Science.gov

Sample records for activity measurements revealed

  1. Frequency specific interactions of MEG resting state activity within and across brain networks as revealed by the multivariate interaction measure.

    PubMed

    Marzetti, L; Della Penna, S; Snyder, A Z; Pizzella, V; Nolte, G; de Pasquale, F; Romani, G L; Corbetta, M

    2013-10-01

    Resting state networks (RSNs) are sets of brain regions exhibiting temporally coherent activity fluctuations in the absence of imposed task structure. RSNs have been extensively studied with fMRI in the infra-slow frequency range (nominally <10(-1)Hz). The topography of fMRI RSNs reflects stationary temporal correlation over minutes. However, neuronal communication occurs on a much faster time scale, at frequencies nominally in the range of 10(0)-10(2)Hz. We examined phase-shifted interactions in the delta (2-3.5 Hz), theta (4-7 Hz), alpha (8-12 Hz) and beta (13-30 Hz) frequency bands of resting-state source space MEG signals. These analyses were conducted between nodes of the dorsal attention network (DAN), one of the most robust RSNs, and between the DAN and other networks. Phase shifted interactions were mapped by the multivariate interaction measure (MIM), a measure of true interaction constructed from the maximization of imaginary coherency in the virtual channels comprised of voxel signals in source space. Non-zero-phase interactions occurred between homologous left and right hemisphere regions of the DAN in the delta and alpha frequency bands. Even stronger non-zero-phase interactions were detected between networks. Visual regions bilaterally showed phase-shifted interactions in the alpha band with regions of the DAN. Bilateral somatomotor regions interacted with DAN nodes in the beta band. These results demonstrate the existence of consistent, frequency specific phase-shifted interactions on a millisecond time scale between cortical regions within RSN as well as across RSNs. PMID:23631996

  2. 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

  3. Measuring Physical Activity Environments

    PubMed Central

    Sallis, James F.

    2010-01-01

    Physical activity is usually done in specific types of places, referred to as physical activity environments. These often include parks, trails, fitness centers, schools, and streets. In recent years, scientific interest has increased notably in measuring physical activity environments. The present paper provides an historical overview of the contributions of the health, planning, and leisure studies fields to the development of contemporary measures. The emphasis is on attributes of the built environment that can be affected by policies to contribute to the promotion of physical activity. Researchers from health fields assessed a wide variety of built environment variables expected to be related to recreational physical activity. Settings of interest were schools, workplaces, and recreation facilities, and most early measures used direct observation methods with demonstrated inter-observer reliability. Investigators from the city planning field evaluated aspects of community design expected to be related to people’s ability to walk from homes to destinations. GIS was used to assess walkability defined by the 3Ds of residential density, land-use diversity, and pedestrian-oriented designs. Evaluating measures for reliability or validity was rarely done in the planning-related fields. Researchers in the leisure studies and recreation fields studied mainly people’s use of leisure time rather than physical characteristics of parks and other recreation facilities. Although few measures of physical activity environments were developed, measures of aesthetic qualities are available. Each of these fields made unique contributions to the contemporary methods used to assess physical activity environments. PMID:19285214

  4. Frantic activity revealed in dusty stellar factories

    NASA Astrophysics Data System (ADS)

    2009-01-01

    Thanks to the Very Large Telescope's acute and powerful near-infrared eye, astronomers have uncovered a host of new young, massive and dusty stellar nurseries in nearby galaxy NGC 253. The centre of this galaxy appears to harbour a twin of our own Milky Way's supermassive black hole. ESO PR Photo 02a/09 The Spiral Galaxy NGC 253 Astronomers from the Instituto de Astrofísica de Canarias (Spain) used NACO, a sharp-eyed adaptive optics instrument on ESO's Very Large Telescope (VLT), to study the fine detail in NGC 253, one of the brightest and dustiest spiral galaxies in the sky. Adaptive Optics (AO) corrects for the blurring effect introduced by the Earth's atmosphere. This turbulence causes the stars to twinkle in a way that delights poets, but frustrates astronomers, since it smears out the images. With AO in action the telescope can produce images that are as sharp as is theoretically possible, as if the telescope were in space. NACO revealed features in the galaxy that were only 11 light-years across. "Our observations provide us with so much spatially resolved detail that we can, for the first time, compare them with the finest radio maps for this galaxy -- maps that have existed for more than a decade," says Juan Antonio Fernández-Ontiveros, the lead author of the paper reporting the results [1]. Astronomers identified 37 distinct bright regions, a threefold increase on previous results, packed into a tiny region at the core of the galaxy, comprising just one percent of the galaxy's total size. The astronomers combined their NACO images with data from another VLT instrument, VISIR, as well as with images from the NASA/ESA Hubble Space Telescope and radio observations made by the Very Large Array and the Very Large Baseline Interferometer. Combining these observations, taken in different wavelength regimes, provided a clue to the nature of these regions. "We now think that these are probably very active nurseries that contain many stars bursting from their

  5. Shocking Detail of Superstar's Activity Revealed

    NASA Astrophysics Data System (ADS)

    1999-10-01

    NASA's Chandra X-ray Observatory has imaged Eta Carinae and revealed a hot inner core around this mysterious superstar. The new X-ray observation shows three distinct structures: an outer, horseshoe shaped ring about two light years in diameter, a hot inner core about 3 light months in diameter, and a hot central source less than a light month in diameter which may contain the superstar. All three structures are thought to represent shock waves produced by matter rushing away from the superstar at supersonic speeds. The temperature of the shock-heated gas ranges from 60 million degrees Celsius in the central regions to 3 million degrees Celsius on the outer structure. An earlier image of Eta Carinae by the Hubble Space Telescope revealed two spectacular bubbles of gas expanding in opposite directions away from a central bright region at speeds in excess of a million miles per hour. The inner region visible in the Chandra image has never been resolved before, and appears to be associated with a central disk of high velocity gas rushing out at much higher speeds perpendicular to the bipolar optical nebula. "It is not what I expected," said Dr. Fred Seward of the Harvard-Smithsonian Center for Astrophysics. "I expected to see a strong point source with a little diffuse emission cloud around it. Instead, we see just the opposite- a bright cloud of diffuse emission, and much less radiation from the center." "The Chandra image contains some puzzles for existing ideas of how a star can produce such hot and intense X-rays," agreed Prof. Kris Davidson of the University of Minnesota. "In the most popular theory, X-rays are made by colliding gas streams from two stars so close together that they'd look like a point source to us. But what happens to gas streams that escape to farther distances? The extended hot stuff in the middle of the new image gives demanding new conditions for any theory to meet." Eta Carinae is one of the most enigmatic and intriguing objects in our

  6. Covert Waking Brain Activity Reveals Instantaneous Sleep Depth

    PubMed Central

    McKinney, Scott M.; Dang-Vu, Thien Thanh; Buxton, Orfeu M.; Solet, Jo M.; Ellenbogen, Jeffrey M.

    2011-01-01

    The neural correlates of the wake-sleep continuum remain incompletely understood, limiting the development of adaptive drug delivery systems for promoting sleep maintenance. The most useful measure for resolving early positions along this continuum is the alpha oscillation, an 8–13 Hz electroencephalographic rhythm prominent over posterior scalp locations. The brain activation signature of wakefulness, alpha expression discloses immediate levels of alertness and dissipates in concert with fading awareness as sleep begins. This brain activity pattern, however, is largely ignored once sleep begins. Here we show that the intensity of spectral power in the alpha band actually continues to disclose instantaneous responsiveness to noise—a measure of sleep depth—throughout a night of sleep. By systematically challenging sleep with realistic and varied acoustic disruption, we found that sleepers exhibited markedly greater sensitivity to sounds during moments of elevated alpha expression. This result demonstrates that alpha power is not a binary marker of the transition between sleep and wakefulness, but carries rich information about immediate sleep stability. Further, it shows that an empirical and ecologically relevant form of sleep depth is revealed in real-time by EEG spectral content in the alpha band, a measure that affords prediction on the order of minutes. This signal, which transcends the boundaries of classical sleep stages, could potentially be used for real-time feedback to novel, adaptive drug delivery systems for inducing sleep. PMID:21408616

  7. Measurement of Physical Activity.

    ERIC Educational Resources Information Center

    Dishman, Rod K.; Washburn, Richard A.; Schoeller, Dale A.

    2001-01-01

    Valid assessment of physical activity must be unobtrusive, practical to administer, and specific about physical activity type, frequency, duration, and intensity. Assessment methods can be categorized according to whether they provide direct or indirect (e.g., self-report) observation of physical activity, body motion, physiological response…

  8. Silicon-wafer-surface damage revealed by surface photovoltage measurements

    NASA Astrophysics Data System (ADS)

    Goodman, Alvin M.

    1982-11-01

    Anomalous results of surface photovoltage (SPV) measurements on Si wafers are shown to be associated with a damaged region beneath the illuminated surface of the wafer being measured. The anomaly is a concave-upward curvature of the I0(α-1) plot with an r2 value, derived from linear regression analysis, less than the normally observed minimum value (˜0.98). Removal of the damaged region by an appropriate etching procedure allows subsequent SPV measurements whose results are substantially free of the previously observed anomaly. The qualitative character of the anomaly can be reproduced by a simple theoretical model in which only one effect of the damage is considered; this effect is a diminished quantum efficiency for hole-electron pair generation by photon absorption in the damaged region. The results suggest the use of SPV measurements as a test procedure for revealing the presence of surface damage in Si wafers.

  9. Nonclassical light revealed by the joint statistics of simultaneous measurements.

    PubMed

    Luis, Alfredo

    2016-04-15

    Nonclassicality cannot be a single-observable property, since the statistics of any quantum observable is compatible with classical physics. We develop a general procedure to reveal nonclassical behavior of light states from the joint statistics arising in the practical measurement of multiple observables. Beside embracing previous approaches, this protocol can disclose nonclassical features for standard examples of classical-like behavior, such as SU(2) and Glauber coherent states. When combined with other criteria, this would imply that every light state is nonclassical. PMID:27082346

  10. Carbohydrate active enzymes revealed in Coptotermes formosanus transcriptome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A normalized cDNA library of Coptotermes formosanus was constructed using mixed RNA isolated from workers, soldiers, nymphs and alates of both sexes. Sequencing of this library generated 131,637 EST and 25,939 unigenes were assembled. Carbohydrate active enzymes (CAZymes) revealed in this library we...

  11. Topological structure dynamics revealing collective evolution in active nematics

    PubMed Central

    Shi, Xia-qing; Ma, Yu-qiang

    2013-01-01

    Topological defects frequently emerge in active matter like bacterial colonies, cytoskeleton extracts on substrates, self-propelled granular or colloidal layers and so on, but their dynamical properties and the relations to large-scale organization and fluctuations in these active systems are seldom touched. Here we reveal, through a simple model for active nematics using self-driven hard elliptic rods, that the excitation, annihilation and transportation of topological defects differ markedly from those in non-active media. These dynamical processes exhibit strong irreversibility in active nematics in the absence of detailed balance. Moreover, topological defects are the key factors in organizing large-scale dynamic structures and collective flows, resulting in multi-spatial temporal effects. These findings allow us to control the self-organization of active matter through topological structures. PMID:24346733

  12. Radioactive waste reality as revealed by neutron measurements

    SciTech Connect

    Schultz, F.J.

    1995-12-31

    To comprehend certain aspects of the contents of a radioactive waste container is not a trivial matter, especially if one is not allowed to open the container and peer inside. One of the suite of tools available to a practioner in the art of nondestructive assay is based upon neutron measurements. Neutrons, both naturally occuring and induced, are penertrating radiations that can be detected external to the waste container. The practioner should be skilled in applying the proper technique(s) to selected waste types. Available techniques include active and passive neutron measurements, each with their own strengths and weaknesses. The waste material itself can compromise the assay results by occluding a portion of the mass of fissile material present, or by multiplying the number of neutrons produced by a spontaneously fissioning mass. This paper will discuss the difficult, but albeit necessary marriage, between radiioactive waste types and alternative neutron measurement techniques.

  13. ACTIVITIES: Centimeter and Millimeter Measurements

    ERIC Educational Resources Information Center

    Bolster, L. Carey

    1974-01-01

    An activity is suggested which will give junior high school students practice in estimating and measuring in centimeters and millimeters. Three worksheets are given, one of which is a model for making a metric caliper. (LS)

  14. Combining complexity measures of EEG data: multiplying measures reveal previously hidden information

    PubMed Central

    Burns, Thomas; Rajan, Ramesh

    2015-01-01

    Many studies have noted significant differences among human electroencephalograph (EEG) results when participants or patients are exposed to different stimuli, undertaking different tasks, or being affected by conditions such as epilepsy or Alzheimer's disease. Such studies often use only one or two measures of complexity and do not regularly justify their choice of measure beyond the fact that it has been used in previous studies. If more measures were added to such studies, however, more complete information might be found about these reported differences. Such information might be useful in confirming the existence or extent of such differences, or in understanding their physiological bases. In this study we analysed publically-available EEG data using a range of complexity measures to determine how well the measures correlated with one another. The complexity measures did not all significantly correlate, suggesting that different measures were measuring unique features of the EEG signals and thus revealing information which other measures were unable to detect. Therefore, the results from this analysis suggests that combinations of complexity measures reveal unique information which is in addition to the information captured by other measures of complexity in EEG data. For this reason, researchers using individual complexity measures for EEG data should consider using combinations of measures to more completely account for any differences they observe and to ensure the robustness of any relationships identified. PMID:26594331

  15. Combining complexity measures of EEG data: multiplying measures reveal previously hidden information.

    PubMed

    Burns, Thomas; Rajan, Ramesh

    2015-01-01

    Many studies have noted significant differences among human electroencephalograph (EEG) results when participants or patients are exposed to different stimuli, undertaking different tasks, or being affected by conditions such as epilepsy or Alzheimer's disease. Such studies often use only one or two measures of complexity and do not regularly justify their choice of measure beyond the fact that it has been used in previous studies. If more measures were added to such studies, however, more complete information might be found about these reported differences. Such information might be useful in confirming the existence or extent of such differences, or in understanding their physiological bases. In this study we analysed publically-available EEG data using a range of complexity measures to determine how well the measures correlated with one another. The complexity measures did not all significantly correlate, suggesting that different measures were measuring unique features of the EEG signals and thus revealing information which other measures were unable to detect. Therefore, the results from this analysis suggests that combinations of complexity measures reveal unique information which is in addition to the information captured by other measures of complexity in EEG data. For this reason, researchers using individual complexity measures for EEG data should consider using combinations of measures to more completely account for any differences they observe and to ensure the robustness of any relationships identified. PMID:26594331

  16. Drought sensitivity of Amazonian carbon balance revealed by atmospheric measurements.

    PubMed

    Gatti, L V; Gloor, M; Miller, J B; Doughty, C E; Malhi, Y; Domingues, L G; Basso, L S; Martinewski, A; Correia, C S C; Borges, V F; Freitas, S; Braz, R; Anderson, L O; Rocha, H; Grace, J; Phillips, O L; Lloyd, J

    2014-02-01

    Feedbacks between land carbon pools and climate provide one of the largest sources of uncertainty in our predictions of global climate. Estimates of the sensitivity of the terrestrial carbon budget to climate anomalies in the tropics and the identification of the mechanisms responsible for feedback effects remain uncertain. The Amazon basin stores a vast amount of carbon, and has experienced increasingly higher temperatures and more frequent floods and droughts over the past two decades. Here we report seasonal and annual carbon balances across the Amazon basin, based on carbon dioxide and carbon monoxide measurements for the anomalously dry and wet years 2010 and 2011, respectively. We find that the Amazon basin lost 0.48 ± 0.18 petagrams of carbon per year (Pg C yr(-1)) during the dry year but was carbon neutral (0.06 ± 0.1 Pg C yr(-1)) during the wet year. Taking into account carbon losses from fire by using carbon monoxide measurements, we derived the basin net biome exchange (that is, the carbon flux between the non-burned forest and the atmosphere) revealing that during the dry year, vegetation was carbon neutral. During the wet year, vegetation was a net carbon sink of 0.25 ± 0.14 Pg C yr(-1), which is roughly consistent with the mean long-term intact-forest biomass sink of 0.39 ± 0.10 Pg C yr(-1) previously estimated from forest censuses. Observations from Amazonian forest plots suggest the suppression of photosynthesis during drought as the primary cause for the 2010 sink neutralization. Overall, our results suggest that moisture has an important role in determining the Amazonian carbon balance. If the recent trend of increasing precipitation extremes persists, the Amazon may become an increasing carbon source as a result of both emissions from fires and the suppression of net biome exchange by drought. PMID:24499918

  17. Memory activation reveals abnormal EEG in preclinical Huntington's disease.

    PubMed

    van der Hiele, Karin; Jurgens, Caroline K; Vein, Alla A; Reijntjes, Robert H A M; Witjes-Ané, Marie-Noëlle W; Roos, Raymund A C; van Dijk, Gert; Middelkoop, Huub A M

    2007-04-15

    The EEG is potentially useful as a marker of early Huntington's disease (HD). In dementia, the EEG during a memory activation challenge showed abnormalities where the resting EEG did not. We investigated whether memory activation also reveals EEG abnormalities in preclinical HD. Sixteen mutation carriers for HD and 13 nonmutation carriers underwent neurological, neuropsychological, MRI and EEG investigations. The EEG was registered during a rest condition, i.e. eyes closed, and a working memory task. In each condition we determined absolute power in the theta (4-8 Hz) and alpha (8-13 Hz) bands and subsequently calculated relative alpha power. The EEG during eyes closed did not differ between groups. The EEG during memory activation showed less relative alpha power in mutation carriers as compared to nonmutation carriers, even though memory performance was similar [F (1,27) = 10.87; P = 0.003]. Absolute powers also showed less alpha power [F (1,27) = 7.02; P = 0.013] but similar theta power. No correlations were found between absolute and relative alpha power on the one hand and neuropsychological scores, motor scores or number of CAG repeats on the other. In conclusion, memory activation reveals functional brain changes in Huntington's disease before clinical signs become overt. PMID:17266047

  18. Small molecules reveal an alternative mechanism of Bax activation

    PubMed Central

    Brahmbhatt, Hetal; Uehling, David; Al-awar, Rima; Leber, Brian; Andrews, David

    2016-01-01

    The pro-apoptotic protein Bax commits a cell to death by permeabilizing the mitochondrial outer membrane (MOM). To obtain small-molecule probes for elucidating the molecular mechanism(s) of Bax activation, we screened for compounds that induced Bax-mediated liposome permeabilization. We identified five structurally different small molecules that promoted both Bax targeting to and oligomerization at membranes. All five compounds initiated Bax oligomerization in the absence of membranes by a mechanism unlike Bax activation by Bcl-2 homology 3 domain (BH3) proteins. Some of the compounds induced Bax/Bak-dependent apoptosis in cells. Activation of Bax by the most active compound was poorly inhibited by the anti-apoptotic protein Bcl-XL and requires a cysteine residue at position 126 of Bax that is not required for activation by BH3 proteins. Our results reveal a novel pathway for Bax activation independent of pro-apoptotic BH3 proteins that may have important implications for the regulation of Bax activity in cells. PMID:26916338

  19. Small molecules reveal an alternative mechanism of Bax activation.

    PubMed

    Brahmbhatt, Hetal; Uehling, David; Al-Awar, Rima; Leber, Brian; Andrews, David

    2016-04-15

    The pro-apoptotic protein Bax commits a cell to death by permeabilizing the mitochondrial outer membrane (MOM). To obtain small-molecule probes for elucidating the molecular mechanism(s) of Bax activation, we screened for compounds that induced Bax-mediated liposome permeabilization. We identified five structurally different small molecules that promoted both Bax targeting to and oligomerization at membranes. All five compounds initiated Bax oligomerization in the absence of membranes by a mechanism unlike Bax activation by Bcl-2 homology 3 domain (BH3) proteins. Some of the compounds induced Bax/Bak-dependent apoptosis in cells. Activation of Bax by the most active compound was poorly inhibited by the anti-apoptotic protein Bcl-XL and requires a cysteine residue at position 126 of Bax that is not required for activation by BH3 proteins. Our results reveal a novel pathway for Bax activation independent of pro-apoptotic BH3 proteins that may have important implications for the regulation of Bax activity in cells. PMID:26916338

  20. Neural measures reveal a fixed item limit in subitizing

    PubMed Central

    Ester, Edward F.; Drew, Trafton; Klee, Daniel; Vogel, Edward K.; Awh, Edward

    2012-01-01

    For centuries, it has been known that humans can rapidly and accurately enumerate small sets of items, a process referred to as subitizing. However, there is still active debate regarding the mechanisms that mediate this ability. For example, some have argued that subitizing reflects the operation of a fixed-capacity individuation mechanism that enables concurrent access to a small number of items. However, others have argued that subitizing reflects the operation of a continuous numerical estimation mechanism whose precision varies with numerosity in a manner consistent with Weber's law. Critically, quantitative models based on either of these predictions can provide a reasonable description of subitizing performance, making it difficult to discriminate between these alternatives solely on the basis of subjects' behavioral performance. Here, we attempted to discriminate between fixed-capacity and continuous estimation models of subitizing using neural measures. In two experiments, we recorded EEG while subjects performed a demanding subitizing task and examined set-size dependent changes in a neurophysiological marker of visual selection (the N2pc ERP component) evoked by an array of to-be-enumerated items. In both experiments, N2pc amplitudes increased monotonically within the subitizing range before reaching an asymptotic limit at around 3 items. Moreover, inter-participant differences in the location of this asymptote were strongly predictive of behavioral estimates of subitizing span derived from a fixed-capacity model. Thus, neural activity linked with subitizing ability shows evidence of an early and discrete limit in the number of items that can be concurrently apprehended, supporting a fixed-capacity model of this process. PMID:22623661

  1. Aberrant Activity in Degenerated Retinas Revealed by Electrical Imaging

    PubMed Central

    Zeck, Günther

    2016-01-01

    In this review, I present and discuss the current understanding of aberrant electrical activity found in the ganglion cell layer (GCL) of rod-degenerated (rd) mouse retinas. The reported electrophysiological properties revealed by electrical imaging using high-density microelectrode arrays can be subdivided between spiking activity originating from retinal ganglion cells (RGCs) and local field potentials (LFPs) reflecting strong trans-membrane currents within the GCL. RGCs in rd retinas show increased and rhythmic spiking compared to age-matched wild-type retinas. Fundamental spiking frequencies range from 5 to 15 Hz in various mouse models. The rhythmic RGC spiking is driven by a presynaptic network comprising AII amacrine and bipolar cells. In the healthy retina this rhythm-generating circuit is inhibited by photoreceptor input. A unique physiological feature of rd retinas is rhythmic LFP manifested as spatially-restricted low-frequency (5–15 Hz) voltage changes. Their spatiotemporal characterization revealed propagation and correlation with RGC spiking. LFPs rely on gap-junctional coupling and are shaped by glycinergic and by GABAergic transmission. The aberrant RGC spiking and LFPs provide a simple readout of the functionality of the remaining retinal circuitry which can be used in the development of improved vision restoration strategies. PMID:26903810

  2. Sensors at Centrosomes Reveal Determinants of Local Separase Activity

    PubMed Central

    Agircan, Fikret Gurkan; Schiebel, Elmar

    2014-01-01

    Separase is best known for its function in sister chromatid separation at the metaphase-anaphase transition. It also has a role in centriole disengagement in late mitosis/G1. To gain insight into the activity of separase at centrosomes, we developed two separase activity sensors: mCherry-Scc1(142-467)-ΔNLS-eGFP-PACT and mCherry-kendrin(2059-2398)-eGFP-PACT. Both localize to the centrosomes and enabled us to monitor local separase activity at the centrosome in real time. Both centrosomal sensors were cleaved by separase before anaphase onset, earlier than the corresponding H2B-mCherry-Scc1(142-467)-eGFP sensor at chromosomes. This indicates that substrate cleavage by separase is not synchronous in the cells. Depletion of the proteins astrin or Aki1, which have been described as inhibitors of centrosomal separase, did not led to a significant activation of separase at centrosomes, emphasizing the importance of direct separase activity measurements at the centrosomes. Inhibition of polo-like kinase Plk1, on the other hand, decreased the separase activity towards the Scc1 but not the kendrin reporter. Together these findings indicate that Plk1 regulates separase activity at the level of substrate affinity at centrosomes and may explain in part the role of Plk1 in centriole disengagement. PMID:25299182

  3. Active Mars Revealed through HiRISE DTMs and Orthoimages

    NASA Astrophysics Data System (ADS)

    Mattson, Sarah; McEwen, Alfred S.; Bridges, Nathan; Byrne, Shane; Chojnacki, Matthew; Daubar, Ingrid; Dundas, Colin; Russell, Patrick

    2014-11-01

    Before the arrival of the Mars Reconnaissance Orbiter (MRO) with the High-Resolution Imaging Science Experiment (HiRISE), the amount of surface activity on Mars was not well known. HiRISE repeat imaging (often at ~30 cm/pixel), combined with the ability to take stereo images and generate high resolution Digital Terrain Models (DTMs) reveals the many types of surface processes that are currently active on Mars. Examples of active processes on Mars studied with HiRISE data include aeolian activity [Bridges et al., 2012, Nature 485; Chojnacki et al., 2014, Icarus 232], Recurring Slope Lineae (RSL) [McEwen et al., 2011, Science 333; 2014, Nature Geoscience 7], active gullies [Dundas et al., 2012, Icarus 220], polar processes [Hansen et al., 2011, Science 331; Portyankina et al. 2013, AGU], new impacts [Byrne et al., 2009, Science 325; Daubar et al., 2013, Icarus 225; Dundas et al., 2014, JGR 119], and north polar scarp avalanches [Russell et al., 2008, GRL 35, 2014, LPSC]. These studies utilize images from multiple Mars years and seasons. We generate animated gifs with sequences of orthorectified images to analyze temporal changes (see http://www.uahirise.org/sim/). HiRISE DTMs and orthoimages can be used to quantitatively map and record changes in geospatial software. More than 200 DTMs and 400 orthoimages are available through the Planetary Data System (see http://uahirise.org/dtm). Three-band color (blue-green, red, and near infrared) orthoimages are also available in many cases. The ability to monitor the surface of Mars at high spatial and temporal resolution provides insight into seasonal and annual changes, further increasing our understanding of Mars as an active planet.

  4. Measuring activity in ant colonies

    NASA Astrophysics Data System (ADS)

    Noda, C.; Fernández, J.; Pérez-Penichet, C.; Altshuler, E.

    2006-12-01

    Ants, as paradigm of social insects, have become a recurrent example of efficient problem solvers via self-organization. In spite of the simple behavior of each individual, the colony as a whole displays "swarm intelligence:" the organization of ant trails for foraging is a typical output of it. But conventional techniques of observation can hardly record the amount of data needed to get a detailed understanding of self-organization of ant swarms in the wild. Here we are presenting a measurement system intended to monitor ant activity in the field comprising massive data acquisition and high sensitivity. A central role is played by an infrared sensor devised specifically to monitor relevant parameters to the activity of ants through the exits of the nest, although other sensors detecting temperature and luminosity are added to the system. We study the characteristics of the activity sensor and its performance in the field. Finally, we present massive data measured at one exit of a nest of Atta insularis, an ant endemic to Cuba, to illustrate the potential of our system.

  5. Real-time Redox Measurements during Endoplasmic Reticulum Stress Reveal Interlinked Protein Folding Functions

    PubMed Central

    Merksamer, Philip I.; Trusina, Ala; Papa, Feroz R.

    2008-01-01

    SUMMARY Disruption of protein folding in the endoplasmic reticulum (ER) causes unfolded proteins to accumulate, triggering the unfolded protein response (UPR). UPR outputs in turn decrease ER unfolded proteins to close a negative feedback loop. However, because it is infeasible to directly measure the concentration of unfolded proteins in vivo, cells are generically described as experiencing “ER stress” whenever the UPR is active. Because ER redox potential is optimized for oxidative protein folding, we reasoned that measureable redox changes should accompany unfolded protein accumulation. To test this concept, we employed fluorescent protein reporters to dynamically measure ER redox status and UPR activity in single cells. Using these tools, we show that diverse stressors, both experimental and physiological, compromise ER protein oxidation when UPR-imposed homeostatic control is lost. Using genetic analysis we uncovered redox heterogeneities in isogenic cell populations, and revealed functional interlinks between ER protein folding, modification, and quality control systems. PMID:19026441

  6. Blood Sugar Measurement in Zebrafish Reveals Dynamics of Glucose Homeostasis

    PubMed Central

    Eames, Stefani C.; Philipson, Louis H.; Prince, Victoria E.

    2010-01-01

    Abstract The adult zebrafish has the potential to become an important model for diabetes-related research. To realize this potential, small-scale methods for analyzing pancreas function are required. The measurement of blood glucose level is a commonly used method for assessing β-cell function, but the small size of the zebrafish presents challenges both for collecting blood samples and for measuring glucose. We have developed methods for collecting microsamples of whole blood and plasma for the measurement of hematocrit and blood glucose. We demonstrate that two hand-held glucose meters designed for use by human diabetics return valid results with zebrafish blood. Additionally, we present methods for fasting and for performing postprandial glucose and intraperitoneal glucose tolerance tests. We find that the dynamics of zebrafish blood glucose homeostasis are consistent with patterns reported for other omnivorous teleost fish. PMID:20515318

  7. Cassava root membrane proteome reveals activities during storage root maturation.

    PubMed

    Naconsie, Maliwan; Lertpanyasampatha, Manassawe; Viboonjun, Unchera; Netrphan, Supatcharee; Kuwano, Masayoshi; Ogasawara, Naotake; Narangajavana, Jarunya

    2016-01-01

    Cassava (Manihot esculenta Crantz) is one of the most important crops of Thailand. Its storage roots are used as food, feed, starch production, and be the important source for biofuel and biodegradable plastic production. Despite the importance of cassava storage roots, little is known about the mechanisms involved in their formation. This present study has focused on comparison of the expression profiles of cassava root proteome at various developmental stages using two-dimensional gel electrophoresis and LC-MS/MS. Based on an anatomical study using Toluidine Blue, the secondary growth was confirmed to be essential during the development of cassava storage root. To investigate biochemical processes occurring during storage root maturation, soluble and membrane proteins were isolated from storage roots harvested from 3-, 6-, 9-, and 12-month-old cassava plants. The proteins with differential expression pattern were analysed and identified to be associated with 8 functional groups: protein folding and degradation, energy, metabolism, secondary metabolism, stress response, transport facilitation, cytoskeleton, and unclassified function. The expression profiling of membrane proteins revealed the proteins involved in protein folding and degradation, energy, and cell structure were highly expressed during early stages of development. Integration of these data along with the information available in genome and transcriptome databases is critical to expand knowledge obtained solely from the field of proteomics. Possible role of identified proteins were discussed in relation with the activities during storage root maturation in cassava. PMID:26547558

  8. Mars Exospheric Temperature Trends as Revealed by MAVEN NGIMS Measurements

    NASA Astrophysics Data System (ADS)

    Bougher, Stephen W.; Olsen, Kirk; Roeten, Kali; Bell, Jared; Mahaffy, Paul; Benna, Mehdi; Elrod, Meredith; Jakosky, Bruce

    2015-11-01

    The Martian dayside upper thermosphere and exosphere temperatures (Texo) have been the subject of considerable debate and study since the first Mariner ultraviolet spectrometer (UVS) measurements (1969-1972), up to recent Mars Express SPICAM UVS measurements (2004-present) (e.g., see reviews by Stewart 1987; Bougher et al. 2000, 2014; Müeller-Wodarg et al. 2008; Stiepen et al. 2014). Prior to MAVEN, the Martian upper atmosphere thermal structure was poorly constrained by a limited number of both in-situ and remote sensing measurements at selected locations, seasons, and periods scattered throughout the solar cycle. Nevertheless, it is recognized that the Mars orbit eccentricity determines that both the solar cycle and seasonal variations in upper atmosphere temperatures must be considered together. The MAVEN NGIMS instrument measures the neutral composition of the major gas species (e.g. He, N, O, CO, N2, O2, NO, Ar and CO2) and their major isotopes, with a vertical resolution of ~5 km for targeted species and a target accuracy of <25% for most of these species (Mahaffy et al. 2014; 2015). Corresponding temperatures can now be derived from the neutral scale heights (especially CO2, Ar, and N2) (e.g. Mahaffy et al. 2015; Bougher et al. 2015). Texo mean temperatures spanning ~200 to 300 km are examined for both Deep Dip and Science orbits over 11-February 2015 (Ls ~ 290) to 14-July 2015 (Ls ~ 12). During these times, dayside sampling below 300 km occurred from the dusk terminator, across the dayside, and approaching the dawn terminator. NGIMS temperatures are investigated to extract spatial (e.g. SZA) and temporal (e.g. orbit-to-orbit, seasonal, solar rotational) variability and trends over this sampling period. Solar and seasonal driven trends in Texo are clearly visible, but orbit-to-orbit variability is significant, and demands further investigation to uncover the major drivers that are responsible.

  9. Lyin’ Eyes: Ocular-motor Measures of Reading Reveal Deception

    PubMed Central

    Cook, Anne E.; Hacker, Douglas J.; Webb, Andrea K.; Osher, Dahvyn; Kristjansson, Sean; Woltz, Dan J.; Kircher, John C.

    2013-01-01

    Our goal was to evaluate an alternative to current methods for detecting deception in security screening contexts. We evaluated a new cognitive-based test of deception that measured participants’ ocular-motor responses (pupil responses and reading behaviors) while they read and responded to statements on a computerized questionnaire. In Experiment 1, participants from a university community were randomly assigned to either a “guilty” group that committed one of two mock crimes or an “innocent” group that only learned about the crime. Participants then reported for testing, where they completed the computer-administered questionnaire that addressed their possible involvement in the crimes. Experiment 2 also manipulated participants’ incentive to pass the test and difficulty of statements on the test. In both experiments, guilty participants had increased pupil responses to statements answered deceptively; however, they spent less time fixating on, reading, and re-reading those statements than statements answered truthfully. These ocular-motor measures were optimally weighted in a discrimination function that correctly classified 85% of participants as either guilty or innocent. Findings from Experiment 2 indicated that group discrimination was improved with greater incentives to pass the test and the use of statements with simple syntax. The present findings suggest that two cognitive processes are involved in deception -- vigilance and strategy -- and that these processes are reflected in different ocular-motor measures. The ocular-motor test reported here represents a new approach to detecting deception that may fill an important need in security screening contexts. PMID:22545928

  10. Partial radiogenic heat model for Earth revealed by geoneutrino measurements

    NASA Astrophysics Data System (ADS)

    Kamland Collaboration; Gando, A.; Gando, Y.; Ichimura, K.; Ikeda, H.; Inoue, K.; Kibe, Y.; Kishimoto, Y.; Koga, M.; Minekawa, Y.; Mitsui, T.; Morikawa, T.; Nagai, N.; Nakajima, K.; Nakamura, K.; Narita, K.; Shimizu, I.; Shimizu, Y.; Shirai, J.; Suekane, F.; Suzuki, A.; Takahashi, H.; Takahashi, N.; Takemoto, Y.; Tamae, K.; Watanabe, H.; Xu, B. D.; Yabumoto, H.; Yoshida, H.; Yoshida, S.; Enomoto, S.; Kozlov, A.; Murayama, H.; Grant, C.; Keefer, G.; Piepke, A.; Banks, T. I.; Bloxham, T.; Detwiler, J. A.; Freedman, S. J.; Fujikawa, B. K.; Han, K.; Kadel, R.; O'Donnell, T.; Steiner, H. M.; Dwyer, D. A.; McKeown, R. D.; Zhang, C.; Berger, B. E.; Lane, C. E.; Maricic, J.; Miletic, T.; Batygov, M.; Learned, J. G.; Matsuno, S.; Sakai, M.; Horton-Smith, G. A.; Downum, K. E.; Gratta, G.; Tolich, K.; Efremenko, Y.; Perevozchikov, O.; Karwowski, H. J.; Markoff, D. M.; Tornow, W.; Heeger, K. M.; Decowski, M. P.

    2011-09-01

    The Earth has cooled since its formation, yet the decay of radiogenic isotopes, and in particular uranium, thorium and potassium, in the planet's interior provides a continuing heat source. The current total heat flux from the Earth to space is 44.2+/-1.0TW, but the relative contributions from residual primordial heat and radiogenic decay remain uncertain. However, radiogenic decay can be estimated from the flux of geoneutrinos, electrically neutral particles that are emitted during radioactive decay and can pass through the Earth virtually unaffected. Here we combine precise measurements of the geoneutrino flux from the Kamioka Liquid-Scintillator Antineutrino Detector, Japan, with existing measurements from the Borexino detector, Italy. We find that decay of uranium-238 and thorium-232 together contribute TW to Earth's heat flux. The neutrinos emitted from the decay of potassium-40 are below the limits of detection in our experiments, but are known to contribute 4TW. Taken together, our observations indicate that heat from radioactive decay contributes about half of Earth's total heat flux. We therefore conclude that Earth's primordial heat supply has not yet been exhausted.

  11. Single cell activity reveals direct electron transfer in methanotrophic consortia.

    PubMed

    McGlynn, Shawn E; Chadwick, Grayson L; Kempes, Christopher P; Orphan, Victoria J

    2015-10-22

    Multicellular assemblages of microorganisms are ubiquitous in nature, and the proximity afforded by aggregation is thought to permit intercellular metabolic coupling that can accommodate otherwise unfavourable reactions. Consortia of methane-oxidizing archaea and sulphate-reducing bacteria are a well-known environmental example of microbial co-aggregation; however, the coupling mechanisms between these paired organisms is not well understood, despite the attention given them because of the global significance of anaerobic methane oxidation. Here we examined the influence of interspecies spatial positioning as it relates to biosynthetic activity within structurally diverse uncultured methane-oxidizing consortia by measuring stable isotope incorporation for individual archaeal and bacterial cells to constrain their potential metabolic interactions. In contrast to conventional models of syntrophy based on the passage of molecular intermediates, cellular activities were found to be independent of both species intermixing and distance between syntrophic partners within consortia. A generalized model of electric conductivity between co-associated archaea and bacteria best fit the empirical data. Combined with the detection of large multi-haem cytochromes in the genomes of methanotrophic archaea and the demonstration of redox-dependent staining of the matrix between cells in consortia, these results provide evidence for syntrophic coupling through direct electron transfer. PMID:26375009

  12. Single cell activity reveals direct electron transfer in methanotrophic consortia

    NASA Astrophysics Data System (ADS)

    McGlynn, Shawn E.; Chadwick, Grayson L.; Kempes, Christopher P.; Orphan, Victoria J.

    2015-10-01

    Multicellular assemblages of microorganisms are ubiquitous in nature, and the proximity afforded by aggregation is thought to permit intercellular metabolic coupling that can accommodate otherwise unfavourable reactions. Consortia of methane-oxidizing archaea and sulphate-reducing bacteria are a well-known environmental example of microbial co-aggregation; however, the coupling mechanisms between these paired organisms is not well understood, despite the attention given them because of the global significance of anaerobic methane oxidation. Here we examined the influence of interspecies spatial positioning as it relates to biosynthetic activity within structurally diverse uncultured methane-oxidizing consortia by measuring stable isotope incorporation for individual archaeal and bacterial cells to constrain their potential metabolic interactions. In contrast to conventional models of syntrophy based on the passage of molecular intermediates, cellular activities were found to be independent of both species intermixing and distance between syntrophic partners within consortia. A generalized model of electric conductivity between co-associated archaea and bacteria best fit the empirical data. Combined with the detection of large multi-haem cytochromes in the genomes of methanotrophic archaea and the demonstration of redox-dependent staining of the matrix between cells in consortia, these results provide evidence for syntrophic coupling through direct electron transfer.

  13. Energy Landscape Topography Reveals the Underlying Link Between Binding Specificity and Activity of Enzymes.

    PubMed

    Chu, Wen-Ting; Wang, Jin

    2016-01-01

    Enzyme activity (often quantified by kcat/Km) is the main function of enzyme when it is active against the specific substrate. Higher or lower activities are highly desired for the design of novel enzyme and drug resistance. However, it is difficult to measure the activities of all possible variants and find the "hot-spot" within the limit of experimental time. In this study, we explore the underlying energy landscape of enzyme-substrate interactions and introduce the intrinsic specificity ratio (ISR), which reflects the landscape topography. By studying two concrete systems, we uncover the statistical correlation between the intrinsic specificity and the enzyme activity kcat/Km. This physics-based concept and method show that the energy landscape topography is valuable for understanding the relationship between enzyme specificity and activity. In addition, it can reveal the underlying mechanism of enzyme-substrate actions and has potential applications on enzyme design. PMID:27298067

  14. Energy Landscape Topography Reveals the Underlying Link Between Binding Specificity and Activity of Enzymes

    PubMed Central

    Chu, Wen-Ting; Wang, Jin

    2016-01-01

    Enzyme activity (often quantified by kcat/Km) is the main function of enzyme when it is active against the specific substrate. Higher or lower activities are highly desired for the design of novel enzyme and drug resistance. However, it is difficult to measure the activities of all possible variants and find the “hot-spot” within the limit of experimental time. In this study, we explore the underlying energy landscape of enzyme-substrate interactions and introduce the intrinsic specificity ratio (ISR), which reflects the landscape topography. By studying two concrete systems, we uncover the statistical correlation between the intrinsic specificity and the enzyme activity kcat/Km. This physics-based concept and method show that the energy landscape topography is valuable for understanding the relationship between enzyme specificity and activity. In addition, it can reveal the underlying mechanism of enzyme-substrate actions and has potential applications on enzyme design. PMID:27298067

  15. Energy Landscape Topography Reveals the Underlying Link Between Binding Specificity and Activity of Enzymes

    NASA Astrophysics Data System (ADS)

    Chu, Wen-Ting; Wang, Jin

    2016-06-01

    Enzyme activity (often quantified by kcat/Km) is the main function of enzyme when it is active against the specific substrate. Higher or lower activities are highly desired for the design of novel enzyme and drug resistance. However, it is difficult to measure the activities of all possible variants and find the “hot-spot” within the limit of experimental time. In this study, we explore the underlying energy landscape of enzyme-substrate interactions and introduce the intrinsic specificity ratio (ISR), which reflects the landscape topography. By studying two concrete systems, we uncover the statistical correlation between the intrinsic specificity and the enzyme activity kcat/Km. This physics-based concept and method show that the energy landscape topography is valuable for understanding the relationship between enzyme specificity and activity. In addition, it can reveal the underlying mechanism of enzyme-substrate actions and has potential applications on enzyme design.

  16. Multiscale comparative spectral analysis of satellite total solar irradiance measurements from 2003 to 2013 reveals a planetary modulation of solar activity and its nonlinear dependence on the 11 yr solar cycle

    NASA Astrophysics Data System (ADS)

    Scafetta, N.; Willson, R. C.

    2013-11-01

    Herein we adopt a multiscale dynamical spectral analysis technique to compare and study the dynamical evolution of the harmonic components of the overlapping ACRIMSAT/ACRIM3 (Active Cavity Radiometer Irradiance Monitor Satellite/Active Cavity Radiometer Irradiance Monitor 3), SOHO/VIRGO (Solar and Heliopheric Observatory/Variability of solar Irradiance and Gravity Oscillations), and SORCE/TIM (Solar Radiation and Climate Experiment/Total Irradiance Monitor) total solar irradiance (TSI) records during 2003.15 to 2013.16 in solar cycles 23 and 24. The three TSI time series present highly correlated patterns. Significant power spectral peaks are common to these records and are observed at the following periods: ~ 0.070 yr, ~ 0.097 yr, ~ 0.20 yr, ~ 0.25 yr, ~ 0.30-0.34 yr, and ~ 0.39 yr. Less certain spectral peaks occur at about 0.55 yr, 0.60-0.65 yr and 0.7-0.9 yr. Four main frequency periods at ~ 4.8 days (~ 0.068 yr), ~ 27.3 days (~ 0.075 yr), at ~ 34-35 days (~ 0.093-0.096 yr), and ~ 36-38 days (~ 0.099-0.104 yr) characterize the solar rotation cycle. The amplitude of these oscillations, in particular of those with periods larger than 0.5 yr, appears to be modulated by the ~ 11 yr solar cycle. Similar harmonics have been found in other solar indices. The observed periodicities are found highly coherent with the spring, orbital and synodic periods of Mercury, Venus, Earth and Jupiter. We conclude that solar activity is likely modulated by planetary gravitational and electromagnetic forces acting on the Sun. The strength of the Sun's response to planetary forcing depends nonlinearly on the state of internal solar dynamics; planetary-Sun coupling effects are enhanced during solar activity maxima and attenuated during minima.

  17. Activities on Facebook Reveal the Depressive State of Users

    PubMed Central

    Kwak, Jinah

    2013-01-01

    Background As online social media have become prominent, much effort has been spent on identifying users with depressive symptoms in order to aim at early diagnosis, treatment, and even prevention by using various online social media. In this paper, we focused on Facebook to discern any correlations between the platform’s features and users’ depressive symptoms. This work may be helpful in trying to reach and detect large numbers of depressed individuals more easily. Objective Our goal was to develop a Web application and identify depressive symptom–related features from users of Facebook, a popular social networking platform. Methods 55 Facebook users (male=40, female=15, mean age 24.43, SD 3.90) were recruited through advertisement fliers distributed to students in a large university in Korea. Using EmotionDiary, the Facebook application we developed, we evaluated depressive symptoms using the Center for Epidemiological Studies-Depression (CES-D) scale. We also provided tips and facts about depression to participants and measured their responses using EmotionDiary. To identify the Facebook features related to depression, correlation analyses were performed between CES-D and participants’ responses to tips and facts or Facebook social features. Last, we interviewed depressed participants (CES-D≥25) to assess their depressive symptoms by a psychiatrist. Results Facebook activities had predictive power in distinguishing depressed and nondepressed individuals. Participants’ response to tips and facts, which can be explained by the number of app tips viewed and app points, had a positive correlation (P=.04 for both cases), whereas the number of friends and location tags had a negative correlation with the CES-D scale (P=.08 and P=.045 respectively). Furthermore, in finding group differences in Facebook social activities, app tips viewed and app points resulted in significant differences (P=.01 and P=.03 respectively) between probably depressed and

  18. Disease Activity Measures in Paediatric Rheumatic Diseases

    PubMed Central

    Luca, Nadia J.; Feldman, Brian M.

    2013-01-01

    Disease activity refers to potentially reversible aspects of a disease. Measurement of disease activity in paediatric rheumatic diseases is a critical component of patient care and clinical research. Disease activity measures are developed systematically, often involving consensus methods. To be useful, a disease activity measure must be feasible, valid, and interpretable. There are several challenges in quantifying disease activity in paediatric rheumatology; namely, the conditions are multidimensional, the level of activity must be valuated in the context of treatment being received, there is no gold standard for disease activity, and it is often difficult to incorporate the patient's perspective of their disease activity. To date, core sets of response variables are defined for juvenile idiopathic arthritis, juvenile systemic lupus erythematosus, and juvenile dermatomyositis, as well as definitions for improvement in response to therapy. Several specific absolute disease activity measures also exist for each condition. Further work is required to determine the optimal disease activity measures in paediatric rheumatology. PMID:24089617

  19. Structure-Based Simulations Reveal Concerted Dynamics of GPCR Activation

    PubMed Central

    Leioatts, Nicholas; Suresh, Pooja; Romo, Tod D.; Grossfield, Alan

    2014-01-01

    G protein-coupled receptors (GPCRs) are a vital class of proteins that transduce biological signals across the cell membrane. However, their allosteric activation mechanism is not fully understood; crystal structures of active and inactive receptors have been reported, but the functional pathway between these two states remains elusive. Here, we employ structure-based (Gō-like) models to simulate activation of two GPCRs, rhodopsin and the β2 adrenergic receptor (β2AR). We used data-derived reaction coordinates that capture the activation mechanism for both proteins, showing that activation proceeds through quantitatively different paths in the two systems. Both reaction coordinates are determined from the dominant concerted motions in the simulations so the technique is broadly applicable. There were two surprising results. First, the main structural changes in the simulations were distributed throughout the transmembrane bundle, and not localized to the obvious areas of interest, such as the intracellular portion of helix 6. Second, the activation (and deactivation) paths were distinctly non-monotonic, populating states that were not simply interpolations between the inactive and active structures. These transitions also suggest a functional explanation for β2AR’s basal activity: it can proceed through a more broadly defined path during the observed transitions. PMID:24889093

  20. Recombinant Human Peptidoglycan Recognition Proteins Reveal Antichlamydial Activity.

    PubMed

    Bobrovsky, Pavel; Manuvera, Valentin; Polina, Nadezhda; Podgorny, Oleg; Prusakov, Kirill; Govorun, Vadim; Lazarev, Vassili

    2016-07-01

    Peptidoglycan recognition proteins (PGLYRPs) are innate immune components that recognize the peptidoglycan and lipopolysaccharides of bacteria and exhibit antibacterial activity. Recently, the obligate intracellular parasite Chlamydia trachomatis was shown to have peptidoglycan. However, the antichlamydial activity of PGLYRPs has not yet been demonstrated. The aim of our study was to test whether PGLYRPs exhibit antibacterial activity against C. trachomatis Thus, we cloned the regions containing the human Pglyrp1, Pglyrp2, Pglyrp3, and Pglyrp4 genes for subsequent expression in human cell lines. We obtained stable HeLa cell lines that secrete recombinant human PGLYRPs into culture medium. We also generated purified recombinant PGLYRP1, -2, and -4 and confirmed their activities against Gram-positive (Bacillus subtilis) and Gram-negative (Escherichia coli) bacteria. Furthermore, we examined the activities of recombinant PGLYRPs against C. trachomatis and determined their MICs. We also observed a decrease in the infectious ability of chlamydial elementary bodies in the next generation after a single exposure to PGLYRPs. Finally, we demonstrated that PGLYRPs attach to C. trachomatis elementary bodies and activate the expression of the chlamydial two-component stress response system. Thus, PGLYRPs inhibit the development of chlamydial infection. PMID:27160295

  1. Activation energy measurements of cheese

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Temperature sweeps of cheeses using small amplitude oscillatory shear tests produced values for activation energy of flow (Ea) between 30 and 44 deg C. Soft goat cheese and Queso Fresco, which are high-moisture cheeses and do not flow when heated, exhibited Ea values between 30 and 60 kJ/mol. The ...

  2. Enceladus's activity as revealed by Cassini-Huygens

    NASA Astrophysics Data System (ADS)

    Schmidt, Juergen

    2015-08-01

    The activity of Enceladus has been monitored by Cassini for nearly one decade after its discovery (see Science, 2006, 311, special issue). Thus, crucial properties of the vapor and dust plumes, heat output, surface properties, and the gravity field of the satellite are constrained in a fairly detailed manner. In this paper I review key observational facts and discuss implications for the vent geometries as well as interior structure and composition. Special emphasize I will give to data recorded by the Cassini Cosmic Dust Analyzer, and the conclusions drawn from it, concerning the number, size, and composition of grains ejected by the plumes associated with the south polar activity.

  3. Sleeping Beauty screen reveals Pparg activation in metastatic prostate cancer.

    PubMed

    Ahmad, Imran; Mui, Ernest; Galbraith, Laura; Patel, Rachana; Tan, Ee Hong; Salji, Mark; Rust, Alistair G; Repiscak, Peter; Hedley, Ann; Markert, Elke; Loveridge, Carolyn; van der Weyden, Louise; Edwards, Joanne; Sansom, Owen J; Adams, David J; Leung, Hing Y

    2016-07-19

    Prostate cancer (CaP) is the most common adult male cancer in the developed world. The paucity of biomarkers to predict prostate tumor biology makes it important to identify key pathways that confer poor prognosis and guide potential targeted therapy. Using a murine forward mutagenesis screen in a Pten-null background, we identified peroxisome proliferator-activated receptor gamma (Pparg), encoding a ligand-activated transcription factor, as a promoter of metastatic CaP through activation of lipid signaling pathways, including up-regulation of lipid synthesis enzymes [fatty acid synthase (FASN), acetyl-CoA carboxylase (ACC), ATP citrate lyase (ACLY)]. Importantly, inhibition of PPARG suppressed tumor growth in vivo, with down-regulation of the lipid synthesis program. We show that elevated levels of PPARG strongly correlate with elevation of FASN in human CaP and that high levels of PPARG/FASN and PI3K/pAKT pathway activation confer a poor prognosis. These data suggest that CaP patients could be stratified in terms of PPARG/FASN and PTEN levels to identify patients with aggressive CaP who may respond favorably to PPARG/FASN inhibition. PMID:27357679

  4. Sleeping Beauty screen reveals Pparg activation in metastatic prostate cancer

    PubMed Central

    Ahmad, Imran; Mui, Ernest; Galbraith, Laura; Patel, Rachana; Tan, Ee Hong; Salji, Mark; Rust, Alistair G.; Repiscak, Peter; Hedley, Ann; Markert, Elke; Loveridge, Carolyn; van der Weyden, Louise; Edwards, Joanne; Sansom, Owen J.; Adams, David J.; Leung, Hing Y.

    2016-01-01

    Prostate cancer (CaP) is the most common adult male cancer in the developed world. The paucity of biomarkers to predict prostate tumor biology makes it important to identify key pathways that confer poor prognosis and guide potential targeted therapy. Using a murine forward mutagenesis screen in a Pten-null background, we identified peroxisome proliferator-activated receptor gamma (Pparg), encoding a ligand-activated transcription factor, as a promoter of metastatic CaP through activation of lipid signaling pathways, including up-regulation of lipid synthesis enzymes [fatty acid synthase (FASN), acetyl-CoA carboxylase (ACC), ATP citrate lyase (ACLY)]. Importantly, inhibition of PPARG suppressed tumor growth in vivo, with down-regulation of the lipid synthesis program. We show that elevated levels of PPARG strongly correlate with elevation of FASN in human CaP and that high levels of PPARG/FASN and PI3K/pAKT pathway activation confer a poor prognosis. These data suggest that CaP patients could be stratified in terms of PPARG/FASN and PTEN levels to identify patients with aggressive CaP who may respond favorably to PPARG/FASN inhibition. PMID:27357679

  5. Revealing Student Blogging Activities Using RSS Feeds and LMS Logs

    ERIC Educational Resources Information Center

    Derntl, Michael

    2010-01-01

    Blogs are an easy-to-use, free alternative to classic means of computer-mediated communication. Moreover, they are authentically aligned with web activity patterns of today's students. The body of studies on integrating and implementing blogs in various educational settings has grown rapidly recently; however, it is often difficult to distill…

  6. Metaproteomic analysis reveals microbial metabolic activities in the deep ocean

    NASA Astrophysics Data System (ADS)

    Wang, Da-Zhi; Xie, Zhang-Xian; Zhang, Shu-Feng; Wang, Ming-Hua; Zhang, Hao; Kong, Ling-Fen; Lin, Lin

    2016-04-01

    The deep sea is the largest habitat on earth and holds many and varied microbial life forms. However, little is known about their metabolic activities in the deep ocean. Here, we characterized protein profiles of particulate (>0.22 μm) and dissolved (between 10 kDa and 0.22 μm) fractions collected from the deep South China Sea using a shotgun proteomic approach. SAR324, Alteromonadales and SAR11 were the most abundant groups, while Prasinophyte contributed most to eukaryotes and cyanophage to viruses. The dominant heterotrophic activity was evidenced by the abundant transporters (33%). Proteins participating in nitrification, methanogenesis, methyltrophy and CO2 fixation were detected. Notably, the predominance of unique cellular proteins in dissolved fraction suggested the presence of membrane structures. Moreover, the detection of translation proteins related to phytoplankton indicated that other process rather than sinking particles might be the downward export of living cells. Our study implied that novel extracellular activities and the interaction of deep water with its overlying water could be crucial to the microbial world of deep sea.

  7. Metatranscriptomics reveals overall active bacterial composition in caries lesions

    PubMed Central

    Simón-Soro, Aurea; Guillen-Navarro, Miriam; Mira, Alex

    2014-01-01

    Background Identifying the microbial species in caries lesions is instrumental to determine the etiology of dental caries. However, a significant proportion of bacteria in carious lesions have not been cultured, and the use of molecular methods has been limited to DNA-based approaches, which detect both active and inactive or dead microorganisms. Objective To identify the RNA-based, metabolically active bacterial composition of caries lesions at different stages of disease progression in order to provide a list of potential etiological agents of tooth decay. Design Non-cavitated enamel caries lesions (n=15) and dentin caries lesions samples (n=12) were collected from 13 individuals. RNA was extracted and cDNA was constructed, which was used to amplify the 16S rRNA gene. The resulting 780 bp polymerase chain reaction products were pyrosequenced using Titanium-plus chemistry, and the sequences obtained were used to determine the bacterial composition. Results A mean of 4,900 sequences of the 16S rRNA gene with an average read length of 661 bp was obtained per sample, giving a comprehensive view of the active bacterial communities in caries lesions. Estimates of bacterial diversity indicate that the microbiota of cavities is highly complex, each sample containing between 70 and 400 metabolically active species. The composition of these bacterial consortia varied among individuals and between caries lesions of the same individuals. In addition, enamel and dentin lesions had a different bacterial makeup. Lactobacilli were found almost exclusively in dentin cavities. Streptococci accounted for 40% of the total active community in enamel caries, and 20% in dentin caries. However, Streptococcus mutans represented only 0.02–0.73% of the total bacterial community. Conclusions The data indicate that the etiology of dental caries is tissue dependent and that the disease has a clear polymicrobial origin. The low proportion of mutans streptococci detected confirms that they

  8. Youth Physical Activity Resources Use and Activity Measured by Accelerometry

    PubMed Central

    Maslow, Andréa L.; Colabianchi, Natalie

    2014-01-01

    Objectives To examine whether utilization of physical activity resources (eg, parks) was associated with daily physical activity measured by accelerometry. Methods 111 adolescents completed a travel diary with concurrent accelerometry. The main exposure was self-reported utilization of a physical activity resource (none/1+ resources). The main outcomes were total minutes spent in daily 1) moderate-vigorous physical activity and 2) vigorous physical activity. Results Utilizing a physical activity resource was significantly associated with total minutes in moderate-vigorous physical activity. African-Americans and males had significantly greater moderate-vigorous physical activity. Conclusions Results from this study support the development and use of physical activity resources. PMID:21204684

  9. Oscillatory brain activity reveals linguistic prints in the quantity code.

    PubMed

    Salillas, Elena; Barraza, Paulo; Carreiras, Manuel

    2015-01-01

    Number representations change through education, although it is currently unclear whether and how language could impact the magnitude representation that we share with other species. The most prominent view is that language does not play any role in modulating the core numeric representation involved in the contrast of quantities. Nevertheless, possible cultural hints on the numerical magnitude representation are currently on discussion focus. In fact, the acquisition of number words provides linguistic input that the quantity system may not ignore. Bilingualism offers a window to the study of this question, especially in bilinguals where the two number wording systems imply also two different numerical systems, such as in Basque-Spanish bilinguals. The present study evidences linguistic prints in the core number representational system through the analysis of EEG oscillatory activity during a simple number comparison task. Gamma band synchronization appears when Basque-Spanish bilinguals compare pairs of Arabic numbers linked through the Basque base-20 wording system, but it does not if the pairs are related through the base-10 system. Crucially, this gamma activity, originated in a left fronto-parietal network, only appears in bilinguals who learned math in Basque and not in equivalent proficiency bilinguals who learned math in Spanish. Thus, this neural index reflected in gamma band synchrony appears to be triggered by early learning experience with the base-20 numerical associations in Basque number words. PMID:25875210

  10. Autotaxin Structure Activity Relationships Revealed through Lysophosphatidylcholine Analogs

    PubMed Central

    North, E. Jeffrey; Osborne, Daniel A.; Bridson, Peter K.; Baker, Daniel L.; Parrill, Abby L.

    2009-01-01

    Autotaxin (ATX) catalyzes the hydrolysis of lysophosphatidylcholine (LPC) to form the bioactive lipid lysophosphatidic acid (LPA). LPA stimulates cell proliferation, cell survival, and cell migration and is involved in obesity, rheumatoid arthritis, neuropathic pain, atherosclerosis and various cancers, suggesting that ATX inhibitors have broad therapeutic potential. Product feedback inhibition of ATX by LPA has stimulated structure activity studies focused on LPA analogs. However, LPA displays mixed mode inhibition, indicating it can bind to both the enzyme and the enzyme-substrate complex. This suggests that LPA may not interact solely with the catalytic site. In this report we have prepared LPC analogs to help map out substrate structure activity relationships. The structural variances include length and unsaturation of the fatty tail, choline and polar linker presence, acyl versus ether linkage of the hydrocarbon chain, and methylene and nitrogen replacement of the choline oxygen. All LPC analogs were assayed in competition with the synthetic substrate, FS-3, to show the preference ATX has for each alteration. Choline presence and methylene replacement of the choline oxygen were detrimental to ATX recognition. These findings provide insights into the structure of the enzyme in the vicinity of the catalytic site as well as suggesting that ATX produces rate enhancement, at least in part, by substrate destabilization. PMID:19345587

  11. Oscillatory Brain Activity Reveals Linguistic Prints in the Quantity Code

    PubMed Central

    Salillas, Elena; Barraza, Paulo; Carreiras, Manuel

    2015-01-01

    Number representations change through education, although it is currently unclear whether and how language could impact the magnitude representation that we share with other species. The most prominent view is that language does not play any role in modulating the core numeric representation involved in the contrast of quantities. Nevertheless, possible cultural hints on the numerical magnitude representation are currently on discussion focus. In fact, the acquisition of number words provides linguistic input that the quantity system may not ignore. Bilingualism offers a window to the study of this question, especially in bilinguals where the two number wording systems imply also two different numerical systems, such as in Basque-Spanish bilinguals. The present study evidences linguistic prints in the core number representational system through the analysis of EEG oscillatory activity during a simple number comparison task. Gamma band synchronization appears when Basque-Spanish bilinguals compare pairs of Arabic numbers linked through the Basque base-20 wording system, but it does not if the pairs are related through the base-10 system. Crucially, this gamma activity, originated in a left fronto-parietal network, only appears in bilinguals who learned math in Basque and not in equivalent proficiency bilinguals who learned math in Spanish. Thus, this neural index reflected in gamma band synchrony appears to be triggered by early learning experience with the base-20 numerical associations in Basque number words. PMID:25875210

  12. Metatranscriptomic Analysis of Groundwater Reveals an Active Anammox Bacterial Population

    NASA Astrophysics Data System (ADS)

    Jewell, T. N. M.; Karaoz, U.; Thomas, B. C.; Banfield, J. F.; Brodie, E.; Williams, K. H.; Beller, H. R.

    2014-12-01

    Groundwater is a major natural resource, yet little is known about the contribution of microbial anaerobic ammonium oxidation (anammox) activity to subsurface nitrogen cycling. During anammox, energy is generated as ammonium is oxidized under anaerobic conditions to dinitrogen gas, using nitrite as the final electron acceptor. This process is a global sink for fixed nitrogen. Only a narrow range of monophyletic bacteria within the Planctomycetes carries out anammox, and the full extent of their metabolism, and subsequent impact on nitrogen cycling and microbial community structure, is still unknown. Here, we employ a metatranscriptomic analysis on enriched mRNA to identify the abundance and activity of a population of anammox bacteria within an aquifer at Rifle, CO. Planktonic biomass was collected over a two-month period after injection of up to 1.5 mM nitrate. Illumina-generated sequences were mapped to a phylogenetically binned Rifle metagenome database. We identified transcripts for genes with high protein sequence identities (81-98%) to those of anammox strain KSU-1 and to two of the five anammox bacteria genera, Brocadia and Kuenenia, suggesting an active, if not diverse, anammox population. Many of the most abundant anammox transcripts mapped to a single scaffold, indicative of a single dominant anammox species. Transcripts of the genes necessary for the anammox pathway were present, including an ammonium transporter (amtB), nitrite/formate transporter, nitrite reductase (nirK), and hydrazine oxidoreductase (hzoB). The form of nitrite reductase encoded by anammox is species-dependent, and we only identified nirK, with no evidence of anammox nirS. In addition to the anammox pathway we saw evidence of the anammox bacterial dissimilatory nitrate reduction to ammonium pathway (narH, putative nrfA, and nrfB), which provides an alternate means of generating substrates for anammox from nitrate, rather than relying on an external pool. Transcripts for hydroxylamine

  13. Hidden Stages of Cognition Revealed in Patterns of Brain Activation.

    PubMed

    Anderson, John R; Pyke, Aryn A; Fincham, Jon M

    2016-09-01

    To advance cognitive theory, researchers must be able to parse the performance of a task into its significant mental stages. In this article, we describe a new method that uses functional MRI brain activation to identify when participants are engaged in different cognitive stages on individual trials. The method combines multivoxel pattern analysis to identify cognitive stages and hidden semi-Markov models to identify their durations. This method, applied to a problem-solving task, identified four distinct stages: encoding, planning, solving, and responding. We examined whether these stages corresponded to their ascribed functions by testing whether they are affected by appropriate factors. Planning-stage duration increased as the method for solving the problem became less obvious, whereas solving-stage duration increased as the number of calculations to produce the answer increased. Responding-stage duration increased with the difficulty of the motor actions required to produce the answer. PMID:27440808

  14. 19th century auroral observations reveal solar activity patterns

    NASA Astrophysics Data System (ADS)

    Silverman, Sam

    Growing interest in the aurora in the early part of the eighteenth century, which resulted from the spectacular reappearance of the aurora in 1707 and 1716, followed a relative scarcity of great auroras during the Maunder minimum, a period of prolonged reduced solar activity from about 1645-1715. Observations in the early eighteenth century led to questions about the geographical extent, nature, and temporal variability of the auroras. Typically, such observations were included as part of recorded meteorological notations, though occasionally early astronomers, such as Tycho Brahe in the 1590s, included auroras in their observations. Meteorological observations were important because of the effects of weather and climate on agriculture, and, according to the belief at the time, on disease.

  15. Metallic Magnetic Calorimeters for Absolute Activity Measurement

    NASA Astrophysics Data System (ADS)

    Loidl, M.; Leblanc, E.; Rodrigues, M.; Bouchard, J.; Censier, B.; Branger, T.; Lacour, D.

    2008-05-01

    We present a prototype of metallic magnetic calorimeters that we are developing for absolute activity measurements of low energy emitting radionuclides. We give a detailed description of the realization of the prototype, containing an 55Fe source inside the detector absorber. We present the analysis of first data taken with this detector and compare the result of activity measurement with liquid scintillation counting. We also propose some ways for reducing the uncertainty on the activity determination with this new technique.

  16. The Retrocausal Nature of Quantum Measurement Revealed by Partial and Weak Measurements

    SciTech Connect

    Elitzur, Avshalom C.; Cohen, Eliahu

    2011-11-29

    Quantum measurement is sometimes more effective when its result is not definite. Partial measurement turns the initial superposition not into a certain state but to a greater probability for it, enabling probing the quantum state in cases where complete measurement makes the noncommuting variables inaccessible. It also enables full quantum erasure that, unlike prevailing method, can be carried out even on recorded results. Aharonov's weak measurement is another method of imprecisely measuring quantum variables, outsmarting the uncertainty principle in even subtler ways. Happily, the two methods complement and corroborate one another in several interesting ways. We gedankenly apply these measurements to the EPR case. A pair of entangled particles undergoes more than one pair of partial and weak measurements, which, unlike complete measurements, leave them partially correlated. Their erasure is then shown to be as nonlocal as measurement itself. Surprisingly, the temporal relations between such measurements in the EPR setting do not follow the temporal sequence perceived by an external observer. For each particle, the measurements performed on the other operate as if they occurred (with signs reversed) in its own past, and in reversed order. This fully accords with Cramer's transactional interpretation and Aharonov's two state-vector formalism.

  17. Youth Physical Activity Resource Use and Activity Measured by Accelerometry

    ERIC Educational Resources Information Center

    Maslow, Andra L.; Colabianchi, Natalie

    2011-01-01

    Objectives: To examine whether use of physical activity resources (e.g., parks) was associated with daily physical activity measured by accelerometry. Methods: One hundred eleven adolescents completed a travel diary with concurrent accelerometry. The main exposure was self-reported use of a physical activity resource (none /1 resources). The main…

  18. Measurement of Larval Activity in the Drosophila Activity Monitor

    PubMed Central

    McParland, Aidan L.; Follansbee, Taylor L.; Ganter, Geoffrey K.

    2016-01-01

    Drosophila larvae are used in many behavioral studies, yet a simple device for measuring basic parameters of larval activity has not been available. This protocol repurposes an instrument often used to measure adult activity, the TriKinetics Drosophila activity monitor (MB5 Multi-Beam Activity Monitor) to study larval activity. The instrument can monitor the movements of animals in 16 individual 8 cm glass assay tubes, using 17 infrared detection beams per tube. Logging software automatically saves data to a computer, recording parameters such as number of moves, times sensors were triggered, and animals’ positions within the tubes. The data can then be analyzed to represent overall locomotion and/or position preference as well as other measurements. All data are easily accessible and compatible with basic graphing and data manipulation software. This protocol will discuss how to use the apparatus, how to operate the software and how to run a larval activity assay from start to finish. PMID:25993121

  19. Measuring Homework Completion in Behavioral Activation

    ERIC Educational Resources Information Center

    Busch, Andrew M.; Uebelacker, Lisa A.; Kalibatseva, Zornitsa; Miller, Ivan W.

    2010-01-01

    The aim of this study was to develop and validate an observer-based coding system for the characterization and completion of homework assignments during Behavioral Activation (BA). Existing measures of homework completion are generally unsophisticated, and there is no current measure of homework completion designed to capture the particularities…

  20. Single-molecule spectroscopy reveals how calmodulin activates NO synthase by controlling its conformational fluctuation dynamics

    PubMed Central

    He, Yufan; Haque, Mohammad Mahfuzul; Stuehr, Dennis J.; Lu, H. Peter

    2015-01-01

    Mechanisms that regulate the nitric oxide synthase enzymes (NOS) are of interest in biology and medicine. Although NOS catalysis relies on domain motions, and is activated by calmodulin binding, the relationships are unclear. We used single-molecule fluorescence resonance energy transfer (FRET) spectroscopy to elucidate the conformational states distribution and associated conformational fluctuation dynamics of the two electron transfer domains in a FRET dye-labeled neuronal NOS reductase domain, and to understand how calmodulin affects the dynamics to regulate catalysis. We found that calmodulin alters NOS conformational behaviors in several ways: It changes the distance distribution between the NOS domains, shortens the lifetimes of the individual conformational states, and instills conformational discipline by greatly narrowing the distributions of the conformational states and fluctuation rates. This information was specifically obtainable only by single-molecule spectroscopic measurements, and reveals how calmodulin promotes catalysis by shaping the physical and temporal conformational behaviors of NOS. PMID:26311846

  1. Single-molecule spectroscopy reveals how calmodulin activates NO synthase by controlling its conformational fluctuation dynamics.

    PubMed

    He, Yufan; Haque, Mohammad Mahfuzul; Stuehr, Dennis J; Lu, H Peter

    2015-09-22

    Mechanisms that regulate the nitric oxide synthase enzymes (NOS) are of interest in biology and medicine. Although NOS catalysis relies on domain motions, and is activated by calmodulin binding, the relationships are unclear. We used single-molecule fluorescence resonance energy transfer (FRET) spectroscopy to elucidate the conformational states distribution and associated conformational fluctuation dynamics of the two electron transfer domains in a FRET dye-labeled neuronal NOS reductase domain, and to understand how calmodulin affects the dynamics to regulate catalysis. We found that calmodulin alters NOS conformational behaviors in several ways: It changes the distance distribution between the NOS domains, shortens the lifetimes of the individual conformational states, and instills conformational discipline by greatly narrowing the distributions of the conformational states and fluctuation rates. This information was specifically obtainable only by single-molecule spectroscopic measurements, and reveals how calmodulin promotes catalysis by shaping the physical and temporal conformational behaviors of NOS. PMID:26311846

  2. Detection of Telomerase Activity Using Capacitance Measurements

    NASA Astrophysics Data System (ADS)

    Kang, Bong Keun; Lee, Ri Mi; Choi, Ahmi; Jung, Hyo-Il; Yoo, Kyung-Hwa

    2007-03-01

    Telomerase activity has been found in about 85% cancer cells, while no activity observed in normal cells, so that telomerase has been proposed as a marker for cancer detection. Here, we describe electrical detection of telomerase activity using capacitance measurements. We have investigated the length dependence of capacitance on DNA solutions and found that the capacitance of DNA solutions were dependent on the DNA length. In addition, upon adding telomerase into the solution of telomeric substrate primer, the capacitance was observed to change as a function of time due to the telomeric elongation. These results suggest that this novel nanosensor may be used for rapid detection of telomerase activity.

  3. Transport into the Northern Hemisphere lowermost stratosphere revealed by in situ tracer measurements

    NASA Astrophysics Data System (ADS)

    Ray, Eric A.; Moore, Fred L.; Elkins, James W.; Dutton, Geoffrey S.; Fahey, David W.; VöMel, Holger; Oltmans, Samuel J.; Rosenlof, Karen H.

    1999-11-01

    The Lightweight Airborne Chromatograph Experiment (LACE) has made in situ measurements of several long-lived trace gases in the upper troposphere and lower to middle stratosphere as part of the Observations of the Middle Stratosphere (OMS) balloon program. The tracers measured by LACE include several photolytic species (CFC-11, CFC-12, and halon-1211) as well as SF6. LACE measurements of these long-lived tracers as well as nearly simultaneous measurements of water vapor and CO2 are used to investigate transport into the lowermost stratosphere, a region where few in situ measurements exist. The measured photolytic species and water vapor are used in a simple mass balance calculation to estimate the mixture of tropospheric and overworld (θ>380 K) air in the lowermost stratosphere. In the northern midlatitudes during September 1996, most of the air in the lowermost stratosphere sampled at the flight location (34.5°N) was transported quasi-isentropically from the troposphere. Measurements from both a May 1998 midlatitude flight and a June 1997 high-latitude flight (64.5°N) revealed the air sampled in the lowermost stratosphere to be dominated by downward advection from the overworld. Atmospheric SF6 and CO2 can uniquely reveal timescales and spatial scales of transport due to these species' large growth rates and subsequent latitudinal surface and free tropospheric gradients. Measurements in the lowermost stratosphere from the September northern midlatitude flight coupled with surface measurements of these species revealed a transport timescale of no more than 1.5 months from the surface to the lowermost stratosphere. The SF6 and CO2 mixing ratios were also consistent with mostly Northern Hemisphere tropospheric air in the lowermost stratosphere. These results point out the usefulness of high-resolution in situ measurements of long-lived tracers to help determine timescales and spatial scales of transport in the region of the upper troposphere and lowermost

  4. Dynamic Allostery of the Catabolite Activator Protein Revealed by Interatomic Forces

    PubMed Central

    Louet, Maxime; Seifert, Christian; Hensen, Ulf; Gräter, Frauke

    2015-01-01

    The Catabolite Activator Protein (CAP) is a showcase example for entropic allostery. For full activation and DNA binding, the homodimeric protein requires the binding of two cyclic AMP (cAMP) molecules in an anti-cooperative manner, the source of which appears to be largely of entropic nature according to previous experimental studies. We here study at atomic detail the allosteric regulation of CAP with Molecular dynamics (MD) simulations. We recover the experimentally observed entropic penalty for the second cAMP binding event with our recently developed force covariance entropy estimator and reveal allosteric communication pathways with Force Distribution Analyses (FDA). Our observations show that CAP binding results in characteristic changes in the interaction pathways connecting the two cAMP allosteric binding sites with each other, as well as with the DNA binding domains. We identified crucial relays in the mostly symmetric allosteric activation network, and suggest point mutants to test this mechanism. Our study suggests inter-residue forces, as opposed to coordinates, as a highly sensitive measure for structural adaptations that, even though minute, can very effectively propagate allosteric signals. PMID:26244893

  5. A chimeric prokaryotic pentameric ligand–gated channel reveals distinct pathways of activation

    PubMed Central

    Schmandt, Nicolaus; Velisetty, Phanindra; Chalamalasetti, Sreevatsa V.; Stein, Richard A.; Bonner, Ross; Talley, Lauren; Parker, Mark D.; Mchaourab, Hassane S.; Yee, Vivien C.; Lodowski, David T.

    2015-01-01

    Recent high resolution structures of several pentameric ligand–gated ion channels have provided unprecedented details of their molecular architecture. However, the conformational dynamics and structural rearrangements that underlie gating and allosteric modulation remain poorly understood. We used a combination of electrophysiology, double electron–electron resonance (DEER) spectroscopy, and x-ray crystallography to investigate activation mechanisms in a novel functional chimera with the extracellular domain (ECD) of amine-gated Erwinia chrysanthemi ligand–gated ion channel, which is activated by primary amines, and the transmembrane domain of Gloeobacter violaceus ligand–gated ion channel, which is activated by protons. We found that the chimera was independently gated by primary amines and by protons. The crystal structure of the chimera in its resting state, at pH 7.0 and in the absence of primary amines, revealed a closed-pore conformation and an ECD that is twisted with respect to the transmembrane region. Amine- and pH-induced conformational changes measured by DEER spectroscopy showed that the chimera exhibits a dual mode of gating that preserves the distinct conformational changes of the parent channels. Collectively, our findings shed light on both conserved and divergent features of gating mechanisms in this class of channels, and will facilitate the design of better allosteric modulators. PMID:26415570

  6. Dynamic Allostery of the Catabolite Activator Protein Revealed by Interatomic Forces.

    PubMed

    Louet, Maxime; Seifert, Christian; Hensen, Ulf; Gräter, Frauke

    2015-08-01

    The Catabolite Activator Protein (CAP) is a showcase example for entropic allostery. For full activation and DNA binding, the homodimeric protein requires the binding of two cyclic AMP (cAMP) molecules in an anti-cooperative manner, the source of which appears to be largely of entropic nature according to previous experimental studies. We here study at atomic detail the allosteric regulation of CAP with Molecular dynamics (MD) simulations. We recover the experimentally observed entropic penalty for the second cAMP binding event with our recently developed force covariance entropy estimator and reveal allosteric communication pathways with Force Distribution Analyses (FDA). Our observations show that CAP binding results in characteristic changes in the interaction pathways connecting the two cAMP allosteric binding sites with each other, as well as with the DNA binding domains. We identified crucial relays in the mostly symmetric allosteric activation network, and suggest point mutants to test this mechanism. Our study suggests inter-residue forces, as opposed to coordinates, as a highly sensitive measure for structural adaptations that, even though minute, can very effectively propagate allosteric signals. PMID:26244893

  7. Chlorophyll a fluorescence lifetime reveals reversible UV-induced photosynthetic activity in the green algae Tetraselmis.

    PubMed

    Kristoffersen, Arne S; Hamre, Børge; Frette, Øyvind; Erga, Svein R

    2016-04-01

    The fluorescence lifetime is a very useful parameter for investigating biological materials on the molecular level as it is mostly independent of the fluorophore concentration. The green alga Tetraselmis blooms in summer, and therefore its response to UV irradiation is of particular interest. In vivo fluorescence lifetimes of chlorophyll a were measured under both normal and UV-stressed conditions of Tetraselmis. Fluorescence was induced by two-photon excitation using a femtosecond laser and laser scanning microscope. The lifetimes were measured in the time domain by time-correlated single-photon counting. Under normal conditions, the fluorescence lifetime was 262 ps, while after 2 h of exposure to UV radiation the lifetime increased to 389 ps, indicating decreased photochemical quenching, likely caused by a damaged and down-regulated photosynthetic apparatus. This was supported by a similar increase in the lifetime to 425 ps when inhibiting photosynthesis chemically using DCMU. Furthermore, the UV-stressed sample was dark-adapted overnight, resulting in a return of the lifetime to 280 ps, revealing that the damage caused by UV radiation is repairable on a relatively short time scale. This reversal of photosynthetic activity was also confirmed by [Formula: see text] measurements. PMID:26538330

  8. Measuring the Built Environment for Physical Activity

    PubMed Central

    Brownson, Ross C.; Hoehner, Christine M.; Day, Kristen; Forsyth, Ann; Sallis, James F.

    2009-01-01

    Physical inactivity is one of the most important public health issues in the U.S. and internationally. Increasingly, links are being identified between various elements of the physical—or built—environment and physical activity. To understand the impact of the built environment on physical activity, the development of high-quality measures is essential. Three categories of built environment data are being used: (1) perceived measures obtained by telephone interview or self-administered questionnaires; (2) observational measures obtained using systematic observational methods (audits); and (3) archival data sets that are often layered and analyzed with GIS. This review provides a critical assessment of these three types of built-environment measures relevant to the study of physical activity. Among perceived measures, 19 questionnaires were reviewed, ranging in length from 7 to 68 questions. Twenty audit tools were reviewed that cover community environments (i.e., neighborhoods, cities), parks, and trails. For GIS-derived measures, more than 50 studies were reviewed. A large degree of variability was found in the operationalization of common GIS measures, which include population density, land-use mix, access to recreational facilities, and street pattern. This first comprehensive examination of built-environment measures demonstrates considerable progress over the past decade, showing diverse environmental variables available that use multiple modes of assessment. Most can be considered first-generation measures, so further development is needed. In particular, further research is needed to improve the technical quality of measures, understand the relevance to various population groups, and understand the utility of measures for science and public health. PMID:19285216

  9. Measuring Active Learning to Predict Course Quality

    ERIC Educational Resources Information Center

    Taylor, John E.; Ku, Heng-Yu

    2011-01-01

    This study investigated whether active learning within computer-based training courses can be measured and whether it serves as a predictor of learner-perceived course quality. A major corporation participated in this research, providing access to internal employee training courses, training representatives, and historical course evaluation data.…

  10. Measurements of thermospheric response to auroral activities

    NASA Technical Reports Server (NTRS)

    Okano, S.; Kim, J. S.

    1986-01-01

    The Joule heating produced by auroral electrojets and its thermospheric response can be studied by monitoring the thermospheric temperatures by optical methods; simultaneously, the concurrent auroral electrojet activities can be investigated by using geomagnetic records obtained from stations along a meridian close to the observation site of optical measurements. The measurements are reported of thermospheric response to auroral activities which were made at Albany (42.68 deg N, 73.82 deg W), New York on September 2, 1978 (UT) when an isolated substorm occured. The thermospheric temperatures were measured by using a high resolution Fabry-Perot interferometer that determines the line profiles of the (OI) 6300A line emission. The intensities and latitudinal positions of auroral electrojets were obtained by the analysis of magnetograms from the IMS Fort Churchill meridian chain stations.

  11. A new autoinhibited kinase conformation reveals a salt-bridge switch in kinase activation

    PubMed Central

    Wei, Qiang; Yang, Shaoyuan; Li, Dan; Zhang, Xiaoying; Zheng, Jimin; Jia, Zongchao

    2016-01-01

    In the structure of autoinhibited EphA2 tyrosine kinase reported herein, we have captured the entire activation segment, revealing a previously unknown role of the conserved Arg762 in kinase autoinhibition by interacting with the essential Mg2+-chelating Asp757. While it is well known that this Arg residue is involved in an electrostatic interaction with the phospho-residue of the activation loop to stabilize the active conformation, our structure determination revealed a new role for the Arg, acting as a switch between the autoinhibited and activated conformations. Mutation of Arg762 to Ala in EphA2 sensitized Mg2+ response, resulting in enhanced kinase catalytic activity and Mg2+ cooperativity. Furthermore, mutation of the corresponding Arg/Lys to Ala in PKA and p38MAPK also exhibited similar behavior. This new salt bridge-mediated switch may thus be an important mechanism of activation on a broader scope for kinases which utilize autophosphorylation. PMID:27324091

  12. Activity measurements of radon from construction materials.

    PubMed

    Fior, L; Nicolosi Corrêa, J; Paschuk, S A; Denyak, V V; Schelin, H R; Soreanu Pecequilo, B R; Kappke, J

    2012-07-01

    This work presents the results of radon concentration measurements of construction materials used in the Brazilian industry, such as clay (red) bricks and concrete blocks. The measurements focused on the detection of indoor radon activity during different construction stages and the analysis of radionuclides present in the construction materials. For this purpose, sealed chambers with internal dimensions of approximately 60×60×60 cm3 were built within a protected and isolated laboratory environment, and stable air humidity and temperature levels were maintained. These chambers were also used for radon emanation reduction tests. The chambers were built in four major stages: (1) assembly of the walls using clay (red) bricks, concrete blocks, and mortar; (2) installation of plaster; (3) finishing of wall surface using lime; and (4) insulation of wall surface and finishing using paint. Radon measurements were performed using polycarbonate etched track detectors. By comparing the three layers applied to the masonry walls, it was concluded that only the last step (wall painting using acrylic varnish) reduced the radon emanation, by a factor of approximately 2. Samples of the construction materials (clay bricks and concrete blocks) were ground, homogenized, and subjected to gamma-ray spectrometry analysis to evaluate the activity concentrations of 226Ra, 232Th and 40K. The values for the index of the activity concentration (I), radium equivalent activity (Raeq), and external hazard index (Hext) showed that these construction materials could be used without restrictions or concern about the equivalent dose limit (1 mSv/year). PMID:22280793

  13. Measuring segregation: an activity space approach

    PubMed Central

    Shaw, Shih-Lung

    2010-01-01

    While the literature clearly acknowledges that individuals may experience different levels of segregation across their various socio-geographical spaces, most measures of segregation are intended to be used in the residential space. Using spatially aggregated data to evaluate segregation in the residential space has been the norm and thus individual’s segregation experiences in other socio-geographical spaces are often de-emphasized or ignored. This paper attempts to provide a more comprehensive approach in evaluating segregation beyond the residential space. The entire activity spaces of individuals are taken into account with individuals serving as the building blocks of the analysis. The measurement principle is based upon the exposure dimension of segregation. The proposed measure reflects the exposure of individuals of a referenced group in a neighborhood to the populations of other groups that are found within the activity spaces of individuals in the referenced group. Using the travel diary data collected from the tri-county area in southeast Florida and the imputed racial–ethnic data, this paper demonstrates how the proposed segregation measurement approach goes beyond just measuring population distribution patterns in the residential space and can provide a more comprehensive evaluation of segregation by considering various socio-geographical spaces. PMID:21643546

  14. Measuring segregation: an activity space approach

    NASA Astrophysics Data System (ADS)

    Wong, David W. S.; Shaw, Shih-Lung

    2011-06-01

    While the literature clearly acknowledges that individuals may experience different levels of segregation across their various socio-geographical spaces, most measures of segregation are intended to be used in the residential space. Using spatially aggregated data to evaluate segregation in the residential space has been the norm and thus individual's segregation experiences in other socio-geographical spaces are often de-emphasized or ignored. This paper attempts to provide a more comprehensive approach in evaluating segregation beyond the residential space. The entire activity spaces of individuals are taken into account with individuals serving as the building blocks of the analysis. The measurement principle is based upon the exposure dimension of segregation. The proposed measure reflects the exposure of individuals of a referenced group in a neighborhood to the populations of other groups that are found within the activity spaces of individuals in the referenced group. Using the travel diary data collected from the tri-county area in southeast Florida and the imputed racial-ethnic data, this paper demonstrates how the proposed segregation measurement approach goes beyond just measuring population distribution patterns in the residential space and can provide a more comprehensive evaluation of segregation by considering various socio-geographical spaces.

  15. Angiogenesis Interactome and Time Course Microarray Data Reveal the Distinct Activation Patterns in Endothelial Cells

    PubMed Central

    Chu, Liang-Hui; Lee, Esak; Bader, Joel S.; Popel, Aleksander S.

    2014-01-01

    Angiogenesis involves stimulation of endothelial cells (EC) by various cytokines and growth factors, but the signaling mechanisms are not completely understood. Combining dynamic gene expression time-course data for stimulated EC with protein-protein interactions associated with angiogenesis (the “angiome”) could reveal how different stimuli result in different patterns of network activation and could implicate signaling intermediates as points for control or intervention. We constructed the protein-protein interaction networks of positive and negative regulation of angiogenesis comprising 367 and 245 proteins, respectively. We used five published gene expression datasets derived from in vitro assays using different types of blood endothelial cells stimulated by VEGFA (vascular endothelial growth factor A). We used the Short Time-series Expression Miner (STEM) to identify significant temporal gene expression profiles. The statistically significant patterns between 2D fibronectin and 3D type I collagen substrates for telomerase-immortalized EC (TIME) show that different substrates could influence the temporal gene activation patterns in the same cell line. We investigated the different activation patterns among 18 transmembrane tyrosine kinase receptors, and experimentally measured the protein level of the tyrosine-kinase receptors VEGFR1, VEGFR2 and VEGFR3 in human umbilical vein EC (HUVEC) and human microvascular EC (MEC). The results show that VEGFR1–VEGFR2 levels are more closely coupled than VEGFR1–VEGFR3 or VEGFR2–VEGFR3 in HUVEC and MEC. This computational methodology can be extended to investigate other molecules or biological processes such as cell cycle. PMID:25329517

  16. Cryo-EM structure of the activated NAIP2-NLRC4 inflammasome reveals nucleated polymerization.

    PubMed

    Zhang, Liman; Chen, Shuobing; Ruan, Jianbin; Wu, Jiayi; Tong, Alexander B; Yin, Qian; Li, Yang; David, Liron; Lu, Alvin; Wang, Wei Li; Marks, Carolyn; Ouyang, Qi; Zhang, Xinzheng; Mao, Youdong; Wu, Hao

    2015-10-23

    The NLR family apoptosis inhibitory proteins (NAIPs) bind conserved bacterial ligands, such as the bacterial rod protein PrgJ, and recruit NLR family CARD-containing protein 4 (NLRC4) as the inflammasome adapter to activate innate immunity. We found that the PrgJ-NAIP2-NLRC4 inflammasome is assembled into multisubunit disk-like structures through a unidirectional adenosine triphosphatase polymerization, primed with a single PrgJ-activated NAIP2 per disk. Cryo-electron microscopy (cryo-EM) reconstruction at subnanometer resolution revealed a ~90° hinge rotation accompanying NLRC4 activation. Unlike in the related heptameric Apaf-1 apoptosome, in which each subunit needs to be conformationally activated by its ligand before assembly, a single PrgJ-activated NAIP2 initiates NLRC4 polymerization in a domino-like reaction to promote the disk assembly. These insights reveal the mechanism of signal amplification in NAIP-NLRC4 inflammasomes. PMID:26449474

  17. Partial pressure measurements with an active spectrometer

    SciTech Connect

    Brooks, N.H.; Jensen, T.H.; Colchin, R.J.; Maingi, R.; Wade, M.R.; Finkenthal, D.F.; Naumenko, N.; Tugarinov, S.

    1998-07-01

    Partial pressure neutral ga measurements have been made using a commercial Penning gauge in conjunction with an active spectrometer. In prior work utilizing bandpass filters and conventional spectrometers, trace concentrations of the hydrogen isotopes H, D, T and of the noble gases He, Ne and Ar were determined from characteristic spectral lines in the light emitted by the neutral species of these elements. For all the elements mentioned, the sensitivity was limited by spectral contamination from a pervasive background of molecular hydrogen radiation. The active spectrometer overcomes this limitations by means of a digital lock-in method and correlation with reference spectra. Preliminary measurements of an admixture containing a trace amount of neon in deuterium show better than a factor of 20 improvement in sensitivity over conventional techniques. This can be further improved by correlating the relative intensities of multiple lines to sets of reference spectra.

  18. Apoptotic human neutrophil peptide-1 anti-tumor activity revealed by cellular biomechanics.

    PubMed

    Gaspar, Diana; Freire, João M; Pacheco, Teresa R; Barata, João T; Castanho, Miguel A R B

    2015-02-01

    Cancer remains a major cause of morbidity and mortality worldwide. Although progress has been made regarding chemotherapeutic agents, new therapies that combine increased selectivity and efficacy with low resistance are still needed. In the search for new anticancer agents, therapies based on biologically active peptides, in particular, antimicrobial peptides (AMPs), have attracted attention for their decreased resistance development and low cytotoxicity. Many AMPs have proved to be tumoricidal agents against human cancer cells, but their mode of action is still controversial. The existence of common properties shared by the membranes of bacteria and tumor cells points to similar lipid-targeting mechanisms in both cases. On the other hand, anticancer peptides (ACPs) also induce apoptosis and inhibit angiogenesis. Human neutrophil peptide-1 (HNP-1) is an endogenous AMP that has been implicated in different cellular phenomena such as tumor proliferation. The presence of HNP-1 in the serum/plasma of oncologic patients turns this peptide into a potential tumor biomarker. The present work reveals the different effects of HNP-1 on the biophysical and nanomechanical properties of solid and hematological tumor cells. Studies on cellular morphology, cellular stiffness, and membrane ultrastructure and charge using atomic force microscopy (AFM) and zeta potential measurements show a preferential binding of HNP-1 to solid tumor cells from human prostate adenocarcinoma when compared to human leukemia cells. AFM also reveals induction of apoptosis with cellular membrane defects at very low peptide concentrations. Understanding ACPs mode(s) of action will certainly open innovative pathways for drug development in cancer treatment. PMID:25447543

  19. Patterns of Activity Revealed by a Time Lag Analysis of a Model Active Region

    NASA Astrophysics Data System (ADS)

    Bradshaw, Stephen; Viall, Nicholeen

    2016-05-01

    We investigate the global activity patterns predicted from a model active region heated by distributions of nanoflares that have a range of average frequencies. The activity patterns are manifested in time lag maps of narrow-band instrument channel pairs. We combine an extrapolated magnetic skeleton with hydrodynamic and forward modeling codes to create a model active region, and apply the time lag method to synthetic observations. Our aim is to recover some typical properties and patterns of activity observed in active regions. Our key findings are: 1. Cooling dominates the time lag signature and the time lags between the channel pairs are generally consistent with observed values. 2. Shorter coronal loops in the core cool more quickly than longer loops at the periphery. 3. All channel pairs show zero time lag when the line-of-sight passes through coronal loop foot-points. 4. There is strong evidence that plasma must be re-energized on a time scale comparable to the cooling timescale to reproduce the observed coronal activity, but it is likely that a relatively broad spectrum of heating frequencies operates across active regions. 5. Due to their highly dynamic nature, we find nanoflare trains produce zero time lags along entire flux tubes in our model active region that are seen between the same channel pairs in observed active regions.

  20. Measurement of glutathione in activated sludges.

    PubMed

    Dziurla, M A; Leroy, P; Strünkmann, G W; Salhi, M; Lee, D U; Camacho, P; Heinz, V; Müller, J A; Paul, E; Ginestet, Ph; Audic, J M; Block, J C

    2004-01-01

    Thermal, electric, mechanical or oxidative stress seem a promising way to reduce the production of excess activated sludge during biological wastewater treatment. However, the adaptation and the resistance of the sludge microbial ecosystem to stress conditions is a major question as it may definitively limit the effect of some treatments. Defence mechanisms developed by aerobic organisms, in particular, in response to oxidative stress involve various antioxidant activities and compounds such as glutathione. An HPLC method was developed for measuring reduced and total glutathione (GSH and GSHt) in perchloric acid sludge extracts. The method was sensitive, highly specific and validated for linearity, precision and recovery. Considering the extraction yield and the oxidation of GSH during extract storage, the measured GSH concentration was estimated to represent 60% of the GSH content from activated sludges. GSHt ranged from 0.32 to 3.34micromolg(-1) volatile solids and the GSH/GSHt ratio ranged from 32% to 91%. Measurements performed on sludges stressed in precise conditions selected to reach a reduction of sludge production showed a decrease of GSH and GSHt concentrations with thermal, mechanical, electric and ozone stress. PMID:14630122

  1. Status of LDEF activation measurements and archive

    NASA Technical Reports Server (NTRS)

    Harmon, B. Alan; Parnell, Thomas A.; Laird, Christopher E.

    1995-01-01

    We review the status of induced radioactivity measurements for the LDEF spacecraft which includes studies of the nuclide, target, directional and depth dependences of the activation. Analysis of the data has focused on extraction of the specific activities for many materials to develop a global picture of the low Earth orbital environment to which the LDEF was subjected. Preliminary comparisons of data in a previous review showed that it was possible to make meaningful intercomparisons between results obtained at different facilities. Generally these comparisons were good and gave results to within 10-20 percent, although some analysis remains. These results clearly provide constraints for recent calculations being performed of the radiation environment of the LDEF. We are not anticipating a period of production of final activation results. An archive is being prepared jointly between NASA/Marshall and Eastern Kentucky University which will include gamma ray spectra and other intermediate results.

  2. Neutron and proton activation measurements from Skylab

    NASA Technical Reports Server (NTRS)

    Fishman, G. J.

    1974-01-01

    Radioactivity induced by high-energy protons and secondary neutrons (from nuclear interactions) in various samples returned from different locations in Skylab was measured directly by gamma-ray spectroscopy measurements of decay gamma rays from the samples. Incident fluxes were derived from the activation measurements, using known nuclear cross-section. Neutron and proton flux values were found to range from 0.2 to 5 particles/sq cm-sec, depending on the energy range and location in Skylab. The thermal neutron flux was less than 0.07 neutrons/sq cm-sec. The results are useful for data analysis and planning of future high-energy astronomy experiments.

  3. High-speed in vivo calcium imaging reveals neuronal network activity with near-millisecond precision.

    PubMed

    Grewe, Benjamin F; Langer, Dominik; Kasper, Hansjörg; Kampa, Björn M; Helmchen, Fritjof

    2010-05-01

    Two-photon calcium imaging of neuronal populations enables optical recording of spiking activity in living animals, but standard laser scanners are too slow to accurately determine spike times. Here we report in vivo imaging in mouse neocortex with greatly improved temporal resolution using random-access scanning with acousto-optic deflectors. We obtained fluorescence measurements from 34-91 layer 2/3 neurons at a 180-490 Hz sampling rate. We detected single action potential-evoked calcium transients with signal-to-noise ratios of 2-5 and determined spike times with near-millisecond precision and 5-15 ms confidence intervals. An automated 'peeling' algorithm enabled reconstruction of complex spike trains from fluorescence traces up to 20-30 Hz frequency, uncovering spatiotemporal trial-to-trial variability of sensory responses in barrel cortex and visual cortex. By revealing spike sequences in neuronal populations on a fast time scale, high-speed calcium imaging will facilitate optical studies of information processing in brain microcircuits. PMID:20400966

  4. A Global Genomic Screening Strategy Reveals Diverse Activators of Constitutive Activated Receptor (CAR)

    EPA Science Inventory

    A comprehensive survey of conditions that activate CAR in the mouse liver has not been carried out but would be useful in understanding their impact on CAR-dependent liver tumor induction. A gene signature dependent on CAR activation was identified by comparing the transcript pr...

  5. Noninvasive ambulatory measurement system of cardiac activity.

    PubMed

    Pino, Esteban J; Chavez, Javier A P; Aqueveque, Pablo

    2015-08-01

    This work implements a noninvasive system that measures the movements caused by cardiac activity. It uses unobtrusive Electro-Mechanical Films (EMFi) on the seat and on the backrest of a regular chair. The system detects ballistocardiogram (BCG) and respiration movements. Real data was obtained from 54 volunteers. 19 of them were measured in the laboratory and 35 in a hospital waiting room. Using a BIOPAC acquisition system, the ECG was measured simultaneously to the BCG for comparison. Wavelet Transform (WT) is a better option than Empirical Mode Decomposition (EMD) for signal extraction and produces higher effective measurement time. In the laboratory, the best results are obtained on the seat. The correlation index was 0.9800 and the Bland-Altman limits of agreement were 0.7136 ± 4.3673 [BPM]. In the hospital waiting room, the best results are also from the seat sensor. The correlation index was 0.9840, and the limits of agreement were 0.4386 ± 3.5884 [BPM]. The system is able to measure BCG in an unobtrusive way and determine the cardiac frequency with high precision. It is simple to use, which means the system can easily be used in non-standard settings: resting in a chair or couch, at the gym, schools or in a hospital waiting room, as shown. PMID:26738057

  6. Expression of the vertebrate Gli proteins in Drosophila reveals a distribution of activator and repressor activities.

    PubMed

    Aza-Blanc, P; Lin, H Y; Ruiz i Altaba, A; Kornberg, T B

    2000-10-01

    The Cubitus interruptus (Ci) and Gli proteins are transcription factors that mediate responses to Hedgehog proteins (Hh) in flies and vertebrates, respectively. During development of the Drosophila wing, Ci transduces the Hh signal and regulates transcription of different target genes at different locations. In vertebrates, the three Gli proteins are expressed in overlapping domains and are partially redundant. To assess how the vertebrate Glis correlate with Drosophila Ci, we expressed each in Drosophila and monitored their behaviors and activities. We found that each Gli has distinct activities that are equivalent to portions of the regulatory arsenal of Ci. Gli2 and Gli1 have activator functions that depend on Hh. Gli2 and Gli3 are proteolyzed to produce a repressor form able to inhibit hh expression. However, while Gli3 repressor activity is regulated by Hh, Gli2 repressor activity is not. These observations suggest that the separate activator and repressor functions of Ci are unevenly partitioned among the three Glis, yielding proteins with related yet distinct properties. PMID:10976059

  7. Comparisons of activity measurements with radionuclide calibrators.

    PubMed

    Oropesa, P; Hernández, A T; Serra, R; Martínez, E; Varela, C

    2003-01-01

    The correct administration to a patient of the prescribed activity of a radiopharmaceutical is an important factor to ensure the confidence in the diagnosis or the therapeutic efficiency, while at the same time keeping the unnecessary human exposure as low as possible. Comparisons of activity measurements for 131I, 201Tl and 99mTc with radionuclide calibrators were organized the first time in Cuba during 2002 with the aim of obtaining information about the quality of administration of radiopharmaceuticals. Ten Cuban nuclear medicine departments and the laboratories involved in the production of these kinds of compounds participated in the comparison runs. The results presented in this paper facilitated the identification of several problems and initiated corrective actions. In addition, they indicate the necessity of establishing Quality Systems in nuclear medicine in Cuba. PMID:14622940

  8. Coupled surface-subsurface hydrologic measurements reveal infiltration, recharge, and discharge dynamics across the swash zone of a sandy beach

    NASA Astrophysics Data System (ADS)

    Heiss, James W.; Puleo, Jack A.; Ullman, William J.; Michael, Holly A.

    2015-11-01

    Swash-groundwater interactions affect the biogeochemistry of beach aquifers and the transport of solutes and sediment across the beachface. Improved understanding of the complex, coupled dynamics of surface and subsurface flow processes in the swash zone is required to better estimate chemical fluxes to the sea and predict the morphological evolution of beaches. Simultaneous high-frequency measurements of saturation, water table elevation, and the cross-shore locations of runup and the boundary between the saturated and unsaturated beachface (surface saturation boundary) were collected on a sandy beach to link groundwater flow dynamics with swash zone forcing. Saturation and lysimeter measurements showed the dynamic response of subsurface saturation to swash events and permitted estimation of infiltration rates. Surface and subsurface observations revealed a decoupling of the surface saturation boundary and the intersection between the water table and the beachface. Surface measurements alone were insufficient to delineate the infiltration and discharge zones, which moved independently of the surface saturation boundary. Results show for the first time the motion and areal extent of infiltration and recharge zones, and constrain the maximum size of the subaerial discharge zone over swash and tidal time scales. The width of the infiltration zone was controlled by swash processes, and subaerial discharge was controlled primarily by tidal processes. These dynamics reveal the tightly coupled nature of surface and subsurface processes over multiple time scales, with implications for sediment transport and fluid and solute fluxes through the hydrologically and biogeochemically active intertidal zone of sandy beaches.

  9. Transcriptomic Sequencing Reveals a Set of Unique Genes Activated by Butyrate-Induced Histone Modification.

    PubMed

    Li, Cong-Jun; Li, Robert W; Baldwin, Ransom L; Blomberg, Le Ann; Wu, Sitao; Li, Weizhong

    2016-01-01

    Butyrate is a nutritional element with strong epigenetic regulatory activity as a histone deacetylase inhibitor. Based on the analysis of differentially expressed genes in the bovine epithelial cells using RNA sequencing technology, a set of unique genes that are activated only after butyrate treatment were revealed. A complementary bioinformatics analysis of the functional category, pathway, and integrated network, using Ingenuity Pathways Analysis, indicated that these genes activated by butyrate treatment are related to major cellular functions, including cell morphological changes, cell cycle arrest, and apoptosis. Our results offered insight into the butyrate-induced transcriptomic changes and will accelerate our discerning of the molecular fundamentals of epigenomic regulation. PMID:26819550

  10. Transcriptomic Sequencing Reveals a Set of Unique Genes Activated by Butyrate-Induced Histone Modification

    PubMed Central

    Li, Cong-Jun; Li, Robert W.; Baldwin, Ransom L.; Blomberg, Le Ann; Wu, Sitao; Li, Weizhong

    2016-01-01

    Butyrate is a nutritional element with strong epigenetic regulatory activity as a histone deacetylase inhibitor. Based on the analysis of differentially expressed genes in the bovine epithelial cells using RNA sequencing technology, a set of unique genes that are activated only after butyrate treatment were revealed. A complementary bioinformatics analysis of the functional category, pathway, and integrated network, using Ingenuity Pathways Analysis, indicated that these genes activated by butyrate treatment are related to major cellular functions, including cell morphological changes, cell cycle arrest, and apoptosis. Our results offered insight into the butyrate-induced transcriptomic changes and will accelerate our discerning of the molecular fundamentals of epigenomic regulation. PMID:26819550

  11. Photocatalytic Active Radiation Measurements and Use

    NASA Technical Reports Server (NTRS)

    Davis, Bruce A.; Underwood, Lauren W.

    2011-01-01

    Photocatalytic materials are being used to purify air, to kill microbes, and to keep surfaces clean. A wide variety of materials are being developed, many of which have different abilities to absorb various wavelengths of light. Material variability, combined with both spectral illumination intensity and spectral distribution variability, will produce a wide range of performance results. The proposed technology estimates photocatalytic active radiation (PcAR), a unit of radiation that normalizes the amount of light based on its spectral distribution and on the ability of the material to absorb that radiation. Photocatalytic reactions depend upon the number of electron-hole pairs generated at the photocatalytic surface. The number of electron-hole pairs produced depends on the number of photons per unit area per second striking the surface that can be absorbed and whose energy exceeds the bandgap of the photocatalytic material. A convenient parameter to describe the number of useful photons is the number of moles of photons striking the surface per unit area per second. The unit of micro-einsteins (or micromoles) of photons per m2 per sec is commonly used for photochemical and photoelectric-like phenomena. This type of parameter is used in photochemistry, such as in the conversion of light energy for photosynthesis. Photosynthetic response correlates with the number of photons rather than by energy because, in this photochemical process, each molecule is activated by the absorption of one photon. In photosynthesis, the number of photons absorbed in the 400 700 nm spectral range is estimated and is referred to as photosynthetic active radiation (PAR). PAR is defined in terms of the photosynthetic photon flux density measured in micro-einsteins of photons per m2 per sec. PcAR is an equivalent, similarly modeled parameter that has been defined for the photocatalytic processes. Two methods to measure the PcAR level are being proposed. In the first method, a calibrated

  12. Kinetic Measurements Reveal Enhanced Protein-Protein Interactions at Intercellular Junctions

    PubMed Central

    Shashikanth, Nitesh; Kisting, Meridith A.; Leckband, Deborah E.

    2016-01-01

    The binding properties of adhesion proteins are typically quantified from measurements with soluble fragments, under conditions that differ radically from the confined microenvironment of membrane bound proteins in adhesion zones. Using classical cadherin as a model adhesion protein, we tested the postulate that confinement within quasi two-dimensional intercellular gaps exposes weak protein interactions that are not detected in solution binding assays. Micropipette-based measurements of cadherin-mediated, cell-cell binding kinetics identified a unique kinetic signature that reflects both adhesive (trans) bonds between cadherins on opposing cells and lateral (cis) interactions between cadherins on the same cell. In solution, proposed lateral interactions were not detected, even at high cadherin concentrations. Mutations postulated to disrupt lateral cadherin association altered the kinetic signatures, but did not affect the adhesive (trans) binding affinity. Perturbed kinetics further coincided with altered cadherin distributions at junctions, wound healing dynamics, and paracellular permeability. Intercellular binding kinetics thus revealed cadherin interactions that occur within confined, intermembrane gaps but not in solution. Findings further demonstrate the impact of these revealed interactions on the organization and function of intercellular junctions. PMID:27009566

  13. Kinetic Measurements Reveal Enhanced Protein-Protein Interactions at Intercellular Junctions.

    PubMed

    Shashikanth, Nitesh; Kisting, Meridith A; Leckband, Deborah E

    2016-01-01

    The binding properties of adhesion proteins are typically quantified from measurements with soluble fragments, under conditions that differ radically from the confined microenvironment of membrane bound proteins in adhesion zones. Using classical cadherin as a model adhesion protein, we tested the postulate that confinement within quasi two-dimensional intercellular gaps exposes weak protein interactions that are not detected in solution binding assays. Micropipette-based measurements of cadherin-mediated, cell-cell binding kinetics identified a unique kinetic signature that reflects both adhesive (trans) bonds between cadherins on opposing cells and lateral (cis) interactions between cadherins on the same cell. In solution, proposed lateral interactions were not detected, even at high cadherin concentrations. Mutations postulated to disrupt lateral cadherin association altered the kinetic signatures, but did not affect the adhesive (trans) binding affinity. Perturbed kinetics further coincided with altered cadherin distributions at junctions, wound healing dynamics, and paracellular permeability. Intercellular binding kinetics thus revealed cadherin interactions that occur within confined, intermembrane gaps but not in solution. Findings further demonstrate the impact of these revealed interactions on the organization and function of intercellular junctions. PMID:27009566

  14. Nuclear RNA-seq of single neurons reveals molecular signatures of activation

    PubMed Central

    Lacar, Benjamin; Linker, Sara B.; Jaeger, Baptiste N.; Krishnaswami, Suguna; Barron, Jerika; Kelder, Martijn; Parylak, Sarah; Paquola, Apuã; Venepally, Pratap; Novotny, Mark; O'Connor, Carolyn; Fitzpatrick, Conor; Erwin, Jennifer; Hsu, Jonathan Y.; Husband, David; McConnell, Michael J.; Lasken, Roger; Gage, Fred H.

    2016-01-01

    Single-cell sequencing methods have emerged as powerful tools for identification of heterogeneous cell types within defined brain regions. Application of single-cell techniques to study the transcriptome of activated neurons can offer insight into molecular dynamics associated with differential neuronal responses to a given experience. Through evaluation of common whole-cell and single-nuclei RNA-sequencing (snRNA-seq) methods, here we show that snRNA-seq faithfully recapitulates transcriptional patterns associated with experience-driven induction of activity, including immediate early genes (IEGs) such as Fos, Arc and Egr1. SnRNA-seq of mouse dentate granule cells reveals large-scale changes in the activated neuronal transcriptome after brief novel environment exposure, including induction of MAPK pathway genes. In addition, we observe a continuum of activation states, revealing a pseudotemporal pattern of activation from gene expression alone. In summary, snRNA-seq of activated neurons enables the examination of gene expression beyond IEGs, allowing for novel insights into neuronal activation patterns in vivo. PMID:27090946

  15. Nuclear RNA-seq of single neurons reveals molecular signatures of activation.

    PubMed

    Lacar, Benjamin; Linker, Sara B; Jaeger, Baptiste N; Krishnaswami, Suguna; Barron, Jerika; Kelder, Martijn; Parylak, Sarah; Paquola, Apuã; Venepally, Pratap; Novotny, Mark; O'Connor, Carolyn; Fitzpatrick, Conor; Erwin, Jennifer; Hsu, Jonathan Y; Husband, David; McConnell, Michael J; Lasken, Roger; Gage, Fred H

    2016-01-01

    Single-cell sequencing methods have emerged as powerful tools for identification of heterogeneous cell types within defined brain regions. Application of single-cell techniques to study the transcriptome of activated neurons can offer insight into molecular dynamics associated with differential neuronal responses to a given experience. Through evaluation of common whole-cell and single-nuclei RNA-sequencing (snRNA-seq) methods, here we show that snRNA-seq faithfully recapitulates transcriptional patterns associated with experience-driven induction of activity, including immediate early genes (IEGs) such as Fos, Arc and Egr1. SnRNA-seq of mouse dentate granule cells reveals large-scale changes in the activated neuronal transcriptome after brief novel environment exposure, including induction of MAPK pathway genes. In addition, we observe a continuum of activation states, revealing a pseudotemporal pattern of activation from gene expression alone. In summary, snRNA-seq of activated neurons enables the examination of gene expression beyond IEGs, allowing for novel insights into neuronal activation patterns in vivo. PMID:27090946

  16. Measuring Homework Completion in Behavioral Activation

    PubMed Central

    Busch, Andrew M.; Uebelacker, Lisa A.; Kalibatseva, Zornitsa; Miller, Ivan W.

    2010-01-01

    The aim of this study was to develop and validate an observer-based coding system for the characterization and completion of homework assignments during Behavioral Activation (BA). Existing measures of homework completion are generally unsophisticated, and there is no current measure of homework completion designed to capture the particularities of BA. The tested scale sought to capture the type of assignment, realm of functioning targeted, extent of completion, and assignment difficulty. Homework assignments were drawn from 12 (mean age = 48, 83% female) clients in two trials of a 10-session BA manual targeting treatment-resistant depression in primary care. The two coders demonstrated acceptable or better reliability on most codes, and unreliable codes were dropped from the proposed scale. In addition, correlations between homework completion and outcome were strong, providing some support for construct validity. Ultimately, this line of research aims to develop a user-friendly, reliable measure of BA homework completion that can be completed by a therapist during session. PMID:20562324

  17. Survey of activated kinase proteins reveals potential targets for cholangiocarcinoma treatment.

    PubMed

    Dokduang, Hasaya; Juntana, Sirinun; Techasen, Anchalee; Namwat, Nisana; Yongvanit, Puangrat; Khuntikeo, Narong; Riggins, Gregory J; Loilome, Watcharin

    2013-12-01

    Improving therapy for patients with cholangiocarcinoma (CCA) presents a significant challenge. This is made more difficult by a lack of a clear understanding of potential molecular targets, such as deregulated kinases. In this work, we profiled the activated kinases in CCA in order to apply them as the targets for CCA therapy. Human phospho-receptor tyrosine kinases (RTKs) and phospho-kinase array analyses revealed that multiple kinases are activated in both CCA cell lines and human CCA tissues that included cell growth, apoptosis, cell to cell interaction, movement, and angiogenesis RTKs. Predominately, the kinases activated downstream were those in the PI3K/Akt, Ras/MAPK, JAK/STAT, and Wnt/β-catenin signaling pathways. Western blot analysis confirms that Erk1/2 and Akt activation were increased in CCA tissues when compared with their normal adjacent tissue. The inhibition of kinase activation using multi-targeted kinase inhibitors, sorafenib and sunitinib led to significant cell growth inhibition and apoptosis induction via suppression of Erk1/2 and Akt activation, whereas drugs with specificity to a single kinase showed less potency. In conclusion, our study reveals the involvement of multiple kinase proteins in CCA growth that might serve as therapeutic targets for combined kinase inhibition. PMID:23812726

  18. Functional Screening of Hydrolytic Activities Reveals an Extremely Thermostable Cellulase from a Deep-Sea Archaeon

    PubMed Central

    Leis, Benedikt; Heinze, Simon; Angelov, Angel; Pham, Vu Thuy Trang; Thürmer, Andrea; Jebbar, Mohamed; Golyshin, Peter N.; Streit, Wolfgang R.; Daniel, Rolf; Liebl, Wolfgang

    2015-01-01

    Extreme habitats serve as a source of enzymes that are active under extreme conditions and are candidates for industrial applications. In this work, six large-insert mixed genomic libraries were screened for hydrolase activities in a broad temperature range (8–70°C). Among a variety of hydrolytic activities, one fosmid clone, derived from a library of pooled isolates of hyperthermophilic archaea from deep sea vents, displayed hydrolytic activity on carboxymethyl cellulose substrate plates at 70°C but not at lower temperatures. Sequence analysis of the fosmid insert revealed a gene encoding a novel glycoside hydrolase family 12 (GHF12) endo-1,4-β-glucanase, termed Cel12E. The enzyme shares 45% sequence identity with a protein from the archaeon Thermococcus sp. AM4 and displays a unique multidomain architecture. Biochemical characterization of Cel12E revealed a remarkably thermostable protein, which appears to be of archaeal origin. The enzyme displayed maximum activity at 92°C and was active on a variety of linear 1,4-β-glucans like carboxymethyl cellulose, β-glucan, lichenan, and phosphoric acid swollen cellulose. The protein is able to bind to various insoluble β-glucans. Product pattern analysis indicated that Cel12E is an endo-cleaving β-glucanase. Cel12E expands the toolbox of hyperthermostable archaeal cellulases with biotechnological potential. PMID:26191525

  19. Engagement in activities revealing the body and psychosocial adjustment in adults with a trans-tibial prosthesis.

    PubMed

    Donovan-Hall, M K; Yardley, L; Watts, R J

    2002-04-01

    The purpose of this study was to examine the effects of the appearance of a prosthesis on social behaviour, social discomfort and psychological well-being in eleven amputees taking delivery of a prosthesis with a silicone cover. Two new scales were developed: the 'Engagement in everyday activities involving revealing the body' (EEARB); and the 'Discomfort-Engagement in everyday activities involving revealing the body' (Discomfort-EEARB) scales. The psychometric properties of these scales were determined using a sample of 101 able-bodied adults. The Hospital Anxiety and Depression Scale and the Rosenberg Self-Esteem Scale were also used to measure psychological well-being in the amputee sample. The EEARB and Discomfort-EEARB proved to have good reliability and validity. Comparison of amputees' scores prior to receiving the silicone cosmesis with those of the able-bodied adults revealed significant behavioural limitations and social discomfort, associated with low self-esteem, anxiety and depression. There was a significant increase in amputees' scores three months afier taking delivery of their prosthesis, indicating that amputees reported engaging in more activities which involved revealing their body, and that they would feel more comfortable in situations which involved revealing the body. As the amputee sample available was small and self-selected, it is not possible to generalise these findings to the amputee population as a whole. However, since there is little previous research investigating the effects of the appearance of the prosthesis, these findings demonstrate the need for further research in this area. PMID:12043922

  20. Targeted massively parallel sequencing of angiosarcomas reveals frequent activation of the mitogen activated protein kinase pathway

    PubMed Central

    Murali, Rajmohan; Chandramohan, Raghu; Möller, Inga; Scholz, Simone L.; Berger, Michael; Huberman, Kety; Viale, Agnes; Pirun, Mono; Socci, Nicholas D.; Bouvier, Nancy; Bauer, Sebastian; Artl, Monika; Schilling, Bastian; Schimming, Tobias; Sucker, Antje; Schwindenhammer, Benjamin; Grabellus, Florian; Speicher, Michael R.; Schaller, Jörg; Hillen, Uwe; Schadendorf, Dirk; Mentzel, Thomas; Cheng, Donavan T.; Wiesner, Thomas; Griewank, Klaus G.

    2015-01-01

    Angiosarcomas are rare malignant mesenchymal tumors of endothelial differentiation. The clinical behavior is usually aggressive and the prognosis for patients with advanced disease is poor with no effective therapies. The genetic bases of these tumors have been partially revealed in recent studies reporting genetic alterations such as amplifications of MYC (primarily in radiation-associated angiosarcomas), inactivating mutations in PTPRB and R707Q hotspot mutations of PLCG1. Here, we performed a comprehensive genomic analysis of 34 angiosarcomas using a clinically-approved, hybridization-based targeted next-generation sequencing assay for 341 well-established oncogenes and tumor suppressor genes. Over half of the angiosarcomas (n = 18, 53%) harbored genetic alterations affecting the MAPK pathway, involving mutations in KRAS, HRAS, NRAS, BRAF, MAPK1 and NF1, or amplifications in MAPK1/CRKL, CRAF or BRAF. The most frequently detected genetic aberrations were mutations in TP53 in 12 tumors (35%) and losses of CDKN2A in 9 tumors (26%). MYC amplifications were generally mutually exclusive of TP53 alterations and CDKN2A loss and were identified in 8 tumors (24%), most of which (n = 7, 88%) arose post-irradiation. Previously reported mutations in PTPRB (n = 10, 29%) and one (3%) PLCG1 R707Q mutation were also identified. Our results demonstrate that angiosarcomas are a genetically heterogeneous group of tumors, harboring a wide range of genetic alterations. The high frequency of genetic events affecting the MAPK pathway suggests that targeted therapies inhibiting MAPK signaling may be promising therapeutic avenues in patients with advanced angiosarcomas. PMID:26440310

  1. 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.

  2. Fibrinogen adsorption mechanisms at the gold substrate revealed by QCM-D measurements and RSA modeling.

    PubMed

    Kubiak, Katarzyna; Adamczyk, Zbigniew; Cieśla, Michał

    2016-03-01

    Adsorption kinetics of fibrinogen at a gold substrate at various pHs was thoroughly studied using the QCM-D method. The experimental were interpreted in terms of theoretical calculations performed according to the random sequential adsorption model (RSA). In this way, the hydration functions and water factors of fibrinogen monolayers were quantitatively evaluated at various pHs. It was revealed that for the lower range of fibrinogen coverage the hydration function were considerably lower than previously obtained for the silica sensor [33]. The lower hydration of fibrinogen monolayers on the gold sensor was attributed to its higher roughness. However, for higher fibrinogen coverage the hydration functions for both sensors became identical exhibiting an universal behavior. By using the hydration functions, the fibrinogen adsorption/desorption runs derived from QCM-D measurements were converted to the Γd vs. the time relationships. This allowed to precisely determine the maximum coverage that varied between 1.6mgm(-2) at pH 3.5 and 4.5mgm(-2) at pH 7.4 (for ionic strength of 0.15M). These results agree with theoretical eRSA modeling and previous experimental data derived by using ellipsometry, OWLS and TIRF. Various fibrinogen adsorption mechanisms were revealed by exploiting the maximum coverage data. These results allow one to develop a method for preparing fibrinogen monolayers of well-controlled coverage and molecule orientation. PMID:26705826

  3. Satellite measurements reveal persistent small-scale features in ocean winds.

    PubMed

    Chelton, Dudley B; Schlax, Michael G; Freilich, Michael H; Milliff, Ralph F

    2004-02-13

    Four-year averages of 25-kilometer-resolution measurements of near-surface wind speed and direction over the global ocean from the QuikSCAT satellite radar scatterometer reveal the existence of surprisingly persistent small-scale features in the dynamically and thermodynamically important curl and divergence of the wind stress. Air-sea interaction over sea surface temperature fronts throughout the world ocean is evident in both the curl and divergence fields, as are the influences of islands and coastal mountains. Ocean currents such as the Gulf Stream generate distinctive patterns in the curl field. These previously unresolved features have important implications for oceanographic and air-sea interaction research. PMID:14726595

  4. Simultaneous Measurement of Amyloid Fibril Formation by Dynamic Light Scattering and Fluorescence Reveals Complex Aggregation Kinetics

    PubMed Central

    Streets, Aaron M.; Sourigues, Yannick; Kopito, Ron R.; Melki, Ronald; Quake, Stephen R.

    2013-01-01

    An apparatus that combines dynamic light scattering and Thioflavin T fluorescence detection is used to simultaneously probe fibril formation in polyglutamine peptides, the aggregating subunit associated with Huntington's disease, in vitro. Huntington's disease is a neurodegenerative disorder in a class of human pathologies that includes Alzheimer's and Parkinson's disease. These pathologies are all related by the propensity of their associated protein or polypeptide to form insoluble, β-sheet rich, amyloid fibrils. Despite the wide range of amino acid sequence in the aggregation prone polypeptides associated with these diseases, the resulting amyloids display strikingly similar physical structure, an observation which suggests a physical basis for amyloid fibril formation. Thioflavin T fluorescence reports β-sheet fibril content while dynamic light scattering measures particle size distributions. The combined techniques allow elucidation of complex aggregation kinetics and are used to reveal multiple stages of amyloid fibril formation. PMID:23349924

  5. Natural and semisynthetic analogues of manadoperoxide B reveal new structural requirements for trypanocidal activity.

    PubMed

    Chianese, Giuseppina; Scala, Fernando; Calcinai, Barbara; Cerrano, Carlo; Dien, Henny A; Kaiser, Marcel; Tasdemir, Deniz; Taglialatela-Scafati, Orazio

    2013-09-01

    Chemical analysis of the Indonesian sponge Plakortis cfr. lita afforded two new analogues of the potent trypanocidal agent manadoperoxide B (1), namely 12-isomanadoperoxide B (2) and manadoperoxidic acid B (3). These compounds were isolated along with a new short chain dicarboxylate monoester (4), bearing some interesting relationships with the polyketide endoperoxides found in this sponge. Some semi-synthetic analogues of manadoperoxide B (6-8) were prepared and evaluated for antitrypanosomal activity and cytotoxicity. These studies revealed crucial structure-activity relationships that should be taken into account in the design of optimized and simplified endoperoxyketal trypanocidal agents. PMID:23989650

  6. A High-Throughput Screen Reveals New Small-Molecule Activators and Inhibitors of Pantothenate Kinases

    PubMed Central

    2016-01-01

    Pantothenate kinase (PanK) is a regulatory enzyme that controls coenzyme A (CoA) biosynthesis. The association of PanK with neurodegeneration and diabetes suggests that chemical modifiers of PanK activity may be useful therapeutics. We performed a high throughput screen of >520000 compounds from the St. Jude compound library and identified new potent PanK inhibitors and activators with chemically tractable scaffolds. The HTS identified PanK inhibitors exemplified by the detailed characterization of a tricyclic compound (7) and a preliminary SAR. Biophysical studies reveal that the PanK inhibitor acts by binding to the ATP–enzyme complex. PMID:25569308

  7. Early activation of Broca's area in grammar processing as revealed by the syntactic mismatch negativity and distributed source analysis.

    PubMed

    Hanna, Jeff; Mejias, Sandrine; Schelstraete, Marie-Anne; Pulvermüller, Friedemann; Shtyrov, Yury; Van der Lely, Heather K J

    2014-01-01

    Though activation of Broca's region in the combinatorial processing of symbols (language, music) has been revealed by neurometabolic studies, most previous neurophysiological research found the earliest grammar indices in the temporal cortex, with inferior-frontal generators becoming active at relatively late stages. We use the attention- and task-free syntactic mismatch negativity (sMMN) event-related potential (ERP) to measure rapid and automatic sensitivity of the human brain to grammatical information in participants' native language (French). Further, sources underlying the MMN were estimated by applying the Parametrical Empirical Bayesian (PEB) approach, with the Multiple Sparse Priors (MSP) technique. Results showed reliable grammar-related activation focused on Broca's region already in the 150-190 ms time window, providing robust documentation of its involvement in the first stages of syntactic processing. PMID:24279717

  8. DNA polymerase beta reveals enhanced activity and processivity in reverse micelles.

    PubMed

    Anarbaev, Rashid O; Rogozina, Anastasia L; Lavrik, Olga I

    2009-04-01

    Water is essential for the stability and functions of proteins and DNA. Reverse micelles are simple model systems where the structure and dynamics of water are controlled. We have estimated the size of complex reverse micelles by light scattering technique and examined the local microenvironment using fluorescein as molecular probe. The micelle size and water polarity inside reverse micelles depend on water volume fraction. We have investigated the different hydration and confinement effects on activity, processivity, and stability of mammalian DNA polymerase beta in reverse micelles. The enzyme displays high processivity on primed single-stranded M13mp19 DNA with maximal activity at 10% of water content. The processivity and activity of DNA polymerase strongly depend on the protein concentration. The enzyme reveals also the enhanced stability in the presence of template-primer and at high protein concentration. The data provide direct evidence for strong influence of microenvironment on DNA polymerase activity. PMID:19138815

  9. Measurement of gene regulation in individual cells reveals rapid switching between promoter states.

    PubMed

    Sepúlveda, Leonardo A; Xu, Heng; Zhang, Jing; Wang, Mengyu; Golding, Ido

    2016-03-11

    In vivo mapping of transcription-factor binding to the transcriptional output of the regulated gene is hindered by probabilistic promoter occupancy, the presence of multiple gene copies, and cell-to-cell variability. We demonstrate how to overcome these obstacles in the lysogeny maintenance promoter of bacteriophage lambda, P(RM). We simultaneously measured the concentration of the lambda repressor CI and the number of messenger RNAs (mRNAs) from P(RM) in individual Escherichia coli cells, and used a theoretical model to identify the stochastic activity corresponding to different CI binding configurations. We found that switching between promoter configurations is faster than mRNA lifetime and that individual gene copies within the same cell act independently. The simultaneous quantification of transcription factor and promoter activity, followed by stochastic theoretical analysis, provides a tool that can be applied to other genetic circuits. PMID:26965629

  10. New Aspects of Photocurrent Generation at Graphene pn Junctions Revealed by Ultrafast Optical Measurements

    NASA Astrophysics Data System (ADS)

    Aivazian, Grant; Sun, Dong; Jones, Aaron; Ross, Jason; Yao, Wang; Cobden, David; Xu, Xiaodong

    2012-02-01

    The remarkable electrical and optical properties of graphene make it a promising material for new optoelectronic applications. However, one important, but so far unexplored, property is the role of hot carriers in charge and energy transport at graphene interfaces. Here we investigate the photocurrent (PC) dynamics at a tunable graphene pn junction using ultrafast scanning PC microscopy. Pump-probe measurements show a temperature dependent relaxation time of photogenerated carriers that increases from 1.5ps at 290K to 4ps at 20K; while the amplitude of the PC is independent of the lattice temperature. These observations imply that it is hot carriers, not phonons, which dominate ultrafast energy transport. Gate dependent measurements show many interesting features such as pump induced saturation, enhancement, and sign reversal of probe generated PC. These observations reveal that the underlying PC mechanism is a combination of the thermoelectric and built-in electric field effects. Our results enhance the understanding of non-equilibrium electron dynamics, electron-electron interactions, and electron-phonon interactions in graphene. They also determine fundamental limits on ultrafast device operation speeds (˜500 GHz) for graphene-based photodetectors.

  11. Characterization of Drosophila CMP-sialic acid synthetase activity reveals unusual enzymatic properties.

    PubMed

    Mertsalov, Ilya B; Novikov, Boris N; Scott, Hilary; Dangott, Lawrence; Panin, Vladislav M

    2016-07-01

    CMP-sialic acid synthetase (CSAS) is a key enzyme of the sialylation pathway. CSAS produces the activated sugar donor, CMP-sialic acid, which serves as a substrate for sialyltransferases to modify glycan termini with sialic acid. Unlike other animal CSASs that normally localize in the nucleus, Drosophila melanogaster CSAS (DmCSAS) localizes in the cell secretory compartment, predominantly in the Golgi, which suggests that this enzyme has properties distinct from those of its vertebrate counterparts. To test this hypothesis, we purified recombinant DmCSAS and characterized its activity in vitro Our experiments revealed several unique features of this enzyme. DmCSAS displays specificity for N-acetylneuraminic acid as a substrate, shows preference for lower pH and can function with a broad range of metal cofactors. When tested at a pH corresponding to the Golgi compartment, the enzyme showed significant activity with several metal cations, including Zn(2+), Fe(2+), Co(2+) and Mn(2+), whereas the activity with Mg(2+) was found to be low. Protein sequence analysis and site-specific mutagenesis identified an aspartic acid residue that is necessary for enzymatic activity and predicted to be involved in co-ordinating a metal cofactor. DmCSAS enzymatic activity was found to be essential in vivo for rescuing the phenotype of DmCSAS mutants. Finally, our experiments revealed a steep dependence of the enzymatic activity on temperature. Taken together, our results indicate that DmCSAS underwent evolutionary adaptation to pH and ionic environment different from that of counterpart synthetases in vertebrates. Our data also suggest that environmental temperatures can regulate Drosophila sialylation, thus modulating neural transmission. PMID:27114558

  12. Phosphoproteomic network analysis in the sea urchin Strongylocentrotus purpuratus reveals new candidates in egg activation.

    PubMed

    Guo, Hongbo; Garcia-Vedrenne, Ana Elisa; Isserlin, Ruth; Lugowski, Andrew; Morada, Anthony; Sun, Alex; Miao, Yishen; Kuzmanov, Uros; Wan, Cuihong; Ma, Hongyue; Foltz, Kathy; Emili, Andrew

    2015-12-01

    Fertilization triggers a dynamic symphony of molecular transformations induced by a rapid rise in intracellular calcium. Most prominent are surface alterations, metabolic activation, cytoskeletal reorganization, and cell-cycle reentry. While the activation process appears to be broadly evolutionarily conserved, and protein phosphorylation is known to play a key role, the signaling networks mediating the response to fertilization are not well described. To address this gap, we performed a time course phosphoproteomic analysis of egg activation in the sea urchin Strongylocentrotus purpuratus, a system that offers biochemical tractability coupled with exquisite synchronicity. By coupling large-scale phosphopeptide enrichment with unbiased quantitative MS, we identified striking changes in global phosphoprotein patterns at 2- and 5-min postfertilization as compared to unfertilized eggs. Overall, we mapped 8796 distinct phosphosite modifications on 2833 phosphoproteins, of which 15% were differentially regulated in early egg activation. Activated kinases were identified by phosphosite mapping, while enrichment analyses revealed conserved signaling cascades not previously associated with egg activation. This work represents the most comprehensive study of signaling associated with egg activation to date, suggesting novel mechanisms that can be experimentally tested and providing a valuable resource for the broader research community. All MS data have been deposited in the ProteomeXchange with identifier PXD002239 (http://proteomecentral.proteomexchange.org/dataset/PXD002239). PMID:26227301

  13. Crystal structure of an avian influenza polymerase PA[subscript N] reveals an endonuclease active site

    SciTech Connect

    Yuan, Puwei; Bartlam, Mark; Lou, Zhiyong; Chen, Shoudeng; Zhou, Jie; He, Xiaojing; Lv, Zongyang; Ge, Ruowen; Li, Xuemei; Deng, Tao; Fodor, Ervin; Rao, Zihe; Liu, Yingfang

    2009-11-10

    The heterotrimeric influenza virus polymerase, containing the PA, PB1 and PB2 proteins, catalyses viral RNA replication and transcription in the nucleus of infected cells. PB1 holds the polymerase active site and reportedly harbours endonuclease activity, whereas PB2 is responsible for cap binding. The PA amino terminus is understood to be the major functional part of the PA protein and has been implicated in several roles, including endonuclease and protease activities as well as viral RNA/complementary RNA promoter binding. Here we report the 2.2 angstrom (A) crystal structure of the N-terminal 197 residues of PA, termed PA(N), from an avian influenza H5N1 virus. The PA(N) structure has an alpha/beta architecture and reveals a bound magnesium ion coordinated by a motif similar to the (P)DX(N)(D/E)XK motif characteristic of many endonucleases. Structural comparisons and mutagenesis analysis of the motif identified in PA(N) provide further evidence that PA(N) holds an endonuclease active site. Furthermore, functional analysis with in vivo ribonucleoprotein reconstitution and direct in vitro endonuclease assays strongly suggest that PA(N) holds the endonuclease active site and has critical roles in endonuclease activity of the influenza virus polymerase, rather than PB1. The high conservation of this endonuclease active site among influenza strains indicates that PA(N) is an important target for the design of new anti-influenza therapeutics.

  14. Single molecule analysis reveals reversible and irreversible steps during spliceosome activation

    PubMed Central

    Hoskins, Aaron A; Rodgers, Margaret L; Friedman, Larry J; Gelles, Jeff; Moore, Melissa J

    2016-01-01

    The spliceosome is a complex machine composed of small nuclear ribonucleoproteins (snRNPs) and accessory proteins that excises introns from pre-mRNAs. After assembly the spliceosome is activated for catalysis by rearrangement of subunits to form an active site. How this rearrangement is coordinated is not well-understood. During activation, U4 must be released to allow U6 conformational change, while Prp19 complex (NTC) recruitment is essential for stabilizing the active site. We used multi-wavelength colocalization single molecule spectroscopy to directly observe the key events in Saccharomyces cerevisiae spliceosome activation. Following binding of the U4/U6.U5 tri-snRNP, the spliceosome either reverses assembly by discarding tri-snRNP or proceeds to activation by irreversible U4 loss. The major pathway for NTC recruitment occurs after U4 release. ATP stimulates both the competing U4 release and tri-snRNP discard processes. The data reveal the activation mechanism and show that overall splicing efficiency may be maintained through repeated rounds of disassembly and tri-snRNP reassociation. DOI: http://dx.doi.org/10.7554/eLife.14166.001 PMID:27244240

  15. Whole-brain activity maps reveal stereotyped, distributed networks for visuomotor behavior

    PubMed Central

    Portugues, Ruben; Feierstein, Claudia E.; Engert, Florian; Orger, Michael B.

    2014-01-01

    Summary Most behaviors, even simple innate reflexes, are mediated by circuits of neurons spanning areas throughout the brain. However, in most cases, the distribution and dynamics of firing patterns of these neurons during behavior are not known. We imaged activity, with cellular resolution, throughout the whole brains of zebrafish performing the optokinetic response. We found a sparse, broadly distributed network that has an elaborate, but ordered, pattern, with a bilaterally symmetrical organization. Activity patterns fell into distinct clusters reflecting sensory and motor processing. By correlating neuronal responses with an array of sensory and motor variables, we find that the network can be clearly divided into distinct functional modules. Comparing aligned data from multiple fish, we find that the spatiotemporal activity dynamics and functional organization are highly stereotyped across individuals. These experiments reveal, for the first time in a vertebrate, the comprehensive functional architecture of the neural circuits underlying a sensorimotor behavior. PMID:24656252

  16. Integrative analysis of breast cancer reveals prognostic haematopoietic activity and patient-specific immune response profiles

    PubMed Central

    Varn, Frederick S.; Andrews, Erik H.; Mullins, David W.; Cheng, Chao

    2016-01-01

    Transcriptional programmes active in haematopoietic cells enable a variety of functions including dedifferentiation, innate immunity and adaptive immunity. Understanding how these programmes function in the context of cancer can provide valuable insights into host immune response, cancer severity and potential therapy response. Here we present a method that uses the transcriptomes of over 200 murine haematopoietic cells, to infer the lineage-specific haematopoietic activity present in human breast tumours. Correlating this activity with patient survival and tumour purity reveals that the transcriptional programmes of many cell types influence patient prognosis and are found in environments of high lymphocytic infiltration. Collectively, these results allow for a detailed and personalized assessment of the patient immune response to a tumour. When combined with routinely collected patient biopsy genomic data, this method can enable a richer understanding of the complex interplay between the host immune system and cancer. PMID:26725977

  17. Integrative analysis of breast cancer reveals prognostic haematopoietic activity and patient-specific immune response profiles.

    PubMed

    Varn, Frederick S; Andrews, Erik H; Mullins, David W; Cheng, Chao

    2016-01-01

    Transcriptional programmes active in haematopoietic cells enable a variety of functions including dedifferentiation, innate immunity and adaptive immunity. Understanding how these programmes function in the context of cancer can provide valuable insights into host immune response, cancer severity and potential therapy response. Here we present a method that uses the transcriptomes of over 200 murine haematopoietic cells, to infer the lineage-specific haematopoietic activity present in human breast tumours. Correlating this activity with patient survival and tumour purity reveals that the transcriptional programmes of many cell types influence patient prognosis and are found in environments of high lymphocytic infiltration. Collectively, these results allow for a detailed and personalized assessment of the patient immune response to a tumour. When combined with routinely collected patient biopsy genomic data, this method can enable a richer understanding of the complex interplay between the host immune system and cancer. PMID:26725977

  18. Latent luciferase activity in the fruit fly revealed by a synthetic luciferin

    PubMed Central

    Mofford, David M.; Reddy, Gadarla Randheer; Miller, Stephen C.

    2014-01-01

    Beetle luciferases are thought to have evolved from fatty acyl-CoA synthetases present in all insects. Both classes of enzymes activate fatty acids with ATP to form acyl-adenylate intermediates, but only luciferases can activate and oxidize d-luciferin to emit light. Here we show that the Drosophila fatty acyl-CoA synthetase CG6178, which cannot use d-luciferin as a substrate, is able to catalyze light emission from the synthetic luciferin analog CycLuc2. Bioluminescence can be detected from the purified protein, live Drosophila Schneider 2 cells, and from mammalian cells transfected with CG6178. Thus, the nonluminescent fruit fly possesses an inherent capacity for bioluminescence that is only revealed upon treatment with a xenobiotic molecule. This result expands the scope of bioluminescence and demonstrates that the introduction of a new substrate can unmask latent enzymatic activity that differs significantly from an enzyme’s normal function without requiring mutation. PMID:24616520

  19. A biosensor for the protease TACE reveals actin damage induced TACE activation

    PubMed Central

    Chapnick, Douglas A.; Bunker, Eric; Liu, Xuedong

    2016-01-01

    Ligand shedding has gained increased attention as a major posttranslational modification mechanism used by cells to respond to diverse environmental conditions. The TACEadam17 protease is a critical mediator of such ligand shedding, regulating the maturation and release of an impressive range of extracellular substrates that drive diverse cellular responses. Exactly how this protease is itself activated remains unclear, in part due to the lack of available tools to measure TACE activity with temporal and spatial resolution in live cells. We have developed a FRET based biosensor for TACE activity (TSen), which is capable of reporting TACE activation kinetics in live cells with a high degree of specificity. TSen was used in combination with chemical biology to probe the dependence of various means of TACE activation on p38 and Erk kinase activities, as well as to identify a novel connection between actin cytoskeletal disruption and TACE activation. Such cytoskeletal disruption leads to rapid and robust TACE activation in some cell types and accumulation of TACE at the plasma membrane, allowing for increased cleavage of endogenous substrates. Our study highlights both the versatility of TSen as a tool to understand the mechanisms of TACE activation in live cells and the importance of actin cytoskeletal integrity as a modulator of TACE activity. PMID:25714465

  20. Revealing the water cycle on Mars via D/H isotopic measurements

    NASA Astrophysics Data System (ADS)

    Villanueva, Geronimo L.; Mumma, Michael J.; Novak, Robert E.; Käufl, Hans-Ullrich; Hartogh, Paul; Encrenaz, Therese; Tokunaga, Alan; Khayat, Alain

    2014-11-01

    Deuterium fractionation is a powerful metric revealing information about the cycle of water on Mars, and most importantly informing about its stability on short-term (diurnal) and long-term (seasonal) scales. The vapor pressures of HDO and H2O differ significantly, making the condensation/sublimation cycle of the isotopologues strongly susceptible to the ambient temperature, saturation level and existence of condensation nuclei. Until recently, only isolated (in time and in space) measurements of D/H in the atmosphere were available, which were incorrectly assumed to be representative of the bulk atmosphere. Spatially resolved measurements of D/H at different times of day and seasons are necessary to disentangle local from global phenomena, and to possibly identify newy found sources of water on Mars. We have addressed these concerns by acquiring full 2D maps of Mars for a broad range of seasons using high spectral resolution data at ground-based telescopes (Keck/NIRSPEC, VLT/CRIRES, NASA-IRTF/CSHELL). Our maps sample the full observable disk of Mars on 8 dates, spanning from late northern winter to late northern spring on Mars (Ls = 335°, 50°, 71°, 83°). The dates encompass the critical time as the northern polar cap sublimes and replenishes the atmosphere with water. By stepping the instrument’s slit across the planet, we obtained full E-W and N-S coverage across the observable disk, allowing us to sample the short-term diurnal variations and the hemispheric seasonal effects. Our maps reveal significant diurnal and seasonal variability, together with a noticeable variation of the D/H ratio with topography (that we associate to the formation of clouds). We will present global maps of D/H acquired from 2008-2014, and will discuss possible scenarios to explain the observations.This work was partially funded by grants from NASA's Planetary Astronomy Program (344-32-51-96), NASA’s Mars Fundamental Research Program (203959.02.02.20.29), NASA’s Astrobiology

  1. Metabolomics reveal 1-palmitoyl lysophosphatidylcholine production by peroxisome proliferator-activated receptor α.

    PubMed

    Takahashi, Haruya; Goto, Tsuyoshi; Yamazaki, Yota; Kamakari, Kosuke; Hirata, Mariko; Suzuki, Hideyuki; Shibata, Daisuke; Nakata, Rieko; Inoue, Hiroyasu; Takahashi, Nobuyuki; Kawada, Teruo

    2015-02-01

    PPARα is well known as a master regulator of lipid metabolism. PPARα activation enhances fatty acid oxidation and decreases the levels of circulating and cellular lipids in obese diabetic patients. Although PPARα target genes are widely known, little is known about the alteration of plasma and liver metabolites during PPARα activation. Here, we report that metabolome analysis-implicated upregulation of many plasma lysoGP species during bezafibrate (PPARα agonist) treatment. In particular, 1-palmitoyl lysophosphatidylcholine [LPC(16:0)] is increased by bezafibrate treatment in both plasma and liver. In mouse primary hepatocytes, the secretion of LPC(16:0) increased on PPARα activation, and this effect was attenuated by PPARα antagonist treatment. We demonstrated that Pla2g7 gene expression levels in the murine hepatocytes were increased by PPARα activation, and the secretion of LPC(16:0) was suppressed by Pla2g7 siRNA treatment. Interestingly, LPC(16:0) activates PPARα and induces the expression of PPARα target genes in hepatocytes. Furthermore, we showed that LPC(16:0) has the ability to recover glucose uptake in adipocytes induced insulin resistance. These results reveal that LPC(16:0) is induced by PPARα activation in hepatocytes; LPC(16:0) contributes to the upregulation of PPARα target genes in hepatocytes and the recovery of glucose uptake in insulin-resistant adipocytes. PMID:25510248

  2. Structural snapshots reveal distinct mechanisms of procaspase-3 and -7 activation

    PubMed Central

    Thomsen, Nathan D.; Koerber, James T.; Wells, James A.

    2013-01-01

    Procaspase-3 (P3) and procaspase-7 (P7) are activated through proteolytic maturation to form caspase-3 (C3) and caspase-7 (C7), respectively, which serve overlapping but nonredundant roles as the executioners of apoptosis in humans. However, it is unclear if differences in P3 and P7 maturation mechanisms underlie their unique biological functions, as the structure of P3 remains unknown. Here, we report structures of P3 in a catalytically inactive conformation, structures of P3 and P7 bound to covalent peptide inhibitors that reveal the active conformation of the zymogens, and the structure of a partially matured C7:P7 heterodimer. Along with a biochemical analysis, we show that P3 is catalytically inactive and matures through a symmetric all-or-nothing process. In contrast, P7 contains latent catalytic activity and matures through an asymmetric and tiered mechanism, suggesting a lower threshold for activation. Finally, we use our structures to design a selection strategy for conformation specific antibody fragments that stimulate procaspase activity, showing that executioner procaspase conformational equilibrium can be rationally modulated. Our studies provide a structural framework that may help to explain the unique roles of these important proapoptotic enzymes, and suggest general strategies for the discovery of proenzyme activators. PMID:23650375

  3. Metabolomics reveal 1-palmitoyl lysophosphatidylcholine production by peroxisome proliferator-activated receptor α[S

    PubMed Central

    Takahashi, Haruya; Goto, Tsuyoshi; Yamazaki, Yota; Kamakari, Kosuke; Hirata, Mariko; Suzuki, Hideyuki; Shibata, Daisuke; Nakata, Rieko; Inoue, Hiroyasu; Takahashi, Nobuyuki; Kawada, Teruo

    2015-01-01

    PPARα is well known as a master regulator of lipid metabolism. PPARα activation enhances fatty acid oxidation and decreases the levels of circulating and cellular lipids in obese diabetic patients. Although PPARα target genes are widely known, little is known about the alteration of plasma and liver metabolites during PPARα activation. Here, we report that metabolome analysis-implicated upregulation of many plasma lysoGP species during bezafibrate (PPARα agonist) treatment. In particular, 1-palmitoyl lysophosphatidylcholine [LPC(16:0)] is increased by bezaf­ibrate treatment in both plasma and liver. In mouse primary hepatocytes, the secretion of LPC(16:0) increased on PPARα activation, and this effect was attenuated by PPARα antagonist treatment. We demonstrated that Pla2g7 gene expression levels in the murine hepatocytes were increased by PPARα activation, and the secretion of LPC(16:0) was suppressed by Pla2g7 siRNA treatment. Interestingly, LPC(16:0) activates PPARα and induces the expression of PPARα target genes in hepatocytes. Furthermore, we showed that LPC(16:0) has the ability to recover glucose uptake in adipocytes induced insulin resistance. These results reveal that LPC(16:0) is induced by PPARα activation in hepatocytes; LPC(16:0) contributes to the upregulation of PPARα target genes in hepatocytes and the recovery of glucose uptake in insulin-resistant adipocytes. PMID:25510248

  4. Small business activity does not measure entrepreneurship.

    PubMed

    Henrekson, Magnus; Sanandaji, Tino

    2014-02-01

    Entrepreneurship policy mainly aims to promote innovative Schumpeterian entrepreneurship. However, the rate of entrepreneurship is commonly proxied using quantity-based metrics, such as small business activity, the self-employment rate, or the number of startups. We argue that those metrics give rise to misleading inferences regarding high-impact Schumpeterian entrepreneurship. To unambiguously identify high-impact entrepreneurs we focus on self-made billionaires (in US dollars) who appear on Forbes Magazine's list and who became wealthy by founding new firms. We identify 996 such billionaire entrepreneurs in 50 countries in 1996-2010, a systematic cross-country study of billionaire entrepreneurs. The rate of billionaire entrepreneurs correlates negatively with self-employment, small business ownership, and firm startup rates. Countries with higher income, higher trust, lower taxes, more venture capital investment, and lower regulatory burdens have higher billionaire entrepreneurship rates but less self-employment. Despite its limitations, the number of billionaire entrepreneurs appears to be a plausible cross-country measure of Schumpeterian entrepreneurship. PMID:24449873

  5. Small business activity does not measure entrepreneurship

    PubMed Central

    Henrekson, Magnus; Sanandaji, Tino

    2014-01-01

    Entrepreneurship policy mainly aims to promote innovative Schumpeterian entrepreneurship. However, the rate of entrepreneurship is commonly proxied using quantity-based metrics, such as small business activity, the self-employment rate, or the number of startups. We argue that those metrics give rise to misleading inferences regarding high-impact Schumpeterian entrepreneurship. To unambiguously identify high-impact entrepreneurs we focus on self-made billionaires (in US dollars) who appear on Forbes Magazine’s list and who became wealthy by founding new firms. We identify 996 such billionaire entrepreneurs in 50 countries in 1996–2010, a systematic cross-country study of billionaire entrepreneurs. The rate of billionaire entrepreneurs correlates negatively with self-employment, small business ownership, and firm startup rates. Countries with higher income, higher trust, lower taxes, more venture capital investment, and lower regulatory burdens have higher billionaire entrepreneurship rates but less self-employment. Despite its limitations, the number of billionaire entrepreneurs appears to be a plausible cross-country measure of Schumpeterian entrepreneurship. PMID:24449873

  6. Discoveries from Revisiting Apollo Direct Active Measurements of Lunar Dust

    NASA Astrophysics Data System (ADS)

    O'Brien, Brian

    2010-05-01

    New missions to the moon being developed by China, Japan, India, USA, Russia and Europe and possibilities of human missions about 2020 face the reality that 6 Apollo expeditions did not totally manage or mitigate effects of easily-mobilised and very "sticky" lunar dust on humans and hardware. Laboratory and theoretical modelling cannot reliably simulate the complex lunar environments that affect dynamical movements of lunar dust. The only direct active measurements of lunar dust during Apollo were made by matchbox-sized minimalist Dust Detector Experiments (DDEs) deployed to transmit some 30 million digital measurements from Apollo 11, 12, 14 and 15. These were misplaced or relatively ignored until 2009, when a self-funded suite of discoveries (O'Brien Geophys. Research Letters FIX 6 May 2099) revealed unexpected properties of lunar dust, such as the adhesive force being stronger as illumination increased. We give the first reports of contrasting effects, contamination or cleansing, from rocket exhausts of Apollo 11, 12, 14 and 15 Lunar Modules leaving the moon. We further strengthen the importance of collateral dust inadvertently splashed on Apollo hardware by human activities. Dust management designs and mission plans require optimum use of such in situ measurements, extended by laboratory simulations and theoretical modelling.

  7. Phenotype Specific Analyses Reveal Distinct Regulatory Mechanism for Chronically Activated p53

    PubMed Central

    Cairns, Jonathan M.; Menon, Suraj; Pérez-Mancera, Pedro A.; Tomimatsu, Kosuke; Bermejo-Rodriguez, Camino; Ito, Yoko; Chandra, Tamir; Narita, Masako; Lyons, Scott K.; Lynch, Andy G.; Kimura, Hiroshi; Ohbayashi, Tetsuya; Tavaré, Simon; Narita, Masashi

    2015-01-01

    The downstream functions of the DNA binding tumor suppressor p53 vary depending on the cellular context, and persistent p53 activation has recently been implicated in tumor suppression and senescence. However, genome-wide information about p53-target gene regulation has been derived mostly from acute genotoxic conditions. Using ChIP-seq and expression data, we have found distinct p53 binding profiles between acutely activated (through DNA damage) and chronically activated (in senescent or pro-apoptotic conditions) p53. Compared to the classical ‘acute’ p53 binding profile, ‘chronic’ p53 peaks were closely associated with CpG-islands. Furthermore, the chronic CpG-island binding of p53 conferred distinct expression patterns between senescent and pro-apoptotic conditions. Using the p53 targets seen in the chronic conditions together with external high-throughput datasets, we have built p53 networks that revealed extensive self-regulatory ‘p53 hubs’ where p53 and many p53 targets can physically interact with each other. Integrating these results with public clinical datasets identified the cancer-associated lipogenic enzyme, SCD, which we found to be directly repressed by p53 through the CpG-island promoter, providing a mechanistic link between p53 and the ‘lipogenic phenotype’, a hallmark of cancer. Our data reveal distinct phenotype associations of chronic p53 targets that underlie specific gene regulatory mechanisms. PMID:25790137

  8. Field-scale tracking of active methane-oxidizing communities in a landfill cover soil reveals spatial and seasonal variability.

    PubMed

    Henneberger, Ruth; Chiri, Eleonora; Bodelier, Paul E L; Frenzel, Peter; Lüke, Claudia; Schroth, Martin H

    2015-05-01

    Aerobic methane-oxidizing bacteria (MOB) in soils mitigate methane (CH4 ) emissions. We assessed spatial and seasonal differences in active MOB communities in a landfill cover soil characterized by highly variable environmental conditions. Field-based measurements of CH4 oxidation activity and stable-isotope probing of polar lipid-derived fatty acids (PLFA-SIP) were complemented by microarray analysis of pmoA genes and transcripts, linking diversity and function at the field scale. In situ CH4 oxidation rates varied between sites and were generally one order of magnitude lower in winter compared with summer. Results from PLFA-SIP and pmoA transcripts were largely congruent, revealing distinct spatial and seasonal clustering. Overall, active MOB communities were highly diverse. Type Ia MOB, specifically Methylomonas and Methylobacter, were key drivers for CH4 oxidation, particularly at a high-activity site. Type II MOB were mainly active at a site showing substantial fluctuations in CH4 loading and soil moisture content. Notably, Upland Soil Cluster-gamma-related pmoA transcripts were also detected, indicating concurrent oxidation of atmospheric CH4 . Spatial separation was less distinct in winter, with Methylobacter and uncultured MOB mediating CH4 oxidation. We propose that high diversity of active MOB communities in this soil is promoted by high variability in environmental conditions, facilitating substantial removal of CH4 generated in the waste body. PMID:25186436

  9. Cofactor bypass variants reveal a conformational control mechanism governing cell wall polymerase activity.

    PubMed

    Markovski, Monica; Bohrhunter, Jessica L; Lupoli, Tania J; Uehara, Tsuyoshi; Walker, Suzanne; Kahne, Daniel E; Bernhardt, Thomas G

    2016-04-26

    To fortify their cytoplasmic membrane and protect it from osmotic rupture, most bacteria surround themselves with a peptidoglycan (PG) exoskeleton synthesized by the penicillin-binding proteins (PBPs). As their name implies, these proteins are the targets of penicillin and related antibiotics. We and others have shown that the PG synthases PBP1b and PBP1a of Escherichia coli require the outer membrane lipoproteins LpoA and LpoB, respectively, for their in vivo function. Although it has been demonstrated that LpoB activates the PG polymerization activity of PBP1b in vitro, the mechanism of activation and its physiological relevance have remained unclear. We therefore selected for variants of PBP1b (PBP1b*) that bypass the LpoB requirement for in vivo function, reasoning that they would shed light on LpoB function and its activation mechanism. Several of these PBP1b variants were isolated and displayed elevated polymerization activity in vitro, indicating that the activation of glycan polymer growth is indeed one of the relevant functions of LpoB in vivo. Moreover, the location of amino acid substitutions causing the bypass phenotype on the PBP1b structure support a model in which polymerization activation proceeds via the induction of a conformational change in PBP1b initiated by LpoB binding to its UB2H domain, followed by its transmission to the glycosyl transferase active site. Finally, phenotypic analysis of strains carrying a PBP1b* variant revealed that the PBP1b-LpoB complex is most likely not providing an important physical link between the inner and outer membranes at the division site, as has been previously proposed. PMID:27071112

  10. Dynamic Transcription Factor Activity Profiles Reveal Key Regulatory Interactions During Megakaryocytic and Erythroid Differentiation

    PubMed Central

    Duncan, Mark T.; Shin, Seungjin; Wu, Jia J.; Mays, Zachary; Weng, Stanley; Bagheri, Neda; Miller, William M.; Shea, Lonnie D.

    2014-01-01

    The directed differentiation toward erythroid (E) or megakaryocytic (MK) lineages by the MK-E progenitor (MEP) could enhance the ex vivo generation of red blood cells and platelets for therapeutic transfusions. The lineage choice at the MEP bifurcation is controlled in large part by activity within the intracellular signal transduction network, the output of which determines the activity of transcription factors (TFs) and ultimately gene expression. Although many TFs have been implicated, E or MK differentiation is a complex process requiring multiple days, and the dynamics of TF activities during commitment and terminal maturation are relatively unexplored. Herein, we applied a living cell array for the large-scale, dynamic quantification of TF activities during MEP bifurcation. A panel of hematopoietic TFs (GATA-1, GATA-2, SCL/TAL1, FLI-1, NF-E2, PU.1, c-Myb) was characterized during E and MK differentiation of bipotent K562 cells. Dynamic TF activity profiles associated with differentiation towards each lineage were identified, and validated with previous reports. From these activity profiles, we show that GATA-1 is an important hub during early hemin- and PMA-induced differentiation, and reveal several characteristic TF interactions for E and MK differentiation that confirm regulatory mechanisms documented in the literature. Additionally, we highlight several novel TF interactions at various stages of E and MK differentiation. Furthermore, we investigated the mechanism by which nicotinamide (NIC) promoted terminal MK maturation using an MK-committed cell line, CHRF-288-11 (CHRF). Concomitant with its enhancement of ploidy, NIC strongly enhanced the activity of three TFs with known involvement in terminal MK maturation: FLI-1, NF-E2, and p53. Dynamic profiling of TF activity represents a novel tool to complement traditional assays focused on mRNA and protein expression levels to understand progenitor cell differentiation. PMID:24853077

  11. Dynamic transcription factor activity profiles reveal key regulatory interactions during megakaryocytic and erythroid differentiation.

    PubMed

    Duncan, Mark T; Shin, Seungjin; Wu, Jia J; Mays, Zachary; Weng, Stanley; Bagheri, Neda; Miller, William M; Shea, Lonnie D

    2014-10-01

    The directed differentiation toward erythroid (E) or megakaryocytic (MK) lineages by the MK-E progenitor (MEP) could enhance the ex vivo generation of red blood cells and platelets for therapeutic transfusions. The lineage choice at the MEP bifurcation is controlled in large part by activity within the intracellular signal transduction network, the output of which determines the activity of transcription factors (TFs) and ultimately gene expression. Although many TFs have been implicated, E or MK differentiation is a complex process requiring multiple days, and the dynamics of TF activities during commitment and terminal maturation are relatively unexplored. Herein, we applied a living cell array for the large-scale, dynamic quantification of TF activities during MEP bifurcation. A panel of hematopoietic TFs (GATA-1, GATA-2, SCL/TAL1, FLI-1, NF-E2, PU.1, c-Myb) was characterized during E and MK differentiation of bipotent K562 cells. Dynamic TF activity profiles associated with differentiation towards each lineage were identified, and validated with previous reports. From these activity profiles, we show that GATA-1 is an important hub during early hemin- and PMA-induced differentiation, and reveal several characteristic TF interactions for E and MK differentiation that confirm regulatory mechanisms documented in the literature. Additionally, we highlight several novel TF interactions at various stages of E and MK differentiation. Furthermore, we investigated the mechanism by which nicotinamide (NIC) promoted terminal MK maturation using an MK-committed cell line, CHRF-288-11 (CHRF). Concomitant with its enhancement of ploidy, NIC strongly enhanced the activity of three TFs with known involvement in terminal MK maturation: FLI-1, NF-E2, and p53. Dynamic profiling of TF activity represents a novel tool to complement traditional assays focused on mRNA and protein expression levels to understand progenitor cell differentiation. PMID:24853077

  12. Active-Site Monovalent Cations Revealed in a 1.55 Å Resolution Hammerhead Ribozyme Structure

    PubMed Central

    Anderson, Michael; Schultz, Eric P.; Martick, Monika; Scott, William G.

    2013-01-01

    We have obtained a 1.55 Å crystal structure of a hammerhead ribozyme derived from Schistosoma mansoni in conditions that permit detailed observations of Na+ ion binding in the ribozyme's active site. At least two such Na+ ions are observed. The first Na+ ion binds to the N7 of G10.1 and the adjacent A9 phosphate in a manner identical to that previously observed for divalent cations. A second Na+ ion binds to the Hoogsteen face of G12, the general base in the hammerhead cleavage reaction, thereby potentially dissipating the negative charge of the catalytically active enolate form of the nucleotide base. A potential but more ambiguous third site bridges the A9 and scissile phosphates in a manner consistent with previous predictions. Hammerhead ribozymes have been observed to be active in the presence of high concentrations of monovalent cations, including Na+, but the mechanism by which monovalent cations substitute for divalent cations in hammerhead catalysis remains unclear. Our results enable us to suggest that Na+ directly and specifically substitutes for divalent cations in the hammerhead active site. The detailed geometry of the pre-catalytic active site complex is also revealed with a new level of precision, thanks to the quality of the electron density maps obtained from what is currently the highest resolution ribozyme structure in the protein data bank. PMID:23711504

  13. Active sensing associated with spatial learning reveals memory-based attention in an electric fish.

    PubMed

    Jun, James J; Longtin, André; Maler, Leonard

    2016-05-01

    Active sensing behaviors reveal what an animal is attending to and how it changes with learning. Gymnotus sp, a gymnotiform weakly electric fish, generates an electric organ discharge (EOD) as discrete pulses to actively sense its surroundings. We monitored freely behaving gymnotid fish in a large dark "maze" and extracted their trajectories and EOD pulse pattern and rate while they learned to find food with electrically detectable landmarks as cues. After training, they more rapidly found food using shorter, more stereotyped trajectories and spent more time near the food location. We observed three forms of active sensing: sustained high EOD rates per unit distance (sampling density), transient large increases in EOD rate (E-scans) and stereotyped scanning movements (B-scans) were initially strong at landmarks and food, but, after learning, intensified only at the food location. During probe (no food) trials, after learning, the fish's search area and intense active sampling was still centered on the missing food location, but now also increased near landmarks. We hypothesize that active sensing is a behavioral manifestation of attention and essential for spatial learning; the fish use spatial memory of landmarks and path integration to reach the expected food location and confine their attention to this region. PMID:26961107

  14. Equilibrium physics breakdown reveals the active nature of red blood cell flickering

    NASA Astrophysics Data System (ADS)

    Turlier, Herve; Fedosov, Dmitry; Auth, Thorsten; Gov, Nir S.; Sykes, Cecile; Joanny, Jean-Francois; Gompper, Gerhard; Betz, Timo

    2015-03-01

    Red blood cell membrane flickering stimulated an abundant biological, biophysical and biochemical literature over the past 50 years. While the phenomenon has been interpreted as thermal fluctuations of the cell membrane, recent results suggest the involvement of metabolic processes. However, to date there is no direct and conclusive evidence that an active force drives membrane flickering. By comparing membrane undulations and active microrheology measurements on single human erythrocytes, we show that flickering is partly driven by an active metabolic process, as it does not satisfy the equilibrium fluctuation-dissipation relation on timescales slower than 100ms. Analytical and numerical models of the red blood cell reproduce experimental results. The analytical model assumes that membrane activity results from reversible binding of the elastic spectrin network to the lipid bilayer and predicts active fluctuations to increase with local curvature and extensional prestress in the cytoskeleton. Our mean-field calculation shows that the strength and kinetics of the binding activity regulates thereupon both passive and active mechanical properties of the red blood cell. Numerical simulations explore other possible origins of active forces on the membrane and predict coherent timescales for the molecular underlying metabolic processes.

  15. 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

  16. Cloud-based simulations on Google Exacycle reveal ligand-modulation of GPCR activation pathways

    PubMed Central

    Bowman, Gregory R.; Konerding, David E.; Belov, Dan; Altman, Russ B.; Pande, Vijay S.

    2014-01-01

    Simulations can provide tremendous insight into atomistic details of biological mechanisms, but micro- to milliseconds timescales are historically only accessible on dedicated supercomputers. We demonstrate that cloud computing is a viable alternative, bringing long-timescale processes within reach of a broader community. We used Google's Exacycle cloud computing platform to simulate 2 milliseconds of dynamics of the β2 adrenergic receptor — a major drug target G protein-coupled receptor (GPCR). Markov state models aggregate independent simulations into a single statistical model that is validated by previous computational and experimental results. Moreover, our models provide an atomistic description of the activation of a GPCR, revealing multiple activation pathways. Agonists and inverse agonists interact differentially with these pathways, with profound implications for drug design PMID:24345941

  17. Single-cell transcriptome analyses reveal signals to activate dormant neural stem cells.

    PubMed

    Luo, Yuping; Coskun, Volkan; Liang, Aibing; Yu, Juehua; Cheng, Liming; Ge, Weihong; Shi, Zhanping; Zhang, Kunshan; Li, Chun; Cui, Yaru; Lin, Haijun; Luo, Dandan; Wang, Junbang; Lin, Connie; Dai, Zachary; Zhu, Hongwen; Zhang, Jun; Liu, Jie; Liu, Hailiang; deVellis, Jean; Horvath, Steve; Sun, Yi Eve; Li, Siguang

    2015-05-21

    The scarcity of tissue-specific stem cells and the complexity of their surrounding environment have made molecular characterization of these cells particularly challenging. Through single-cell transcriptome and weighted gene co-expression network analysis (WGCNA), we uncovered molecular properties of CD133(+)/GFAP(-) ependymal (E) cells in the adult mouse forebrain neurogenic zone. Surprisingly, prominent hub genes of the gene network unique to ependymal CD133(+)/GFAP(-) quiescent cells were enriched for immune-responsive genes, as well as genes encoding receptors for angiogenic factors. Administration of vascular endothelial growth factor (VEGF) activated CD133(+) ependymal neural stem cells (NSCs), lining not only the lateral but also the fourth ventricles and, together with basic fibroblast growth factor (bFGF), elicited subsequent neural lineage differentiation and migration. This study revealed the existence of dormant ependymal NSCs throughout the ventricular surface of the CNS, as well as signals abundant after injury for their activation. PMID:26000486

  18. Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

    NASA Astrophysics Data System (ADS)

    Kohlhoff, Kai J.; Shukla, Diwakar; Lawrenz, Morgan; Bowman, Gregory R.; Konerding, David E.; Belov, Dan; Altman, Russ B.; Pande, Vijay S.

    2014-01-01

    Simulations can provide tremendous insight into the atomistic details of biological mechanisms, but micro- to millisecond timescales are historically only accessible on dedicated supercomputers. We demonstrate that cloud computing is a viable alternative that brings long-timescale processes within reach of a broader community. We used Google's Exacycle cloud-computing platform to simulate two milliseconds of dynamics of a major drug target, the G-protein-coupled receptor β2AR. Markov state models aggregate independent simulations into a single statistical model that is validated by previous computational and experimental results. Moreover, our models provide an atomistic description of the activation of a G-protein-coupled receptor and reveal multiple activation pathways. Agonists and inverse agonists interact differentially with these pathways, with profound implications for drug design.

  19. TAF4 Inactivation Reveals the 3 Dimensional Growth Promoting Activities of Collagen 6A3

    PubMed Central

    Duluc, Isabelle; Vicaire, Serge; Philipps, Muriel; Freund, Jean-Noel; Davidson, Irwin

    2014-01-01

    Collagen 6A3 (Col6a3), a component of extracellular matrix, is often up-regulated in tumours and is believed to play a pro-oncogenic role. However the mechanisms of its tumorigenic activity are poorly understood. We show here that Col6a3 is highly expressed in densely growing mouse embryonic fibroblasts (MEFs). In MEFs where the TAF4 subunit of general transcription factor IID (TFIID) has been inactivated, elevated Col6a3 expression prevents contact inhibition promoting their 3 dimensional growth as foci and fibrospheres. Analyses of gene expression in densely growing Taf4−/− MEFs revealed repression of the Hippo pathway and activation of Wnt signalling. The Hippo activator Kibra/Wwc1 is repressed under dense conditions in Taf4−/− MEFs, leading to nuclear accumulation of the proliferation factor YAP1 in the cells forming 3D foci. At the same time, Wnt9a is activated and the Sfrp2 antagonist of Wnt signalling is repressed. Surprisingly, treatment of Taf4−/− MEFs with all-trans retinoic acid (ATRA) restores contact inhibition suppressing 3D growth. ATRA represses Col6a3 expression independently of TAF4 expression and Col6a3 silencing is sufficient to restore contact inhibition in Taf4−/− MEFs and to suppress 3D growth by reactivating Kibra expression to induce Hippo signalling and by inducing Sfrp2 expression to antagonize Wnt signalling. All together, these results reveal a critical role for Col6a3 in regulating both Hippo and Wnt signalling to promote 3D growth, and show that the TFIID subunit TAF4 is essential to restrain the growth promoting properties of Col6a3. Our data provide new insight into the role of extra cellular matrix components in regulating cell growth. PMID:24498316

  20. Methods to Measure Physical Activity Behaviors in Health Education Research

    ERIC Educational Resources Information Center

    Fitzhugh, Eugene C.

    2015-01-01

    Regular physical activity (PA) is an important concept to measure in health education research. The health education researcher might need to measure physical activity because it is the primary measure of interest, or PA might be a confounding measure that needs to be controlled for in statistical analysis. The purpose of this commentary is to…

  1. Microfluidic Investigation Reveals Distinct Roles for Actin Cytoskeleton and Myosin II Activity in Capillary Leukocyte Trafficking

    PubMed Central

    Gabriele, Sylvain; Benoliel, Anne-Marie; Bongrand, Pierre; Théodoly, Olivier

    2009-01-01

    Circulating leukocyte sequestration in pulmonary capillaries is arguably the initiating event of lung injury in acute respiratory distress syndrome. We present a microfluidic investigation of the roles of actin organization and myosin II activity during the different stages of leukocyte trafficking through narrow capillaries (entry, transit and shape relaxation) using specific drugs (latrunculin A, jasplakinolide, and blebbistatin). The deformation rate during entry reveals that cell stiffness depends strongly on F-actin organization and hardly on myosin II activity, supporting a microfilament role in leukocyte sequestration. In the transit stage, cell friction is influenced by stiffness, demonstrating that the actin network is not completely broken after a forced entry into a capillary. Conversely, membrane unfolding was independent of leukocyte stiffness. The surface area of sequestered leukocytes increased by up to 160% in the absence of myosin II activity, showing the major role of molecular motors in microvilli wrinkling and zipping. Finally, cell shape relaxation was largely independent of both actin organization and myosin II activity, whereas a deformed state was required for normal trafficking through capillary segments. PMID:19450501

  2. Rapid ester biosynthesis screening reveals a high activity alcohol-O-acyltransferase (AATase) from tomato fruit.

    PubMed

    Lin, Jyun-Liang; Zhu, Jie; Wheeldon, Ian

    2016-05-01

    Ethyl and acetate esters are naturally produced in various yeasts, plants, and bacteria. The biosynthetic pathways that produce these esters share a common reaction step, the condensation of acetyl/acyl-CoA with an alcohol by alcohol-O-acetyl/acyltransferase (AATase). Recent metabolic engineering efforts exploit AATase activity to produce fatty acid ethyl esters as potential diesel fuel replacements as well as short- and medium-chain volatile esters as fragrance and flavor compounds. These efforts have been limited by the lack of a rapid screen to quantify ester biosynthesis. Enzyme engineering efforts have also been limited by the lack of a high throughput screen for AATase activity. Here, we developed a high throughput assay for AATase activity and used this assay to discover a high activity AATase from tomato fruit, Solanum lycopersicum (Atf-S.l). Atf1-S.l exhibited broad specificity towards acyl-CoAs with chain length from C4 to C10 and was specific towards 1-pentanol. The AATase screen also revealed new acyl-CoA substrate specificities for Atf1, Atf2, Eht1, and Eeb1 from Saccharomyces cerevisiae, and Atf-C.m from melon fruit, Cucumis melo, thus increasing the pool of characterized AATases that can be used in ester biosynthesis of ester-based fragrance and flavor compounds as well as fatty acid ethyl ester biofuels. PMID:26814045

  3. Interdomain conformational changes in Akt activation revealed by chemical cross-linking and tandem mass spectrometry.

    PubMed

    Huang, Bill X; Kim, Hee-Yong

    2006-06-01

    Akt, a serine/threonine kinase, plays a critical role in cell survival. Upon growth factor receptor stimulation, cytosolic Akt is recruited to the plasma membrane by phospholipid binding and activated through phosphorylation at Thr(308) and Ser(473). Although crystal structures for the parts of Akt have been reported, neither the three-dimensional structure of the whole molecule nor sequential conformational changes during activation have been demonstrated. In this study, we demonstrated that Akt undergoes dramatic interdomain conformational changes during activation processes by probing the three-dimensional structure of full-length Akt in solution using chemical cross-linking and tandem mass spectrometry. The cross-linking results not only provided new structural information but also revealed distinctive spatial arrangements of individual domains in the Akt molecule in resting, membrane-interacted, phosphorylated, and substrate-bound states. Our data allowed a new model for stepwise interdomain conformational changes in Akt activation sequence, setting a stage for the further investigation on Akt-membrane, Akt-protein, and/or Akt-drug interactions in solution to understand molecular mechanisms involved in physiological and pathophysiological processes of cell survival. PMID:16531397

  4. Concentration-Discharge Patterns Revealed from High Resolution Nitrate Measurements in Agricultural Landscapes

    NASA Astrophysics Data System (ADS)

    Boland, S. J.; Basu, N. B.

    2012-12-01

    Riverine export of nutrients is a major component of nutrient cycles, particularly with respect to nitrogen; ~ 25 percent of terrestrially applied nitrogen (N) is removed via riverine export. Understanding the patterns in N export during a storm event is critical for developing a conceptual model of the dominant processes and pathways of N transformation, and designing appropriate management strategies to mitigate N pollution in streams and receiving water bodies. Most studies however, are limited by the lack of high-resolution water quality data to elucidate these pathways and mechanisms. We explored concentration-discharge relationships using high-resolution (15 minute) discharge (Q) and nitrate concentration (C) data (measured using an in-situ Nitratax Sonde) at multiple nested scales (from 151.3 km2 to 8900 km2) in two watersheds in Iowa: Clear Creek Watershed and the Raccoon River watershed. Three distinct regimes of nitrate transport were revealed: (1) a linear regime in which C increases with increasing Q, (2) a saturation regime in which C remains constant against increasing Q, and (3) a dilution regime in which concentration decreases as Q increases. The tight clustering of the data along these patterns is indicative of emergent behavior in such human-dominated systems. All three regimes were apparent in the Raccoon River Watershed, while only the saturation and dilution regimes were apparent in the Clear Creek Watershed. We hypothesize that surface flow is dominant in the Clear Creek Watershed leading to a saturation/dilution regimes, while subsurface flow is dominant in the more heavily tile-drained Raccoon River Watershed, leading to the occurrence of all three regimes. A parsimonious model was developed to test the hypothesis and develop C-Q patterns as a function of the partitioning of flow through the different pathways.

  5. The interior of 67P/C-G nucleus revealed by CONSERT measurements and simulations

    NASA Astrophysics Data System (ADS)

    Levasseur-Regourd, A.; Kofman, Wlodek; Herique, Alain; Ciarletti, Valérie; Heggy, Essam; Lasue, Jérémie

    2015-11-01

    The CONSERT bistatic radar onboard the Rosetta spacecraft and the Philae lander has begun to reveal the internal structure of Comet 67P/Churyumov-Gerasimenko, through radio tomographic mapping between the lander and main spacecraft. The small lobe was found to be structurally homogeneous, at the spatial scale of ten meters, corresponding to a few wavelengths of CONSERT instrument [1]. The real part of the relative permittivity has been derived from the travel time of the strongest signals obtained on 12-13 November 2014, from Philae final landing site. Since the final position of the lander was not accurately defined, numerous ray-tracing simulations were performed to constrain the ambiguities on Philae position using the known position of Rosetta and the propagation time and paths inside and outside the nucleus. A least square statistical analysis between measurements and simulations lead to deduce a bulk relative permittivity about (1.27 ± 0.1); meanwhile, the uncertainty in the lander location was reduced to an area of about 21 by 34 square meters [1].Ongoing theoretical and experimental simulations are providing more insights on the nucleus properties. Numerical ray-tracing simulations of the propagation at grazing angles have been performed for various subsurface permittivity models. They establish that a permittivity gradient in the shallow sub-surface would have a strong effect on the wave propagation. The permittivity probably decreases with depth, suggesting that a significant increase of dust/ice ratio with depth is unlikely [2]. Laboratory simulations of the permittivity of subsurface cometary analog materials [3], and of surface porous analog samples [4] have taken place. Results suggest 67P dielectric properties to be mainly controlled by porosity, the dust/ice volumetric ratio to range from 0.4 to 2.6 and the porosity to range from 75 to 85% [1]. Further on-going laboratory measurements will be discussed.Supports from CNES and NASA are acknowledged

  6. Characterization of the circulating hemocytes in mud crab (Scylla olivacea) revealed phenoloxidase activity.

    PubMed

    Mangkalanan, Seksan; Sanguanrat, Piyachat; Utairangsri, Tanatchaporn; Sritunyalucksana, Kallaya; Krittanai, Chartchai

    2014-05-01

    This study focused on an isolation and characterization of the circulating hemocytes in mud crab, Scylla olivacea. Isolation of specific cell types of hemocytes from crab hemolymph was accomplished by using 60% Percoll density gradient centrifugation. Four separated bands of the hemocytes were successfully obtained. Characterization of these isolated hemocytes by light microscope using trypan blue-rose bengal staining, rose bengal-hematoxilin staining, and phase contrast revealed four distinct types of hemocyte cells. Using their specific morphology and granularity, they were identified as hyaline cell (HC), small granular cell (SGC), large granular cell (LGC) and mixed granular cell (MGC). Transmission electron microscopy (TEM) revealed more details on specific cell size, size of cytoplasmic granule, and nuclear to cytoplasmic ratio, and confirmed the classification. Relative abundance of these cells types in the hemolymph of an adult crab were 15.50±8.22% for HC, 55.50±7.15% for SGC, 13.50±5.28% for LGC, and 15.50±3.50% for MGC. Proteomic analysis of protein expression for each specific cell types by two-dimensional electrophoresis identified two highly abundant proteins, prophenoloxidase (ProPO) and peroxinectin in LGC. Determination of phenoloxidase (PO) activity in each isolated cell types using in vitro and in situ chemical assays confirmed the presence of PO activity only in LGC. Based on an increased PO activity of crab hemolymph during the course of White Spot Syndrome Virus (WSSV) infection, these results suggest that prophenoloxidase pathway was employed for host defense mechanism against WSSV and it may link to the role of large granular hemocyte. PMID:24316230

  7. Protrusion force microscopy reveals oscillatory force generation and mechanosensing activity of human macrophage podosomes.

    PubMed

    Labernadie, Anna; Bouissou, Anaïs; Delobelle, Patrick; Balor, Stéphanie; Voituriez, Raphael; Proag, Amsha; Fourquaux, Isabelle; Thibault, Christophe; Vieu, Christophe; Poincloux, Renaud; Charrière, Guillaume M; Maridonneau-Parini, Isabelle

    2014-01-01

    Podosomes are adhesion structures formed in monocyte-derived cells. They are F-actin-rich columns perpendicular to the substrate surrounded by a ring of integrins. Here, to measure podosome protrusive forces, we designed an innovative experimental setup named protrusion force microscopy (PFM), which consists in measuring by atomic force microscopy the deformation induced by living cells onto a compliant Formvar sheet. By quantifying the heights of protrusions made by podosomes onto Formvar sheets, we estimate that a single podosome generates a protrusion force that increases with the stiffness of the substratum, which is a hallmark of mechanosensing activity. We show that the protrusive force generated at podosomes oscillates with a constant period and requires combined actomyosin contraction and actin polymerization. Finally, we elaborate a model to explain the mechanical and oscillatory activities of podosomes. Thus, PFM shows that podosomes are mechanosensing cell structures exerting a protrusive force. PMID:25385672

  8. Protrusion force microscopy reveals oscillatory force generation and mechanosensing activity of human macrophage podosomes

    NASA Astrophysics Data System (ADS)

    Labernadie, Anna; Bouissou, Anaïs; Delobelle, Patrick; Balor, Stéphanie; Voituriez, Raphael; Proag, Amsha; Fourquaux, Isabelle; Thibault, Christophe; Vieu, Christophe; Poincloux, Renaud; Charrière, Guillaume M.; Maridonneau-Parini, Isabelle

    2014-11-01

    Podosomes are adhesion structures formed in monocyte-derived cells. They are F-actin-rich columns perpendicular to the substrate surrounded by a ring of integrins. Here, to measure podosome protrusive forces, we designed an innovative experimental setup named protrusion force microscopy (PFM), which consists in measuring by atomic force microscopy the deformation induced by living cells onto a compliant Formvar sheet. By quantifying the heights of protrusions made by podosomes onto Formvar sheets, we estimate that a single podosome generates a protrusion force that increases with the stiffness of the substratum, which is a hallmark of mechanosensing activity. We show that the protrusive force generated at podosomes oscillates with a constant period and requires combined actomyosin contraction and actin polymerization. Finally, we elaborate a model to explain the mechanical and oscillatory activities of podosomes. Thus, PFM shows that podosomes are mechanosensing cell structures exerting a protrusive force.

  9. Relationship between balance and physical activity measured by an activity monitor in elderly COPD patients

    PubMed Central

    Iwakura, Masahiro; Okura, Kazuki; Shibata, Kazuyuki; Kawagoshi, Atsuyoshi; Sugawara, Keiyu; Takahashi, Hitomi; Shioya, Takanobu

    2016-01-01

    Background Little is known regarding the relationship between balance impairments and physical activity in COPD. There has been no study investigating the relationship between balance and objectively measured physical activity. Here we investigated the association between balance and physical activity measured by an activity monitor in elderly COPD patients. Materials and methods Twenty-two outpatients with COPD (mean age, 72±7 years; forced expiratory volume in 1 second, 53%±21% predicted) and 13 age-matched healthy control subjects (mean age, 72±6 years) participated in the study. We assessed all 35 subjects’ balance (one-leg standing test [OLST] times, Short Physical Performance Battery total scores, standing balance test scores, 4 m gait speed, and five-times sit-to-stand test [5STST]) and physical activity (daily steps and time spent in moderate-to-vigorous physical activity per day [MV-PA]). Possible confounders were assessed in the COPD group. The between-group differences in balance test scores and physical activity were analyzed. A correlation analysis and multivariate regression analysis were conducted in the COPD group. Results The COPD patients exhibited significant reductions in OLST times (P=0.033), Short Physical Performance Battery scores (P=0.013), 4 m gait speed (P<0.001), five-times sit-to-stand times (P=0.002), daily steps (P=0.003), and MV-PA (P=0.022) compared to the controls; the exception was the standing balance test scores. The correlation and multivariate regression analyses revealed significant independent associations between OLST times and daily steps (P<0.001) and between OLST times and MV-PA (P=0.014) in the COPD group after adjusting for possible confounding factors. Conclusion Impairments in balance and reductions in physical activity were observed in the COPD group. Deficits in balance are independently associated with physical inactivity. PMID:27445470

  10. Active mechanics in living oocytes reveal molecular-scale force kinetics

    NASA Astrophysics Data System (ADS)

    Ahmed, Wylie; Fodor, Etienne; Almonacid, Maria; Bussonnier, Matthias; Verlhac, Marie-Helene; Gov, Nir; Visco, Paolo; van Wijland, Frederic; Betz, Timo

    Unlike traditional materials, living cells actively generate forces at the molecular scale that change their structure and mechanical properties. This nonequilibrium activity is essential for cellular function, and drives processes such as cell division. Single molecule studies have uncovered the detailed force kinetics of isolated motor proteins in-vitro, however their behavior in-vivo has been elusive due to the complex environment inside the cell. Here, we quantify active forces and intracellular mechanics in living oocytes using in-vivo optical trapping and laser interferometry of endogenous vesicles. We integrate an experimental and theoretical framework to connect mesoscopic measurements of nonequilibrium properties to the underlying molecular- scale force kinetics. Our results show that force generation by myosin-V drives the cytoplasmic-skeleton out-of-equilibrium (at frequencies below 300 Hz) and actively softens the environment. In vivo myosin-V activity generates a force of F ~ 0 . 4 pN, with a power-stroke of length Δx ~ 20 nm and duration τ ~ 300 μs, that drives vesicle motion at vv ~ 320 nm/s. This framework is widely applicable to characterize living cells and other soft active materials.

  11. Transcriptomic Analysis of Musca domestica to Reveal Key Genes of the Prophenoloxidase-Activating System

    PubMed Central

    Li, Dianxiang; Liang, Yongli; Wang, Xianwei; Wang, Lei; Qi, Mei; Yu, Yang; Luan, Yuanyuan

    2015-01-01

    The proPO system regulates melanization in arthropods. However, the genes that are involved in the proPO system in housefly Musca domestica remain unclear. Thus, this study analyzed the combined transcriptome obtained from M. domestica larvae, pupae, and adults that were either normal or bacteria-challenged by an Escherichia coli and Staphylococcus aureus mixture. A total of 54,821,138 clean reads (4.93 Gb) were yielded by Illumina sequencing, which were de novo assembled into 89,842 unigenes. Of the 89,842 unigenes, based on a similarity search with known genes in other insects, 24 putative genes related to the proPO system were identified. Eight of the identified genes encoded for peptidoglycan recognition receptors, two encoded for prophenoloxidases, three encoded for prophenoloxidase-activating enzymes, and 11 encoded for serine proteinase inhibitors. The expression levels of these identified genes were investigated by qRT-PCR assay, which were consistent with expected activation process of the proPO system, and their activation functions were confirmed by the measurement of phenoloxidase activity in bacteria-infected larvae after proPO antibody blockage, suggesting these candidate genes might have potentially different roles in the activation of proPO system. Collectively, this study has provided the comprehensive transcriptomic data of an insect and some fundamental basis toward achieving understanding of the activation mechanisms and immune functions of the proPO system in M. domestica. PMID:26156588

  12. Activity Patterns of Free-Ranging Koalas (Phascolarctos cinereus) Revealed by Accelerometry

    PubMed Central

    Ryan, Michelle A.; Whisson, Desley A.; Holland, Greg J.; Arnould, John P. Y.

    2013-01-01

    An understanding of koala activity patterns is important for measuring the behavioral response of this species to environmental change, but to date has been limited by the logistical challenges of traditional field methodologies. We addressed this knowledge gap by using tri-axial accelerometer data loggers attached to VHF radio collars to examine activity patterns of adult male and female koalas in a high-density population at Cape Otway, Victoria, Australia. Data were obtained from 27 adult koalas over two 7-d periods during the breeding season: 12 in the early-breeding season in November 2010, and 15 in the late-breeding season in January 2011. Multiple 15 minute observation blocks on each animal were used for validation of activity patterns determined from the accelerometer data loggers. Accelerometry was effective in distinguishing between inactive (sleeping, resting) and active (grooming, feeding and moving) behaviors. Koalas were more active during the early-breeding season with a higher index of movement (overall dynamic body acceleration [ODBA]) for both males and females. Koalas showed a distinct temporal pattern of behavior, with most activity occurring from mid-afternoon to early morning. Accelerometry has potential for examining fine-scale behavior of a wide range of arboreal and terrestrial species. PMID:24224050

  13. On the way of revealing coactivator complexes cross-talk during transcriptional activation.

    PubMed

    Krasnov, Aleksey N; Mazina, Marina Yu; Nikolenko, Julia V; Vorobyeva, Nadezhda E

    2016-01-01

    Transcriptional activation is a complex, multistage process implemented by hundreds of proteins. Many transcriptional proteins are organized into coactivator complexes, which participate in transcription regulation at numerous genes and are a driver of this process. The molecular action mechanisms of coactivator complexes remain largely understudied. Relevant publications usually deal with the involvement of these complexes in the entire process of transcription, and only a few studies are aimed to elucidate their functions at its particular stages. This review summarizes available information on the participation of key coactivator complexes in transcriptional activation. The timing of coactivator complex binding/removal has been used for restructuring previously described information about the transcriptional process. Several major stages of transcriptional activation have been distinguished based on the presence of covalent histone modifications and general transcriptional factors, and the recruitment and/or removal phases have been determined for each coactivator included in analysis. Recruitment of Mediator, SWItch/Sucrose Non-Fermentable and NUcleosome Remodeling Factor complexes during transcription activation has been investigated thoroughly; CHD and INOsitol auxotrophy 80 families are less well studied. In most cases, the molecular mechanisms responsible for the removal of certain coactivator complexes after the termination of their functions at the promoters are still not understood. On the basis of the summarized information, we propose a scheme that illustrates the involvement of coactivator complexes in different stages of the transcription activation process. This scheme may help to gain a deeper insight into the molecular mechanism of functioning of coactivator complexes, find novel participants of the process, and reveal novel structural or functional connections between different coactivators. PMID:26913181

  14. Identification of Chronic Stress Activated Regions Reveals a Potential Recruited Circuit in Rat Brain

    PubMed Central

    Flak, Jonathan N.; Solomon, Matia B.; Jankord, Ryan; Krause, Eric G.; Herman, James P.

    2015-01-01

    Chronic stress induces pre-synaptic and post-synaptic modifications in the paraventricular nucleus of the hypothalamus (PVN) that are consistent with enhanced excitatory hypothalamo-pituitary-adrenocortical (HPA) axis drive. The brain regions mediating these molecular modifications are not known. We hypothesized that chronic variable stress (CVS) tonically activates stress-excitatory regions that interact with the PVN, culminating in stress facilitation. In order to identify chronically activated brain regions, ΔFosB, a documented marker of tonic neuronal activation, was assessed in known stress regulatory limbic and brainstem sites. Four experimental groups were included: CVS, repeated restraint (RR) (control for HPA habituation), animals weight-matched (WM) to CVS animals (control for changes in circulating metabolic factors due to reduced weight gain), and non-handled controls. CVS, but not RR or WM, induced adrenal hypertrophy, indicating that sustained HPA axis drive only occurred in the CVS group. CVS (but not RR or WM) selectively increased the number of FosB/ΔFosB nuclei in the nucleus of the solitary tract, posterior hypothalamic nucleus, and both the infralimbic and prelimbic divisions of the medial prefrontal cortex, indicating an involvement of these regions in chronic drive of the HPA axis. Increases in FosB/ΔFosB-immunoreactive cells were observed following both RR and CVS in the other regions (e.g., the dorsomedial hypothalamus), suggesting activation by both habituating and non-habituating stress conditions. The data suggest that unpredictable stress uniquely activates interconnected cortical, hypothalamic, and brainstem nuclei, potentially revealing the existence of a recruited circuitry mediating chronic drive of brain stress effector systems. PMID:22789020

  15. Lost for emotion words: what motor and limbic brain activity reveals about autism and semantic theory.

    PubMed

    Moseley, Rachel L; Shtyrov, Yury; Mohr, Bettina; Lombardo, Michael V; Baron-Cohen, Simon; Pulvermüller, Friedemann

    2015-01-01

    Autism spectrum conditions (ASC) are characterised by deficits in understanding and expressing emotions and are frequently accompanied by alexithymia, a difficulty in understanding and expressing emotion words. Words are differentially represented in the brain according to their semantic category and these difficulties in ASC predict reduced activation to emotion-related words in limbic structures crucial for affective processing. Semantic theories view 'emotion actions' as critical for learning the semantic relationship between a word and the emotion it describes, such that emotion words typically activate the cortical motor systems involved in expressing emotion actions such as facial expressions. As ASC are also characterised by motor deficits and atypical brain structure and function in these regions, motor structures would also be expected to show reduced activation during emotion-semantic processing. Here we used event-related fMRI to compare passive processing of emotion words in comparison to abstract verbs and animal names in typically-developing controls and individuals with ASC. Relatively reduced brain activation in ASC for emotion words, but not matched control words, was found in motor areas and cingulate cortex specifically. The degree of activation evoked by emotion words in the motor system was also associated with the extent of autistic traits as revealed by the Autism Spectrum Quotient. We suggest that hypoactivation of motor and limbic regions for emotion word processing may underlie difficulties in processing emotional language in ASC. The role that sensorimotor systems and their connections might play in the affective and social-communication difficulties in ASC is discussed. PMID:25278250

  16. Lost for emotion words: What motor and limbic brain activity reveals about autism and semantic theory

    PubMed Central

    Moseley, Rachel L.; Shtyrov, Yury; Mohr, Bettina; Lombardo, Michael V.; Baron-Cohen, Simon; Pulvermüller, Friedemann

    2015-01-01

    Autism spectrum conditions (ASC) are characterised by deficits in understanding and expressing emotions and are frequently accompanied by alexithymia, a difficulty in understanding and expressing emotion words. Words are differentially represented in the brain according to their semantic category and these difficulties in ASC predict reduced activation to emotion-related words in limbic structures crucial for affective processing. Semantic theories view ‘emotion actions’ as critical for learning the semantic relationship between a word and the emotion it describes, such that emotion words typically activate the cortical motor systems involved in expressing emotion actions such as facial expressions. As ASC are also characterised by motor deficits and atypical brain structure and function in these regions, motor structures would also be expected to show reduced activation during emotion-semantic processing. Here we used event-related fMRI to compare passive processing of emotion words in comparison to abstract verbs and animal names in typically-developing controls and individuals with ASC. Relatively reduced brain activation in ASC for emotion words, but not matched control words, was found in motor areas and cingulate cortex specifically. The degree of activation evoked by emotion words in the motor system was also associated with the extent of autistic traits as revealed by the Autism Spectrum Quotient. We suggest that hypoactivation of motor and limbic regions for emotion word processing may underlie difficulties in processing emotional language in ASC. The role that sensorimotor systems and their connections might play in the affective and social-communication difficulties in ASC is discussed. PMID:25278250

  17. Comparative Proteomic Analysis Reveals Activation of Mucosal Innate Immune Signaling Pathways during Cholera

    PubMed Central

    LaRocque, Regina C.; Uddin, Taher; Krastins, Bryan; Mayo-Smith, Leslie M.; Sarracino, David; Karlsson, Elinor K.; Rahman, Atiqur; Shirin, Tahmina; Bhuiyan, Taufiqur R.; Chowdhury, Fahima; Khan, Ashraful Islam; Ryan, Edward T.; Calderwood, Stephen B.; Qadri, Firdausi

    2015-01-01

    Vibrio cholerae O1 is a major cause of acute watery diarrhea in over 50 countries. Evidence suggests that V. cholerae O1 may activate inflammatory pathways, and a recent study of a Bangladeshi population showed that variants in innate immune genes play a role in mediating susceptibility to cholera. We analyzed human proteins present in the small intestine of patients infected with V. cholerae O1 to characterize the host response to this pathogen. We collected duodenal biopsy specimens from patients with acute cholera after stabilization and again 30 days after initial presentation. Peptides extracted from biopsy specimens were sequenced and quantified using label-free mass spectrometry and SEQUEST. Twenty-seven host proteins were differentially abundant between the acute and convalescent stages of infection; the majority of these have known roles in innate defense, cytokine production, and apoptosis. Immunostaining confirmed that two proteins, WARS and S100A8, were more abundant in lamina propria cells during the acute stage of cholera. Analysis of the differentially abundant proteins revealed the activation of key regulators of inflammation by the innate immune system, including Toll-like receptor 4, nuclear factor kappa-light-chain-enhancer of activated B cells, mitogen-activated protein kinases, and caspase-dependent inflammasomes. Interleukin-12β (IL-12β) was a regulator of several proteins that were activated during cholera, and we confirmed that IL-12β was produced by lymphocytes recovered from duodenal biopsy specimens of cholera patients. Our study shows that a broad inflammatory response is generated in the gut early after onset of cholera, which may be critical in the development of long-term mucosal immunity against V. cholerae O1. PMID:25561705

  18. Comparative proteomic analysis reveals activation of mucosal innate immune signaling pathways during cholera.

    PubMed

    Ellis, Crystal N; LaRocque, Regina C; Uddin, Taher; Krastins, Bryan; Mayo-Smith, Leslie M; Sarracino, David; Karlsson, Elinor K; Rahman, Atiqur; Shirin, Tahmina; Bhuiyan, Taufiqur R; Chowdhury, Fahima; Khan, Ashraful Islam; Ryan, Edward T; Calderwood, Stephen B; Qadri, Firdausi; Harris, Jason B

    2015-03-01

    Vibrio cholerae O1 is a major cause of acute watery diarrhea in over 50 countries. Evidence suggests that V. cholerae O1 may activate inflammatory pathways, and a recent study of a Bangladeshi population showed that variants in innate immune genes play a role in mediating susceptibility to cholera. We analyzed human proteins present in the small intestine of patients infected with V. cholerae O1 to characterize the host response to this pathogen. We collected duodenal biopsy specimens from patients with acute cholera after stabilization and again 30 days after initial presentation. Peptides extracted from biopsy specimens were sequenced and quantified using label-free mass spectrometry and SEQUEST. Twenty-seven host proteins were differentially abundant between the acute and convalescent stages of infection; the majority of these have known roles in innate defense, cytokine production, and apoptosis. Immunostaining confirmed that two proteins, WARS and S100A8, were more abundant in lamina propria cells during the acute stage of cholera. Analysis of the differentially abundant proteins revealed the activation of key regulators of inflammation by the innate immune system, including Toll-like receptor 4, nuclear factor kappa-light-chain-enhancer of activated B cells, mitogen-activated protein kinases, and caspase-dependent inflammasomes. Interleukin-12β (IL-12β) was a regulator of several proteins that were activated during cholera, and we confirmed that IL-12β was produced by lymphocytes recovered from duodenal biopsy specimens of cholera patients. Our study shows that a broad inflammatory response is generated in the gut early after onset of cholera, which may be critical in the development of long-term mucosal immunity against V. cholerae O1. PMID:25561705

  19. Multimodal imaging reveals temporal and spatial microglia and matrix metalloproteinase activity after experimental stroke

    PubMed Central

    Zinnhardt, Bastian; Viel, Thomas; Wachsmuth, Lydia; Vrachimis, Alexis; Wagner, Stefan; Breyholz, Hans-Jörg; Faust, Andreas; Hermann, Sven; Kopka, Klaus; Faber, Cornelius; Dollé, Frédéric; Pappata, Sabina; Planas, Anna M; Tavitian, Bertrand; Schäfers, Michael; Sorokin, Lydia M; Kuhlmann, Michael T; Jacobs, Andreas H

    2015-01-01

    Stroke is the most common cause of death and disability from neurologic disease in humans. Activation of microglia and matrix metalloproteinases (MMPs) is involved in positively and negatively affecting stroke outcome. Novel, noninvasive, multimodal imaging methods visualizing microglial and MMP alterations were employed. The spatio-temporal dynamics of these parameters were studied in relation to blood flow changes. Micro positron emission tomography (μPET) using [18F]BR-351 showed MMP activity within the first days after transient middle cerebral artery occlusion (tMCAo), followed by increased [18F]DPA-714 uptake as a marker for microglia activation with a maximum at 14 days after tMCAo. The inflammatory response was spatially located in the infarct core and in adjacent (penumbral) tissue. For the first time, multimodal imaging based on PET, single photon emission computed tomography, and magnetic resonance imaging revealed insight into the spatio-temporal distribution of critical parameters of poststroke inflammation. This allows further evaluation of novel treatment paradigms targeting the postischemic inflammation. PMID:26126867

  20. Multimodal imaging reveals temporal and spatial microglia and matrix metalloproteinase activity after experimental stroke.

    PubMed

    Zinnhardt, Bastian; Viel, Thomas; Wachsmuth, Lydia; Vrachimis, Alexis; Wagner, Stefan; Breyholz, Hans-Jörg; Faust, Andreas; Hermann, Sven; Kopka, Klaus; Faber, Cornelius; Dollé, Frédéric; Pappata, Sabina; Planas, Anna M; Tavitian, Bertrand; Schäfers, Michael; Sorokin, Lydia M; Kuhlmann, Michael T; Jacobs, Andreas H

    2015-11-01

    Stroke is the most common cause of death and disability from neurologic disease in humans. Activation of microglia and matrix metalloproteinases (MMPs) is involved in positively and negatively affecting stroke outcome. Novel, noninvasive, multimodal imaging methods visualizing microglial and MMP alterations were employed. The spatio-temporal dynamics of these parameters were studied in relation to blood flow changes. Micro positron emission tomography (μPET) using [(18)F]BR-351 showed MMP activity within the first days after transient middle cerebral artery occlusion (tMCAo), followed by increased [(18)F]DPA-714 uptake as a marker for microglia activation with a maximum at 14 days after tMCAo. The inflammatory response was spatially located in the infarct core and in adjacent (penumbral) tissue. For the first time, multimodal imaging based on PET, single photon emission computed tomography, and magnetic resonance imaging revealed insight into the spatio-temporal distribution of critical parameters of poststroke inflammation. This allows further evaluation of novel treatment paradigms targeting the postischemic inflammation. PMID:26126867

  1. Community Lenses Revealing the Role of Sociocultural Environment on Physical Activity

    PubMed Central

    Belon, Ana Paula; Nieuwendyk, Laura M.; Vallianatos, Helen; Nykiforuk, Candace I. J.

    2016-01-01

    Purpose To identify perceptions of how sociocultural environment enabled and hindered physical activity (PA) participation. Design Community-based participatory research. Setting Two semirural and two urban communities located in Alberta, Canada. Participants Thirty-five people (74.3% females, 71.4% aged 25–64 years) across the four communities. Method PhotoVoice activities occurred over 3 months during the spring of 2009. Participants were asked to document perceived environmental attributes that might foster or inhibit PA in their community. Photographs and narratives were shared in one-on-one interviews. Line-by-line coding of the transcripts was independently conducted by two researchers using an inductive approach. Codes were arranged into themes and subthemes, which were then organized into the Analysis Grid for Environments Linked to Obesity (ANGELO) framework. Results Six main themes (accompanied by subthemes) emerged: sociocultural aesthetics, safety, social involvement, PA motivation, cultural ideas of recreation, and car culture. Representative quotes and photographs illustrate enablers and obstacles identified by participants. Conclusion This PhotoVoice study revealed how aspects of participants’ sociocultural environments shaped their decisions to be physically active. Providing more PA resources is only one step in the promotion of supportive environments. Strategies should also account for the beautification and maintenance of communities, increasing feelings of safety, enhancement of social support among community members, popularization of PA, and mitigating car culture, among others. PMID:25973966

  2. Stepwise multiphoton activation fluorescence reveals a new method of melanin detection

    NASA Astrophysics Data System (ADS)

    Lai, Zhenhua; Kerimo, Josef; Mega, Yair; DiMarzio, Charles A.

    2013-06-01

    The stepwise multiphoton activated fluorescence (SMPAF) of melanin, activated by a continuous-wave mode near infrared (NIR) laser, reveals a broad spectrum extending from the visible spectra to the NIR and has potential application for a low-cost, reliable method of detecting melanin. SMPAF images of melanin in mouse hair and skin are compared with conventional multiphoton fluorescence microscopy and confocal reflectance microscopy (CRM). By combining CRM with SMPAF, we can locate melanin reliably. However, we have the added benefit of eliminating background interference from other components inside mouse hair and skin. The melanin SMPAF signal from the mouse hair is a mixture of a two-photon process and a third-order process. The melanin SMPAF emission spectrum is activated by a 1505.9-nm laser light, and the resulting spectrum has a peak at 960 nm. The discovery of the emission peak may lead to a more energy-efficient method of background-free melanin detection with less photo-bleaching.

  3. Timing of posterior parahippocampal gyrus activity reveals multiple scene processing stages.

    PubMed

    Bastin, Julien; Committeri, Giorgia; Kahane, Philippe; Galati, Gaspare; Minotti, Lorella; Lachaux, Jean-Philippe; Berthoz, Alain

    2013-06-01

    Posterior parahippocampal gyrus (PPHG) is strongly involved during scene recognition and spatial cognition. How PPHG electrophysiological activity could underlie these functions, and whether they share similar timing mechanisms is unknown. We addressed this question in two intracerebral experiments which revealed that PPHG neural activity dissociated an early stimulus-driven effect (>200 and <500 ms) and a late task-related effect (>600 and <800 ms). Strongest PPHG gamma band (50-150 Hz) activities were found early when subjects passively viewed scenes (scene selectivity effect) and lately when they had to estimate the position of an object relative to the environment (allocentric effect). Based on single trial analyses, we were able to predict when patients viewed scenes (compared to other visual categories) and when they performed allocentric judgments (compared to other spatial judgments). The anatomical location corresponding to the strongest effects was in the depth of the collateral sulcus. Our findings directly affect current theories of visual scene processing and spatial orientation by providing new timing constraints and by demonstrating the existence of separable information processing stages in the functionally defined parahippocampal place area. PMID:22287281

  4. Measurement of optical activity of honey bee

    NASA Astrophysics Data System (ADS)

    Ortiz-Gutiérrez, Mauricio; Olivares-Pérez, Arturo; Salgado-Verduzco, Marco Antonio; Ibarra-Torres, Juan Carlos

    2016-03-01

    Optical activity of some substances, such as chiral molecules, often exhibits circular birefringence. Circular birefringence causes rotation of the vibration plane of the plane polarized light as it passes through the substance. In this work we present optical characterization of honey as function of the optical activity when it is placed in a polariscope that consists of a light source and properly arranged polarizing elements.

  5. 454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants

    PubMed Central

    Zhang, Tong; Shao, Ming-Fei; Ye, Lin

    2012-01-01

    Activated sludge (AS) contains highly complex microbial communities. In this study, PCR-based 454 pyrosequencing was applied to investigate the bacterial communities of AS samples from 14 sewage treatment plants of Asia (mainland China, Hong Kong, and Singapore), and North America (Canada and the United States). A total of 259 K effective sequences of 16S rRNA gene V4 region were obtained from these AS samples. These sequences revealed huge amount of operational taxonomic units (OTUs) in AS, that is, 1183–3567 OTUs in a sludge sample, at 3% cutoff level and sequencing depth of 16 489 sequences. Clear geographical differences among the AS samples from Asia and North America were revealed by (1) cluster analyses based on abundances of OTUs or the genus/family/order assigned by Ribosomal Database Project (RDP) and (2) the principal coordinate analyses based on OTUs abundances, RDP taxa abundances and UniFrac of OTUs and their distances. In addition to certain unique bacterial populations in each AS sample, some genera were dominant, and core populations shared by multiple samples, including two commonly reported genera of Zoogloea and Dechloromonas, three genera not frequently reported (i.e., Prosthecobacter, Caldilinea and Tricoccus) and three genera not well described so far (i.e., Gp4 and Gp6 in Acidobacteria and Subdivision3 genera incertae sedis of Verrucomicrobia). Pyrosequencing analyses of multiple AS samples in this study also revealed the minority populations that are hard to be explored by traditional molecular methods and showed that a large proportion of sequences could not be assigned to taxonomic affiliations even at the phylum/class levels. PMID:22170428

  6. Spatio-Temporal Analysis of Micro Economic Activities in Rome Reveals Patterns of Mixed-Use Urban Evolution.

    PubMed

    Fiasconaro, Alessandro; Strano, Emanuele; Nicosia, Vincenzo; Porta, Sergio; Latora, Vito

    2016-01-01

    Understanding urban growth is one with understanding how society evolves to satisfy the needs of its individuals in sharing a common space and adapting to the territory. We propose here a quantitative analysis of the historical development of a large urban area by investigating the spatial distribution and the age of commercial activities in the whole city of Rome. We find that the age of activities of various categories presents a very interesting double exponential trend, with a transition possibly related to the long-term economical effects determined by the oil crisis of the Seventies. The diversification of commercial categories, studied through various measures of entropy, shows, among other interesting features, a saturating behaviour with the density of activities. Moreover, different couples of commercial categories exhibit over the years a tendency to attract in space. Our results demonstrate that the spatio-temporal distribution of commercial activities can provide important insights on the urbanisation processes at work, revealing specific and non trivial socio-economical dynamics, as the presence of crisis periods and expansion trends, and contributing to the characterisation of the maturity of urban areas. PMID:26982028

  7. Interaction of Rio1 Kinase with Toyocamycin Reveals a Conformational Switch That Controls Oligomeric State and Catalytic Activity

    SciTech Connect

    Kiburu, Irene N.; LaRonde-LeBlanc, Nicole

    2012-10-10

    Rio1 kinase is an essential ribosome-processing factor required for proper maturation of 40 S ribosomal subunit. Although its structure is known, several questions regarding its functional remain to be addressed. We report that both Archaeoglobus fulgidus and human Rio1 bind more tightly to an adenosine analog, toyocamycin, than to ATP. Toyocamycin has antibiotic, antiviral and cytotoxic properties, and is known to inhibit ribosome biogenesis, specifically the maturation of 40 S. We determined the X-ray crystal structure of toyocamycin bound to Rio1 at 2.0 {angstrom} and demonstrated that toyocamycin binds in the ATP binding pocket of the protein. Despite this, measured steady state kinetics were inconsistent with strict competitive inhibition by toyocamycin. In analyzing this interaction, we discovered that Rio1 is capable of accessing multiple distinct oligomeric states and that toyocamycin may inhibit Rio1 by stabilizing a less catalytically active oligomer. We also present evidence of substrate inhibition by high concentrations of ATP for both archaeal and human Rio1. Oligomeric state studies show both proteins access a higher order oligomeric state in the presence of ATP. The study revealed that autophosphorylation by Rio1 reduces oligomer formation and promotes monomerization, resulting in the most active species. Taken together, these results suggest the activity of Rio1 may be modulated by regulating its oligomerization properties in a conserved mechanism, identifies the first ribosome processing target of toyocamycin and presents the first small molecule inhibitor of Rio1 kinase activity.

  8. Spatio-Temporal Analysis of Micro Economic Activities in Rome Reveals Patterns of Mixed-Use Urban Evolution

    PubMed Central

    Fiasconaro, Alessandro; Strano, Emanuele; Nicosia, Vincenzo; Porta, Sergio; Latora, Vito

    2016-01-01

    Understanding urban growth is one with understanding how society evolves to satisfy the needs of its individuals in sharing a common space and adapting to the territory. We propose here a quantitative analysis of the historical development of a large urban area by investigating the spatial distribution and the age of commercial activities in the whole city of Rome. We find that the age of activities of various categories presents a very interesting double exponential trend, with a transition possibly related to the long-term economical effects determined by the oil crisis of the Seventies. The diversification of commercial categories, studied through various measures of entropy, shows, among other interesting features, a saturating behaviour with the density of activities. Moreover, different couples of commercial categories exhibit over the years a tendency to attract in space. Our results demonstrate that the spatio-temporal distribution of commercial activities can provide important insights on the urbanisation processes at work, revealing specific and non trivial socio-economical dynamics, as the presence of crisis periods and expansion trends, and contributing to the characterisation of the maturity of urban areas. PMID:26982028

  9. PARTICULATE EMISSION MEASUREMENTS FROM CONTROLLED CONSTRUCTION ACTIVITIES

    EPA Science Inventory

    The report summarized the results of field testing of the effectiveness of control measures for sources of fugitive particulate emissions found at construction sites. The effectiveness of watering temporary, unpaved travel surfaces on emissions of particulate matter with aerodyna...

  10. 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.

  11. Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

    PubMed

    Ferreira, Ari J S; Siam, Rania; Setubal, João C; Moustafa, Ahmed; Sayed, Ahmed; Chambergo, Felipe S; Dawe, Adam S; Ghazy, Mohamed A; Sharaf, Hazem; Ouf, Amged; Alam, Intikhab; Abdel-Haleem, Alyaa M; Lehvaslaiho, Heikki; Ramadan, Eman; Antunes, André; Stingl, Ulrich; Archer, John A C; Jankovic, Boris R; Sogin, Mitchell; Bajic, Vladimir B; El-Dorry, Hamza

    2014-01-01

    Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light. PMID:24921648

  12. Core Microbial Functional Activities in Ocean Environments Revealed by Global Metagenomic Profiling Analyses

    PubMed Central

    Ferreira, Ari J. S.; Siam, Rania; Setubal, João C.; Moustafa, Ahmed; Sayed, Ahmed; Chambergo, Felipe S.; Dawe, Adam S.; Ghazy, Mohamed A.; Sharaf, Hazem; Ouf, Amged; Alam, Intikhab; Abdel-Haleem, Alyaa M.; Lehvaslaiho, Heikki; Ramadan, Eman; Antunes, André; Stingl, Ulrich; Archer, John A. C.; Jankovic, Boris R.; Sogin, Mitchell; Bajic, Vladimir B.; El-Dorry, Hamza

    2014-01-01

    Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light. PMID:24921648

  13. 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

  14. A contrast agent recognizing activated platelets reveals murine cerebral malaria pathology undetectable by conventional MRI.

    PubMed

    von Zur Muhlen, Constantin; Sibson, Nicola R; Peter, Karlheinz; Campbell, Sandra J; Wilainam, Panop; Grau, Georges E; Bode, Christoph; Choudhury, Robin P; Anthony, Daniel C

    2008-03-01

    Human and murine cerebral malaria are associated with elevated levels of cytokines in the brain and adherence of platelets to the microvasculature. Here we demonstrated that the accumulation of platelets in the brain microvasculature can be detected with MRI, using what we believe to be a novel contrast agent, at a time when the pathology is undetectable by conventional MRI. Ligand-induced binding sites (LIBS) on activated platelet glycoprotein IIb/IIIa receptors were detected in the brains of malaria-infected mice 6 days after inoculation with Plasmodium berghei using microparticles of iron oxide (MPIOs) conjugated to a single-chain antibody specific for the LIBS (LIBS-MPIO). No binding of the LIBS-MPIO contrast agent was detected in uninfected animals. A combination of LIBS-MPIO MRI, confocal microscopy, and transmission electron microscopy revealed that the proinflammatory cytokine TNF-alpha, but not IL-1beta or lymphotoxin-alpha (LT-alpha), induced adherence of platelets to cerebrovascular endothelium. Peak platelet adhesion was found 12 h after TNF-alpha injection and was readily detected with LIBS-MPIO contrast-enhanced MRI. Temporal studies revealed that the level of MPIO-induced contrast was proportional to the number of platelets bound. Thus, the LIBS-MPIO contrast agent enabled noninvasive detection of otherwise undetectable cerebral pathology by in vivo MRI before the appearance of clinical disease, highlighting the potential of targeted contrast agents for diagnostic, mechanistic, and therapeutic studies. PMID:18274670

  15. A contrast agent recognizing activated platelets reveals murine cerebral malaria pathology undetectable by conventional MRI

    PubMed Central

    von zur Muhlen, Constantin; Sibson, Nicola R.; Peter, Karlheinz; Campbell, Sandra J.; Wilainam, Panop; Grau, Georges E.; Bode, Christoph; Choudhury, Robin P.; Anthony, Daniel C.

    2008-01-01

    Human and murine cerebral malaria are associated with elevated levels of cytokines in the brain and adherence of platelets to the microvasculature. Here we demonstrated that the accumulation of platelets in the brain microvasculature can be detected with MRI, using what we believe to be a novel contrast agent, at a time when the pathology is undetectable by conventional MRI. Ligand-induced binding sites (LIBS) on activated platelet glycoprotein IIb/IIIa receptors were detected in the brains of malaria-infected mice 6 days after inoculation with Plasmodium berghei using microparticles of iron oxide (MPIOs) conjugated to a single-chain antibody specific for the LIBS (LIBS-MPIO). No binding of the LIBS-MPIO contrast agent was detected in uninfected animals. A combination of LIBS-MPIO MRI, confocal microscopy, and transmission electron microscopy revealed that the proinflammatory cytokine TNF-α, but not IL-1β or lymphotoxin-α (LT-α), induced adherence of platelets to cerebrovascular endothelium. Peak platelet adhesion was found 12 h after TNF-α injection and was readily detected with LIBS-MPIO contrast-enhanced MRI. Temporal studies revealed that the level of MPIO-induced contrast was proportional to the number of platelets bound. Thus, the LIBS-MPIO contrast agent enabled noninvasive detection of otherwise undetectable cerebral pathology by in vivo MRI before the appearance of clinical disease, highlighting the potential of targeted contrast agents for diagnostic, mechanistic, and therapeutic studies. PMID:18274670

  16. Structures of two superoxide dismutases from Bacillus anthracis reveal a novel active centre

    SciTech Connect

    Boucher, Ian W.; Kalliomaa, Anne K.; Levdikov, Vladimir M.; Blagova, Elena V.; Fogg, Mark J.; Brannigan, James A. Wilson, Keith S.; Wilkinson, Anthony J.

    2005-07-01

    The crystal structures of two manganese superoxide dismutases from B. anthracis were solved by X-ray crystallography using molecular replacement. The BA4499 and BA5696 genes of Bacillus anthracis encode proteins homologous to manganese superoxide dismutase, suggesting that this organism has an expanded repertoire of antioxidant proteins. Differences in metal specificity and quaternary structure between the dismutases of prokaryotes and higher eukaryotes may be exploited in the development of therapeutic antibacterial compounds. Here, the crystal structure of two Mn superoxide dismutases from B. anthracis solved to high resolution are reported. Comparison of their structures reveals that a highly conserved residue near the active centre is substituted in one of the proteins and that this is a characteristic feature of superoxide dismutases from the B. cereus/B. anthracis/B. thuringiensis group of organisms.

  17. Structures of two superoxide dismutases from Bacillus anthracis reveal a novel active centre

    PubMed Central

    Boucher, Ian W.; Kalliomaa, Anne K.; Levdikov, Vladimir M.; Blagova, Elena V.; Fogg, Mark J.; Brannigan, James A.; Wilson, Keith S.; Wilkinson, Anthony J.

    2005-01-01

    The BA4499 and BA5696 genes of Bacillus anthracis encode proteins homologous to manganese superoxide dismutase, suggesting that this organism has an expanded repertoire of antioxidant proteins. Differences in metal specificity and quaternary structure between the dismutases of prokaryotes and higher eukaryotes may be exploited in the development of therapeutic antibacterial compounds. Here, the crystal structure of two Mn superoxide dismutases from B. anthracis solved to high resolution are reported. Comparison of their structures reveals that a highly conserved residue near the active centre is substituted in one of the proteins and that this is a characteristic feature of superoxide dismutases from the B. cereus/B. anthracis/B. thuringiensis group of organisms. PMID:16511113

  18. 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

  19. The structure of Plasmodium falciparum serine hydroxymethyltransferase reveals a novel redox switch that regulates its activities

    SciTech Connect

    Chitnumsub, Penchit Ittarat, Wanwipa; Jaruwat, Aritsara; Noytanom, Krittikar; Amornwatcharapong, Watcharee; Pornthanakasem, Wichai; Chaiyen, Pimchai; Yuthavong, Yongyuth; Leartsakulpanich, Ubolsree

    2014-06-01

    The crystal structure of P. falciparum SHMT revealed snapshots of an intriguing disulfide/sulfhydryl switch controlling the functional activity. Plasmodium falciparum serine hydroxymethyltransferase (PfSHMT), an enzyme in the dTMP synthesis cycle, is an antimalarial target because inhibition of its expression or function has been shown to be lethal to the parasite. As the wild-type enzyme could not be crystallized, protein engineering of residues on the surface was carried out. The surface-engineered mutant PfSHMT-F292E was successfully crystallized and its structure was determined at 3 Å resolution. The PfSHMT-F292E structure is a good representation of PfSHMT as this variant revealed biochemical properties similar to those of the wild type. Although the overall structure of PfSHMT is similar to those of other SHMTs, unique features including the presence of two loops and a distinctive cysteine pair formed by Cys125 and Cys364 in the tetrahydrofolate (THF) substrate binding pocket were identified. These structural characteristics have never been reported in other SHMTs. Biochemical characterization and mutation analysis of these two residues confirm that they act as a disulfide/sulfhydryl switch to regulate the THF-dependent catalytic function of the enzyme. This redox switch is not present in the human enzyme, in which the cysteine pair is absent. The data reported here can be further exploited as a new strategy to specifically disrupt the activity of the parasite enzyme without interfering with the function of the human enzyme.

  20. Genetically encoded proton sensors reveal activity-dependent pH changes in neurons

    PubMed Central

    Raimondo, Joseph V.; Irkle, Agnese; Wefelmeyer, Winnie; Newey, Sarah E.; Akerman, Colin J.

    2011-01-01

    The regulation of hydrogen ion concentration (pH) is fundamental to cell viability, metabolism, and enzymatic function. Within the nervous system, the control of pH is also involved in diverse and dynamic processes including development, synaptic transmission, and the control of network excitability. As pH affects neuronal activity, and can also itself be altered by neuronal activity, the existence of tools to accurately measure hydrogen ion fluctuations is important for understanding the role pH plays under physiological and pathological conditions. Outside of their use as a marker of synaptic release, genetically encoded pH sensors have not been utilized to study hydrogen ion fluxes associated with network activity. By combining whole-cell patch clamp with simultaneous two-photon or confocal imaging, we quantified the amplitude and time course of neuronal, intracellular, acidic transients evoked by epileptiform activity in two separate in vitro models of temporal lobe epilepsy. In doing so, we demonstrate the suitability of three genetically encoded pH sensors: deGFP4, E2GFP, and Cl-sensor for investigating activity-dependent pH changes at the level of single neurons. PMID:22666186

  1. Are Preschool Children Active Enough? Objectively Measured Physical Activity Levels

    ERIC Educational Resources Information Center

    Cardon, Greet M.; De Bourdeaudhuij, Ilse M. M.

    2008-01-01

    The present study aimed to describe accelerometer-based physical activity levels in 4- and 5-year-old children (N = 76) on 2 weekdays and 2 weekend days. The children were sedentary for 9.6 hr (85%) daily, while they engaged in moderate to vigorous physical activity (MVPA) for 34 min (5%). Only 7% of the children engaged in MVPA for 60 min per…

  2. Complex Regulation Pattern of IRF3 Activation Revealed by a Novel Dimerization Reporter System.

    PubMed

    Wang, Zining; Ji, Jingyun; Peng, Di; Ma, Feng; Cheng, Genhong; Qin, F Xiao-Feng

    2016-05-15

    Induction of type I IFN (IFN-I) is essential for host antiviral immune responses. However, IFN-I also plays divergent roles in antibacterial immunity, persistent viral infections, autoimmune diseases, and tumorigenesis. IFN regulatory factor 3 (IRF3) is the master transcription factor that controls IFN-I production via phosphorylation-dependent dimerization in most cell types in response to viral infections and various innate stimuli by pathogen-associated molecular patterns (PAMPs). To monitor the dynamic process of IRF3 activation, we developed a novel IRF3 dimerization reporter based on bimolecular luminescence complementation (BiLC) techniques, termed the IRF3-BiLC reporter. Robust induction of luciferase activity of the IRF3-BiLC reporter was observed upon viral infection and PAMP stimulation with a broad dynamic range. Knockout of TANK-binding kinase 1, the critical upstream kinase of IRF3, as well as the mutation of serine 386, the essential phosphorylation site of IRF3, completely abolished the luciferase activity of IRF3-BiLC reporter, confirming the authenticity of IRF3 activation. Taken together, these results demonstrated that the IRF3-BiLC reporter is a highly specific, reliable, and sensitive system to measure IRF3 activity. Using this reporter system, we further observed that the temporal pattern and magnitude of IRF3 activation induced by various PAMPs are highly complex with distinct cell type-specific characteristics, and IRF3 dimerization is a direct regulatory node for IFN-α/β receptor-mediated feed-forward regulation and crosstalk with other pathways. Therefore, the IRF3-BiLC reporter has multiple potential applications, including mechanistic studies as well as the identification of novel compounds that can modulate IRF3 activation. PMID:27045107

  3. MEASURING CHOLINESTERASE ACTIVITY IN HUMAN SALIVA

    EPA Science Inventory

    To assess the potential for using saliva in pesticide biomonitoring, the consistency of cholinesterase activity in human saliva collected over time was examined. In this pilot study, saliva was collected from 20 healthy adults once per week for 5 consecutive weeks using 2 differe...

  4. MEASURING CHOLINESTERASE ACTIVITY IN HUMAN SALIVA.

    EPA Science Inventory

    To assess the potential for using saliva in pesticide biomonitoring, the consistency of cholinesterase activity in human saliva collected over time was examined. In this pilot study, saliva was collected from 20 healthy adults once per week for 5 consecutive weeks using 2 differe...

  5. Comparative analyses of Podospora anserina secretomes reveal a large array of lignocellulose-active enzymes.

    PubMed

    Poidevin, Laetitia; Berrin, Jean-Guy; Bennati-Granier, Chloé; Levasseur, Anthony; Herpoël-Gimbert, Isabelle; Chevret, Didier; Coutinho, Pedro M; Henrissat, Bernard; Heiss-Blanquet, Senta; Record, Eric

    2014-09-01

    The genome of the coprophilous fungus Podospora anserina harbors a large and highly diverse set of putative lignocellulose-acting enzymes. In this study, we investigated the enzymatic diversity of a broad range of P. anserina secretomes induced by various carbon sources (dextrin, glucose, xylose, arabinose, lactose, cellobiose, saccharose, Avicel, Solka-floc, birchwood xylan, wheat straw, maize bran, and sugar beet pulp (SBP)). Compared with the Trichoderma reesei enzymatic cocktail, P. anserina secretomes displayed similar cellulase, xylanase, and pectinase activities and greater arabinofuranosidase, arabinanase, and galactanase activities. The secretomes were further tested for their capacity to supplement a T. reesei cocktail. Four of them improved significantly the saccharification yield of steam-exploded wheat straw up to 48 %. Fine analysis of the P. anserina secretomes produced with Avicel and SBP using proteomics revealed a large array of CAZymes with a high number of GH6 and GH7 cellulases, CE1 esterases, GH43 arabinofuranosidases, and AA1 laccase-like multicopper oxidases. Moreover, a preponderance of AA9 (formerly GH61) was exclusively produced in the SBP condition. This study brings additional insights into the P. anserina enzymatic machinery and will facilitate the selection of promising targets for the development of future biorefineries. PMID:24695830

  6. Context Differences Reveal Insulator and Activator Functions of a Su(Hw) Binding Region

    PubMed Central

    Wehling, Misty D.; Geyer, Pamela K.

    2008-01-01

    Insulators are DNA elements that divide chromosomes into independent transcriptional domains. The Drosophila genome contains hundreds of binding sites for the Suppressor of Hairy-wing [Su(Hw)] insulator protein, corresponding to locations of the retroviral gypsy insulator and non-gypsy binding regions (BRs). The first non-gypsy BR identified, 1A-2, resides in cytological region 1A. Using a quantitative transgene system, we show that 1A-2 is a composite insulator containing enhancer blocking and facilitator elements. We discovered that 1A-2 separates the yellow (y) gene from a previously unannotated, non-coding RNA gene, named yar for y-achaete (ac) intergenic RNA. The role of 1A-2 was elucidated using homologous recombination to excise these sequences from the natural location, representing the first deletion of any Su(Hw) BR in the genome. Loss of 1A-2 reduced yar RNA accumulation, without affecting mRNA levels from the neighboring y and ac genes. These data indicate that within the 1A region, 1A-2 acts an activator of yar transcription. Taken together, these studies reveal that the properties of 1A-2 are context-dependent, as this element has both insulator and enhancer activities. These findings imply that the function of non-gypsy Su(Hw) BRs depends on the genomic environment, predicting that Su(Hw) BRs represent a diverse collection of genomic regulatory elements. PMID:18704163

  7. High-throughput mutagenesis reveals functional determinants for DNA targeting by activation-induced deaminase.

    PubMed

    Gajula, Kiran S; Huwe, Peter J; Mo, Charlie Y; Crawford, Daniel J; Stivers, James T; Radhakrishnan, Ravi; Kohli, Rahul M

    2014-09-01

    Antibody maturation is a critical immune process governed by the enzyme activation-induced deaminase (AID), a member of the AID/APOBEC DNA deaminase family. AID/APOBEC deaminases preferentially target cytosine within distinct preferred sequence motifs in DNA, with specificity largely conferred by a small 9-11 residue protein loop that differs among family members. Here, we aimed to determine the key functional characteristics of this protein loop in AID and to thereby inform our understanding of the mode of DNA engagement. To this end, we developed a methodology (Sat-Sel-Seq) that couples saturation mutagenesis at each position across the targeting loop, with iterative functional selection and next-generation sequencing. This high-throughput mutational analysis revealed dominant characteristics for residues within the loop and additionally yielded enzymatic variants that enhance deaminase activity. To rationalize these functional requirements, we performed molecular dynamics simulations that suggest that AID and its hyperactive variants can engage DNA in multiple specific modes. These findings align with AID's competing requirements for specificity and flexibility to efficiently drive antibody maturation. Beyond insights into the AID-DNA interface, our Sat-Sel-Seq approach also serves to further expand the repertoire of techniques for deep positional scanning and may find general utility for high-throughput analysis of protein function. PMID:25064858

  8. Inner workings of thrombolites: spatial gradients of metabolic activity as revealed by metatranscriptome profiling

    PubMed Central

    Mobberley, J. M.; Khodadad, C. L. M.; Visscher, P. T.; Reid, R. P.; Hagan, P.; Foster, J. S.

    2015-01-01

    Microbialites are sedimentary deposits formed by the metabolic interactions of microbes and their environment. These lithifying microbial communities represent one of the oldest ecosystems on Earth, yet the molecular mechanisms underlying the function of these communities are poorly understood. In this study, we used comparative metagenomic and metatranscriptomic analyses to characterize the spatial organization of the thrombolites of Highborne Cay, The Bahamas, an actively forming microbialite system. At midday, there were differences in gene expression throughout the spatial profile of the thrombolitic mat with a high abundance of transcripts encoding genes required for photosynthesis, nitrogen fixation and exopolymeric substance production in the upper three mm of the mat. Transcripts associated with denitrification and sulfate reduction were in low abundance throughout the depth profile, suggesting these metabolisms were less active during midday. Comparative metagenomics of the Bahamian thrombolites with other known microbialite ecosystems from across the globe revealed that, despite many shared core pathways, the thrombolites represented genetically distinct communities. This study represents the first time the metatranscriptome of living microbialite has been characterized and offers a new molecular perspective on those microbial metabolisms, and their underlying genetic pathways, that influence the mechanisms of carbonate precipitation in lithifying microbial mat ecosystems. PMID:26213359

  9. Structural characterization reveals the keratinolytic activity of an arthrobacter nicotinovorans protease.

    PubMed

    Sone, Teruo; Haraguchi, Yumiko; Kuwahara, Aki; Ose, Toyoyuki; Takano, Megumi; Abe, Ayumi; Tanaka, Michiko; Tanaka, Isao; Asano, Kozo

    2015-01-01

    Elevated cadmium (Cd) concentrations in fishery byproducts are an environmental concern, that might be reduced by enzymatic removal and adsorption of the contaminants during recycling the byproducts as animal food. We cloned the gene for Arthrobacter nicotinovorans serine protease (ANISEP), which was isolated from the hepatopancreas of the Japanese scallop (Patiopecten yessoensis) and has been found to be an effective enzyme for Cd(II) removal. The gene is 993 bp in length and encodes 330 amino acids, including the pre (1-30) and pro (31-111) sequences. The catalytic triad consists of His, Asp, and Ser. Sequence similarities indicate that ANISEP is a extracellular serine protease. X-ray crystallography revealed structural similarities between ANISEP and the trypsin-like serine protease NAALP from Nesterenkonia sp. Site-directed mutagenesis identified Ser171 as catalytic residue. The keratinolytic activity of ANISEP was 10-fold greater than that of trypsin. ANISEP digested Cd(II)-bound recombinant metallothionein MT-10a from Laternula elliptica, but did not release Cd. These results further suggest ANISEP is a trypsin-like serine protease that can release Cd from the Japanese scallop hepatopancreas because of its strong keratinolytic activity. PMID:25256266

  10. High-throughput mutagenesis reveals functional determinants for DNA targeting by activation-induced deaminase

    PubMed Central

    Gajula, Kiran S.; Huwe, Peter J.; Mo, Charlie Y.; Crawford, Daniel J.; Stivers, James T.; Radhakrishnan, Ravi; Kohli, Rahul M.

    2014-01-01

    Antibody maturation is a critical immune process governed by the enzyme activation-induced deaminase (AID), a member of the AID/APOBEC DNA deaminase family. AID/APOBEC deaminases preferentially target cytosine within distinct preferred sequence motifs in DNA, with specificity largely conferred by a small 9–11 residue protein loop that differs among family members. Here, we aimed to determine the key functional characteristics of this protein loop in AID and to thereby inform our understanding of the mode of DNA engagement. To this end, we developed a methodology (Sat-Sel-Seq) that couples saturation mutagenesis at each position across the targeting loop, with iterative functional selection and next-generation sequencing. This high-throughput mutational analysis revealed dominant characteristics for residues within the loop and additionally yielded enzymatic variants that enhance deaminase activity. To rationalize these functional requirements, we performed molecular dynamics simulations that suggest that AID and its hyperactive variants can engage DNA in multiple specific modes. These findings align with AID's competing requirements for specificity and flexibility to efficiently drive antibody maturation. Beyond insights into the AID-DNA interface, our Sat-Sel-Seq approach also serves to further expand the repertoire of techniques for deep positional scanning and may find general utility for high-throughput analysis of protein function. PMID:25064858

  11. Structure analysis reveals the flexibility of the ADAMTS-5 active site.

    PubMed

    Shieh, Huey-Sheng; Tomasselli, Alfredo G; Mathis, Karl J; Schnute, Mark E; Woodard, Scott S; Caspers, Nicole; Williams, Jennifer M; Kiefer, James R; Munie, Grace; Wittwer, Arthur; Malfait, Anne-Marie; Tortorella, Micky D

    2011-04-01

    A ((1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl) succinamide derivative (here referred to as Compound 12) shows significant activity toward many matrix metalloproteinases (MMPs), including MMP-2, MMP-8, MMP-9, and MMP-13. Modeling studies had predicted that this compound would not bind to ADAMTS-5 (a disintegrin and metalloproteinase with thrombospondin motifs-5) due to its shallow S1' pocket. However, inhibition analysis revealed it to be a nanomolar inhibitor of both ADAMTS-4 and -5. The observed inconsistency was explained by analysis of crystallographic structures, which showed that Compound 12 in complex with the catalytic domain of ADAMTS-5 (cataTS5) exhibits an unusual conformation in the S1' pocket of the protein. This first demonstration that cataTS5 can undergo an induced conformational change in its active site pocket by a molecule like Compound 12 should enable the design of new aggrecanase inhibitors with better potency and selectivity profiles. PMID:21370305

  12. Neuroinformatics analyses reveal GABAt and SSADH as major proteins involved in anticonvulsant activity of valproic acid.

    PubMed

    Piplani, Sakshi; Verma, Prabhakar Kumar; Kumar, Ajit

    2016-07-01

    The unequivocal hypotheses about anticonvulsant activity of valproic acid (VPA) have always been a basic hurdle in designing next generation neurotherapeutics, particularly the anti-epileptic drugs. The present study reports about a comprehensive in-silico investigation into qualitative and quantitative binding of VPA and corresponding natural ligands of four major enzymes involved in neurotransmissions, namely-GABA transaminase (GABAt), α-keto glutarate dehydrogenase (α-KGDH), Succinate Semialdehyde dehydrogenase (SSADH) and Glutamate Decarboxylase (GAD), respectively. The molecular docking analyses revealed that VPA inhibits GABAt and α-KGDH through allosteric while SSADH through competitive mode of binding. There is an observed elevation in binding of glutamate over GAD in the presence of VPA. The docking inhibition constant (Ki) of VPA to all the studied enzymatic receptors were observed to be well below the therapeutic concentration of VPA in blood, except for α-KGDH, thus favouring GABAergic over glutamatergic mode of anticonvulsant activity of VPA. The report is probably the first comprehensive in-silico molecular study about VPA action. PMID:27261619

  13. Inner workings of thrombolites: spatial gradients of metabolic activity as revealed by metatranscriptome profiling

    NASA Astrophysics Data System (ADS)

    Mobberley, J. M.; Khodadad, C. L. M.; Visscher, P. T.; Reid, R. P.; Hagan, P.; Foster, J. S.

    2015-07-01

    Microbialites are sedimentary deposits formed by the metabolic interactions of microbes and their environment. These lithifying microbial communities represent one of the oldest ecosystems on Earth, yet the molecular mechanisms underlying the function of these communities are poorly understood. In this study, we used comparative metagenomic and metatranscriptomic analyses to characterize the spatial organization of the thrombolites of Highborne Cay, The Bahamas, an actively forming microbialite system. At midday, there were differences in gene expression throughout the spatial profile of the thrombolitic mat with a high abundance of transcripts encoding genes required for photosynthesis, nitrogen fixation and exopolymeric substance production in the upper three mm of the mat. Transcripts associated with denitrification and sulfate reduction were in low abundance throughout the depth profile, suggesting these metabolisms were less active during midday. Comparative metagenomics of the Bahamian thrombolites with other known microbialite ecosystems from across the globe revealed that, despite many shared core pathways, the thrombolites represented genetically distinct communities. This study represents the first time the metatranscriptome of living microbialite has been characterized and offers a new molecular perspective on those microbial metabolisms, and their underlying genetic pathways, that influence the mechanisms of carbonate precipitation in lithifying microbial mat ecosystems.

  14. Towards Fast In-line Measurement of Water Activity

    NASA Astrophysics Data System (ADS)

    Nielsen, J.; Andreasen, M. B.; Pedersen, M.; Rasmussen, M. K.

    2015-03-01

    Water activity is widely used as a key parameter in controlling the quality of food and feed products, among others. For determining the water activity, the material is sampled from the manufacturing process and measured in the laboratory with water activity analyzers. The sampling procedure can lead to non-representative measurements, the measurement process is time consuming, and much of the produced material may be wasted before the measurement results are available. To reduce waste and to be able to optimize production processes, industry requires in-line measurement of relevant quality determining parameters, hereunder the water activity. In cooperation with a manufacturer of systems for automatic in-line sampling and measurement of moisture, density, and the size of items, a project was defined to also enable the manufacturer's existing products to perform automatic measurement of the water activity in a sample. The aim was to develop a measurement system with the ability to operate in an industrial environment, which in the end would increase the measurement speed significantly and minimize the problems related to the handling of samples. In the paper the selection and characterization of the sensors, the design of a measurement chamber, and various issues of modeling and methods to reduce measurement time are discussed. The paper also presents water activity measurements obtained from food and feed products with the system, and shows that reliable results can be obtained in a few minutes with a proper design of the measurement chamber and selection of a model.

  15. Electrocorticography reveals the temporal dynamics of posterior parietal cortical activity during recognition memory decisions

    PubMed Central

    Gonzalez, Alex; Hutchinson, J. Benjamin; Uncapher, Melina R.; Chen, Janice; LaRocque, Karen F.; Foster, Brett L.; Rangarajan, Vinitha; Parvizi, Josef; Wagner, Anthony D.

    2015-01-01

    Theories of the neurobiology of episodic memory predominantly focus on the contributions of medial temporal lobe structures, based on extensive lesion, electrophysiological, and imaging evidence. Against this backdrop, functional neuroimaging data have unexpectedly implicated left posterior parietal cortex (PPC) in episodic retrieval, revealing distinct activation patterns in PPC subregions as humans make memory-related decisions. To date, theorizing about the functional contributions of PPC has been hampered by the absence of information about the temporal dynamics of PPC activity as retrieval unfolds. Here, we leveraged electrocorticography to examine the temporal profile of high gamma power (HGP) in dorsal PPC subregions as participants made old/new recognition memory decisions. A double dissociation in memory-related HGP was observed, with activity in left intraparietal sulcus (IPS) and left superior parietal lobule (SPL) differing in time and sign for recognized old items (Hits) and correctly rejected novel items (CRs). Specifically, HGP in left IPS increased for Hits 300–700 ms poststimulus onset, and decayed to baseline ∼200 ms preresponse. By contrast, HGP in left SPL increased for CRs early after stimulus onset (200−300 ms) and late in the memory decision (from 700 ms to response). These memory-related effects were unique to left PPC, as they were not observed in right PPC. Finally, memory-related HGP in left IPS and SPL was sufficiently reliable to enable brain-based decoding of the participant’s memory state at the single-trial level, using multivariate pattern classification. Collectively, these data provide insights into left PPC temporal dynamics as humans make recognition memory decisions. PMID:26283375

  16. Glycan structure of Gc Protein-derived Macrophage Activating Factor as revealed by mass spectrometry.

    PubMed

    Borges, Chad R; Rehder, Douglas S

    2016-09-15

    Disagreement exists regarding the O-glycan structure attached to human vitamin D binding protein (DBP). Previously reported evidence indicated that the O-glycan of the Gc1S allele product is the linear core 1 NeuNAc-Gal-GalNAc-Thr trisaccharide. Here, glycan structural evidence is provided from glycan linkage analysis and over 30 serial glycosidase-digestion experiments which were followed by analysis of the intact protein by electrospray ionization mass spectrometry (ESI-MS). Results demonstrate that the O-glycan from the Gc1F protein is the same linear trisaccharide found on the Gc1S protein and that the hexose residue is galactose. In addition, the putative anti-cancer derivative of DBP known as Gc Protein-derived Macrophage Activating Factor (GcMAF, which is formed by the combined action of β-galactosidase and neuraminidase upon DBP) was analyzed intact by ESI-MS, revealing that the activating E. coli β-galactosidase cleaves nothing from the protein-leaving the glycan structure of active GcMAF as a Gal-GalNAc-Thr disaccharide, regardless of the order in which β-galactosidase and neuraminidase are applied. Moreover, glycosidase digestion results show that α-N-Acetylgalactosamindase (nagalase) lacks endoglycosidic function and only cleaves the DBP O-glycan once it has been trimmed down to a GalNAc-Thr monosaccharide-precluding the possibility of this enzyme removing the O-glycan trisaccharide from cancer-patient DBP in vivo. PMID:27503803

  17. Extensive hydrothermal activity in the NE Lau basin revealed by ROV dives

    NASA Astrophysics Data System (ADS)

    Embley, R. W.; Resing, J. A.; Tebo, B.; Baker, E. T.; Butterfield, D. A.; Chadwick, B.; Davis, R.; de Ronde, C. E. J.; Lilley, M. D.; Lupton, J. E.; Merle, S. G.; Rubin, K. H.; Shank, T. M.; Walker, S. L.; Arculus, R. J.; Bobbitt, A. M.; Buck, N. J.; Caratori Tontini, F.; Crowhurst, P. V.; Mitchell, E.; Olson, E. J.; Ratmeyer, V.; Richards, S.; Roe, K. K.; Kenner-Chavis, P.; Martinez-Lyons, A.; Sheehan, C.; Brian, R.

    2014-12-01

    Dives with the QUEST 4000 ROV (Remotely Operated Vehicle) in September 2012 discovered nine hydrothermal sites in the arc and rear-arc region of the NE Lau Basin in 1150 m to 2630 m depth. These sites, originally detected by water column and seafloor surveys conducted in 2008-2011, include: (1) a paired sulfur-rich/black smoker field on the summit of a tectonically deformed magmatic arc volcano (Niua), (2) fracture-controlled black smoker venting on several small en echelon seamounts (north Matas) that lie between the magmatic arc and the backarc spreading center and (3) a magmatic degassing site on the summit of a dacite cone within a large (~12 km diameter) caldera volcano (Niuatahi). Dives at West Mata Seamount, which was undergoing strombolian volcanic activity and effusive rift-zone eruptions from 2008 to 2010, revealed a dormant volcanic phase in September 2012, with continued low-temperature diffuse venting. The high-temperature venting is likely driven by magmatic heat indicative of underlying partial melt zones and/or melt pockets distributed through the region. The occurrence of the youngest known boninite eruptions on the Mata volcanoes is consistent with subduction fluid flux melting extending into the rear-arc zone. Extension related to the transition from subduction to strike-slip motion of the northern Tonga Arc over the active Subduction-Transform Edge Propagator (STEP) fault probably contributes to the enhanced volcanism/hydrothermal activity in the NE Lau Basin. Chemosynthetic ecosystems at these sites range from mostly motile, lower diversity ecosystems at the eruptive/magmatically-degassing sites to higher diversity ecosystems with less mobile faunal components at the black-smoker systems. The wide range of fluid chemistry, water depth and geologic settings of the hydrothermal systems in this area provides an intriguing template to study the interaction of hydrothermal fluid chemistry, chemosynthetic habitats and their geologic underpinning

  18. Hyperactive hydrothermal activity in the NE Lau basin revealed by ROV dives

    NASA Astrophysics Data System (ADS)

    Embley, R. W.; Resing, J. A.; Tebo, B.; Baker, E. T.; Butterfield, D. A.; Chadwick, B.; Davis, R.; de Ronde, C. E.; Lilley, M. D.; Lupton, J. E.; Merle, S. G.; Rubin, K. H.; Shank, T. M.; Walker, S. L.; Arculus, R. J.; Bobbitt, A. M.; Buck, N.; Caratori Tontini, F.; Crowhurst, P. V.; Mitchell, E.; Olson, E. J.; Ratmeyer, V.; Richards, S.; Roe, K. K.; Keener, P.; Martinez Lyons, A.; Sheehan, C.; Brian, R.

    2013-12-01

    Dives with the QUEST 4000 ROV (Remotely Operated Vehicle) in September 2012 discovered nine hydrothermal sites in the arc and rear-arc region of the NE Lau Basin in 1150 m to 2630 m depth. These sites, originally detected by water column and seafloor surveys conducted in 2008-2011, include: (1) a paired sulfur-rich/black smoker field on the summit of a tectonically deformed magmatic arc volcano (Niua), (2) fracture-controlled black smoker venting on several small en echelon seamounts (north Matas) that lie between the magmatic arc and the backarc spreading center and (3) a magmatic degassing site on the summit of a dacite cone within a large (~12 km diameter) caldera volcano (Niuatahi). Dives at West Mata Seamount, which was undergoing strombolian volcanic activity and effusive rift-zone eruptions from 2008 to 2010, revealed a dormant volcanic phase in September 2012, with continued low-temperature diffuse venting. The high-temperature venting is likely driven by magmatic heat indicative of underlying partial melt zones and/or melt pockets distributed through the region. The occurrence of the youngest known boninite eruptions on the Mata volcanoes is consistent with subduction fluid flux melting extending into the rear-arc zone. Extension related to the transition from subduction to strike-slip motion of the northern Tonga Arc over the active Subduction-Transform Edge Propagator (STEP) fault probably contributes to the enhanced volcanism/hydrothermal activity in the NE Lau Basin. Chemosynthetic ecosystems at these sites range from mostly motile, lower diversity ecosystems at the eruptive/magmatically-degassing sites to higher diversity ecosystems with less mobile faunal components at the black-smoker systems. The wide range of fluid chemistry, water depth and geologic settings of the hydrothermal systems in this area provides an intriguing template to study the interaction of hydrothermal fluid chemistry, chemosynthetic habitats and their geologic underpinning

  19. Optogenetic activation of mechanically insensitive afferents in mouse colorectum reveals chemosensitivity.

    PubMed

    Feng, Bin; Joyce, Sonali C; Gebhart, G F

    2016-05-15

    The sensory innervation of the distal colorectum includes mechanically insensitive afferents (MIAs; ∼25%), which acquire mechanosensitivity in persistent visceral hypersensitivity and thus generate de novo input to the central nervous system. We utilized an optogenetic approach to bypass the process of transduction (generator potential) and focus on transformation (spike initiation) at colorectal MIA sensory terminals, which is otherwise not possible in typical functional studies. From channelrhodopsin2-expressing mice (driven by Advillin-Cre), the distal colorectum with attached pelvic nerve was harvested for ex vivo single-fiber recordings. Afferent receptive fields (RFs) were identified by electrical stimulation and tested for response to mechanical stimuli (probing, stroking, and stretch), and afferents were classified as either MIAs or mechanosensitive afferents (MSAs). All MIA and MSA RFs were subsequently stimulated optically and MIAs were also tested for activation/sensitization with inflammatory soup (IS), acidic hypertonic solution (AHS), and/or bile salts (BS). Responses to pulsed optical stimuli (1-10 Hz) were comparable between MSAs and MIAs whereas 43% of MIAs compared with 86% of MSAs responded tonically to stepped optical stimuli. Tonic-spiking MIAs responded preferentially to AHS (an osmotic stimulus) whereas non-tonic-spiking MIAs responded to IS (an inflammatory stimulus). A significant proportion of MIAs were also sensitized by BS. These results reveal transformation as a critical factor underlying the differences between MIAs (osmosensors vs. inflammatory sensors), revealing a previously unappreciated heterogeneity of MIA endings. The current study draws attention to the sensory encoding of MIA nerve endings that likely contribute to afferent sensitization and thus have important roles in visceral pain. PMID:26950857

  20. Metagenomics, metatranscriptomics and single cell genomics reveal functional response of active Oceanospirillales to Gulf oil spill

    SciTech Connect

    Mason, Olivia U.; Hazen, Terry C.; Borglin, Sharon; Chain, Patrick S. G.; Dubinsky, Eric A.; Fortney, Julian L.; Han, James; Holman, Hoi-Ying N.; Hultman, Jenni; Lamendella, Regina; Mackelprang, Rachel; Malfatti, Stephanie; Tom, Lauren M.; Tringe, Susannah G.; Woyke, Tanja; Zhou, Jizhong; Rubin, Edward M.; Jansson, Janet K.

    2012-06-12

    The Deepwater Horizon oil spill in the Gulf of Mexico resulted in a deep-sea hydrocarbon plume that caused a shift in the indigenous microbial community composition with unknown ecological consequences. Early in the spill history, a bloom of uncultured, thus uncharacterized, members of the Oceanospirillales was previously detected, but their role in oil disposition was unknown. Here our aim was to determine the functional role of the Oceanospirillales and other active members of the indigenous microbial community using deep sequencing of community DNA and RNA, as well as single-cell genomics. Shotgun metagenomic and metatranscriptomic sequencing revealed that genes for motility, chemotaxis and aliphatic hydrocarbon degradation were significantly enriched and expressed in the hydrocarbon plume samples compared with uncontaminated seawater collected from plume depth. In contrast, although genes coding for degradation of more recalcitrant compounds, such as benzene, toluene, ethylbenzene, total xylenes and polycyclic aromatic hydrocarbons, were identified in the metagenomes, they were expressed at low levels, or not at all based on analysis of the metatranscriptomes. Isolation and sequencing of two Oceanospirillales single cells revealed that both cells possessed genes coding for n-alkane and cycloalkane degradation. Specifically, the near-complete pathway for cyclohexane oxidation in the Oceanospirillales single cells was elucidated and supported by both metagenome and metatranscriptome data. The draft genome also included genes for chemotaxis, motility and nutrient acquisition strategies that were also identified in the metagenomes and metatranscriptomes. These data point towards a rapid response of members of the Oceanospirillales to aliphatic hydrocarbons in the deep sea.

  1. Crystal Structures of a Multidrug-Resistant Human Immunodeficiency Virus Type 1 Protease Reveal an Expanded Active-Site Cavity

    SciTech Connect

    Logsdon, Bradley C.; Vickrey, John F.; Martin, Philip; Proteasa, Gheorghe; Koepke, Jay I.; Terlecky, Stanley R.; Wawrzak, Zdzislaw; Winters, Mark A.; Merigan, Thomas C.; Kovari, Ladislau C.

    2010-03-08

    The goal of this study was to use X-ray crystallography to investigate the structural basis of resistance to human immunodeficiency virus type 1 (HIV-1) protease inhibitors. We overexpressed, purified, and crystallized a multidrug-resistant (MDR) HIV-1 protease enzyme derived from a patient failing on several protease inhibitor-containing regimens. This HIV-1 variant contained codon mutations at positions 10, 36, 46, 54, 63, 71, 82, 84, and 90 that confer drug resistance to protease inhibitors. The 1.8-{angstrom} crystal structure of this MDR patient isolate reveals an expanded active-site cavity. The active-site expansion includes position 82 and 84 mutations due to the alterations in the amino acid side chains from longer to shorter (e.g., V82A and I84V). The MDR isolate 769 protease 'flaps' stay open wider, and the difference in the flap tip distances in the MDR 769 variant is 12 {angstrom}. The MDR 769 protease crystal complexes with lopinavir and DMP450 reveal completely different binding modes. The network of interactions between the ligands and the MDR 769 protease is completely different from that seen with the wild-type protease-ligand complexes. The water molecule-forming hydrogen bonds bridging between the two flaps and either the substrate or the peptide-based inhibitor are lacking in the MDR 769 clinical isolate. The S1, S1', S3, and S3' pockets show expansion and conformational change. Surface plasmon resonance measurements with the MDR 769 protease indicate higher k{sub off} rates, resulting in a change of binding affinity. Surface plasmon resonance measurements provide k{sub on} and k{sub off} data (K{sub d} = k{sub off}/k{sub on}) to measure binding of the multidrug-resistant protease to various ligands. This MDR 769 protease represents a new antiviral target, presenting the possibility of designing novel inhibitors with activity against the open and expanded protease forms.

  2. Length and activity of the root apical meristem revealed in vivo by infrared imaging.

    PubMed

    Bizet, François; Hummel, Irène; Bogeat-Triboulot, Marie-Béatrice

    2015-03-01

    Understanding how cell division and cell elongation influence organ growth and development is a long-standing issue in plant biology. In plant roots, most of the cell divisions occur in a short and specialized region, the root apical meristem (RAM). Although RAM activity has been suggested to be of high importance to understand how roots grow and how the cell cycle is regulated, few experimental and numeric data are currently available. The characterization of the RAM is difficult and essentially based upon cell length measurements through destructive and time-consuming microscopy approaches. Here, a new non-invasive method is described that couples infrared light imaging and kinematic analyses and that allows in vivo measurements of the RAM length. This study provides a detailed description of the RAM activity, especially in terms of cell flux and cell division rate. We focused on roots of hydroponic grown poplars and confirmed our method on maize roots. How the RAM affects root growth rate is studied by taking advantage of the high inter-individual variability of poplar root growth. An osmotic stress was applied and did not significantly affect the RAM length, highlighting its homeostasis in short to middle-term responses. The methodology described here simplifies a lot experimental procedures, allows an increase in the number of individuals that can be taken into account in experiments, and means new experiments can be formulated that allow temporal monitoring of the RAM length. PMID:25540436

  3. Length and activity of the root apical meristem revealed in vivo by infrared imaging

    PubMed Central

    Bizet, François; Hummel, Irène; Bogeat-Triboulot, Marie-Béatrice

    2015-01-01

    Understanding how cell division and cell elongation influence organ growth and development is a long-standing issue in plant biology. In plant roots, most of the cell divisions occur in a short and specialized region, the root apical meristem (RAM). Although RAM activity has been suggested to be of high importance to understand how roots grow and how the cell cycle is regulated, few experimental and numeric data are currently available. The characterization of the RAM is difficult and essentially based upon cell length measurements through destructive and time-consuming microscopy approaches. Here, a new non-invasive method is described that couples infrared light imaging and kinematic analyses and that allows in vivo measurements of the RAM length. This study provides a detailed description of the RAM activity, especially in terms of cell flux and cell division rate. We focused on roots of hydroponic grown poplars and confirmed our method on maize roots. How the RAM affects root growth rate is studied by taking advantage of the high inter-individual variability of poplar root growth. An osmotic stress was applied and did not significantly affect the RAM length, highlighting its homeostasis in short to middle-term responses. The methodology described here simplifies a lot experimental procedures, allows an increase in the number of individuals that can be taken into account in experiments, and means new experiments can be formulated that allow temporal monitoring of the RAM length. PMID:25540436

  4. Differences in Fidelity of Implementation Measures: What Videos and Surveys Reveal about Algebra Instruction

    ERIC Educational Resources Information Center

    Durkin, Kelley; Pollack, Courtney; Star, Jon R.; Rittle-Johnson, Bethany

    2012-01-01

    The current paper investigated the following research questions regarding measures of fidelity: (1) Is there a significant relationship between two different measures of fidelity of implementation: a survey of instructional practices and coded videos of classroom lessons? Does the strength of this relationship differ between treatment and control…

  5. Neutron Yield Measurements via Aluminum Activation

    SciTech Connect

    1999-12-08

    Neutron activation of aluminum may occur by several neutron capture reactions. Four such reactions are described here: {sup 27}Al + n = {sup 28}Al, {sup 27}Al(n,{alpha}){sup 24}Na, {sup 27}Al(n, 2n){sup 26}Al and {sup 27}Al(n,p){sup 27}Mg. The radioactive nuclei {sup 28}Al, {sup 24}Na, and {sup 27}Mg, which are produced via the {sup 27}Al + n = {sup 28}Al, {sup 27}Al(n,{alpha}){sup 24}Na and {sup 27}Al(n,p){sup 27}Mg neutron reactions, beta decay to excited states of {sup 28}Si, {sup 24}Mg and {sup 27}Al respectively. These excited states then emit gamma rays as the nuclei de-excite to their respective ground states.

  6. Clumpy tori around type II active galactic nuclei as revealed by X-ray fluorescent lines

    NASA Astrophysics Data System (ADS)

    Liu, Jiren; Liu, Yuan; Li, Xiaobo; Xu, Weiwei; Gou, Lijun; Cheng, Cheng

    2016-06-01

    The reflection spectrum of a torus around an active galactic nucleus (AGN) is characterized by X-ray fluorescent lines, which are most prominent for type II AGNs. A clumpy torus allows photons reflected from the back-side of the torus to leak through the front regions that are free of obscuration. The observed X-ray fluorescent lines are therefore sensitive to the clumpiness of the torus. We analysed a sample of type II AGNs observed with the Chandra High Energy Transmission Grating Spectrometer (HETGS), and measured the fluxes for the Si Kα and Fe Kα lines. The measured Fe Kα/Si Kα ratios, spanning a range between 5 and 60, are far smaller than the ratios predicted from simulations of smooth tori, indicating that the tori of the studied sources have clumpy distributions rather than smooth ones. We compared the measured Fe Kα/Si Kα ratios with simulation results of clumpy tori. The Circinus galaxy has a Fe Kα/Si Kα ratio of ˜60, which is close to the simulation results for N = 5, where N is the average number of clumps along the line of sight. The Fe Kα/Si Kα ratios of the other sources are all below the simulation results for N = 2. Overall, this shows that the non-Fe fluorescent lines in the soft X-ray band are a potentially powerful probe of the clumpiness of tori around AGNs.

  7. Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison

    PubMed Central

    Chen, Luonan; Wu, Ling-Yun; Wang, Yong; Zhang, Shihua; Zhang, Xiang-Sun

    2006-01-01

    Background Protein structure comparison is one of the most important problems in computational biology and plays a key role in protein structure prediction, fold family classification, motif finding, phylogenetic tree reconstruction and protein docking. Results We propose a novel method to compare the protein structures in an accurate and efficient manner. Such a method can be used to not only reveal divergent evolution, but also identify circular permutations and further detect active-sites. Specifically, we define the structure alignment as a multi-objective optimization problem, i.e., maximizing the number of aligned atoms and minimizing their root mean square distance. By controlling a single distance-related parameter, theoretically we can obtain a variety of optimal alignments corresponding to different optimal matching patterns, i.e., from a large matching portion to a small matching portion. The number of variables in our algorithm increases with the number of atoms of protein pairs in almost a linear manner. In addition to solid theoretical background, numerical experiments demonstrated significant improvement of our approach over the existing methods in terms of quality and efficiency. In particular, we show that divergent evolution, circular permutations and active-sites (or structural motifs) can be identified by our method. The software SAMO is available upon request from the authors, or from and . Conclusion A novel formulation is proposed to accurately align protein structures in the framework of multi-objective optimization, based on a sequence order-independent strategy. A fast and accurate algorithm based on the bipartite matching algorithm is developed by exploiting the special features. Convergence of computation is shown in experiments and is also theoretically proven. PMID:16948858

  8. ACTIVE LONGITUDES REVEALED BY LARGE-SCALE AND LONG-LIVED CORONAL STREAMERS

    SciTech Connect

    Li Jing

    2011-07-10

    We use time-series ultraviolet full sun images to construct limb-synoptic maps of the Sun. On these maps, large-scale, long-lived coronal streamers appear as repetitive sinusoid-like arcs projected over the polar regions. They are caused by high altitude plasma produced from sunspot-rich regions at latitudes generally far from the poles. The non-uniform longitudinal distribution of these streamers reveals four longitudinal zones at the surface of the Sun from which sunspots erupt preferentially over the 5 year observing interval (2006 January to 2011 April). Spots in these zones (or clusters) have individual lifetimes short compared to the lifetimes of the coronal features which they sustain, and they erupt at different times. The four sunspot clusters contain >75% of all numbered sunspots in this period. They occupy two distinct longitudinal zones separated by {approx}180{sup 0} and each spanning {approx}100{sup 0} in longitude. The rotation rates of the spot clusters are {approx}5% faster than the rates at both the surface and the bottom of the convection zone. While no convincing theoretical framework exists to interpret the sunspot clusters in the longitude-time space, their persistent and nonuniform distribution indicates long-lived, azimuthal structures beneath the surface, and are compatible with the existence of previously reported active longitudes on the Sun.

  9. In vivo role of the HNF4α AF-1 activation domain revealed by exon swapping

    PubMed Central

    Briançon, Nadège; Weiss, Mary C

    2006-01-01

    The gene encoding the nuclear receptor hepatocyte nuclear factor 4α (HNF4α) generates isoforms HNF4α1 and HNF4α7 from usage of alternative promoters. In particular, HNF4α7 is expressed in the pancreas whereas HNF4α1 is found in liver, and mutations affecting HNF4α function cause impaired insulin secretion and/or hepatic defects in humans and in tissue-specific ‘knockout' mice. HNF4α1 and α7 isoforms differ exclusively by amino acids encoded by the first exon which, in HNF4α1 but not in HNF4α7, includes the activating function (AF)-1 transactivation domain. To investigate the roles of HNF4α1 and HNF4α7 in vivo, we generated mice expressing only one isoform under control of both promoters, via reciprocal swapping of the isoform-specific first exons. Unlike Hnf4α gene disruption which causes embryonic lethality, these ‘α7-only' and ‘α1-only' mice are viable, indicating functional redundancy of the isoforms. However, the former show dyslipidemia and preliminary results indicate impaired glucose tolerance for the latter, revealing functional specificities of the isoforms. These ‘knock-in' mice provide the first test in vivo of the HNF4α AF-1 function and have permitted identification of AF-1-dependent target genes. PMID:16498401

  10. Activation of Nanoscale Allosteric Protein Domain Motion Revealed by Neutron Spin Echo Spectroscopy

    PubMed Central

    Farago, Bela; Li, Jianquan; Cornilescu, Gabriel; Callaway, David J.E.; Bu, Zimei

    2010-01-01

    NHERF1 is a multidomain scaffolding protein that assembles signaling complexes, and regulates the cell surface expression and endocytic recycling of a variety of membrane proteins. The ability of the two PDZ domains in NHERF1 to assemble protein complexes is allosterically modulated by the membrane-cytoskeleton linker protein ezrin, whose binding site is located as far as 110 Ångstroms away from the PDZ domains. Here, using neutron spin echo (NSE) spectroscopy, selective deuterium labeling, and theoretical analyses, we reveal the activation of interdomain motion in NHERF1 on nanometer length-scales and on submicrosecond timescales upon forming a complex with ezrin. We show that a much-simplified coarse-grained model suffices to describe interdomain motion of a multidomain protein or protein complex. We expect that future NSE experiments will benefit by exploiting our approach of selective deuteration to resolve the specific domain motions of interest from a plethora of global translational and rotational motions. Our results demonstrate that the dynamic propagation of allosteric signals to distal sites involves changes in long-range coupled domain motions on submicrosecond timescales, and that these coupled motions can be distinguished and characterized by NSE. PMID:21081097

  11. Ribosome•RelA structures reveal the mechanism of stringent response activation

    PubMed Central

    Loveland, Anna B; Bah, Eugene; Madireddy, Rohini; Zhang, Ying; Brilot, Axel F; Grigorieff, Nikolaus; Korostelev, Andrei A

    2016-01-01

    Stringent response is a conserved bacterial stress response underlying virulence and antibiotic resistance. RelA/SpoT-homolog proteins synthesize transcriptional modulators (p)ppGpp, allowing bacteria to adapt to stress. RelA is activated during amino-acid starvation, when cognate deacyl-tRNA binds to the ribosomal A (aminoacyl-tRNA) site. We report four cryo-EM structures of E. coli RelA bound to the 70S ribosome, in the absence and presence of deacyl-tRNA accommodating in the 30S A site. The boomerang-shaped RelA with a wingspan of more than 100 Å wraps around the A/R (30S A-site/RelA-bound) tRNA. The CCA end of the A/R tRNA pins the central TGS domain against the 30S subunit, presenting the (p)ppGpp-synthetase domain near the 30S spur. The ribosome and A/R tRNA are captured in three conformations, revealing hitherto elusive states of tRNA engagement with the ribosomal decoding center. Decoding-center rearrangements are coupled with the step-wise 30S-subunit 'closure', providing insights into the dynamics of high-fidelity tRNA decoding. DOI: http://dx.doi.org/10.7554/eLife.17029.001 PMID:27434674

  12. Multimodular biosensors reveal a novel platform for activation of G proteins by growth factor receptors

    PubMed Central

    Midde, Krishna K.; Aznar, Nicolas; Laederich, Melanie B.; Ma, Gary S.; Kunkel, Maya T.; Newton, Alexandra C.; Ghosh, Pradipta

    2015-01-01

    Environmental cues are transmitted to the interior of the cell via a complex network of signaling hubs. Receptor tyrosine kinases (RTKs) and trimeric G proteins are two such major signaling hubs in eukaryotes. Conventionally, canonical signal transduction via trimeric G proteins is thought to be triggered exclusively by G protein-coupled receptors. Here we used molecular engineering to develop modular fluorescent biosensors that exploit the remarkable specificity of bimolecular recognition, i.e., of both G proteins and RTKs, and reveal the workings of a novel platform for activation of G proteins by RTKs in single living cells. Comprised of the unique modular makeup of guanidine exchange factor Gα-interacting vesicle-associated protein (GIV)/girdin, a guanidine exchange factor that links G proteins to a variety of RTKs, these biosensors provide direct evidence that RTK–GIV–Gαi ternary complexes are formed in living cells and that Gαi is transactivated within minutes after growth factor stimulation at the plasma membrane. Thus, GIV-derived biosensors provide a versatile strategy for visualizing, monitoring, and manipulating the dynamic association of Gαi with RTKs for noncanonical transactivation of G proteins in cells and illuminate a fundamental signaling event regulated by GIV during diverse cellular processes and pathophysiologic states. PMID:25713130

  13. Metabolomics Reveals that Aryl Hydrocarbon Receptor Activation by Environmental Chemicals Induces Systemic Metabolic Dysfunction in Mice

    PubMed Central

    Zhang, Limin; Hatzakis, Emmanuel; Nichols, Robert G.; Hao, Ruixin; Correll, Jared; Smith, Philip B.; Chiaro, Christopher R.; Perdew, Gary H.; Patterson, Andrew D.

    2016-01-01

    Environmental exposure to dioxins and dioxin-like compounds poses a significant health risk for human health. Developing a better understanding of the mechanisms of toxicity through activation of the aryl hydrocarbon receptor (AHR) is likely to improve the reliability of risk assessment. In this study, the AHR-dependent metabolic response of mice exposed to 2,3,7,8-tetrachlorodibenzofuran (TCDF) were assessed using global 1H nuclear magnetic resonance (NMR)-based metabolomics and targeted metabolic profiling of extracts obtained from serum and liver. 1H NMR analyses revealed that TCDF exposure suppressed gluconeogenesis and glycogenolysis, stimulated lipogenesis, and triggered inflammatory gene expression in an Ahr-dependent manner. Targeted analyses using gas chromatography mass spectrometry showed TCDF treatment altered the ratio of unsaturated/saturated fatty acids. Consistent with this observation, an increase in hepatic expression of stearoyl coenzyme A desaturase 1 was also observed. In addition, TCDF exposure resulted in inhibition of de novo fatty acid biosynthesis manifested by down-regulation of acetyl-CoA, malonyl-CoA and palmitoyl-CoA metabolites and related mRNA levels. In contrast, no significant changes in the levels of glucose and lipid were observed in serum and liver obtained from Ahr-null mice following TCDF treatment, thus strongly supporting the important role of the AHR in mediating the metabolic effects seen following TCDF exposure. PMID:26023891

  14. Revealing a new activity of the human Dicer DUF283 domain in vitro

    PubMed Central

    Kurzynska-Kokorniak, Anna; Pokornowska, Maria; Koralewska, Natalia; Hoffmann, Weronika; Bienkowska-Szewczyk, Krystyna; Figlerowicz, Marek

    2016-01-01

    The ribonuclease Dicer is a multidomain enzyme that plays a fundamental role in the biogenesis of small regulatory RNAs (srRNAs), which control gene expression by targeting complementary transcripts and inducing their cleavage or repressing their translation. Recent studies of Dicer’s domains have permitted to propose their roles in srRNA biogenesis. For all of Dicer’s domains except one, called DUF283 (domain of unknown function), their involvement in RNA substrate recognition, binding or cleavage has been postulated. For DUF283, the interaction with Dicer’s protein partners has been the only function suggested thus far. In this report, we demonstrate that the isolated DUF283 domain from human Dicer is capable of binding single-stranded nucleic acids in vitro. We also show that DUF283 can act as a nucleic acid annealer that accelerates base-pairing between complementary RNA/DNA molecules in vitro. We further demonstrate an annealing activity of full length human Dicer. The overall results suggest that Dicer, presumably through its DUF283 domain, might facilitate hybridization between short RNAs and their targets. The presented findings reveal the complex nature of Dicer, whose functions may extend beyond the biogenesis of srRNAs. PMID:27045313

  15. The anti-obesity drug orlistat reveals anti-viral activity.

    PubMed

    Ammer, Elisabeth; Nietzsche, Sandor; Rien, Christian; Kühnl, Alexander; Mader, Theresa; Heller, Regine; Sauerbrei, Andreas; Henke, Andreas

    2015-12-01

    The administration of drugs to inhibit metabolic pathways not only reduces the risk of obesity-induced diseases in humans but may also hamper the replication of different viral pathogens. In order to investigate the value of the US Food and Drug Administration-approved anti-obesity drug orlistat in view of its anti-viral activity against different human-pathogenic viruses, several anti-viral studies, electron microscopy analyses as well as fatty acid uptake experiments were performed. The results indicate that administrations of non-cytotoxic concentrations of orlistat reduced the replication of coxsackievirus B3 (CVB3) in different cell types significantly. Moreover, orlistat revealed cell protective effects and modified the formation of multi-layered structures in CVB3-infected cells, which are necessary for viral replication. Lowering fatty acid uptake from the extracellular environment by phloretin administrations had only marginal impact on CVB3 replication. Finally, orlistat reduced also the replication of varicella-zoster virus moderately but had no significant influence on the replication of influenza A viruses. The data support further experiments into the value of orlistat as an inhibitor of the fatty acid synthase to develop new anti-viral compounds, which are based on the modulation of cellular metabolic pathways. PMID:25680890

  16. Detailed investigation of the microbial community in foaming activated sludge reveals novel foam formers

    PubMed Central

    Guo, Feng; Wang, Zhi-Ping; Yu, Ke; Zhang, T.

    2015-01-01

    Foaming of activated sludge (AS) causes adverse impacts on wastewater treatment operation and hygiene. In this study, we investigated the microbial communities of foam, foaming AS and non-foaming AS in a sewage treatment plant via deep-sequencing of the taxonomic marker genes 16S rRNA and mycobacterial rpoB and a metagenomic approach. In addition to Actinobacteria, many genera (e.g., Clostridium XI, Arcobacter, Flavobacterium) were more abundant in the foam than in the AS. On the other hand, deep-sequencing of rpoB did not detect any obligate pathogenic mycobacteria in the foam. We found that unknown factors other than the abundance of Gordonia sp. could determine the foaming process, because abundance of the same species was stable before and after a foaming event over six months. More interestingly, although the dominant Gordonia foam former was the closest with G. amarae, it was identified as an undescribed Gordonia species by referring to the 16S rRNA gene, gyrB and, most convincingly, the reconstructed draft genome from metagenomic reads. Our results, based on metagenomics and deep sequencing, reveal that foams are derived from diverse taxa, which expands previous understanding and provides new insight into the underlying complications of the foaming phenomenon in AS. PMID:25560234

  17. Ribosome•RelA structures reveal the mechanism of stringent response activation.

    PubMed

    Loveland, Anna B; Bah, Eugene; Madireddy, Rohini; Zhang, Ying; Brilot, Axel F; Grigorieff, Nikolaus; Korostelev, Andrei A

    2016-01-01

    Stringent response is a conserved bacterial stress response underlying virulence and antibiotic resistance. RelA/SpoT-homolog proteins synthesize transcriptional modulators (p)ppGpp, allowing bacteria to adapt to stress. RelA is activated during amino-acid starvation, when cognate deacyl-tRNA binds to the ribosomal A (aminoacyl-tRNA) site. We report four cryo-EM structures of E. coli RelA bound to the 70S ribosome, in the absence and presence of deacyl-tRNA accommodating in the 30S A site. The boomerang-shaped RelA with a wingspan of more than 100 Å wraps around the A/R (30S A-site/RelA-bound) tRNA. The CCA end of the A/R tRNA pins the central TGS domain against the 30S subunit, presenting the (p)ppGpp-synthetase domain near the 30S spur. The ribosome and A/R tRNA are captured in three conformations, revealing hitherto elusive states of tRNA engagement with the ribosomal decoding center. Decoding-center rearrangements are coupled with the step-wise 30S-subunit 'closure', providing insights into the dynamics of high-fidelity tRNA decoding. PMID:27434674

  18. Detailed investigation of the microbial community in foaming activated sludge reveals novel foam formers

    NASA Astrophysics Data System (ADS)

    Guo, Feng; Wang, Zhi-Ping; Yu, Ke; Zhang, T.

    2015-01-01

    Foaming of activated sludge (AS) causes adverse impacts on wastewater treatment operation and hygiene. In this study, we investigated the microbial communities of foam, foaming AS and non-foaming AS in a sewage treatment plant via deep-sequencing of the taxonomic marker genes 16S rRNA and mycobacterial rpoB and a metagenomic approach. In addition to Actinobacteria, many genera (e.g., Clostridium XI, Arcobacter, Flavobacterium) were more abundant in the foam than in the AS. On the other hand, deep-sequencing of rpoB did not detect any obligate pathogenic mycobacteria in the foam. We found that unknown factors other than the abundance of Gordonia sp. could determine the foaming process, because abundance of the same species was stable before and after a foaming event over six months. More interestingly, although the dominant Gordonia foam former was the closest with G. amarae, it was identified as an undescribed Gordonia species by referring to the 16S rRNA gene, gyrB and, most convincingly, the reconstructed draft genome from metagenomic reads. Our results, based on metagenomics and deep sequencing, reveal that foams are derived from diverse taxa, which expands previous understanding and provides new insight into the underlying complications of the foaming phenomenon in AS.

  19. Quantifying Ant Activity Using Vibration Measurements

    PubMed Central

    Oberst, Sebastian; Baro, Enrique Nava; Lai, Joseph C. S.; Evans, Theodore A.

    2014-01-01

    Ant behaviour is of great interest due to their sociality. Ant behaviour is typically observed visually, however there are many circumstances where visual observation is not possible. It may be possible to assess ant behaviour using vibration signals produced by their physical movement. We demonstrate through a series of bioassays with different stimuli that the level of activity of meat ants (Iridomyrmex purpureus) can be quantified using vibrations, corresponding to observations with video. We found that ants exposed to physical shaking produced the highest average vibration amplitudes followed by ants with stones to drag, then ants with neighbours, illuminated ants and ants in darkness. In addition, we devised a novel method based on wavelet decomposition to separate the vibration signal owing to the initial ant behaviour from the substrate response, which will allow signals recorded from different substrates to be compared directly. Our results indicate the potential to use vibration signals to classify some ant behaviours in situations where visual observation could be difficult. PMID:24658467

  20. Infiltration rate measurement by active perfluorocarbon monitoring

    SciTech Connect

    Menzies, K.T.; Pong, C.M.; Randel, M.A. )

    1987-01-01

    The rate of air infiltration in homes and buildings is a significant factor affecting the magnitude of human exposure to air pollutants in the indoor environment. Several techniques have been utilized for the determination of air infiltration. These include building pressurization and tracer analysis, e.g., SF/sub 6/. Dietz and Cote at Brookhaven National Laboratory (BNL) have developed a simple, steady-state tracer kit that can be utilized by homeowners. This kit includes a source(s) of perfluorocarbon, i.e., perfluoromethylcyclohexane (PMCH) or perfluorodimethylcyclohexane (PDCH), and a passive sampling tube containing Ambersorb XE-347. Typically, the sampling tube is deployed for several days and then returned to a laboratory for analysis by thermal desorption/gas chromatography/electron capture detection. The authors developed an alternative sampling and analysis technique for PMCH/PDCH in homes. In order to facilitate monitoring of short-term infiltration rates (i.e., less than one day) they developed an active sorbent sampling method and solvent desorption/gas chromatography/electron capture detection analytical method. The method is based on the collection of PMCH on charcoal. The method validation, which is discussed in this article, includes analytical method development, selection of a solid sorbent, determination of desorption efficiency, analysis of breakthrough, testing of storage stability, and assessment of precision and accuracy in both the laboratory and field environment.

  1. Integrated Experimental and Model-based Analysis Reveals the Spatial Aspects of EGFR Activation Dynamics

    SciTech Connect

    Shankaran, Harish; Zhang, Yi; Chrisler, William B.; Ewald, Jonathan A.; Wiley, H. S.; Resat, Haluk

    2012-10-02

    The epidermal growth factor receptor (EGFR) belongs to the ErbB family of receptor tyrosine kinases, and controls a diverse set of cellular responses relevant to development and tumorigenesis. ErbB activation is a complex process involving receptor-ligand binding, receptor dimerization, phosphorylation, and trafficking (internalization, recycling and degradation), which together dictate the spatio-temporal distribution of active receptors within the cell. The ability to predict this distribution, and elucidation of the factors regulating it, would help to establish a mechanistic link between ErbB expression levels and the cellular response. Towards this end, we constructed mathematical models for deconvolving the contributions of receptor dimerization and phosphorylation to EGFR activation, and to examine the dependence of these processes on sub-cellular location. We collected experimental datasets for EGFR activation dynamics in human mammary epithelial cells, with the specific goal of model parameterization, and used the data to estimate parameters for several alternate models. Model-based analysis indicated that: 1) signal termination via receptor dephosphorylation in late endosomes, prior to degradation, is an important component of the response, 2) less than 40% of the receptors in the cell are phosphorylated at any given time, even at saturating ligand doses, and 3) receptor dephosphorylation rates at the cell surface and early endosomes are comparable. We validated the last finding by measuring EGFR dephosphorylation rates at various times following ligand addition both in whole cells, and in endosomes using ELISAs and fluorescent imaging. Overall, our results provide important information on how EGFR phosphorylation levels are regulated within cells. Further, the mathematical model described here can be extended to determine receptor dimer abundances in cells co-expressing various levels of ErbB receptors. This study demonstrates that an iterative cycle of

  2. Rhythmic Components in Extracranial Brain Signals Reveal Multifaceted Task Modulation of Overlapping Neuronal Activity.

    PubMed

    van der Meij, Roemer; van Ede, Freek; Maris, Eric

    2016-01-01

    Oscillatory neuronal activity is implicated in many cognitive functions, and its phase coupling between sensors may reflect networks of communicating neuronal populations. Oscillatory activity is often studied using extracranial recordings and compared between experimental conditions. This is challenging, because there is overlap between sensor-level activity generated by different sources, and this can obscure differential experimental modulations of these sources. Additionally, in extracranial data, sensor-level phase coupling not only reflects communicating populations, but can also be generated by a current dipole, whose sensor-level phase coupling does not reflect source-level interactions. We present a novel method, which is capable of separating and characterizing sources on the basis of their phase coupling patterns as a function of space, frequency and time (trials). Importantly, this method depends on a plausible model of a neurobiological rhythm. We present this model and an accompanying analysis pipeline. Next, we demonstrate our approach, using magnetoencephalographic (MEG) recordings during a cued tactile detection task as a case study. We show that the extracted components have overlapping spatial maps and frequency content, which are difficult to resolve using conventional pairwise measures. Because our decomposition also provides trial loadings, components can be readily contrasted between experimental conditions. Strikingly, we observed heterogeneity in alpha and beta sources with respect to whether their activity was suppressed or enhanced as a function of attention and performance, and this happened both in task relevant and irrelevant regions. This heterogeneity contrasts with the common view that alpha and beta amplitude over sensory areas are always negatively related to attention and performance. PMID:27336159

  3. Active Trans-Plasma Membrane Water Cycling in Yeast Is Revealed by NMR

    PubMed Central

    Zhang, Yajie; Poirier-Quinot, Marie; Springer, Charles S.; Balschi, James A.

    2011-01-01

    Plasma membrane water transport is a crucial cellular phenomenon. Net water movement in response to an osmotic gradient changes cell volume. Steady-state exchange of water molecules, with no net flux or volume change, occurs by passive diffusion through the phospholipid bilayer and passage through membrane proteins. The hypothesis is tested that plasma membrane water exchange also correlates with ATP-driven membrane transport activity in yeast (Saccharomyces cerevisiae). Longitudinal 1H2O NMR relaxation time constant (T1) values were measured in yeast suspensions containing extracellular relaxation reagent. Two-site-exchange analysis quantified the reversible exchange kinetics as the mean intracellular water lifetime (τi), where τi−1 is the pseudo-first-order rate constant for water efflux. To modulate cellular ATP, yeast suspensions were bubbled with 95%O2/5%CO2 (O2) or 95%N2/5%CO2 (N2). ATP was high during O2, and τi−1 was 3.1 s−1 at 25°C. After changing to N2, ATP decreased and τi−1 was 1.8 s−1. The principal active yeast ion transport protein is the plasma membrane H+-ATPase. Studies using the H+-ATPase inhibitor ebselen or a yeast genetic strain with reduced H+-ATPase found reduced τi−1, notwithstanding high ATP. Steady-state water exchange correlates with H+-ATPase activity. At volume steady state, water is cycling across the plasma membrane in response to metabolic transport activity. PMID:22261073

  4. Rhythmic Components in Extracranial Brain Signals Reveal Multifaceted Task Modulation of Overlapping Neuronal Activity

    PubMed Central

    van Ede, Freek; Maris, Eric

    2016-01-01

    Oscillatory neuronal activity is implicated in many cognitive functions, and its phase coupling between sensors may reflect networks of communicating neuronal populations. Oscillatory activity is often studied using extracranial recordings and compared between experimental conditions. This is challenging, because there is overlap between sensor-level activity generated by different sources, and this can obscure differential experimental modulations of these sources. Additionally, in extracranial data, sensor-level phase coupling not only reflects communicating populations, but can also be generated by a current dipole, whose sensor-level phase coupling does not reflect source-level interactions. We present a novel method, which is capable of separating and characterizing sources on the basis of their phase coupling patterns as a function of space, frequency and time (trials). Importantly, this method depends on a plausible model of a neurobiological rhythm. We present this model and an accompanying analysis pipeline. Next, we demonstrate our approach, using magnetoencephalographic (MEG) recordings during a cued tactile detection task as a case study. We show that the extracted components have overlapping spatial maps and frequency content, which are difficult to resolve using conventional pairwise measures. Because our decomposition also provides trial loadings, components can be readily contrasted between experimental conditions. Strikingly, we observed heterogeneity in alpha and beta sources with respect to whether their activity was suppressed or enhanced as a function of attention and performance, and this happened both in task relevant and irrelevant regions. This heterogeneity contrasts with the common view that alpha and beta amplitude over sensory areas are always negatively related to attention and performance. PMID:27336159

  5. Substituent-induced intermolecular interaction in organic crystals revealed by precise band-dispersion measurements.

    PubMed

    Yamane, Hiroyuki; Kosugi, Nobuhiro

    2013-08-23

    We reveal quite small but different intermolecular valence band dispersions of sub-100-meV scale in crystalline films of Zn and Mn phthalocyanine (ZnPc and MnPc) and fluorinated ZnPc (F16ZnPc). The intermolecular transfer integrals are found to be reasonably dependent on the intermolecular distance with the 75±5 meV/Å relation. Furthermore, the angle-resolved photoemission spectra show anomalous dispersive behaviors such as phase flips and local-dimerization-derived periodicities, which originate from the site-specific intermolecular interaction induced by substituents. PMID:24010459

  6. Substituent-Induced Intermolecular Interaction in Organic Crystals Revealed by Precise Band-Dispersion Measurements

    NASA Astrophysics Data System (ADS)

    Yamane, Hiroyuki; Kosugi, Nobuhiro

    2013-08-01

    We reveal quite small but different intermolecular valence band dispersions of sub-100-meV scale in crystalline films of Zn and Mn phthalocyanine (ZnPc and MnPc) and fluorinated ZnPc (F16ZnPc). The intermolecular transfer integrals are found to be reasonably dependent on the intermolecular distance with the 75±5meV/Å relation. Furthermore, the angle-resolved photoemission spectra show anomalous dispersive behaviors such as phase flips and local-dimerization-derived periodicities, which originate from the site-specific intermolecular interaction induced by substituents.

  7. The Measurement of Physical Activity in Young Children.

    ERIC Educational Resources Information Center

    Noland, Melody; And Others

    1990-01-01

    Presents data from two studies determining the validity of various measures of physical activity in preschool children. One explored how certain measures of activity predicted observed behavior. The other examined the Caltrac motion sensor's predictive validity. Results indicate the Caltrac monitor is sensitive to children's individual differences…

  8. 12 CFR 1806.201 - Measuring and reporting Qualified Activities.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 7 2010-01-01 2010-01-01 false Measuring and reporting Qualified Activities. 1806.201 Section 1806.201 Banks and Banking COMMUNITY DEVELOPMENT FINANCIAL INSTITUTIONS FUND, DEPARTMENT OF THE TREASURY BANK ENTERPRISE AWARD PROGRAM Awards § 1806.201 Measuring and reporting Qualified Activities. (a) General. An Applicant...

  9. Measuring Reading Activity: An Inventory. Instructional Resource No. 4.

    ERIC Educational Resources Information Center

    Guthrie, John T.; And Others

    Noting that the amount of reading students do is related to their reading achievement, this booklet presents an instrument designed to measure the amount and breadth of students' reading in and out of school. The first part of the booklet discusses the Reading Activity Inventory (RAI) and how it differs from other reading activity measures, uses…

  10. A Measurement Activity to Encourage Exploration of Calculus Concepts

    ERIC Educational Resources Information Center

    McGuffey, William

    2015-01-01

    This article describes an activity that incorporates measurement in order to lead students to discover and explore fundamental concepts of calculus. Students are provided with an experientially real starting point involving measurement and are encouraged to engage in mathematical discussions in a low-stakes environment. I describe the activity as…

  11. Electromagnetic Measurements in an Active Oilfield Environment

    NASA Astrophysics Data System (ADS)

    Schramm, K. A.; Aldridge, D. F.; Bartel, L. C.; Knox, H. A.; Weiss, C. J.

    2015-12-01

    An important issue in oilfield development pertains to mapping and monitoring of the fracture distributions (either natural or man-made) controlling subsurface fluid flow. Although microseismic monitoring and analysis have been used for this purpose for several decades, there remain several ambiguities and uncertainties with this approach. We are investigating a novel electromagnetic (EM) technique for detecting and mapping hydraulic fractures in a petroleum reservoir by injecting an electrically conductive contrast agent into an open fracture. The fracture is subsequently illuminated by a strong EM field radiated by a large engineered antenna. Specifically, a grounded electric current source is applied directly to the steel casing of the borehole, either at/near the wellhead or at a deep downhole point. Transient multicomponent EM signals (both electric and magnetic) scattered by the conductivity contrast are then recorded by a surface receiver array. We are presently utilizing advanced 3D numerical modeling algorithms to accurately simulate fracture responses, both before and after insertion of the conductive contrast agent. Model results compare favorably with EM field data recently acquired in a Permian Basin oilfield. However, extraction of the very-low-amplitude fracture signatures from noisy data requires effective noise suppression strategies such as long stacking times, rejection of outliers, and careful treatment of natural magnetotelluric fields. Dealing with the ever-present "episodic EM noise" typical in an active oilfield environment (associated with drilling, pumping, machinery, traffic, etc.) constitutes an ongoing problem. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the US Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  12. Quantitative measures to reveal coordinated cytoskeleton-nucleus reorganization during in vitro invasion of cancer cells

    NASA Astrophysics Data System (ADS)

    Dvir, Liron; Nissim, Ronen; Alvarez-Elizondo, Martha B.; Weihs, Daphne

    2015-04-01

    Metastasis formation is a major cause of mortality in cancer patients and includes tumor cell relocation to distant organs. A metastatic cell invades through other cells and extracellular matrix by biochemical attachment and mechanical force application. Force is used to move on or through a 2- or 3-dimensional (3D) environment, respectively, or to penetrate a 2D substrate. We have previously shown that even when a gel substrate is impenetrable, metastatic breast cancer cells can still indent it by applying force. Cells typically apply force through the acto-myosin network, which is mechanically connected to the nucleus. We develop a 3D image-analysis to reveal relative locations of the cell elements, and show that as cells apply force to the gel, a coordinated process occurs that involves cytoskeletal remodeling and repositioning of the nucleus. Our approach shows that the actin and microtubules reorganize in the cell, bringing the actin to the leading edge of the cell. In parallel, the nucleus is transported behind the actin, likely by the cytoskeleton, into the indentation dimple formed in the gel. The nucleus volume below the gel surface correlates with indentation depth, when metastatic breast cancer cells indent gels deeply. However, the nucleus always remains above the gel in benign cells, even when small indentations are observed. Determining mechanical processes during metastatic cell invasion can reveal how cells disseminate in the body and can uncover targets for diagnosis and treatment.

  13. Twin Knudsen Cell Configuration for Activity Measurements by Mass Spectrometry

    NASA Technical Reports Server (NTRS)

    Jacobson, N. S.

    1996-01-01

    A twin Knudsen cell apparatus for alloy activity measurements by mass spectrometry is described. Two Knudsen cells - one containing an alloy and one containing a pure component - are mounted on a single flange and translated into the sampling region via a motorized x-y table. Mixing of the molecular beams from the cells is minimized by a novel system of shutters. Activity measurements were taken on two well-characterized alloys to verify the operation of the system. Silver activity measurements are reported for Ag-Cu alloys and aluminum activity measurements are reported for Fe-Al alloys. The temperature dependence of activity for a 0.474 mol fraction Al-Fe alloy gives a partial molar heat of aluminum. Measurements taken with the twin cell show good agreement with literature values for these alloys.

  14. Impedance spectroscopy of micro-Droplets reveals activation of Bacterial Mechanosensitive Channels in Hypotonic Solutions

    NASA Astrophysics Data System (ADS)

    Ebrahimi, Aida; Alam, Muhammad A.

    Rapid detection of bacterial pathogens is of great importance in healthcare, food safety, environmental monitoring, and homeland security. Most bacterial detection platforms rely on binary fission (i.e. cell growth) to reach a threshold cell population that can be resolved by the sensing method. Since cell division depends on the bacteria type, the detection time of such methods can vary from hours to days. In contrast, in this work, we show that bacteria cells can be detected within minutes by relying on activation of specific protein channels, i.e. mechanosensitive channels (MS channels). When cells are exposed to hypotonic solutions, MS channels allow efflux of solutes to the external solution which leads to release the excessive membrane tension. Release of the cytoplasmic solutes, in turn, results in increase of the electrical conductance measured by droplet-based impedance sensing. The approach can be an effective technique for fast, pre-screening of bacterial contamination at ultra-low concentration.

  15. Metaproteogenomics reveals the soil microbial communities active in nutrient cycling processes under different tree species

    NASA Astrophysics Data System (ADS)

    Keiblinger, Katharina Maria; Masse, Jacynthe; Zühlke, Daniela; Riedel, Katharina; Zechmeister-Boltenstern, Sophie; Prescott, Cindy E.; Grayston, Sue

    2016-04-01

    Tree species exert strong effects on microbial communities in litter and soil and may alter rates of soil processes fundamental to nutrient cycling and carbon fluxes (Prescott and Grayston 2013). However, the influence of tree species on decomposition processes are still contradictory and poorly understood. An understanding of the mechanisms underlying plant influences on soil processes is important for our ability to predict ecosystem response to altered global/environmental conditions. In order to link microbial community structure and function to forest-floor nutrient cycling processes, we sampled forest floors under western redcedar (Thuja plicata), Douglas-fir (Pseudotsuga menziesii) and Sitka spruce (Picea sitchensis) grown in nutrient-poor sites in common garden experiments on Vancouver island (Canada). We measured forest-floor total N, total C, initial NH4+ and NO3‑ concentrations, DOC, Cmic and Nmic. Gross rates of ammonification and NH4+ consumption were measured using the 15N pool-dilution method. Organic carbon quality was assessed through FTIR analyses. Microbial community structure was analysed by a metaproteogenomic approach using 16S and ITS amplification and sequencing with MiSeq platform. Proteins were extracted and peptides characterized via LC-MS/MS on a Velos Orbitrap to assess the active microbial community. Different microbial communities were active under the three tree species and variation in process rates were observed and will be discussed. This research provides new insights on microbial processes during organic matter decomposition. The metaproteogenomic approach enables us to investigate these changes with respect to possible effects on soil C-storage at even finer taxonomic resolution.

  16. Test-retest Stability Analysis of Resting Brain Activity Revealed by BOLD fMRI

    PubMed Central

    Li, Zhengjun; Kadivar, Aniseh; Pluta, John; Dunlop, John; Wang, Ze

    2012-01-01

    Purpose To assess test-retest stability of four fMRI-derived resting brain activity metrics: the seed-region-based functional connectivity (SRFC), independent component analysis (ICA)-derived network-based FC (NTFC), regional homogeneity (ReHo), and the amplitude of low frequency fluctuation (ALFF). Methods Simulations were used to assess the sensitivity of SRFC, ReHo, and ALFF to noise interference. Repeat resting blood-oxygen-level-dependent (BOLD) fMRI were acquired from 32 healthy subjects. The intra-class correlation coefficient (ICC) was used to assess the stability of the 4 metrics. Results Random noise yielded small random SRFC, small but consistent ReHo and ALFF. A neighborhood size greater than 20 voxels should be used for calculating ReHo in order to reduce the noise interference. Both the anterior cingulate cortex (ACC) and posterior cingulate cortex (PCC)-based SRFC were reproducible in more spatially extended regions than ICA NTFC. The two regional spontaneous brain activity (SBA) measures, ReHo and ALFF, showed test-retest reproducibility in almost the whole grey matter. Conclusion SRFC, ReHo, and ALFF are robust to random noise interference. The neighborhood size for calculating ReHo should be larger than 20 voxels. ICC>0.5 and cluster size>11 should be used to assess the ICC maps for ACC/PCC SRFC, ReHo and ALFF. BOLD fMRI-based SBA can be reliably measured using ACC/PCC SRFC, ReHo and ALFF after two months. PMID:22535702

  17. Transcriptomes reveal alterations in gravity impact circadian clocks and activate mechanotransduction pathways with adaptation through epigenetic change.

    PubMed

    Casey, Theresa; Patel, Osman V; Plaut, Karen

    2015-04-01

    Few studies have investigated the impact of alterations in gravity on mammalian transcriptomes. Here, we describe the impact of spaceflight on mammary transcriptome of late pregnant rats and the effect of hypergravity exposure on mammary, liver, and adipose transcriptomes in late pregnancy and at the onset of lactation. RNA was isolated from mammary collected on pregnancy day 20 from rats exposed to spaceflight from days 11 to 20 of gestation. To measure the impact of hypergravity on mammary, liver, and adipose transcriptomes we isolated RNA from tissues collected on P20 and lactation day 1 from rats exposed to hypergravity beginning on pregnancy day 9. Gene expression was measured with Affymetrix GeneChips. Microarray analysis of variance revealed alterations in gravity affected the expression of genes that regulate circadian clocks and activate mechanotransduction pathways. Changes in these systems may explain global gene expression changes in immune response, metabolism, and cell proliferation. Expression of genes that modify chromatin structure and methylation was affected, suggesting adaptation to gravity alterations may proceed through epigenetic change. Altered gravity experiments offer insights into the role of forces omnipresent on Earth that shape genomes in heritable ways. Our study is the first to analyze the impact of alterations in gravity on transcriptomes of pregnant and lactating mammals. Findings provide insight into systems that sense gravity and the way in which they affect phenotype, as well as the possibility of sustaining life beyond Earth's orbit. PMID:25649141

  18. Measurement of uterine activity in vitro by integrating muscle tension

    PubMed Central

    Styles, P. R.; Sullivan, T. J.

    1962-01-01

    Spontaneous or electrically stimulated activity of the uterus is measured isometrically in vitro by integrating tension against time. Uterine contractions move the operating rod of a potentiometer transducer, the output voltage from which is coupled to an electrical integrator motor and a servo recorder. Several parameters of uterine activity can be expressed in a single measurement, and a record of isometric contractions is obtained simultaneously. Oxytocin can be assayed accurately and the effect of drugs on uterine motility can be measured. PMID:13918066

  19. Active Learning: The Importance of Developing a Comprehensive Measure

    ERIC Educational Resources Information Center

    Carr, Rodney; Palmer, Stuart; Hagel, Pauline

    2015-01-01

    This article reports on an investigation into the validity of a widely used scale for measuring the extent to which higher education students employ active learning strategies. The scale is the active learning scale in the Australasian Survey of Student Engagement. This scale is based on the Active and Collaborative Learning scale of the National…

  20. The extended Saturnian neutral cloud as revealed by global ENA simulations using Cassini/MIMI measurements

    NASA Astrophysics Data System (ADS)

    Dialynas, K.; Brandt, P. C.; Krimigis, S. M.; Mitchell, D. G.; Hamilton, D. C.; Krupp, N.; Rymer, A. M.

    2013-06-01

    We show that the neutral gas vertical distribution at Saturn must be ~3-4 times more extended than previously thought for the >5 RSregions, while the neutral H distribution is consistent with H densities that reach up to ~150/cm3close to the orbit of Titan. We utilize a technique to retrieve the global neutral gas distribution in Saturn's magnetosphere, using energetic ion and energetic neutral atom (ENA) measurements, obtained by the Magnetospheric Imaging Instrument (MIMI) onboard the Cassini spacecraft. Our ENA measurements are consistent with a neutral cloud that consists of H2O, OH, H, and O, while the overall shapes and densities numbers concerning the neutral gas distributions are constrained according to already existing models as well as recent observations. The neutral gas distribution at Saturn is determined by simulating a 24-55 keV hydrogen image of the Saturnian magnetosphere, measured by the Ion and Neutral Camera (INCA), averaged over the time period from 1 July 2004 to 23 August 2005. The ionic input of the model includes a proton distribution of combined Charge Energy Mass Spectrometer (CHEMS, 3-230 keV/e), Low Energy Magnetospheric Measurements System (LEMMS, 30.7 keV to 2.3 MeV), and INCA (5-300 keV) in situ measurements. These measurements cover several passes from 1 July 2004 to 10 April 2007, at various local times over the dipole L range 5< L <20RS. A parameterized neutral gas distribution is changed until agreement between the simulated and average INCA image is obtained.

  1. Coseismic landslides reveal near-surface rock strength in a high-relief tectonically active setting

    USGS Publications Warehouse

    Gallen, Sean F; Clark, Marin K; Godt, Jonathan W.

    2014-01-01

    We present quantitative estimates of near-surface rock strength relevant to landscape evolution and landslide hazard assessment for 15 geologic map units of the Longmen Shan, China. Strength estimates are derived from a novel method that inverts earthquake peak ground acceleration models and coseismic landslide inventories to obtain material proper- ties and landslide thickness. Aggregate rock strength is determined by prescribing a friction angle of 30° and solving for effective cohesion. Effective cohesion ranges are from 70 kPa to 107 kPa for 15 geologic map units, and are approximately an order of magnitude less than typical laboratory measurements, probably because laboratory tests on hand-sized specimens do not incorporate the effects of heterogeneity and fracturing that likely control near-surface strength at the hillslope scale. We find that strength among the geologic map units studied varies by less than a factor of two. However, increased weakening of units with proximity to the range front, where precipitation and active fault density are the greatest, suggests that cli- matic and tectonic factors overwhelm lithologic differences in rock strength in this high-relief tectonically active setting.

  2. Molecular Network Analysis of Endometriosis Reveals a Novel Role for c-Jun Regulated Macrophage Activation

    PubMed Central

    Beste, Michael T.; Pfäffle-Doyle, Nicole; Prentice, Emily A.; Morris, Stephanie N.; Lauffenburger, Douglas A.; Isaacson, Keith B.; Griffith, Linda G.

    2014-01-01

    Clinical management of endometriosis is limited by the complex relationship between symptom severity, heterogeneous surgical presentations, and variability in clinical outcomes. As a complement to visual classification schemes, molecular profiles of disease activity may improve risk stratification to better inform treatment decisions and identify novel approaches to targeted treatment. Here, we employ a network analysis of information flow within and between inflammatory cells to discern consensus behaviors characterizing patient sub-populations. Unsupervised multivariate analysis of cytokine profiles quantified by multiplex immunoassays identified a subset of patients with a shared “consensus signature” of thirteen elevated cytokines that was associated with common clinical features, but was not observed among patient subpopulations defined by morphologic presentation alone. Enrichment analysis of consensus markers reinforced the primacy of peritoneal macrophage infiltration and activation, which was demonstrably elevated in ex vivo cultures. Although familiar targets of the NFκB family emerged among over-represented transcriptional binding sites for consensus markers, our analysis provides evidence for a previously unrecognized contribution from c-Jun, c-Fos, and AP-1 effectors of mitogen associated kinase signaling. Their crucial involvement in propagation of macrophage-driven inflammatory networks was confirmed via targeted inhibition of upstream kinases. Collectively, these analyses provide in vivo validation of a clinically relevant inflammatory network that may serve as an objective measure for guiding treatment decisions for endometriosis management, and in the future may provide a mechanistic endpoint for assessing efficacy of novel agents aimed at curtailing inflammatory mechanisms that drive disease progression. PMID:24500404

  3. A Systematic Analysis Reveals Heterogeneous Changes in the Endocytic Activities of Cancer Cells

    PubMed Central

    Elkin, Sarah R.; Bendris, Nawal; Reis, Carlos R.; Zhou, Yunyun; Xie, Yang; Huffman, Kenneth E.; Minna, John D.; Schmid, Sandra L.

    2016-01-01

    Metastasis is a multistep process requiring cancer cell signaling, invasion, migration, survival, and proliferation. These processes require dynamic modulation of cell surface proteins by endocytosis. Given this functional connection, it has been suggested that endocytosis is dysregulated in cancer. To test this, we developed In-Cell ELISA assays to measure three different endocytic pathways: clathrin-mediated endocytosis, caveolae-mediated endocytosis, and clathrin-independent endocytosis and compared these activities using two different syngeneic models for normal and oncogene-transformed human lung epithelial cells. We found that all endocytic activities were reduced in the transformed versus normal counterparts. However, when we screened 29 independently isolated non–small cell lung cancer (NSCLC) cell lines to determine whether these changes were systematic, we observed significant heterogeneity. Nonetheless, using hierarchical clustering based on their combined endocytic properties, we identified two phenotypically distinct clusters of NSCLCs. One co-clustered with mutations in KRAS, a mesenchymal phenotype, increased invasion through collagen and decreased growth in soft agar, whereas the second was enriched in cells with an epithelial phenotype. Interestingly, the two clusters also differed significantly in clathrin-independent internalization and surface expression of CD44 and CD59. Taken together, our results suggest that endocytotic alterations in cancer cells that affect cell surface expression of critical molecules have a significant influence on cancer-relevant phenotypes, with potential implications for interventions to control cancer by modulating endocytic dynamics. PMID:26359453

  4. The dynamic surface tension of atmospheric aerosol surfactants reveals new aspects of cloud activation

    PubMed Central

    Nozière, Barbara; Baduel, Christine; Jaffrezo, Jean-Luc

    2014-01-01

    The activation of aerosol particles into cloud droplets in the Earth’s atmosphere is both a key process for the climate budget and a main source of uncertainty. Its investigation is facing major experimental challenges, as no technique can measure the main driving parameters, the Raoult’s term and surface tension, σ, for sub-micron atmospheric particles. In addition, the surfactant fraction of atmospheric aerosols could not be isolated until recently. Here we present the first dynamic investigation of the total surfactant fraction of atmospheric aerosols, evidencing adsorption barriers that limit their gradient (partitioning) in particles and should enhance their cloud-forming efficiency compared with current models. The results also show that the equilibration time of surfactants in sub-micron atmospheric particles should be beyond the detection of most on-line instruments. Such instrumental and theoretical shortcomings would be consistent with atmospheric and laboratory observations and could have limited the understanding of cloud activation until now. PMID:24566451

  5. Aberrant spontaneous brain activity in chronic tinnitus patients revealed by resting-state functional MRI

    PubMed Central

    Chen, Yu-Chen; Zhang, Jian; Li, Xiao-Wei; Xia, Wenqing; Feng, Xu; Gao, Bo; Ju, Sheng-Hong; Wang, Jian; Salvi, Richard; Teng, Gao-Jun

    2014-01-01

    Objective The neural mechanisms that give rise to the phantom sound of tinnitus are poorly understood. This study aims to investigate whether aberrant spontaneous brain activity exists in chronic tinnitus patients using resting-state functional magnetic resonance imaging (fMRI) technique. Materials and methods A total of 31 patients with chronic tinnitus patients and 32 healthy age-, sex-, and education-matched healthy controls were prospectively examined. Both groups had normal hearing thresholds. We calculated the amplitude of low-frequency fluctuations (ALFFs) of fMRI signals to measure spontaneous neuronal activity and detect the relationship between fMRI information and clinical data of tinnitus. Results Compared with healthy controls, we observed significant increased ALFF within several selected regions including the right middle temporal gyrus (MTG), right superior frontal gyrus (SFG), and right angular gyrus; decreased ALFF was detected in the left cuneus, right middle occipital gyrus and bilateral thalamus. Moreover, tinnitus distress correlated positively with increased ALFF in right MTG and right SFG; tinnitus duration correlated positively with higher ALFF values in right SFG. Conclusions The present study confirms that chronic tinnitus patients have aberrant ALFF in many brain regions, which is associated with specific clinical tinnitus characteristics. ALFF disturbance in specific brain regions might be used to identify the neuro-pathophysiological mechanisms in chronic tinnitus patients. PMID:25379434

  6. Quantitative cell signalling analysis reveals down-regulation of MAPK pathway activation in colorectal cancer.

    PubMed

    Gulmann, Christian; Sheehan, Katherine M; Conroy, Ronán M; Wulfkuhle, Julia D; Espina, Virginia; Mullarkey, Michelle J; Kay, Elaine W; Liotta, Lance A; Petricoin, Emanuel F

    2009-08-01

    Mitogen-activated protein kinases (MAPK) are considered to play significant roles in colonic carcinogenesis and kinase inhibitor therapy has been proposed as a potential tool in the treatment of this disease. Reverse-phase microarray assays using phospho-specific antibodies can directly measure levels of phosphorylated protein isoforms. In the current study, samples from 35 cases of untreated colorectal cancer colectomies were laser capture-microdissected to isolate epithelium and stroma from cancer as well as normal (i.e. uninvolved) mucosa. Lysates generated from these four tissue types were spotted onto reverse-phase protein microarrays and probed with a panel of antibodies to ERK, p-ERK, p38, p-p38, p-JNK, MEK and p-MEK. Whereas total protein levels were unchanged, or slightly elevated (p38, p = 0.0025) in cancers, activated isoforms, including p-ERK, p-p38 and p-JNK, were decreased two- to four-fold in cancers compared with uninvolved mucosa (p < 0.0023 in all cases except for p-JNK in epithelium, where decrement was non-significant). This was backed up by western blotting. Dukes' stage B and C cancers displayed lower p-ERK and p-p38 expression than Dukes' stage A cancers, although this was not statistically significant. It is concluded that MAPK activity may be down-regulated in colorectal cancer and that further exploration of inhibitory therapy in this system should be carefully evaluated if this finding is confirmed in larger series. PMID:19396842

  7. Your Mind Wanders Weakly, Your Mind Wanders Deeply: Objective Measures Reveal Mindless Reading at Different Levels

    ERIC Educational Resources Information Center

    Schad, Daniel J.; Nuthmann, Antje; Engbert, Ralf

    2012-01-01

    Time Factors (Learning);When the mind wanders, attention turns away from the external environment and cognitive processing is decoupled from perceptual information. Mind wandering is usually treated as a dichotomy (dichotomy-hypothesis), and is often measured using self-reports. Here, we propose the levels of inattention hypothesis, which…

  8. Resin {sup 90}Y microsphere activity measurements for liver brachytherapy

    SciTech Connect

    Dezarn, William A.; Kennedy, Andrew S.

    2007-06-15

    The measurement of the radioactivity administered to the patient is one of the major components of {sup 90}Y microsphere liver brachytherapy. The activity of {sup 90}Y microspheres in a glass delivery vial was measured in a dose calibrator. The calibration value to use for {sup 90}Y in the dose calibrator was verified using an activity calibration standard provided by the microsphere manufacturer. This method allowed for the determination of a consistent, reproducible local activity standard. Additional measurements were made to determine some of the factors that could affect activity measurement. The axial response of the dose calibrator was determined by the ratio of activity measurements at the bottom and center of the dose calibrator. The axial response was 0.964 for a glass shipping vial, 1.001 for a glass V-vial, and 0.988 for a polycarbonate V-vial. Comparisons between activity measurements in the dose calibrator and those using a radiation survey meter were found to agree within 10%. It was determined that the dose calibrator method was superior to the survey meter method because the former allowed better defined measurement geometry and traceability of the activity standard back to the manufacturer. Part of the preparation of resin {sup 90}Y microspheres for patient delivery is to draw out a predetermined activity from a shipping vial and place it into a V-vial for delivery to the patient. If the drawn activity was placed in a glass V-vial, the activity measured in the dose calibrator with a glass V-vial was 4% higher than the drawn activity from the shipping vial standard. If the drawn activity was placed in a polycarbonate V-vial, the activity measured in the dose calibrator with a polycarbonate V-vial activity was 20% higher than the drawn activity from the shipping vial standard. Careful characterization of the local activity measurement standard is recommended instead of simply accepting the calibration value of the dose calibrator manufacturer.

  9. Wide-field Ca2+ imaging reveals visually evoked activity in the retrosplenial area

    PubMed Central

    Murakami, Tomonari; Yoshida, Takashi; Matsui, Teppei; Ohki, Kenichi

    2015-01-01

    Due to recent advances of genetic manipulation, mouse brain has become a useful model for studying brain function, which demands whole brain functional mapping techniques in the mouse brain. In the present study, to finely map visual responsive areas in the mouse brain, we combined high-resolution wide-field optical imaging with transgenic mice containing the genetically encoded Ca2+ indicator, GCaMP3. With the high signal amplitude of GCaMP3 expressing in excitatory neurons, this system allowed neural activity to be observed with relatively fine spatial resolution and cell-type specificity. To evaluate this system, we examined whether non-visual areas exhibited a visual response over the entire surface of the mouse hemisphere. We found that two association areas, the retrosplenial area (RS) and secondary motor/anterior cingulate area (M2/AC), were significantly responsive to drifting gratings. Examination using gratings with distinct spatiotemporal frequency parameters revealed that the RS strongly responded to high-spatial and low-temporal frequency gratings. The M2/AC exhibited a response property similar to that of the RS, though it was not statistically significant. Finally, we performed cellular imaging using two-photon microscopy to examine orientation and direction selectivity of individual neurons, and found that a minority of neurons in the RS clearly showed visual responses sharply selective for orientation and direction. These results suggest that neurons in RS encode visual information of fine spatial details in images. Thus, the present study shows the usefulness of the functional mapping method using a combination of wide-field and two-photon Ca2+ imaging, which allows for whole brain mapping with high spatiotemporal resolution and cell-type specificity. PMID:26106292

  10. Metatranscriptome Analysis of Aquifer Samples Reveals Unexpected Metabolic Lifestyles Relevant to Active Biogeochemical Cycling

    NASA Astrophysics Data System (ADS)

    Beller, H. R.; Jewell, T. N. M.; Karaoz, U.; Banfield, J. F.; Brodie, E.; Williams, K. H.

    2015-12-01

    Modern molecular ecology techniques are revealing the metabolic potential of uncultivated microorganisms, but there is still much to be learned about the actual biogeochemical roles of microbes that have cultivated relatives. Here, we present metatranscriptomic and metagenomic data from a field study that provides evidence of coupled redox processes that have not been documented in cultivated relatives and, indeed, represent strains with metabolic traits that are novel with respect to closely related isolates. The data come from omics analysis of groundwater samples collected during an experiment in which nitrate (a native electron acceptor) was injected into a perennially suboxic aquifer in Rifle (CO). Transcriptional data indicated that just two groups of chemolithoautotrophic bacteria accounted for a very large portion (~80%) of overall community gene expression: (1) members of the Fe(II)-oxidizing Gallionellaceae family and (2) strains of the S-oxidizing species, Sulfurimonas denitrificans. Metabolic lifestyles for Gallionellaceae strains that were novel compared to cultivated representatives included nitrate-dependent Fe(II) oxidation and S oxidation. Evidence for these metabolisms included highly correlated temporal expression in binned data of nitrate reductase (e.g., narGHI) genes (which have never been reported in Gallionellaceae genomes) and Fe(II) oxidation genes (e.g., mtoA) or S oxidation genes (e.g., dsrE, aprA). Of the two most active strains of S. denitrificans, only one showed strong expression of S oxidation genes, whereas the other was apparently using an unexpected (as-yet unidentified) primary electron donor. Transcriptional data added considerable interpretive value to this study, as (1) metagenomic data would not have highlighted these organisms, which had a disproportionately large role in community metabolism relative to their populations, and (2) co-expression of coupled pathway genes could not be predicted based solely on metagenomic data.

  11. Active fault creep variations at Chihshang, Taiwan, revealed by creep meter monitoring, 1998-2001

    NASA Astrophysics Data System (ADS)

    Lee, Jian-Cheng; Angelier, Jacques; Chu, Hao-Tsu; Hu, Jyr-Ching; Jeng, Fu-Shu; Rau, Ruey-Juin

    2003-11-01

    The daily creep meter data recorded at Chihshang in 1998-2001 are presented. The Chihshang creep meter experiment was set up across the Chihshang thrust fault, the most active segment of the Longitudinal Valley Fault, which is the present-day plate suture between the Eurasian and the Philippine Sea plates in eastern Taiwan. Near-continuous data recording at two sites revealed different surface fault motions yet similar annual shortening rates: 16.2 mm at the Tapo site (comprising two connected creep meters) and 15.0 mm at the Chinyuan site (three creep meters straddling parallel fault branches). Four of the five creep meters showed a seasonal variation, with the fault moving steadily during the rainy season from April to October, and remaining quiescent during the rest of the year. The only exception was recorded by the creep meter located on a mélange-composed hillslope, where local gravitational landsliding played an additional role other than tectonic faulting. Through comparison with daily precipitation data, we inferred that moderate rainfall suffices to trigger or facilitate slippage on the surface fault, during the transition period of the dry/wet season. During the observation period from 1998 to 2001, the subsurface seismicity exhibited clusters of microearthquakes on the Chihshang Fault at depths of 10-25 km. Recurrent earthquakes occurred regardless of whether the season was wet or dry, indicating that the stress relaxation associated with seismicity in the seismogenic zone did not transfer immediately up to the surface. The accumulated strain on the Chihshang Fault at shallow surface levels was released through creep during the wet season. In addition to these short-term seasonal variations, an apparent decrease in the annual slipping rate on the Chihshang Fault during the last few years deserves further investigation in order to mitigate against seismic hazard.

  12. Saccharomyces cerevisiae a-Factor Mutants Reveal Residues Critical for Processing, Activity, and Export

    PubMed Central

    Huyer, Gregory; Kistler, Amy; Nouvet, Franklin J.; George, Carolyn M.; Boyle, Meredith L.; Michaelis, Susan

    2006-01-01

    The Saccharomyces cerevisiae mating pheromone a-factor provides a paradigm for understanding the biogenesis of prenylated fungal pheromones. The biogenesis of a-factor involves multiple steps: (i) C-terminal CAAX modification (where C is cysteine, A is aliphatic, and X is any residue) which includes prenylation, proteolysis, and carboxymethylation (by Ram1p/Ram2p, Ste24p or Rce1p, and Ste14p, respectively); (ii) N-terminal processing, involving two sequential proteolytic cleavages (by Ste24p and Axl1p); and (iii) nonclassical export (by Ste6p). Once exported, mature a-factor interacts with the Ste3p receptor on MATα cells to stimulate mating. The a-factor biogenesis machinery is well defined, as is the CAAX motif that directs C-terminal modification; however, very little is known about the sequence determinants within a-factor required for N-terminal processing, activity, and export. Here we generated a large collection of a-factor mutants and identified residues critical for the N-terminal processing steps mediated by Ste24p and Axl1p. We also identified mutants that fail to support mating but do not affect biogenesis or export, suggesting a defective interaction with the Ste3p receptor. Mutants significantly impaired in export were also found, providing evidence that the Ste6p transporter recognizes sequence determinants as well as CAAX modifications. We also performed a phenotypic analysis of the entire set of isogenic a-factor biogenesis machinery mutants, which revealed information about the dependency of biogenesis steps upon one another, and demonstrated that export by Ste6p requires the completion of all processing events. Overall, this comprehensive analysis will provide a useful framework for the study of other fungal pheromones, as well as prenylated metazoan proteins involved in development and aging. PMID:16963638

  13. Transcriptional Analysis of a Dehalococcoides-Containing Microbial Consortium Reveals Prophage Activation

    PubMed Central

    Waller, Alison S.; Hug, Laura A.; Mo, Kaiguo; Radford, Devon R.; Maxwell, Karen L.

    2012-01-01

    Chlorinated solvents are among the most prevalent groundwater contaminants in the industrialized world. Biodegradation with Dehalococcoides-containing mixed cultures is an effective remediation technology. To elucidate transcribed genes in a Dehalococcoides-containing mixed culture, a shotgun metagenome microarray was created and used to investigate gene transcription during vinyl chloride (VC) dechlorination and during starvation (no chlorinated compounds) by a microbial enrichment culture called KB-1. In both treatment conditions, methanol was amended as an electron donor. Subsequently, spots were sequenced that contained the genes most differentially transcribed between the VC-degrading and methanol-only conditions, as well as spots with the highest intensities. Sequencing revealed that during VC degradation Dehalococcoides genes involved in transcription, translation, metabolic energy generation, and amino acid and lipid metabolism and transport were overrepresented in the transcripts compared to the average Dehalococcoides genome. KB-1 rdhA14 (vcrA) was the only reductive dehalogenase homologous (RDH) gene with higher transcript levels during VC degradation, while multiple RDH genes had higher transcript levels in the absence of VC. Numerous hypothetical genes from Dehalococcoides also had higher transcript levels in methanol-only treatments, indicating that many uncharacterized proteins are involved in cell maintenance in the absence of chlorinated substrates. In addition, microarray results prompted biological experiments confirming that electron acceptor limiting conditions activated a Dehalococcoides prophage. Transcripts from Spirochaetes, Chloroflexi, Geobacter, and methanogens demonstrate the importance of non-Dehalococcoides organisms to the culture, and sequencing of identified shotgun clones of interest provided information for follow-on targeted studies. PMID:22179237

  14. Robust dynamic classes revealed by measuring the response function of a social system

    PubMed Central

    Crane, Riley; Sornette, Didier

    2008-01-01

    We study the relaxation response of a social system after endogenous and exogenous bursts of activity using the time series of daily views for nearly 5 million videos on YouTube. We find that most activity can be described accurately as a Poisson process. However, we also find hundreds of thousands of examples in which a burst of activity is followed by an ubiquitous power-law relaxation governing the timing of views. We find that these relaxation exponents cluster into three distinct classes and allow for the classification of collective human dynamics. This is consistent with an epidemic model on a social network containing two ingredients: a power-law distribution of waiting times between cause and action and an epidemic cascade of actions becoming the cause of future actions. This model is a conceptual extension of the fluctuation-dissipation theorem to social systems [Ruelle, D (2004) Phys Today 57:48–53] and [Roehner BM, et al., (2004) Int J Mod Phys C 15:809–834], and provides a unique framework for the investigation of timing in complex systems. PMID:18824681

  15. Comparison of (90)Y activity measurements in nuclear medicine in Germany.

    PubMed

    Kossert, Karsten; Bokeloh, Karen; Ehlers, Marion; Nähle, Ole; Scheibe, Olaf; Schwarz, Uwe; Thieme, Klaus

    2016-03-01

    In 2014, PTB and the company Eckert & Ziegler organized a national comparison exercise to determine the activity of a (90)Y solution. One aim of the comparison was to assess the measurement capability of hospitals and medical practices in Germany. P6-type vials were filled with aliquots of a radioactive (90)Y solution and then sent to 19 participants who were asked to measure the activity in the ampoules as well as in their own standard geometry using syringes. Most of the submitted results have a deviation of less than ±10% from the PTB reference activity when measured in the P6-type vials. The spread is somewhat larger when measured in a syringe geometry. The comparison revealed that some participants have difficulties in applying decay corrections and only a few participants were capable of estimating realistic measurement uncertainties. PMID:26597654

  16. Charged fusion product loss measurements using nuclear activation.

    PubMed

    Bonheure, G; Hult, M; González de Orduña, R; Arnold, D; Dombrowski, H; Laubenstein, M; Wieslander, E; Vermaercke, P; Murari, A; Popovichev, S; Mlynar, J

    2010-10-01

    In ITER, α particle loss measurements will be required in order to understand the alpha particle physics. Techniques capable of operating in a fusion reactor environment need further development. Recent experimental studies on JET demonstrated the potential of nuclear activation to measure the flux of escaping MeV ions. New results from MeV ion induced activation of metallic, ceramic, and crystal samples placed near the plasma edge are reported. Activation products were measured as function of orientation with respect to the magnetic field as well as function of the distance to the plasma. Sample activity was measured using ultralow-level gamma-ray spectrometry. Distribution of 14.68 MeV fusion proton induced activation products is strongly anisotropic in agreement with simulations and falls off sharply with increasing distance to the plasma. Prospects for using the technique in ITER are discussed. PMID:21058458

  17. Geochemistry of the lunar highlands as revealed by measurements of thermal neutrons

    NASA Astrophysics Data System (ADS)

    Peplowski, Patrick N.; Beck, Andrew W.; Lawrence, David J.

    2016-03-01

    Thermal neutron emissions from the lunar surface provide a direct measure of bulk elemental composition that can be used to constrain the chemical properties of near-surface (depth <1 m) lunar materials. We present a new calibration of the Lunar Prospector thermal neutron map, providing a direct link between measured count rates and bulk elemental composition. The data are used to examine the chemical and mineralogical composition of the lunar surface, with an emphasis on constraining the plagioclase concentration across the highlands. We observe that the regions of lowest neutron absorption, which correspond to estimated plagioclase concentrations of >85%, are generally associated with large impact basins and are colocated with clusters of nearly pure plagioclase identified with spectral reflectance data.

  18. Gas Nonideality at One Atmosphere Revealed through Speed of Sound Measurements and Heat Capacity Determinations

    ERIC Educational Resources Information Center

    Halpern, Arthur M.; Liu, Allen

    2008-01-01

    Using an easy-to-make cylindrical resonator, students can measure the speed of sound in a gas, u, with sufficiently high precision (by locating standing-wave Lissajous patterns on an oscilloscope) to observe real gas properties at one atmosphere and 300 K. For CO[subscript 2] and SF[subscript 6], u is found to be 268.83 and 135.25 m s[superscript…

  19. Eigencentrality based on dissimilarity measures reveals central nodes in complex networks

    NASA Astrophysics Data System (ADS)

    Alvarez-Socorro, A. J.; Herrera-Almarza, G. C.; González-Díaz, L. A.

    2015-11-01

    One of the most important problems in complex network’s theory is the location of the entities that are essential or have a main role within the network. For this purpose, the use of dissimilarity measures (specific to theory of classification and data mining) to enrich the centrality measures in complex networks is proposed. The centrality method used is the eigencentrality which is based on the heuristic that the centrality of a node depends on how central are the nodes in the immediate neighbourhood (like rich get richer phenomenon). This can be described by an eigenvalues problem, however the information of the neighbourhood and the connections between neighbours is not taken in account, neglecting their relevance when is one evaluates the centrality/importance/influence of a node. The contribution calculated by the dissimilarity measure is parameter independent, making the proposed method is also parameter independent. Finally, we perform a comparative study of our method versus other methods reported in the literature, obtaining more accurate and less expensive computational results in most cases.

  20. Environmental controls of frost cracking revealed through in situ acoustic emission measurements in steep bedrock

    NASA Astrophysics Data System (ADS)

    Girard, Lucas; Gruber, Stephan; Weber, Samuel; Beutel, Jan

    2013-05-01

    Frost cracking, the breakdown of rock by freezing, is one of the most important mechanical weathering processes acting on Earth's surface. Insights on the mechanisms driving frost cracking stem mainly from laboratory and theoretical studies. Transferring insights from such studies to natural conditions, involving jointed bedrock and heterogeneous thermal and hydrological properties, is a major challenge. We address this problem with simultaneous in situ measurements of acoustic emissions, used as proxy of rock damage, and rock temperature/moisture content. The 1 year data set acquired in an Alpine rock wall shows that (1) liquid water content has an important impact on freezing-induced rock damage, (2) sustained freezing can yield much stronger damage than repeated freeze-thaw cycling, and (3) that frost cracking occurs over the full range of temperatures measured extending from 0 down to -15°C. These new measurements yield a slightly different picture than previous field studies where ice segregation appears to play an important role.

  1. Eigencentrality based on dissimilarity measures reveals central nodes in complex networks

    PubMed Central

    Alvarez-Socorro, A. J.; Herrera-Almarza, G. C.; González-Díaz, L. A.

    2015-01-01

    One of the most important problems in complex network’s theory is the location of the entities that are essential or have a main role within the network. For this purpose, the use of dissimilarity measures (specific to theory of classification and data mining) to enrich the centrality measures in complex networks is proposed. The centrality method used is the eigencentrality which is based on the heuristic that the centrality of a node depends on how central are the nodes in the immediate neighbourhood (like rich get richer phenomenon). This can be described by an eigenvalues problem, however the information of the neighbourhood and the connections between neighbours is not taken in account, neglecting their relevance when is one evaluates the centrality/importance/influence of a node. The contribution calculated by the dissimilarity measure is parameter independent, making the proposed method is also parameter independent. Finally, we perform a comparative study of our method versus other methods reported in the literature, obtaining more accurate and less expensive computational results in most cases. PMID:26603652

  2. Method for measuring surface activity of silicon nitride powder

    NASA Technical Reports Server (NTRS)

    Kanno, Y.; Imai, H.

    1985-01-01

    Amorphous, alpha-, and beta-Si3N4 powders were activated by vibration ball milling in purified MeOH, and the surface activity of ground powders was determined by the temperature programmed desorption (TPD) method using NH3 gas. The concentration of active sites with a potential energy equivalent to the peak temperature in the spectrum increased was markedly by ball milling the amorphous Si3N4. The alpha- and beta-Si3N4 also had active sites produced by ball milling. The concentration of active site increased with increased ball milling time. A method for measuring surface activity of ceramic raw materials by TPD is proposed.

  3. Temperature dependent measurements reveal similarities between muscle and non-muscle myosin motility

    PubMed Central

    Yengo, Christopher M.; Takagi, Yasuharu; Sellers, James R.

    2013-01-01

    We examined the temperature dependence of muscle and non-muscle myosin (heavy meromyosin, HMM) with in vitro motility and actin-activated ATPase assays. Our results indicate that myosin V (MV) has a temperature dependence that is similar in both ATPase and motility assays. We demonstrate that skeletal muscle myosin (SK), smooth muscle myosin (SM), and non-muscle myosin IIA (NM) have a different temperature dependence in ATPase compared to in vitro motility assays. In the class II myosins we examined (SK, SM, and NM) the rate-limiting step in ATPase assays is thought to be attachment to actin or phosphate release, while for in vitro motility assays it is controversial. In myosin V the rate-limiting step for both in vitro motility and ATPase assays is known to be ADP release. Consequently, in MV the temperature dependence of the ADP release rate constant is similar to the temperature dependence of in vitro motility. Interestingly, the temperature dependence of the ADP release rate constant of SM and NM was shifted toward the in vitro motility temperature dependence. Our results suggest that the rate-limiting step in SK, SM, and NM may shift from attachment-limited in solution to detachment-limited in the in vitro motility assay. Internal strain within the myosin molecule or by neighboring myosin motors may slow ADP release which becomes rate-limiting in the in vitro motility assay. Within this small subset of myosins examined, the in vitro sliding velocity correlates reasonably well with actin-activated ATPase activity, which was suggested by the original study by Barany et al. (Barany 1967). PMID:22930330

  4. Atomic force microscopy measurements reveal multiple bonds between Helicobacter pylori blood group antigen binding adhesin and Lewis b ligand

    PubMed Central

    Parreira, P.; Shi, Q.; Magalhaes, A.; Reis, C. A.; Bugaytsova, J.; Borén, T.; Leckband, D.; Martins, M. C. L.

    2014-01-01

    The strength of binding between the Helicobacter pylori blood group antigen-binding adhesin (BabA) and its cognate glycan receptor, the Lewis b blood group antigen (Leb), was measured by means of atomic force microscopy. High-resolution measurements of rupture forces between single receptor–ligand pairs were performed between the purified BabA and immobilized Leb structures on self-assembled monolayers. Dynamic force spectroscopy revealed two similar but statistically different bond populations. These findings suggest that the BabA may form different adhesive attachments to the gastric mucosa in ways that enhance the efficiency and stability of bacterial adhesion. PMID:25320070

  5. Spatial variability of the subsurface water storage revealed by relative gravity measurements in Southwest Niger

    NASA Astrophysics Data System (ADS)

    Pfeffer, J.; Champollion, C.; Favreau, G.; Hinderer, J.; Cappelaere, B.; Mouyen, M.; Boucher, M.; Nazoumou, Y.; Oi, M.; Robert, O.; Le Moigne, N.; Deroussi, S.; Demarty, J.; Benarrosh, N.; Charvet, G.; Chazarin, J.

    2011-12-01

    A major challenge in water resources research is to document the spatial and temporal variability of the hydrological processes over short time and space scales. Indeed, the quality of model predictions for resource assessment is dependent on reliable datasets, representative of the hydrological regime and its variations. This issue is particularly sensitive in Sahelian Africa, where available hydrological datasets are scarce. In this study, the variability of the water storage was investigated at the subcatchment scale (< 1km) by an intensive microgravity field campaign. Weekly microgravity surveys were carried out in a small endoreic catchment in Southwest Niger, during three months of the rainy season in 2009. Gravity measurements were performed at 16 stations located near a temporary pond, where rapid infiltration towards the aquifer occurs. The highest (63 μGal) gravity signal was measured on a station located above the pond and is well explained by the direct effect of the pond water volume changes throughout the wet season. Gravity signals of smaller amplitude (≤ 22 μGal) were measured in the pond surroundings and coupled to hydrodynamic data (pond level, soil moisture and water table level) to evaluate the intraseasonal variability of the water storage in the vicinity of the pond. The gravity signals related to the water storage in the subsurface exhibits a significant spatial variability. The heterogeneity of the water storage in the vadose zone appears as the main reason for the dispersion of the gravity values at local scale. This experiment evidences the ability of time lapse microgravity survey to detect the spatial variations of the water storage at intraseasonal scale in Sahelian Africa. Combined with hydrodynamic data, such a spatially distributed dataset may be a useful tool to calibrate or validate hydrological models and should be taken into account for scaling issue such as satellite gravimetry validation.

  6. One-neutron removal measurement reveals 24O as a new doubly magic nucleus.

    PubMed

    Kanungo, R; Nociforo, C; Prochazka, A; Aumann, T; Boutin, D; Cortina-Gil, D; Davids, B; Diakaki, M; Farinon, F; Geissel, H; Gernhäuser, R; Gerl, J; Janik, R; Jonson, B; Kindler, B; Knöbel, R; Krücken, R; Lantz, M; Lenske, H; Litvinov, Y; Lommel, B; Mahata, K; Maierbeck, P; Musumarra, A; Nilsson, T; Otsuka, T; Perro, C; Scheidenberger, C; Sitar, B; Strmen, P; Sun, B; Szarka, I; Tanihata, I; Utsuno, Y; Weick, H; Winkler, M

    2009-04-17

    The first measurement of the momentum distribution for one-neutron removal from (24)O at 920A MeV performed at GSI, Darmstadt is reported. The observed distribution has a width (FWHM) of 99 +/- 4 MeV/c in the projectile rest frame and a one-neutron removal cross section of 63 +/- 7 mb. The results are well explained with a nearly pure 2s_{1/2} neutron spectroscopic factor of 1.74 +/- 0.19 within the eikonal model. This large s-wave probability shows a spherical shell closure thereby confirming earlier suggestions that (24)O is a new doubly magic nucleus. PMID:19518623

  7. Altered Spontaneous Activity in Patients with Persistent Somatoform Pain Disorder Revealed by Regional Homogeneity

    PubMed Central

    Yan, Chao; Lu, Jing; Li, Xuzhou; Tang, Chaozheng; Fan, Mingxia; Luo, Yanli

    2016-01-01

    Persistent somatoform pain disorder (PSPD) is a mental disorder un-associated with any somatic injury and can cause severe somatosensory and emotional impairments in patients. However, so far, the neuro-pathophysiological mechanism of the functional impairments in PSPD is still unclear. The present study assesses the difference in regional spontaneous activity between PSPD and healthy controls (HC) during a resting state, in order to elucidate the neural mechanisms underlying PSPD. Resting-state functional Magnetic Resonance Imaging data were obtained from 13 PSPD patients and 23 age- and gender-matched HC subjects in this study. Kendall’s coefficient of concordance was used to measure regional homogeneity (ReHo), and a two-sample t-test was subsequently performed to investigate the ReHo difference between PSPD and HC. Additionally, the correlations between the mean ReHo of each survived area and the clinical assessments were further analyzed. Compared with the HC group, patients with PSPD exhibited decreased ReHo in the bilateral primary somatosensory cortex, posterior cerebellum, and occipital lobe, while increased ReHo in the prefrontal cortex (PFC) and default mode network (including the medial PFC, right inferior parietal lobe (IPL), and left supramarginal gyrus). In addition, significant positive correlations were found between the mean ReHo of both right IPL and left supramarginal gyrus and participants’ Self-Rating Anxiety Scale (SAS) scores, and between the mean ReHo of the left middle frontal gyrus and Visual Analogue Scale (VAS) scores. Our results suggest that abnormal spontaneous brain activity in specific brain regions during a resting state may be associated with the dysfunctions in pain, memory and emotional processing commonly observed in patients with PSPD. These findings help us to understand the neural mechanisms underlying PSPD and suggest that the ReHo metric could be used as a clinical marker for PSPD. PMID:26977802

  8. Altered Spontaneous Activity in Patients with Persistent Somatoform Pain Disorder Revealed by Regional Homogeneity.

    PubMed

    Huang, Tianming; Zhao, Zhiyong; Yan, Chao; Lu, Jing; Li, Xuzhou; Tang, Chaozheng; Fan, Mingxia; Luo, Yanli

    2016-01-01

    Persistent somatoform pain disorder (PSPD) is a mental disorder un-associated with any somatic injury and can cause severe somatosensory and emotional impairments in patients. However, so far, the neuro-pathophysiological mechanism of the functional impairments in PSPD is still unclear. The present study assesses the difference in regional spontaneous activity between PSPD and healthy controls (HC) during a resting state, in order to elucidate the neural mechanisms underlying PSPD. Resting-state functional Magnetic Resonance Imaging data were obtained from 13 PSPD patients and 23 age- and gender-matched HC subjects in this study. Kendall's coefficient of concordance was used to measure regional homogeneity (ReHo), and a two-sample t-test was subsequently performed to investigate the ReHo difference between PSPD and HC. Additionally, the correlations between the mean ReHo of each survived area and the clinical assessments were further analyzed. Compared with the HC group, patients with PSPD exhibited decreased ReHo in the bilateral primary somatosensory cortex, posterior cerebellum, and occipital lobe, while increased ReHo in the prefrontal cortex (PFC) and default mode network (including the medial PFC, right inferior parietal lobe (IPL), and left supramarginal gyrus). In addition, significant positive correlations were found between the mean ReHo of both right IPL and left supramarginal gyrus and participants' Self-Rating Anxiety Scale (SAS) scores, and between the mean ReHo of the left middle frontal gyrus and Visual Analogue Scale (VAS) scores. Our results suggest that abnormal spontaneous brain activity in specific brain regions during a resting state may be associated with the dysfunctions in pain, memory and emotional processing commonly observed in patients with PSPD. These findings help us to understand the neural mechanisms underlying PSPD and suggest that the ReHo metric could be used as a clinical marker for PSPD. PMID:26977802

  9. Atmospheric CO2 measurements reveal strong drought sensitivity of Amazonian carbon balance

    NASA Astrophysics Data System (ADS)

    Miller, J. B.; Gatti, L.; Gloor, M.; Doughty, C.; Malhi, Y.; Domingues, L. G.; Basso, L. S.; Martinewski, A.; Correia, C.; Borges, V.; Freitas, S. R.; Braz, R.; Anderson, L.; Rocha, H.; Grace, J.; Phillips, O.; Lloyd, J.

    2013-12-01

    Potential feedbacks between land carbon pools and climate are one of the largest sources of uncertainty for predicting future global climate, but estimates of their sensitivity to climate anomalies in the tropics and determination of underlying mechanisms are either incomplete or strongly model-based. Amazonia alone stores ~150-200 Pg of labile carbon, and has experienced an increasing trend in temperature and extreme floods and droughts over the last two decades. Here we report the first Amazon Basin-wide seasonal and annual carbon balances based on tropospheric greenhouse gas sampling, during an anomalously dry and a wet year, 2010 and 2011, providing the first whole-system assessment of sensitivity to such conditions. During 2010, the Amazon Basin lost 0.5×0.2 PgCyr-1 while in 2011 it was approximately carbon neutral (0.06×0.1 PgCyr-1). Carbon loss via fire was 0.5×0.1 PgCyr-1 in 2010 and 0.3×0.1 PgCyr-1 in 2011, as derived from Basin-wide carbon monoxide (CO) enhancements. Subtracting fire emissions from total carbon flux to derive Basin net biome exchange (NBE) reveals that in 2010 the non-fire regions of the Basin were carbon neutral; in 2011 they were a net carbon sink of -0.3×0.1 PgC yr-1, roughly consistent with a three-decade long intact-forest biomass sink of ~ -0.5×0.3 PgCyr-1 estimated from forest censuses. Altogether, our results suggest that if the recent trend of precipitation extremes persists, the Amazon region may become an increasing carbon source as a result of both emissions from fires and suppression of NBE by drought.

  10. Two distinct overstretched DNA structures revealed by single-molecule thermodynamics measurements

    PubMed Central

    Zhang, Xinghua; Chen, Hu; Fu, Hongxia; Doyle, Patrick S.; Yan, Jie

    2012-01-01

    Double-stranded DNA is a dynamic molecule whose structure can change depending on conditions. While there is consensus in the literature about many structures DNA can have, the state of highly-stretched DNA is still not clear. Several groups have shown that DNA in the torsion-unconstrained B-form undergoes an “overstretching” transition at a stretching force of around 65 pN, which leads to approximately 1.7-fold elongation of the DNA contour length. Recent experiments have revealed that two distinct structural transitions are involved in the overstretching process: (i) a hysteretic “peeling” off one strand from its complementary strand, and (ii) a nonhysteretic transition that leads to an undetermined DNA structure. We report the first simultaneous determination of the entropy (ΔS) and enthalpy changes (ΔH) pertaining to these respective transitions. For the hysteretic peeling transition, we determined ΔS ∼ 20 cal/(K.mol) and ΔH ∼ 7 kcal/mol. In the case of the nonhysteretic transition, ΔS ∼ -3 cal/(K.mol) and ΔH ∼ 1 kcal/mol. Furthermore, the response of the transition force to salt concentration implies that the two DNA strands are spatially separated after the hysteretic peeling transition. In contrast, the corresponding response after the nonhysteretic transition indicated that the strands remained in close proximity. The selection between the two transitions depends on DNA base-pair stability, and it can be illustrated by a multidimensional phase diagram. Our results provide important insights into the thermodynamics of DNA overstretching and conformational structures of overstretched DNA that may play an important role in vivo. PMID:22532662

  11. Ice nucleus activity measurements of solid rocket motor exhaust particles

    NASA Technical Reports Server (NTRS)

    Keller, V. W. (Compiler)

    1986-01-01

    The ice Nucleus activity of exhaust particles generated from combustion of Space Shuttle propellant in small rocket motors has been measured. The activity at -20 C was substantially lower than that of aerosols generated by unpressurized combustion of propellant samples in previous studies. The activity decays rapidly with time and is decreased further in the presence of moist air. These tests corroborate the low effectivity ice nucleus measurement results obtained in the exhaust ground cloud of the Space Shuttle. Such low ice nucleus activity implies that Space Shuttle induced inadvertent weather modification via an ice phase process is extremely unlikely.

  12. Extended carrier lifetimes and diffusion in hybrid perovskites revealed by Hall effect and photoconductivity measurements

    NASA Astrophysics Data System (ADS)

    Chen, Y.; Yi, H. T.; Wu, X.; Haroldson, R.; Gartstein, Y. N.; Rodionov, Y. I.; Tikhonov, K. S.; Zakhidov, A.; Zhu, X.-Y.; Podzorov, V.

    2016-08-01

    Impressive performance of hybrid perovskite solar cells reported in recent years still awaits a comprehensive understanding of its microscopic origins. In this work, the intrinsic Hall mobility and photocarrier recombination coefficient are directly measured in these materials in steady-state transport studies. The results show that electron-hole recombination and carrier trapping rates in hybrid perovskites are very low. The bimolecular recombination coefficient (10-11 to 10-10 cm3 s-1) is found to be on par with that in the best direct-band inorganic semiconductors, even though the intrinsic Hall mobility in hybrid perovskites is considerably lower (up to 60 cm2 V-1 s-1). Measured here, steady-state carrier lifetimes (of up to 3 ms) and diffusion lengths (as long as 650 μm) are significantly longer than those in high-purity crystalline inorganic semiconductors. We suggest that these experimental findings are consistent with the polaronic nature of charge carriers, resulting from an interaction of charges with methylammonium dipoles.

  13. Water revealed as molecular mirror when measuring low concentrations of sugar with near infrared light.

    PubMed

    Bázár, György; Kovacs, Zoltan; Tanaka, Mariko; Furukawa, Akane; Nagai, Airi; Osawa, Manami; Itakura, Yukari; Sugiyama, Hiroshi; Tsenkova, Roumiana

    2015-10-01

    Near infrared spectroscopy is an overtone spectroscopy regarded as a quick and non-destructive method that provides analytical solutions for components that represent approximately 1% or more of the total mass of the investigated composite samples. Aquaphotomics offers the possibility for disentanglement of information remaining hidden in the spectra when conventional data evaluation methods are used, since this concept utilizes changes of the water structure induced by the measured solute as specific molecular vibrations at water bands. Here, near infrared technique and aquaphotomics are applied for non-destructive identification and quantification of mono- and di-saccharide solutes at 100-0.02 mM concentration that is accepted as unachievable with near infrared spectroscopy. The results presented in this study support the aquaphotomics' water molecular mirror concept that explores spectral changes related to water molecular rearrangements caused by minute changes of the solutes in the aqueous systems. The method provides quick and accurate alternative for classical analytical measurements of saccharides even at millimolar concentration levels. PMID:26481987

  14. Carbon-depleted outer core revealed by sound velocity measurements of liquid iron-carbon alloy.

    PubMed

    Nakajima, Yoichi; Imada, Saori; Hirose, Kei; Komabayashi, Tetsuya; Ozawa, Haruka; Tateno, Shigehiko; Tsutsui, Satoshi; Kuwayama, Yasuhiro; Baron, Alfred Q R

    2015-01-01

    The relative abundance of light elements in the Earth's core has long been controversial. Recently, the presence of carbon in the core has been emphasized, because the density and sound velocities of the inner core may be consistent with solid Fe7C3. Here we report the longitudinal wave velocity of liquid Fe84C16 up to 70 GPa based on inelastic X-ray scattering measurements. We find the velocity to be substantially slower than that of solid iron and Fe3C and to be faster than that of liquid iron. The thermodynamic equation of state for liquid Fe84C16 is also obtained from the velocity data combined with previous density measurements at 1 bar. The longitudinal velocity of the outer core, about 4% faster than that of liquid iron, is consistent with the presence of 4-5 at.% carbon. However, that amount of carbon is too small to account for the outer core density deficit, suggesting that carbon cannot be a predominant light element in the core. PMID:26596912

  15. Extended carrier lifetimes and diffusion in hybrid perovskites revealed by Hall effect and photoconductivity measurements

    PubMed Central

    Chen, Y.; Yi, H. T.; Wu, X.; Haroldson, R.; Gartstein, Y. N.; Rodionov, Y. I.; Tikhonov, K. S.; Zakhidov, A.; Zhu, X. -Y.; Podzorov, V.

    2016-01-01

    Impressive performance of hybrid perovskite solar cells reported in recent years still awaits a comprehensive understanding of its microscopic origins. In this work, the intrinsic Hall mobility and photocarrier recombination coefficient are directly measured in these materials in steady-state transport studies. The results show that electron-hole recombination and carrier trapping rates in hybrid perovskites are very low. The bimolecular recombination coefficient (10−11 to 10−10 cm3 s−1) is found to be on par with that in the best direct-band inorganic semiconductors, even though the intrinsic Hall mobility in hybrid perovskites is considerably lower (up to 60 cm2 V−1 s−1). Measured here, steady-state carrier lifetimes (of up to 3 ms) and diffusion lengths (as long as 650 μm) are significantly longer than those in high-purity crystalline inorganic semiconductors. We suggest that these experimental findings are consistent with the polaronic nature of charge carriers, resulting from an interaction of charges with methylammonium dipoles. PMID:27477058

  16. Field measurement of beef pen manure methane and nitrous oxide reveals a surprise for inventory calculations.

    PubMed

    Redding, M R; Devereux, J; Phillips, F; Lewis, R; Naylor, T; Kearton, T; Hill, C J; Weidemann, S

    2015-05-01

    Few data exist on direct greenhouse gas emissions from pen manure at beef feedlots. However, emission inventories attempt to account for these emissions. This study used a large chamber to isolate NO and CH emissions from pen manure at two Australian commercial beef feedlots (stocking densities, 13-27 m head) and related these emissions to a range of potential emission control factors, including masses and concentrations of volatile solids, NO, total N, NH, and organic C (OC), and additional factors such as total manure mass, cattle numbers, manure pack depth and density, temperature, and moisture content. Mean measured pen NO emissions were 0.428 kg ha d (95% confidence interval [CI], 0.252-0.691) and 0.00405 kg ha d (95% CI, 0.00114-0.0110) for the northern and southern feedlots, respectively. Mean measured CH emission was 0.236 kg ha d (95% CI, 0.163-0.332) for the northern feedlot and 3.93 kg ha d (95% CI, 2.58-5.81) for the southern feedlot. Nitrous oxide emission increased with density, pH, temperature, and manure mass, whereas negative relationships were evident with moisture and OC. Strong relationships were not evident between NO emission and masses or concentrations of NO or total N in the manure. This is significant because many standard inventory calculation protocols predict NO emissions using the mass of N excreted by the animal. PMID:26024253

  17. Measurement on isolated lithium iron phosphate particles reveals heterogeneity in material properties distribution

    NASA Astrophysics Data System (ADS)

    Snowden, Michael E.; Dayeh, Malak; Payne, Nicholas A.; Gervais, Simon; Mauzeroll, Janine; Schougaard, Steen B.

    2016-09-01

    We present herein localized galvanostatic and potentiodynamic measurements on lithium iron phosphate (LFP) particles, using the combination of a scanning micropipette contact method (SMCM) and scanning electron microscopy (SEM). The proposed technique allows small substrate areas (∼10 μm in diameter) decorated with LFP particles to be probed within a lithium electrolyte solution in organic carbonate solvents (0.1 M LiClO4 in propylene carbonate in the present study). SEM images of the scanned area allow the correlation of each electrochemical response to the number, and volume of the probed particles. Under favorable conditions, single particles are found within the measurement areas, thus enabling the determination of single particle properties in an anaerobic environment without the additional complications arising from the presence of binders and electronically conductive fillers. The ability to analyze a material with complementary experimental techniques at the single particle level should create new opportunities for fundamental studies and for the quality control of granular materials.

  18. Carbon-depleted outer core revealed by sound velocity measurements of liquid iron–carbon alloy

    PubMed Central

    Nakajima, Yoichi; Imada, Saori; Hirose, Kei; Komabayashi, Tetsuya; Ozawa, Haruka; Tateno, Shigehiko; Tsutsui, Satoshi; Kuwayama, Yasuhiro; Baron, Alfred Q. R.

    2015-01-01

    The relative abundance of light elements in the Earth's core has long been controversial. Recently, the presence of carbon in the core has been emphasized, because the density and sound velocities of the inner core may be consistent with solid Fe7C3. Here we report the longitudinal wave velocity of liquid Fe84C16 up to 70 GPa based on inelastic X-ray scattering measurements. We find the velocity to be substantially slower than that of solid iron and Fe3C and to be faster than that of liquid iron. The thermodynamic equation of state for liquid Fe84C16 is also obtained from the velocity data combined with previous density measurements at 1 bar. The longitudinal velocity of the outer core, about 4% faster than that of liquid iron, is consistent with the presence of 4–5 at.% carbon. However, that amount of carbon is too small to account for the outer core density deficit, suggesting that carbon cannot be a predominant light element in the core. PMID:26596912

  19. Extended carrier lifetimes and diffusion in hybrid perovskites revealed by Hall effect and photoconductivity measurements.

    PubMed

    Chen, Y; Yi, H T; Wu, X; Haroldson, R; Gartstein, Y N; Rodionov, Y I; Tikhonov, K S; Zakhidov, A; Zhu, X-Y; Podzorov, V

    2016-01-01

    Impressive performance of hybrid perovskite solar cells reported in recent years still awaits a comprehensive understanding of its microscopic origins. In this work, the intrinsic Hall mobility and photocarrier recombination coefficient are directly measured in these materials in steady-state transport studies. The results show that electron-hole recombination and carrier trapping rates in hybrid perovskites are very low. The bimolecular recombination coefficient (10(-11) to 10(-10) cm(3) s(-1)) is found to be on par with that in the best direct-band inorganic semiconductors, even though the intrinsic Hall mobility in hybrid perovskites is considerably lower (up to 60 cm(2) V(-1) s(-1)). Measured here, steady-state carrier lifetimes (of up to 3 ms) and diffusion lengths (as long as 650 μm) are significantly longer than those in high-purity crystalline inorganic semiconductors. We suggest that these experimental findings are consistent with the polaronic nature of charge carriers, resulting from an interaction of charges with methylammonium dipoles. PMID:27477058

  20. Leaf Phenology of Amazonian Canopy Trees as Revealed by Spectral and Physiochemical Measurements

    NASA Astrophysics Data System (ADS)

    Chavana-Bryant, C.; Gerard, F. F.; Malhi, Y.; Enquist, B. J.; Asner, G. P.

    2013-12-01

    The phenological dynamics of terrestrial ecosystems reflect the response of the Earth's biosphere to inter- and intra-annual dynamics of climatic and hydrological regimes. Some Dynamic Global Vegetation Models (GDVMs) have predicted that by 2050 the Amazon rainforest will begin to dieback (Cox et al. 2000, Nature) or that the ecosystem will become unsustainable (Salazar et al. 2007, GRL). One major component in DGVMs is the simulation of vegetation phenology, however, modelers are challenged with the estimation of tropical phenology which is highly complex. Current modeled phenology is based on observations of temperate vegetation and accurate representation of tropical phenology is long overdue. Remote sensing (RS) data are a key tool in monitoring vegetation dynamics at regional and global scales. Of the many RS techniques available, time-series analysis of vegetation indices (VIs) has become the most common approach in monitoring vegetation phenology (Samanta et al. 2010, GRL; Bradley et al. 2011, GCB). Our research focuses on investigating the influence that age related variation in the spectral reflectance and physiochemical properties of leaves may have on VIs of tropical canopies. In order to do this, we collected a unique leaf and canopy phenological dataset at two different Amazonian sites: Inselberg, French Guyana (FG) and Tambopata, Peru (PE). Hyperspectral reflectance measurements were collected from 4,102 individual leaves sampled to represent different leaf ages and vertical canopy positions (top, mid and low canopy) from 20 different canopy tree species (8 in FG and 12 in PE). These leaf spectra were complemented with 1) leaf physical measurements: fresh and dry weight, area and thickness, LMA and LWC and 2) leaf chemical measurements: %N, %C, %P, C:N and d13C. Canopy level observations included top-of-canopy reflectance measurements obtained using a multispectral 16-band radiometer, leaf demography (tot. number and age distribution) and branch

  1. Structure of recombinant Leishmania donovani pteridine reductase reveals a disordered active site

    PubMed Central

    Barrack, Keri L.; Tulloch, Lindsay B.; Burke, Lynsey-Ann; Fyfe, Paul K.; Hunter, William N.

    2011-01-01

    Pteridine reductase (PTR1) is a potential target for drug development against parasitic Trypanosoma and Leishmania species, protozoa that are responsible for a range of serious diseases found in tropical and subtropical parts of the world. As part of a structure-based approach to inhibitor development, specifically targeting Leishmania species, well ordered crystals of L. donovani PTR1 were sought to support the characterization of complexes formed with inhibitors. An efficient system for recombinant protein production was prepared and the enzyme was purified and crystallized in an orthorhombic form with ammonium sulfate as the precipitant. Diffraction data were measured to 2.5 Å resolution and the structure was solved by molecular replacement. However, a sulfate occupies a phosphate-binding site used by NADPH and occludes cofactor binding. The nicotinamide moiety is a critical component of the active site and without it this part of the structure is disordered. The crystal form obtained under these conditions is therefore unsuitable for the characterization of inhibitor complexes. PMID:21206018

  2. Actinomycin D binding mode reveals the basis for its potent HIV-1 and cancer activity

    NASA Astrophysics Data System (ADS)

    Paramanathan, Thayaparan; Vladescu, Ioana D.; McCauley, Micah J.; Rouzina, Ioulia; Williams, Mark C.

    2011-03-01

    Actinomycin D (ActD) is one of the most studied antibiotics, which has been used as an anti-cancer agent and also shown to inhibit HIV reverse transcription. Initial studies with ActD established that it intercalates double stranded DNA (dsDNA). However, recent studies have shown that ActD binds with even higher affinity to single stranded DNA (ssDNA). In our studies we use optical tweezers to stretch and hold single dsDNA molecule at constant force in the presence of varying ActD concentrations until the binding reaches equilibrium. The change in dsDNA length upon ActD binding measured as a function of time yields the rate of binding in addition to the equilibrium lengthening of DNA. The results suggest extremely slow kinetics, on the order of several minutes and 0.52 +/- 0.06 μ M binding affinity. Holding DNA at constant force while stretching and relaxing suggests that ActD binds to two single strands that are close to each other rather than to pure dsDNA or ssDNA. This suggests that biological activity of ActD that contributes towards the inhibition of cellular replication is due to its ability to bind at DNA bubbles during RNA transcription, thereby stalling the transcription process.

  3. Microfluidic glucose stimulation reveals limited coordination of intracellular Ca2+ activity oscillations in pancreatic islets

    PubMed Central

    Rocheleau, Jonathan V.; Walker, Glenn M.; Head, W. Steven; McGuinness, Owen P.; Piston, David W.

    2004-01-01

    The pancreatic islet is a functional microorgan involved in maintaining normoglycemia through regulated secretion of insulin and other hormones. Extracellular glucose stimulates insulin secretion from islet β cells through an increase in redox state, which can be measured by NAD(P)H autofluorescence. Glucose concentrations over ≈7 mM generate synchronous oscillations in β cell intracellular Ca2+ concentration ([Ca2+]i), which lead to pulsatile insulin secretion. Prevailing models assume that the pancreatic islet acts as a functional syncytium, and the whole islet [Ca2+]i response has been modeled in terms of islet bursting and pacemaker models. To test these models, we developed a microfluidic device capable of partially stimulating an islet, while allowing observation of the NAD(P)H and [Ca2+]i responses. We show that β cell [Ca2+]i oscillations occur only within regions stimulated with more than ≈6.6 mM glucose. Furthermore, we show that tolbutamide, an antagonist of the ATP-sensitive K+ channel, allows these oscillations to travel farther into the nonstimulated regions of the islet. Our approach shows that the extent of Ca2+ propagation across the islet depends on a delicate interaction between the degree of coupling and the extent of ATP-sensitive K+-channel activation and illustrates an experimental paradigm that will have utility for many other biological systems. PMID:15317941

  4. Optical Coherence Tomography angiography reveals laminar microvascular hemodynamics in the rat somatosensory cortex during activation

    PubMed Central

    Srinivasan, Vivek J.; Radhakrishnan, Harsha

    2014-01-01

    The BOLD (blood-oxygen-level dependent) fMRI (functional Magnetic Resonance Imaging) signal is shaped, in part, by changes in red blood cell (RBC) content and flow across vascular compartments over time. These complex dynamics have been challenging to characterize directly due to a lack of appropriate imaging modalities. In this study, making use of infrared light scattering from RBCs, depth-resolved Optical Coherence Tomography (OCT) angiography was applied to image laminar functional hyperemia in the rat somatosensory cortex. After defining and validating depth-specific metrics for changes in RBC content and speed, laminar hemodynamic responses in microvasculature up to cortical depths of >1 mm were measured during a forepaw stimulus. The results provide a comprehensive picture of when and where changes in RBC content and speed occur during and immediately following cortical activation. In summary, the earliest and largest microvascular RBC content changes occurred in the middle cortical layers, while post-stimulus undershoots were most prominent superficially. These laminar variations in positive and negative responses paralleled known distributions of excitatory and inhibitory synapses, suggesting neuronal underpinnings. Additionally, the RBC speed response consistently returned to baseline more promptly than RBC content after the stimulus across cortical layers, supporting a “flow-volume mismatch” of hemodynamic origin. PMID:25111471

  5. Nano-rheology measurements reveal that the hydration layer of enzymes partially controls conformational dynamics

    NASA Astrophysics Data System (ADS)

    Alavi, Zahra; Ariyaratne, Amila; Zocchi, Giovanni

    2015-05-01

    For a typical (20 kD, 4 nm size) monomeric enzyme, more than 50 % of the residues are at the surface. The mechanics of these soft, heterogeneous nanoparticles was recently shown to be viscoelastic. Here, we explore the contribution of the enzyme's surface to the mechanics of the molecule. Nano-rheology provides sub- Å resolution measurements of the reversible deformation of the enzyme subject to an oscillatory mechanical stress. We perturb the surface of the enzyme by adding small amounts of DMSO (dimethyl sulfoxide), believed to affect ordering of the enzyme-water interface. We observe a dramatic though reversible change in the mechanics of the enzyme, which becomes more viscous. On the other hand, the catalytic speed is unaffected, while at higher DMSO concentrations ( >1 % ) it even increases.

  6. One-Neutron Removal Measurement Reveals {sup 24}O as a New Doubly Magic Nucleus

    SciTech Connect

    Kanungo, R.; Perro, C.; Nociforo, C.; Aumann, T.; Geissel, H.; Gerl, J.; Kindler, B.; Litvinov, Y.; Lommel, B.; Mahata, K.; Scheidenberger, C.; Sun, B.; Weick, H.; Winkler, M.; Prochazka, A.; Farinon, F.; Knoebel, R.; Boutin, D.; Lenske, H.; Cortina-Gil, D.

    2009-04-17

    The first measurement of the momentum distribution for one-neutron removal from {sup 24}O at 920A MeV performed at GSI, Darmstadt is reported. The observed distribution has a width (FWHM) of 99{+-}4 MeV/c in the projectile rest frame and a one-neutron removal cross section of 63{+-}7 mb. The results are well explained with a nearly pure 2s{sub 1/2} neutron spectroscopic factor of 1.74{+-}0.19 within the eikonal model. This large s-wave probability shows a spherical shell closure thereby confirming earlier suggestions that {sup 24}O is a new doubly magic nucleus.

  7. Polyethylene glycol and divalent salt-induced DNA reentrant condensation revealed by single molecule measurements.

    PubMed

    Cheng, Chao; Jia, Jun-Li; Ran, Shi-Yong

    2015-05-21

    In this study, we investigated the DNA condensation induced by polyethylene glycol (PEG) with different molecular weights (PEG 600 and PEG 6000) in the presence of NaCl or MgCl2 by using magnetic tweezers (MT) and atomic force microscopy (AFM). The MT measurements show that with increasing NaCl concentration, the critical condensation force in the PEG 600-DNA or PEG 6000-DNA system increased approximately linearly. PEG 6000 solution has a larger critical force than PEG 600 solution at a given NaCl concentration. In comparison, a parabolic trend of the critical condensation force was observed with increasing MgCl2 concentration, indicating that DNA undergoes a reentrant condensation. The AFM results show that the morphologies of the compacted DNA-PEG complexes depended on the salt concentration and were consistent with the MT results. PMID:25871460

  8. Planetary science. Low-altitude magnetic field measurements by MESSENGER reveal Mercury's ancient crustal field.

    PubMed

    Johnson, Catherine L; Phillips, Roger J; Purucker, Michael E; Anderson, Brian J; Byrne, Paul K; Denevi, Brett W; Feinberg, Joshua M; Hauck, Steven A; Head, James W; Korth, Haje; James, Peter B; Mazarico, Erwan; Neumann, Gregory A; Philpott, Lydia C; Siegler, Matthew A; Tsyganenko, Nikolai A; Solomon, Sean C

    2015-05-22

    Magnetized rocks can record the history of the magnetic field of a planet, a key constraint for understanding its evolution. From orbital vector magnetic field measurements of Mercury taken by the MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) spacecraft at altitudes below 150 kilometers, we have detected remanent magnetization in Mercury's crust. We infer a lower bound on the average age of magnetization of 3.7 to 3.9 billion years. Our findings indicate that a global magnetic field driven by dynamo processes in the fluid outer core operated early in Mercury's history. Ancient field strengths that range from those similar to Mercury's present dipole field to Earth-like values are consistent with the magnetic field observations and with the low iron content of Mercury's crust inferred from MESSENGER elemental composition data. PMID:25953822

  9. Multifractality as a Measure of Complexity in Solar Flare Activity

    NASA Astrophysics Data System (ADS)

    Sen, Asok K.

    2007-03-01

    In this paper we use the notion of multifractality to describe the complexity in H α flare activity during the solar cycles 21, 22, and 23. Both northern and southern hemisphere flare indices are analyzed. Multifractal behavior of the flare activity is characterized by calculating the singularity spectrum of the daily flare index time series in terms of the Hölder exponent. The broadness of the singularity spectrum gives a measure of the degree of multifractality or complexity in the flare index data. The broader the spectrum, the richer and more complex is the structure with a higher degree of multifractality. Using this broadness measure, complexity in the flare index data is compared between the northern and southern hemispheres in each of the three cycles, and among the three cycles in each of the two hemispheres. Other parameters of the singularity spectrum can also provide information about the fractal properties of the flare index data. For instance, an asymmetry to the left or right in the singularity spectrum indicates a dominance of high or low fractal exponents, respectively, reflecting a relative abundance of large or small fluctuations in the total energy emitted by the flares. Our results reveal that in the even (22nd) cycle the singularity spectra are very similar for the northern and southern hemispheres, whereas in the odd cycles (21st and 23rd) they differ significantly. In particular, we find that in cycle 21, the northern hemisphere flare index data have higher complexity than its southern counterpart, with an opposite pattern prevailing in cycle 23. Furthermore, small-scale fluctuations in the flare index time series are predominant in the northern hemisphere in the 21st cycle and are predominant in the southern hemisphere in the 23rd cycle. Based on these findings one might suggest that, from cycle to cycle, there exists a smooth switching between the northern and southern hemispheres in the multifractality of the flaring process. This new

  10. In situ measures of foraging success and prey encounter reveal marine habitat-dependent search strategies.

    PubMed

    Thums, Michele; Bradshaw, Corey J A; Hindelli, Mark A

    2011-06-01

    Predators are thought to reduce travel speed and increase turning rate in areas where resources are relatively more abundant, a behavior termed "area-restricted search." However, evidence for this is rare, and few empirical data exist for large predators. Animals exhibiting foraging site fidelity could also be spatially aware of suitable feeding areas based on prior experience; changes in movement patterns might therefore arise from the anticipation of higher prey density. We tested the hypothesis that regions of area-restricted search were associated with a higher number of daily speed spikes (a proxy for potential prey encounter rate) and foraging success in southern elephant seals (Mirounga leonina), a species exhibiting both area-restricted searches and high interannual foraging site fidelity. We used onshore morphological measurements and diving data from archival tags deployed during winter foraging trips. Foraging success was inferred from in situ changes in relative lipid content derived from measured changes in buoyancy, and first-passage time analysis was used to identify area-restricted search behavior. Seals exhibited relatively direct southerly movement on average, with intensive search behavior predominantly located at the distal end of tracks. The probability of being in search mode was positively related to changes in relative lipid content; thus, intensively searched areas were associated with the highest foraging success. However, there was high foraging success during the outward transit even though seals moved through quickly without slowing down and increasing turning rate to exploit these areas. In addition, the probability of being in search mode was negatively related to the number of daily speed spikes. These results suggest that movement patterns represent a response to prior expectation of the location of predictable and profitable resources. Shelf habitat was 4-9 times more profitable than the other habitats, emphasizing the importance

  11. Force measurements on natural membrane nanovesicles reveal a composition-independent, high Young's modulus

    NASA Astrophysics Data System (ADS)

    Calò, Annalisa; Reguera, David; Oncins, Gerard; Persuy, Marie-Annick; Sanz, Guenhaël; Lobasso, Simona; Corcelli, Angela; Pajot-Augy, Edith; Gomila, Gabriel

    2014-01-01

    Mechanical properties of nano-sized vesicles made up of natural membranes are crucial to the development of stable, biocompatible nanocontainers with enhanced functional, recognition and sensing capabilities. Here we measure and compare the mechanical properties of plasma and inner membrane nanovesicles ~80 nm in diameter obtained from disrupted yeast Saccharomyces cerevisiae cells. We provide evidence of a highly deformable behaviour for these vesicles, able to support repeated wall-to-wall compressions without irreversible deformations, accompanied by a noticeably high Young's modulus (~300 MPa) compared to that obtained for reconstituted artificial liposomes of similar size and approaching that of some virus particles. Surprisingly enough, the results are approximately similar for plasma and inner membrane nanovesicles, in spite of their different lipid compositions, especially on what concerns the ergosterol content. These results point towards an important structural role of membrane proteins in the mechanical response of natural membrane vesicles and open the perspective to their potential use as robust nanocontainers for bioapplications.Mechanical properties of nano-sized vesicles made up of natural membranes are crucial to the development of stable, biocompatible nanocontainers with enhanced functional, recognition and sensing capabilities. Here we measure and compare the mechanical properties of plasma and inner membrane nanovesicles ~80 nm in diameter obtained from disrupted yeast Saccharomyces cerevisiae cells. We provide evidence of a highly deformable behaviour for these vesicles, able to support repeated wall-to-wall compressions without irreversible deformations, accompanied by a noticeably high Young's modulus (~300 MPa) compared to that obtained for reconstituted artificial liposomes of similar size and approaching that of some virus particles. Surprisingly enough, the results are approximately similar for plasma and inner membrane nanovesicles, in

  12. Novel fluorescence resonance energy transfer-based reporter reveals differential calcineurin activation in neonatal and adult cardiomyocytes.

    PubMed

    Bazzazi, Hojjat; Sang, Lingjie; Dick, Ivy E; Joshi-Mukherjee, Rosy; Yang, Wanjun; Yue, David T

    2015-09-01

    Novel fluorescence resonance energy transfer-based genetically encoded reporters of calcineurin are constructed by fusing the two subunits of calcineurin with P2A-based linkers retaining the expected native conformation of calcineurin. Calcineurin reporters display robust responses to calcium transients in HEK293 cells. The sensor responses are correlated with NFATc1 translocation dynamics in HEK293 cells. The sensors are uniformly distributed in neonatal myocytes and respond efficiently to single electrically evoked calcium transients and show cumulative activation at frequencies of 0.5 and 1 Hz. In adult myocytes, the calcineurin sensors appear to be localized to the cardiac z-lines, and respond to cumulative calcium transients at frequencies of 0.5 and 1 Hz. The phosphatase calcineurin is a central component of many calcium signalling pathways, relaying calcium signals from the plasma membrane to the nucleus. It has critical functions in a multitude of systems, including immune, cardiac and neuronal. Given the widespread importance of calcineurin in both normal and pathological conditions, new tools that elucidate the spatiotemporal dynamics of calcineurin activity would be invaluable. Here we develop two separate genetically encoded fluorescence resonance energy transfer (FRET)-based sensors of calcineurin activation, DuoCaN and UniCaN. Both sensors showcase a large dynamic range and rapid response kinetics, differing primarily in the linker structure between the FRET pairs. Both sensors were calibrated in HEK293 cells and their responses correlated well with NFAT translocation to the nucleus, validating the biological relevance of the sensor readout. The sensors were subsequently expressed in neonatal rat ventricular myocytes and acutely isolated adult guinea pig ventricular myocytes. Both sensors demonstrated robust responses in myocytes and revealed kinetic differences in calcineurin activation during changes in pacing rate for neonatal versus adult myocytes

  13. Microvascular pressure measurement reveals a coronary vascular waterfall in arterioles larger than 110 microm.

    PubMed

    Versluis, J P; Heslinga, J W; Sipkema, P; Westerhof, N

    2001-11-01

    Pressure-flow relationships at the entrance of the coronary circulation in the diastolic myocardium exhibit a zero-flow pressure intercept (P(int)). We tested whether this intercept is the same throughout the vascular bed. Microvascular pressure-flow relationships were therefore measured in vessels of various sizes of the maximally dilated vasculature of perfused unstimulated papillary muscle using the servo-null technique. From these relationships, P(int) were calculated with nonlinear regression. The P(int) at the level of the septal artery (diameter, 150-250 microm) was 23.2 +/- 4.4 cmH2O (n = 12). In arterioles with a diameter range between 24 and 110 microm, P(int) was 1.7 +/- 0.5 cmH2O (n = 6, P < 0.01), significantly lower than in the septal artery but significantly higher than zero, and not dependent on vessel size. In venules with the same diameters, P(int) was 1.1 +/- 1.1 cmH2O (n = 4), which was not different from zero. We conclude that, in the dilated vascular bed of the papillary muscle, two vascular waterfalls are found. The first waterfall is located in arterioles between 150 and 110 microm. The second waterfall is probably located in the small postcapillary venules. PMID:11668051

  14. Gel-expanded to gel-condensed transition in neurofilament networks revealed by direct force measurements

    NASA Astrophysics Data System (ADS)

    Beck, Roy; Deek, Joanna; Jones, Jayna B.; Safinya, Cyrus R.

    2010-01-01

    Neurofilaments (NF)-the principal cytoskeletal constituent of myelinated axons in vertebrates-consist of three molecular-weight subunit proteins NF-L (low), NF-M (medium) and NF-H (high), assembled to form mature filaments with protruding unstructured C-terminus side arms. Liquid-crystal gel networks of side-arm-mediated neurofilament assemblies have a key role in the mechanical stability of neuronal processes. Disruptions of the neurofilament network, owing to neurofilament over-accumulation or incorrect side-arm interactions, are a hallmark of motor-neuron diseases including amyotrophic lateral sclerosis. Using synchrotron X-ray scattering, we report on a direct measurement of forces in reconstituted neurofilament gels under osmotic pressure (P). With increasing pressure near physiological salt and average phosphorylation conditions, NF-LMH, comprising the three subunits near in vivo composition, or NF-LH gels, undergo for P>Pc~10kPa, an abrupt non-reversible gel-expanded to gel-condensed transition. The transition indicates side-arm-mediated attractions between neurofilaments consistent with an electrostatic model of interpenetrating chains. In contrast, NF-LM gels remain in a collapsed state for PPc. These findings, which delineate the distinct roles of NF-M and NF-H in regulating neurofilament interactions, shed light on possible mechanisms for disruptions of optimal mechanical network properties.

  15. Inferring brain-computational mechanisms with models of activity measurements.

    PubMed

    Kriegeskorte, Nikolaus; Diedrichsen, Jörn

    2016-10-01

    High-resolution functional imaging is providing increasingly rich measurements of brain activity in animals and humans. A major challenge is to leverage such data to gain insight into the brain's computational mechanisms. The first step is to define candidate brain-computational models (BCMs) that can perform the behavioural task in question. We would then like to infer which of the candidate BCMs best accounts for measured brain-activity data. Here we describe a method that complements each BCM by a measurement model (MM), which simulates the way the brain-activity measurements reflect neuronal activity (e.g. local averaging in functional magnetic resonance imaging (fMRI) voxels or sparse sampling in array recordings). The resulting generative model (BCM-MM) produces simulated measurements. To avoid having to fit the MM to predict each individual measurement channel of the brain-activity data, we compare the measured and predicted data at the level of summary statistics. We describe a novel particular implementation of this approach, called probabilistic representational similarity analysis (pRSA) with MMs, which uses representational dissimilarity matrices (RDMs) as the summary statistics. We validate this method by simulations of fMRI measurements (locally averaging voxels) based on a deep convolutional neural network for visual object recognition. Results indicate that the way the measurements sample the activity patterns strongly affects the apparent representational dissimilarities. However, modelling of the measurement process can account for these effects, and different BCMs remain distinguishable even under substantial noise. The pRSA method enables us to perform Bayesian inference on the set of BCMs and to recognize the data-generating model in each case.This article is part of the themed issue 'Interpreting BOLD: a dialogue between cognitive and cellular neuroscience'. PMID:27574316

  16. The inner jet of an active galactic nucleus as revealed by a radio-to-gamma-ray outburst.

    PubMed

    Marscher, Alan P; Jorstad, Svetlana G; D'Arcangelo, Francesca D; Smith, Paul S; Williams, G Grant; Larionov, Valeri M; Oh, Haruki; Olmstead, Alice R; Aller, Margo F; Aller, Hugh D; McHardy, Ian M; Lähteenmäki, Anne; Tornikoski, Merja; Valtaoja, Esko; Hagen-Thorn, Vladimir A; Kopatskaya, Eugenia N; Gear, Walter K; Tosti, Gino; Kurtanidze, Omar; Nikolashvili, Maria; Sigua, Lorand; Miller, H Richard; Ryle, Wesley T

    2008-04-24

    Blazars are the most extreme active galactic nuclei. They possess oppositely directed plasma jets emanating at near light speeds from accreting supermassive black holes. According to theoretical models, such jets are propelled by magnetic fields twisted by differential rotation of the black hole's accretion disk or inertial-frame-dragging ergosphere. The flow velocity increases outward along the jet in an acceleration and collimation zone containing a coiled magnetic field. Detailed observations of outbursts of electromagnetic radiation, for which blazars are famous, can potentially probe the zone. It has hitherto not been possible to either specify the location of the outbursts or verify the general picture of jet formation. Here we report sequences of high-resolution radio images and optical polarization measurements of the blazar BL Lacertae. The data reveal a bright feature in the jet that causes a double flare of radiation from optical frequencies to TeV gamma-ray energies, as well as a delayed outburst at radio wavelengths. We conclude that the event starts in a region with a helical magnetic field that we identify with the acceleration and collimation zone predicted by the theories. The feature brightens again when it crosses a standing shock wave corresponding to the bright 'core' seen on the images. PMID:18432239

  17. Tearing of the Indian lithospheric slab beneath southern Tibet revealed by SKS-wave splitting measurements

    NASA Astrophysics Data System (ADS)

    Chen, Yun; Li, Wei; Yuan, Xiaohui; Badal, José; Teng, Jiwen

    2015-03-01

    Shear wave birefringence is a direct diagnostic of seismic anisotropy. It is often used to infer the northern limit of the underthrusting Indian lithosphere, based on the seismic anisotropy contrast between the Indian and Eurasian plates. Most studies have been made through several near north-south trending passive-source seismic experiments in southern Tibet. To investigate the geometry and the nature of the underthrusting Indian lithosphere, an east-west trending seismic array consisting of 48 seismographs was operated in the central Lhasa block from September 2009 to November 2010. Splitting of SKS waves was measured and verified with different methods. Along the profile, the direction of fast wave polarization is about 60° in average with small fluctuations. The delay time generally increases from east to west between 0.2 s and 1.0 s, and its variation correlates spatially with north-south oriented rifts in southern Tibet. The SKS wave arrives 1.0-2.0 s later at stations in the eastern part of the profile than in the west. The source of the anisotropy, estimated by non-overlapped parts of the Fresnel zones at stations with different splitting parameters, is concentrated above ca. 195 km depth. All the first-order features suggest that the geometry of the underthrusting Indian lithospheric slab in the Himalayan-Tibetan collision zone beneath southern Tibet is characterized by systematic lateral variations. A slab tearing and/or breakoff model of Indian lithosphere with different subduction angles is likely a good candidate to explain the observations.

  18. Airborne methane remote measurements reveal heavy-tail flux distribution in Four Corners region.

    PubMed

    Frankenberg, Christian; Thorpe, Andrew K; Thompson, David R; Hulley, Glynn; Kort, Eric Adam; Vance, Nick; Borchardt, Jakob; Krings, Thomas; Gerilowski, Konstantin; Sweeney, Colm; Conley, Stephen; Bue, Brian D; Aubrey, Andrew D; Hook, Simon; Green, Robert O

    2016-08-30

    Methane (CH4) impacts climate as the second strongest anthropogenic greenhouse gas and air quality by influencing tropospheric ozone levels. Space-based observations have identified the Four Corners region in the Southwest United States as an area of large CH4 enhancements. We conducted an airborne campaign in Four Corners during April 2015 with the next-generation Airborne Visible/Infrared Imaging Spectrometer (near-infrared) and Hyperspectral Thermal Emission Spectrometer (thermal infrared) imaging spectrometers to better understand the source of methane by measuring methane plumes at 1- to 3-m spatial resolution. Our analysis detected more than 250 individual methane plumes from fossil fuel harvesting, processing, and distributing infrastructures, spanning an emission range from the detection limit [Formula: see text] 2 kg/h to 5 kg/h through [Formula: see text] 5,000 kg/h. Observed sources include gas processing facilities, storage tanks, pipeline leaks, and well pads, as well as a coal mine venting shaft. Overall, plume enhancements and inferred fluxes follow a lognormal distribution, with the top 10% emitters contributing 49 to 66% to the inferred total point source flux of 0.23 Tg/y to 0.39 Tg/y. With the observed confirmation of a lognormal emission distribution, this airborne observing strategy and its ability to locate previously unknown point sources in real time provides an efficient and effective method to identify and mitigate major emissions contributors over a wide geographic area. With improved instrumentation, this capability scales to spaceborne applications [Thompson DR, et al. (2016) Geophys Res Lett 43(12):6571-6578]. Further illustration of this potential is demonstrated with two detected, confirmed, and repaired pipeline leaks during the campaign. PMID:27528660

  19. Earthworm Biomass Measurement: A Science Activity for Middle School.

    ERIC Educational Resources Information Center

    Haskett, Jonathan; Levine, Elissa; Carey, Pauline B.; Niepold III, Frank

    2000-01-01

    Describes an activity on biomass measurement which, in this case, is the weight of a group of living things in a given area. The earthworm activity gives students a greater understanding of ecology, practical math applications, and the scientific method. (ASK)

  20. Seasonality in Children's Pedometer-Measured Physical Activity Levels

    ERIC Educational Resources Information Center

    Beighle, Aaron; Alderman, Brandon; Morgan, Charles F.; Le Masurier, Guy

    2008-01-01

    Seasonality appears to have an impact on children's physical activity levels, but equivocal findings demand more study in this area. With the increased use of pedometers in both research and practice, collecting descriptive data in various seasons to examine the impact of seasonality on pedometer-measured physical activity among children is…

  1. A Simple and Accurate Method for Measuring Enzyme Activity.

    ERIC Educational Resources Information Center

    Yip, Din-Yan

    1997-01-01

    Presents methods commonly used for investigating enzyme activity using catalase and presents a new method for measuring catalase activity that is more reliable and accurate. Provides results that are readily reproduced and quantified. Can also be used for investigations of enzyme properties such as the effects of temperature, pH, inhibitors,…

  2. Should soil testing services measure soil biological activity?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Health of agricultural soils depends largely on conservation management to promote soil organic C accumulation. Total soil organic C changes slowly, but active fractions are more dynamic. A key indicator of healthy soil is potential biological activity, which could be measured rapidly with soil te...

  3. LOFT experimental measurements uncertainty analyses. Volume XX. Fluid-velocity measurement using pulsed-neutron activation

    SciTech Connect

    Lassahn, G.D.; Taylor, D.J.N.

    1982-08-01

    Analyses of uncertainty components inherent in pulsed-neutron-activation (PNA) measurements in general and the Loss-of-Fluid-Test (LOFT) system in particular are given. Due to the LOFT system's unique conditions, previously-used techniques were modified to make the volocity measurement. These methods render a useful, cost-effective measurement with an estimated uncertainty of 11% of reading.

  4. Measurement of action spectra of light-activated processes

    NASA Astrophysics Data System (ADS)

    Ross, Justin; Zvyagin, Andrei V.; Heckenberg, Norman R.; Upcroft, Jacqui; Upcroft, Peter; Rubinsztein-Dunlop, Halina H.

    2006-01-01

    We report on a new experimental technique suitable for measurement of light-activated processes, such as fluorophore transport. The usefulness of this technique is derived from its capacity to decouple the imaging and activation processes, allowing fluorescent imaging of fluorophore transport at a convenient activation wavelength. We demonstrate the efficiency of this new technique in determination of the action spectrum of the light mediated transport of rhodamine 123 into the parasitic protozoan Giardia duodenalis.

  5. Behavioral Analysis of Dopaminergic Activation in Zebrafish and Rats Reveals Similar Phenotypes.

    PubMed

    Ek, Fredrik; Malo, Marcus; Åberg Andersson, Madelene; Wedding, Christoffer; Kronborg, Joel; Svensson, Peder; Waters, Susanna; Petersson, Per; Olsson, Roger

    2016-05-18

    Zebrafish is emerging as a complement to mammals in behavioral studies; however, there is a lack of comparative studies with rodents and humans to establish the zebrafish as a predictive translational model. Here we present a detailed phenotype evaluation of zebrafish larvae, measuring 300-3000 variables and analyzing them using multivariate analysis to identify the most important ones for further evaluations. The dopamine agonist apomorphine has previously been shown to have a complex U-shaped dose-response relationship in the variable distance traveled. In this study, we focused on breaking down distance traveled into more detailed behavioral phenotypes for both zebrafish and rats and identified in the multivariate analysis low and high dose phenotypes with characteristic behavioral features. Further analysis of single parameters also identified an increased activity at the lowest concentration indicative of a U-shaped dose-response. Apomorphine increased the distance of each swim movement (bout) at both high and low doses, but the underlying behavior of this increase is different; at high dose, both bout duration and frequency increased whereas bout max speed was higher at low dose. Larvae also displayed differences in place preference. The low dose phenotype spent more time in the center, indicative of an anxiolytic effect, while the high-dose phenotype had a wall preference. These dose-dependent effects corroborated findings in a parallel rat study and previous observations in humans. The translational value of pharmacological zebrafish studies was further evaluated by comparing the amino acid sequence of the dopamine receptors (D1-D4), between zebrafish, rats and humans. Humans and zebrafish share 100% of the amino acids in the binding site for D1 and D3 whereas D2 and D4 receptors share 85-95%. Molecular modeling of dopamine D2 and D4 receptors indicated that nonconserved amino acids have limited influence on important ligand-receptor interactions. PMID

  6. Revealing the Functional States in the Active Site of BLUF Photoreceptors from Electrochromic Shift Calculations

    PubMed Central

    2014-01-01

    Photoexcitation with blue light of the flavin chromophore in BLUF photoreceptors induces a switch into a metastable signaling state that is characterized by a red-shifted absorption maximum. The red shift is due to a rearrangement in the hydrogen bond pattern around Gln63 located in the immediate proximity of the isoalloxazine ring system of the chromophore. There is a long-lasting controversy between two structural models, named Q63A and Q63J in the literature, on the local conformation of the residues Gln63 and Tyr21 in the dark state of the photoreceptor. As regards the mechanistic details of the light-activation mechanism, rotation of Gln63 is opposed by tautomerism in the Q63A and Q63J models, respectively. We provide a structure-based simulation of electrochromic shifts of the flavin chromophore in the wild type and in various site-directed mutants. The excellent overall agreement between experimental and computed data allows us to evaluate the two structural models. Compelling evidence is obtained that the Q63A model is incorrect, whereas the Q63J is fully consistent with the present computations. Finally, we confirm independently that a keto–enol tautomerization of the glutamine at position 63, which was proposed as molecular mechanism for the transition between the dark and the light-adapted state, explains the measured 10 to 15 nm red shift in flavin absorption between these two states of the protein. We believe that the accurateness of our results provides evidence that the BLUF photoreceptors absorption is fine-tuned through electrostatic interactions between the chromophore and the protein matrix, and finally that the simplicity of our theoretical model is advantageous as regards easy reproducibility and further extensions. PMID:25153778

  7. 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.

  8. Development of the Patient Activation Measure for mental health.

    PubMed

    Green, Carla A; Perrin, Nancy A; Polen, Michael R; Leo, Michael C; Hibbard, Judith H; Tusler, Martin

    2010-07-01

    Our objective was to adapt the physical health Patient Activation Measure (PAM) for use among people with mental health conditions (PAM-MH). Data came from three studies among people with chronic mental health conditions and were combined in Rasch analyses. The PAM-MH's psychometric properties equal those of the original 13-item PAM. Test-retest reliability and concurrent validity were good, and the PAM-MH showed sensitivity to change. The PAM-MH appears to be a reliable and valid measure of patient activation among individuals with mental health problems. It appears to have potential for use in assessing change in activation. PMID:19728074

  9. Measurements of Salivary Alpha Amylase and Salivary Cortisol in Hominoid Primates Reveal Within-Species Consistency and Between-Species Differences

    PubMed Central

    Behringer, Verena; Borchers, Claudia; Deschner, Tobias; Möstl, Erich; Selzer, Dieter; Hohmann, Gottfried

    2013-01-01

    Salivary alpha amylase (sAA) is the most abundant enzyme in saliva. Studies in humans found variation in enzymatic activity of sAA across populations that could be linked to the copy number of loci for salivary amylase (AMY1), which was seen as an adaptive response to the intake of dietary starch. In addition to diet dependent variation, differences in sAA activity have been related to social stress. In a previous study, we found evidence for stress-induced variation in sAA activity in the bonobos, a hominoid primate that is closely related to humans. In this study, we explored patterns of variation in sAA activity in bonobos and three other hominoid primates, chimpanzee, gorilla, and orangutan to (a) examine if within-species differences in sAA activity found in bonobos are characteristic for hominoids and (b) assess the extent of variation in sAA activity between different species. The results revealed species-differences in sAA activity with gorillas and orangutans having higher basal sAA activity when compared to Pan. To assess the impact of stress, sAA values were related to cortisol levels measured in the same saliva samples. Gorillas and orangutans had low salivary cortisol concentrations and the highest cortisol concentration was found in samples from male bonobos, the group that also showed the highest sAA activity. Considering published information, the differences in sAA activity correspond with differences in AMY1 copy numbers and match with general features of natural diet. Studies on sAA activity have the potential to complement molecular studies and may contribute to research on feeding ecology and nutrition. PMID:23613746

  10. Measurements of salivary alpha amylase and salivary cortisol in hominoid primates reveal within-species consistency and between-species differences.

    PubMed

    Behringer, Verena; Borchers, Claudia; Deschner, Tobias; Möstl, Erich; Selzer, Dieter; Hohmann, Gottfried

    2013-01-01

    Salivary alpha amylase (sAA) is the most abundant enzyme in saliva. Studies in humans found variation in enzymatic activity of sAA across populations that could be linked to the copy number of loci for salivary amylase (AMY1), which was seen as an adaptive response to the intake of dietary starch. In addition to diet dependent variation, differences in sAA activity have been related to social stress. In a previous study, we found evidence for stress-induced variation in sAA activity in the bonobos, a hominoid primate that is closely related to humans. In this study, we explored patterns of variation in sAA activity in bonobos and three other hominoid primates, chimpanzee, gorilla, and orangutan to (a) examine if within-species differences in sAA activity found in bonobos are characteristic for hominoids and (b) assess the extent of variation in sAA activity between different species. The results revealed species-differences in sAA activity with gorillas and orangutans having higher basal sAA activity when compared to Pan. To assess the impact of stress, sAA values were related to cortisol levels measured in the same saliva samples. Gorillas and orangutans had low salivary cortisol concentrations and the highest cortisol concentration was found in samples from male bonobos, the group that also showed the highest sAA activity. Considering published information, the differences in sAA activity correspond with differences in AMY1 copy numbers and match with general features of natural diet. Studies on sAA activity have the potential to complement molecular studies and may contribute to research on feeding ecology and nutrition. PMID:23613746

  11. MCG measurement in the environment of active magnetic shield.

    PubMed

    Yamazaki, K; Kato, K; Kobayashi, K; Igarashi, A; Sato, T; Haga, A; Kasai, N

    2004-01-01

    MCG (Magnetocardiography) measurement by a SQUID gradiometer was attempted with only active magnetic shielding (active shielding). A three-axis-canceling-coil active shielding system, where three 16-10-16 turns-coil sets were put in the orthogonal directions, produces a homogeneous magnetic field in a considerable volume surrounding the center. Fluxgate sensors were used as the reference sensors of the system. The system can reduce environmental magnetic noise at low frequencies of less than a few Hz, at 50 Hz and at 150 Hz. Reducing such disturbances stabilizes biomagnetic measurement conditions for SQUIDs in the absence of magnetically shielded rooms (MSR). After filtering and averaging the measured MCG data by a first-order SQUID gradiometer with only the active shielding during the daytime, the QRS complex and T wave was clearly presented. PMID:16012640

  12. Solar irradiance measurements - Minimum through maximum solar activity

    NASA Technical Reports Server (NTRS)

    Lee, R. B., III; Gibson, M. A.; Shivakumar, N.; Wilson, R.; Kyle, H. L.; Mecherikunnel, A. T.

    1991-01-01

    The Earth Radiation Budget Satellite (ERBS) and the NOAA-9 spacecraft solar monitors were used to measure the total solar irradiance during the period October 1984 to December 1989. Decreasing trends in the irradiance measurements were observed as sunspot activity decreased to minimum levels in 1986; after 1986, increasing trends were observed as sunspot activity increased. The magnitude of the irradiance variability was found to be approximately 0.1 percent between sunspot minimum and maximum (late 1989). When compared with the 1984 to 1989 indices of solar magnetic activity, the irradiance trends appear to be in phase with the 11-year sunspot cycle. Both irradiance series yielded 1,365/sq Wm as the mean value of the solar irradiance, normalized to the mean earth/sun distance. The monitors are electrical substitution, active-cavity radiometers with estimated measurement precisions and accuracies of less than 0.02 and 0.2 percent, respectively.

  13. Measurement of actinides and strontium-90 in high activity waste

    SciTech Connect

    Maxwell, S.L. III; Nelson, M.R.

    1994-08-01

    The reliable measurement of trace radionuclides in high activity waste is important to support waste processing activities at SRS (F and H Area Waste Tanks, Extended Sludge Processing (ESP) and In-Tank precipitation (ITP) processing). Separation techniques are needed to remove high levels of gamma activity and alpha/beta interferences prior to analytical measurement. Using new extraction chromatographic resins from EiChrom Industries, Inc., the SRS Central Laboratory has developed new high speed separation methods that enable measurement of neptunium, thorium, uranium, plutonium, americium and strontium-90 in high activity waste solutions. Small particle size resin and applied vacuum are used to reduce analysis times and enhance column performance. Extraction chromatographic resins are easy to use and eliminate the generation of contaminated liquid organic waste.

  14. A proteomic approach reveals integrin activation state-dependent control of microtubule cortical targeting.

    PubMed

    Byron, Adam; Askari, Janet A; Humphries, Jonathan D; Jacquemet, Guillaume; Koper, Ewa J; Warwood, Stacey; Choi, Colin K; Stroud, Matthew J; Chen, Christopher S; Knight, David; Humphries, Martin J

    2015-01-01

    Integrin activation, which is regulated by allosteric changes in receptor conformation, enables cellular responses to the chemical, mechanical and topological features of the extracellular microenvironment. A global view of how activation state converts the molecular composition of the region proximal to integrins into functional readouts is, however, lacking. Here, using conformation-specific monoclonal antibodies, we report the isolation of integrin activation state-dependent complexes and their characterization by mass spectrometry. Quantitative comparisons, integrating network, clustering, pathway and image analyses, define multiple functional protein modules enriched in a conformation-specific manner. Notably, active integrin complexes are specifically enriched for proteins associated with microtubule-based functions. Visualization of microtubules on micropatterned surfaces and live cell imaging demonstrate that active integrins establish an environment that stabilizes microtubules at the cell periphery. These data provide a resource for the interrogation of the global molecular connections that link integrin activation to adhesion signalling. PMID:25609142

  15. Alanine-Scanning Mutational Analysis of Durancin GL Reveals Residues Important for Its Antimicrobial Activity.

    PubMed

    Ju, Xingrong; Chen, Xinquan; Du, Lihui; Wu, Xueyou; Liu, Fang; Yuan, Jian

    2015-07-22

    Durancin GL is a novel class IIa bacteriocin with 43 residues produced by Enterococcus durans 41D. This bacteriocin demonstrates narrow inhibition spectrum and potent antimicrobial activity against several Listeria monocytogenes strains, including nisin-resistant L. monocytogenes NR30. A systematic alanine-scanning mutational analysis with site-directed mutagenesis was performed to analyze durancin GL residues important for antimicrobial activity and specificity. Results showed that three mutations lost their antimicrobial activity, ten mutations demonstrated a decreased effect on the activity, and seven mutations exhibited relatively high activity. With regard to inhibitory spectrum, four mutants demonstrated a narrower antimicrobial spectrum than wild-type durancin GL. Another four mutants displayed a broader target cell spectrum and increased potency relative to wild-type durancin GL. These findings broaden our understanding of durancin GL residues important for its antimicrobial activity and contribute to future rational design of variants with increased potency. PMID:26168032

  16. A FRET biosensor reveals spatiotemporal activation and functions of aurora kinase A in living cells.

    PubMed

    Bertolin, Giulia; Sizaire, Florian; Herbomel, Gaëtan; Reboutier, David; Prigent, Claude; Tramier, Marc

    2016-01-01

    Overexpression of AURKA is a major hallmark of epithelial cancers. It encodes the multifunctional serine/threonine kinase aurora A, which is activated at metaphase and is required for cell cycle progression; assessing its activation in living cells is mandatory for next-generation drug design. We describe here a Förster's resonance energy transfer (FRET) biosensor detecting the conformational changes of aurora kinase A induced by its autophosphorylation on Thr288. The biosensor functionally replaces the endogenous kinase in cells and allows the activation of the kinase to be followed throughout the cell cycle. Inhibiting the catalytic activity of the kinase prevents the conformational changes of the biosensor. Using this approach, we discover that aurora kinase A activates during G1 to regulate the stability of microtubules in cooperation with TPX2 and CEP192. These results demonstrate that the aurora kinase A biosensor is a powerful tool to identify new regulatory pathways controlling aurora kinase A activation. PMID:27624869

  17. A proteomic approach reveals integrin activation state-dependent control of microtubule cortical targeting

    PubMed Central

    Byron, Adam; Askari, Janet A.; Humphries, Jonathan D.; Jacquemet, Guillaume; Koper, Ewa J.; Warwood, Stacey; Choi, Colin K.; Stroud, Matthew J.; Chen, Christopher S.; Knight, David; Humphries, Martin J.

    2015-01-01

    Integrin activation, which is regulated by allosteric changes in receptor conformation, enables cellular responses to the chemical, mechanical and topological features of the extracellular microenvironment. A global view of how activation state converts the molecular composition of the region proximal to integrins into functional readouts is, however, lacking. Here, using conformation-specific monoclonal antibodies, we report the isolation of integrin activation state-dependent complexes and their characterization by mass spectrometry. Quantitative comparisons, integrating network, clustering, pathway and image analyses, define multiple functional protein modules enriched in a conformation-specific manner. Notably, active integrin complexes are specifically enriched for proteins associated with microtubule-based functions. Visualization of microtubules on micropatterned surfaces and live cell imaging demonstrate that active integrins establish an environment that stabilizes microtubules at the cell periphery. These data provide a resource for the interrogation of the global molecular connections that link integrin activation to adhesion signalling. PMID:25609142

  18. Active-passive airborne ocean color measurement. II - Applications

    NASA Technical Reports Server (NTRS)

    Hoge, F. E.; Swift, R. N.; Yungel, J. K.

    1986-01-01

    Reported here for the first time is the use of a single airborne instrument to make concurrent measurements of oceanic chlorophyll concentration by (1) laser-induced fluorescence, (2) passive upwelling radiance, and (3) solar-induced chlorophyll fluorescence. Results from field experiments conducted with the NASA airborne oceanographic lidar (AOL) in the New York Bight demonstrate the capability of a single active-passive instrument to perform new and potentially important ocean color studies related to (1) active lidar validation of passive ocean color in-water algorithms, (2) chlorophyll a in vivo fluorescence yield variability, (3) calibration of active multichannel lidar systems, (4) effect of sea state on passive and active ocean color measurements, (5) laser/solar-induced chlorophyll fluorescence investigations, and (6) subsequent improvement of satellite-borne ocean color scanners. For validation and comparison purposes a separate passive ocean color sensor was also flown along with the new active-passive sensor during these initial field trials.

  19. Stimulus-Specific Distinctions in Spatial and Temporal Dynamics of Stress-Activated Protein Kinase Kinase Kinases Revealed by a Fluorescence Resonance Energy Transfer Biosensor▿

    PubMed Central

    Tomida, Taichiro; Takekawa, Mutsuhiro; O'Grady, Pauline; Saito, Haruo

    2009-01-01

    The stress-activated protein kinases (SAPKs), namely, p38 and JNK, are members of the mitogen-activated protein kinase family and are important determinants of cell fate when cells are exposed to environmental stresses such as UV and osmostress. SAPKs are activated by SAPK kinases (SAP2Ks), which are in turn activated by various SAP2K kinases (SAP3Ks). Because conventional methods, such as immunoblotting using phospho-specific antibodies, measure the average activity of SAP3Ks in a cell population, the intracellular dynamics of SAP3K activity are largely unknown. Here, we developed a reporter of SAP3K activity toward the MKK6 SAP2K, based on fluorescence resonance energy transfer, that can uncover the dynamic behavior of SAP3K activation in cells. Using this reporter, we demonstrated that SAP3K activation occurs either synchronously or asynchronously among a cell population and in different cellular compartments in single cells, depending on the type of stress applied. In particular, SAP3Ks are activated by epidermal growth factor and osmostress on the plasma membrane, by anisomycin and UV in the cytoplasm, and by etoposide in the nucleus. These observations revealed previously unknown heterogeneity in SAPK responses and supplied answers to the question of the cellular location in which various stresses induce stimulus-specific SAPK responses. PMID:19737916

  20. Measure for Measure: What Combining Diverse Measures Reveals about Children's Understanding of the Equal Sign as An Indicator of Mathematical Equality

    ERIC Educational Resources Information Center

    Matthews, Percival; Rittle-Johnson, Bethany; McEldoon, Katherine; Taylor, Roger

    2012-01-01

    Knowledge of the equal sign as an indicator of mathematical equality is foundational to children's mathematical development and serves as a key link between arithmetic and algebra. The current findings reaffirmed a past finding that diverse items can be integrated onto a single scale, revealed the wide variability in children's knowledge of the…

  1. A 220-nucleotide deletion of the intronic enhancer reveals an epigenetic hierarchy in immunoglobulin heavy chain locus activation

    PubMed Central

    Chakraborty, Tirtha; Perlot, Thomas; Subrahmanyam, Ramesh; Jani, Anant; Goff, Peter H.; Zhang, Yu; Ivanova, Irina; Alt, Frederick W.

    2009-01-01

    A tissue-specific transcriptional enhancer, Eμ, has been implicated in developmentally regulated recombination and transcription of the immunoglobulin heavy chain (IgH) gene locus. We demonstrate that deleting 220 nucleotides that constitute the core Eμ results in partially active locus, characterized by reduced histone acetylation, chromatin remodeling, transcription, and recombination, whereas other hallmarks of tissue-specific locus activation, such as loss of H3K9 dimethylation or gain of H3K4 dimethylation, are less affected. These observations define Eμ-independent and Eμ-dependent phases of locus activation that reveal an unappreciated epigenetic hierarchy in tissue-specific gene expression. PMID:19414554

  2. Advanced Active-Magnetic-Bearing Thrust-Measurement System

    NASA Technical Reports Server (NTRS)

    Imlach, Joseph; Kasarda, Mary; Blumber, Eric

    2008-01-01

    An advanced thrust-measurement system utilizes active magnetic bearings to both (1) levitate a floating frame in all six degrees of freedom and (2) measure the levitation forces between the floating frame and a grounded frame. This system was developed for original use in measuring the thrust exerted by a rocket engine mounted on the floating frame, but can just as well be used in other force-measurement applications. This system offers several advantages over prior thrust-measurement systems based on mechanical support by flexures and/or load cells: The system includes multiple active magnetic bearings for each degree of freedom, so that by selective use of one, some, or all of these bearings, it is possible to test a given article over a wide force range in the same fixture, eliminating the need to transfer the article to different test fixtures to obtain the benefit of full-scale accuracy of different force-measurement devices for different force ranges. Like other active magnetic bearings, the active magnetic bearings of this system include closed-loop control subsystems, through which the stiffness and damping characteristics of the magnetic bearings can be modified electronically. The design of the system minimizes or eliminates cross-axis force-measurement errors. The active magnetic bearings are configured to provide support against movement along all three orthogonal Cartesian axes, and such that the support along a given axis does not produce force along any other axis. Moreover, by eliminating the need for such mechanical connections as flexures used in prior thrust-measurement systems, magnetic levitation of the floating frame eliminates what would otherwise be major sources of cross-axis forces and the associated measurement errors. Overall, relative to prior mechanical-support thrust-measurement systems, this system offers greater versatility for adaptation to a variety of test conditions and requirements. The basic idea of most prior active

  3. Comparative Validity of Physical Activity Measures in Older Adults

    PubMed Central

    COLBERT, LISA H.; MATTHEWS, CHARLES E.; HAVIGHURST, THOMAS C.; KIM, KYUNGMANN; SCHOELLER, DALE A.

    2012-01-01

    Purpose To compare the validity of various physical activity measures with doubly labeled water (DLW)–measured physical activity energy expenditure (PAEE) in free-living older adults. Methods Fifty-six adults aged ≥65 yr wore three activity monitors (New Lifestyles pedometer, ActiGraph accelerometer, and a SenseWear (SW) armband) during a 10-d free-living period and completed three different surveys (Yale Physical Activity Survey (YPAS), Community Health Activities Model Program for Seniors (CHAMPS), and a modified Physical Activity Scale for the Elderly (modPASE)). Total energy expenditure was measured using DLW, resting metabolic rate was measured with indirect calorimetry, the thermic effect of food was estimated, and from these, estimates of PAEE were calculated. The degree of linear association between the various measures and PAEE was assessed, as were differences in group PAEE, when estimable by a given measure. Results All three monitors were significantly correlated with PAEE (r = 0.48–0.60, P < 0.001). Of the questionnaires, only CHAMPS was significantly correlated with PAEE (r = 0.28, P = 0.04). Statistical comparison of the correlations suggested that the monitors were superior to YPAS and modPASE. Mean squared errors for all correlations were high, and the median PAEE from the different tools was significantly different from DLW for all but the YPAS and regression-estimated PAEE from the ActiGraph. Conclusions Objective devices more appropriately rank PAEE than self-reported instruments in older adults, but absolute estimates of PAEE are not accurate. Given the cost differential and ease of use, pedometers seem most useful in this population when ranking by physical activity level is adequate. PMID:20881882

  4. Assessing Built Environment Walkability using Activity-Space Summary Measures

    PubMed Central

    Tribby, Calvin P.; Miller, Harvey J.; Brown, Barbara B.; Werner, Carol M.; Smith, Ken R.

    2015-01-01

    There is increasing emphasis on active transportation, such as walking, in transportation planning as a sustainable form of mobility and in public health as a means of achieving recommended physical activity and better health outcomes. A research focus is the influence of the built environment on walking, with the ultimate goal of identifying environmental modifications that invite more walking. However, assessments of the built environment for walkability are typically at a spatially disaggregate level (such as street blocks) or at a spatially aggregate level (such as census block groups). A key issue is determining the spatial units for walkability measures so that they reflect potential walking behavior. This paper develops methods for assessing walkability within individual activity spaces: the geographic region accessible to an individual during a given walking trip. We first estimate street network-based activity spaces using the shortest path between known trip starting/ending points and a travel time budget that reflects potential alternative paths. Based on objective walkability measures of the street blocks, we use three summary measures for walkability within activity spaces: i) the average walkability score across block segments (representing the general level of walkability in the activity space); ii) the standard deviation (representing the walkability variation), and; iii) the network autocorrelation (representing the spatial coherence of the walkability pattern). We assess the method using data from an empirical study of built environment walkability and walking behavior in Salt Lake City, Utah, USA. We visualize and map these activity space summary measures to compare walkability among individuals’ trips within their neighborhoods. We also compare summary measures for activity spaces versus census block groups, with the result that they agree less than half of the time. PMID:27213027

  5. Measurement of the components of nonexercise activity thermogenesis.

    PubMed

    Levine, J; Melanson, E L; Westerterp, K R; Hill, J O

    2001-10-01

    Nonexercise activity thermogenesis (NEAT) accounts for the vast majority of nonresting metabolic rate and changes in NEAT-predicted susceptibility to fat gain with overfeeding. Measuring physical activity and its components in free-living humans has been a long-standing challenge. In this study, we combine information about lightweight sensors that capture data on body position and motion with laboratory measures of energy expenditure to calculate nonfidgeting NEAT. This measurement of nonfidgeting NEAT was compared with total NEAT measured in a room calorimeter in 11 healthy subjects. The measurement of nonfidgeting NEAT accounted for 85 +/- 9% of total NEAT measured in the room calorimeter. The intraclass correlation coefficient for the two methods was 0.86 (95% confidence interval 0.56, 0.96; P < 0.05). This suggests that 86% of the variance is attributable to between-subject variance and 14% to between-method disagreement. These instruments are applicable to free-living subjects; they are stand-alone, are lightweight, and allow normal daily activities. This novel technology has potential application for not only assessing NEAT but also tracking physical activity in free-living humans. PMID:11551842

  6. Equilibrium physics breakdown reveals the active nature of red blood cell flickering

    NASA Astrophysics Data System (ADS)

    Turlier, H.; Fedosov, D. A.; Audoly, B.; Auth, T.; Gov, N. S.; Sykes, C.; Joanny, J.-F.; Gompper, G.; Betz, T.

    2016-05-01

    Red blood cells, or erythrocytes, are seen to flicker under optical microscopy, a phenomenon initially described as thermal fluctuations of the cell membrane. But recent studies have suggested the involvement of non-equilibrium processes, without definitively ruling out equilibrium interpretations. Using active and passive microrheology to directly compare the membrane response and fluctuations on single erythrocytes, we report here a violation of the fluctuation-dissipation relation, which is a direct demonstration of the non-equilibrium nature of flickering. With an analytical model of the composite erythrocyte membrane and realistic stochastic simulations, we show that several molecular mechanisms may explain the active fluctuations, and we predict their kinetics. We demonstrate that tangential metabolic activity in the network formed by spectrin, a cytoskeletal protein, can generate curvature-mediated active membrane motions. We also show that other active membrane processes represented by direct normal force dipoles may explain the observed membrane activity. Our findings provide solid experimental and theoretical frameworks for future investigations of the origin and function of active motion in cells.

  7. Knockin of Cre Gene at Ins2 Locus Reveals No Cre Activity in Mouse Hypothalamic Neurons

    PubMed Central

    Li, Ling; Gao, Lin; Wang, Kejia; Ma, Xianhua; Chang, Xusheng; Shi, Jian-Hui; Zhang, Ye; Yin, Kai; Liu, Zhimin; Shi, Yuguang; Xie, Zhifang; Zhang, Weiping J.

    2016-01-01

    The recombination efficiency and cell specificity of Cre driver lines are critical for exploring pancreatic β cell biology with the Cre/LoxP approach. Some commonly used Cre lines are based on the short Ins2 promoter fragment and show recombination activity in hypothalamic neurons; however, whether this stems from endogenous Ins2 promoter activity remains controversial. In this study, we generated Ins2-Cre knockin mice with a targeted insertion of IRES-Cre at the Ins2 locus and demonstrated with a cell lineage tracing study that the Ins2 gene is not transcriptionally active in the hypothalamus. The Ins2-Cre driver line displayed robust Cre expression and activity in pancreatic β cells without significant alterations in insulin expression. In the brain, Cre activity was mainly restricted to the choroid plexus, without significant recombination detected in the hippocampus or hypothalamus by the LacZ or fluorescent tdTomato reporters. Furthermore, Ins2-Cre mice exhibited normal glucose tolerance and insulin secretion upon glucose stimulation in vivo. In conclusion, this Ins2-Cre driver line allowed high-fidelity detection of endogenous Ins2 promoter activity in vivo, and the negative activity in the hypothalamus demonstrated that this system is a promising alternative tool for studying β cell biology. PMID:26830324

  8. Properties of active nucleosomes as revealed by HMG 14 and 17 chromatography.

    PubMed Central

    Weisbrod, S T

    1982-01-01

    Nucleosomes from actively transcribed genes (active nucleosomes) contain nonhistone proteins HMG 14 and 17 and are preferentially sensitive to digestion by DNAse I. Active nucleosomes isolated by chromatography on an HMG 14 and 17 glass bead affinity column were analyzed with respect to overall structure, accessory nonhistone components and modifications to the DNA and histones. The experiments lead to the following conclusions: the DNA in the active nucleosome is undermethylated compared to bulk DNA; topoisomerase I is a non-stoichiometric component of the active nucleosome fraction; the level of histone acetylation is enriched in active nucleosomes, but the extent of enrichment cannot account for HMG binding; and the two histone H3 molecules in the active nucleosome can dimerize more readily and are, therefore, probably closer together than those in the bulk of the nucleosomes. Additionally it is shown that HMG 14 and 17 prefer to bind to single- vs. double-stranded nucleic acids. The role of HMG 14 and 17 in producing a highly DNAse I sensitive structure and correspondingly helping to facilitate transcription is discussed in terms of these properties. Images PMID:6210882

  9. Bacterial biofilm formation inhibitory activity revealed for plant derived natural compounds.

    PubMed

    Artini, M; Papa, R; Barbato, G; Scoarughi, G L; Cellini, A; Morazzoni, P; Bombardelli, E; Selan, L

    2012-01-15

    Use of herbal plant remedies to treat infectious diseases is a common practice in many countries in traditional and alternative medicine. However to date there are only few antimicrobial agents derived from botanics. Based on microbiological screening tests of crude plant extracts we identified four compounds derived from Krameria, Aesculus hippocastanum and Chelidonium majus that showed a potentially interesting antimicrobial activity. In this work we present an in depth characterization of the inhibition activity of these pure compounds on the formation of biofilm of Staphylococcus aureus as well as of Staphylococcus epidermidis strains. We show that two of these compounds possess interesting potential to become active principles of new drugs. PMID:22182580

  10. Methodological considerations for measuring spontaneous physical activity in rodents

    PubMed Central

    Perez-Leighton, Claudio E.; Billington, Charles J.; Kotz, Catherine M.

    2014-01-01

    When exploring biological determinants of spontaneous physical activity (SPA), it is critical to consider whether methodological factors differentially affect rodents and the measured SPA. We determined whether acclimation time, sensory stimulation, vendor, or chamber size affected measures in rodents with varying propensity for SPA. We used principal component analysis to determine which SPA components (ambulatory and vertical counts, time in SPA, and distance traveled) best described the variability in SPA measurements. We compared radiotelemetry and infrared photobeams used to measure SPA and exploratory activity. Acclimation time, sensory stimulation, vendor, and chamber size independently influenced SPA, and the effect was moderated by the propensity for SPA. A 24-h acclimation period prior to SPA measurement was sufficient for habituation. Principal component analysis showed that ambulatory and vertical measurements of SPA describe different dimensions of the rodent's SPA behavior. Smaller testing chambers and a sensory attenuation cubicle around the chamber reduced SPA. SPA varies between rodents purchased from different vendors. Radiotelemetry and infrared photobeams differ in their sensitivity to detect phenotypic differences in SPA and exploratory activity. These data highlight methodological considerations in rodent SPA measurement and a need to standardize SPA methodology. PMID:24598463

  11. A biosensor of local kinesin activity reveals roles of PKC and EB1 in KIF17 activation

    PubMed Central

    Espenel, Cedric; Acharya, Bipul R.

    2013-01-01

    We showed previously that the kinesin-2 motor KIF17 regulates microtubule (MT) dynamics and organization to promote epithelial differentiation. How KIF17 activity is regulated during this process remains unclear. Several kinesins, including KIF17, adopt compact and extended conformations that reflect autoinhibited and active states, respectively. We designed biosensors of KIF17 to monitor its activity directly in single cells using fluorescence lifetime imaging to detect Förster resonance energy transfer. Lifetime data are mapped on a phasor plot, allowing us to resolve populations of active and inactive motors in individual cells. Using this biosensor, we demonstrate that PKC contributes to the activation of KIF17 and that this is required for KIF17 to stabilize MTs in epithelia. Furthermore, we show that EB1 recruits KIF17 to dynamic MTs, enabling its accumulation at MT ends and thus promoting MT stabilization at discrete cellular domains. PMID:24189273

  12. Microbial metabolic activity in soil as measured by dehydrogenase determinations

    NASA Technical Reports Server (NTRS)

    Casida, L. E., Jr.

    1977-01-01

    The dehydrogenase technique for measuring the metabolic activity of microorganisms in soil was modified to use a 6-h, 37 C incubation with either glucose or yeast extract as the electron-donating substrate. The rate of formazan production remained constant during this time interval, and cellular multiplication apparently did not occur. The technique was used to follow changes in the overall metabolic activities of microorganisms in soil undergoing incubation with a limiting concentration of added nutrient. The sequence of events was similar to that obtained by using the Warburg respirometer to measure O2 consumption. However, the major peaks of activity occurred earlier with the respirometer. This possibly is due to the lack of atmospheric CO2 during the O2 consumption measurements.

  13. Spores of most common airborne fungi reveal no ice nucleation activity

    NASA Astrophysics Data System (ADS)

    Pummer, B. G.; Atanasova, L.; Bauer, H.; Bernardi, J.; Druzhinina, I. S.; Grothe, H.

    2013-06-01

    Fungal spores are ubiquitous biological aerosols, which are considered to show ice nucleation (IN) activity. In this study the respective IN activity was tested in oil emulsion in the immersion freezing mode. The focus was laid on species of economical, ecological or sanitary significance. For the first time, not only common moulds, but also edible mushrooms (Basidiomycota, Agaricomycetes) were investigated, as they contribute massively to the total amount of fungal spores in the atmosphere. Only Fusarium avenaceum showed freezing events at low subzero-temperatures, while the other investigated fungal spores showed no significant IN activity. Furthermore, we selected a set of fungal strains from different sites and exposed them to occasional freezing stress during cultivation. Although the total protein expression was altered by this treatment, it had no significant impact on the IN activity.

  14. Active-site mobility revealed by the crystal structure of arylmalonate decarboxylase from Bordetella bronchiseptica.

    PubMed

    Kuettner, E Bartholomeus; Keim, Antje; Kircher, Markus; Rosmus, Susann; Sträter, Norbert

    2008-03-21

    Arylmalonate decarboxylase (AMDase) from Bordetella bronchiseptica catalyzes the enantioselective decarboxylation of arylmethylmalonates without the need for an organic cofactor or metal ion. The decarboxylation reaction is of interest for the synthesis of fine chemicals. As basis for an analysis of the catalytic mechanism of AMDase and for a rational enzyme design, we determined the X-ray structure of the enzyme up to 1.9 A resolution. Like the distantly related aspartate or glutamate racemases, AMDase has an aspartate transcarbamoylase fold consisting of two alpha/beta domains related by a pseudo dyad. However, the domain orientation of AMDase differs by about 30 degrees from that of the glutamate racemases, and also significant differences in active-site structures are observed. In the crystals, four independent subunits showing different conformations of active-site loops are present. This finding is likely to reflect the active-site mobility necessary for catalytic activity. PMID:18258259

  15. Structure of Escherichia coli tyrosine Kinase Etk Reveals a Novel Activation Mechanism

    SciTech Connect

    Lee,D.; Zheng, J.; She, Y.; Jia, Z.

    2008-01-01

    While protein tyrosine (Tyr) kinases (PTKs) have been extensively characterized in eukaryotes, far less is known about their emerging counterparts in prokaryotes. The inner-membrane Wzc/Etk protein belongs to the bacterial PTK family, which has an important function in regulating the polymerization and transport of virulence-determining capsular polysaccharide (CPS). The kinase uses a unique two-step activation process involving intra-phosphorylation of a Tyr residue, although the molecular mechanism remains unknown. Herein, we report the first crystal structure of a bacterial PTK, the C-terminal kinase domain of Escherichia coli Tyr kinase (Etk) at 2.5-Angstroms resolution. The fold of the Etk kinase domain differs markedly from that of eukaryotic PTKs. Based on the observed structure and supporting mass spectrometric evidence of Etk, a unique activation mechanism is proposed that involves the phosphorylated Tyr residue, Y574, at the active site and its specific interaction with a previously unidentified key Arg residue, R614, to unblock the active site. Both in vitro kinase activity and in vivo antibiotics resistance studies using structure-guided mutants further support the novel activation mechanism.

  16. Dynamic BRG1 Recruitment during T Helper Differentiation and Activation Reveals Distal Regulatory Elements▿§

    PubMed Central

    De, Supriyo; Wurster, Andrea L.; Precht, Patricia; Wood, William H.; Becker, Kevin G.; Pazin, Michael J.

    2011-01-01

    T helper cell differentiation and activation require specific transcriptional programs accompanied by changes in chromatin structure. However, little is known about the chromatin remodeling enzymes responsible. We performed genome-wide analysis to determine the general principles of BRG1 binding, followed by analysis of specific genes to determine whether these general rules were typical of key T cell genes. We found that binding of the remodeling protein BRG1 was programmed by both lineage and activation signals. BRG1 binding positively correlated with gene activity at protein-coding and microRNA (miRNA) genes. BRG1 binding was found at promoters and distal regions, including both novel and previously validated distal regulatory elements. Distal BRG1 binding correlated with expression, and novel distal sites in the Gata3 locus possessed enhancer-like activity, suggesting a general role for BRG1 in long-distance gene regulation. BRG1 recruitment to distal sites in Gata3 was impaired in cells lacking STAT6, a transcription factor that regulates lineage-specific genes. Together, these findings suggest that BRG1 interprets both differentiation and activation signals and plays a causal role in gene regulation, chromatin structure, and cell fate. Our findings suggest that BRG1 binding is a useful marker for identifying active cis-regulatory regions in protein-coding and miRNA genes. PMID:21262765

  17. An in vitro screening with emerging contaminants reveals inhibition of carboxylesterase activity in aquatic organisms.

    PubMed

    Solé, Montserrat; Sanchez-Hernandez, Juan C

    2015-12-01

    Pharmaceuticals and personal care products (PPCPs) form part of the new generation of pollutants present in many freshwater and marine ecosystems. Although environmental concentrations of these bioactive substances are low, they cause sublethal effects (e.g., enzyme inhibition) in non-target organisms. However, little is known on metabolism of PPCPs by non-mammal species. Herein, an in vitro enzyme trial was performed to explore sensitivity of carboxylesterase (CE) activity of aquatic organisms to fourteen PPCPs. The esterase activity was determined in the liver of Mediterranean freshwater fish (Barbus meridionalis and Squalius laietanus), coastal marine fish (Dicentrarchus labrax and Solea solea), middle-slope fish (Trachyrhynchus scabrus), deep-sea fish (Alepocephalus rostratus and Cataetix laticeps), and in the digestive gland of a decapod crustacean (Aristeus antennatus). Results showed that 100μM of the lipid regulators simvastatin and fenofibrate significantly inhibited (30-80% of controls) the CE activity of all target species. Among the personal care products, nonylphenol and triclosan were strong esterase inhibitors in most species (36-68% of controls). Comparison with literature data suggests that fish CE activity is as sensitive to inhibition by some PPCPs as that of mammals, although their basal activity levels are lower than in mammals. Pending further studies on the interaction between PPCPs and CE activity, we postulate that this enzyme may act as a molecular sink for certain PPCPs in a comparable way than that described for the organophosphorus pesticides. PMID:26562051

  18. Protein phosphorylation changes reveal new candidates in the regulation of egg activation and early embryogenesis in D. melanogaster

    PubMed Central

    Krauchunas, Amber R.; Horner, Vanessa L.; Wolfner, Mariana F.

    2012-01-01

    Egg activation is the series of events that must occur for a mature oocyte to become capable of supporting embryogenesis. These events include changes to the egg’s outer coverings, the resumption and completion of meiosis, the translation of new proteins, and the degradation of specific maternal mRNAs. While we know some of the molecules that direct the initial events of egg activation, it remains unclear how multiple pathways are coordinated to change the cellular state from mature oocyte to activated egg. Using a proteomic approach we have identified new candidates for the regulation and progression of egg activation. Reasoning that phosphorylation can simultaneously and rapidly modulate the activity of many proteins, we identified proteins that are post-translationally modified during the transition from oocyte to activated egg in Drosophila melanogaster. We find that at least 311 proteins change in phosphorylation state between mature oocytes and activated eggs. These proteins fall into various functional classes related to the events of egg activation including calcium binding, proteolysis, and protein translation. Our set of candidates includes genes already associated with egg activation, as well as many genes not previously studied during this developmental period. RNAi knockdown of a subset of these genes revealed a new gene, mrityu, necessary for embryonic development past the first mitosis. Thus, by identifying phospho-modulated proteins we have produced a focused candidate set for future genetic studies to test their roles in egg activation and the initiation of embryogenesis. PMID:22884528

  19. An Alternative Measure of Solar Activity from Detailed Sunspot Datasets

    NASA Astrophysics Data System (ADS)

    Muraközy, J.; Baranyi, T.; Ludmány, A.

    2016-05-01

    The sunspot number is analyzed by using detailed sunspot data, including aspects of observability, sunspot sizes, and proper identification of sunspot groups as discrete entities of solar activity. The tests show that in addition to the subjective factors there are also objective causes of the ambiguities in the series of sunspot numbers. To introduce an alternative solar-activity measure, the physical meaning of the sunspot number has to be reconsidered. It contains two components whose numbers are governed by different physical mechanisms and this is one source of the ambiguity. This article suggests an activity index, which is the amount of emerged magnetic flux. The only long-term proxy measure is the detailed sunspot-area dataset with proper calibration to the magnetic flux. The Debrecen sunspot databases provide an appropriate source for the establishment of the suggested activity index.

  20. Photospheric Magnetic Diffusion by Measuring Moments of Active Regions

    NASA Astrophysics Data System (ADS)

    Engell, Alexander; Longcope, D.

    2013-07-01

    Photospheric magnetic surface diffusion is an important constraint for the solar dynamo. The HMI Active Region Patches (HARPs) program automatically identify all magnetic regions above a certain flux. In our study we measure the moments of ARs that are no longer actively emerging and can thereby give us good statistical constraints on photospheric diffusion. We also present the diffusion properties as a function of latitude, flux density, and single polarity (leading or following) within each HARP.

  1. β-Arrestin biosensors reveal a rapid, receptor-dependent activation/deactivation cycle.

    PubMed

    Nuber, Susanne; Zabel, Ulrike; Lorenz, Kristina; Nuber, Andreas; Milligan, Graeme; Tobin, Andrew B; Lohse, Martin J; Hoffmann, Carsten

    2016-03-31

    (β-)Arrestins are important regulators of G-protein-coupled receptors (GPCRs). They bind to active, phosphorylated GPCRs and thereby shut off 'classical' signalling to G proteins, trigger internalization of GPCRs via interaction with the clathrin machinery and mediate signalling via 'non-classical' pathways. In addition to two visual arrestins that bind to rod and cone photoreceptors (termed arrestin1 and arrestin4), there are only two (non-visual) β-arrestin proteins (β-arrestin1 and β-arrestin2, also termed arrestin2 and arrestin3), which regulate hundreds of different (non-visual) GPCRs. Binding of these proteins to GPCRs usually requires the active form of the receptors plus their phosphorylation by G-protein-coupled receptor kinases (GRKs). The binding of receptors or their carboxy terminus as well as certain truncations induce active conformations of (β-)arrestins that have recently been solved by X-ray crystallography. Here we investigate both the interaction of β-arrestin with GPCRs, and the β-arrestin conformational changes in real time and in living human cells, using a series of fluorescence resonance energy transfer (FRET)-based β-arrestin2 biosensors. We observe receptor-specific patterns of conformational changes in β-arrestin2 that occur rapidly after the receptor-β-arrestin2 interaction. After agonist removal, these changes persist for longer than the direct receptor interaction. Our data indicate a rapid, receptor-type-specific, two-step binding and activation process between GPCRs and β-arrestins. They further indicate that β-arrestins remain active after dissociation from receptors, allowing them to remain at the cell surface and presumably signal independently. Thus, GPCRs trigger a rapid, receptor-specific activation/deactivation cycle of β-arrestins, which permits their active signalling. PMID:27007855

  2. Spectrometric measurements of radioisotope activity in the thyroid

    NASA Astrophysics Data System (ADS)

    Osko, Jakub; Golnik, Natalia

    2008-01-01

    The results of measurements of iodine 131I and technetium 99mTc uptake in human thyroid, performed with scintillation or semiconductor detectors can exhibit a considerable uncertainty due to the differences in the thyroid position in the patient's neck. Basic physical laws of radiation attenuation and scattering show that the final shape of the registered spectrum should depends on the thyroid position in the neck and on the thickness of the tissue between the thyroid and the detector. The use of the spectrometric measuring method is proposed in this work for determination of the iodine gathering effective depth. The performed studies showed that the measurements results can be used for improving the accuracy of the iodine 131I activity in thyroid measurements and for selection of the group of patients for whom the anatomical position of the thyroid or the spatial distribution of the iodine gathering is much different than the standard one, assumed during the calibration of the counters. The results of the measurements were in agreement with Monte-Carlo calculations of the detector response. The method was used in routine monitoring of occupationally exposed persons, using the thyroid counter. A group of six persons with measurable internal contamination was selected and the measurements were performed on consecutive days, so the results could be registered at decreasing iodine activities in the thyroid. Larger series of measurements were performed at Brodno Regional Hospital in Warsaw, for a group of 95 patients after diagnostic administration of iodine 131I.

  3. The influence of thoron on instruments measuring radon activity concentration.

    PubMed

    Michielsen, N; Bondiguel, S

    2015-11-01

    Thoron, the isotope 220 of radon, is a radionuclide whose concentration may influence the measurement of the activity concentration of (222)Rn in the air. If in the case of continuous and active sampling measuring instruments, using a pump for example, the influence of thoron on radon measurement is obvious and is taken into account in the apparatus, it is often assumed that in the case of a passive sampling, by diffusion through a filter for example, this thoron influence is negligible. This is due to the very short radioactive half-life of thoron, 55.6 s (3.82 d for (222)Rn), and the assumption that the diffusion time of thoron in the detection chamber is long enough beside that of the thoron half-life. The objective of this study is to check whether this assumption is true or not for different kinds of commercial electronic apparatus used to measure radon activity concentration from soil to dwellings. First of all, the devices were calibrated in activity concentration of radon, and then they were exposed to a controlled thoron atmosphere. The experiments concerning the thoron aimed to investigate the sensitivity to thoron in the radon measuring mode of the apparatus. Results of these experiments show that all devices have a very quick answer to thoron atmosphere, even though the sensitivities vary from one instrument to another. Results clearly show that this influence on radon measurement due to the thoron is observed also after the exposition because of the decay of (212)Pb and its progenies. In conclusion, the sensitivity to thoron in the radon measuring mode depends strongly on the type of instruments. The results of the present investigation show that for some apparatus, the influence of thoron cannot be disregarded especially when measuring radon in soil. PMID:25953787

  4. From Blame to Punishment: Disrupting Prefrontal Cortex Activity Reveals Norm Enforcement Mechanisms.

    PubMed

    Buckholtz, Joshua W; Martin, Justin W; Treadway, Michael T; Jan, Katherine; Zald, David H; Jones, Owen; Marois, René

    2015-09-23

    The social welfare provided by cooperation depends on the enforcement of social norms. Determining blameworthiness and assigning a deserved punishment are two cognitive cornerstones of norm enforcement. Although prior work has implicated the dorsolateral prefrontal cortex (DLPFC) in norm-based judgments, the relative contribution of this region to blameworthiness and punishment decisions remains poorly understood. Here, we used repetitive transcranial magnetic stimulation (rTMS) and fMRI to determine the specific role of DLPFC function in norm-enforcement behavior. DLPFC rTMS reduced punishment for wrongful acts without affecting blameworthiness ratings, and fMRI revealed punishment-selective DLPFC recruitment, suggesting that these two facets of norm-based decision making are neurobiologically dissociable. Finally, we show that DLPFC rTMS affects punishment decision making by altering the integration of information about culpability and harm. Together, these findings reveal a selective, causal role for DLPFC in norm enforcement: representational integration of the distinct information streams used to make punishment decisions. PMID:26386518

  5. Representing Microbial Dormancy in Soil Decomposition Models Improves Model Performance and Reveals Key Ecosystem Controls on Microbial Activity

    NASA Astrophysics Data System (ADS)

    He, Y.; Yang, J.; Zhuang, Q.; Wang, G.; Liu, Y.

    2014-12-01

    Climate feedbacks from soils can result from environmental change and subsequent responses of plant and microbial communities and nutrient cycling. Explicit consideration of microbial life history traits and strategy may be necessary to predict climate feedbacks due to microbial physiology and community changes and their associated effect on carbon cycling. In this study, we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of dormancy at six temperate forest sites with observed soil efflux ranged from 4 to 10 years across different forest types. We then extrapolated the model to all temperate forests in the Northern Hemisphere (25-50°N) to investigate spatial controls on microbial and soil C dynamics. Both models captured the observed soil heterotrophic respiration (RH), yet no-dormancy model consistently exhibited large seasonal amplitude and overestimation in microbial biomass. Spatially, the total RH from temperate forests based on dormancy model amounts to 6.88PgC/yr, and 7.99PgC/yr based on no-dormancy model. However, no-dormancy model notably overestimated the ratio of microbial biomass to SOC. Spatial correlation analysis revealed key controls of soil C:N ratio on the active proportion of microbial biomass, whereas local dormancy is primarily controlled by soil moisture and temperature, indicating scale-dependent environmental and biotic controls on microbial and SOC dynamics. These developments should provide essential support to modeling future soil carbon dynamics and enhance the avenue for collaboration between empirical soil experiment and modeling in the sense that more microbial physiological measurements are needed to better constrain and evaluate the models.

  6. FRET analysis using sperm-activating peptides tagged with fluorescent proteins reveals that ligand-binding sites exist as clusters.

    PubMed

    Arcos-Hernández, César; Romero, Francisco; Sánchez-Guevara, Yoloxochitl; Beltrán, Carmen; Nishigaki, Takuya

    2016-02-01

    Long-range cellular communication between the sperm and egg is critical for external fertilization. Sperm-activating peptides (SAPs) are diffusible components of the outer layer of eggs in echinoderms, and function as chemoattractants for spermatozoa. The decapeptide named speract is the best-characterized sea urchin SAP. Biochemical and physiological actions of speract have been studied with purified or chemically synthesized peptides. In this work, we prepared recombinant speract fused to a fluorescent protein (FP; FP-speract) using three color variants: a cyan (eCFP), a yellow (mVenus) and a large Stokes shift yellow (mAmetrine) FP. Although these fluorescence tags are 20 times larger than speract, competitive binding experiments using mAmetrine-speract revealed that this FP-speract has binding affinity to the receptor that is comparable (7.6-fold less) to that of non-labeled speract. Indeed, 10 nmol l(-1) eCFP-speract induces physiological sperm responses such as membrane potential changes and increases in intracellular pH and Ca(2+) concentrations similar to those triggered by 10 nmol l(-1) speract. Furthermore, FP-speract maintains its fluorescence upon binding to its receptor. Using this property, we performed fluorescence resonance energy transfer (FRET) measurements with eCFP-speract and mVenus-speract as probes and obtained a positive FRET signal upon binding to the receptor, which suggests that the speract receptor exists as an oligomer, at least as a dimer, or alternatively that a single speract receptor protein possesses multiple binding sites. This property could partially account for the positive and/or negative cooperative binding of speract to the receptor. PMID:26889001

  7. Small-angle neutron and X-ray scattering reveal conformational changes in rhodopsin activation

    NASA Astrophysics Data System (ADS)

    Shrestha, Utsab R.; Bhowmik, Debsindhu; Perera, Suchitrhanga M. C. D.; Chawla, Udeep; Struts, Andrey V.; Graziono, Vito; Pingali, Sai Venkatesh; Heller, William T.; Qian, Shuo; Brown, Michael F.; Chu, Xiang-Qiang

    2015-03-01

    Understanding G-protein-coupled receptor (GPCR) activation plays a crucial role in the development of novel improved molecular drugs. During photo-activation, the retinal chromophore of the visual GPCR rhodopsin isomerizes from 11-cis to all-trans conformation, yielding an equilibrium between inactive Meta-I and active Meta-II states. The principal goals of this work are to address whether the activation of rhodopsin leads to a single state or a conformational ensemble, and how protein organizational structure changes with detergent environment in solution. We use both small-angle neutron scattering (SANS) and small-angle X-ray scattering (SAXS) techniques to answer the above questions. For the first time we observe the change in protein conformational ensemble upon photo-activation by SANS with contrast variation, which enables the separate study of the protein structure within the detergent assembly. In addition, SAXS study of protein structure within detergent assembly suggests that the detergent molecules form a belt of monolayer (micelle) around protein with different geometrical shapes to keep the protein in folded state.

  8. Mutant N143P Reveals How Na[superscript +] Activates Thrombin

    SciTech Connect

    Niu, Weiling; Chen, Zhiwei; Bush-Pelc, Leslie A.; Bah, Alaji; Gandhi, Prafull S.; Di Cera, Enrico

    2010-01-12

    The molecular mechanism of thrombin activation by Na{sup +} remains elusive. Its kinetic formulation requires extension of the classical Botts-Morales theory for the action of a modifier on an enzyme to correctly account for the contribution of the E*, E, and E:Na{sup +} forms. The extended scheme establishes that analysis of k{sub cat} unequivocally identifies allosteric transduction of Na{sup +} binding into enhanced catalytic activity. The thrombin mutant N143P features no Na{sup +}-dependent enhancement of k{sub cat} yet binds Na{sup +} with an affinity comparable to that of wild type. Crystal structures of the mutant in the presence and absence of Na{sup +} confirm that Pro{sup 143} abrogates the important H-bond between the backbone N atom of residue 143 and the carbonyl O atom of Glu{sup 192}, which in turn controls the orientation of the Glu{sup 192}-Gly{sup 193} peptide bond and the correct architecture of the oxyanion hole. We conclude that Na{sup +} activates thrombin by securing the correct orientation of the Glu{sup 192}-Gly{sup 193} peptide bond, which is likely flipped in the absence of cation. Absolute conservation of the 143-192 H-bond in trypsin-like proteases and the importance of the oxyanion hole in protease function suggest that this mechanism of Na{sup +} activation is present in all Na{sup +}-activated trypsin-like proteases.

  9. fMRI reveals neural activity overlap between adult and infant pain

    PubMed Central

    Goksan, Sezgi; Hartley, Caroline; Emery, Faith; Cockrill, Naomi; Poorun, Ravi; Moultrie, Fiona; Rogers, Richard; Campbell, Jon; Sanders, Michael; Adams, Eleri; Clare, Stuart; Jenkinson, Mark; Tracey, Irene; Slater, Rebeccah

    2015-01-01

    Limited understanding of infant pain has led to its lack of recognition in clinical practice. While the network of brain regions that encode the affective and sensory aspects of adult pain are well described, the brain structures involved in infant nociceptive processing are less well known, meaning little can be inferred about the nature of the infant pain experience. Using fMRI we identified the network of brain regions that are active following acute noxious stimulation in newborn infants, and compared the activity to that observed in adults. Significant infant brain activity was observed in 18 of the 20 active adult brain regions but not in the infant amygdala or orbitofrontal cortex. Brain regions that encode sensory and affective components of pain are active in infants, suggesting that the infant pain experience closely resembles that seen in adults. This highlights the importance of developing effective pain management strategies in this vulnerable population. DOI: http://dx.doi.org/10.7554/eLife.06356.001 PMID:25895592

  10. Structural interpretation of activity cliffs revealed by systematic analysis of structure-activity relationships in analog series.

    PubMed

    Sisay, Mihiret T; Peltason, Lisa; Bajorath, Jürgen

    2009-10-01

    Discontinuity in structure-activity relationships (SARs) is caused by so-called activity cliffs and represents one of the major caveats in SAR modeling and lead optimization. At activity cliffs, small structural modifications of compounds lead to substantial differences in potency that are essentially unpredictable using quantitative structure-activity relationship (QSAR) methods. In order to better understand SAR discontinuity at the molecular level of detail, we have analyzed different compound series in combinatorial analog graphs and determined substitution patterns that introduce activity cliffs of varying magnitude. So identified SAR determinants were then analyzed on the basis of complex crystal structures to enable a structural interpretation of SAR discontinuity and underlying activity cliffs. In some instances, SAR discontinuity detected within analog series could be well rationalized on the basis of structural data, whereas in others a structural explanation was not possible. This reflects the intrinsic complexity of small molecule SARs and suggests that the analysis of short-range receptor-ligand interactions seen in X-ray structures is insufficient to comprehensively account for SAR discontinuity. However, in other cases, SAR information extracted from ligands was incomplete but could be deduced taking X-ray data into account. Thus, taken together, these findings illustrate the complementarity of ligand-based SAR analysis and structural information. PMID:19761254

  11. Measuring emotion in advertising research: prefrontal brain activity.

    PubMed

    Silberstein, Richard B; Nield, Geoffrey E

    2012-01-01

    With the current interest in the role of emotion in advertising and advertising research, there has been an increasing interest in the use of various brain activity measures to access nonverbal emotional responses. One such approach relies on measuring the difference between left and right hemisphere prefrontal cortical activity to assess like and dislike. This approach is based on electroencephalography (EEG) and neuroimaging work, suggesting that the approach/withdrawal (frequently but not always associated with like/dislike) dimension of emotion is indicated by the balance of activity between the left and right prefrontal cortex. Much of this work was initiated by Richard Davidson in the early 1990s. An early study by Davidson et al. measured brain electrical activity to assess patterns of activation during the experience of happiness and disgust. The authors reported that disgust was found to be associated with increased right-sided activation in the frontal and anterior temporal regions compared with happiness. In contrast, happiness was found to be accompanied by left-sided activation in the anterior temporal region compared with disgust. Early reports suggested that frontal laterality indexes motivational valence with positive emotions (happy, like) associated with left greater than the right frontal activity and vice versa. Although these findings appear to be consistent with personality traits (e.g., optimism pessimism), state changes in frontal laterality appears to index approach withdraw rather than emotional valence. Interestingly, the behavioral and motivational correlates of prefrontal asymmetric activity are not restricted to humans or even primates but have been observed in numerous species such as birds and fish (see [4]). Henceforth, we use the term motivational valence (MV) rather than the more cumbersome term approach withdraw. PMID:22678836

  12. The effect of different inter-pad distances on the determination of active drag using the Measuring Active Drag system.

    PubMed

    Schreven, S; Toussaint, H M; Smeets, J B J; Beek, P J

    2013-07-26

    The Measuring Active Drag (MAD) system was developed to determine active drag in swimming by measuring the push-off force exerted at fixed pads placed below the waterline. The imposed inter-pad distance, which to date has been kept constant while using the MAD system, could affect the active drag because it requires the use of different stroke frequencies. The aim of the present study was therefore to determine the effect of inter-pad distance on active drag at a given speed. In particular, drag-velocity curves at three different inter-pad distances (1.25m, 1.35m and 1.45m) were determined using the MAD system for eleven competitive swimmers. Variation of 16% in inter-pad distance (14% change in stroke frequency) revealed no significant difference in calculated active drag between different inter-pad distances and a low (<5%) average coefficient of variation over different inter-pad distances was found. In addition, inter-test reliability, which was determined for the two 1.35m conditions only, was high (ICC>0.90) for measurements on two consecutive days. The results suggest that it may not be necessary to adapt the inter-pad distance of the MAD system based on anthropometric characteristics of the subject or the velocity-related stroke length in free swimming. PMID:23791187

  13. Structures of apicomplexan calcium-dependent protein kinases reveal mechanism of activation by calcium

    PubMed Central

    Wernimont, Amy K.; Artz, Jennifer D.; Finerty, Patrick; Lin, Y.; Amani, Mehrnaz; Allali-Hassani, Abdellah; Senisterra, Guillermo; Vedadi, Masoud; Tempel, Wolfram; Mackenzie, Farrell; Chau, Irene; Lourido, Sebastian; Sibley, L. David; Hui, Raymond

    2013-01-01

    Calcium-dependent protein kinases (CDPKs) play pivotal roles in the calcium-signaling pathway in plants, ciliates and apicomplexan parasites, and comprise a CaMK-like kinase domain regulated by a calcium-binding domain in the C-terminus. To understand this intramolecular mechanism of activation, we solved the structures of the autoinhibited (apo) and activated (calcium-bound) conformations of CDPKs from the apicomplexan parasites Toxoplasma gondii and Cryptosporidium parvum. In the apo form, the C-terminal CDPK activation domain (CAD) resembles a calmodulin protein with an unexpected long helix in the N-terminus that inhibits the kinase domain in the same manner as CaMKII. Calcium binding triggers the reorganization of the CAD into a highly intricate fold, leading to its relocation around the base of the kinase domain to a site remote from the substrate-binding site. This large conformational change constitutes a distinct mechanism in calcium signal transduction pathways. PMID:20436473

  14. Structural investigation of heteroyohimbine alkaloid synthesis reveals active site elements that control stereoselectivity.

    PubMed

    Stavrinides, Anna; Tatsis, Evangelos C; Caputi, Lorenzo; Foureau, Emilien; Stevenson, Clare E M; Lawson, David M; Courdavault, Vincent; O'Connor, Sarah E

    2016-01-01

    Plants produce an enormous array of biologically active metabolites, often with stereochemical variations on the same molecular scaffold. These changes in stereochemistry dramatically impact biological activity. Notably, the stereoisomers of the heteroyohimbine alkaloids show diverse pharmacological activities. We reported a medium chain dehydrogenase/reductase (MDR) from Catharanthus roseus that catalyses formation of a heteroyohimbine isomer. Here we report the discovery of additional heteroyohimbine synthases (HYSs), one of which produces a mixture of diastereomers. The crystal structures for three HYSs have been solved, providing insight into the mechanism of reactivity and stereoselectivity, with mutation of one loop transforming product specificity. Localization and gene silencing experiments provide a basis for understanding the function of these enzymes in vivo. This work sets the stage to explore how MDRs evolved to generate structural and biological diversity in specialized plant metabolism and opens the possibility for metabolic engineering of new compounds based on this scaffold. PMID:27418042

  15. Structural investigation of heteroyohimbine alkaloid synthesis reveals active site elements that control stereoselectivity

    PubMed Central

    Stavrinides, Anna; Tatsis, Evangelos C.; Caputi, Lorenzo; Foureau, Emilien; Stevenson, Clare E. M.; Lawson, David M.; Courdavault, Vincent; O'Connor, Sarah E.

    2016-01-01

    Plants produce an enormous array of biologically active metabolites, often with stereochemical variations on the same molecular scaffold. These changes in stereochemistry dramatically impact biological activity. Notably, the stereoisomers of the heteroyohimbine alkaloids show diverse pharmacological activities. We reported a medium chain dehydrogenase/reductase (MDR) from Catharanthus roseus that catalyses formation of a heteroyohimbine isomer. Here we report the discovery of additional heteroyohimbine synthases (HYSs), one of which produces a mixture of diastereomers. The crystal structures for three HYSs have been solved, providing insight into the mechanism of reactivity and stereoselectivity, with mutation of one loop transforming product specificity. Localization and gene silencing experiments provide a basis for understanding the function of these enzymes in vivo. This work sets the stage to explore how MDRs evolved to generate structural and biological diversity in specialized plant metabolism and opens the possibility for metabolic engineering of new compounds based on this scaffold. PMID:27418042

  16. Analysis of protein phosphorylation in nerve terminal reveals extensive changes in active zone proteins upon exocytosis.

    PubMed

    Kohansal-Nodehi, Mahdokht; Chua, John Je; Urlaub, Henning; Jahn, Reinhard; Czernik, Dominika

    2016-01-01

    Neurotransmitter release is mediated by the fast, calcium-triggered fusion of synaptic vesicles with the presynaptic plasma membrane, followed by endocytosis and recycling of the membrane of synaptic vesicles. While many of the proteins governing these processes are known, their regulation is only beginning to be understood. Here we have applied quantitative phosphoproteomics to identify changes in phosphorylation status of presynaptic proteins in resting and stimulated nerve terminals isolated from the brains of Wistar rats. Using rigorous quantification, we identified 252 phosphosites that are either up- or downregulated upon triggering calcium-dependent exocytosis. Particularly pronounced were regulated changes of phosphosites within protein constituents of the presynaptic active zone, including bassoon, piccolo, and RIM1. Additionally, we have mapped kinases and phosphatases that are activated upon stimulation. Overall, our study provides a snapshot of phosphorylation changes associated with presynaptic activity and provides a foundation for further functional analysis of key phosphosites involved in presynaptic plasticity. PMID:27115346

  17. Structures of apicomplexan calcium-dependent protein kinases reveal mechanism of activation by calcium

    SciTech Connect

    Wernimont, Amy K; Artz, Jennifer D.; Jr, Patrick Finerty; Lin, Yu-Hui; Amani, Mehrnaz; Allali-Hassani, Abdellah; Senisterra, Guillermo; Vedadi, Masoud; Tempel, Wolfram; Mackenzie, Farrell; Chau, Irene; Lourido, Sebastian; Sibley, L. David; Hui, Raymond

    2010-09-21

    Calcium-dependent protein kinases (CDPKs) have pivotal roles in the calcium-signaling pathway in plants, ciliates and apicomplexan parasites and comprise a calmodulin-dependent kinase (CaMK)-like kinase domain regulated by a calcium-binding domain in the C terminus. To understand this intramolecular mechanism of activation, we solved the structures of the autoinhibited (apo) and activated (calcium-bound) conformations of CDPKs from the apicomplexan parasites Toxoplasma gondii and Cryptosporidium parvum. In the apo form, the C-terminal CDPK activation domain (CAD) resembles a calmodulin protein with an unexpected long helix in the N terminus that inhibits the kinase domain in the same manner as CaMKII. Calcium binding triggers the reorganization of the CAD into a highly intricate fold, leading to its relocation around the base of the kinase domain to a site remote from the substrate binding site. This large conformational change constitutes a distinct mechanism in calcium signal-transduction pathways.

  18. Brain Activation of Negative Feedback in Rule Acquisition Revealed in a Segmented Wisconsin Card Sorting Test

    PubMed Central

    Wang, Jing; Cao, Bihua; Cai, Xueli; Gao, Heming; Li, Fuhong

    2015-01-01

    The present study is to investigate the brain activation associated with the informative value of negative feedback in rule acquisition. In each trial of a segmented Wisconsin Card Sorting Test, participants were provided with three reference cards and one target card, and were asked to match one of three reference cards to the target card based on a classification rule. Participants received feedback after each match. Participants would acquire the rule after one negative feedback (1-NF condition) or two successive negative feedbacks (2-NF condition). The functional magnetic resonance imaging (fMRI) results indicated that lateral prefrontal-to-parietal cortices were more active in the 2-NF condition than in the 1-NF condition. The activation in the right lateral prefrontal cortex and left posterior parietal cortex increased gradually with the amount of negative feedback. These results demonstrate that the informative value of negative feedback in rule acquisition might be modulated by the lateral prefronto-parietal loop. PMID:26469519

  19. A SPECTROPHOTOMETRIC ASSAY TO MEASURE RUBISCO ACTIVASE ACTIVATION ACTIVITY UNDER VARYING ATP:ADP RATIOS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The ratio of ATP to ADP in the stroma is an important regulatory mechanism for controlling the activation state of Rubisco via Rubisco activase (activase). Understanding the response of activase to a varying ATP:ADP ratio should reveal insights into the regulation of photosynthesis. However, the cur...

  20. In vivo imaging of alphaherpesvirus infection reveals synchronized activity dependent on axonal sorting of viral proteins

    PubMed Central

    Granstedt, Andrea E.; Bosse, Jens B.; Thiberge, Stephan Y.; Enquist, Lynn W.

    2013-01-01

    A clinical hallmark of human alphaherpesvirus infections is peripheral pain or itching. Pseudorabies virus (PRV), a broad host range alphaherpesvirus, causes violent pruritus in many different animals, but the mechanism is unknown. Previous in vitro studies have shown that infected, cultured peripheral nervous system (PNS) neurons exhibited aberrant electrical activity after PRV infection due to the action of viral membrane fusion proteins, yet it is unclear if such activity occurs in infected PNS ganglia in living animals and if it correlates with disease symptoms. Using two-photon microscopy, we imaged autonomic ganglia in living mice infected with PRV strains expressing GCaMP3, a genetically encoded calcium indicator, and used the changes in calcium flux to monitor the activity of many neurons simultaneously with single-cell resolution. Infection with virulent PRV caused these PNS neurons to fire synchronously and cyclically in highly correlated patterns among infected neurons. This activity persisted even when we severed the presynaptic axons, showing that infection-induced firing is independent of input from presynaptic brainstem neurons. This activity was not observed after infections with an attenuated PRV recombinant used for circuit tracing or with PRV mutants lacking either viral glycoprotein B, required for membrane fusion, or viral membrane protein Us9, required for sorting virions and viral glycoproteins into axons. We propose that the viral fusion proteins produced by virulent PRV infection induce electrical coupling in unmyelinated axons in vivo. This action would then give rise to the synchronous and cyclical activity in the ganglia and contribute to the characteristic peripheral neuropathy. PMID:23980169

  1. Revealing the activation pathway for TMEM16A chloride channels from macroscopic currents and kinetic models.

    PubMed

    Contreras-Vite, Juan A; Cruz-Rangel, Silvia; De Jesús-Pérez, José J; Figueroa, Iván A Aréchiga; Rodríguez-Menchaca, Aldo A; Pérez-Cornejo, Patricia; Hartzell, H Criss; Arreola, Jorge

    2016-07-01

    TMEM16A (ANO1), the pore-forming subunit of calcium-activated chloride channels, regulates several physiological and pathophysiological processes such as smooth muscle contraction, cardiac and neuronal excitability, salivary secretion, tumour growth and cancer progression. Gating of TMEM16A is complex because it involves the interplay between increases in intracellular calcium concentration ([Ca(2+)]i), membrane depolarization, extracellular Cl(-) or permeant anions and intracellular protons. Our goal here was to understand how these variables regulate TMEM16A gating and to explain four observations. (a) TMEM16A is activated by voltage in the absence of intracellular Ca(2+). (b) The Cl(-) conductance is decreased after reducing extracellular Cl(-) concentration ([Cl(-)]o). (c) ICl is regulated by physiological concentrations of [Cl(-)]o. (d) In cells dialyzed with 0.2 μM [Ca(2+)]i, Cl(-) has a bimodal effect: at [Cl(-)]o <30 mM TMEM16A current activates with a monoexponential time course, but above 30 mM, [Cl(-)]o ICl activation displays fast and slow kinetics. To explain the contribution of Vm, Ca(2+) and Cl(-) to gating, we developed a 12-state Markov chain model. This model explains TMEM16A activation as a sequential, direct, and Vm-dependent binding of two Ca(2+) ions coupled to a Vm-dependent binding of an external Cl(-) ion, with Vm-dependent transitions between states. Our model predicts that extracellular Cl(-) does not alter the apparent Ca(2+) affinity of TMEM16A, which we corroborated experimentally. Rather, extracellular Cl(-) acts by stabilizing the open configuration induced by Ca(2+) and by contributing to the Vm dependence of activation. PMID:27138167

  2. Thermal activation of a group II intron ribozyme reveals multiple conformational states.

    PubMed

    Franzen, J S; Zhang, M; Chay, T R; Peebles, C L

    1994-09-20

    Conformational changes often accompany biological catalysis. Group II introns promote a variety of reactions in vitro that show an unusually sharp temperature dependence. This suggests that the chemical steps are accompanied by the conversion of a folded-but-inactive form to a differently folded active state. We report here the kinetic analysis of 5'-splice-junction hydrolysis (SJH) by E1:12345, a transcript containing the 5'-exon plus the first five of six intron secondary structure domains. The pseudo-first-order SJH reaction shows (1) activation by added KCl to 1.5 M; (2) cooperative activation by added MgCl2, nHill = 4.1-4.3, and [MgCl2]vmax/2 approximately 0.040 M; and (3) a rather high apparent activation energy, Ea approximately 50 kcal mol-l. In contrast, the 5'-terminal phosphodiester bond of a domain 5 transcript (GGD5) was hydrolyzed with Ea approximately 30 kcal mol-1 under SJH conditions; the 5'-GG leader dinucleotide presumably lacks secondary structure constraints. The effect of adding the chaotropic salt tetraethylammonium chloride (TEA) was also investigated. TEA reduced the melting temperatures of GGD5 and E1:12345. TEA also shifted the profile of rate versus temperature for SJH by E1:12345 toward lower temperatures without affecting the maximum rate. TEA had little effect on the rate of hydrolysis of the 5'-phosphodiester bond of GGD5. The high apparent activation enthalpy and entropy for SJH along with the effect of TEA on these parameters imply that conversion of an inactive form of E1:12345 to an active conformation accompanies enhanced occupation of the transition state as the temperature is raised to that for maximum SJH. Analytical modeling indicates that either a two-state model (open and disordered, with open being active) or a three-state model (compact, open, and disordered) could account for the temperature dependence of kSJH. However, the three-state model is clearly preferable, since it does not require that the activation parameters

  3. Satellite chlorophyll fluorescence measurements reveal large-scale decoupling of photosynthesis and greenness dynamics in boreal evergreen forests.

    PubMed

    Walther, Sophia; Voigt, Maximilian; Thum, Tea; Gonsamo, Alemu; Zhang, Yongguang; Köhler, Philipp; Jung, Martin; Varlagin, Andrej; Guanter, Luis

    2016-09-01

    Mid-to-high latitude forests play an important role in the terrestrial carbon cycle, but the representation of photosynthesis in boreal forests by current modelling and observational methods is still challenging. In particular, the applicability of existing satellite-based proxies of greenness to indicate photosynthetic activity is hindered by small annual changes in green biomass of the often evergreen tree population and by the confounding effects of background materials such as snow. As an alternative, satellite measurements of sun-induced chlorophyll fluorescence (SIF) can be used as a direct proxy of photosynthetic activity. In this study, the start and end of the photosynthetically active season of the main boreal forests are analysed using spaceborne SIF measurements retrieved from the GOME-2 instrument and compared to that of green biomass, proxied by vegetation indices including the Enhanced Vegetation Index (EVI) derived from MODIS data. We find that photosynthesis and greenness show a similar seasonality in deciduous forests. In high-latitude evergreen needleleaf forests, however, the length of the photosynthetically active period indicated by SIF is up to 6 weeks longer than the green biomass changing period proxied by EVI, with SIF showing a start-of-season of approximately 1 month earlier than EVI. On average, the photosynthetic spring recovery as signalled by SIF occurs as soon as air temperatures exceed the freezing point (2-3 °C) and when the snow on the ground has not yet completely melted. These findings are supported by model data of gross primary production and a number of other studies which evaluated in situ observations of CO2 fluxes, meteorology and the physiological state of the needles. Our results demonstrate the sensitivity of space-based SIF measurements to light-use efficiency of boreal forests and their potential for an unbiased detection of photosynthetic activity even under the challenging conditions interposed by evergreen

  4. Determination of the physiological 2:2 TLR5:flagellin activation stoichiometry revealed by the activity of a fusion receptor

    SciTech Connect

    Ivičak-Kocjan, Karolina; Panter, Gabriela; Benčina, Mojca; Jerala, Roman

    2013-05-24

    Highlights: •The chimeric protein fusing flagellin to the TLR5 ectodomain is constitutively active. •Mutation P736H within the BB-loop of TLR5 TIR domain renders the receptor inactive. •The R90D mutation in flagellin inactivated autoactivation of the chimeric protein. •The 2:2 stoichiometry of the TLR5:flagellin complex is physiologically relevant. -- Abstract: Toll-like receptor 5 (TLR5) recognizes flagellin of most flagellated bacteria, enabling activation of the MyD88-dependent signaling pathway. The recently published crystal structure of a truncated zebrafish TLR5 ectodomain in complex with an inactive flagellin fragment indicated binding of two flagellin molecules to a TLR5 homodimer, however this complex did not dimerize in solution. In the present study, we aimed to determine the physiological stoichiometry of TLR5:flagellin activation by the use of a chimeric protein composed of an active flagellin fragment linked to the N-terminus of human TLR5 (SF-TLR5). This construct was constitutively active. Inactivation by the R90D mutation within flagellin demonstrated that autoactivation of the chimeric protein depended solely on the specific interaction between TLR5 and flagellin. Addition of wild-type hTLR5 substantially lowered autoactivation of SF-TLR5 in a concentration dependent manner, an effect which was reversible by the addition of exogenous Salmonella typhimurium flagellin, indicating the biological activity of a TLR5:flagellin complex with a 2:2 stoichiometry. These results, in addition to the combinations of inactive P736H mutation within the BB-loop of the TIR domain of TLR5 and SF-TLR5, further confirm the mechanism of TLR5 activation.

  5. Activity profiling reveals changes in the diversity and activity of proteins in Arabidopsis roots in response to nematode infection.

    PubMed

    Hütten, Marion; Geukes, Melanie; Misas-Villamil, Johana C; van der Hoorn, Renier A L; Grundler, Florian M W; Siddique, Shahid

    2015-12-01

    Cyst nematodes are obligate, sedentary endoparasites with a highly specialised biology and a huge economic impact in agriculture. Successful parasitism involves morphological and physiological modifications of the host cells which lead to the formation of specialised syncytial feeding structures in roots. The development of the syncytium is aided by a cocktail of nematode effectors that manipulate the host plant activities in a complex network of interactions through post-translational modifications. Traditional transcriptomic and proteomic approaches cannot display this functional proteomic information. Activity-based protein profiling (ABPP) is a powerful technology that can be used to investigate the activity of the proteome through activity-based probes. To better understand the functional proteomics of syncytium, ABPP was conducted on syncytia induced by the beet cyst nematode Heterodera schachtii in Arabidopsis roots. Our results demonstrated that the activity of several enzymes is differentially regulated in the syncytium compared to the control roots. Among those specifically activated in the syncytium are a putative S-formyl-glutathione hydrolase (SFGH), a putative methylesterase (MES) and two unidentified enzymes. In contrast, the activities of vacuolar processing enzymes (VPEs) are specifically suppressed in the syncytium. Competition labelling, quantitative gene expression and T-DNA knock-out mutants were used to further characterise the roles of the differentially regulated enzymes during plant-nematode interaction. In conclusion, our study will open the door to generate a comprehensive and integrated view of the host-pathogen warfare that results in the formation of long-term feeding sites for pathogens. PMID:26408809

  6. Active role of the liquid phase of developer in revealing surface flaws by capillary methods

    SciTech Connect

    Prokhorenko, P.P.; Dezhkunov, N.V.; Stoicheva, I.V.

    1988-08-01

    The article investigates the interaction of two chemically nonreacting liquids after they have been brought into contact with each other in a capillary. It is established that the liquid phase of the developer is not only a passive carrier of the developing component but also exerts an active influence on the process of development, and consequently, on the detectability of flaws.

  7. Single Particle Tracking Reveals that EGFR Signaling Activity Is Amplified in Clathrin-Coated Pits

    PubMed Central

    Ibach, Jenny; Radon, Yvonne; Gelléri, Márton; Sonntag, Michael H.; Brunsveld, Luc; Bastiaens, Philippe I. H.; Verveer, Peter J.

    2015-01-01

    Signaling from the epidermal growth factor receptor (EGFR) via phosphorylation on its C-terminal tyrosine residues requires self-association, which depends on the diffusional properties of the receptor and its density in the plasma membrane. Dimerization is a key event for EGFR activation, but the role of higher order clustering is unknown. We employed single particle tracking to relate the mobility and aggregation of EGFR to its signaling activity. EGFR mobility alternates between short-lived free, confined and immobile states. In the immobile state, EGFR tends to aggregate in clathrin-coated pits, which is further enhanced in a phosphorylation-dependent manner and does not require ligand binding. EGFR phosphorylation is further amplified by cross-phosphorylation in clathrin-coated pits. Because phosphorylated receptors can escape from the pits, local gradients of signaling active EGFR are formed. These results show that amplification of EGFR phosphorylation by receptor clustering in clathrin-coated pits supports signal activation at the plasma membrane. PMID:26575183

  8. Ensemble Activation of G-Protein -Coupled Receptors Revealed by Small-Angle Neutron Scattering

    NASA Astrophysics Data System (ADS)

    Chu, Xiang-Qiang; Perera, Suchithranga; Shrestha, Utsab; Chawla, Udeep; Struts, Andrey; Qian, Shuo; Brown, Michael

    2014-03-01

    Rhodopsin is a G-protein -coupled receptor (GPCR) involved in visual light perception and occurs naturally in a membrane lipid environment. Rhodopsin photoactivation yields cis-trans isomerization of retinal giving equilibrium between inactive Meta-I and active Meta-II states. Does photoactivation lead to a single Meta-II conformation, or do substates exist as described by an ensemble-activation mechanism (EAM)? We use small-angle neutron scattering (SANS) to investigate conformational changes in rhodopsin-detergent and rhodopsin-lipid complexes upon photoactivation. Meta-I state is stabilized in CHAPS-solubilized rhodopsin, while Meta-II is trapped in DDM-solubilized rhodopsin. SANS data are acquired from 80% D2O solutions and at contrast-matching points for both DDM and CHAPS samples. Our experiments demonstrate that for detergent-solubilized rhodopsin, SANS with contrast variation can detect structural differences between the rhodopsin dark-state, Meta-I, Meta-II, and ligand-free opsin states. Dark-state rhodopsin has more conformational flexibility in DDM micelles compared to CHAPS, which is consistent with an ensemble of activated Meta-II states. Furthermore, time-resolved SANS enables study of the time-dependent structural transitions between Meta-I and Meta-II, which is crucial to understanding the ensemble-based activation.

  9. Single molecule microscopy reveals mechanistic insight into RNA polymerase II preinitiation complex assembly and transcriptional activity

    PubMed Central

    Horn, Abigail E.; Kugel, Jennifer F.; Goodrich, James A.

    2016-01-01

    Transcription by RNA polymerase II (Pol II) is a complex process that requires general transcription factors and Pol II to assemble on DNA into preinitiation complexes that can begin RNA synthesis upon binding of NTPs (nucleoside triphosphate). The pathways by which preinitiation complexes form, and how this impacts transcriptional activity are not completely clear. To address these issues, we developed a single molecule system using TIRF (total internal reflection fluorescence) microscopy and purified human transcription factors, which allows us to visualize transcriptional activity at individual template molecules. We see that stable interactions between polymerase II (Pol II) and a heteroduplex DNA template do not depend on general transcription factors; however, transcriptional activity is highly dependent upon TATA-binding protein, TFIIB and TFIIF. We also found that subsets of general transcription factors and Pol II can form stable complexes that are precursors for functional transcription complexes upon addition of the remaining factors and DNA. Ultimately we found that Pol II, TATA-binding protein, TFIIB and TFIIF can form a quaternary complex in the absence of promoter DNA, indicating that a stable network of interactions exists between these proteins independent of promoter DNA. Single molecule studies can be used to learn how different modes of preinitiation complex assembly impact transcriptional activity. PMID:27112574

  10. Fractal analysis reveals subclasses of neurons and suggests an explanation of their spontaneous activity.

    PubMed

    Favela, Luis H; Coey, Charles A; Griff, Edwin R; Richardson, Michael J

    2016-07-28

    The present work used fractal time series analysis (detrended fluctuation analysis; DFA) to examine the spontaneous activity of single neurons in an anesthetized animal model, specifically, the mitral cells in the rat main olfactory bulb. DFA bolstered previous research in suggesting two subclasses of mitral cells. Although there was no difference in the fractal scaling of the interspike interval series at the shorter timescales, there was a significant difference at longer timescales. Neurons in Group B exhibited fractal, power-law scaled interspike intervals, whereas neurons in Group A exhibited random variation. These results raise questions about the role of these different cells within the olfactory bulb and potential explanations of their dynamics. Specifically, self-organized criticality has been proposed as an explanation of fractal scaling in many natural systems, including neural systems. However, this theory is based on certain assumptions that do not clearly hold in the case of spontaneous neural activity, which likely reflects intrinsic cell dynamics rather than activity driven by external stimulation. Moreover, it is unclear how self-organized criticality might account for the random dynamics observed in Group A, and how these random dynamics might serve some functional role when embedded in the typical activity of the olfactory bulb. These theoretical considerations provide direction for additional experimental work. PMID:27189719

  11. Vector analysis of ecoenzyme activities reveal constraints on coupled C, N and P dynamics

    EPA Science Inventory

    We developed a quantitative method for estimating resource allocation strategies of microbial communities based on the proportional activities of four, key extracellular enzymes, 1,4-ß-glucosidase (BG), leucine amino-peptidase (LAP), 1,4-ß-N-acetylglucosaminidase (NAG...

  12. Skipped-Stimulus Approach Reveals That Short-Term Plasticity Dominates Synaptic Strength during Ongoing Activity

    PubMed Central

    Yang, Hua

    2015-01-01

    All synapses show activity-dependent changes in strength, which affect the fidelity of postsynaptic spiking. This is particularly important at auditory nerve synapses, where the presence and timing of spikes carry information about a sound's structure, which must be passed along for proper processing. However, it is not clear how synaptic plasticity influences spiking during ongoing activity. Under these conditions, conventional analyses erroneously suggest that synaptic plasticity has no influence on EPSC amplitude or spiking. Therefore, we developed new approaches to study how ongoing activity influences synaptic strength, using voltage- and current-clamp recordings from bushy cells in brain slices from mouse anteroventral cochlear nucleus. We applied identical trains of stimuli, except for one skipped stimulus, and found that EPSC amplitude was affected for 60 ms following a skipped stimulus. We further showed that the initial probability of release, calcium-dependent mechanisms of recovery, and desensitization all play a role even during ongoing activity. Current-clamp experiments indicated that these processes had a significant effect on postsynaptic spiking, as did the refractory period to a smaller extent. Thus short-term plasticity has real, important functional consequences. PMID:26019343

  13. Beyond Rhyme or Reason: ERPs Reveal Task-Specific Activation of Orthography on Spoken Language

    ERIC Educational Resources Information Center

    Pattamadilok, Chotiga; Perre, Laetitia; Ziegler, Johannes C.

    2011-01-01

    Metaphonological tasks, such as rhyme judgment, have been the primary tool for the investigation of the effects of orthographic knowledge on spoken language. However, it has been recently argued that the orthography effect in rhyme judgment does not reflect the automatic activation of orthographic codes but rather stems from sophisticated response…

  14. Transcriptomic sequencing reveals a set of unique genes activated by butyrate-induced histone modification

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Butyrate is a nutritional element with strong epigenetic regulatory activity as an inhibitor of histone deacetylases (HDACs). Based on the analysis of differentially expressed genes induced by butyrate in the bovine epithelial cell using deep RNA-sequencing technology (RNA-seq), a set of unique gen...

  15. Event-related potentials reveal early activation of body part representations in action concept comprehension.

    PubMed

    Lu, Aitao; Liu, Jing; Zhang, John X

    2012-03-01

    With tasks involving action concept comprehension, many fMRI studies have reported brain activations in sensori-motor regions specific to effectors of the referent action. There is relatively less evidence whether such activations reflect early semantic access or late conceptual re-processing. Here we recorded event-related potentials when participants recognized noun-verb pairs. For Congruent pairs, the verb was the one most commonly associated with the noun (e.g., football-kick). Compared with a control condition, verbs in Congruent pairs showed priming effects in the time windows of 100-150 ms and 210-260 ms. Such activation seems to be specific to body part but not other aspects of the action as similar priming effect was also found when the noun and verb involved different actions though sharing the same body part (e.g., football-jump), documenting for the first time the early activation of body part representations in action concept comprehension. PMID:22306088

  16. Suppression of voluntary motor activity revealed using transcranial magnetic stimulation of the motor cortex in man.

    PubMed Central

    Davey, N J; Romaiguère, P; Maskill, D W; Ellaway, P H

    1994-01-01

    1. Suppression of voluntary muscle activity of hand and arm muscles in response to transcranial magnetic stimulation (TMS) of the motor cortex has been investigated in man. 2. Suppression could be elicited by low levels of TMS without any prior excitatory response. The latency of the suppression was 3-8 ms longer than the excitation observed at a higher stimulus intensity. The duration of the suppression ranged from 8 to 26 ms. 3. A circular stimulating coil was used to determine threshold intensity for excitation and suppression of contraction of thenar muscles in response to TMS at different locations over the motor cortex. The locations for lowest threshold excitation coincided with those for lowest threshold suppression. Suppression was elicited at a lower threshold than excitation at all locations. 4. A figure-of-eight stimulating coil was positioned over the left motor cortex at the lowest threshold point for excitation of the right thenar muscles. The orientation for the lowest threshold excitatory and inhibitory responses was the same for all subjects. That orientation induced a stimulating current travelling in an antero-medial direction. Suppression was invariably elicited at lower thresholds than excitation. 5. When antagonistic muscles (second and third dorsal interosseus) were co-contracted, TMS evoked coincident suppression of voluntary EMG in the two muscles without prior excitation of either muscle. This suggests that the suppression is not mediated via corticospinal activation of spinal interneurones. 6. Test responses to electrical stimulation of the cervical spinal cord were evoked in both relaxed and activated thenar muscles. In the relaxed muscle, prior TMS at an intensity that would suppress voluntary activity failed to influence the test responses, suggesting absence of inhibition at a spinal level. However, in the activated muscle, prior TMS could reduce the test response. This may be explained by disfacilitation of motoneurones due to

  17. Structure of inorganic pyrophosphatase from Staphylococcus aureus reveals conformational flexibility of the active site.

    PubMed

    Gajadeera, Chathurada S; Zhang, Xinyi; Wei, Yinan; Tsodikov, Oleg V

    2015-02-01

    Cytoplasmic inorganic pyrophosphatase (PPiase) is an enzyme essential for survival of organisms, from bacteria to human. PPiases are divided into two structurally distinct families: family I PPiases are Mg(2+)-dependent and present in most archaea, eukaryotes and prokaryotes, whereas the relatively less understood family II PPiases are Mn(2+)-dependent and present only in some archaea, bacteria and primitive eukaryotes. Staphylococcus aureus (SA), a dangerous pathogen and a frequent cause of hospital infections, contains a family II PPiase (PpaC), which is an attractive potential target for development of novel antibacterial agents. We determined a crystal structure of SA PpaC in complex with catalytic Mn(2+) at 2.1Å resolution. The active site contains two catalytic Mn(2+) binding sites, each half-occupied, reconciling the previously observed 1:1 Mn(2+):enzyme stoichiometry with the presence of two divalent metal ion sites in the apo-enzyme. Unexpectedly, despite the absence of the substrate or products in the active site, the two domains of SA PpaC form a closed active site, a conformation observed in structures of other family II PPiases only in complex with substrate or product mimics. A region spanning residues 295-298, which contains a conserved substrate binding RKK motif, is flipped out of the active site, an unprecedented conformation for a PPiase. Because the mutant of Arg295 to an alanine is devoid of activity, this loop likely undergoes an induced-fit conformational change upon substrate binding and product dissociation. This closed conformation of SA PPiase may serve as an attractive target for rational design of inhibitors of this enzyme. PMID:25576794

  18. High resolution Hall measurements across the VO2 metal-insulator transition reveal impact of spatial phase separation

    PubMed Central

    Yamin, Tony; Strelniker, Yakov M.; Sharoni, Amos

    2016-01-01

    Many strongly correlated transition metal oxides exhibit a metal-insulator transition (MIT), the manipulation of which is essential for their application as active device elements. However, such manipulation is hindered by lack of microscopic understanding of mechanisms involved in these transitions. A prototypical example is VO2, where previous studies indicated that the MIT resistance change correlate with changes in carrier density and mobility. We studied the MIT using Hall measurements with unprecedented resolution and accuracy, simultaneously with resistance measurements. Contrast to prior reports, we find that the MIT is not correlated with a change in mobility, but rather, is a macroscopic manifestation of the spatial phase separation which accompanies the MIT. Our results demonstrate that, surprisingly, properties of the nano-scale spatially-separated metallic and semiconducting domains actually retain their bulk properties. This study highlights the importance of taking into account local fluctuations and correlations when interpreting transport measurements in highly correlated systems. PMID:26783076

  19. High resolution Hall measurements across the VO2 metal-insulator transition reveal impact of spatial phase separation

    NASA Astrophysics Data System (ADS)

    Yamin, Tony; Strelniker, Yakov M.; Sharoni, Amos

    2016-01-01

    Many strongly correlated transition metal oxides exhibit a metal-insulator transition (MIT), the manipulation of which is essential for their application as active device elements. However, such manipulation is hindered by lack of microscopic understanding of mechanisms involved in these transitions. A prototypical example is VO2, where previous studies indicated that the MIT resistance change correlate with changes in carrier density and mobility. We studied the MIT using Hall measurements with unprecedented resolution and accuracy, simultaneously with resistance measurements. Contrast to prior reports, we find that the MIT is not correlated with a change in mobility, but rather, is a macroscopic manifestation of the spatial phase separation which accompanies the MIT. Our results demonstrate that, surprisingly, properties of the nano-scale spatially-separated metallic and semiconducting domains actually retain their bulk properties. This study highlights the importance of taking into account local fluctuations and correlations when interpreting transport measurements in highly correlated systems.

  20. Fractionation of a Herbal Antidiarrheal Medicine Reveals Eugenol as an Inhibitor of Ca2+-Activated Cl− Channel TMEM16A

    PubMed Central

    Yao, Zhen; Namkung, Wan; Ko, Eun A.; Park, Jinhong; Tradtrantip, Lukmanee; Verkman, A. S.

    2012-01-01

    The Ca2+-activated Cl− channel TMEM16A is involved in epithelial fluid secretion, smooth muscle contraction and neurosensory signaling. We identified a Thai herbal antidiarrheal formulation that inhibited TMEM16A Cl− conductance. C18-reversed-phase HPLC fractionation of the herbal formulation revealed >98% of TMEM16A inhibition activity in one out of approximately 20 distinct peaks. The purified, active compound was identified as eugenol (4-allyl-2-methoxyphenol), the major component of clove oil. Eugenol fully inhibited TMEM16A Cl− conductance with single-site IC50∼150 µM. Eugenol inhibition of TMEM16A in interstitial cells of Cajal produced strong inhibition of intestinal contraction in mouse ileal segments. TMEM16A Cl− channel inhibition adds to the list of eugenol molecular targets and may account for some of its biological activities. PMID:22666439

  1. Fractionation of a herbal antidiarrheal medicine reveals eugenol as an inhibitor of Ca2+-Activated Cl- channel TMEM16A.

    PubMed

    Yao, Zhen; Namkung, Wan; Ko, Eun A; Park, Jinhong; Tradtrantip, Lukmanee; Verkman, A S

    2012-01-01

    The Ca(2+)-activated Cl(-) channel TMEM16A is involved in epithelial fluid secretion, smooth muscle contraction and neurosensory signaling. We identified a Thai herbal antidiarrheal formulation that inhibited TMEM16A Cl(-) conductance. C18-reversed-phase HPLC fractionation of the herbal formulation revealed >98% of TMEM16A inhibition activity in one out of approximately 20 distinct peaks. The purified, active compound was identified as eugenol (4-allyl-2-methoxyphenol), the major component of clove oil. Eugenol fully inhibited TMEM16A Cl(-) conductance with single-site IC(50)~150 µM. Eugenol inhibition of TMEM16A in interstitial cells of Cajal produced strong inhibition of intestinal contraction in mouse ileal segments. TMEM16A Cl(-) channel inhibition adds to the list of eugenol molecular targets and may account for some of its biological activities. PMID:22666439

  2. Multichannel brain recordings in behaving Drosophila reveal oscillatory activity and local coherence in response to sensory stimulation and circuit activation

    PubMed Central

    Paulk, Angelique C.; Zhou, Yanqiong; Stratton, Peter; Liu, Li

    2013-01-01

    Neural networks in vertebrates exhibit endogenous oscillations that have been associated with functions ranging from sensory processing to locomotion. It remains unclear whether oscillations may play a similar role in the insect brain. We describe a novel “whole brain” readout for Drosophila melanogaster using a simple multichannel recording preparation to study electrical activity across the brain of flies exposed to different sensory stimuli. We recorded local field potential (LFP) activity from >2,000 registered recording sites across the fly brain in >200 wild-type and transgenic animals to uncover specific LFP frequency bands that correlate with: 1) brain region; 2) sensory modality (olfactory, visual, or mechanosensory); and 3) activity in specific neural circuits. We found endogenous and stimulus-specific oscillations throughout the fly brain. Central (higher-order) brain regions exhibited sensory modality-specific increases in power within narrow frequency bands. Conversely, in sensory brain regions such as the optic or antennal lobes, LFP coherence, rather than power, best defined sensory responses across modalities. By transiently activating specific circuits via expression of TrpA1, we found that several circuits in the fly brain modulate LFP power and coherence across brain regions and frequency domains. However, activation of a neuromodulatory octopaminergic circuit specifically increased neuronal coherence in the optic lobes during visual stimulation while decreasing coherence in central brain regions. Our multichannel recording and brain registration approach provides an effective way to track activity simultaneously across the fly brain in vivo, allowing investigation of functional roles for oscillations in processing sensory stimuli and modulating behavior. PMID:23864378

  3. Exploring Patient Activation in the Clinic: Measurement from Three Perspectives

    ERIC Educational Resources Information Center

    Ledford, Christy J. W.; Ledford, Christopher C.; Childress, Marc A.

    2013-01-01

    Objective. To further conceptualize and operationalize patient activation (PA), using measures from patient, physician, and researcher perspectives. Data Source/Study Setting. Multimethod observation in 2010 within a family medicine clinic. Study Design. Part of an intervention with 130 patients with type 2 diabetes, this observational study…

  4. Measuring Perceived Benefits and Perceived Barriers for Physical Activity

    ERIC Educational Resources Information Center

    Brown, Seth A.

    2005-01-01

    Objectives: To evaluate the psychometric properties and relationship to physical activity levels of the Exercise Benefits/Barriers Scale (EBBS) among college students. Methods: A total of 398 college students completed the EBBS and a measure of self-efficacy, the Physical Exercise Self-Efficacy Scale. In addition, a subsample of 275 students also…

  5. Measurement of the Construct of Attitude Toward Student Activism.

    ERIC Educational Resources Information Center

    Gold, Joel A.; And Others

    The study measures individual differences in attitude toward student activism on an 18-item Likert type scale. A validity comparison of a known extreme group with a sample from the general student population yielded a significant difference between the means of the groups. Construct validity was evaluated by first testing the differences between…

  6. A Self-Report Measure of Physical Activity

    ERIC Educational Resources Information Center

    Siegel, Donald

    2005-01-01

    There are multiple approaches to measuring physical activity. Among these are direct observation, electronic monitoring, direct and indirect calorimetry, and self-report instruments. Self-report instruments are the most practical and cost effective option for use with a large group. In a study by Motl, Dishman, Dowda, and Pate (2004), two groups…

  7. Measurement for Work. Teaching Guide and Sample Learning Activities.

    ERIC Educational Resources Information Center

    Angel, Margo; Bolton, Chris

    This document is intended to help Australian technical and further education instructors in New South Wales (TAFE NSW) identify teaching principles and learning activities that they can use to help adult learners master the mathematics processes, knowledge, and skills needed to perform basic measurement tasks in today's workplace. The materials…

  8. Measurement of Perceived School Climate for Active Travel in Children

    ERIC Educational Resources Information Center

    Evenson, Kelly R.; Motl, Robert W.; Birnbaum, Amanda S.; Ward, Dianne S.

    2007-01-01

    Objectives: To describe the development of an original scale that measures perceived school climate for active travel in fourth- and fifth-grade girls and boys. Methods: The data were analyzed using confirmatory factor analysis (CFA) to provide evidence of factorial validity, factorial invariance, and construct validity. Results: The CFA supported…

  9. 10Be surface exposure dating reveals strong active deformation in the central Andean backarc interior

    NASA Astrophysics Data System (ADS)

    García Morabito, Ezequiel; Terrizzano, Carla; Zech, Roland; Willett, Sean; Yamin, Marcela; Haghipour, Negar; Wuethrich, Lorenz; Christl, Marcus; María Cortes, José; Ramos, Victor

    2016-04-01

    Understanding the deformation associated with active thrust wedges is essential to evaluate seismic hazard. How is active faulting distributed throughout the wedge, and how much deformation is taken up by individual structures? We address these questions for our study region, the central Andean backarc of Argentina. We combined a structural and geomorphological approach with surface exposure dating (10Be) of alluvial fans and strath terraces in two key localities at ~32° S: the Cerro Salinas, located in the active orogenic front of the Precordillera, and the Barreal block in the interior of the Andean mountain range. We analysed 22 surface samples and 6 depth profiles. At the thrust front, the oldest terrace (T1) yields an age of 100-130 ka, the intermediate terrace (T2) between 40-95 ka, and the youngest terrace (T3) an age of ~20 ka. In the Andean interior, T1´ dates to 117-146 ka, T2´ to ~70 ka, and T3´ to ~20 ka, all calculations assuming negligible erosion and using the scaling scheme for spallation based on Lal 1991, Stone 2000. Vertical slip rates of fault offsets are 0.3-0.5 mm/yr and of 0.6-1.2 mm/yr at the thrust front and in the Andean interior, respectively. Our results highlight: i) fault activity related to the growth of the Andean orogenic wedge is not only limited to a narrow thrust front zone. Internal structures have been active during the last 150 ka, ii) deformation rates in the Andean interior are comparable or even higher that those estimated and reported along the emerging thrust front, iii) distribution of active faulting seems to account for unsteady state conditions, and iv) seismic hazards may be more relevant in the internal parts of the Andean orogen than assumed so far. References Lal, D., 1991: Cosmic ray labeling of erosion surfaces: In situ nuclide production rates and erosion models. Earth and Planetary Science Letters 104: 424-439. Stone, J.O., 2000: Air pressure and cosmogenic isotope production. Journal of Geophysical

  10. A Global Genomic Screening Strategy Reveals Genetic and Chemical Activators ofPeroxisome Proliferator-Activated Receptor alpha (PPARalpha)

    EPA Science Inventory

    A comprehensive survey of chemical, diet and genetic perturbations that activate PPARalpha in the mouse liver has not been carried out but would be useful to identify the factors that may contribute to PPARalpha-dependent liver tumors. A gene signature dependent on PPARalpha ac...

  11. Conformational study reveals amino acid residues essential for hemagglutinating and anti-proliferative activities of Clematis montana lectin.

    PubMed

    Lu, Bangmin; Zhang, Bin; Qi, Wei; Zhu, Yanan; Zhao, Yan; Zhou, Nan; Sun, Rong; Bao, Jinku; Wu, Chuanfang

    2014-11-01

    Clematis montana lectin (CML), a novel mannose-binding lectin purified from C. montana Buch.-Ham stem (Ranunculaceae), has been proved to have hemagglutinating activity in rabbit erythrocytes and apoptosis-inducing activity in tumor cells. However, the biochemical properties of CML have not revealed and its structural information still needs to be elucidated. In this study, it was found that CML possessed quite good thermostability and alkaline resistance, and its hemagglutinating activity was bivalent metal cation dependent. In addition, hemagglutination test and fluorescence spectroscopy proved that GuHCl, urea, and sodium dodecyl sulfate could change the conformation of CML and further caused the loss of hemagglutination activity. Moreover, the changes of fluorescence spectrum indicated that the tryptophan (Trp) microenvironment conversion might be related to the conformation and bioactivities of CML. In addition, it was also found that Trp residues, arginine (Arg) residues, and sulfhydryl were important for the hemagglutinating activity of CML, but only Trp was proved to be crucial for the CML conformation. Furthermore, the Trp, Arg, and sulfhydryl-modified CML exhibited 97.17%, 76.99%, and 49.64% loss of its anti-proliferative activity, respectively, which was consistent with the alterations of its hemagglutinating activity. Given these findings, Trp residues on the surface of CML are essential for the active center to form substrate-accessible conformation and suitable environment for carbohydrate binding. PMID:25239139

  12. Targeted mutagenesis of the human papillomavirus type 16 E2 transactivation domain reveals separable transcriptional activation and DNA replication functions.

    PubMed

    Sakai, H; Yasugi, T; Benson, J D; Dowhanick, J J; Howley, P M

    1996-03-01

    The E2 gene products of papillomavirus play key roles in viral replication, both as regulators of viral transcription and as auxiliary factors that act with E1 in viral DNA replication. We have carried out a detailed structure-function analysis of conserved amino acids within the N-terminal domain of the human papillomavirus type 16 (HPV16) E2 protein. These mutants were tested for their transcriptional activation activities as well as transient DNA replication and E1 binding activities. Analysis of the stably expressed mutants revealed that the transcriptional activation and replication activities of HPV16 E2 could be dissociated. The 173A mutant was defective for the transcriptional activation function but retained wild-type DNA replication activity, whereas the E39A mutant wild-type transcriptional activation function but was defective in transient DNA replication assays. The E39A mutant was also defective for HPV16 E1 binding in vitro, suggesting that the ability of E2 protein to form a complex with E1 appears to be essential for its function as an auxiliary replication factor. PMID:8627680

  13. Revealing the Origin of Activity in Nitrogen-Doped Nanocarbons towards Electrocatalytic Reduction of Carbon Dioxide.

    PubMed

    Xu, Junyuan; Kan, Yuhe; Huang, Rui; Zhang, Bingsen; Wang, Bolun; Wu, Kuang-Hsu; Lin, Yangming; Sun, Xiaoyan; Li, Qingfeng; Centi, Gabriele; Su, Dangsheng

    2016-05-23

    Carbon nanotubes (CNTs) are functionalized with nitrogen atoms for reduction of carbon dioxide (CO2 ). The investigation explores the origin of the catalyst's activity and the role of nitrogen chemical states therein. The catalysts show excellent performances, with about 90 % current efficiency for CO formation and stability over 60 hours. The Tafel analyses and density functional theory calculations suggest that the reduction of CO2 proceeds through an initial rate-determining transfer of one electron to CO2 , which leads to the formation of carbon dioxide radical anion (CO2 (.-) ). The initial reduction barrier is too high on pristine CNTs, resulting in a very high overpotentials at which the hydrogen evolution reaction dominates over CO2 reduction. The doped nitrogen atoms stabilize the radical anion, thereby lowering the initial reduction barrier and improving the intrinsic activity. The most efficient nitrogen chemical state for this reaction is quaternary nitrogen, followed by pyridinic and pyrrolic nitrogen. PMID:27100272

  14. Stepwise multi-photon activation fluorescence reveals a new method of melanoma imaging for dermatologists

    NASA Astrophysics Data System (ADS)

    Lai, Zhenhua; Lian, Christine; Ma, Jie; Yu, Jingyi; Gu, Zetong; Rajadhyaksha, Milind; DiMarzio, Charles A.

    2014-02-01

    Previous research has shown that the stepwise multi-photon activated fluorescence (SMPAF) of melanin, activated by a continuous-wave (CW) mode near infrared (NIR) laser, is a low cost and reliable method of detecting melanin. SMPAF images of melanin in a mouse hair and a formalin fixed mouse melanoma were compared with conventional multiphoton fluorescence microscopy (MPFM) images and confocal reflectance microscopy (CRM) images, all of which were acquired at an excitation wavelength of 920 nm, to further prove the effectiveness of SMPAF in detecting melanin. SMPAF images add specificity for melanin detection to MPFM images and CRM images. Melanin SMPAF can be a promising technology to enable melanoma imaging for dermatologists.

  15. Genome sequence of Wickerhamomyces anomalus DSM 6766 reveals genetic basis of biotechnologically important antimicrobial activities.

    PubMed

    Schneider, Jessica; Rupp, Oliver; Trost, Eva; Jaenicke, Sebastian; Passoth, Volkmar; Goesmann, Alexander; Tauch, Andreas; Brinkrolf, Karina

    2012-05-01

    The ascomycetous yeast Wickerhamomyces anomalus (formerly Pichia anomala and Hansenula anomala) exhibits antimicrobial activities and flavoring features that are responsible for its frequent association with food, beverage and feed products. However, limited information on the genetic background of this yeast and its multiple capabilities are currently available. Here, we present the draft genome sequence of the neotype strain W. anomalus DSM 6766. On the basis of pyrosequencing, a de novo assembly of this strain resulted in a draft genome sequence with a total size of 25.47 Mbp. An automatic annotation using RAPYD generated 11 512 protein-coding sequences. This annotation provided the basis to analyse metabolic capabilities, phylogenetic relationships, as well as biotechnologically important features and yielded novel candidate genes of W. anomalus DSM 6766 coding for proteins participating in antimicrobial activities. PMID:22292503

  16. Aromatic C-H bond activation revealed by infrared multiphoton dissociation spectroscopy.

    PubMed

    Jašíková, Lucie; Hanikýřová, Eva; Schröder, Detlef; Roithová, Jana

    2012-04-01

    Metal-oxide cations are models of catalyst mediating the C-H bond activation of organic substrates. One of the most powerful reagents suggested in the gas phase is based on CuO(+) . Here, we describe the activation of the aromatic C-H bonds of phenanthroline in its complex with CuO(+) . The reaction sequence starts with a hydrogen atom abstraction by the oxygen atom from the 2-position of the phenanthroline ring, followed by OH migration to the ring. Using infrared multiphoton spectroscopy, it is shown that the reaction can be energetically facilitated by additional coordination of a water ligand to the copper ion. As the reaction is intramolecular, a spectroscopic characterization of the product is mandatory in order to unambiguously address the reaction mechanism. PMID:22689621

  17. Synthesis of Isomeric Phosphoubiquitin Chains Reveals that Phosphorylation Controls Deubiquitinase Activity and Specificity.

    PubMed

    Huguenin-Dezot, Nicolas; De Cesare, Virginia; Peltier, Julien; Knebel, Axel; Kristaryianto, Yosua Adi; Rogerson, Daniel T; Kulathu, Yogesh; Trost, Matthias; Chin, Jason W

    2016-07-26

    Ubiquitin is post-translationally modified by phosphorylation at several sites, but the consequences of these modifications are largely unknown. Here, we synthesize multi-milligram quantities of ubiquitin phosphorylated at serine 20, serine 57, and serine 65 via genetic code expansion. We use these phosphoubiquitins for the enzymatic assembly of 20 isomeric phosphoubiquitin dimers, with different sites of isopeptide linkage and/or phosphorylation. We discover that phosphorylation of serine 20 on ubiquitin converts UBE3C from a dual-specificity E3 ligase into a ligase that primarily synthesizes K48 chains. We profile the activity of 31 deubiquitinases on the isomeric phosphoubiquitin dimers in 837 reactions, and we discover that phosphorylation at distinct sites in ubiquitin can activate or repress cleavage of a particular linkage by deubiquitinases and that phosphorylation at a single site in ubiquitin can control the specificity of deubiquitinases for distinct ubiquitin linkages. PMID:27425610

  18. Unexpected hormonal activity of a catechol equine estrogen metabolite reveals reversible glutathione conjugation

    PubMed Central

    Peng, Kuan-Wei; Chang, Minsun; Wang, Yue-Ting; Wang, Zhican; Qin, Zhihui; Bolton, Judy L.; Thatcher, Gregory R. J.

    2010-01-01

    4-Hydroxyequilenin (4-OHEN) is a major phase I metabolite of the equine estrogens present in widely prescribed hormone replacement formulations. 4-OHEN is autoxidized to an electrophilic o-quinone that has been shown to redox cycle, generating ROS, and to covalently modify proteins and DNA and thus potentially to act as a chemical carcinogen. To establish the ability of 4-OHEN to act as a hormonal carcinogen at the estrogen receptor (ER), estrogen responsive gene expression and proliferation were studied in ER(+) breast cancer cells. Recruitment by 4-OHEN of ER to estrogen responsive elements (ERE) of DNA in MCF-7 cells was also studied and observed. 4-OHEN was a potent estrogen, with additional weak activity associated with binding to the arylhydrocarbon receptor (AhR). The potency of 4-OHEN towards classical ERα mediated activity was unexpected given the reported rapid autoxidation and trapping of the resultant quinone by GSH. Addition of thiols to cell cultures did not attenuate the estrogenic activity of 4-OHEN and pre-formed thiol conjugates added to cell incubations only marginally reduced ERE-luciferase induction. On reaction of the 4OHEN-GSH conjugate with NADPH, 4-OHEN was observed to be regenerated at a rate dependent upon NADPH concentration, indicating that intracellular non-enzymatic and enzymatic regeneration of 4-OHEN accounts for the observed estrogenic activity of 4-OHEN. 4-OHEN is therefore capable of inducing chemical and hormonal pathways that may contribute to estrogen-dependent carcinogenesis, and trapping by cellular thiols does not provide a mechanism of termination of these pathways. PMID:20540524

  19. Revealing the surface and bulk regimes of isothermal graphene growth on Ni with in situ kinetic measurements and modeling

    SciTech Connect

    Puretzky, Alexander A; Merkulov, Igor A; Rouleau, Christopher M; Eres, Gyula; Geohegan, David B

    2014-01-01

    In situ optical diagnostics are used to reveal the isothermal nucleation and growth mechanisms of graphene on Ni across a wide temperature range (560 C < T < 840 C) by chemical vapor deposition from single, sub-second pulses of acetylene. An abrupt, two-orders of magnitude change in growth times (~ 100s to 1s) is revealed at T = 680 C. Below and above this temperature, similar sigmoidal kinetics are measured and attributed to autocatalytic growth reactions but by two different mechanisms, surface assembly and dissolution/precipitation, respectively. These data are used to develop a simple and general kinetic model for graphene growth that includes the nucleation phase and includes the effects of carbon solubility in metals, describes delayed nucleation, and allows the interpretation of the competition between surface and bulk growth modes. The sharp transition in growth kinetics at T = 680 C is explained by a change in defect site density required for nucleation due to a transition in the carbon-induced mobility of the Ni surface. The easily-implemented optical reflectivity diagnostics and the simple kinetic model described here allow a pathway to optimize the growth of graphene on metals with arbitrary carbon solubility.

  20. Structure of Human Acid Sphingomyelinase Reveals the Role of the Saposin Domain in Activating Substrate Hydrolysis.

    PubMed

    Xiong, Zi-Jian; Huang, Jingjing; Poda, Gennady; Pomès, Régis; Privé, Gilbert G

    2016-07-31

    Acid sphingomyelinase (ASM) is a lysosomal phosphodiesterase that catalyzes the hydrolysis of sphingomyelin to produce ceramide and phosphocholine. While other lysosomal sphingolipid hydrolases require a saposin activator protein for full activity, the ASM polypeptide incorporates a built-in N-terminal saposin domain and does not require an external activator protein. Here, we report the crystal structure of human ASM and describe the organization of the three main regions of the enzyme: the N-terminal saposin domain, the proline-rich connector, and the catalytic domain. The saposin domain is tightly associated along an edge of the large, bowl-shaped catalytic domain and adopts an open form that exposes a hydrophobic concave surface approximately 30Å from the catalytic center. The calculated electrostatic potential of the enzyme is electropositive at the acidic pH of the lysosome, consistent with the strict requirement for the presence of acidic lipids in target membranes. Docking studies indicate that sphingomyelin binds with the ceramide-phosphate group positioned at the binuclear zinc center and molecular dynamic simulations indicate that the intrinsic flexibility of the saposin domain is important for monomer-dimer exchange and for membrane interactions. Overall, ASM uses a combination of electrostatic and hydrophobic interactions to cause local disruptions of target bilayers in order to bring the lipid headgroup to the catalytic center in a membrane-bound reaction. PMID:27349982

  1. Force and power generating mechanism(s) in active muscle as revealed from temperature perturbation studies.

    PubMed

    Ranatunga, K W

    2010-10-01

    The basic characteristics of the process of force and power generation in active muscle that have emerged from temperature studies are examined. This is done by reviewing complementary findings from temperature-dependence studies and rapid temperature-jump (T-jump) experiments and from intact and skinned fast mammalian muscle fibres. In isometric muscle, a small T-jump leads to a characteristic rise in force showing that crossbridge force generation is endothermic (heat absorbed) and associated with increased entropy (disorder). The sensitivity of the T-jump force generation to added inorganic phosphate (Pi) indicates that a T-jump enhances an early step in the actomyosin (crossbridge) ATPase cycle before Pi-release. During muscle lengthening when steady force is increased, the T-jump force generation is inhibited. Conversely, during shortening when steady force is decreased, the T-jump force generation is enhanced in a velocity-dependent manner, showing that T-jump force generation is strain sensitive. Within the temperature range of ∼5–35◦C, the temperature dependence of steady active force is sigmoidal both in isometric and in shortening muscle. However, in shortening muscle, the endothermic character of force generation becomes more pronounced with increased velocity and this can, at least partly, account for the marked increase with warming of the mechanical power output of active muscle. PMID:20660565

  2. Familial autoinflammation with neutrophilic dermatosis reveals a regulatory mechanism of pyrin activation.

    PubMed

    Masters, Seth L; Lagou, Vasiliki; Jéru, Isabelle; Baker, Paul J; Van Eyck, Lien; Parry, David A; Lawless, Dylan; De Nardo, Dominic; Garcia-Perez, Josselyn E; Dagley, Laura F; Holley, Caroline L; Dooley, James; Moghaddas, Fiona; Pasciuto, Emanuela; Jeandel, Pierre-Yves; Sciot, Raf; Lyras, Dena; Webb, Andrew I; Nicholson, Sandra E; De Somer, Lien; van Nieuwenhove, Erika; Ruuth-Praz, Julia; Copin, Bruno; Cochet, Emmanuelle; Medlej-Hashim, Myrna; Megarbane, Andre; Schroder, Kate; Savic, Sinisa; Goris, An; Amselem, Serge; Wouters, Carine; Liston, Adrian

    2016-03-30

    Pyrin responds to pathogen signals and loss of cellular homeostasis by forming an inflammasome complex that drives the cleavage and secretion of interleukin-1β (IL-1β). Mutations in the B30.2/SPRY domain cause pathogen-independent activation of pyrin and are responsible for the autoinflammatory disease familial Mediterranean fever (FMF). We studied a family with a dominantly inherited autoinflammatory disease, distinct from FMF, characterized by childhood-onset recurrent episodes of neutrophilic dermatosis, fever, elevated acute-phase reactants, arthralgia, and myalgia/myositis. The disease was caused by a mutation in MEFV, the gene encoding pyrin (S242R). The mutation results in the loss of a 14-3-3 binding motif at phosphorylated S242, which was not perturbed by FMF mutations in the B30.2/SPRY domain. However, loss of both S242 phosphorylation and 14-3-3 binding was observed for bacterial effectors that activate the pyrin inflammasome, such as Clostridium difficile toxin B (TcdB). The S242R mutation thus recapitulated the effect of pathogen sensing, triggering inflammasome activation and IL-1β production. Successful therapy targeting IL-1β has been initiated in one patient, resolving pyrin-associated autoinflammation with neutrophilic dermatosis. This disease provides evidence that a guard-like mechanism of pyrin regulation, originally identified for Nod-like receptors in plant innate immunity, also exists in humans. PMID:27030597

  3. Molecular Dynamics Simulations Reveal the Mechanisms of Allosteric Activation of Hsp90 by Designed Ligands

    NASA Astrophysics Data System (ADS)

    Vettoretti, Gerolamo; Moroni, Elisabetta; Sattin, Sara; Tao, Jiahui; Agard, David A.; Bernardi, Anna; Colombo, Giorgio

    2016-04-01

    Controlling biochemical pathways through chemically designed modulators may provide novel opportunities to develop therapeutic drugs and chemical tools. The underlying challenge is to design new molecular entities able to act as allosteric chemical switches that selectively turn on/off functions by modulating the conformational dynamics of their target protein. We examine the origins of the stimulation of ATPase and closure kinetics in the molecular chaperone Hsp90 by allosteric modulators through atomistic molecular dynamics (MD) simulations and analysis of protein-ligand interactions. In particular, we focus on the cross-talk between allosteric ligands and protein conformations and its effect on the dynamic properties of the chaperone’s active state. We examine the impact of different allosteric modulators on the stability, structural and internal dynamics properties of Hsp90 closed state. A critical aspect of this study is the development of a quantitative model that correlates Hsp90 activation to the presence of a certain compound, making use of information on the dynamic adaptation of protein conformations to the presence of the ligand, which allows to capture conformational states relevant in the activation process. We discuss the implications of considering the conformational dialogue between allosteric ligands and protein conformations for the design of new functional modulators.

  4. Acetohydroxyacid synthase activity and transcripts profiling reveal tissue-specific regulation of ahas genes in sunflower.

    PubMed

    Ochogavía, Ana C; Breccia, Gabriela; Vega, Tatiana; Felitti, Silvina A; Picardi, Liliana A; Nestares, Graciela

    2014-07-01

    Acetohydroxyacid synthase (AHAS) is the target site of several herbicides and catalyses the first step in the biosynthesis of branched chain amino acid. Three genes coding for AHAS catalytic subunit (ahas1, ahas2 and ahas3) have been reported for sunflower. The aim of this work was to study the expression pattern of ahas genes family and AHAS activity in sunflower (Helianthus annuus L.). Different organs (leaves, hypocotyls, roots, flowers and embryos) were evaluated at several developmental stages. The transcriptional profile was studied through RT-qPCR. The highest expression for ahas1 was shown in leaves, where all the induced and natural gene mutations conferring herbicide resistance were found. The maximal expression of ahas2 and ahas3 occurred in immature flowers and embryos. The highest AHAS activity was found in leaves and immature embryos. Correlation analysis among ahas gene expression and AHAS activity was discussed. Our results show that differences in ahas genes expression are tissue-specific and temporally regulated. Moreover, the conservation of multiple AHAS isoforms in sunflower seems to result from different expression requirements controlled by tissue-specific regulatory mechanisms at different developmental stages. PMID:24908515

  5. Molecular Dynamics Simulations Reveal the Mechanisms of Allosteric Activation of Hsp90 by Designed Ligands

    PubMed Central

    Vettoretti, Gerolamo; Moroni, Elisabetta; Sattin, Sara; Tao, Jiahui; Agard, David A.; Bernardi, Anna; Colombo, Giorgio

    2016-01-01

    Controlling biochemical pathways through chemically designed modulators may provide novel opportunities to develop therapeutic drugs and chemical tools. The underlying challenge is to design new molecular entities able to act as allosteric chemical switches that selectively turn on/off functions by modulating the conformational dynamics of their target protein. We examine the origins of the stimulation of ATPase and closure kinetics in the molecular chaperone Hsp90 by allosteric modulators through atomistic molecular dynamics (MD) simulations and analysis of protein-ligand interactions. In particular, we focus on the cross-talk between allosteric ligands and protein conformations and its effect on the dynamic properties of the chaperone’s active state. We examine the impact of different allosteric modulators on the stability, structural and internal dynamics properties of Hsp90 closed state. A critical aspect of this study is the development of a quantitative model that correlates Hsp90 activation to the presence of a certain compound, making use of information on the dynamic adaptation of protein conformations to the presence of the ligand, which allows to capture conformational states relevant in the activation process. We discuss the implications of considering the conformational dialogue between allosteric ligands and protein conformations for the design of new functional modulators. PMID:27032695

  6. Polycomb repressive complex 2 structure with inhibitor reveals a mechanism of activation and drug resistance

    PubMed Central

    Brooun, Alexei; Gajiwala, Ketan S.; Deng, Ya-Li; Liu, Wei; Bolaños, Ben; Bingham, Patrick; He, You-Ai; Diehl, Wade; Grable, Nicole; Kung, Pei-Pei; Sutton, Scott; Maegley, Karen A.; Yu, Xiu; Stewart, Al E.

    2016-01-01

    Polycomb repressive complex 2 (PRC2) mediates gene silencing through chromatin reorganization by methylation of histone H3 lysine 27 (H3K27). Overexpression of the complex and point mutations in the individual subunits of PRC2 have been shown to contribute to tumorigenesis. Several inhibitors of the PRC2 activity have shown efficacy in EZH2-mutated lymphomas and are currently in clinical development, although the molecular basis of inhibitor recognition remains unknown. Here we report the crystal structures of the inhibitor-bound wild-type and Y641N PRC2. The structures illuminate an important role played by a stretch of 17 residues in the N-terminal region of EZH2, we call the activation loop, in the stimulation of the enzyme activity, inhibitor recognition and the potential development of the mutation-mediated drug resistance. The work presented here provides new avenues for the design and development of next-generation PRC2 inhibitors through establishment of a structure-based drug design platform. PMID:27122193

  7. Mechanistic Studies of Bismuth(V)-Mediated Thioglycoside Activation Reveal Differential Reactivity of Anomers.

    PubMed

    Goswami, Manibarsha; Ashley, Daniel C; Baik, Mu-Hyun; Pohl, Nicola L B

    2016-07-15

    The mechanism of bismuth(V)-mediated thioglycoside activation was examined using reaction kinetics and quantum chemical reaction models. NMR experiments show an unusual nonlinear growth/decay curve for the glycosylation reaction. Further studies suggest an anomeric inversion of the β-glycoside donor to the α-donor during its activation, even in the presence of a neighboring 2-position acetate. Interestingly, in situ anomerization was not observed in the activation of an α-glycoside donor, and this anomer also showed faster reaction times and higher product diastereoselectivites. Density functional theory calculations identify the structure of the promoter triphenyl bismuth ditriflate, [Ph3Bi(OTf)2, 1], in solution and map out the energetics of its interactions with the two thioglycoside anomers. These calculations suggest that 1 must bind the thiopropyl arm to induce triflate loss. The computational analyses also show that, unlike most O-glycosides, the β- and α-donor S-glycosides are similar in energy. One energetically reasonable anomerization pathway of the donors is an SN1-like mechanism promoted by forming a bismuth-sulfonium adduct with the Lewis acidic Bi(V) for the formation of an oxacarbenium intermediate. Finally, the computed energy compensations needed to form these α vs β Bi adducts is a possible explanation for the differential reactivity of these donors. PMID:27295299

  8. A Sleeping Beauty screen reveals NF-kB activation in CLL mouse model.

    PubMed

    Zanesi, Nicola; Balatti, Veronica; Riordan, Jesse; Burch, Aaron; Rizzotto, Lara; Palamarchuk, Alexey; Cascione, Luciano; Lagana, Alessandro; Dupuy, Adam J; Croce, Carlo M; Pekarsky, Yuri

    2013-05-23

    TCL1 oncogene is overexpressed in aggressive form of human chronic lymphocytic leukemia (CLL) and its dysregulation in mouse B cells causes a CD5-positive leukemia similar to the aggressive form of human CLLs. To identify oncogenes that cooperate with Tcl1, we performed genetic screen in Eμ-TCL1 mice using Sleeping Beauty transposon-mediated mutagenesis. Analysis of transposon common insertion sites identified 7 genes activated by transposon insertions. Overexpression of these genes in mouse CLL was confirmed by real time reverse transcription-polymerase chain reaction. Interestingly, the main known function of 4 of 7 genes (Nfkb1, Tab2, Map3K14, and Nfkbid) is participation in or activation of the nuclear factor-kB (NF-kB) pathway. In addition, activation of the NF-kB is 1 of main functions of Akt2, also identified in the screen. These findings demonstrate cooperation of Tcl1 and the NF-kB pathway in the pathogenesis of aggressive CLL. Identification cooperating cancer genes will result in the development of combinatorial therapies to treat CLL. PMID:23591791

  9. Large heterogeneities in comet 67P as revealed by active pits from sinkhole collapse.

    PubMed

    Vincent, Jean-Baptiste; Bodewits, Dennis; Besse, Sébastien; Sierks, Holger; Barbieri, Cesare; Lamy, Philippe; Rodrigo, Rafael; Koschny, Detlef; Rickman, Hans; Keller, Horst Uwe; Agarwal, Jessica; A'Hearn, Michael F; Auger, Anne-Thérèse; Barucci, M Antonella; Bertaux, Jean-Loup; Bertini, Ivano; Capanna, Claire; Cremonese, Gabriele; Da Deppo, Vania; Davidsson, Björn; Debei, Stefano; De Cecco, Mariolino; El-Maarry, Mohamed Ramy; Ferri, Francesca; Fornasier, Sonia; Fulle, Marco; Gaskell, Robert; Giacomini, Lorenza; Groussin, Olivier; Guilbert-Lepoutre, Aurélie; Gutierrez-Marques, P; Gutiérrez, Pedro J; Güttler, Carsten; Hoekzema, Nick; Höfner, Sebastian; Hviid, Stubbe F; Ip, Wing-Huen; Jorda, Laurent; Knollenberg, Jörg; Kovacs, Gabor; Kramm, Rainer; Kührt, Ekkehard; Küppers, Michael; La Forgia, Fiorangela; Lara, Luisa M; Lazzarin, Monica; Lee, Vicky; Leyrat, Cédric; Lin, Zhong-Yi; Lopez Moreno, Josè J; Lowry, Stephen; Magrin, Sara; Maquet, Lucie; Marchi, Simone; Marzari, Francesco; Massironi, Matteo; Michalik, Harald; Moissl, Richard; Mottola, Stefano; Naletto, Giampiero; Oklay, Nilda; Pajola, Maurizio; Preusker, Frank; Scholten, Frank; Thomas, Nicolas; Toth, Imre; Tubiana, Cecilia

    2015-07-01

    Pits have been observed on many cometary nuclei mapped by spacecraft. It has been argued that cometary pits are a signature of endogenic activity, rather than impact craters such as those on planetary and asteroid surfaces. Impact experiments and models cannot reproduce the shapes of most of the observed cometary pits, and the predicted collision rates imply that few of the pits are related to impacts. Alternative mechanisms like explosive activity have been suggested, but the driving process remains unknown. Here we report that pits on comet 67P/Churyumov-Gerasimenko are active, and probably created by a sinkhole process, possibly accompanied by outbursts. We argue that after formation, pits expand slowly in diameter, owing to sublimation-driven retreat of the walls. Therefore, pits characterize how eroded the surface is: a fresh cometary surface will have a ragged structure with many pits, while an evolved surface will look smoother. The size and spatial distribution of pits imply that large heterogeneities exist in the physical, structural or compositional properties of the first few hundred metres below the current nucleus surface. PMID:26135448

  10. Large heterogeneities in comet 67P as revealed by active pits from sinkhole collapse

    NASA Astrophysics Data System (ADS)

    Vincent, Jean-Baptiste; Bodewits, Dennis; Besse, Sébastien; Sierks, Holger; Barbieri, Cesare; Lamy, Philippe; Rodrigo, Rafael; Koschny, Detlef; Rickman, Hans; Keller, Horst Uwe; Agarwal, Jessica; A'Hearn, Michael F.; Auger, Anne-Thérèse; Barucci, M. Antonella; Bertaux, Jean-Loup; Bertini, Ivano; Capanna, Claire; Cremonese, Gabriele; da Deppo, Vania; Davidsson, Björn; Debei, Stefano; de Cecco, Mariolino; El-Maarry, Mohamed Ramy; Ferri, Francesca; Fornasier, Sonia; Fulle, Marco; Gaskell, Robert; Giacomini, Lorenza; Groussin, Olivier; Guilbert-Lepoutre, Aurélie; Gutierrez-Marques, P.; Gutiérrez, Pedro J.; Güttler, Carsten; Hoekzema, Nick; Höfner, Sebastian; Hviid, Stubbe F.; Ip, Wing-Huen; Jorda, Laurent; Knollenberg, Jörg; Kovacs, Gabor; Kramm, Rainer; Kührt, Ekkehard; Küppers, Michael; La Forgia, Fiorangela; Lara, Luisa M.; Lazzarin, Monica; Lee, Vicky; Leyrat, Cédric; Lin, Zhong-Yi; Lopez Moreno, Josè J.; Lowry, Stephen; Magrin, Sara; Maquet, Lucie; Marchi, Simone; Marzari, Francesco; Massironi, Matteo; Michalik, Harald; Moissl, Richard; Mottola, Stefano; Naletto, Giampiero; Oklay, Nilda; Pajola, Maurizio; Preusker, Frank; Scholten, Frank; Thomas, Nicolas; Toth, Imre; Tubiana, Cecilia

    2015-07-01

    Pits have been observed on many cometary nuclei mapped by spacecraft. It has been argued that cometary pits are a signature of endogenic activity, rather than impact craters such as those on planetary and asteroid surfaces. Impact experiments and models cannot reproduce the shapes of most of the observed cometary pits, and the predicted collision rates imply that few of the pits are related to impacts. Alternative mechanisms like explosive activity have been suggested, but the driving process remains unknown. Here we report that pits on comet 67P/Churyumov-Gerasimenko are active, and probably created by a sinkhole process, possibly accompanied by outbursts. We argue that after formation, pits expand slowly in diameter, owing to sublimation-driven retreat of the walls. Therefore, pits characterize how eroded the surface is: a fresh cometary surface will have a ragged structure with many pits, while an evolved surface will look smoother. The size and spatial distribution of pits imply that large heterogeneities exist in the physical, structural or compositional properties of the first few hundred metres below the current nucleus surface.

  11. A Sleeping Beauty screen reveals NF-kB activation in CLL mouse model

    PubMed Central

    Zanesi, Nicola; Balatti, Veronica; Riordan, Jesse; Burch, Aaron; Rizzotto, Lara; Palamarchuk, Alexey; Cascione, Luciano; Lagana, Alessandro; Dupuy, Adam J.; Croce, Carlo M.

    2013-01-01

    TCL1 oncogene is overexpressed in aggressive form of human chronic lymphocytic leukemia (CLL) and its dysregulation in mouse B cells causes a CD5-positive leukemia similar to the aggressive form of human CLLs. To identify oncogenes that cooperate with Tcl1, we performed genetic screen in Eμ−TCL1 mice using Sleeping Beauty transposon-mediated mutagenesis. Analysis of transposon common insertion sites identified 7 genes activated by transposon insertions. Overexpression of these genes in mouse CLL was confirmed by real time reverse transcription-polymerase chain reaction. Interestingly, the main known function of 4 of 7 genes (Nfkb1, Tab2, Map3K14, and Nfkbid) is participation in or activation of the nuclear factor-kB (NF-kB) pathway. In addition, activation of the NF-kB is 1 of main functions of Akt2, also identified in the screen. These findings demonstrate cooperation of Tcl1 and the NF-kB pathway in the pathogenesis of aggressive CLL. Identification cooperating cancer genes will result in the development of combinatorial therapies to treat CLL. PMID:23591791

  12. Analysis of protein phosphorylation in nerve terminal reveals extensive changes in active zone proteins upon exocytosis

    PubMed Central

    Kohansal-Nodehi, Mahdokht; Chua, John JE; Urlaub, Henning; Jahn, Reinhard; Czernik, Dominika

    2016-01-01

    Neurotransmitter release is mediated by the fast, calcium-triggered fusion of synaptic vesicles with the presynaptic plasma membrane, followed by endocytosis and recycling of the membrane of synaptic vesicles. While many of the proteins governing these processes are known, their regulation is only beginning to be understood. Here we have applied quantitative phosphoproteomics to identify changes in phosphorylation status of presynaptic proteins in resting and stimulated nerve terminals isolated from the brains of Wistar rats. Using rigorous quantification, we identified 252 phosphosites that are either up- or downregulated upon triggering calcium-dependent exocytosis. Particularly pronounced were regulated changes of phosphosites within protein constituents of the presynaptic active zone, including bassoon, piccolo, and RIM1. Additionally, we have mapped kinases and phosphatases that are activated upon stimulation. Overall, our study provides a snapshot of phosphorylation changes associated with presynaptic activity and provides a foundation for further functional analysis of key phosphosites involved in presynaptic plasticity. DOI: http://dx.doi.org/10.7554/eLife.14530.001 PMID:27115346

  13. Spores of many common airborne fungi reveal no ice nucleation activity in oil immersion freezing experiments

    NASA Astrophysics Data System (ADS)

    Pummer, B. G.; Atanasova, L.; Bauer, H.; Bernardi, J.; Druzhinina, I. S.; Fröhlich-Nowoisky, J.; Grothe, H.

    2013-12-01

    Fungal spores are ubiquitous biological aerosols, which are considered to act as ice nuclei. In this study the ice nucleation (IN) activity of spores harvested from 29 fungal strains belonging to 21 different species was tested in the immersion freezing mode by microscopic observation of water-in-oil emulsions. Spores of 8 of these strains were also investigated in a microdroplet freezing array instrument. The focus was laid on species of economical, ecological or sanitary significance. Besides common molds (Ascomycota), some representatives of the widespread group of mushrooms (Basidiomycota) were also investigated. Fusarium avenaceum was the only sample showing IN activity at relatively high temperatures (about 264 K), while the other investigated fungal spores showed no freezing above 248 K. Many of the samples indeed froze at homogeneous ice nucleation temperatures (about 237 K). In combination with other studies, this suggests that only a limited number of species may act as atmospheric ice nuclei. This would be analogous to what is already known for the bacterial ice nuclei. Apart from that, we selected a set of fungal strains from different sites and exposed them to occasional freezing stress during their cultivation. This was in order to test if the exposure to a cold environment encourages the expression of ice nuclei during growth as a way of adaptation. Although the total protein expression was altered by this treatment, it had no significant impact on the IN activity.

  14. Using Carbohydrate Interaction Assays to Reveal Novel Binding Sites in Carbohydrate Active Enzymes.

    PubMed

    Cockburn, Darrell; Wilkens, Casper; Dilokpimol, Adiphol; Nakai, Hiroyuki; Lewińska, Anna; Abou Hachem, Maher; Svensson, Birte

    2016-01-01

    Carbohydrate active enzymes often contain auxiliary binding sites located either on independent domains termed carbohydrate binding modules (CBMs) or as so-called surface binding sites (SBSs) on the catalytic module at a certain distance from the active site. The SBSs are usually critical for the activity of their cognate enzyme, though they are not readily detected in the sequence of a protein, but normally require a crystal structure of a complex for their identification. A variety of methods, including affinity electrophoresis (AE), insoluble polysaccharide pulldown (IPP) and surface plasmon resonance (SPR) have been used to study auxiliary binding sites. These techniques are complementary as AE allows monitoring of binding to soluble polysaccharides, IPP to insoluble polysaccharides and SPR to oligosaccharides. Here we show that these methods are useful not only for analyzing known binding sites, but also for identifying new ones, even without structural data available. We further verify the chosen assays discriminate between known SBS/CBM containing enzymes and negative controls. Altogether 35 enzymes are screened for the presence of SBSs or CBMs and several novel binding sites are identified, including the first SBS ever reported in a cellulase. This work demonstrates that combinations of these methods can be used as a part of routine enzyme characterization to identify new binding sites and advance the study of SBSs and CBMs, allowing them to be detected in the absence of structural data. PMID:27504624

  15. A new autocatalytic activation mechanism for cysteine proteases revealed by Prevotella intermedia interpain A

    PubMed Central

    Mallorquí-Fernández, Noemí; Manandhar, Surya P.; Mallorquí-Fernández, Goretti; Usón, Isabel; Wawrzonek, Katarzyna; Kantyka, Tomasz; Solà, Maria; Thøgersen, Ida B.; Enghild, Jan J.; Potempa, Jan; Gomis-Rüth, F.Xavier

    2009-01-01

    Prevotella intermedia is a major periodontopathogen contributing to human gingivitis and periodontitis. Such pathogens release proteases as virulence factors that cause deterrence of host defences and tissue destruction. A new cysteine protease from the cysteine-histidine-dyad class, interpain A, was studied in its zymogenic and its self-processed mature form. The latter consists of a bivalved moiety made up by two subdomains. In the structure of a catalytic cysteine-to-alanine zymogen variant, the right subdomain interacts with an unusual prodomain, thus contributing to latency. Unlike the catalytic cysteine residue, already in its competent conformation in the zymogen, the catalytic histidine is swung out from its active conformation and trapped in a cage shaped by a backing helix, a zymogenic hairpin and a latency flap in the zymogen. Dramatic rearrangement of up to 20Å of these elements triggered by a tryptophan switch occurs during activation and accounts for a new activation mechanism for proteolytic enzymes. These findings can be extrapolated to related potentially pathogenic cysteine proteases such as Streprococcus pyogenes SpeB and Porphyromonas gingivalis periodontain. PMID:17993455

  16. Retinal orientation and interactions in rhodopsin reveal a two-stage trigger mechanism for activation.

    PubMed

    Kimata, Naoki; Pope, Andreyah; Eilers, Markus; Opefi, Chikwado A; Ziliox, Martine; Hirshfeld, Amiram; Zaitseva, Ekaterina; Vogel, Reiner; Sheves, Mordechai; Reeves, Philip J; Smith, Steven O

    2016-01-01

    The 11-cis retinal chromophore is tightly packed within the interior of the visual receptor rhodopsin and isomerizes to the all-trans configuration following absorption of light. The mechanism by which this isomerization event drives the outward rotation of transmembrane helix H6, a hallmark of activated G protein-coupled receptors, is not well established. To address this question, we use solid-state NMR and FTIR spectroscopy to define the orientation and interactions of the retinal chromophore in the active metarhodopsin II intermediate. Here we show that isomerization of the 11-cis retinal chromophore generates strong steric interactions between its β-ionone ring and transmembrane helices H5 and H6, while deprotonation of its protonated Schiff's base triggers the rearrangement of the hydrogen-bonding network involving residues on H6 and within the second extracellular loop. We integrate these observations with previous structural and functional studies to propose a two-stage mechanism for rhodopsin activation. PMID:27585742

  17. Using Carbohydrate Interaction Assays to Reveal Novel Binding Sites in Carbohydrate Active Enzymes

    PubMed Central

    Wilkens, Casper; Dilokpimol, Adiphol; Nakai, Hiroyuki; Lewińska, Anna; Abou Hachem, Maher; Svensson, Birte

    2016-01-01

    Carbohydrate active enzymes often contain auxiliary binding sites located either on independent domains termed carbohydrate binding modules (CBMs) or as so-called surface binding sites (SBSs) on the catalytic module at a certain distance from the active site. The SBSs are usually critical for the activity of their cognate enzyme, though they are not readily detected in the sequence of a protein, but normally require a crystal structure of a complex for their identification. A variety of methods, including affinity electrophoresis (AE), insoluble polysaccharide pulldown (IPP) and surface plasmon resonance (SPR) have been used to study auxiliary binding sites. These techniques are complementary as AE allows monitoring of binding to soluble polysaccharides, IPP to insoluble polysaccharides and SPR to oligosaccharides. Here we show that these methods are useful not only for analyzing known binding sites, but also for identifying new ones, even without structural data available. We further verify the chosen assays discriminate between known SBS/CBM containing enzymes and negative controls. Altogether 35 enzymes are screened for the presence of SBSs or CBMs and several novel binding sites are identified, including the first SBS ever reported in a cellulase. This work demonstrates that combinations of these methods can be used as a part of routine enzyme characterization to identify new binding sites and advance the study of SBSs and CBMs, allowing them to be detected in the absence of structural data. PMID:27504624

  18. Measurement of voluntary activation of fresh and fatigued human muscles using transcranial magnetic stimulation

    PubMed Central

    Todd, Gabrielle; Taylor, Janet L; Gandevia, S C

    2003-01-01

    Recently, transcranial magnetic stimulation of the motor cortex (TMS) revealed impaired voluntary activation of muscles during maximal efforts. Hence, we evaluated its use as a measure of voluntary activation over a range of contraction strengths in both fresh and fatigued muscles, and compared it with standard twitch interpolation using nerve stimulation. Subjects contracted the elbow flexors isometrically while force and EMG from biceps and triceps were recorded. In one study, eight subjects made submaximal and maximal test contractions with rests to minimise fatigue. In the second study, eight subjects made sustained maximal contractions to reduce force to 60 % of the initial value, followed by brief test contractions. Force responses were recorded following TMS or electrical stimulation of the biceps motor nerve. In other contractions, EMG responses to TMS (motor evoked potentials, MEPs) or to stimulation at the brachial plexus (maximal M waves, Mmax) were recorded. During contractions of 50 % maximum, TMS elicited large MEPs in biceps (> 90 % Mmax) which decreased in size (to ≈70 % Mmax) with maximal efforts. This suggests that faster firing rates made some motor units effectively refractory. With fatigue, MEPs were also smaller but remained > 70 % Mmax for contractions of 50–100 % maximum. For fresh and fatigued muscle, the superimposed twitch evoked by motor nerve and motor cortex stimulation decreased with increasing contraction strength. For nerve stimulation the relation was curvilinear, and for TMS it was linear for contractions of 50–100 % maximum (r2 = 1.00). Voluntary activation was derived using the expression: (1 – superimposed twitch/resting twitch) × 100. The resting twitch was measured directly for nerve stimulation and for TMS, it was estimated by extrapolation of the linear regression between the twitch and voluntary force. For cortical stimulation, this resulted in a highly linear relation between voluntary activation and force

  19. In-Plane Electronic Anisotropy of Underdoped ___122___ Fe-Arsenide Superconductors Revealed by Measurements of Detwinned Single Crystals

    SciTech Connect

    Fisher, Ian Randal

    2012-05-08

    The parent phases of the Fe-arsenide superconductors harbor an antiferromagnetic ground state. Significantly, the Neel transition is either preceded or accompanied by a structural transition that breaks the four fold symmetry of the high-temperature lattice. Borrowing language from the field of soft condensed matter physics, this broken discrete rotational symmetry is widely referred to as an Ising nematic phase transition. Understanding the origin of this effect is a key component of a complete theoretical description of the occurrence of superconductivity in this family of compounds, motivating both theoretical and experimental investigation of the nematic transition and the associated in-plane anisotropy. Here we review recent experimental progress in determining the intrinsic in-plane electronic anisotropy as revealed by resistivity, reflectivity and ARPES measurements of detwinned single crystals of underdoped Fe arsenide superconductors in the '122' family of compounds.

  20. Revealing the hidden faults in the SE flank of Mt. Etna using radon in-soil gas measurement.

    PubMed

    Johnová, K; Thinová, L; Giammanco, S

    2014-07-01

    Although there are many methods for investigating tectonic structures, many faults remain hidden, and they can endanger the life and property of people living along them. The slopes of volcanoes are covered with such hidden faults, near which strong earthquakes and gas releases can appear. Revealing hidden faults can therefore contribute significantly to the protection of people living in volcanic areas. In the study, seven different techniques were used for making measurements of in-soil radon concentrations in order to search for hidden faults on the SE flank of the Mt. Etna volcano. These reported methods had previously been proved to be useful tools for investigating fault structures. The main aim of the experiment presented here was to evaluate the usability of these methods in the geological conditions of the Mt. Etna region, and to find the best place for continual radon monitoring using a permanent station in the near future. PMID:24729558

  1. Spin-Triplet Superconductivity in UNi2Al3 Revealed by the 27Al Knight Shift Measurement

    NASA Astrophysics Data System (ADS)

    Ishida, K.; Ozaki, D.; Kamatsuka, T.; Tou, H.; Kyogaku, M.; Kitaoka, Y.; Tateiwa, N.; Sato, N. K.; Aso, N.; Geibel, C.; Steglich, F.

    2002-06-01

    We report 27Al Knight shift ( 27K) measurement on a single-crystal UNi2Al3 that reveals a coexistence of superconductivity and a spin-density-wave (SDW) type of magnetic ordering ( TSDW = 4.5 K). The spin part of 27K, 27Ks, does not change down to 50 mK across the superconducting (SC) transition temperature Tc~0.9 K. In contrast with the isostructural compound UPd2Al3 ( Tc~2 K), which was identified to be a spin-singlet d-wave superconductor, the behavior of 27K strongly supports that UNi2Al3, like UPt3 and Sr2RuO4, belongs to a class of spin-triplet SC pairing state superconductors.

  2. Active faults in the deformation zone off Noto Peninsula, Japan, revealed by high- resolution seismic profiles

    NASA Astrophysics Data System (ADS)

    Inoue, T.; Okamura, Y.; Murakami, F.; Kimura, H.; Ikehara, K.

    2008-12-01

    Recently, a lot of earthquakes occur in Japan. The deformation zone which many faults and folds have concentrated exists on the Japan Sea side of Japan. The 2007 Noto Hanto Earthquake (MJMA 6.9) and 2007 Chuetsu-oki Earthquake (MJMA 6.8) were caused by activity of parts of faults in this deformation zone. The Noto Hanto Earthquake occurred on 25 March, 2007 under the northwestern coast of Noto Peninsula, Ishikawa Prefecture, Japan. This earthquake is located in Quaternary deformation zone that is continued from northern margin of Noto Peninsula to southeast direction (Okamura, 2007a). National Institute of Advanced Industrial Science and Technology (AIST) carried out high-resolution seismic survey using Boomer and 12 channels short streamer cable in the northern part off Noto Peninsula, in order to clarify distribution and activities of active faults in the deformation zone. A twelve channels short streamer cable with 2.5 meter channel spacing developed by AIST and private corporation is designed to get high resolution seismic profiles in shallow sea area. The multi-channel system is possible to equip on a small fishing boat, because the data acquisition system is based on PC and the length of the cable is short and easy to handle. Moreover, because the channel spacing is short, this cable is very effective for a high- resolution seismic profiling survey in the shallow sea, and seismic data obtained by multi-channel cable can be improved by velocity analysis and CDP stack. In the northern part off Noto Peninsula, seismic profiles depicting geologic structure up to 100 meters deep under sea floor were obtained. The most remarkable reflection surface recognized in the seismic profiles is erosion surface at the Last Glacial Maximum (LGM). In the western part, sediments about 30 meters (40 msec) thick cover the erosional surface that is distributed under the shelf shallower than 100m in depth and the sediments thin toward offshore and east. Flexures like deformation in

  3. A direct measurement of strontium-89 activity in bone metastases.

    PubMed

    Ben-Josef, E; Maughan, R L; Vasan, S; Porter, A T

    1995-06-01

    The total absorbed dose after systemic administration of 89Sr has been determined by measuring directly its activity in bone metastases. Autoradiography was performed on sections of bones obtained from patients treated with 89Sr to study the pattern of deposition. Discs of 5 and 8 mm diameter were cut from metastatic sites and normal bone. The beta-ray activity was determined with a scintillation counter, which was calibrated using similar bovine cancellous bone discs, onto which a known activity of 89Sr was transferred by pipette. From the activity measured, the initial activity (at the time of 89Sr administration) was calculated. The absorbed dose was estimated using the methodology described in NCRP Report No. 58. The estimated initial activity of 89Sr in the bone metastases varied from 2.3 to 240 MBq kg-1, with a mean value of 31 +/- 27 MBq kg-1. The total absorbed dose ranged from 1.3 to 64 Gy, with a mean of 18 +/- 16 Gy. The average total dose to normal bone sites was 1.1 +/- 0.4 Gy. The metastases to normal bone dose ratio in individual samples varied from 8 +/- 4 to 40 +/- 25. These estimates are in agreement with those obtained previously by indirect methods. PMID:7675358

  4. Being PRO-ACTive: What can a Clinical Trial Database Reveal About ALS?

    PubMed

    Zach, Neta; Ennist, David L; Taylor, Albert A; Alon, Hagit; Sherman, Alexander; Kueffner, Robert; Walker, Jason; Sinani, Ervin; Katsovskiy, Igor; Cudkowicz, Merit; Leitner, Melanie L

    2015-04-01

    Advancing research and clinical care, and conducting successful and cost-effective clinical trials requires characterizing a given patient population. To gather a sufficiently large cohort of patients in rare diseases such as amyotrophic lateral sclerosis (ALS), we developed the Pooled Resource Open-Access ALS Clinical Trials (PRO-ACT) platform. The PRO-ACT database currently consists of >8600 ALS patient records from 17 completed clinical trials, and more trials are being incorporated. The database was launched in an open-access mode in December 2012; since then, >400 researchers from >40 countries have requested the data. This review gives an overview on the research enabled by this resource, through several examples of research already carried out with the goal of improving patient care and understanding the disease. These examples include predicting ALS progression, the simulation of future ALS clinical trials, the verification of previously proposed predictive features, the discovery of novel predictors of ALS progression and survival, the newly identified stratification of patients based on their disease progression profiles, and the development of tools for better clinical trial recruitment and monitoring. Results from these approaches clearly demonstrate the value of large datasets for developing a better understanding of ALS natural history, prognostic factors, patient stratification, and more. The increasing use by the community suggests that further analyses of the PRO-ACT database will continue to reveal more information about this disease that has for so long defied our understanding. PMID:25613183

  5. Stability of active mantle upwelling revealed by net characteristics of plate tectonics.

    PubMed

    Conrad, Clinton P; Steinberger, Bernhard; Torsvik, Trond H

    2013-06-27

    Viscous convection within the mantle is linked to tectonic plate motions and deforms Earth's surface across wide areas. Such close links between surface geology and deep mantle dynamics presumably operated throughout Earth's history, but are difficult to investigate for past times because the history of mantle flow is poorly known. Here we show that the time dependence of global-scale mantle flow can be deduced from the net behaviour of surface plate motions. In particular, we tracked the geographic locations of net convergence and divergence for harmonic degrees 1 and 2 by computing the dipole and quadrupole moments of plate motions from tectonic reconstructions extended back to the early Mesozoic era. For present-day plate motions, we find dipole convergence in eastern Asia and quadrupole divergence in both central Africa and the central Pacific. These orientations are nearly identical to the dipole and quadrupole orientations of underlying mantle flow, which indicates that these 'net characteristics' of plate motions reveal deeper flow patterns. The positions of quadrupole divergence have not moved significantly during the past 250 million years, which suggests long-term stability of mantle upwelling beneath Africa and the Pacific Ocean. These upwelling locations are positioned above two compositionally and seismologically distinct regions of the lowermost mantle, which may organize global mantle flow as they remain stationary over geologic time. PMID:23803848

  6. Motif module map reveals enforcement of aging by continual NF-κB activity

    PubMed Central

    Adler, Adam S.; Sinha, Saurabh; Kawahara, Tiara L.A.; Zhang, Jennifer Y.; Segal, Eran; Chang, Howard Y.

    2007-01-01

    Aging is characterized by specific alterations in gene expression, but their underlying mechanisms and functional consequences are not well understood. Here we develop a systematic approach to identify combinatorial cis-regulatory motifs that drive age-dependent gene expression across different tissues and organisms. Integrated analysis of 365 microarrays spanning nine tissue types predicted fourteen motifs as major regulators of age-dependent gene expression in human and mouse. The motif most strongly associated with aging was that of the transcription factor NF-κB. Inducible genetic blockade of NF-κB for 2 wk in the epidermis of chronologically aged mice reverted the tissue characteristics and global gene expression programs to those of young mice. Age-specific NF-κB blockade and orthogonal cell cycle interventions revealed that NF-κB controls cell cycle exit and gene expression signature of aging in parallel but not sequential pathways. These results identify a conserved network of regulatory pathways underlying mammalian aging and show that NF-κB is continually required to enforce many features of aging in a tissue-specific manner. PMID:18055696

  7. Seven Years (2004-2011) of Cassini Measurements Reveal Strong Local Time Asymmetry of the Saturnian Ring Current

    NASA Astrophysics Data System (ADS)

    Sergis, N.; Krimigis, S.; Thomsen, M.; Roelof, E.; Mitchell, D.; Hamilton, D.; Krupp, N.; Dougherty, M.; Crary, F.

    2012-04-01

    The Saturnian ring current, initially inferred from magnetic field and particle measurements after the Voyager 1 and 2 flybys, has been studied in substantial detail via in-situ and remote measurements since the July 2004 Cassini orbit insertion. The ring current of Saturn, located between 7 and 15 RS and primarily composed of O+ ions, is characterized by increased suprathermal (> 3 keV) particle pressure with high (> 1) plasma β values and intense dynamic behavior, as revealed by the analysis of combined particle data from the Cassini Magnetospheric Imaging Instrument (MIMI) and the Cassini Plasma Spectrometer instrument (CAPS), and magnetic field measurements from the Cassini magnetometer (MAG). Among the most important findings so far is that the azimuthal ring current flows primarily to balance inertial centrifugal forces inside ~8 RS, but increasingly it is driven by the non-thermal pressure gradient beyond its maximum region (8-12 RS, 100-150 pA/m2) and certainly it dominates farther out. Beyond ~ 10RS, the non-thermal pressure decreases with radial distance faster than the previously assumed 1/r rate and results in a magnetic perturbation of 10-15 nT. In this work we present the most complete (2004-2011) and up-to-date results, focusing on the local time asymmetry of the ring current properties (e.g. particle pressure, current density), and the relative contribution of different components to the radial force balance. The comprehensive spatial and local time coverage provided by the Cassini orbits has revealed that the suprathermal pressure and its corresponding pressure gradient is higher by a factor of 3 to 8 on the night side, in agreement with the observed distribution of energetic particle injections and energetic neutral atom (ENA) emissions. In addition to in-situ measurements, ENA images from the Ion and Neutral Camera (INCA) of Cassini, offer a unique overview of large parts of the Saturnian magnetosphere, depicting the rotation and dynamics of the

  8. Structure of the nisin leader peptidase NisP revealing a C-terminal autocleavage activity.

    PubMed

    Xu, Yueyang; Li, Xin; Li, Ruiqing; Li, Shanshan; Ni, Hongqian; Wang, Hui; Xu, Haijin; Zhou, Weihong; Saris, Per E J; Yang, Wen; Qiao, Mingqiang; Rao, Zihe

    2014-06-01

    Nisin is a widely used antibacterial lantibiotic polypeptide produced by Lactococcus lactis. NisP belongs to the subtilase family and functions in the last step of nisin maturation as the leader-peptide peptidase. Deletion of the nisP gene in LAC71 results in the production of a non-active precursor peptide with the leader peptide unremoved. Here, the 1.1 Å resolution crystal structure of NisP is reported. The structure shows similarity to other subtilases, which can bind varying numbers of Ca atoms. However, no calcium was found in this NisP structure, and the predicted calcium-chelating residues were placed so as to not allow NisP to bind a calcium ion in this conformation. Interestingly, a short peptide corresponding to its own 635-647 sequence was found to bind to the active site of NisP. Biochemical assays and native mass-spectrometric analysis confirmed that NisP possesses an auto-cleavage site between residues Arg647 and Ser648. Further, it was shown that NisP mutated at the auto-cleavage site (R647P/S648P) had full catalytic activity for nisin leader-peptide cleavage, although the C-terminal region of NisP was no longer cleaved. Expressing this mutant in L. lactis LAC71 did not affect the production of nisin but did decrease the proliferation rate of the bacteria, suggesting the biological significance of the C-terminal auto-cleavage of NisP. PMID:24914961

  9. Molecular genetics of blood-fleshed peach reveals activation of anthocyanin biosynthesis by NAC transcription factors.

    PubMed

    Zhou, Hui; Lin-Wang, Kui; Wang, Huiliang; Gu, Chao; Dare, Andrew P; Espley, Richard V; He, Huaping; Allan, Andrew C; Han, Yuepeng

    2015-04-01

    Anthocyanin pigmentation is an important consumer trait in peach (Prunus persica). In this study, the genetic basis of the blood-flesh trait was investigated using the cultivar Dahongpao, which shows high levels of cyanidin-3-glucoside in the mesocarp. Elevation of anthocyanin levels in the flesh was correlated with the expression of an R2R3 MYB transcription factor, PpMYB10.1. However, PpMYB10.1 did not co-segregate with the blood-flesh trait. The blood-flesh trait was mapped to a 200-kb interval on peach linkage group (LG) 5. Within this interval, a gene encoding a NAC domain transcription factor (TF) was found to be highly up-regulated in blood-fleshed peaches when compared with non-red-fleshed peaches. This NAC TF, designated blood (BL), acts as a heterodimer with PpNAC1 which shows high levels of expression in fruit at late developmental stages. We show that the heterodimer of BL and PpNAC1 can activate the transcription of PpMYB10.1, resulting in anthocyanin pigmentation in tobacco. Furthermore, silencing the BL gene reduces anthocyanin pigmentation in blood-fleshed peaches. The transactivation activity of the BL-PpNAC1 heterodimer is repressed by a SQUAMOSA promoter-binding protein-like TF, PpSPL1. Low levels of PpMYB10.1 expression in fruit at early developmental stages is probably attributable to lower levels of expression of PpNAC1 plus the presence of high levels of repressors such as PpSPL1. We present a mechanism whereby BL is the key gene for the blood-flesh trait in peach via its activation of PpMYB10.1 in maturing fruit. Partner TFs such as basic helix-loop-helix proteins and NAC1 are required, as is the removal of transcriptional repressors. PMID:25688923

  10. Widely Used Pesticides with Previously Unknown Endocrine Activity Revealed as in Vitro Antiandrogens

    PubMed Central

    Orton, Frances; Rosivatz, Erika; Scholze, Martin; Kortenkamp, Andreas

    2011-01-01

    Background Evidence suggests that there is widespread decline in male reproductive health and that antiandrogenic pollutants may play a significant role. There is also a clear disparity between pesticide exposure and data on endocrine disruption, with most of the published literature focused on pesticides that are no longer registered for use in developed countries. Objective We used estimated human exposure data to select pesticides to test for antiandrogenic activity, focusing on highest use pesticides. Methods We used European databases to select 134 candidate pesticides based on highest exposure, followed by a filtering step according to known or predicted receptor-mediated antiandrogenic potency, based on a previously published quantitative structure–activity relationship (QSAR) model. In total, 37 pesticides were tested for in vitro androgen receptor (AR) antagonism. Of these, 14 were previously reported to be AR antagonists (“active”), 4 were predicted AR antagonists using the QSAR, 6 were predicted to not be AR antagonists (“inactive”), and 13 had unknown activity, which were “out of domain” and therefore could not be classified with the QSAR (“unknown”). Results All 14 pesticides with previous evidence of AR antagonism were confirmed as antiandrogenic in our assay, and 9 previously untested pesticides were identified as antiandrogenic (dimethomorph, fenhexamid, quinoxyfen, cyprodinil, λ-cyhalothrin, pyrimethanil, fludioxonil, azinphos-methyl, pirimiphos-methyl). In addition, we classified 7 compounds as androgenic. Conclusions Due to estimated antiandrogenic potency, current use, estimated exposure, and lack of previous data, we strongly recommend that dimethomorph, fludioxonil, fenhexamid, imazalil, ortho-phenylphenol, and pirimiphos-methyl be tested for antiandrogenic effects in vivo. The lack of human biomonitoring data for environmentally relevant pesticides presents a barrier to current risk assessment of pesticides on humans. PMID

  11. Native Electrophoresis-Coupled Activity Assays Reveal Catalytically-Active Protein Aggregates of Escherichia coli β-Glucuronidase

    PubMed Central

    Burchett, Gina G.; Folsom, Charles G.; Lane, Kimberly T.

    2015-01-01

    β-glucuronidase is found as a functional homotetramer in a variety of organisms, including humans and other animals, as well as a number of bacteria. This enzyme is important in these organisms, catalyzing the hydrolytic removal of a glucuronide moiety from substrate molecules. This process serves to break down sugar conjugates in animals and provide sugars for metabolism in bacteria. While β-glucuronidase is primarily found as a homotetramer, previous studies have indicated that the human form of the protein is also catalytically active as a dimer. Here we present evidence for not only an active dimer of the E. coli form of the protein, but also for several larger active complexes, including an octomer and a 16-mer. Additionally, we propose a model for the structures of these large complexes, based on computationally-derived molecular modeling studies. These structures may have application in the study of human disease, as several diseases have been associated with the aggregation of proteins. PMID:26121040

  12. Directed random walks and constraint programming reveal active pathways in hepatocyte growth factor signaling.

    PubMed

    Kittas, Aristotelis; Delobelle, Aurélien; Schmitt, Sabrina; Breuhahn, Kai; Guziolowski, Carito; Grabe, Niels

    2016-01-01

    An effective means to analyze mRNA expression data is to take advantage of established knowledge from pathway databases, using methods such as pathway-enrichment analyses. However, pathway databases are not case-specific and expression data could be used to infer gene-regulation patterns in the context of specific pathways. In addition, canonical pathways may not always describe the signaling mechanisms properly, because interactions can frequently occur between genes in different pathways. Relatively few methods have been proposed to date for generating and analyzing such networks, preserving the causality between gene interactions and reasoning over the qualitative logic of regulatory effects. We present an algorithm (MCWalk) integrated with a logic programming approach, to discover subgraphs in large-scale signaling networks by random walks in a fully automated pipeline. As an exemplary application, we uncover the signal transduction mechanisms in a gene interaction network describing hepatocyte growth factor-stimulated cell migration and proliferation from gene-expression measured with microarray and RT-qPCR using in-house perturbation experiments in a keratinocyte-fibroblast co-culture. The resulting subgraphs illustrate possible associations of hepatocyte growth factor receptor c-Met nodes, differentially expressed genes and cellular states. Using perturbation experiments and Answer Set programming, we are able to select those which are more consistent with the experimental data. We discover key regulator nodes by measuring the frequency with which they are traversed when connecting signaling between receptors and significantly regulated genes and predict their expression-shift consistently with the measured data. The Java implementation of MCWalk is publicly available under the MIT license at: https://bitbucket.org/akittas/biosubg. PMID:26518250

  13. High-Throughput Sequencing Reveals Circulating miRNAs as Potential Biomarkers for Measuring Puberty Onset in Chicken (Gallus gallus)

    PubMed Central

    Su, Yijun; Li, Guohui; Qu, Liang; Zhang, Huiyong; Wang, Kehua; Zou, Jianmin; Liu, Honglin

    2016-01-01

    There are still no highly sensitive and unique biomarkers for measurement of puberty onset. Circulating miRNAs have been shown to be promising biomarkers for diagnosis of various diseases. To identify circulating miRNAs that could be served as biomarkers for measuring chicken (Gallus gallus) puberty onset, the Solexa deep sequencing was performed to analyze the miRNA expression profiles in serum and plasma of hens from two different pubertal stages, before puberty onset (BO) and after puberty onset (AO). 197 conserved and 19 novel miRNAs (reads > 10) were identified as serum/plasma-expressed miRNAs in the chicken. The common miRNA amounts and their expression changes from BO to AO between serum and plasma were very similar, indicating the different treatments to generate serum and plasma had quite small influence on the miRNAs. 130 conserved serum-miRNAs were showed to be differentially expressed (reads > 10, P < 0.05) from BO to AO, with 68 up-regulated and 62 down-regulated. 4829 putative genes were predicted as the targets of the 40 most differentially expressed miRNAs (|log2(fold-change)|>1.0, P < 0.01). Functional analysis revealed several pathways that were associated with puberty onset. Further quantitative real-time PCR (RT-qPCR) test found that a seven-miRNA panel, including miR-29c, miR-375, miR-215, miR-217, miR-19b, miR-133a and let-7a, had great potentials to serve as novel biomarkers for measuring puberty onset in chicken. Due to highly conserved nature of miRNAs, the findings could provide cues for measurement of puberty onset in other animals as well as humans. PMID:27149515

  14. Structure of protease-cleaved Escherichia coli α-2-macroglobulin reveals a putative mechanism of conformational activation for protease entrapment

    SciTech Connect

    Fyfe, Cameron D.; Grinter, Rhys; Josts, Inokentijs; Mosbahi, Khedidja; Roszak, Aleksander W.; Cogdell, Richard J.; Wall, Daniel M.; Burchmore, Richard J. S.; Byron, Olwyn; Walker, Daniel

    2015-06-30

    The X-ray structure of protease-cleaved E. coli α-2-macroglobulin is described, which reveals a putative mechanism of activation and conformational change essential for protease inhibition. Bacterial α-2-macroglobulins have been suggested to function in defence as broad-spectrum inhibitors of host proteases that breach the outer membrane. Here, the X-ray structure of protease-cleaved Escherichia coli α-2-macroglobulin is described, which reveals a putative mechanism of activation and conformational change essential for protease inhibition. In this competitive mechanism, protease cleavage of the bait-region domain results in the untethering of an intrinsically disordered region of this domain which disrupts native interdomain interactions that maintain E. coli α-2-macroglobulin in the inactivated form. The resulting global conformational change results in entrapment of the protease and activation of the thioester bond that covalently links to the attacking protease. Owing to the similarity in structure and domain architecture of Escherichia coli α-2-macroglobulin and human α-2-macroglobulin, this protease-activation mechanism is likely to operate across the diverse members of this group.

  15. Mapping the Human Platelet Lipidome Reveals Cytosolic Phospholipase A2 as a Regulator of Mitochondrial Bioenergetics during Activation.

    PubMed

    Slatter, David A; Aldrovandi, Maceler; O'Connor, Anne; Allen, Stuart M; Brasher, Christopher J; Murphy, Robert C; Mecklemann, Sven; Ravi, Saranya; Darley-Usmar, Victor; O'Donnell, Valerie B

    2016-05-10

    Human platelets acutely increase mitochondrial energy generation following stimulation. Herein, a lipidomic circuit was uncovered whereby the substrates for this are exclusively provided by cPLA2, including multiple fatty acids and oxidized species that support energy generation via β-oxidation. This indicates that acute lipid membrane remodeling is required to support energetic demands during platelet activation. Phospholipase activity is linked to energy metabolism, revealing cPLA2 as a central regulator of both lipidomics and energy flux. Using a lipidomic approach (LipidArrays), we also estimated the total number of lipids in resting, thrombin-activated, and aspirinized platelets. Significant diversity between genetically unrelated individuals and a wealth of species was revealed. Resting platelets demonstrated ∼5,600 unique species, with only ∼50% being putatively identified. Thrombin elevated ∼900 lipids >2-fold with 86% newly appearing and 45% inhibited by aspirin supplementation, indicating COX-1 is required for major activation-dependent lipidomic fluxes. Many lipids were structurally identified. With ∼50% of the lipids being absent from databases, a major opportunity for mining lipids relevant to human health and disease is presented. PMID:27133131

  16. Fibroblast Growth Factor 2 Internal Ribosome Entry Site (Ires) Activity Ex Vivo and in Transgenic Mice Reveals a Stringent Tissue-Specific Regulation

    PubMed Central

    Créancier, Laurent; Morello, Dominique; Mercier, Pascale; Prats, Anne-Catherine

    2000-01-01

    Fibroblast growth factor 2 (FGF-2) is a powerful mitogen involved in proliferation, differentiation, and survival of various cells including neurons. FGF-2 expression is translationally regulated; in particular, the FGF-2 mRNA contains an internal ribosome entry site (IRES) allowing cap-independent translation. Here, we have analyzed FGF-2 IRES tissue specificity ex vivo and in vivo by using a dual luciferase bicistronic vector. This IRES was active in most transiently transfected human and nonhuman cell types, with a higher activity in p53 −/− osteosarcoma and neuroblastoma cell lines. Transgenic mice were generated using bicistronic transgenes with FGF-2 IRES or encephalomyocarditis virus (EMCV) IRES. Measurements of luciferase activity revealed high FGF-2 IRES activity in 11-d-old embryos (E11) but not in the placenta; activity was high in the heart and brain of E16. FGF-2 IRES activity was low in most organs of the adult, but exceptionally high in the brain. Such spatiotemporal variations were not observed with the EMCV IRES. These data, demonstrating the strong tissue specificity of a mammalian IRES in vivo, suggest a pivotal role of translational IRES- dependent activation of FGF-2 expression during embryogenesis and in adult brain. FGF-2 IRES could constitute, thus, a powerful tool for gene transfer in the central nervous system. PMID:10893274

  17. Measurements of the PLT and PDX device activation

    SciTech Connect

    Stavely, J.; Barnes, C.W.; Chrien, R.E.; Strachan, J.D.

    1981-09-01

    Measurements of the activation levels around the PLT and PDX tokamaks have been made using a Ge(Li) gamma spectrometer and a Geiger counter. The activation results from radiation induced in the plasma by 14 MeV neutrons from the d(t,n)..cap alpha.. fusion reaction, 14.7 MeV protons from the d(/sup 3/He,p)..cap alpha.. fusion reaction, 10 ..-->.. 20 MeV hard x-rays from runaway electron induced bremmstrahlung, and 2.5 MeV neutrons from the d(d,n)/sup 3/He fusion reaction. The magnitude of the activation is compared to that predicted for PDX on the basis of one-dimensional activation codes.

  18. Prodigiosin inhibits motility and activates bacterial cell death revealing molecular biomarkers of programmed cell death.

    PubMed

    Darshan, N; Manonmani, H K

    2016-12-01

    The antimicrobial activity of prodigiosin from Serratia nematodiphila darsh1, a bacterial pigment was tested against few food borne bacterial pathogens Bacillus cereus, Staphylococcus aureus, Pseudomonas aeruginosa and Escherichia coli. The mode of action of prodigiosin was studied. Prodigiosin induced bactericidal activity indicating a stereotypical set of biochemical and morphological feature of Programmed cell death (PCD). PCD involves DNA fragmentation, generation of ROS, and expression of a protein with caspase-like substrate specificity in bacterial cells. Prodigiosin was observed to be internalized into bacterial cells and was localized predominantly in the membrane and the nuclear fraction, thus, facilitating intracellular trafficking and then binding of prodigiosin to the bacterial DNA. Corresponding to an increasing concentration of prodigiosin, the level of certain proteases were observed to increase in bacteria studied, thus initiating the onset of PCD. Prodigiosin at a sub-inhibitory concentration inhibits motility of pathogens. Our observations indicated that prodigiosin could be a promising antibacterial agent and could be used in the prevention of bacterial infections. PMID:27460563

  19. Transcriptional activity around bacterial cell death reveals molecular biomarkers for cell viability

    PubMed Central

    Kort, Remco; Keijser, Bart J; Caspers, Martien PM; Schuren, Frank H; Montijn, Roy

    2008-01-01

    Background In bacteriology, the ability to grow in selective media and to form colonies on nutrient agar plates is routinely used as a retrospective criterion for the detection of living bacteria. However, the utilization of indicators for bacterial viability-such as the presence of specific transcripts or membrane integrity-would overcome bias introduced by cultivation and reduces the time span of analysis from initiation to read out. Therefore, we investigated the correlation between transcriptional activity, membrane integrity and cultivation-based viability in the Gram-positive model bacterium Bacillus subtilis. Results We present microbiological, cytological and molecular analyses of the physiological response to lethal heat stress under accurately defined conditions through systematic sampling of bacteria from a single culture exposed to gradually increasing temperatures. We identified a coherent transcriptional program including known heat shock responses as well as the rapid expression of a small number of sporulation and competence genes, the latter only known to be active in the stationary growth phase. Conclusion The observed coordinated gene expression continued even after cell death, in other words after all bacteria permanently lost their ability to reproduce. Transcription of a very limited number of genes correlated with cell viability under the applied killing regime. The transcripts of the expressed genes in living bacteria – but silent in dead bacteria-include those of essential genes encoding chaperones of the protein folding machinery and can serve as molecular biomarkers for bacterial cell viability. PMID:19061518

  20. Covalent Inhibition of Ubc13 Affects Ubiquitin Signaling and Reveals Active Site Elements Important for Targeting

    PubMed Central

    Hodge, Curtis D.; Edwards, Ross A.; Markin, Craig J.; McDonald, Darin; Pulvino, Mary; Huen, Michael S. Y.; Zhao, Jiyong; Spyracopoulos, Leo; Hendzel, Michael J.; Glover, J.N. Mark

    2015-01-01

    Ubc13 is an E2 ubiquitin conjugating enzyme that functions in nuclear DNA damage signaling and cytoplasmic NF-κB signaling. Here we present the structures of complexes of Ubc13 with two inhibitors, NSC697923 and BAY 11-7082, which inhibit DNA damage and NF-κB signaling in human cells. NSC697923 and BAY 11-7082 both inhibit Ubc13 by covalent adduct formation through a Michael addition at the Ubc13 active site cysteine. The resulting adducts of both compounds exploit a binding groove unique to Ubc13. We developed a Ubc13 mutant which resists NSC697923 inhibition and, using this mutant, we show that the inhibition of cellular DNA damage and NF-κB signaling by NSC697923 is largely due to specific Ubc13 inhibition. We propose that unique structural features near the Ubc13 active site could provide a basis for the rational development and design of specific Ubc13 inhibitors. PMID:25909880

  1. Covalent Inhibition of Ubc13 Affects Ubiquitin Signaling and Reveals Active Site Elements Important for Targeting.

    PubMed

    Hodge, Curtis D; Edwards, Ross A; Markin, Craig J; McDonald, Darin; Pulvino, Mary; Huen, Michael S Y; Zhao, Jiyong; Spyracopoulos, Leo; Hendzel, Michael J; Glover, J N Mark

    2015-07-17

    Ubc13 is an E2 ubiquitin conjugating enzyme that functions in nuclear DNA damage signaling and cytoplasmic NF-κB signaling. Here, we present the structures of complexes of Ubc13 with two inhibitors, NSC697923 and BAY 11-7082, which inhibit DNA damage and NF-κB signaling in human cells. NSC697923 and BAY 11-7082 both inhibit Ubc13 by covalent adduct formation through a Michael addition at the Ubc13 active site cysteine. The resulting adducts of both compounds exploit a binding groove unique to Ubc13. We developed a Ubc13 mutant which resists NSC697923 inhibition and, using this mutant, we show that the inhibition of cellular DNA damage and NF-κB signaling by NSC697923 is largely due to specific Ubc13 inhibition. We propose that unique structural features near the Ubc13 active site could provide a basis for the rational development and design of specific Ubc13 inhibitors. PMID:25909880

  2. Activation of TRPM3 by a potent synthetic ligand reveals a role in peptide release

    PubMed Central

    Held, Katharina; Kichko, Tatjana; De Clercq, Katrien; Klaassen, Hugo; Van Bree, Rieta; Vanherck, Jean-Christophe; Marchand, Arnaud; Reeh, Peter W.; Chaltin, Patrick; Voets, Thomas; Vriens, Joris

    2015-01-01

    Transient receptor potential (TRP) cation channel subfamily M member 3 (TRPM3), a member of the TRP channel superfamily, was recently identified as a nociceptor channel in the somatosensory system, where it is involved in the detection of noxious heat; however, owing to the lack of potent and selective agonists, little is known about other potential physiological consequences of the opening of TRPM3. Here we identify and characterize a synthetic TRPM3 activator, CIM0216, whose potency and apparent affinity greatly exceeds that of the canonical TRPM3 agonist, pregnenolone sulfate (PS). In particular, a single application of CIM0216 causes opening of both the central calcium-conducting pore and the alternative cation permeation pathway in a membrane-delimited manner. CIM0216 evoked robust calcium influx in TRPM3-expressing somatosensory neurons, and intradermal injection of the compound induced a TRPM3-dependent nocifensive behavior. Moreover, CIM0216 elicited the release of the peptides calcitonin gene-related peptide (CGRP) from sensory nerve terminals and insulin from isolated pancreatic islets in a TRPM3-dependent manner. These experiments identify CIM0216 as a powerful tool for use in investigating the physiological roles of TRPM3, and indicate that TRPM3 activation in sensory nerve endings can contribute to neurogenic inflammation. PMID:25733887

  3. Characterization of 10-hydroxygeraniol dehydrogenase from Catharanthus roseus reveals cascaded enzymatic activity in iridoid biosynthesis.

    PubMed

    Krithika, Ramakrishnan; Srivastava, Prabhakar Lal; Rani, Bajaj; Kolet, Swati P; Chopade, Manojkumar; Soniya, Mantri; Thulasiram, Hirekodathakallu V

    2015-01-01

    Catharanthus roseus [L.] is a major source of the monoterpene indole alkaloids (MIAs), which are of significant interest due to their therapeutic value. These molecules are formed through an intermediate, cis-trans-nepetalactol, a cyclized product of 10-oxogeranial. One of the key enzymes involved in the biosynthesis of MIAs is an NAD(P)(+) dependent oxidoreductase system, 10-hydroxygeraniol dehydrogenase (Cr10HGO), which catalyses the formation of 10-oxogeranial from 10-hydroxygeraniol via 10-oxogeraniol or 10-hydroxygeranial. This work describes the cloning and functional characterization of Cr10HGO from C. roseus and its role in the iridoid biosynthesis. Substrate specificity studies indicated that, Cr10HGO has good activity on substrates such as 10-hydroxygeraniol, 10-oxogeraniol or 10-hydroxygeranial over monohydroxy linear terpene derivatives. Further it was observed that incubation of 10-hydroxygeraniol with Cr10HGO and iridoid synthase (CrIDS) in the presence of NADP(+) yielded a major metabolite, which was characterized as (1R, 4aS, 7S, 7aR)-nepetalactol by comparing its retention time, mass fragmentation pattern, and co-injection studies with that of the synthesized compound. These results indicate that there is concerted activity of Cr10HGO with iridoid synthase in the formation of (1R, 4aS, 7S, 7aR)-nepetalactol, an important intermediate in iridoid biosynthesis. PMID:25651761

  4. Cortical Effects on Ipsilateral Hindlimb Muscles Revealed with Stimulus-Triggered Averaging of EMG Activity.

    PubMed

    Messamore, William G; Van Acker, Gustaf M; Hudson, Heather M; Zhang, Hongyu Y; Kovac, Anthony; Nazzaro, Jules; Cheney, Paul D

    2016-07-01

    While a large body of evidence supports the view that ipsilateral motor cortex may make an important contribution to normal movements and to recovery of function following cortical injury (Chollet et al. 1991; Fisher 1992; Caramia et al. 2000; Feydy et al. 2002), relatively little is known about the properties of output from motor cortex to ipsilateral muscles. Our aim in this study was to characterize the organization of output effects on hindlimb muscles from ipsilateral motor cortex using stimulus-triggered averaging of EMG activity. Stimulus-triggered averages of EMG activity were computed from microstimuli applied at 60-120 μA to sites in both contralateral and ipsilateral M1 of macaque monkeys during the performance of a hindlimb push-pull task. Although the poststimulus effects (PStEs) from ipsilateral M1 were fewer in number and substantially weaker, clear and consistent effects were obtained at an intensity of 120 μA. The mean onset latency of ipsilateral poststimulus facilitation was longer than contralateral effects by an average of 0.7 ms. However, the shortest latency effects in ipsilateral muscles were as short as the shortest latency effects in the corresponding contralateral muscles suggesting a minimal synaptic linkage that is equally direct in both cases. PMID:26088970

  5. Deep Sequencing of Subseafloor Eukaryotic rRNA Reveals Active Fungi across Marine Subsurface Provinces

    PubMed Central

    Orsi, William; Biddle, Jennifer F.; Edgcomb, Virginia

    2013-01-01

    The deep marine subsurface is a vast habitat for microbial life where cells may live on geologic timescales. Because DNA in sediments may be preserved on long timescales, ribosomal RNA (rRNA) is suggested to be a proxy for the active fraction of a microbial community in the subsurface. During an investigation of eukaryotic 18S rRNA by amplicon pyrosequencing, unique profiles of Fungi were found across a range of marine subsurface provinces including ridge flanks, continental margins, and abyssal plains. Subseafloor fungal populations exhibit statistically significant correlations with total organic carbon (TOC), nitrate, sulfide, and dissolved inorganic carbon (DIC). These correlations are supported by terminal restriction length polymorphism (TRFLP) analyses of fungal rRNA. Geochemical correlations with fungal pyrosequencing and TRFLP data from this geographically broad sample set suggests environmental selection of active Fungi in the marine subsurface. Within the same dataset, ancient rRNA signatures were recovered from plants and diatoms in marine sediments ranging from 0.03 to 2.7 million years old, suggesting that rRNA from some eukaryotic taxa may be much more stable than previously considered in the marine subsurface. PMID:23418556

  6. Proteomic analysis of tylosin-resistant Mycoplasma gallisepticum reveals enzymatic activities associated with resistance.

    PubMed

    Xia, Xi; Wu, Congming; Cui, Yaowen; Kang, Mengjiao; Li, Xiaowei; Ding, Shuangyang; Shen, Jianzhong

    2015-01-01

    Mycoplasma gallisepticum is a significant pathogenic bacterium that infects poultry, causing chronic respiratory disease and sinusitis in chickens and turkeys, respectively. M. gallisepticum infection poses a substantial economic threat to the poultry industry, and this threat is made worse by the emergence of antibiotic-resistant strains. The mechanisms of resistance are often difficult to determine; for example, little is known about antibiotic resistance of M. gallisepticum at the proteome level. In this study, we performed comparative proteomic analyses of an antibiotic (tylosin)-resistant M. gallisepticum mutant and a susceptible parent strain using a combination of two-dimensional differential gel electrophoresis and nano-liquid chromatography-quadrupole-time of flight mass spectrometry. Thirteen proteins were identified as differentially expressed in the resistant strain compared to the susceptible strain. Most of these proteins were related to catalytic activity, including catalysis that promotes the formylation of initiator tRNA and energy production. Elongation factors Tu and G were over-expressed in the resistant strains, and this could promote the binding of tRNA to ribosomes and catalyze ribosomal translocation, the coordinated movement of tRNA, and conformational changes in the ribosome. Taken together, our results indicate that M. gallisepticum develops resistance to tylosin by regulating associated enzymatic activities. PMID:26584633

  7. Active sites of two orthologous cytochromes P450 2E1: Differences revealed by spectroscopic methods

    SciTech Connect

    Anzenbacherova, Eva; Hudecek, Jiri; Murgida, Daniel; Hildebrandt, Peter; Marchal, Stephane; Lange, Reinhard; Anzenbacher, Pavel . E-mail: anzen@tunw.upol.cz

    2005-12-09

    Cytochromes P450 2E1 of human and minipig origin were examined by absorption spectroscopy under high hydrostatic pressure and by resonance Raman spectroscopy. Human enzyme tends to denature to the P420 form more easily than the minipig form; moreover, the apparent compressibility of the heme active site (as judged from a redshift of the absorption maximum with pressure) is greater than that of the minipig counterpart. Relative compactness of the minipig enzyme is also seen in the Raman spectra, where the presence of planar heme conformation was inferred from band positions characteristic of the low-spin heme with high degree of symmetry. In this respect, the CYP2E1 seems to be another example of P450 conformational heterogeneity as shown, e.g., by Davydov et al. for CYP3A4 [Biochem. Biophys. Res. Commun. 312 (2003) 121-130]. The results indicate that the flexibility of the CYP active site is likely one of its basic structural characteristics.

  8. Characterization of 10-Hydroxygeraniol Dehydrogenase from Catharanthus roseus Reveals Cascaded Enzymatic Activity in Iridoid Biosynthesis

    PubMed Central

    Krithika, Ramakrishnan; Srivastava, Prabhakar Lal; Rani, Bajaj; Kolet, Swati P.; Chopade, Manojkumar; Soniya, Mantri; Thulasiram, Hirekodathakallu V.

    2015-01-01

    Catharanthus roseus [L.] is a major source of the monoterpene indole alkaloids (MIAs), which are of significant interest due to their therapeutic value. These molecules are formed through an intermediate, cis-trans-nepetalactol, a cyclized product of 10-oxogeranial. One of the key enzymes involved in the biosynthesis of MIAs is an NAD(P)+ dependent oxidoreductase system, 10-hydroxygeraniol dehydrogenase (Cr10HGO), which catalyses the formation of 10-oxogeranial from 10-hydroxygeraniol via 10-oxogeraniol or 10-hydroxygeranial. This work describes the cloning and functional characterization of Cr10HGO from C. roseus and its role in the iridoid biosynthesis. Substrate specificity studies indicated that, Cr10HGO has good activity on substrates such as 10-hydroxygeraniol, 10-oxogeraniol or 10-hydroxygeranial over monohydroxy linear terpene derivatives. Further it was observed that incubation of 10-hydroxygeraniol with Cr10HGO and iridoid synthase (CrIDS) in the presence of NADP+ yielded a major metabolite, which was characterized as (1R, 4aS, 7S, 7aR)-nepetalactol by comparing its retention time, mass fragmentation pattern, and co-injection studies with that of the synthesized compound. These results indicate that there is concerted activity of Cr10HGO with iridoid synthase in the formation of (1R, 4aS, 7S, 7aR)-nepetalactol, an important intermediate in iridoid biosynthesis. PMID:25651761

  9. Activity-dependent silencing reveals functionally distinct itch-generating sensory neurons

    PubMed Central

    Roberson, David P.; Gudes, Sagi; Sprague, Jared M.; Patoski, Haley A. W.; Robson, Victoria K.; Blasl, Felix; Duan, Bo; Oh, Seog Bae; Bean, Bruce P.; Ma, Qiufu

    2013-01-01

    The peripheral terminals of primary sensory neurons detect histamine and non-histamine itch-provoking ligands through molecularly distinct transduction mechanisms. It remains unclear, however, whether these distinct pruritogens activate the same or different afferent fibers. We utilized a strategy of reversibly silencing specific subsets of murine pruritogen-sensitive sensory axons by targeted delivery of a charged sodium-channel blocker and found that functional blockade of histamine itch did not affect the itch evoked by chloroquine or SLIGRL-NH2, and vice versa. Notably, blocking itch-generating fibers did not reduce pain-associated behavior. However, silencing TRPV1+ or TRPA1+ neurons allowed AITC or capsaicin respectively to evoke itch, implying that certain peripheral afferents may normally indirectly inhibit algogens from eliciting itch. These findings support the presence of functionally distinct sets of itch-generating neurons and suggest that targeted silencing of activated sensory fibers may represent a clinically useful anti-pruritic therapeutic approach for histaminergic and non-histaminergic pruritus. PMID:23685721

  10. Proteomic analysis of tylosin-resistant Mycoplasma gallisepticum reveals enzymatic activities associated with resistance

    PubMed Central

    Xia, Xi; Wu, Congming; Cui, Yaowen; Kang, Mengjiao; Li, Xiaowei; Ding, Shuangyang; Shen, Jianzhong

    2015-01-01

    Mycoplasma gallisepticum is a significant pathogenic bacterium that infects poultry, causing chronic respiratory disease and sinusitis in chickens and turkeys, respectively. M. gallisepticum infection poses a substantial economic threat to the poultry industry, and this threat is made worse by the emergence of antibiotic-resistant strains. The mechanisms of resistance are often difficult to determine; for example, little is known about antibiotic resistance of M. gallisepticum at the proteome level. In this study, we performed comparative proteomic analyses of an antibiotic (tylosin)-resistant M. gallisepticum mutant and a susceptible parent strain using a combination of two-dimensional differential gel electrophoresis and nano-liquid chromatography-quadrupole-time of flight mass spectrometry. Thirteen proteins were identified as differentially expressed in the resistant strain compared to the susceptible strain. Most of these proteins were related to catalytic activity, including catalysis that promotes the formylation of initiator tRNA and energy production. Elongation factors Tu and G were over-expressed in the resistant strains, and this could promote the binding of tRNA to ribosomes and catalyze ribosomal translocation, the coordinated movement of tRNA, and conformational changes in the ribosome. Taken together, our results indicate that M. gallisepticum develops resistance to tylosin by regulating associated enzymatic activities. PMID:26584633

  11. Nuclear Fractionation Reveals Thousands of Chromatin-Tethered Noncoding RNAs Adjacent to Active Genes.

    PubMed

    Werner, Michael S; Ruthenburg, Alexander J

    2015-08-18

    A number of long noncoding RNAs (lncRNAs) have been reported to regulate transcription via recruitment of chromatin modifiers or bridging distal enhancer elements to gene promoters. However, the generality of these modes of regulation and the mechanisms of chromatin attachment for thousands of unstudied human lncRNAs remain unclear. To address these questions, we performed stringent nuclear fractionation coupled to RNA sequencing. We provide genome-wide identification of human chromatin-associated lncRNAs and demonstrate tethering of RNA to chromatin by RNAPII is a pervasive mechanism of attachment. We also uncovered thousands of chromatin-enriched RNAs (cheRNAs) that share molecular properties with known lncRNAs. Although distinct from eRNAs derived from active prototypical enhancers, the production of cheRNAs is strongly correlated with the expression of neighboring protein-coding genes. This work provides an updated framework for nuclear RNA organization that includes a large chromatin-associated transcript population correlated with active genes and may prove useful in de novo enhancer annotation. PMID:26257179

  12. Asymmetric mutations in the tetrameric R67 dihydrofolate reductase reveal high tolerance to active-site substitutions

    PubMed Central

    Ebert, Maximilian C C J C; Morley, Krista L; Volpato, Jordan P; Schmitzer, Andreea R; Pelletier, Joelle N

    2015-01-01

    Type II R67 dihydrofolate reductase (DHFR) is a bacterial plasmid-encoded enzyme that is intrinsically resistant to the widely-administered antibiotic trimethoprim. R67 DHFR is genetically and structurally unrelated to E. coli chromosomal DHFR and has an unusual architecture, in that four identical protomers form a single symmetrical active site tunnel that allows only one substrate binding/catalytic event at any given time. As a result, substitution of an active-site residue has as many as four distinct consequences on catalysis, constituting an atypical model of enzyme evolution. Although we previously demonstrated that no single residue of the native active site is indispensable for function, library selection here revealed a strong bias toward maintenance of two native protomers per mutated tetramer. A variety of such “half-native” tetramers were shown to procure native-like catalytic activity, with similar KM values but kcat values 5- to 33-fold lower, illustrating a high tolerance for active-site substitutions. The selected variants showed a reduced thermal stability (Tm ∼12°C lower), which appears to result from looser association of the protomers, but generally showed a marked increase in resilience to heat denaturation, recovering activity to a significantly greater extent than the variant with no active-site substitutions. Our results suggest that the presence of two native protomers in the R67 DHFR tetramer is sufficient to provide native-like catalytic rate and thus ensure cellular proliferation. PMID:25401264

  13. Thermodynamic Activity Measurements with Knudsen Cell Mass Spectrometry

    NASA Technical Reports Server (NTRS)

    Copland, Evan H.; Jacobson, Nathan S.

    2001-01-01

    Coupling the Knudsen effusion method with mass spectrometry has proven to be one of the most useful experimental techniques for studying the equilibrium between condensed phases and complex vapors. The Knudsen effusion method involves placing a condensed sample in a Knudsen cell, a small "enclosure", that is uniformly heated and held until equilibrium is attained between the condensed and vapor phases. The vapor is continuously sampled by effusion through a small orifice in the cell. A molecular beam is formed from the effusing vapor and directed into a mass spectrometer for identification and pressure measurement of the species in the vapor phase. Knudsen cell mass spectrometry (KCMS) has been used for nearly fifty years now and continues to be a leading technique for obtaining thermodynamic data. Indeed, much of the well-established vapor specie data in the JANAF tables has been obtained from this technique. This is due to the extreme versatility of the technique. All classes of materials can be studied and all constituents of the vapor phase can be measured over a wide range of pressures (approximately 10(exp -4) to 10(exp -11) bar) and temperatures (500-2800 K). The ability to selectively measure different vapor species makes KCMS a very powerful tool for the measurement of component activities in metallic and ceramic solutions. Today several groups are applying KCMS to measure thermodynamic functions in multicomponent metallic and ceramic systems. Thermodynamic functions, especially component activities, are extremely important in the development of CALPHAD (Calculation of Phase Diagrams) type thermodynamic descriptions. These descriptions, in turn, are useful for modeling materials processing and predicting reactions such as oxide formation and fiber/matrix interactions. The leading experimental methods for measuring activities are the Galvanic cell or electro-motive force (EMF) technique and the KCMS technique. Each has specific advantages, depending on

  14. Measuring In Vitro ATPase Activity for Enzymatic Characterization.

    PubMed

    Rule, Chelsea S; Patrick, Marcella; Sandkvist, Maria

    2016-01-01

    Adenosine triphosphate-hydrolyzing enzymes, or ATPases, play a critical role in a diverse array of cellular functions. These dynamic proteins can generate energy for mechanical work, such as protein trafficking and degradation, solute transport, and cellular movements. The protocol described here is a basic assay for measuring the in vitro activity of purified ATPases for functional characterization. Proteins hydrolyze ATP in a reaction that results in inorganic phosphate release, and the amount of phosphate liberated is then quantitated using a colorimetric assay. This highly adaptable protocol can be adjusted to measure ATPase activity in kinetic or endpoint assays. A representative protocol is provided here based on the activity and requirements of EpsE, the AAA+ ATPase involved in Type II Secretion in the bacterium Vibrio cholerae. The amount of purified protein needed to measure activity, length of the assay and the timing and number of sampling intervals, buffer and salt composition, temperature, co-factors, stimulants (if any), etc. may vary from those described here, and thus some optimization may be necessary. This protocol provides a basic framework for characterizing ATPases and can be performed quickly and easily adjusted as necessary. PMID:27584824

  15. Measuring Cysteine Cathepsin Activity to Detect Lysosomal Membrane Permeabilization.

    PubMed

    Repnik, Urška; Česen, Maruša Hafner; Turk, Boris

    2016-01-01

    During lysosomal membrane permeabilization (LMP), lysosomal lumenal contents can be released into the cytosol. Small molecules are more likely to be released, and cysteine cathepsins, with mature forms possessing a mass of 25-30 kDa, are among the smallest lumenal lysosomal enzymes. In addition, specific substrates for cysteine cathepsins are available to investigators, and therefore the measurement of the cathepsin activity as a hallmark of LMP works well. Here, we present a protocol for measuring the activity of these enzymes after selective plasma membrane permeabilization with a low concentration of digitonin and after total cell membrane lysis with a high concentration of digitonin. A fluorogenic substrate can be added either directly to the well with lysed cells to show LMP or to the cell-free extract to show that the lysosomal membrane has been sufficiently destabilized to allow the translocation of lysosomal enzymes. Although the content of lysosomal cysteine cathepsins differs between cell lines, this method has general applicability, is sensitive, and has high throughput. The presented protocol shows how to measure cysteine cathepsin activity in the presence of lysed cells and also in cell-free extracts. Depending on the aim of the study, one or both types of measurements can be performed. PMID:27140915

  16. Tectonic activity revealed by morphostructural analysis: Development of the Sierra de la Candelaria range, northwestern Argentina

    NASA Astrophysics Data System (ADS)

    Barcelona, H.; Peri, G.; Tobal, J.; Sagripanti, L.; Favetto, A.

    2014-12-01

    The tectonically active broken foreland of NW Argentina is a recent analog of the eastern margin of the Puna plateau during Mio-Pliocene times and likely of other broken forelands worldwide. In order to evaluate active tectonism in the broken foreland of the NW Argentine Andes, we examined the complex geomorphology in the vicinity of the basement-cored Sierra de la Candelaria range at ˜26°S and deciphered multiple episodes of crustal deformation spanning the Pliocene to the Quaternary. Digital elevation models, satellite images and geological data within a GIS environment allowed us to analyze the terrain, drainage networks, river dynamics and structure, as well as to obtain detailed geomorphological mapping, active tectonic indices, longitudinal river profiles and structural sections. Three morphostructural segments were defined based on the structural features, the differential vertical dissection pattern over the basement, the faulted Pliocene to recent deposits, the stepwise propagation of anticlines and the distortion over the fluvial system. By combining the several lines of evidence, we concluded that the Sierra de la Candelaria range was subjected to a multi-stage development. The first stage uplifted the central segment concomitant with the formation of the surrounding ranges and with the main partition phase of the foreland. After a significant time lapse, the mountain range was subjected to southward thick-skinned growth and northward growth via stepwise thin-skinned deformation and exerted control over the dynamics of the Río Rosario. Taking into account the surrounding basins and ranges of the Sierra de la Candelaria, the southern Santa Bárbara System is characterized by partially isolated intramontane basins (Choromoro and Rosario) limited by shielded ranges that caused moisture block and shows continuous deformation. These features were related to early stages of a broken foreland evolution model and modern analogs were found at the northern

  17. Systematically Altering Bacterial SOS Activity under Stress Reveals Therapeutic Strategies for Potentiating Antibiotics.

    PubMed

    Mo, Charlie Y; Manning, Sara A; Roggiani, Manuela; Culyba, Matthew J; Samuels, Amanda N; Sniegowski, Paul D; Goulian, Mark; Kohli, Rahul M

    2016-01-01

    The bacterial SOS response is a DNA damage repair network that is strongly implicated in both survival and acquired drug resistance under antimicrobial stress. The two SOS regulators, LexA and RecA, have therefore emerged as potential targets for adjuvant therapies aimed at combating resistance, although many open questions remain. For example, it is not well understood whether SOS hyperactivation is a viable therapeutic approach or whether LexA or RecA is a better target. Furthermore, it is important to determine which antimicrobials could serve as the best treatment partners with SOS-targeting adjuvants. Here we derived Escherichia coli strains that have mutations in either lexA or recA genes in order to cover the full spectrum of possible SOS activity levels. We then systematically analyzed a wide range of antimicrobials by comparing the mean inhibitory concentrations (MICs) and induced mutation rates for each drug-strain combination. We first show that significant changes in MICs are largely confined to DNA-damaging antibiotics, with strains containing a constitutively repressed SOS response impacted to a greater extent than hyperactivated strains. Second, antibiotic-induced mutation rates were suppressed when SOS activity was reduced, and this trend was observed across a wider spectrum of antibiotics. Finally, perturbing either LexA or RecA proved to be equally viable strategies for targeting the SOS response. Our work provides support for multiple adjuvant strategies, while also suggesting that the combination of an SOS inhibitor with a DNA-damaging antibiotic could offer the best potential for lowering MICs and decreasing acquired drug resistance. IMPORTANCE Our antibiotic arsenal is becoming depleted, in part, because bacteria have the ability to rapidly adapt and acquire resistance to our best agents. The SOS pathway, a widely conserved DNA damage stress response in bacteria, is activated by many antibiotics and has been shown to play central role in

  18. Systematically Altering Bacterial SOS Activity under Stress Reveals Therapeutic Strategies for Potentiating Antibiotics

    PubMed Central

    Mo, Charlie Y.; Manning, Sara A.; Roggiani, Manuela; Culyba, Matthew J.; Samuels, Amanda N.; Sniegowski, Paul D.; Goulian, Mark

    2016-01-01

    ABSTRACT The bacterial SOS response is a DNA damage repair network that is strongly implicated in both survival and acquired drug resistance under antimicrobial stress. The two SOS regulators, LexA and RecA, have therefore emerged as potential targets for adjuvant therapies aimed at combating resistance, although many open questions remain. For example, it is not well understood whether SOS hyperactivation is a viable therapeutic approach or whether LexA or RecA is a better target. Furthermore, it is important to determine which antimicrobials could serve as the best treatment partners with SOS-targeting adjuvants. Here we derived Escherichia coli strains that have mutations in either lexA or recA genes in order to cover the full spectrum of possible SOS activity levels. We then systematically analyzed a wide range of antimicrobials by comparing the mean inhibitory concentrations (MICs) and induced mutation rates for each drug-strain combination. We first show that significant changes in MICs are largely confined to DNA-damaging antibiotics, with strains containing a constitutively repressed SOS response impacted to a greater extent than hyperactivated strains. Second, antibiotic-induced mutation rates were suppressed when SOS activity was reduced, and this trend was observed across a wider spectrum of antibiotics. Finally, perturbing either LexA or RecA proved to be equally viable strategies for targeting the SOS response. Our work provides support for multiple adjuvant strategies, while also suggesting that the combination of an SOS inhibitor with a DNA-damaging antibiotic could offer the best potential for lowering MICs and decreasing acquired drug resistance. IMPORTANCE Our antibiotic arsenal is becoming depleted, in part, because bacteria have the ability to rapidly adapt and acquire resistance to our best agents. The SOS pathway, a widely conserved DNA damage stress response in bacteria, is activated by many antibiotics and has been shown to play central role

  19. Analysis of Geminivirus AL2 and L2 Proteins Reveals a Novel AL2 Silencing Suppressor Activity

    PubMed Central

    Jackel, Jamie N.; Buchmann, R. Cody; Singhal, Udit

    2014-01-01

    ABSTRACT Both posttranscriptional and transcriptional gene silencing (PTGS and TGS, respectively) participate in defense against the DNA-containing geminiviruses. As a countermeasure, members of the genus Begomovirus (e.g., Cabbage leaf curl virus) encode an AL2 protein that is both a transcriptional activator and a silencing suppressor. The related L2 protein of Beet curly top virus (genus Curtovirus) lacks transcription activation activity. Previous studies showed that both AL2 and L2 suppress silencing by a mechanism that correlates with adenosine kinase (ADK) inhibition, while AL2 in addition activates transcription of cellular genes that negatively regulate silencing pathways. The goal of this study was to clarify the general means by which these viral proteins inhibit various aspects of silencing. We confirmed that AL2 inhibits systemic silencing spread by a mechanism that requires transcription activation activity. Surprisingly, we also found that reversal of PTGS and TGS by ADK inactivation depended on whether experiments were conducted in vegetative or reproductive Nicotiana benthamiana plants (i.e., before or after the vegetative-to-reproductive transition). While AL2 was able to reverse silencing in both vegetative and reproductive plants, L2 and ADK inhibition were effective only in vegetative plants. This suggests that silencing maintenance mechanisms can change during development or in response to stress. Remarkably, we also observed that AL2 lacking its transcription activation domain could reverse TGS in reproductive plants, revealing a third, previously unsuspected AL2 suppression mechanism that depends on neither ADK inactivation nor transcription activation. IMPORTANCE RNA silencing in plants is a multivalent antiviral defense, and viruses respond by elaborating multiple and sometimes multifunctional proteins that inhibit various aspects of silencing. The studies described here add an additional layer of complexity to this interplay. By examining

  20. Structure of protease-cleaved Escherichia coli α-2-macroglobulin reveals a putative mechanism of conformational activation for protease entrapment

    PubMed Central

    Fyfe, Cameron D.; Grinter, Rhys; Josts, Inokentijs; Mosbahi, Khedidja; Roszak, Aleksander W.; Cogdell, Richard J.; Wall, Daniel M.; Burchmore, Richard J. S.; Byron, Olwyn; Walker, Daniel

    2015-01-01

    Bacterial α-2-macroglobulins have been suggested to function in defence as broad-spectrum inhibitors of host proteases that breach the outer membrane. Here, the X-ray structure of protease-cleaved Escherichia coli α-2-macroglobulin is described, which reveals a putative mechanism of activation and conformational change essential for protease inhibition. In this competitive mechanism, protease cleavage of the bait-region domain results in the untethering of an intrinsically disordered region of this domain which disrupts native interdomain interactions that maintain E. coli α-2-macroglobulin in the inactivated form. The resulting global conformational change results in entrapment of the protease and activation of the thioester bond that covalently links to the attacking protease. Owing to the similarity in structure and domain architecture of Escherichia coli α-2-macroglobulin and human α-2-macro­globulin, this protease-activation mechanism is likely to operate across the diverse members of this group. PMID:26143919

  1. In vivo activation of azipropofol prolongs anesthesia and reveals synaptic targets.

    PubMed

    Weiser, Brian P; Kelz, Max B; Eckenhoff, Roderic G

    2013-01-11

    General anesthetic photolabels have been instrumental in discovering and confirming protein binding partners and binding sites of these promiscuous ligands. We report the in vivo photoactivation of meta-azipropofol, a potent analog of propofol, in Xenopus laevis tadpoles. Covalent adduction of meta-azipropofol in vivo prolongs the primary pharmacologic effect of general anesthetics in a behavioral phenotype we termed "optoanesthesia." Coupling this behavior with a tritiated probe, we performed unbiased, time-resolved gel proteomics to identify neuronal targets of meta-azipropofol in vivo. We have identified synaptic binding partners, such as synaptosomal-associated protein 25, as well as voltage-dependent anion channels as potential facilitators of the general anesthetic state. Pairing behavioral phenotypes elicited by the activation of efficacious photolabels in vivo with time-resolved proteomics provides a novel approach to investigate molecular mechanisms of general anesthetics. PMID:23184948

  2. Preparatory EMG activity reveals a rapid adaptation pattern in humans performing landing movements in blindfolded condition.

    PubMed

    Magalhães, Fernando Henrique; Goroso, Daniel Gustavo

    2009-10-01

    The main questions addressed in this work were whether and how adaptation to suppression of visual information occurs in a free-fall paradigm, and the extent to which vision availability influences the control of landing movements. The prelanding modulation of EMG timing and amplitude of four lower-limb muscles was investigated. Participants performed six consecutive drop-landings from four different heights in two experimental conditions: with and without vision. Experimental design precluded participants from estimating the height of the drop. Since cues provided by proprioceptive and vestibular information acquired during the first trials were processed, the nervous system rapidly adapted to the lack of visual information, and hence produced a motor output (i.e., prelanding EMG modulation) similar to that observed when performing the activity with vision available. PMID:20038004

  3. Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site.

    PubMed

    Sunden, Fanny; Peck, Ariana; Salzman, Julia; Ressl, Susanne; Herschlag, Daniel

    2015-01-01

    Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called 'catalytic residues' are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modes of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes. PMID:25902402

  4. Quantifying activity: a new assay reveals T-cell signalling in tiny skin biopsy samples.

    PubMed

    Dornmair, Klaus

    2014-06-01

    Tissue-invasive T cells are observed in many inflammatory dermatological diseases, but in most cases, it is not known how they were attracted, what they might recognize, and to which extent they are activated. Answering these questions is surely essential for understanding pathogeneses of the diseases. In a recent issue of Experimental Dermatology, Smith et al. showed that early signalling events in skin-resident T cells may be investigated by multiplex immunoprecipitation flow cytometry, even if only few T cells are available from skin biopsy samples. This new technology will most likely contribute to elucidating the role of skin-invasive T cells and to understanding the pathology of dermatological diseases. PMID:24665970

  5. Unmasking the ancestral activity of integron integrases reveals a smooth evolutionary transition during functional innovation

    PubMed Central

    Escudero, Jose Antonio; Loot, Celine; Parissi, Vincent; Nivina, Aleksandra; Bouchier, Christiane; Mazel, Didier

    2016-01-01

    Tyrosine (Y)-recombinases have evolved to deliver mechanistically different reactions on a variety of substrates, but these evolutionary transitions are poorly understood. Among them, integron integrases are hybrid systems recombining single- and double-stranded DNA partners. These reactions are asymmetric and need a replicative resolution pathway, an exception to the canonical second strand exchange model of Y-recombinases. Integron integrases possess a specific domain for this specialized pathway. Here we show that despite this, integrases are still capable of efficiently operating the ancestral second strand exchange in symmetrical reactions between double-stranded substrates. During these reactions, both strands are reactive and Holliday junction resolution can follow either pathway. A novel deep-sequencing approach allows mapping of the crossover point for the second strand exchange. The persistence of the ancestral activity in integrases illustrates their robustness and shows that innovation towards new recombination substrates and resolution pathways was a smooth evolutionary process. PMID:26961432

  6. In Vivo Activation of Azipropofol Prolongs Anesthesia and Reveals Synaptic Targets*

    PubMed Central

    Weiser, Brian P.; Kelz, Max B.; Eckenhoff, Roderic G.

    2013-01-01

    General anesthetic photolabels have been instrumental in discovering and confirming protein binding partners and binding sites of these promiscuous ligands. We report the in vivo photoactivation of meta-azipropofol, a potent analog of propofol, in Xenopus laevis tadpoles. Covalent adduction of meta-azipropofol in vivo prolongs the primary pharmacologic effect of general anesthetics in a behavioral phenotype we termed “optoanesthesia.” Coupling this behavior with a tritiated probe, we performed unbiased, time-resolved gel proteomics to identify neuronal targets of meta-azipropofol in vivo. We have identified synaptic binding partners, such as synaptosomal-associated protein 25, as well as voltage-dependent anion channels as potential facilitators of the general anesthetic state. Pairing behavioral phenotypes elicited by the activation of efficacious photolabels in vivo with time-resolved proteomics provides a novel approach to investigate molecular mechanisms of general anesthetics. PMID:23184948

  7. Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses

    PubMed Central

    Schostag, Morten; Stibal, Marek; Jacobsen, Carsten S.; Bælum, Jacob; Taş, Neslihan; Elberling, Bo; Jansson, Janet K.; Semenchuk, Philipp; Priemé, Anders

    2015-01-01

    The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78°N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable organic matter on the bacterial communities. The copy number of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below −10°C. Multivariate statistical analysis of the bacterial diversity data (DNA and cDNA libraries) revealed a season-based clustering of the samples, and, e.g., the relative abundance of potentially active Cyanobacteria peaked in June and Alphaproteobacteria increased over the summer and then declined from October to November. The structure of the bulk (DNA-based) community was significantly correlated with pH and dissolved organic carbon, while the potentially active (RNA-based) community structure was not significantly correlated with any of the measured soil parameters. A large fraction of the 16S rRNA transcripts was assigned to nitrogen-fixing bacteria (up to 24% in June) and phototrophic organisms (up to 48% in June) illustrating the potential importance of nitrogen fixation in otherwise nitrogen poor Arctic ecosystems and of phototrophic bacterial activity on the soil surface. PMID:25983731

  8. Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses

    SciTech Connect

    Schostag, Morten; Stibal, Marek; Jacobsen, Carsten S.; Bælum, Jacob; Taş, Neslihan; Elberling, Bo; Jansson, Janet K.; Semenchuk, Philipp; Priemé, Anders

    2015-04-30

    The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78°N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable organic matter on the bacterial communities. The copy number of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below -10°C. Multivariate statistical analysis of the bacterial diversity data (DNA and cDNA libraries) revealed a season-based clustering of the samples, and, e.g., the relative abundance of potentially active Cyanobacteria peaked in June and Alphaproteobacteria increased over the summer and then declined from October to November. The structure of the bulk (DNA-based) community was significantly correlated with pH and dissolved organic carbon, while the potentially active (RNA-based) community structure was not significantly correlated with any of the measured soil parameters. A large fraction of the 16S rRNA transcripts was assigned to nitrogen-fixing bacteria (up to 24% in June) and phototrophic organisms (up to 48% in June) illustrating the potential importance of nitrogen fixation in otherwise nitrogen poor Arctic ecosystems and of phototrophic bacterial activity on the soil surface.

  9. Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses

    DOE PAGESBeta

    Schostag, Morten; Stibal, Marek; Jacobsen, Carsten S.; Bælum, Jacob; Taş, Neslihan; Elberling, Bo; Jansson, Janet K.; Semenchuk, Philipp; Priemé, Anders

    2015-04-30

    The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78°N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable organic matter on the bacterial communities. The copy numbermore » of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below -10°C. Multivariate statistical analysis of the bacterial diversity data (DNA and cDNA libraries) revealed a season-based clustering of the samples, and, e.g., the relative abundance of potentially active Cyanobacteria peaked in June and Alphaproteobacteria increased over the summer and then declined from October to November. The structure of the bulk (DNA-based) community was significantly correlated with pH and dissolved organic carbon, while the potentially active (RNA-based) community structure was not significantly correlated with any of the measured soil parameters. A large fraction of the 16S rRNA transcripts was assigned to nitrogen-fixing bacteria (up to 24% in June) and phototrophic organisms (up to 48% in June) illustrating the potential importance of nitrogen fixation in otherwise nitrogen poor Arctic ecosystems and of phototrophic bacterial activity on the soil surface.« less

  10. Substrate-bound structures of benzylsuccinate synthase reveal how toluene is activated in anaerobic hydrocarbon degradation.

    PubMed

    Funk, Michael A; Marsh, E Neil G; Drennan, Catherine L

    2015-09-11

    Various bacteria perform anaerobic degradation of small hydrocarbons as a source of energy and cellular carbon. To activate non-reactive hydrocarbons such as toluene, enzymes conjugate these molecules to fumarate in a radical-catalyzed, C-C bond-forming reaction. We have determined x-ray crystal structures of the glycyl radical enzyme that catalyzes the addition of toluene to fumarate, benzylsuccinate synthase (BSS), in two oligomeric states with fumarate alone or with both substrates. We find that fumarate is secured at the bottom of a long active site cavity with toluene bound directly above it. The two substrates adopt orientations that appear ideal for radical-mediated C-C bond formation; the methyl group of toluene is positioned between fumarate and a cysteine that forms a thiyl radical during catalysis, which is in turn adjacent to the glycine that serves as a radical storage residue. Toluene is held in place by fumarate on one face and tight packing by hydrophobic residues on the other face and sides. These hydrophobic residues appear to become ordered, thus encapsulating toluene, only in the presence of BSSβ, a small protein subunit that forms a tight complex with BSSα, the catalytic subunit. Enzymes related to BSS are able to metabolize a wide range of hydrocarbons through attachment to fumarate. Using our structures as a guide, we have constructed homology models of several of these "X-succinate synthases" and determined conservation patterns that will be useful in understanding the basis for catalysis and specificity in this family of enzymes. PMID:26224635

  11. Climate impacts on human settlement and agricultural activities in northern Norway revealed through sediment biogeochemistry

    PubMed Central

    D’Anjou, Robert M.; Bradley, Raymond S.; Balascio, Nicholas L.; Finkelstein, David B.

    2012-01-01

    Disentangling the effects of climate change and anthropogenic activities on the environment is a major challenge in paleoenvironmental research. Here, we used fecal sterols and other biogeochemical compounds in lake sediments from northern Norway to identify both natural and anthropogenic signals of environmental change during the late Holocene. The area was first occupied by humans and their grazing animals at ∼2,250 ± 75 calendar years before 1950 AD (calendar years before present). The arrival of humans is indicated by an abrupt increase in coprostanol (and its epimer epicoprostanol) in the sediments and an associated increase in 5β-stigmastanol (and 5β-epistigmastanol), which resulted from human and animal feces washing into the lake. Human settlement was accompanied by an abrupt increase in landscape fires (indicated by the rise in pyrolytic polycyclic aromatic hydrocarbons) and a decline in woodland (registered by a change in n-alkane chain lengths from leaf waxes), accelerating a process that began earlier in the Holocene. Human activity and associated landscape changes in the region over the last two millennia were mainly driven by summer temperatures, as indicated by independent tree-ring reconstructions, although there were periods when socioeconomic factors played an equally important role. In this study, fecal sterols in lake sediments have been used to provide a record of human occupancy through time. This approach may be useful in many archeological studies, both to confirm the presence of humans and grazing animals, and to distinguish between anthropogenic and natural factors that have influenced the environment in the past. PMID:23185025

  12. Climate impacts on human settlement and agricultural activities in northern Norway revealed through sediment biogeochemistry

    NASA Astrophysics Data System (ADS)

    D'Anjou, Robert M.; Bradley, Raymond S.; Balascio, Nicholas L.; Finkelstein, David B.

    2012-12-01

    Disentangling the effects of climate change and anthropogenic activities on the environment is a major challenge in paleoenvironmental research. Here, we used fecal sterols and other biogeochemical compounds in lake sediments from northern Norway to identify both natural and anthropogenic signals of environmental change during the late Holocene. The area was first occupied by humans and their grazing animals at ∼2,250 ± 75 calendar years before 1950 AD (calendar years before present). The arrival of humans is indicated by an abrupt increase in coprostanol (and its epimer epicoprostanol) in the sediments and an associated increase in 5β-stigmastanol (and 5β-epistigmastanol), which resulted from human and animal feces washing into the lake. Human settlement was accompanied by an abrupt increase in landscape fires (indicated by the rise in pyrolytic polycyclic aromatic hydrocarbons) and a decline in woodland (registered by a change in n-alkane chain lengths from leaf waxes), accelerating a process that began earlier in the Holocene. Human activity and associated landscape changes in the region over the last two millennia were mainly driven by summer temperatures, as indicated by independent tree-ring reconstructions, although there were periods when socioeconomic factors played an equally important role. In this study, fecal sterols in lake sediments have been used to provide a record of human occupancy through time. This approach may be useful in many archeological studies, both to confirm the presence of humans and grazing animals, and to distinguish between anthropogenic and natural factors that have influenced the environment in the past.

  13. Climate impacts on human settlement and agricultural activities in northern Norway revealed through sediment biogeochemistry.

    PubMed

    D'Anjou, Robert M; Bradley, Raymond S; Balascio, Nicholas L; Finkelstein, David B

    2012-12-11

    Disentangling the effects of climate change and anthropogenic activities on the environment is a major challenge in paleoenvironmental research. Here, we used fecal sterols and other biogeochemical compounds in lake sediments from northern Norway to identify both natural and anthropogenic signals of environmental change during the late Holocene. The area was first occupied by humans and their grazing animals at ∼2,250 ± 75 calendar years before 1950 AD (calendar years before present). The arrival of humans is indicated by an abrupt increase in coprostanol (and its epimer epicoprostanol) in the sediments and an associated increase in 5β-stigmastanol (and 5β-epistigmastanol), which resulted from human and animal feces washing into the lake. Human settlement was accompanied by an abrupt increase in landscape fires (indicated by the rise in pyrolytic polycyclic aromatic hydrocarbons) and a decline in woodland (registered by a change in n-alkane chain lengths from leaf waxes), accelerating a process that began earlier in the Holocene. Human activity and associated landscape changes in the region over the last two millennia were mainly driven by summer temperatures, as indicated by independent tree-ring reconstructions, although there were periods when socioeconomic factors played an equally important role. In this study, fecal sterols in lake sediments have been used to provide a record of human occupancy through time. This approach may be useful in many archeological studies, both to confirm the presence of humans and grazing animals, and to distinguish between anthropogenic and natural factors that have influenced the environment in the past. PMID:23185025

  14. Expression and activity analysis reveal that heme oxygenase (decycling) 1 is associated with blue egg formation.

    PubMed

    Wang, Z P; Liu, R F; Wang, A R; Li, J Y; Deng, X M

    2011-04-01

    Biliverdin is responsible for the coloration of blue eggs and is secreted onto the eggshell by the shell gland. Previous studies confirmed that a significant difference exists in biliverdin content between blue eggs and brown eggs, although the reasons are still unknown. Because the pigment is derived from oxidative degradation of heme catalyzed by heme oxygenase (HO), this study compared heme oxygenase (decycling) 1 (HMOX1), the gene encoding HO expression and HO activity, in the shell glands of the Dongxiang blue-shelled chicken (n = 12) and the Dongxiang brown-shelled chicken (n = 12). Results showed that HMOX1 was highly expressed at the mRNA (1.58-fold; P < 0.05) and protein levels in blue-shelled chickens compared with brown-shelled chickens. At the functional level, blue-shelled chickens also showed 1.40-fold (P < 0.05) higher HO activity than brown-shelled chickens. To explore the reasons for the differential expression of HMOX1, an association study of 6 SNP capturing the majority of HMOX1 variants with the blue egg coloration was performed. Results showed no significant association between SNP and the blue egg coloration in HMOX1 (P > 0.05). Taken together, these results show that blue egg formation is associated with high expression of HMOX1 in the shell gland of Dongxiang blue-shelled chickens, and suggest that differential expression of HMOX1 in the 2 groups of chickens is most likely to arise from an alteration in the trans-acting factor. PMID:21406370

  15. Measurement of PIP3 Levels Reveals an Unexpected Role for p110β in Early Adaptive Responses to p110α-Specific Inhibitors in Luminal Breast Cancer

    PubMed Central

    Costa, Carlotta; Ebi, Hiromichi; Martini, Miriam; Beausoleil, Sean A.; Faber, Anthony C.; Jakubik, Charles T.; Huang, Alan; Wang, Youzhen; Nishtala, Madhuri; Hall, Ben; Rikova, Klarisa; Zhao, Jean; Hirsch, Emilio; Benes, Cyril H.

    2016-01-01

    SUMMARY BYL719, which selectively inhibits the alpha isoform of the phosphatidylinositol 3-kinase (PI3K) catalytic subunit (p110α), is currently in clinical trials for the treatment of solid tumors, especially luminal breast cancers with PIK3CA mutations and/or HER2 amplification. This study reveals that, even among these sensitive cancers, the initial efficacy of p110α inhibition is mitigated by rapid re-accumulation of the PI3K product PIP3 produced by the p110β isoform. Importantly, the reactivation of PI3K mediated by p110β does not invariably restore AKT phosphorylation, demonstrating the limitations of using phospho-AKT as a surrogate to measure PI3K activation. Consistently, we show that the addition of the p110β inhibitor to BYL719 prevents the PIP3 rebound and induces greater antitumor efficacy in HER2-amplified and PIK3CA mutant cancers. PMID:25544637

  16. Time Series Measurements of Diffuse Hydrothermal Flow at the ASHES Vent Field Reveal Tidally Modulated Heat and Volume Flux

    NASA Astrophysics Data System (ADS)

    Mittelstaedt, E. L.; Fornari, D. J.; Crone, T. J.

    2015-12-01

    Existing time-series measurements of temperature and velocity of diffuse hydrothermal fluids exhibit variability over a range of periods from seconds to days. Frequency analysis of these measurements reveals differences between studies and field locations including nearly white spectra, as well as spectra with peaks at tidal and inertial periods. Based upon these results, previous authors have suggested several processes that may control diffuse flow rates, including tidally induced currents and 'tidal pumping', and have also suggested that there are no systematic controls. To further investigate the processes that control variability in diffuse flow, we use data from a new, deep-sea camera and temperature measurement system, the Diffuse Effluent Measurement System (DEMS), deployed during the July, 2014 cruise of the R/V Atlantis. The DEMS was deployed with DSV Alvin above a fracture network at the Phoenix vent within the ASHES vent field (Axial Seamount, 1541 mbsl). The system collected 20 seconds of imagery at 20 Hz and 24 seconds of temperature measurements at 1 Hz each hour over the period between July 22 and August 2nd. Velocities of the upwelling fluids were calculated using Diffuse Fluid Velocimetry (DFV; Mittelstaedt et al., 2010). DFV is a cross correlation technique that tracks moving index of refraction anomalies (i.e., hot parcels of fluid) through time. Over the ~12 day deployment, median flow rates ranged from 0.5 cm/s to 6 cm/s and mean fluid temperature anomalies from 0°C up to ~6.5°C, yielding an average heat flux density of 0.23 MW/m2. Spectral analysis of both the measured temperatures and calculated velocities yield a peak in normalized power at the semi-diurnal lunar period (M2, 12.4hrs), but no other spectral peaks above the 95% confidence level. Here, we present these results and discuss their implications for the tidal current and tidal pressure models of diffuse flow variability at the ASHES vent field.

  17. The Meaningful Activity Participation Assessment: A Measure of Engagement in Personally Valued Activities

    ERIC Educational Resources Information Center

    Eakman, Aaron M.; Carlson, Mike E.; Clark, Florence A.

    2010-01-01

    The Meaningful Activity Participation Assessment (MAPA), a recently developed 28-item tool designed to measure the meaningfulness of activity, was tested in a sample of 154 older adults. The MAPA evidenced a sufficient level of internal consistency and test-retest reliability and correlated as theoretically predicted with the Life Satisfaction…

  18. Upwelling characteristics in the Gulf of Finland (Baltic Sea) as revealed by Ferrybox measurements in 2007-2013

    NASA Astrophysics Data System (ADS)

    Kikas, V.; Lips, U.

    2015-11-01

    Ferrybox measurements are carried out between Tallinn and Helsinki in the Gulf of Finland (Baltic Sea) in a regular basis since 1997. The system measures autonomously water temperature, salinity, chlorophyll a fluorescence and turbidity and takes water samples for further analyses at a pre-defined time interval. We aimed to show how the Ferrybox technology could be used to study the coastal upwelling events in the Gulf of Finland. Based on the introduced upwelling index and related criterion, 33 coastal upwelling events were identified in May-September 2007-2013. The number of events as well as frequency of their occurrence and intensity, expressed as a sum of daily average temperature deviations in the 20 km wide coastal area, were almost equal near the northern and southern coast. It is shown that the wind impulse needed to generate upwelling events of similar intensity differ between the two coastal areas whereas this difference is related to the average wind forcing in the area. Two types of upwelling events were identified - one characterized by a strong temperature front and the other revealing gradual decrease of temperature from the open to coastal area with maximum temperature deviation close to the shore.

  19. Upwelling characteristics in the Gulf of Finland (Baltic Sea) as revealed by Ferrybox measurements in 2007-2013

    NASA Astrophysics Data System (ADS)

    Kikas, Villu; Lips, Urmas

    2016-07-01

    Ferrybox measurements have been carried out between Tallinn and Helsinki in the Gulf of Finland (Baltic Sea) on a regular basis since 1997. The system measures autonomously water temperature, salinity, chlorophyll a fluorescence and turbidity and takes water samples for further analyses at a predefined time interval. We aimed to show how the Ferrybox technology could be used to study the coastal upwelling events in the Gulf of Finland. Based on the introduced upwelling index and related criteria, 33 coastal upwelling events were identified in May-September 2007-2013. The number of events, as well as the frequency of their occurrence and intensity expressed as a sum of daily average temperature deviations in the 20 km wide coastal area, were almost equal near the northern and southern coasts. Nevertheless, the wind impulse, which was needed to generate upwelling events of similar intensity, differed between the northern and southern coastal areas. It is suggested that the general thermohaline structure adapted to the prevailing forcing and the estuarine character of the basin weaken the upwelling created by the westerly to southwesterly (up-estuary) winds and strengthen the upwelling created by the easterly to northeasterly (down-estuary) winds. Two types of upwelling events were identified - one characterized by a strong temperature front and the other revealing gradual decrease in temperature from the open sea to the coastal area, with maximum temperature deviation close to the shore.

  20. Revealing energy level structure of individual quantum dots by tunneling rate measured by single-electron sensitive electrostatic force spectroscopy.

    PubMed

    Roy-Gobeil, Antoine; Miyahara, Yoichi; Grutter, Peter

    2015-04-01

    We present theoretical and experimental studies of the effect of the density of states of a quantum dot (QD) on the rate of single-electron tunneling that can be directly measured by electrostatic force microscopy (e-EFM) experiments. In e-EFM, the motion of a biased atomic force microscope cantilever tip modulates the charge state of a QD in the Coulomb blockade regime. The charge dynamics of the dot, which is detected through its back-action on the capacitavely coupled cantilever, depends on the tunneling rate of the QD to a back-electrode. The density of states of the QD can therefore be measured through its effect on the energy dependence of tunneling rate. We present experimental data on individual 5 nm colloidal gold nanoparticles that exhibit a near continuous density of state at 77 K. In contrast, our analysis of already published data on self-assembled InAs QDs at 4 K clearly reveals discrete degenerate energy levels. PMID:25761141