inlet and outlet tubes.

  1. Multispectral imaging probe

    SciTech Connect

    Sandison, David R.; Platzbecker, Mark R.; Descour, Michael R.; Armour, David L.; Craig, Marcus J.; Richards-Kortum, Rebecca

    1999-01-01

    A multispectral imaging probe delivers a range of wavelengths of excitation light to a target and collects a range of expressed light wavelengths. The multispectral imaging probe is adapted for mobile use and use in confined spaces, and is sealed against the effects of hostile environments. The multispectral imaging probe comprises a housing that defines a sealed volume that is substantially sealed from the surrounding environment. A beam splitting device mounts within the sealed volume. Excitation light is directed to the beam splitting device, which directs the excitation light to a target. Expressed light from the target reaches the beam splitting device along a path coaxial with the path traveled by the excitation light from the beam splitting device to the target. The beam splitting device directs expressed light to a collection subsystem for delivery to a detector.

  2. Multispectral imaging probe

    DOEpatents

    Sandison, D.R.; Platzbecker, M.R.; Descour, M.R.; Armour, D.L.; Craig, M.J.; Richards-Kortum, R.

    1999-07-27

    A multispectral imaging probe delivers a range of wavelengths of excitation light to a target and collects a range of expressed light wavelengths. The multispectral imaging probe is adapted for mobile use and use in confined spaces, and is sealed against the effects of hostile environments. The multispectral imaging probe comprises a housing that defines a sealed volume that is substantially sealed from the surrounding environment. A beam splitting device mounts within the sealed volume. Excitation light is directed to the beam splitting device, which directs the excitation light to a target. Expressed light from the target reaches the beam splitting device along a path coaxial with the path traveled by the excitation light from the beam splitting device to the target. The beam splitting device directs expressed light to a collection subsystem for delivery to a detector. 8 figs.

  3. Pioneer III Probe

    NASA Technical Reports Server (NTRS)

    1961-01-01

    Looking more like surgeons, these technicians wearing 'cleanroom' attire inspect the Pioneer III probe before shipping it to Cape Canaveral, Florida. Pioneer III was launched on December 6, 1958 aboard a Juno II rocket at the Atlantic Missile Range, Cape Canaveral, Florida. The mission objectives were to measure the radiation intensity of the Van Allen radiation belt, test long range communication systems, the launch vehicle and other subsystems. The Juno II failed to reach proper orbital escape velocity. The probe re-entered the Earth's atmosphere on December 7th ending its brief mission.

  4. Reproducibility of the cutoff probe for the measurement of electron density

    NASA Astrophysics Data System (ADS)

    Kim, D. W.; You, S. J.; Kwon, J. H.; You, K. H.; Seo, B. H.; Kim, J. H.; Yoon, J.-S.; Oh, W. Y.

    2016-06-01

    Since a plasma processing control based on plasma diagnostics attracted considerable attention in industry, the reproducibility of the diagnostics using in this application has become a great interest. Because the cutoff probe is one of the potential candidates for this application, knowing the reproducibility of the cutoff probe measurement becomes quit important in the cutoff probe application research. To test the reproducibility of the cutoff probe measurement, in this paper, a comparative study among the different cutoff probe measurements was performed. The comparative study revealed remarkable result: the cutoff probe has a great reproducibility for the electron density measurement, i.e., there are little differences among measurements by different probes made by different experimenters. The discussion including the reason for the result was addressed via this paper by using a basic measurement principle of cutoff probe and a comparative experiment with Langmuir probe.

  5. Thermal denaturing of proteins: Equilibrium and transient studies using nonlinear infrared probes

    NASA Astrophysics Data System (ADS)

    Chung, H. S.; Khalil, M.; Smith, A. W.; Ganim, Z.; Tokmakoff, A.

    Thermal unfolding of β-sheets in ribonuclease A and ubiquitin is revealed by disappearance of cross peaks in 2D IR spectra. Transient unfolding probed with vibrational echoes following a temperature jump reveals nanosecond to millisecond dynamics.

  6. Endocavity Ultrasound Probe Manipulators

    PubMed Central

    Stoianovici, Dan; Kim, Chunwoo; Schäfer, Felix; Huang, Chien-Ming; Zuo, Yihe; Petrisor, Doru; Han, Misop

    2014-01-01

    We developed two similar structure manipulators for medical endocavity ultrasound probes with 3 and 4 degrees of freedom (DoF). These robots allow scanning with ultrasound for 3-D imaging and enable robot-assisted image-guided procedures. Both robots use remote center of motion kinematics, characteristic of medical robots. The 4-DoF robot provides unrestricted manipulation of the endocavity probe. With the 3-DoF robot the insertion motion of the probe must be adjusted manually, but the device is simpler and may also be used to manipulate external-body probes. The robots enabled a novel surgical approach of using intraoperative image-based navigation during robot-assisted laparoscopic prostatectomy (RALP), performed with concurrent use of two robotic systems (Tandem, T-RALP). Thus far, a clinical trial for evaluation of safety and feasibility has been performed successfully on 46 patients. This paper describes the architecture and design of the robots, the two prototypes, control features related to safety, preclinical experiments, and the T-RALP procedure. PMID:24795525

  7. Ultrasonic search wheel probe

    DOEpatents

    Mikesell, Charles R.

    1978-01-01

    A device is provided for reducing internal reflections from the tire of an ultrasonic search wheel probe or from within the material being examined. The device includes a liner with an anechoic chamber within which is an ultrasonic transducer. The liner is positioned within the wheel and includes an aperture through which the ultrasonic sound from the transducer is directed.

  8. The Phoenix Pluto Probe

    NASA Technical Reports Server (NTRS)

    Gunning, George R.; Spapperi, Jeff; Wilkinson, Jeffrey P.; Eldred, Jim; Labij, Dennis; Strinni, Meredith

    1990-01-01

    A design proposal for an unmanned probe to Pluto is presented. The topics covered include: (1) scientific instrumentation; (2) mission management, planning, and costing; (3) power and propulsion system; (4) structural subsystem; (5) command, control, and communication; and (6) attitude and articulation control.

  9. Laboratory plasma probe studies

    NASA Technical Reports Server (NTRS)

    Heikkila, W. J.

    1975-01-01

    Diagnostic experiments performed in a collisionless plasma using CO2 as the working gas are described. In particular, simultaneous measurements that have been performed by means of Langmuir- and RF-probes are presented. A resonance occurring above the parallel resonance in the frequency characteristic of a two electrode system is interpreted as being due to the resonant excitation of electroacoustic waves.

  10. Probing the Solar System

    ERIC Educational Resources Information Center

    Wilkinson, John

    2013-01-01

    Humans have always had the vision to one day live on other planets. This vision existed even before the first person was put into orbit. Since the early space missions of putting humans into orbit around Earth, many advances have been made in space technology. We have now sent many space probes deep into the Solar system to explore the planets and…

  11. Experimenting with Temperature Probes.

    ERIC Educational Resources Information Center

    Roth, Wolff-Michael

    1989-01-01

    Presented are four activities which are designed to familiarize children with the multiple uses of computers and help them learn about heat and temperature using temperature probes. Included are the tempering effect of water, heat capacity, caloric content of foods, and weather. Hardware and software are discussed. (CW)

  12. Cervical Neoplasia Probe Control

    Energy Science and Technology Software Center (ESTSC)

    1997-01-24

    This software, which consists of a main executive and several subroutines, performs control of the optics, image acquisition, and Digital Signal Processing (DSP) of this image, of an optical based medical instrument that performs fluoresence detection of precancerous lesions (neoplasia) of the human cervix. The hardware portion of this medical instrument is known by the same name Cervical Neoplasia Probe (CNP)

  13. Endocavity Ultrasound Probe Manipulators.

    PubMed

    Stoianovici, Dan; Kim, Chunwoo; Schäfer, Felix; Huang, Chien-Ming; Zuo, Yihe; Petrisor, Doru; Han, Misop

    2013-06-01

    We developed two similar structure manipulators for medical endocavity ultrasound probes with 3 and 4 degrees of freedom (DoF). These robots allow scanning with ultrasound for 3-D imaging and enable robot-assisted image-guided procedures. Both robots use remote center of motion kinematics, characteristic of medical robots. The 4-DoF robot provides unrestricted manipulation of the endocavity probe. With the 3-DoF robot the insertion motion of the probe must be adjusted manually, but the device is simpler and may also be used to manipulate external-body probes. The robots enabled a novel surgical approach of using intraoperative image-based navigation during robot-assisted laparoscopic prostatectomy (RALP), performed with concurrent use of two robotic systems (Tandem, T-RALP). Thus far, a clinical trial for evaluation of safety and feasibility has been performed successfully on 46 patients. This paper describes the architecture and design of the robots, the two prototypes, control features related to safety, preclinical experiments, and the T-RALP procedure. PMID:24795525

  14. Probing the Higgs vacuum with general relativity

    NASA Technical Reports Server (NTRS)

    Mannheim, Philip D.; Kazanas, Demosthenes

    1991-01-01

    It is shown that the structure of the Higgs vacuum can be revealed in gravitational experiments which probe the Schwarzschild geometry to only one order in MG/r beyond that needed for the classical tests of general relativity. The possibility that deviations from the conventional geometry are at least theoretically conceivable is explored. The deviations obtained provide a diagnostic test for searching for the existence of macroscopic scalar fields and open up the possiblity for further exploring the Higgs mechanism.

  15. Strand-invading linear probe combined with unmodified PNA.

    PubMed

    Asanuma, Hiroyuki; Niwa, Rie; Akahane, Mariko; Murayama, Keiji; Kashida, Hiromu; Kamiya, Yukiko

    2016-09-15

    Efficient strand invasion by a linear probe to fluorescently label double-stranded DNA has been implemented by employing a probe and unmodified PNA. As a fluorophore, we utilized ethynylperylene. Multiple ethynylperylene residues were incorporated into the DNA probe via a d-threoninol scaffold. The ethynylperylene did not significantly disrupt hybridization with complementary DNA. The linear probe self-quenched in the absence of target DNA and did not hybridize with PNA. A gel-shift assay revealed that linear probe and PNA combination invaded the central region of double-stranded DNA upon heat-shock treatment to form a double duplex. To further suppress the background emission and increase the stability of the probe/DNA duplex, a probe containing anthraquinones as well as ethynylperylene was synthesized. This probe and PNA invader pair detected an internal sequence in a double-stranded DNA with high sensitivity when heat shock treatment was used. The probe and PNA pair was able to invade at the terminus of a long double-stranded DNA at 40°C at 100mM NaCl concentration. PMID:27394693

  16. Mechanosensitive membrane probes.

    PubMed

    Dal Molin, Marta; Verolet, Quentin; Soleimanpour, Saeideh; Matile, Stefan

    2015-04-13

    This article assembles pertinent insights behind the concept of planarizable push-pull probes. As a response to the planarization of their polarized ground state, a red shift of their excitation maximum is expected to report on either the disorder, the tension, or the potential of biomembranes. The combination of chromophore planarization and polarization contributes to various, usually more complex processes in nature. Examples include the color change of crabs or lobsters during cooking or the chemistry of vision, particularly color vision. The summary of lessons from nature is followed by an overview of mechanosensitive organic materials. Although often twisted and sometimes also polarized, their change of color under pressure usually originates from changes in their crystal packing. Intriguing exceptions include the planarization of several elegantly twisted phenylethynyl oligomers and polymers. Also mechanosensitive probes in plastics usually respond to stretching by disassembly. True ground-state planarization in response to molecular recognition is best exemplified with the binding of thoughtfully twisted cationic polythiophenes to single- and double-stranded oligonucleotides. Molecular rotors, en vogue as viscosity sensors in cells, operate by deplanarization of the first excited state. Pertinent recent examples are described, focusing on λ-ratiometry and intracellular targeting. Complementary to planarization of the ground state with twisted push-pull probes, molecular rotors report on environmental changes with quenching or shifts in emission rather than absorption. The labeling of mechanosensitive channels is discussed as a bioengineering approach to bypass the challenge to create molecular mechanosensitivity and use biological systems instead to sense membrane tension. With planarizable push-pull probes, this challenge is met not with twistome screening, but with "fluorescent flippers," a new concept to insert large and bright monomers into oligomeric

  17. Ice-Borehole Probe

    NASA Technical Reports Server (NTRS)

    Behar, Alberto; Carsey, Frank; Lane, Arthur; Engelhardt, Herman

    2006-01-01

    An instrumentation system has been developed for studying interactions between a glacier or ice sheet and the underlying rock and/or soil. Prior borehole imaging systems have been used in well-drilling and mineral-exploration applications and for studying relatively thin valley glaciers, but have not been used for studying thick ice sheets like those of Antarctica. The system includes a cylindrical imaging probe that is lowered into a hole that has been bored through the ice to the ice/bedrock interface by use of an established hot-water-jet technique. The images acquired by the cameras yield information on the movement of the ice relative to the bedrock and on visible features of the lower structure of the ice sheet, including ice layers formed at different times, bubbles, and mineralogical inclusions. At the time of reporting the information for this article, the system was just deployed in two boreholes on the Amery ice shelf in East Antarctica and after successful 2000 2001 deployments in 4 boreholes at Ice Stream C, West Antarctica, and in 2002 at Black Rapids Glacier, Alaska. The probe is designed to operate at temperatures from 40 to +40 C and to withstand the cold, wet, high-pressure [130-atm (13.20-MPa)] environment at the bottom of a water-filled borehole in ice as deep as 1.6 km. A current version is being outfitted to service 2.4-km-deep boreholes at the Rutford Ice Stream in West Antarctica. The probe (see figure) contains a sidelooking charge-coupled-device (CCD) camera that generates both a real-time analog video signal and a sequence of still-image data, and contains a digital videotape recorder. The probe also contains a downward-looking CCD analog video camera, plus halogen lamps to illuminate the fields of view of both cameras. The analog video outputs of the cameras are converted to optical signals that are transmitted to a surface station via optical fibers in a cable. Electric power is supplied to the probe through wires in the cable at a

  18. Molecular probes for cardiovascular imaging.

    PubMed

    Liang, Grace; Nguyen, Patricia K

    2016-08-01

    Molecular probes provide imaging signal and contrast for the visualization, characterization, and measurement of biological processes at the molecular level. These probes can be designed to target the cell or tissue of interest and must be retained at the imaging site until they can be detected by the appropriate imaging modality. In this article, we will discuss the basic design of molecular probes, differences among the various types of probes, and general strategies for their evaluation of cardiovascular disease. PMID:27189171

  19. Heavy ion beam probing

    SciTech Connect

    Hickok, R L

    1980-07-01

    This report consists of the notes distributed to the participants at the IEEE Mini-Course on Modern Plasma Diagnostics that was held in Madison, Wisconsin in May 1980. It presents an overview of Heavy Ion Beam Probing that briefly describes the principles and discuss the types of measurements that can be made. The problems associated with implementing beam probes are noted, possible variations are described, estimated costs of present day systems, and the scaling requirements for large plasma devices are presented. The final chapter illustrates typical results that have been obtained on a variety of plasma devices. No detailed calculations are included in the report, but a list of references that will provide more detailed information is included.

  20. Molecular inversion probe assay.

    PubMed

    Absalan, Farnaz; Ronaghi, Mostafa

    2007-01-01

    We have described molecular inversion probe technologies for large-scale genetic analyses. This technique provides a comprehensive and powerful tool for the analysis of genetic variation and enables affordable, large-scale studies that will help uncover the genetic basis of complex disease and explain the individual variation in response to therapeutics. Major applications of the molecular inversion probes (MIP) technologies include targeted genotyping from focused regions to whole-genome studies, and allele quantification of genomic rearrangements. The MIP technology (used in the HapMap project) provides an efficient, scalable, and affordable way to score polymorphisms in case/control populations for genetic studies. The MIP technology provides the highest commercially available multiplexing levels and assay conversion rates for targeted genotyping. This enables more informative, genome-wide studies with either the functional (direct detection) approach or the indirect detection approach. PMID:18025701

  1. Fast Langmuir probe sweeping circuit

    SciTech Connect

    Milnes, K.A.; Ehlers, K.W.; Leung, K.N.; Owren, H.M.; Williams, M.D.

    1980-06-01

    An inexpensive, simple, and fast Langmuir probe sweeping circuit is presented. This sweeper completes a probe trace in 1.4 ms and has a maximum probe current capability of 5 A. It is suitable for pulsemode plasma operation with density greater than 10/sup 12/ ions/cm/sup 3/.

  2. Scanning Probe Microscopy and Spectroscopy

    NASA Astrophysics Data System (ADS)

    Wiesendanger, Roland

    1994-09-01

    Preface; List of acronyms; Introduction; Part I. Experimental Methods and Theoretical Background of Scanning Probe Microscopy and Spectroscopy: 1. Scanning tunnelling microscopy; 2. Scanning force microscopy; 3. Related scanning probe techniques; Part II. Applications of Scanning Probe Microscopy and Spectroscopy: 4. Condensed matter physics; 5. Chemistry; 6. Organic materials; 7. Metrology and standards; 8. Nanotechnology; References; Index.

  3. Properties of Broezel static probe

    NASA Astrophysics Data System (ADS)

    Gašparovič, Peter; Semrád, Karol; Cúttová, Miroslava

    2016-03-01

    The properties of flat static probe designed by Broezel and used in sailplanes are investigated for its planned use in low speed tunnel. Both the numerical CFD model and experiment in low speed wind tunnel confirm yaw insensitivity of the static pressure measured by the probe. The results indicate that the probe is sufficiently accurate for its planned use in wind tunnel measurements.

  4. Galileo probe relay receiver

    NASA Technical Reports Server (NTRS)

    Prouty, D. A.; Von Der Embse, U. A.

    1982-01-01

    For the Jovian mission, the data link from the Galileo probe to the orbiter uses suppressed-carrier Manchester encoded BPSK modulation and is protected with R = 1/2, K = 7 convolutional coding. The receiver closes the link by acquiring, tracking, and demodulating the data. It has to operate in a highly stressed environment with severe frequency offset, frequency rate, wind gust, and antenna spin conditions. Salient features are described and breadboard test data presented.

  5. Droplet monitoring probe

    NASA Technical Reports Server (NTRS)

    Baughman, J. R.; Thys, P. C.

    1973-01-01

    A droplet monitoring system is disclosed for analysis of mixed-phase fluid flow in development of gas turbines. The system uses a probe comprising two electrical wires spaced a known distance apart and connected at one end to means for establishing a dc potential between the wires. A drop in the fluid stream momentarily contacting both wires simultaneously causes and electrical signal which is amplified, detected and counted.

  6. Space Probe Launch

    NASA Technical Reports Server (NTRS)

    1970-01-01

    Managed by Marshall Space Flight Center, the Space Tug was a reusable multipurpose space vehicle designed to transport payloads to different orbital inclinations. Utilizing mission-specific combinations of its three primary modules (crew, propulsion, and cargo) and a variety of supplementary kits, the Space Tug was capable of numerous space applications. This 1970 artist's concept depicts the Tug's propulsion module launching a space probe into lunar orbit.

  7. Cosmological probes of gravity

    NASA Astrophysics Data System (ADS)

    Rassat, Anais Marie Melanie

    This Thesis is concerned with two cosmological probes of linear gravity. The first relates to Large Scale Structure (LSS) in the Universe, probed by galaxy surveys. The second to temperature anisotropics of the Cosmic Microwave Background (CMB), probed by the Wilkinson Microwave Anisotropy Map (WMAP). Both probe the matter and dark energy distributions in the Universe and can be used to test general relativity. The first part of this Thesis (Chapters 2 to 4) is concerned with the analysis of galaxy clustering in redshift space. The second part (Chapters 5 to 7) is concerned with the Integrated Sachs-Wolfe (ISW) effect using LSS-CMB cross-correlations. Chapter 1 introduces the cosmological theory and overviews the subsequent chapters. Chapter 2 gives a review of recent results from the 2 Micron All-Sky Survey (2MASS) and its Redshift Survey (2MRS). It includes work published in Erdogdu (a) et al. (2006) and Erdogdu (b) et al. (2006). Chapter 3 quantifies the clustering of 2MRS galaxies in redshift space. Chapter 4 uses results from Chapter 3 to constrain cosmological parameters. A selection of work from Chapters 3 and 4 will shortly become available in Rassat et al. (2008), entitled 'Redshift Space Analysis of 2MRS'. Chapter 5 overviews the late-time Integrated Sachs-Wolfe effect (ISW) and cross- correlations between the LSS and the CMB. Chapter 6 is also published in Rassat et al. (2007), entitled "Cross-correlation of 2MASS and WMAP3: Implications for the Integrated Sachs-Wolfe effect". It investigates a detection of the ISW effect and correlations which may affect statistical isotropy in the CMB ('Axis of Evil'). Chapter 7 uses the ISW effect to forecast constraints on dark energy parameters and general modifications of general relativity for the next generation of galaxy surveys, particularly the Dark UNiverse Explorer (DUNE) and the Dark Energy Survey (DES). Chapter 8 presents the overall conclusions of this Thesis. Chapter 9 discusses possible extensions to

  8. Ultrafast scanning probe microscopy

    SciTech Connect

    Botkin, D.; Weiss, S.; Ogletree, D.F.; Salmeron, M.; Chemla, D.S.

    1994-01-01

    The authors have developed a general technique which combines the temporal resolution of ultrafast laser spectroscopy with the spatial resolution of scanned probe microscopy (SPM). Using this technique with scanning tunneling microscopy (STM), they have obtained simultaneous 2 ps time resolution and 50 {angstrom} spatial resolution. This improves the time resolution currently attainable with STM by nine orders of magnitude. The potential of this powerful technique for studying ultrafast dynamical phenomena on surfaces with atomic resolution is discussed.

  9. Gravity Probe B Inspection

    NASA Technical Reports Server (NTRS)

    2000-01-01

    The space vehicle Gravity Probe B (GP-B) is the relativity experiment developed at Stanford University to test two extraordinary predictions of Albert Einstein's general theory of relativity. The experiment will measure, very precisely, the expected tiny changes in the direction of the spin axes of four gyroscopes contained in an Earth-orbiting satellite at a 400-mile altitude. So free are the gyroscopes from disturbance that they will provide an almost perfect space-time reference system. They will measure how space and time are very slightly warped by the presence of the Earth, and, more profoundly, how the Earth's rotation very slightly drags space-time around with it. These effects, though small for the Earth, have far-reaching implications for the nature of matter and the structure of the Universe. GP-B is among the most thoroughly researched programs ever undertaken by NASA. This is the story of a scientific quest in which physicists and engineers have collaborated closely over many years. Inspired by their quest, they have invented a whole range of technologies that are already enlivening other branches of science and engineering. In this photograph, engineer Gary Reynolds is inspecting the inside of the probe neck during probe thermal repairs. GP-B is scheduled for launch in April 2004 and managed for NASA by the Marshall Space Flight Center. Development of the GP-B is the responsibility of Stanford University along with major subcontractor Lockheed Martin Corporation. (Image credit to Russ Leese, Gravity Probe B, Stanford University)

  10. Phoenix Conductivity Probe

    NASA Technical Reports Server (NTRS)

    2008-01-01

    This image taken by the Surface Stereo Imager on Sol 49, or the 49th Martian day of the mission (July 14, 2008), shows thermal and electrical conductivity probe on NASA's Phoenix Mars Lander's Robotic Arm.

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is led by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  11. Einstein Inflationary Probe (EIP)

    NASA Technical Reports Server (NTRS)

    Hinshaw, Gary

    2004-01-01

    I will discuss plans to develop a concept for the Einstein Inflation Probe: a mission to detect gravity waves from inflation via the unique signature they impart to the cosmic microwave background (CMB) polarization. A sensitive CMB polarization satellite may be the only way to probe physics at the grand-unified theory (GUT) scale, exceeding by 12 orders of magnitude the energies studied at the Large Hadron Collider. A detection of gravity waves would represent a remarkable confirmation of the inflationary paradigm and set the energy scale at which inflation occurred when the universe was a fraction of a second old. Even a strong upper limit to the gravity wave amplitude would be significant, ruling out many common models of inflation, and pointing to inflation occurring at much lower energy, if at all. Measuring gravity waves via the CMB polarization will be challenging. We will undertake a comprehensive study to identify the critical scientific requirements for the mission and their derived instrumental performance requirements. At the core of the study will be an assessment of what is scientifically and experimentally optimal within the scope and purpose of the Einstein Inflation Probe.

  12. Nanoscale thermal probing

    PubMed Central

    Yue, Yanan; Wang, Xinwei

    2012-01-01

    Nanoscale novel devices have raised the demand for nanoscale thermal characterization that is critical for evaluating the device performance and durability. Achieving nanoscale spatial resolution and high accuracy in temperature measurement is very challenging due to the limitation of measurement pathways. In this review, we discuss four methodologies currently developed in nanoscale surface imaging and temperature measurement. To overcome the restriction of the conventional methods, the scanning thermal microscopy technique is widely used. From the perspective of measuring target, the optical feature size method can be applied by using either Raman or fluorescence thermometry. The near-field optical method that measures nanoscale temperature by focusing the optical field to a nano-sized region provides a non-contact and non-destructive way for nanoscale thermal probing. Although the resistance thermometry based on nano-sized thermal sensors is possible for nanoscale thermal probing, significant effort is still needed to reduce the size of the current sensors by using advanced fabrication techniques. At the same time, the development of nanoscale imaging techniques, such as fluorescence imaging, provides a great potential solution to resolve the nanoscale thermal probing problem. PMID:22419968

  13. Icing Sensor Probe

    NASA Technical Reports Server (NTRS)

    Emery, Edward; Kok, Gregory L.

    2002-01-01

    Aircraft icing is a serious safety problem for the general aviation and some commuter transport airplanes. There has been tremendous growth in the commuter aviation industry in the last few years, Since these type of aircraft generally operate at lower altitudes they consequently spend a far greater proportion of their time operating in icing conditions. For the past thirty years airborne and ground based facilities have relied primarily on two types of cloud physics instrumentation to measure the characteristics of icing clouds: hot wire liquid water content probes and laser based particle sizing probes for the measurement of water droplet size. The instrumentation is severely limited by the technology that was developed during the 1970's and is quite large in size. The goal of this research is to develop one instrument with a wide bandwidth, better response time, higher resolution, user selectability, and small and lightweight. NASA Glenn Research Center, Droplet Measurement Technology, and Meteorology Society of Canada have developed a collaborative effort to develop such an instrument. This paper describes the development and test results of the prototype Icing Sensor Probe.

  14. Magnetic TRAnsition Region Probe (MTRAP)

    NASA Technical Reports Server (NTRS)

    Moore, R. L.; Davis, John; Hathaway, David; Six, N. Frank (Technical Monitor)

    2002-01-01

    MTRAP (Magnetic Transition Region Probe) will reveal the fine-scale physical processes in the Sun's magnetic transition region, the complex layer from the upper photosphere to the upper chromosphere/lower transition region. In the magnetic transition region plasma forces and magnetic forces are of comparable strength, which results in complex interplay of the two, which interplay governs the coupling of the convectively-driven deeper layers to the magnetically-driven upper transition region and inner corona. The fine-scale magnetic structure, processes, and events in the magnetic transition region are key to the genesis of the Sun's entire hot, dynamic outer atmosphere and to the initiation of large eruptive events. MTRAP will be a single spacecraft in Sun-synchronous Earth orbit. Because MTRAP will probe and measure the 3-D structure and dynamics of the magnetic field and plasma in the chromosphere and transition region with unprecedented resolution, the required telescope size and telemetry rates dictate that MTRAP be in Earth orbit, not in deep space. The observations will feature visible and infrared maps of vector magnetic and velocity fields in the magnetic transition region and photosphere. These will have large field of view (greater than 100,000 km), high resolution (greater than 100 km), and high sensitivity (greater than 30 G in transverse field). These observations of the lower atmosphere will be complemented by UV maps of the structure, velocity, and magnetic field (including the full vector field if technically feasible) higher up, in the upper chromosphere and lower transition region. MTRAP will also have an EUV imaging spectrograph observing coronal structure and dynamics in the same field of view with comparable resolution. Specific phenomena to be analyzed include spicules, bright points, jets, the base of plumes, and the triggering of eruptive flares and coronal mass ejections. Additional information is included in the original extended abstract.

  15. Comparative evaluation of probing depth and clinical attachment level using a manual probe and Florida probe

    PubMed Central

    Kour, Amandeep; Kumar, Ashish; Puri, Komal; Khatri, Manish; Bansal, Mansi; Gupta, Geeti

    2016-01-01

    Background: To compare and evaluate the intra- and inter-examiner efficacy and reproducibility of the first-generation manual (Williams) probe and the third-generation Florida probe in terms of measuring pocket probing depth (PD) and clinical attachment level (CAL). Materials and Methods: Forty subjects/4000 sites were included in this comparative, cross-sectional study. Group- and site-wise categorizations were done. Based on gingival index, PD, and CAL, patients were divided into four groups, i.e., periodontally healthy, gingivitis, mild to moderate periodontitis, and severe periodontitis. Further, based on these parameters, a total of 4000 sites, with 1000 sites in each category randomly selected from these 40 patients, were taken. Full mouth PD and CAL measurements were recorded with two probes, by Examiner 1 and on Ramfjord teeth by Examiner 2. Results: Full mouth and Ramfjord teeth group- and site-wise PD obtained with the manual probe by both the examiners were statistically significantly deeper than that obtained with the Florida probe. The full mouth and Ramfjord teeth mean CAL measurement by Florida probe was higher as compared to manual probe in mild to moderate periodontitis group and sites, whereas in severe periodontitis group and sites, manual probe recorded higher CAL as compared to Florida probe. Conclusion: Mean PD and CAL measurements were deeper with the manual probe as compared to the Florida probe in all the groups and sites, except for the mild-moderate periodontitis group and sites where the CAL measurements with the manual probe were less than the Florida probe. Manual probe was more reproducible and showed less interexaminer variability as compared to the Florida probe. PMID:27563204

  16. Electrical conductivity studies on individual conjugated polymer nanowires: two-probe and four-probe results.

    PubMed

    Long, Yunze; Duvail, Jeanluc; Li, Mengmeng; Gu, Changzhi; Liu, Zongwen; Ringer, Simon P

    2009-01-01

    Two- and four-probe electrical measurements on individual conjugated polymer nanowires with different diameters ranging from 20 to 190 nm have been performed to study their conductivity and nanocontact resistance. The two-probe results reveal that all the measured polymer nanowires with different diameters are semiconducting. However, the four-probe results show that the measured polymer nanowires with diameters of 190, 95-100, 35-40 and 20-25 nm are lying in the insulating, critical, metallic and insulting regimes of metal-insulator transition, respectively. The 35-40 nm nanowire displays a metal-insulator transition at around 35 K. In addition, it was found that the nanocontact resistance is in the magnitude of 104Ω at room temperature, which is comparable to the intrinsic resistance of the nanowires. These results demonstrate that four-probe electrical measurement is necessary to explore the intrinsic electronic transport properties of isolated nanowires, especially in the case of metallic nanowires, because the metallic nature of the measured nanowires may be coved by the nanocontact resistance that cannot be excluded by a two-probe technique. PMID:20652139

  17. PROcess Based Diagnostics PROBE

    NASA Technical Reports Server (NTRS)

    Clune, T.; Schmidt, G.; Kuo, K.; Bauer, M.; Oloso, H.

    2013-01-01

    Many of the aspects of the climate system that are of the greatest interest (e.g., the sensitivity of the system to external forcings) are emergent properties that arise via the complex interplay between disparate processes. This is also true for climate models most diagnostics are not a function of an isolated portion of source code, but rather are affected by multiple components and procedures. Thus any model-observation mismatch is hard to attribute to any specific piece of code or imperfection in a specific model assumption. An alternative approach is to identify diagnostics that are more closely tied to specific processes -- implying that if a mismatch is found, it should be much easier to identify and address specific algorithmic choices that will improve the simulation. However, this approach requires looking at model output and observational data in a more sophisticated way than the more traditional production of monthly or annual mean quantities. The data must instead be filtered in time and space for examples of the specific process being targeted.We are developing a data analysis environment called PROcess-Based Explorer (PROBE) that seeks to enable efficient and systematic computation of process-based diagnostics on very large sets of data. In this environment, investigators can define arbitrarily complex filters and then seamlessly perform computations in parallel on the filtered output from their model. The same analysis can be performed on additional related data sets (e.g., reanalyses) thereby enabling routine comparisons between model and observational data. PROBE also incorporates workflow technology to automatically update computed diagnostics for subsequent executions of a model. In this presentation, we will discuss the design and current status of PROBE as well as share results from some preliminary use cases.

  18. Experimental probes of axions

    SciTech Connect

    Chou, Aaron S.; /Fermilab

    2009-10-01

    Experimental searches for axions or axion-like particles rely on semiclassical phenomena resulting from the postulated coupling of the axion to two photons. Sensitive probes of the extremely small coupling constant can be made by exploiting familiar, coherent electromagnetic laboratory techniques, including resonant enhancement of transitions using microwave and optical cavities, Bragg scattering, and coherent photon-axion oscillations. The axion beam may either be astrophysical in origin as in the case of dark matter axion searches and solar axion searches, or created in the laboratory from laser interactions with magnetic fields. This note is meant to be a sampling of recent experimental results.

  19. Vacuum probe surface sampler

    NASA Technical Reports Server (NTRS)

    Zahlava, B. A. (Inventor)

    1973-01-01

    A vacuum probe surface sampler is described for rapidly sampling relatively large surface areas which possess relatively light loading densities of micro-organism, drug particles or the like. A vacuum head with a hollow handle connected to a suitable vacuum source is frictionally attached to a cone assembly terminating in a flared tip adapted to be passed over the surface to be sampled. A fine mesh screen carried by the vacuum head provides support for a membrane filter which collects the microorganisms or other particles. The head assembly is easily removed from the cone assembly without contacting the cone assembly with human hands.

  20. Impedance Characteristics of the Plasma Absorption Probe

    NASA Astrophysics Data System (ADS)

    Yamazawa, Yohei

    2009-10-01

    The plasma absorption probe (PAP) is a diagnostics for determination of spatially resolved electron density.footnotetextH. Kokura, et al., Jpn. J. Appl. Phys. 38 5262 (1999). PAP has attracted considerable interest because of its applicability in a reactive plasma. The simple structure of the probe allows us a robust measurement while the mechanism of the absorption is complicated and there are still some uncertainty.footnotetextM. Lapke, et al., Appl. Phys. Lett. 90, 121502 (2007) In this study, we focus on the frequency characteristics of the impedance instead of the absorption spectrum. An electromagnetic field simulation reveals that there is only one parallel resonance in the impedance characteristics even in a case there are many peaks in absorption spectrum. Thus, the impedance characteristics provide a clue to understanding the mechanism.

  1. Probing magnons with RIXS

    NASA Astrophysics Data System (ADS)

    Ament, Lucas; Ghiringhelli, Giacomo; Moretti Sala, Marco; Braicovich, Lucio; van den Brink, Jeroen

    2010-03-01

    Resonant Inelastic X-ray Scattering (RIXS) at the copper L and M edge can probe single spin-flips, which makes it possible to probe the dispersion of magnetic excitations (for instance magnons) of cuprates such as the high Tc superconductors [1]. The cross section factors into a local, atomic spin flip scattering amplitude and a momentum dependent factor describing the final state excitation. Recently, the single magnon dispersion has been measured and found to coincide with earlier neutron measurements [2]. For the cuprates, these results put RIXS as a technique on the same footing as neutron scattering, opening a new window for experiments on this class of materials. [1] L.J.P. Ament, G. Ghiringhelli, M. Moretti Sala, L. Braicovich, and J. van den Brink, PRL 103, 117003 (2009) [2] L. Braicovich, J. van den Brink, V. Bisogni, M. Moretti Sala, L.J.P. Ament, N.B. Brookes, G.M. De Luca, M. Salluzzo, T. Schmitt, and G. Ghiringhelli, arXiv:0911.0621

  2. High-speed dual Langmuir probe

    SciTech Connect

    Lobbia, Robert B.; Gallimore, Alec D.

    2010-07-15

    In an effort to temporally resolve the electron density, electron temperature, and plasma potential for turbulent plasma discharges, a unique high-speed dual Langmuir probe (HDLP) has been developed. A traditional single Langmuir probe of cylindrical geometry (exposed to the plasma) is swept simultaneously with a nearby capacitance and noise compensating null probe (fully insulated from the plasma) to enable bias sweep rates on a microsecond timescale. Traditional thin-sheath Langmuir probe theory is applied for interpretation of the collected probe data. Data at a sweep rate of 100 kHz are presented; however the developed system is capable of running at 1 MHz--near the upper limit of the applied electrostatic Langmuir probe theory for the investigated plasma conditions. Large sets (100 000 sweeps at each of 352 spatial locations) of contiguous turbulent plasma properties are collected using simple electronics for probe bias driving and current measurement attaining 80 dB signal-to-noise measurements with dc to 1 MHz bandwidth. Near- and far-field plume measurements with the HDLP system are performed downstream from a modern Hall effect thruster where the time-averaged plasma properties exhibit the approximate ranges: electron density n{sub e} from (1x10{sup 15})-(5x10{sup 16}) m{sup -3}, electron temperature T{sub e} from 1 to 3.5 eV, and plasma potential V{sub p} from 5 to 15 V. The thruster discharge of 200 V (constant anode potential) and 2 A (average discharge current) displays strong, 2.2 A peak-to-peak, current oscillations at 19 kHz, characteristic of the thruster ''breathing mode'' ionization instability. Large amplitude discharge current fluctuations are typical for most Hall thrusters, yet the HDLP system reveals the presence of the same 19 kHz fluctuations in n{sub e}(t), T{sub e}(t), and V{sub p}(t) throughout the entire plume with peak-to-peak divided by mean plasma properties that average 94%. The propagation delays between the discharge current

  3. High-speed dual Langmuir probe.

    PubMed

    Lobbia, Robert B; Gallimore, Alec D

    2010-07-01

    In an effort to temporally resolve the electron density, electron temperature, and plasma potential for turbulent plasma discharges, a unique high-speed dual Langmuir probe (HDLP) has been developed. A traditional single Langmuir probe of cylindrical geometry (exposed to the plasma) is swept simultaneously with a nearby capacitance and noise compensating null probe (fully insulated from the plasma) to enable bias sweep rates on a microsecond timescale. Traditional thin-sheath Langmuir probe theory is applied for interpretation of the collected probe data. Data at a sweep rate of 100 kHz are presented; however the developed system is capable of running at 1 MHz-near the upper limit of the applied electrostatic Langmuir probe theory for the investigated plasma conditions. Large sets (100,000 sweeps at each of 352 spatial locations) of contiguous turbulent plasma properties are collected using simple electronics for probe bias driving and current measurement attaining 80 dB signal-to-noise measurements with dc to 1 MHz bandwidth. Near- and far-field plume measurements with the HDLP system are performed downstream from a modern Hall effect thruster where the time-averaged plasma properties exhibit the approximate ranges: electron density n(e) from (1x10(15))-(5x10(16)) m(-3), electron temperature T(e) from 1 to 3.5 eV, and plasma potential V(p) from 5 to 15 V. The thruster discharge of 200 V (constant anode potential) and 2 A (average discharge current) displays strong, 2.2 A peak-to-peak, current oscillations at 19 kHz, characteristic of the thruster "breathing mode" ionization instability. Large amplitude discharge current fluctuations are typical for most Hall thrusters, yet the HDLP system reveals the presence of the same 19 kHz fluctuations in n(e)(t), T(e)(t), and V(p)(t) throughout the entire plume with peak-to-peak divided by mean plasma properties that average 94%. The propagation delays between the discharge current fluctuations and the corresponding plasma

  4. Modeling the Insertion Mechanics of Flexible Neural Probes Coated with Sacrificial Polymers for Optimizing Probe Design

    PubMed Central

    Singh, Sagar; Lo, Meng-Chen; Damodaran, Vinod B.; Kaplan, Hilton M.; Kohn, Joachim; Zahn, Jeffrey D.; Shreiber, David I.

    2016-01-01

    -designed to ensure successful insertion. Probability color maps were generated to visually compare the influence of design parameters. Statistical metrics derived from the color maps and multi-variable regression analysis confirmed that coating thickness and probe length were the most important features in influencing insertion potential. The model also revealed the effects of manufacturing flaws on insertion potential. PMID:26959021

  5. Modeling the Insertion Mechanics of Flexible Neural Probes Coated with Sacrificial Polymers for Optimizing Probe Design.

    PubMed

    Singh, Sagar; Lo, Meng-Chen; Damodaran, Vinod B; Kaplan, Hilton M; Kohn, Joachim; Zahn, Jeffrey D; Shreiber, David I

    2016-01-01

    -designed to ensure successful insertion. Probability color maps were generated to visually compare the influence of design parameters. Statistical metrics derived from the color maps and multi-variable regression analysis confirmed that coating thickness and probe length were the most important features in influencing insertion potential. The model also revealed the effects of manufacturing flaws on insertion potential. PMID:26959021

  6. Development and Application of Multiple-Probe Scanning Probe Microscopes

    SciTech Connect

    Nakayama, T.; Kubo, O.; Shingaya, Y.; Higuchi, S.; Hasegawa, T.; Jiang, C. S.; Okuda, T.; Kuwahara, Y.; Takami, K.; Aono, M.

    2012-04-03

    the research of advanced materials based on nanoscience and nanotechnology, it is often desirable to measure nanoscale local electrical conductivity at a designated position of a given sample. For this purpose, multiple-probe scanning probe microscopes (MP-SPMs), in which two, three or four scanning tunneling microscope (STM) or atomic force microscope (AFM) probes are operated independently, have been developed. Each probe in an MP-SPM is used not only for observing high-resolution STM or AFM images but also for forming an electrical contact enabling nanoscale local electrical conductivity measurement. The world's first double-probe STM (DP-STM) developed by the authors, which was subsequently modified to a triple-probe STM (TP-STM), has been used to measure the conductivities of one-dimensional metal nanowires and carbon nanotubes and also two-dimensional molecular films. A quadruple-probe STM (QP-STM) has also been developed and used to measure the conductivity of two-dimensional molecular films without the ambiguity of contact resistance between the probe and sample. Moreover, a quadruple-probe AFM (QP-AFM) with four conductive tuning-fork-type self-detection force sensing probes has been developed to measure the conductivity of a nanostructure on an insulating substrate. A general-purpose computer software to control four probes at the same time has also been developed and used in the operation of the QP-AFM. These developments and applications of MP-SPMs are reviewed in this paper.

  7. Investigation of the contrast inversion effect on hydrophilic surfaces using Pt/C whisker probes in a scanning force microscope

    NASA Astrophysics Data System (ADS)

    Zhukov, M. V.; Mukhin, I. S.; Levichev, V. V.; Golubok, A. O.

    2015-02-01

    We compare the spatial resolution and image contrast of an erythrocyte surface obtained by means of scanning force microscopy (SFM) with conventional hydrophobic Si probes and probes modified by hydrophilic Pt/C whisker probes. It is shown that probes with Pt/C nanowhiskers provide a higher spatial resolution and contrast when imaging relief on the surface of erythrocytes. The contrast inversion is revealed in some areas of the SFM images when replacing Si probes by probes with Pt/C nanowhiskers. The origin of this inversion in the tapping and contact modes is discussed.

  8. Variable path length spectrophotometric probe

    DOEpatents

    O'Rourke, Patrick E.; McCarty, Jerry E.; Haggard, Ricky A.

    1992-01-01

    A compact, variable pathlength, fiber optic probe for spectrophotometric measurements of fluids in situ. The probe comprises a probe body with a shaft having a polished end penetrating one side of the probe, a pair of optic fibers, parallel and coterminous, entering the probe opposite the reflecting shaft, and a collimating lens to direct light from one of the fibers to the reflecting surface of the shaft and to direct the reflected light to the second optic fiber. The probe body has an inlet and an outlet port to allow the liquid to enter the probe body and pass between the lens and the reflecting surface of the shaft. A linear stepper motor is connected to the shaft to cause the shaft to advance toward or away from the lens in increments so that absorption measurements can be made at each of the incremental steps. The shaft is sealed to the probe body by a bellows seal to allow freedom of movement of the shaft and yet avoid leakage from the interior of the probe.

  9. Heat transfer probe

    DOEpatents

    Frank, Jeffrey I.; Rosengart, Axel J.; Kasza, Ken; Yu, Wenhua; Chien, Tai-Hsin; Franklin, Jeff

    2006-10-10

    Apparatuses, systems, methods, and computer code for, among other things, monitoring the health of samples such as the brain while providing local cooling or heating. A representative device is a heat transfer probe, which includes an inner channel, a tip, a concentric outer channel, a first temperature sensor, and a second temperature sensor. The inner channel is configured to transport working fluid from an inner inlet to an inner outlet. The tip is configured to receive at least a portion of the working fluid from the inner outlet. The concentric outer channel is configured to transport the working fluid from the inner outlet to an outer outlet. The first temperature sensor is coupled to the tip, and the second temperature sensor spaced apart from the first temperature sensor.

  10. Solar Probe Plus

    NASA Technical Reports Server (NTRS)

    Szabo, Adam

    2011-01-01

    The NASA Solar Probe Plus mission is planned to be launched in 2018 to study the upper solar corona with both.in-situ and remote sensing instrumentation. The mission will utilize 6 Venus gravity assist maneuver to gradually lower its perihelion to 9.5 Rs below the expected Alfven pOint to study the sub-alfvenic solar wind that is still at least partially co-rotates with the Sun. The detailed science objectives of this mission will be discussed. SPP will have a strong synergy with The ESA/NASA Solar orbiter mission to be launched a year ahead. Both missions will focus on the inner heliosphere and will have complimentary instrumentations. Strategies to exploit this synergy will be also presented.

  11. New probe of naturalness.

    PubMed

    Craig, Nathaniel; Englert, Christoph; McCullough, Matthew

    2013-09-20

    Any new scalar fields that perturbatively solve the hierarchy problem by stabilizing the Higgs boson mass also generate new contributions to the Higgs boson field-strength renormalization, irrespective of their gauge representation. These new contributions are physical, and in explicit models their magnitude can be inferred from the requirement of quadratic divergence cancellation; hence, they are directly related to the resolution of the hierarchy problem. Upon canonically normalizing the Higgs field, these new contributions lead to modifications of Higgs couplings that are typically great enough that the hierarchy problem and the concept of electroweak naturalness can be probed thoroughly within a precision Higgs boson program. Specifically, at a lepton collider this can be achieved through precision measurements of the Higgs boson associated production cross section. This would lead to indirect constraints on perturbative solutions to the hierarchy problem in the broadest sense, even if the relevant new fields are gauge singlets. PMID:24093250

  12. Nondestructive Test Probe

    NASA Technical Reports Server (NTRS)

    1996-01-01

    Under the Aircraft Structural Integrity program, Langley Research Center invented a device to detect fatigue cracks in aluminum alloy plates. Krautkramer Branson obtained an exclusive license and commercialized a hand-held device, the "CrackFinder," an electromagnetic probe for nondestructive evaluation, used to scan aircraft skins for surface breaks. The technology involves an eddy current, which is an electrical current induced by an alternating magnetic field. The CrackFinder also employs an innovative self-nulling feature, where the device automatically recalibrates to zero so that each flaw detected produces a reading. Compared to conventional testing systems, the CrackFinder is affordable, small, simple to use, and needs no calibration.

  13. Trapping and Probing Antihydrogen

    SciTech Connect

    Wurtele, Jonathan

    2013-03-27

    Precision spectroscopy of antihydrogen is a promising path to sensitive tests of CPT symmetry. The most direct route to achieve this goal is to create and probe antihydrogen in a magnetic minimum trap. Antihydrogen has been synthesized and trapped for 1000s at CERN by the ALPHA Collaboration. Some of the challenges associated with achieving these milestones will be discussed, including mixing cryogenic positron and antiproton plasmas to synthesize antihydrogen with kinetic energy less than the trap potential of .5K. Recent experiments in which hyperfine transitions were resonantly induced with microwaves will be presented. The opportunity for gravitational measurements in traps based on detailed studies of antihydrogen dynamics will be described. The talk will conclude with a discussion future antihydrogen research that will use a new experimental apparatus, ALPHA-I.

  14. Advanced Langmuir Probe (LP)

    NASA Technical Reports Server (NTRS)

    Voronka, N. R.; Block, B. P.; Carignan, G. R.

    1991-01-01

    The dynamic response of the MK-2 version of the Langmuir probe amplifier was studied. The settling time of the step response is increased by: (1) stray node-to-ground capacitance at series connections between high value feedback resistors; and (2) input capacitance due to the input cable, FET switches, and input source follower. The stray node-to-ground capacitances can be reduced to tolerable levels by elevating the string of feedback resistors above the printing board. A new feedback network was considered, with promising results. The design uses resistances having much lower nominal values, thereby minimizing the effect of stray capacitances. Faster settling times can be achieved by using an operational amplifier having a higher gain-bandwidth product.

  15. Single Probes, Double Probes, and the Structure of Memory Traces.

    ERIC Educational Resources Information Center

    Bruce, Darryl

    1980-01-01

    Memory for names was queried by single probes consisting of conceptual information about the persons or by double probes combining two single cues. Results were viewed as consistent with Jones's fragmentation hypothesis and with the general class of associative theories of memory. (Author/RD)

  16. Adaptive scanning probe microscopies

    SciTech Connect

    Swartzentruber, B.S.; Bouchard, A.M.; Osbourn, G.C.

    1997-02-01

    This work is comprised of two major sections. In the first section the authors develop multivariate image classification techniques to distinguish and identify surface electronic species directly from multiple-bias scanning tunneling microscope (STM) images. Multiple measurements at each site are used to distinguish and categorize inequivalent electronic or atomic species on the surface via a computerized classification algorithm. Then, comparison with theory or other suitably chosen experimental data enables the identification of each class. They demonstrate the technique by analyzing dual-polarity constant-current topographs of the Ge(111) surface. Just two measurements, negative- and positive-bias topography height, permit pixels to be separated into seven different classes. Labeling four of the classes as adatoms, first-layer atoms, and two inequivalent rest-atom sites, they find excellent agreement with the c(2 x 8) structure. The remaining classes are associated with structural defects and contaminants. This work represents a first step toward developing a general electronic/chemical classification and identification tool for multivariate scanning probe microscopy imagery. In the second section they report measurements of the diffusion of Si dimers on the Si(001) surface at temperatures between room temperature and 128 C using a novel atom-tracking technique that can resolve every diffusion event. The atom tracker employs lateral-positioning feedback to lock the STM probe tip into position above selected atoms with sub-Angstrom precision. Once locked the STM tracks the position of the atoms as they migrate over the crystal surface. By tracking individual atoms directly, the ability of the instrument to measure dynamic events is increased by a factor of {approximately} 1,000 over conventional STM imaging techniques.

  17. Small rocket tornado probe

    SciTech Connect

    Colgate, S.A.

    1982-01-01

    A (less than 1 lb.) paper rock tornado probe was developed and deployed in an attempt to measure the pressure, temperature, ionization, and electric field variations along a trajectory penetrating a tornado funnel. The requirements of weight and materials were set by federal regulations and a one-meter resolution at a penetration velocity of close to Mach 1 was desired. These requirements were achieved by telemetering a strain gage transducer for pressure, micro size thermister and electric field, and ionization sensors via a pulse time telemetry to a receiver on board an aircraft that digitizes a signal and presents it to a Z80 microcomputer for recording on mini-floppy disk. Recording rate was 2 ms for 8 channels of information that also includes telemetry rf field strength, magnetic field for orientation on the rocket, zero reference voltage for the sensor op amps as well as the previously mentioned items also. The absolute pressure was recorded. Tactically, over 120 h were flown in a Cessna 210 in April and May 1981, and one tornado was encountered. Four rockets were fired at this tornado, missed, and there were many equipment problems. The equipment needs to be hardened and engineered to a significant degree, but it is believed that the feasibility of the probe, tactics, and launch platform for future tornado work has been proven. The logistics of thunderstorm chasing from a remote base in New Mexico is a major difficulty and reliability of the equipment another. Over 50 dummy rockets have been fired to prove trajectories, stability, and photographic capability. Over 25 electronically equipped rockets have been fired to prove sensors transmission, breakaway connections, etc. The pressure recovery factor was calibrated in the Air Force Academy blow-down tunnel. There is a need for more refined engineering and more logistic support.

  18. Probing an ensemble of superconducting devices

    NASA Astrophysics Data System (ADS)

    Sears, Adam; Hover, David; Gudmundsen, Theodore; Yoder, Jonilyn L.; Kamal, Archana; Yan, Fei; Gustavsson, Simon; Kerman, Andrew; Oliver, William

    2015-03-01

    We present experimental results on a system in which we use a flux qubit to probe an ensemble of weakly coupled superconducting devices. We employ standard qubit metrology techniques to reveal global device properties. In addition, we discuss the connection with engineered environmental decoherence. This work is sponsored by the Assistant Secretary of Defense for Research & Engineering under Air Force Contract FA8721-05-0002. Opinions, interpretations, conclusions, and recommendations are those of the authors and are not necessarily endorsed by the United States Government.

  19. Site-Specific Infrared Probes of Proteins

    PubMed Central

    Ma, Jianqiang; Pazos, Ileana M.; Zhang, Wenkai; Culik, Robert M.; Gai, Feng

    2015-01-01

    Infrared spectroscopy has played an instrumental role in studying a wide variety of biological questions. However, in many cases it is impossible or difficult to rely on the intrinsic vibrational modes of biological molecules of interest, such as proteins, to reveal structural and/or environmental information in a site-specific manner. To overcome this limitation, many recent efforts have been dedicated to the development and application of various extrinsic vibrational probes that can be incorporated into biological molecules and used to site-specifically interrogate their structural and/or environmental properties. In this Review, we highlight some recent advancements of this rapidly growing research area. PMID:25580624

  20. Synergy Between probes and Orbiter

    NASA Technical Reports Server (NTRS)

    Young, Richard E.

    2005-01-01

    There are many ways in which the science return from a planetary mission is considerably enhanced by interactions between entry probes and a mission orbiter. Mission configuration aspects that are desirable include delivery of entry probes by the orbiter, and communication between probe and orbiter. Both of these mission aspects could greatly enhance access to key scientific sites that might not otherwise be accessible using delivery from say, a flyby, or employing direct communication from probes to Earth. Examples for Venus and Jupiter will be discussed. A second class of orbiter-probe interaction could better be termed direct probe-orbiter science collaboration. That would include, determining the global context of the entry probe sites from the orbiter, obtaining ground truth from the probe for remote sensing observations from the orbiter, observing the global and vertical distribution of key atmospheric trace species, and measuring the global and vertical distribution of clouds and winds. The importance of each of these items will be illustrated by particular examples.

  1. Magnetic circuitry mutual coupling probe

    NASA Technical Reports Server (NTRS)

    Anthony, P. L.

    1972-01-01

    Development of magnetic probe for nondestructive testing of multilayer printed circuit boards to determine existence of opens or shorts is reported. Components of probe are described and procedures for operation are discussed. Two illustrations are provided to show magnetic circuits and principles of operation.

  2. Cobra Probes Containing Replaceable Thermocouples

    NASA Technical Reports Server (NTRS)

    Jones, John; Redding, Adam

    2007-01-01

    A modification of the basic design of cobra probes provides for relatively easy replacement of broken thermocouples. Cobra probes are standard tube-type pressure probes that may also contain thermocouples and that are routinely used in wind tunnels and aeronautical hardware. They are so named because in side views, they resemble a cobra poised to attack. Heretofore, there has been no easy way to replace a broken thermocouple in a cobra probe: instead, it has been necessary to break the probe apart and then rebuild it, typically at a cost between $2,000 and $4,000 (2004 prices). The modified design makes it possible to replace the thermocouple, in minimal time and at relatively low cost, by inserting new thermocouple wire in a tube.

  3. Electrophoresis-mass spectrometry probe

    DOEpatents

    Andresen, B.D.; Fought, E.R.

    1987-11-10

    The invention involves a new technique for the separation of complex mixtures of chemicals, which utilizes a unique interface probe for conventional mass spectrometers which allows the electrophoretically separated compounds to be analyzed in real-time by a mass spectrometer. This new chemical analysis interface, which couples electrophoresis with mass spectrometry, allows complex mixtures to be analyzed very rapidly, with much greater specificity, and with greater sensitivity. The interface or probe provides a means whereby large and/or polar molecules in complex mixtures to be completely characterized. The preferred embodiment of the probe utilizes a double capillary tip which allows the probe tip to be continually wetted by the buffer, which provides for increased heat dissipation, and results in a continually operating interface which is more durable and electronically stable than the illustrated single capillary tip probe interface. 8 figs.

  4. Electrophoresis-mass spectrometry probe

    DOEpatents

    Andresen, Brian D.; Fought, Eric R.

    1987-01-01

    The invention involves a new technique for the separation of complex mixtures of chemicals, which utilizes a unique interface probe for conventional mass spectrometers which allows the electrophoretically separated compounds to be analyzed in real-time by a mass spectrometer. This new chemical analysis interface, which couples electrophoresis with mass spectrometry, allows complex mixtures to be analyzed very rapidly, with much greater specificity, and with greater sensitivity. The interface or probe provides a means whereby large and/or polar molecules in complex mixtures to be completely characterized. The preferred embodiment of the probe utilizes a double capillary tip which allows the probe tip to be continually wetted by the buffer, which provides for increased heat dissipation, and results in a continually operating interface which is more durable and electronically stable than the illustrated single capillary tip probe interface.

  5. Rotating concave eddy current probe

    DOEpatents

    Roach, Dennis P.; Walkington, Phil; Rackow, Kirk A.; Hohman, Ed

    2008-04-01

    A rotating concave eddy current probe for detecting fatigue cracks hidden from view underneath the head of a raised head fastener, such as a buttonhead-type rivet, used to join together structural skins, such as aluminum aircraft skins. The probe has a recessed concave dimple in its bottom surface that closely conforms to the shape of the raised head. The concave dimple holds the probe in good alignment on top of the rivet while the probe is rotated around the rivet's centerline. One or more magnetic coils are rigidly embedded within the probe's cylindrical body, which is made of a non-conducting material. This design overcomes the inspection impediment associated with widely varying conductivity in fastened joints.

  6. Water cooled static pressure probe

    NASA Technical Reports Server (NTRS)

    Lagen, Nicholas T. (Inventor); Eves, John W. (Inventor); Reece, Garland D. (Inventor); Geissinger, Steve L. (Inventor)

    1991-01-01

    An improved static pressure probe containing a water cooling mechanism is disclosed. This probe has a hollow interior containing a central coolant tube and multiple individual pressure measurement tubes connected to holes placed on the exterior. Coolant from the central tube symmetrically immerses the interior of the probe, allowing it to sustain high temperature (in the region of 2500 F) supersonic jet flow indefinitely, while still recording accurate pressure data. The coolant exits the probe body by way of a reservoir attached to the aft of the probe. The pressure measurement tubes are joined to a single, larger manifold in the reservoir. This manifold is attached to a pressure transducer that records the average static pressure.

  7. Thiol Reactive Probes and Chemosensors

    PubMed Central

    Peng, Hanjing; Chen, Weixuan; Cheng, Yunfeng; Hakuna, Lovemore; Strongin, Robert; Wang, Binghe

    2012-01-01

    Thiols are important molecules in the environment and in biological processes. Cysteine (Cys), homocysteine (Hcy), glutathione (GSH) and hydrogen sulfide (H2S) play critical roles in a variety of physiological and pathological processes. The selective detection of thiols using reaction-based probes and sensors is very important in basic research and in disease diagnosis. This review focuses on the design of fluorescent and colorimetric probes and sensors for thiol detection. Thiol detection methods include probes and labeling agents based on nucleophilic addition and substitution, Michael addition, disulfide bond or Se-N bond cleavage, metal-sulfur interactions and more. Probes for H2S are based on nucleophilic cyclization, reduction and metal sulfide formation. Thiol probe and chemosensor design strategies and mechanism of action are discussed in this review. PMID:23202239

  8. Atom probe tomography of a commercial light emitting diode

    NASA Astrophysics Data System (ADS)

    Larson, D. J.; Prosa, T. J.; Olson, D.; Lefebvre, W.; Lawrence, D.; Clifton, P. H.; Kelly, T. F.

    2013-11-01

    The atomic-scale analysis of a commercial light emitting diode device purchased at retail is demonstrated using a local electrode atom probe. Some of the features are correlated with transmission electron microscopy imaging. Subtle details of the structure that are revealed have potential significance for the design and performance of this device.

  9. Long duration ash probe

    DOEpatents

    Hurley, J.P.; McCollor, D.P.; Selle, S.J.

    1994-07-26

    A long duration ash probe includes a pressure shell connected to a port in a combustor with a sample coupon mounted on a retractable carriage so as to retract the sample coupon within the pressure shell during soot blowing operation of the combustor. A valve mounted at the forward end of the pressure shell is selectively closeable to seal the sample coupon within the shell, and a heating element in the shell is operable to maintain the desired temperature of the sample coupon while retracted within the shell. The carriage is operably mounted on a pair of rails within the shell for longitudinal movement within the shell. A hollow carrier tube connects the hollow cylindrical sample coupon to the carriage, and extends through the carriage and out the rearward end thereof. Air lines are connected to the rearward end of the carrier tube and are operable to permit coolant to pass through the air lines and thence through the carrier tube to the sample coupon so as to cool the sample coupon. 8 figs.

  10. Long duration ash probe

    DOEpatents

    Hurley, John P.; McCollor, Don P.; Selle, Stanley J.

    1994-01-01

    A long duration ash probe includes a pressure shell connected to a port in a combustor with a sample coupon mounted on a retractable carriage so as to retract the sample coupon within the pressure shell during sootblowing operation of the combustor. A valve mounted at the forward end of the pressure shell is selectively closeable to seal the sample coupon within the shell, and a heating element in the shell is operable to maintain the desired temperature of the sample coupon while retracted within the shell. The carriage is operably mounted on a pair of rails within the shell for longitudinal movement within the shell. A hollow carrier tube connects the hollow cylindrical sample coupon to the carriage, and extends through the carriage and out the rearward end thereof. Air lines are connected to the rearward end of the carrier tube and are operable to permit coolant to pass through the air lines and thence through the carrier tube to the sample coupon so as to cool the sample coupon.

  11. Active Dynamic Frictional Probes

    NASA Astrophysics Data System (ADS)

    Steimel, Joshua; Aragones, Juan; Alexander-Katz, Alfredo

    2015-03-01

    In biological systems there are a myriad of interactions occurring instantaneously and these interactions can vary drastically in the strength of the interaction, the speed at which this interaction occurs, and the duration of the interaction. When multiple interactions occur any of these factors can determine which particular interaction is dominant. However, currently it is extremely difficult to measure binding affinity, Kon, and Koff rates in a relatively high throughput manner. Here we propose a novel and versatile system that will be able to detect differences in binding affinity of wide range of transient interactions and will be able to extract the relevant time scales of these interactions. Our system will utilize ferromagnetic particles that can be easily functionalized with a receptor of interest and the substrate will be coated in the corresponding ligand. A rotating magnetic field will cause particles, henceforth referred to as rollers, to rotate and this rotational motion will be converted into translational motion via the effective frictional force induced by interaction that is being probed. By measuring the translation of the rollers to a baseline, where only hydrodynamic friction occurs, we can measure the relative strength of the interactions. We can also potentially measure kinetic information by changing the frequency at which the magnetic field rotates, since changing the frequency at which the bead rotates is akin to changing the time allowed for bond formation. We will measure a wide range of interaction including ionic, metal-ion coordination, IgG-Protein A complex, and biotin-streptavidin complex.

  12. Gravity Probe B Encapsulated

    NASA Technical Reports Server (NTRS)

    2004-01-01

    In this photo, the Gravity Probe B (GP-B) space vehicle is being encapsulated atop the Delta II launch vehicle. The GP-B is the relativity experiment developed at Stanford University to test two extraordinary predictions of Albert Einstein's general theory of relativity. The experiment will measure, very precisely, the expected tiny changes in the direction of the spin axes of four gyroscopes contained in an Earth-orbiting satellite at a 400-mile altitude. So free are the gyroscopes from disturbance that they will provide an almost perfect space-time reference system. They will measure how space and time are very slightly warped by the presence of the Earth, and, more profoundly, how the Earth's rotation very slightly drags space-time around with it. These effects, though small for the Earth, have far-reaching implications for the nature of matter and the structure of the Universe. GP-B is among the most thoroughly researched programs ever undertaken by NASA. This is the story of a scientific quest in which physicists and engineers have collaborated closely over many years. Inspired by their quest, they have invented a whole range of technologies that are already enlivening other branches of science and engineering. Launched April 20, 2004 , the GP-B program was managed for NASA by the Marshall Space Flight Center. Development of the GP-B is the responsibility of Stanford University along with major subcontractor Lockheed Martin Corporation. (Image credit to Russ Underwood, Lockheed Martin Corporation).

  13. Scanning probe nanoimprint lithography

    NASA Astrophysics Data System (ADS)

    Dinelli, F.; Menozzi, C.; Baschieri, P.; Facci, P.; Pingue, P.

    2010-02-01

    The present paper reports on a novel lithographic approach at the nanoscale level, which is based on scanning probe microscopy (SPM) and nanoimprint lithography (NIL). The experimental set-up consists of an atomic force microscope (AFM) operated via software specifically developed for the purpose. In particular, this software allows one to apply a predefined external load for a given lapse of time while monitoring in real-time the relative distance between the tip and the sample as well as the normal and lateral force during the embossing process. Additionally, we have employed AFM tips sculptured by means of focused ion beam in order to create indenting tools of the desired shape. Anti-sticking layers can also be used to functionalize the tips if one needs to investigate the effects of different treatments on the indentation and de-molding processes. The lithographic capabilities of this set-up are demonstrated on a polystyrene NIL-patterned sample, where imprinted features have been obtained upon using different normal load values for increasing time intervals, and on a thermoplastic polymer film, where the imprint process has been monitored in real-time.

  14. Calibration of Langmuir probes against microwaves and plasma oscillation probes

    NASA Astrophysics Data System (ADS)

    Chen, Francis F.; Evans, John D.; Zawalski, Wade

    2012-10-01

    The use of Langmuir probes for measuring plasma density is subject to uncertainty because the theories commonly used to interpret the data give widely differing results. This is especially troublesome in partially ionized plasmas used, for instance, in the semiconductor industry, since no existing theory adequately treats the case when there are a few collisions between ions and neutral atoms. In this work, plasma densities measured by microwave interferometry and plasma-oscillation probes are compared with those from probe data analyzed with Langmuir's orbital motion limited (OML) theory, the Allen-Boyd-Reynolds (ABR) theory and the Bernstein-Rabinowitz-Laframboise (BRL) theory. It is found that ABR underestimates and BRL overestimates the density, the problems being the neglect of ion orbiting in ABR and the effect of ion-neutral collisions in BRL. The best theory is either OML or the geometric mean between the ABR and BRL results. For thicker probes, other methods are suggested.

  15. Measurements With a Split-Fiber Probe in Complex Unsteady Flows

    NASA Technical Reports Server (NTRS)

    Lepicovsky, Jan

    2004-01-01

    A split-fiber probe was used to acquire unsteady data in a research compressor. A calibration method was devised for a split-fiber probe, and a new algorithm was developed to decompose split-fiber probe signals into velocity magnitude and direction. The algorithm is based on the minimum value of a merit function that is built over the entire range of flow velocities for which the probe was calibrated. The split-fiber probe performance and signal decomposition was first verified in a free-jet facility by comparing the data from three thermo-anemometric probes, namely a single-wire, a single-fiber, and the split-fiber probe. All three probes performed extremely well as far as the velocity magnitude was concerned. However, there are differences in the peak values of measured velocity unsteadiness in the jet shear layer. The single-wire probe indicates the highest unsteadiness level, followed closely by the split-fiber probe. The single-fiber probe indicates a noticeably lower level of velocity unsteadiness. Experiments in the NASA Low Speed Axial Compressor facility revealed similar results. The mean velocities agreed well, and differences in the velocity unsteadiness are similar to the case of a free jet. A reason for these discrepancies is in the different frequency response characteristics of probes used. It follows that the single-fiber probe has the slowest frequency response. In summary, the split-fiber probe worked reliably during the entire program. The acquired data averaged in time followed closely data acquired by conventional pneumatic probes.

  16. ESA Venus Entry Probe Study

    NASA Technical Reports Server (NTRS)

    vandenBerg, M. L.; Falkner, P.; Phipps, A.; Underwood, J. C.; Lingard, J. S.; Moorhouse, J.; Kraft, S.; Peacock, A.

    2005-01-01

    The Venus Entry Probe is one of ESA s Technology Reference Studies (TRS). The purpose of the Technology Reference Studies is to provide a focus for the development of strategically important technologies that are of likely relevance for future scientific missions. The aim of the Venus Entry Probe TRS is to study approaches for low cost in-situ exploration of Venus and other planetary bodies with a significant atmosphere. In this paper, the mission objectives and an outline of the mission concept of the Venus Entry Probe TRS are presented.

  17. Optic probe for semiconductor characterization

    DOEpatents

    Sopori, Bhushan L.; Hambarian, Artak

    2008-09-02

    Described herein is an optical probe (120) for use in characterizing surface defects in wafers, such as semiconductor wafers. The optical probe (120) detects laser light reflected from the surface (124) of the wafer (106) within various ranges of angles. Characteristics of defects in the surface (124) of the wafer (106) are determined based on the amount of reflected laser light detected in each of the ranges of angles. Additionally, a wafer characterization system (100) is described that includes the described optical probe (120).

  18. Saturn orbiter dual probe mission

    NASA Technical Reports Server (NTRS)

    Rudd, R. P.

    1978-01-01

    The described Saturn orbiter dual probe mission and spacecraft combines three systems into a multi-purpose Saturn exploration package. The spacecraft consists of: (1) Saturn orbiter; (2) Saturn probe; and (3) Titan probe or lander. This single spacecraft provides the capability to conduct in situ measurements of the Saturn and Titan atmospheres, and, possibly the Titan surface, as well as a variety of remote sensing measurements. The remote sensing capabilities will be used to study the surfaces, interiors and environments of Saturn's satellites, the rings of Saturn, Saturn's magnetosphere, and synoptic properties of Saturn's atmosphere.

  19. Atmospheric probes: needs and prospects

    NASA Astrophysics Data System (ADS)

    Owen, Tobias

    2004-02-01

    There is only one Rosetta Stone in the Solar System; it's in the British Museum. We cannot understand the inner planets by simply studying the Earth, nor can we apprehend the giants by examining only Jupiter. Despite the stunning successes of previous probes to Venus and the Galileo probe to Jupiter, our knowledge of the atmospheres of even these two planets remains tantalizingly incomplete. We must therefore return to Venus and consider the challenge of exploring all of the outer planets with a family of identical probes, a project that could commemorater the vision of multiple worlds championed by Giordano Bruno.

  20. Floating Potential Probe Langmuir Probe Data Reduction Results

    NASA Technical Reports Server (NTRS)

    Morton, Thomas L.; Minow, Joseph I.

    2002-01-01

    During its first five months of operations, the Langmuir Probe on the Floating Potential Probe (FPP) obtained data on ionospheric electron densities and temperatures in the ISS orbit. In this paper, the algorithms for data reduction are presented, and comparisons are made of FPP data with ground-based ionosonde and Incoherent Scattering Radar (ISR) results. Implications for ISS operations are detailed, and the need for a permanent FPP on ISS is examined.

  1. Fiberoptic probe and system for spectral measurements

    DOEpatents

    Dai, S.; Young, J.P.

    1998-10-13

    A fused fiberoptic probe, a system, method and embodiments thereof for conducting spectral measurements are disclosed. The fused fiberoptic probe comprises a probe tip having a specific geometrical configuration, an exciting optical fiber and at least one collection optical fiber fused within a housing, preferably silica. The specific geometrical configurations in which the probe tip can be shaped include a slanted probe tip with an angle greater than 0{degree}, an inverted cone-shaped probe tip, and a lens head. 12 figs.

  2. Fiberoptic probe and system for spectral measurements

    DOEpatents

    Dai, Sheng; Young, Jack P.

    1998-01-01

    A fused fiberoptic probe, a system, method and embodiments thereof for conducting spectral measurements are disclosed. The fused fiberoptic probe comprises a probe tip having a specific geometrical configuration, an exciting optical fiber and at least one collection optical fiber fused within a housing, preferrably silica. The specific geometrical configurations in which the probe tip can be shaped include a slanted probe tip with an angle greater than 0.degree., an inverted cone-shaped probe tip, and a lens head.

  3. Integrated microfluidic probe station.

    PubMed

    Perrault, C M; Qasaimeh, M A; Brastaviceanu, T; Anderson, K; Kabakibo, Y; Juncker, D

    2010-11-01

    The microfluidic probe (MFP) consists of a flat, blunt tip with two apertures for the injection and reaspiration of a microjet into a solution--thus hydrodynamically confining the microjet--and is operated atop an inverted microscope that enables live imaging. By scanning across a surface, the microjet can be used for surface processing with the capability of both depositing and removing material; as it operates under immersed conditions, sensitive biological materials and living cells can be processed. During scanning, the MFP is kept immobile and centered over the objective of the inverted microscope, a few micrometers above a substrate that is displaced by moving the microscope stage and that is flushed continuously with the microjet. For consistent and reproducible surface processing, the gap between the MFP and the substrate, the MFP's alignment, the scanning speed, the injection and aspiration flow rates, and the image capture need all to be controlled and synchronized. Here, we present an automated MFP station that integrates all of these functionalities and automates the key operational parameters. A custom software program is used to control an independent motorized Z stage for adjusting the gap, a motorized microscope stage for scanning the substrate, up to 16 syringe pumps for injecting and aspirating fluids, and an inverted fluorescence microscope equipped with a charge-coupled device camera. The parallelism between the MFP and the substrate is adjusted using manual goniometer at the beginning of the experiment. The alignment of the injection and aspiration apertures along the scanning axis is performed using a newly designed MFP screw holder. We illustrate the integrated MFP station by the programmed, automated patterning of fluorescently labeled biotin on a streptavidin-coated surface. PMID:21133501

  4. Gravity Probe B Assembled

    NASA Technical Reports Server (NTRS)

    2000-01-01

    In this photo, the Gravity Probe B (GP-B) space vehicle is being assembled at the Sunnyvale, California location of the Lockheed Martin Corporation. The GP-B is the relativity experiment developed at Stanford University to test two extraordinary predictions of Albert Einstein's general theory of relativity. The experiment will measure, very precisely, the expected tiny changes in the direction of the spin axes of four gyroscopes contained in an Earth-orbiting satellite at a 400-mile altitude. So free are the gyroscopes from disturbance that they will provide an almost perfect space-time reference system. They will measure how space and time are very slightly warped by the presence of the Earth, and, more profoundly, how the Earth's rotation very slightly drags space-time around with it. These effects, though small for the Earth, have far-reaching implications for the nature of matter and the structure of the Universe. GP-B is among the most thoroughly researched programs ever undertaken by NASA. This is the story of a scientific quest in which physicists and engineers have collaborated closely over many years. Inspired by their quest, they have invented a whole range of technologies that are already enlivening other branches of science and engineering. Launched April 20, 2004 , the GP-B program was managed for NASA by the Marshall Space Flight Center. Development of the GP-B is the responsibility of Stanford University along with major subcontractor Lockheed Martin Corporation. (Image credit to Russ Underwood, Lockheed Martin Corporation).

  5. Integrated microfluidic probe station

    NASA Astrophysics Data System (ADS)

    Perrault, C. M.; Qasaimeh, M. A.; Brastaviceanu, T.; Anderson, K.; Kabakibo, Y.; Juncker, D.

    2010-11-01

    The microfluidic probe (MFP) consists of a flat, blunt tip with two apertures for the injection and reaspiration of a microjet into a solution—thus hydrodynamically confining the microjet—and is operated atop an inverted microscope that enables live imaging. By scanning across a surface, the microjet can be used for surface processing with the capability of both depositing and removing material; as it operates under immersed conditions, sensitive biological materials and living cells can be processed. During scanning, the MFP is kept immobile and centered over the objective of the inverted microscope, a few micrometers above a substrate that is displaced by moving the microscope stage and that is flushed continuously with the microjet. For consistent and reproducible surface processing, the gap between the MFP and the substrate, the MFP's alignment, the scanning speed, the injection and aspiration flow rates, and the image capture need all to be controlled and synchronized. Here, we present an automated MFP station that integrates all of these functionalities and automates the key operational parameters. A custom software program is used to control an independent motorized Z stage for adjusting the gap, a motorized microscope stage for scanning the substrate, up to 16 syringe pumps for injecting and aspirating fluids, and an inverted fluorescence microscope equipped with a charge-coupled device camera. The parallelism between the MFP and the substrate is adjusted using manual goniometer at the beginning of the experiment. The alignment of the injection and aspiration apertures along the scanning axis is performed using a newly designed MFP screw holder. We illustrate the integrated MFP station by the programmed, automated patterning of fluorescently labeled biotin on a streptavidin-coated surface.

  6. A three dimensional probe positioner

    SciTech Connect

    Intrator, T.; Sun, X.; Furno, I.; Dorf, L.; Lapenta, G.

    2008-10-15

    In order to sort out the physics that is important in many plasma experiments, data in three dimensions (3D) are becoming necessary. Access to the usual cylindrical vacuum vessel is typically restricted to radially or axially insertable probes that can pivot. The space that can be explored usually has significant restrictions either because probe travel must be along a travel path, or a 'wobbly' probe positioner requires one to map between a moveable coordinate system and a preferred laboratory coordinate system. This could for example introduce errors in measurements of vector quantities such as magnetic field or flow. We describe the design and implementation of a 3D probe positioner that slides in two dimensions on a double O-ring seal and radially inserts along the third dimension. The net result is that a 3D space can be explored in a laboratory Cartesian reference frame.

  7. Study of alternative probe technologies

    NASA Technical Reports Server (NTRS)

    1977-01-01

    A number of implied technologies for a deep probe mission was examined; i.e., one that would provide the capability to scientifically examine planetary atmospheres at the 1000 bar level. Conditions imposed by current Jupiter, Saturn, and Uranus atmospheric models were considered. The major thrust of the measurements was to determine lower atmosphere composition, even to trace constituents of one part per billion. Two types of instruments having the necessary accuracy to meet the science objectives were considered and integrated into a deep probe configuration. One deep probe option that resulted was identified as a Minimum Technology Development approach. The significant feature of this option is that only three technology developments are required to enable the mission, i.e., (1) science instrument development, (2) advanced data processing, and (3) external high pressure/thermal insulation. It is concluded that a probe designed for a Jupiter mission could, with minor changes, be used for a Saturn or Uranus mission.

  8. The Radiation Belt Storm Probes

    NASA Video Gallery

    The Radiation Belt Storm Probe mission (RBSP) will explore the Van Allen Radiation Belts in the Earth's magnetosphere. The charge particles in these regions can be hazardous to both spacecraft and ...

  9. Monitoring probe for groundwater flow

    DOEpatents

    Looney, B.B.; Ballard, S.

    1994-08-23

    A monitoring probe for detecting groundwater migration is disclosed. The monitor features a cylinder made of a permeable membrane carrying an array of electrical conductivity sensors on its outer surface. The cylinder is filled with a fluid that has a conductivity different than the groundwater. The probe is placed in the ground at an area of interest to be monitored. The fluid, typically saltwater, diffuses through the permeable membrane into the groundwater. The flow of groundwater passing around the permeable membrane walls of the cylinder carries the conductive fluid in the same general direction and distorts the conductivity field measured by the sensors. The degree of distortion from top to bottom and around the probe is precisely related to the vertical and horizontal flow rates, respectively. The electrical conductivities measured by the sensors about the outer surface of the probe are analyzed to determine the rate and direction of the groundwater flow. 4 figs.

  10. Monitoring probe for groundwater flow

    DOEpatents

    Looney, Brian B.; Ballard, Sanford

    1994-01-01

    A monitoring probe for detecting groundwater migration. The monitor features a cylinder made of a permeable membrane carrying an array of electrical conductivity sensors on its outer surface. The cylinder is filled with a fluid that has a conductivity different than the groundwater. The probe is placed in the ground at an area of interest to be monitored. The fluid, typically saltwater, diffuses through the permeable membrane into the groundwater. The flow of groundwater passing around the permeable membrane walls of the cylinder carries the conductive fluid in the same general direction and distorts the conductivity field measured by the sensors. The degree of distortion from top to bottom and around the probe is precisely related to the vertical and horizontal flow rates, respectively. The electrical conductivities measured by the sensors about the outer surface of the probe are analyzed to determine the rate and direction of the groundwater flow.